id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
values | categories stringlengths 8 87 | license stringclasses 9
values | orig_abstract stringlengths 27 3.76k | versions listlengths 1 15 | update_date stringlengths 10 10 | authors_parsed listlengths 1 147 | abstract stringlengths 24 3.75k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2312.15134 | Jakub K\"ory | J. K\"ory, P. S. Stewart, N. A. Hill, X. Y. Luo, A. Pandolfi | A discrete-to-continuum model for the human cornea with application to
keratoconus | 32 pages, 8 figures | null | null | null | q-bio.QM physics.app-ph physics.bio-ph q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | We introduce a discrete mathematical model for the mechanical behaviour of a
planar slice of human corneal tissue, in equilibrium under the action of
physiological intraocular pressure (IOP). The model considers a regular
(two-dimensional) network of structural elements mimicking a discrete number of
parallel collage... | [
{
"created": "Sat, 23 Dec 2023 01:54:08 GMT",
"version": "v1"
}
] | 2023-12-27 | [
[
"Köry",
"J.",
""
],
[
"Stewart",
"P. S.",
""
],
[
"Hill",
"N. A.",
""
],
[
"Luo",
"X. Y.",
""
],
[
"Pandolfi",
"A.",
""
]
] | We introduce a discrete mathematical model for the mechanical behaviour of a planar slice of human corneal tissue, in equilibrium under the action of physiological intraocular pressure (IOP). The model considers a regular (two-dimensional) network of structural elements mimicking a discrete number of parallel collagen ... |
1908.02532 | Youness Azimzade | Youness Azimzade, Mahdi Sasar, V\'ictor M. P\'erez Garc\'ia | Environmental Disorder Regulation of Invasion and Genetic Loss | null | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many physical and natural systems, including the population of species,
evolve in habitats with spatial stochastic variations of the individuals'
motility. We study here the effect of those fluctuations on invasion and
genetic loss. A Langevin equation for the \textit{position} and \textit{border}
of the invasion fro... | [
{
"created": "Wed, 7 Aug 2019 11:28:55 GMT",
"version": "v1"
}
] | 2019-08-08 | [
[
"Azimzade",
"Youness",
""
],
[
"Sasar",
"Mahdi",
""
],
[
"García",
"Víctor M. Pérez",
""
]
] | Many physical and natural systems, including the population of species, evolve in habitats with spatial stochastic variations of the individuals' motility. We study here the effect of those fluctuations on invasion and genetic loss. A Langevin equation for the \textit{position} and \textit{border} of the invasion front... |
2212.14537 | William Marshall | William Marshall, Matteo Grasso, William GP Mayner, Alireza
Zaeemzadeh, Leonardo S Barbosa, Erick Chastain, Graham Findlay, Shuntaro
Sasai, Larissa Albantakis, Giulio Tononi | System Integrated Information | 16 pages, 4 figures | null | 10.3390/e25020334 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Integrated information theory (IIT) starts from consciousness itself and
identifies a set of properties (axioms) that are true of every conceivable
experience. The axioms are translated into a set of postulates about the
substrate of consciousness (called a complex), which are then used to formulate
a mathematical fr... | [
{
"created": "Fri, 30 Dec 2022 03:43:57 GMT",
"version": "v1"
}
] | 2023-03-22 | [
[
"Marshall",
"William",
""
],
[
"Grasso",
"Matteo",
""
],
[
"Mayner",
"William GP",
""
],
[
"Zaeemzadeh",
"Alireza",
""
],
[
"Barbosa",
"Leonardo S",
""
],
[
"Chastain",
"Erick",
""
],
[
"Findlay",
"Graham",
... | Integrated information theory (IIT) starts from consciousness itself and identifies a set of properties (axioms) that are true of every conceivable experience. The axioms are translated into a set of postulates about the substrate of consciousness (called a complex), which are then used to formulate a mathematical fram... |
1904.02610 | Wenping Cui | Wenping Cui, Robert Marsland III and Pankaj Mehta | Diverse communities behave like typical random ecosystems | 24 pages | Phys. Rev. E 104, 034416 (2021) | 10.1103/PhysRevE.104.034416 | null | q-bio.PE cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In 1972, Robert May triggered a worldwide research program studying
ecological communities using random matrix theory. Yet, it remains unclear if
and when we can treat real communities as random ecosystems. Here, we draw on
recent progress in random matrix theory and statistical physics to extend May's
approach to ge... | [
{
"created": "Mon, 1 Apr 2019 23:55:30 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Jun 2019 15:55:33 GMT",
"version": "v2"
},
{
"created": "Wed, 24 Mar 2021 02:26:25 GMT",
"version": "v3"
},
{
"created": "Mon, 27 Sep 2021 17:02:59 GMT",
"version": "v4"
}
] | 2021-09-28 | [
[
"Cui",
"Wenping",
""
],
[
"Marsland",
"Robert",
"III"
],
[
"Mehta",
"Pankaj",
""
]
] | In 1972, Robert May triggered a worldwide research program studying ecological communities using random matrix theory. Yet, it remains unclear if and when we can treat real communities as random ecosystems. Here, we draw on recent progress in random matrix theory and statistical physics to extend May's approach to gene... |
1803.03304 | Ryan Pyle | Ryan Pyle, Robert Rosenbaum | A model of reward-modulated motor learning with parallelcortical and
basal ganglia pathways | null | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many recent studies of the motor system are divided into two distinct
approaches: Those that investigate how motor responses are encoded in cortical
neurons' firing rate dynamics and those that study the learning rules by which
mammals and songbirds develop reliable motor responses. Computationally, the
first approac... | [
{
"created": "Thu, 8 Mar 2018 21:01:02 GMT",
"version": "v1"
},
{
"created": "Fri, 1 Mar 2019 23:25:16 GMT",
"version": "v2"
}
] | 2019-03-05 | [
[
"Pyle",
"Ryan",
""
],
[
"Rosenbaum",
"Robert",
""
]
] | Many recent studies of the motor system are divided into two distinct approaches: Those that investigate how motor responses are encoded in cortical neurons' firing rate dynamics and those that study the learning rules by which mammals and songbirds develop reliable motor responses. Computationally, the first approach ... |
2005.11935 | Min-Liang Wang | Anurag Lal, Ming-Hsien Hu, Pei-Yuan Lee, Min Liang Wang | A Novel Approach of using AR and Smart Surgical Glasses Supported Trauma
Care | 10 pages, 9 Figures, Conference. arXiv admin note: text overlap with
arXiv:1801.01560 by other authors | null | null | null | q-bio.QM cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | BACKGROUND: Augmented reality (AR) is gaining popularity in varying field
such as computer gaming and medical education fields. However, still few of
applications in real surgeries. Orthopedic surgical applications are currently
limited and underdeveloped. - METHODS: The clinic validation was prepared with
the curren... | [
{
"created": "Mon, 25 May 2020 06:03:30 GMT",
"version": "v1"
}
] | 2020-05-27 | [
[
"Lal",
"Anurag",
""
],
[
"Hu",
"Ming-Hsien",
""
],
[
"Lee",
"Pei-Yuan",
""
],
[
"Wang",
"Min Liang",
""
]
] | BACKGROUND: Augmented reality (AR) is gaining popularity in varying field such as computer gaming and medical education fields. However, still few of applications in real surgeries. Orthopedic surgical applications are currently limited and underdeveloped. - METHODS: The clinic validation was prepared with the currentl... |
2202.05889 | Muhammad Ardiyansyah | Muhammad Ardiyansyah, Dimitra Kosta, Jordi Roca-Lacostena | Embeddability of centrosymmetric matrices capturing the double-helix
structure in natural and synthetic DNA | 34 pages, 9 tables | null | null | null | q-bio.PE math.PR | http://creativecommons.org/licenses/by/4.0/ | In this paper, we discuss the embedding problem for centrosymmetric matrices,
which are higher order generalizations of the matrices occurring in Strand
Symmetric Models. These models capture the substitution symmetries arising from
the double helix structure of the DNA. Deciding whether a transition matrix is
embedd... | [
{
"created": "Fri, 11 Feb 2022 20:13:16 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Nov 2022 08:43:13 GMT",
"version": "v2"
}
] | 2022-11-09 | [
[
"Ardiyansyah",
"Muhammad",
""
],
[
"Kosta",
"Dimitra",
""
],
[
"Roca-Lacostena",
"Jordi",
""
]
] | In this paper, we discuss the embedding problem for centrosymmetric matrices, which are higher order generalizations of the matrices occurring in Strand Symmetric Models. These models capture the substitution symmetries arising from the double helix structure of the DNA. Deciding whether a transition matrix is embeddab... |
1509.09104 | Alexander Andreychenko | Alexander Andreychenko, Luca Bortolussi, Ramon Grima, Philipp Thomas,
Verena Wolf | Distribution approximations for the chemical master equation: comparison
of the method of moments and the system size expansion | 28 pages, 6 figures | null | null | null | q-bio.QM cond-mat.stat-mech math.NA q-bio.MN q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The stochastic nature of chemical reactions involving randomly fluctuating
population sizes has lead to a growing research interest in discrete-state
stochastic models and their analysis. A widely-used approach is the description
of the temporal evolution of the system in terms of a chemical master equation
(CME). In... | [
{
"created": "Wed, 30 Sep 2015 09:53:38 GMT",
"version": "v1"
}
] | 2015-10-01 | [
[
"Andreychenko",
"Alexander",
""
],
[
"Bortolussi",
"Luca",
""
],
[
"Grima",
"Ramon",
""
],
[
"Thomas",
"Philipp",
""
],
[
"Wolf",
"Verena",
""
]
] | The stochastic nature of chemical reactions involving randomly fluctuating population sizes has lead to a growing research interest in discrete-state stochastic models and their analysis. A widely-used approach is the description of the temporal evolution of the system in terms of a chemical master equation (CME). In t... |
2005.02071 | Christoph Leitner | Christoph Leitner, Robert Jarolim, Andreas Konrad, Annika Kruse,
Markus Tilp, J\"org Schr\"ottner, Christian Baumgartner | Automatic Tracking of the Muscle Tendon Junction in Healthy and Impaired
Subjects using Deep Learning | Accepted version to be published in 2020, 42nd Annual International
Conference of the IEEE Engineering in Medicine and Biology Society (EMBC),
Montreal, Canada | null | 10.1109/EMBC44109.2020.9176145 | null | q-bio.QM cs.LG eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recording muscle tendon junction displacements during movement, allows
separate investigation of the muscle and tendon behaviour, respectively. In
order to provide a fully-automatic tracking method, we employ a novel deep
learning approach to detect the position of the muscle tendon junction in
ultrasound images. We ... | [
{
"created": "Tue, 5 May 2020 11:24:40 GMT",
"version": "v1"
}
] | 2020-09-09 | [
[
"Leitner",
"Christoph",
""
],
[
"Jarolim",
"Robert",
""
],
[
"Konrad",
"Andreas",
""
],
[
"Kruse",
"Annika",
""
],
[
"Tilp",
"Markus",
""
],
[
"Schröttner",
"Jörg",
""
],
[
"Baumgartner",
"Christian",
""
... | Recording muscle tendon junction displacements during movement, allows separate investigation of the muscle and tendon behaviour, respectively. In order to provide a fully-automatic tracking method, we employ a novel deep learning approach to detect the position of the muscle tendon junction in ultrasound images. We ut... |
2402.13658 | Cedric Sueur | Maxime Herbrich (IPHC), Eythan Cousin, Ivan Puga-Gonzalez, Barbara
Tiddi, Claudia Fichtel, Meg Crofoot, Andrew Jj Macintosh, Erica van de Waal,
C\'edric Sueur (IPHC) | Network nestedness in primates: a structural constraint or a biological
advantage of social complexity? | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This study investigates the prevalence and implications of nestedness within
primate social networks, examining its relationship with cognitive and
structural factors. We analysed data from 51 primate groups across 21 species,
employing network analysis to evaluate nestedness and its correlation with
modularity, neoc... | [
{
"created": "Wed, 21 Feb 2024 09:44:14 GMT",
"version": "v1"
}
] | 2024-02-22 | [
[
"Herbrich",
"Maxime",
"",
"IPHC"
],
[
"Cousin",
"Eythan",
"",
"IPHC"
],
[
"Puga-Gonzalez",
"Ivan",
"",
"IPHC"
],
[
"Tiddi",
"Barbara",
"",
"IPHC"
],
[
"Fichtel",
"Claudia",
"",
"IPHC"
],
[
"Crofoot",
"Meg",... | This study investigates the prevalence and implications of nestedness within primate social networks, examining its relationship with cognitive and structural factors. We analysed data from 51 primate groups across 21 species, employing network analysis to evaluate nestedness and its correlation with modularity, neocor... |
1309.6208 | Eric Frichot | Eric Frichot, Fran\c{c}ois Mathieu, Th\'eo Trouillon, Guillaume
Bouchard, Olivier Fran\c{c}ois | Fast Inference of Admixture Coefficients Using Sparse Non-negative
Matrix Factorization Algorithms | 31 pages, 5 figures, 3 tables, 2 supplementary tables, 4
supplementary figures | null | null | null | q-bio.PE q-bio.QM stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inference of individual admixture coefficients, which is important for
population genetic and association studies, is commonly performed using
compute-intensive likelihood algorithms. With the availability of large
population genomic data sets, fast versions of likelihood algorithms have
attracted considerable attent... | [
{
"created": "Tue, 24 Sep 2013 15:19:38 GMT",
"version": "v1"
}
] | 2013-09-25 | [
[
"Frichot",
"Eric",
""
],
[
"Mathieu",
"François",
""
],
[
"Trouillon",
"Théo",
""
],
[
"Bouchard",
"Guillaume",
""
],
[
"François",
"Olivier",
""
]
] | Inference of individual admixture coefficients, which is important for population genetic and association studies, is commonly performed using compute-intensive likelihood algorithms. With the availability of large population genomic data sets, fast versions of likelihood algorithms have attracted considerable attentio... |
1204.2198 | Eugene Shakhnovich | Shimon Bershtein, Wanmeng Mu, and Eugene I. Shakhnovich | Soluble oligomerization provides a beneficial fitness effect on
destabilizing mutations | null | PNAS, v.109, pp.4857-62 MARCH 27, 2012 | 10.1073/pnas.1118157109 | null | q-bio.BM physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mutations create the genetic diversity on which selective pressures can act,
yet also create structural instability in proteins. How, then, is it possible
for organisms to ameliorate mutation-induced perturbations of protein stability
while maintaining biological fitness and gaining a selective advantage? Here we
use... | [
{
"created": "Tue, 10 Apr 2012 15:42:13 GMT",
"version": "v1"
}
] | 2015-06-04 | [
[
"Bershtein",
"Shimon",
""
],
[
"Mu",
"Wanmeng",
""
],
[
"Shakhnovich",
"Eugene I.",
""
]
] | Mutations create the genetic diversity on which selective pressures can act, yet also create structural instability in proteins. How, then, is it possible for organisms to ameliorate mutation-induced perturbations of protein stability while maintaining biological fitness and gaining a selective advantage? Here we used ... |
2202.02143 | Delfim F. M. Torres | Abdesslem Lamrani Alaoui, Moulay Rchid Sidi Ammi, Mouhcine Tilioua,
Delfim F. M. Torres | Global Stability of a Diffusive SEIR Epidemic Model with Distributed
Delay | This is a preprint whose final form is published by Elsevier in the
book 'Mathematical Analysis of Infectious Diseases', 1st Edition - June 1,
2022. ISBN: 9780323905046 | null | 10.1016/B978-0-32-390504-6.00016-4 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the global dynamics of a reaction-diffusion SEIR infection model
with distributed delay and nonlinear incidence rate. The well-posedness of the
proposed model is proved. By means of Lyapunov functionals, we show that the
disease free equilibrium state is globally asymptotically stable when the basic
reproduc... | [
{
"created": "Tue, 1 Feb 2022 18:41:47 GMT",
"version": "v1"
}
] | 2022-04-21 | [
[
"Alaoui",
"Abdesslem Lamrani",
""
],
[
"Ammi",
"Moulay Rchid Sidi",
""
],
[
"Tilioua",
"Mouhcine",
""
],
[
"Torres",
"Delfim F. M.",
""
]
] | We study the global dynamics of a reaction-diffusion SEIR infection model with distributed delay and nonlinear incidence rate. The well-posedness of the proposed model is proved. By means of Lyapunov functionals, we show that the disease free equilibrium state is globally asymptotically stable when the basic reproducti... |
1806.09900 | Joe Greener | Joe G Greener, Lewis Moffat, David T Jones | Design of metalloproteins and novel protein folds using variational
autoencoders | JGG and LM contributed equally to the work | Scientific Reports 8:16189 (2018) | 10.1038/s41598-018-34533-1 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The design of novel proteins has many applications but remains an attritional
process with success in isolated cases. Meanwhile, deep learning technologies
have exploded in popularity in recent years and are increasingly applicable to
biology due to the rise in available data. We attempt to link protein design
and de... | [
{
"created": "Tue, 26 Jun 2018 11:00:22 GMT",
"version": "v1"
},
{
"created": "Wed, 19 Sep 2018 10:49:41 GMT",
"version": "v2"
},
{
"created": "Fri, 2 Nov 2018 11:23:48 GMT",
"version": "v3"
}
] | 2018-11-07 | [
[
"Greener",
"Joe G",
""
],
[
"Moffat",
"Lewis",
""
],
[
"Jones",
"David T",
""
]
] | The design of novel proteins has many applications but remains an attritional process with success in isolated cases. Meanwhile, deep learning technologies have exploded in popularity in recent years and are increasingly applicable to biology due to the rise in available data. We attempt to link protein design and deep... |
1303.3054 | Xu Yang | Guangwei Si, Min Tang and Xu Yang | A pathway-based mean-field model for E. coli chemotaxis: Mathematical
derivation and Keller-Segel limit | 21 pages, 3 figures | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A pathway-based mean-field theory (PBMFT) was recently proposed for E. coli
chemotaxis in [G. Si, T. Wu, Q. Quyang and Y. Tu, Phys. Rev. Lett., 109 (2012),
048101]. In this paper, we derived a new moment system of PBMFT by using the
moment closure technique in kinetic theory under the assumption that the
methylation ... | [
{
"created": "Tue, 12 Mar 2013 23:21:39 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Apr 2013 05:04:10 GMT",
"version": "v2"
}
] | 2013-04-29 | [
[
"Si",
"Guangwei",
""
],
[
"Tang",
"Min",
""
],
[
"Yang",
"Xu",
""
]
] | A pathway-based mean-field theory (PBMFT) was recently proposed for E. coli chemotaxis in [G. Si, T. Wu, Q. Quyang and Y. Tu, Phys. Rev. Lett., 109 (2012), 048101]. In this paper, we derived a new moment system of PBMFT by using the moment closure technique in kinetic theory under the assumption that the methylation le... |
2403.20239 | Marc Fiammante | Marc Fiammante (1,2), Anne-Isabelle Vermersch (3), Marie Vidailhet
(1,4), Mario Chavez (5) ((1) Paris Brain Institute, Inserm U1127, CNRS
UMR7225, Sorbonne Universite UM75, Inria Paris (Team Nerv), Pitie-Salpetriere
Hospital, Paris, France, (2) Retired IBM Fellow, (3) Physiology & Paediatric
Functional Explorat... | A simple EEG-based decision tool for neonatal therapeutic hypothermia in
hypoxic-ischemic encephalopathy | 20 pages, 1 table, 2 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Indication of therapeutic hypothermia needs an accurate identification of
brain injury in the early neonatal period. Here, we aim to provide a simple
hypothermia decision-making tool for the term neonates with hypoxic-ischemic
encephalopathy (HIE) based on features of conventional electroencephalogram
(EEG) taken les... | [
{
"created": "Fri, 29 Mar 2024 15:33:16 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Apr 2024 16:13:46 GMT",
"version": "v2"
}
] | 2024-04-04 | [
[
"Fiammante",
"Marc",
""
],
[
"Vermersch",
"Anne-Isabelle",
""
],
[
"Vidailhet",
"Marie",
""
],
[
"Chavez",
"Mario",
""
]
] | Indication of therapeutic hypothermia needs an accurate identification of brain injury in the early neonatal period. Here, we aim to provide a simple hypothermia decision-making tool for the term neonates with hypoxic-ischemic encephalopathy (HIE) based on features of conventional electroencephalogram (EEG) taken less ... |
2107.06738 | Antonio Mart\'inez-Sanchez | Antonio Martinez-Sanchez, Wolfgang Baumeister and Vladan Lu\v{c}i\'c | Statistical spatial analysis for cryo-electron tomography | null | Computer Methods and Programs in Biomedicine 218 (2022) 106693 | 10.1016/j.cmpb.2022.106693 | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cryo-electron tomography (cryo-ET) is uniquely suited to precisely localize
macromolecular complexes in situ, that is in a close-to-native state within
their cellular compartments, in three-dimensions at high resolution. Point
pattern analysis (PPA) allows quantitative characterization of the spatial
organization of ... | [
{
"created": "Wed, 14 Jul 2021 14:31:18 GMT",
"version": "v1"
}
] | 2022-03-02 | [
[
"Martinez-Sanchez",
"Antonio",
""
],
[
"Baumeister",
"Wolfgang",
""
],
[
"Lučić",
"Vladan",
""
]
] | Cryo-electron tomography (cryo-ET) is uniquely suited to precisely localize macromolecular complexes in situ, that is in a close-to-native state within their cellular compartments, in three-dimensions at high resolution. Point pattern analysis (PPA) allows quantitative characterization of the spatial organization of pa... |
1811.12499 | Kevin Keys | Alfonso Landeros, Timothy Stutz, Kevin L. Keys, Alexander Alekseyenko,
Janet S. Sinsheimer, Kenneth Lange, Mary Sehl | BioSimulator.jl: Stochastic simulation in Julia | 27 pages, 5 figures, 3 tables | Computer Methods and Programs in Biomedicine, Volume 167, December
2018, Pages 23-35 | 10.1016/j.cmpb.2018.09.009 | null | q-bio.QM math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biological systems with intertwined feedback loops pose a challenge to
mathematical modeling efforts. Moreover, rare events, such as mutation and
extinction, complicate system dynamics. Stochastic simulation algorithms are
useful in generating time-evolution trajectories for these systems because they
can adequately ... | [
{
"created": "Thu, 29 Nov 2018 21:38:16 GMT",
"version": "v1"
}
] | 2018-12-10 | [
[
"Landeros",
"Alfonso",
""
],
[
"Stutz",
"Timothy",
""
],
[
"Keys",
"Kevin L.",
""
],
[
"Alekseyenko",
"Alexander",
""
],
[
"Sinsheimer",
"Janet S.",
""
],
[
"Lange",
"Kenneth",
""
],
[
"Sehl",
"Mary",
""
... | Biological systems with intertwined feedback loops pose a challenge to mathematical modeling efforts. Moreover, rare events, such as mutation and extinction, complicate system dynamics. Stochastic simulation algorithms are useful in generating time-evolution trajectories for these systems because they can adequately ca... |
1609.09421 | Yuri Shestopaloff | Yuri K. Shestopaloff | Physical mechanisms influencing life origin and development.
Physical-biochemical paradigm of Life | 49 pages, 8 figures, 1 table. Mathematical derivations are presented
with more intermediate transformations | Biophysical Reviews and Letters, 2023,
https://www.worldscientific.com/doi/epdf/10.1142/S1793048023500030 | 10.1142/S1793048023500030 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The present view of biological phenomena is based on a biochemical paradigm
that development of living organisms is defined by information stored in a
molecular form as some genetic code. However, new discoveries indicate that
biological phenomena cannot be confined to a biochemical realm alone, but are
also influenc... | [
{
"created": "Thu, 29 Sep 2016 16:45:49 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Nov 2017 01:47:18 GMT",
"version": "v2"
},
{
"created": "Mon, 22 Jan 2018 20:04:13 GMT",
"version": "v3"
},
{
"created": "Fri, 1 Jun 2018 21:24:38 GMT",
"version": "v4"
},
{
"cre... | 2023-11-14 | [
[
"Shestopaloff",
"Yuri K.",
""
]
] | The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological phenomena cannot be confined to a biochemical realm alone, but are also influenced... |
2109.07925 | Christopher Wood | Leonardo V. Castorina, Rokas Petrenas, Kartic Subr and Christopher W.
Wood | PDBench: Evaluating Computational Methods for Protein Sequence Design | 9 pages, 5 figures | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by-sa/4.0/ | Proteins perform critical processes in all living systems: converting solar
energy into chemical energy, replicating DNA, as the basis of highly performant
materials, sensing and much more. While an incredible range of functionality
has been sampled in nature, it accounts for a tiny fraction of the possible
protein u... | [
{
"created": "Thu, 16 Sep 2021 12:20:03 GMT",
"version": "v1"
},
{
"created": "Fri, 17 Sep 2021 09:23:31 GMT",
"version": "v2"
},
{
"created": "Tue, 28 Sep 2021 13:34:33 GMT",
"version": "v3"
}
] | 2021-09-29 | [
[
"Castorina",
"Leonardo V.",
""
],
[
"Petrenas",
"Rokas",
""
],
[
"Subr",
"Kartic",
""
],
[
"Wood",
"Christopher W.",
""
]
] | Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has been sampled in nature, it accounts for a tiny fraction of the possible protein uni... |
0903.4161 | Federico Zertuche | Federico Zertuche | On the Robustness of NK-Kauffman Networks Against Changes in their
Connections and Boolean Functions | 17 pages, 1 figure, Accepted in Journal of Mathematical Physics | null | 10.1063/1.3116166 | null | q-bio.QM math-ph math.MP nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | NK-Kauffman networks {\cal L}^N_K are a subset of the Boolean functions on N
Boolean variables to themselves, \Lambda_N = {\xi: \IZ_2^N \to \IZ_2^N}. To
each NK-Kauffman network it is possible to assign a unique Boolean function on
N variables through the function \Psi: {\cal L}^N_K \to \Lambda_N. The
probability {\c... | [
{
"created": "Tue, 24 Mar 2009 18:56:40 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Zertuche",
"Federico",
""
]
] | NK-Kauffman networks {\cal L}^N_K are a subset of the Boolean functions on N Boolean variables to themselves, \Lambda_N = {\xi: \IZ_2^N \to \IZ_2^N}. To each NK-Kauffman network it is possible to assign a unique Boolean function on N variables through the function \Psi: {\cal L}^N_K \to \Lambda_N. The probability {\cal... |
2208.06360 | Kisung Moon | Kisung Moon, Sunyoung Kwon | 3D Graph Contrastive Learning for Molecular Property Prediction | need to be edited | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Self-supervised learning (SSL) is a method that learns the data
representation by utilizing supervision inherent in the data. This learning
method is in the spotlight in the drug field, lacking annotated data due to
time-consuming and expensive experiments. SSL using enormous unlabeled data has
shown excellent perfor... | [
{
"created": "Tue, 31 May 2022 04:45:31 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Aug 2022 13:10:50 GMT",
"version": "v2"
}
] | 2022-08-19 | [
[
"Moon",
"Kisung",
""
],
[
"Kwon",
"Sunyoung",
""
]
] | Self-supervised learning (SSL) is a method that learns the data representation by utilizing supervision inherent in the data. This learning method is in the spotlight in the drug field, lacking annotated data due to time-consuming and expensive experiments. SSL using enormous unlabeled data has shown excellent performa... |
2008.05897 | Mouhamadou Aliou Mountaga Tall Bald\'e | Fulgence Mansal, Mouhamadou A.M.T. Bald\'e and Alpha O. Bah | Study of COVID-19 anti-pandemic strategies by using optimal control | 21 pages, 32 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this study, we present a new epidemiological model, with contamination
from confirmed and unreported. We also compute equilibria and study their
stability without intervention strategies. Optimal control theory has proven to
be a successful tool in understanding ways to curtail the spread of infectious
diseases by... | [
{
"created": "Sun, 9 Aug 2020 21:42:03 GMT",
"version": "v1"
}
] | 2020-08-14 | [
[
"Mansal",
"Fulgence",
""
],
[
"Baldé",
"Mouhamadou A. M. T.",
""
],
[
"Bah",
"Alpha O.",
""
]
] | In this study, we present a new epidemiological model, with contamination from confirmed and unreported. We also compute equilibria and study their stability without intervention strategies. Optimal control theory has proven to be a successful tool in understanding ways to curtail the spread of infectious diseases by d... |
2401.06199 | Xingyi Cheng | Bo Chen, Xingyi Cheng, Pan Li, Yangli-ao Geng, Jing Gong, Shen Li,
Zhilei Bei, Xu Tan, Boyan Wang, Xin Zeng, Chiming Liu, Aohan Zeng, Yuxiao
Dong, Jie Tang, Le Song | xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering
the Language of Protein | null | null | null | null | q-bio.QM cs.AI cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Protein language models have shown remarkable success in learning biological
information from protein sequences. However, most existing models are limited
by either autoencoding or autoregressive pre-training objectives, which makes
them struggle to handle protein understanding and generation tasks
concurrently. We p... | [
{
"created": "Thu, 11 Jan 2024 15:03:17 GMT",
"version": "v1"
}
] | 2024-01-15 | [
[
"Chen",
"Bo",
""
],
[
"Cheng",
"Xingyi",
""
],
[
"Li",
"Pan",
""
],
[
"Geng",
"Yangli-ao",
""
],
[
"Gong",
"Jing",
""
],
[
"Li",
"Shen",
""
],
[
"Bei",
"Zhilei",
""
],
[
"Tan",
"Xu",
""
],... | Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We pro... |
1501.02124 | Ildefonso De la Fuente M | Ildefonso M. De la Fuente | New insights on the Dynamic Cellular Metabolism | 1 figure | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A large number of studies have shown the existence of metabolic covalent
modifications in different molecular structures, able to store biochemical
information that is not encoded by the DNA. Some of these covalent mark
patterns can be transmitted across generations (epigenetic changes). Recently,
the emergence of Ho... | [
{
"created": "Fri, 9 Jan 2015 12:53:08 GMT",
"version": "v1"
}
] | 2015-01-12 | [
[
"De la Fuente",
"Ildefonso M.",
""
]
] | A large number of studies have shown the existence of metabolic covalent modifications in different molecular structures, able to store biochemical information that is not encoded by the DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopf... |
2105.02811 | Weikai Li | Weikai Li, Yongxiang Tang, Zhengxia Wang, Shuo Hu and Xin Gao | The Reconfiguration Pattern of Individual Brain Metabolic Connectome for
Parkinson's Disease Identification | 9 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Background: Positron Emission Tomography (PET) with 18F-fluorodeoxyglucose
(18F-FDG) reveals metabolic abnormalities in Parkinson's disease (PD) at a
systemic level. Previous metabolic connectome studies derived from groups of
patients have failed to identify the individual neurophysiological details. We
aim to estab... | [
{
"created": "Thu, 29 Apr 2021 06:46:52 GMT",
"version": "v1"
}
] | 2021-05-07 | [
[
"Li",
"Weikai",
""
],
[
"Tang",
"Yongxiang",
""
],
[
"Wang",
"Zhengxia",
""
],
[
"Hu",
"Shuo",
""
],
[
"Gao",
"Xin",
""
]
] | Background: Positron Emission Tomography (PET) with 18F-fluorodeoxyglucose (18F-FDG) reveals metabolic abnormalities in Parkinson's disease (PD) at a systemic level. Previous metabolic connectome studies derived from groups of patients have failed to identify the individual neurophysiological details. We aim to establi... |
2205.13816 | Paolo Muratore | Paolo Muratore, Sina Tafazoli, Eugenio Piasini, Alessandro Laio and
Davide Zoccolan | Prune and distill: similar reformatting of image information along rat
visual cortex and deep neural networks | 11 pages, 5 fiures | Advances in Neural Information Processing Systems (2022) Vol. 35
pp. 30206-30218 | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by/4.0/ | Visual object recognition has been extensively studied in both neuroscience
and computer vision. Recently, the most popular class of artificial systems for
this task, deep convolutional neural networks (CNNs), has been shown to provide
excellent models for its functional analogue in the brain, the ventral stream
in v... | [
{
"created": "Fri, 27 May 2022 08:06:40 GMT",
"version": "v1"
}
] | 2023-06-06 | [
[
"Muratore",
"Paolo",
""
],
[
"Tafazoli",
"Sina",
""
],
[
"Piasini",
"Eugenio",
""
],
[
"Laio",
"Alessandro",
""
],
[
"Zoccolan",
"Davide",
""
]
] | Visual object recognition has been extensively studied in both neuroscience and computer vision. Recently, the most popular class of artificial systems for this task, deep convolutional neural networks (CNNs), has been shown to provide excellent models for its functional analogue in the brain, the ventral stream in vis... |
0807.0499 | Melanie J.I. M\"uller | Melanie J.I. M\"uller, Stefan Klumpp, Reinhard Lipowsky | Tug-of-war as a cooperative mechanism for bidirectional cargo transport
by molecular motors | 17 pages, latex, 11 figures, 4 tables, includes Supporting
Information | Proc. Natl. Acad. Sci. USA 105, 4609-4614 (2008) | 10.1073/pnas.0706825105 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Intracellular transport is based on molecular motors that pull cargos along
cytoskeletal filaments. One motor species always moves in one direction, e.g.
conventional kinesin moves to the microtubule plus end, while cytoplasmic
dynein moves to the microtubule minus end. However, many cellular cargos are
observed to m... | [
{
"created": "Thu, 3 Jul 2008 07:48:23 GMT",
"version": "v1"
}
] | 2008-07-04 | [
[
"Müller",
"Melanie J. I.",
""
],
[
"Klumpp",
"Stefan",
""
],
[
"Lipowsky",
"Reinhard",
""
]
] | Intracellular transport is based on molecular motors that pull cargos along cytoskeletal filaments. One motor species always moves in one direction, e.g. conventional kinesin moves to the microtubule plus end, while cytoplasmic dynein moves to the microtubule minus end. However, many cellular cargos are observed to mov... |
2004.13485 | Nathalie Henrich Bernardoni | Jean-Philippe Epron, Jocelyne Sarfati, Nathalie Henrich Bernardoni
(GIPSA-GAMA) | Callas or the trajectory of the meteor | in French | Revue de Laryngologie Otologie Rhinologie, Revue de Laryngologie,
2010, 131 (1), pp.35-38 | null | null | q-bio.OT physics.class-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The lyric career of Maria Callas, though exceptional, is also noteworthy for
its brevity. The first signs of downturn appeared at the age of 36 and her
voice fell silent at only 40. Though the literature has massively commented on
this premature worsening, few analyses of its characteristics have been made
public so ... | [
{
"created": "Thu, 23 Apr 2020 12:23:45 GMT",
"version": "v1"
}
] | 2020-04-29 | [
[
"Epron",
"Jean-Philippe",
"",
"GIPSA-GAMA"
],
[
"Sarfati",
"Jocelyne",
"",
"GIPSA-GAMA"
],
[
"Bernardoni",
"Nathalie Henrich",
"",
"GIPSA-GAMA"
]
] | The lyric career of Maria Callas, though exceptional, is also noteworthy for its brevity. The first signs of downturn appeared at the age of 36 and her voice fell silent at only 40. Though the literature has massively commented on this premature worsening, few analyses of its characteristics have been made public so fa... |
1606.07221 | Dennis C. Rapaport | D. C. Rapaport | Packaging stiff polymers in small containers: A molecular dynamics study | 4 pages, 4 figures (minor changes in revised version) | Phys. Rev. E 94, 030401 (2016) | 10.1103/PhysRevE.94.030401 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The question of how stiff polymers are able to pack into small containers is
particularly relevant to the study of DNA packaging in viruses. A reduced
version of the problem based on coarse-grained representations of the main
components of the system -- the DNA polymer and the spherical viral capsid --
has been studi... | [
{
"created": "Thu, 23 Jun 2016 08:25:43 GMT",
"version": "v1"
},
{
"created": "Fri, 23 Sep 2016 14:01:49 GMT",
"version": "v2"
}
] | 2016-10-12 | [
[
"Rapaport",
"D. C.",
""
]
] | The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of the system -- the DNA polymer and the spherical viral capsid -- has been studied... |
1307.5728 | Josef Ladenbauer | Josef Ladenbauer, Moritz Augustin and Klaus Obermayer | How adaptation currents change threshold, gain and variability of
neuronal spiking | 20 pages, 8 figures; Journal of Neurophysiology (in press) | null | 10.1152/jn.00586.2013 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many types of neurons exhibit spike rate adaptation, mediated by intrinsic
slow $\mathrm{K}^+$-currents, which effectively inhibit neuronal responses. How
these adaptation currents change the relationship between in-vivo like
fluctuating synaptic input, spike rate output and the spike train statistics,
however, is no... | [
{
"created": "Mon, 22 Jul 2013 14:24:43 GMT",
"version": "v1"
},
{
"created": "Thu, 7 Nov 2013 10:39:01 GMT",
"version": "v2"
}
] | 2013-11-08 | [
[
"Ladenbauer",
"Josef",
""
],
[
"Augustin",
"Moritz",
""
],
[
"Obermayer",
"Klaus",
""
]
] | Many types of neurons exhibit spike rate adaptation, mediated by intrinsic slow $\mathrm{K}^+$-currents, which effectively inhibit neuronal responses. How these adaptation currents change the relationship between in-vivo like fluctuating synaptic input, spike rate output and the spike train statistics, however, is not ... |
2104.03406 | Nicholas Guttenberg | Nicholas Guttenberg | Evolutionary rates of information gain and decay in fluctuating
environments | 7 pages, 4 figures, ALife 2019 | null | null | null | q-bio.PE cs.IT cs.LG math.IT | http://creativecommons.org/licenses/by/4.0/ | In this paper, we wish to investigate the dynamics of information transfer in
evolutionary dynamics. We use information theoretic tools to track how much
information an evolving population has obtained and managed to retain about
different environments that it is exposed to. By understanding the dynamics of
informati... | [
{
"created": "Wed, 7 Apr 2021 21:42:37 GMT",
"version": "v1"
}
] | 2021-04-09 | [
[
"Guttenberg",
"Nicholas",
""
]
] | In this paper, we wish to investigate the dynamics of information transfer in evolutionary dynamics. We use information theoretic tools to track how much information an evolving population has obtained and managed to retain about different environments that it is exposed to. By understanding the dynamics of information... |
2007.15727 | David Mori\~na Prof. | David Mori\~na, Amanda Fern\'andez-Fontelo, Alejandra Caba\~na,
Argimiro Arratia, Gustavo \'Avalos and Pedro Puig | Cumulated burden of Covid-19 in Spain from a Bayesian perspective | null | null | 10.1093/eurpub/ckab118 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The main goal of this work is to estimate the actual number of cases of
Covid-19 in Spain in the period 01-31-2020 / 06-01-2020 by Autonomous
Communities. Based on these estimates, this work allows us to accurately
re-estimate the lethality of the disease in Spain, taking into account
unreported cases. A hierarchical... | [
{
"created": "Thu, 30 Jul 2020 20:28:15 GMT",
"version": "v1"
}
] | 2021-08-18 | [
[
"Moriña",
"David",
""
],
[
"Fernández-Fontelo",
"Amanda",
""
],
[
"Cabaña",
"Alejandra",
""
],
[
"Arratia",
"Argimiro",
""
],
[
"Ávalos",
"Gustavo",
""
],
[
"Puig",
"Pedro",
""
]
] | The main goal of this work is to estimate the actual number of cases of Covid-19 in Spain in the period 01-31-2020 / 06-01-2020 by Autonomous Communities. Based on these estimates, this work allows us to accurately re-estimate the lethality of the disease in Spain, taking into account unreported cases. A hierarchical B... |
1507.06614 | Haralambos Hatzikirou | A. I. Reppas, J. C. L. Alfonso and H. Hatzikirou | In silico tumor control induced via alternating immunostimulating and
immunosuppressive phases | null | null | null | null | q-bio.TO q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite recent advances in the field of Oncoimmunology, the success potential
of immunomodulatory therapies against cancer remains to be elucidated. One of
the reasons is the lack of understanding on the complex interplay between tumor
growth dynamics and the associated immune system responses. Towards this goal,
we ... | [
{
"created": "Wed, 22 Jul 2015 11:30:28 GMT",
"version": "v1"
}
] | 2015-07-24 | [
[
"Reppas",
"A. I.",
""
],
[
"Alfonso",
"J. C. L.",
""
],
[
"Hatzikirou",
"H.",
""
]
] | Despite recent advances in the field of Oncoimmunology, the success potential of immunomodulatory therapies against cancer remains to be elucidated. One of the reasons is the lack of understanding on the complex interplay between tumor growth dynamics and the associated immune system responses. Towards this goal, we co... |
2106.12297 | Victor Popescu | Nicoleta Siminea, Victor Popescu, Jose Angel Sanchez Martin, Daniela
Florea, Georgiana Gavril, Ana-Maria Gheorghe, Corina Itcus, Krishna Kanhaiya,
Octavian Pacioglu, Laura Ioana Popa, Romica Trandafir, Maria Iris Tusa,
Manuela Sidoroff, Mihaela Paun, Eugen Czeizler, Andrei Paun, Ion Petre | Network analytics for drug repurposing in COVID-19 | 21 pages, 3 tables, 9 figures, supplementary information included at
the end, 4 files as supplementary material | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | To better understand the potential of drug repurposing in COVID-19, we
analyzed control strategies over essential host factors for SARS-CoV-2
infection. We constructed comprehensive directed protein-protein interaction
networks integrating the top ranked host factors, drug target proteins, and
directed protein-protei... | [
{
"created": "Wed, 23 Jun 2021 10:32:15 GMT",
"version": "v1"
}
] | 2021-06-24 | [
[
"Siminea",
"Nicoleta",
""
],
[
"Popescu",
"Victor",
""
],
[
"Martin",
"Jose Angel Sanchez",
""
],
[
"Florea",
"Daniela",
""
],
[
"Gavril",
"Georgiana",
""
],
[
"Gheorghe",
"Ana-Maria",
""
],
[
"Itcus",
"Corina"... | To better understand the potential of drug repurposing in COVID-19, we analyzed control strategies over essential host factors for SARS-CoV-2 infection. We constructed comprehensive directed protein-protein interaction networks integrating the top ranked host factors, drug target proteins, and directed protein-protein ... |
2102.03438 | Ekkehard Ullner | Afifurrahman and Ekkehard Ullner and Antonio Politi | Collective dynamics in the presence of finite-width pulses | 12 pages, 12 figures | null | 10.1063/5.0046691 | null | q-bio.NC math.DS nlin.AO | http://creativecommons.org/licenses/by/4.0/ | The idealisation of neuronal pulses as $\delta$-spikes is a convenient
approach in neuroscience but can sometimes lead to erroneous conclusions. We
investigate the effect of a finite pulse-width on the dynamics of balanced
neuronal networks. In particular, we study two populations of identical
excitatory and inhibito... | [
{
"created": "Fri, 5 Feb 2021 22:24:43 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Apr 2021 16:29:30 GMT",
"version": "v2"
}
] | 2024-06-19 | [
[
"Afifurrahman",
"",
""
],
[
"Ullner",
"Ekkehard",
""
],
[
"Politi",
"Antonio",
""
]
] | The idealisation of neuronal pulses as $\delta$-spikes is a convenient approach in neuroscience but can sometimes lead to erroneous conclusions. We investigate the effect of a finite pulse-width on the dynamics of balanced neuronal networks. In particular, we study two populations of identical excitatory and inhibitory... |
1110.0235 | Pablo Cordero | Pablo Cordero, Julius Lucks, Rhiju Das | The Stanford RNA Mapping Database for sharing and visualizing RNA
structure mapping experiments | 20 pages, 2 figures | null | null | null | q-bio.BM cs.DB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have established an RNA Mapping Database (RMDB) to enable a new generation
of structural, thermodynamic, and kinetic studies from quantitative
single-nucleotide-resolution RNA structure mapping (freely available at
http://rmdb.stanford.edu). Chemical and enzymatic mapping is a rapid, robust,
and widespread approac... | [
{
"created": "Sun, 2 Oct 2011 20:56:47 GMT",
"version": "v1"
}
] | 2011-10-04 | [
[
"Cordero",
"Pablo",
""
],
[
"Lucks",
"Julius",
""
],
[
"Das",
"Rhiju",
""
]
] | We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely available at http://rmdb.stanford.edu). Chemical and enzymatic mapping is a rapid, robust, and widespread approach ... |
2405.16357 | Tingting Dan | Tingting Dan and Ziquan Wei and Won Hwa Kim and Guorong Wu | Exploring the Enigma of Neural Dynamics Through A Scattering-Transform
Mixer Landscape for Riemannian Manifold | 15 pages, 6 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The human brain is a complex inter-wired system that emerges spontaneous
functional fluctuations. In spite of tremendous success in the experimental
neuroscience field, a system-level understanding of how brain anatomy supports
various neural activities remains elusive. Capitalizing on the unprecedented
amount of neu... | [
{
"created": "Sat, 25 May 2024 21:35:50 GMT",
"version": "v1"
}
] | 2024-05-28 | [
[
"Dan",
"Tingting",
""
],
[
"Wei",
"Ziquan",
""
],
[
"Kim",
"Won Hwa",
""
],
[
"Wu",
"Guorong",
""
]
] | The human brain is a complex inter-wired system that emerges spontaneous functional fluctuations. In spite of tremendous success in the experimental neuroscience field, a system-level understanding of how brain anatomy supports various neural activities remains elusive. Capitalizing on the unprecedented amount of neuro... |
2008.01692 | Almaz Tesfay | Almaz Tesfay, Daniel Tesfay, James Brannan, Jinqiao Duan | A Logistic-Harvest Model with Allee Effect under Multiplicative Noise | 18 pages, 14 figures | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work is devoted to the study of a stochastic logistic growth model with
and without the Allee effect. Such a model describes the evolution of a
population under environmental stochastic fluctuations and is in the form of a
stochastic differential equation driven by multiplicative Gaussian noise. With
the help of... | [
{
"created": "Tue, 4 Aug 2020 16:50:20 GMT",
"version": "v1"
}
] | 2020-08-05 | [
[
"Tesfay",
"Almaz",
""
],
[
"Tesfay",
"Daniel",
""
],
[
"Brannan",
"James",
""
],
[
"Duan",
"Jinqiao",
""
]
] | This work is devoted to the study of a stochastic logistic growth model with and without the Allee effect. Such a model describes the evolution of a population under environmental stochastic fluctuations and is in the form of a stochastic differential equation driven by multiplicative Gaussian noise. With the help of t... |
1409.7208 | Ruibang Luo | Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane and Tak-Wah
Lam | MEGAHIT: An ultra-fast single-node solution for large and complex
metagenomics assembly via succinct de Bruijn graph | 2 pages, 2 tables, 1 figure, submitted to Oxford Bioinformatics as an
Application Note | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | MEGAHIT is a NGS de novo assembler for assembling large and complex
metagenomics data in a time- and cost-efficient manner. It finished assembling
a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a
single computing node with and without a GPU, respectively. MEGAHIT assembles
the data as a whol... | [
{
"created": "Thu, 25 Sep 2014 10:49:30 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Dec 2014 13:10:03 GMT",
"version": "v2"
}
] | 2014-12-24 | [
[
"Li",
"Dinghua",
""
],
[
"Liu",
"Chi-Man",
""
],
[
"Luo",
"Ruibang",
""
],
[
"Sadakane",
"Kunihiko",
""
],
[
"Lam",
"Tak-Wah",
""
]
] | MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and without a GPU, respectively. MEGAHIT assembles the data as a whole,... |
1304.5952 | Eduardo Eyras | Gael P. Alamancos, Eneritz Agirre, Eduardo Eyras | Methods to study splicing from high-throughput RNA Sequencing data | 31 pages, 1 figure, 9 tables. Small corrections added | Methods Mol Biol. 2014;1126:357-97 | 10.1007/978-1-62703-980-2_26 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The development of novel high-throughput sequencing (HTS) methods for RNA
(RNA-Seq) has provided a very powerful mean to study splicing under multiple
conditions at unprecedented depth. However, the complexity of the information
to be analyzed has turned this into a challenging task. In the last few years,
a plethora... | [
{
"created": "Mon, 22 Apr 2013 13:58:54 GMT",
"version": "v1"
},
{
"created": "Thu, 6 Feb 2014 18:03:30 GMT",
"version": "v2"
},
{
"created": "Thu, 30 Jul 2015 23:15:02 GMT",
"version": "v3"
}
] | 2015-08-03 | [
[
"Alamancos",
"Gael P.",
""
],
[
"Agirre",
"Eneritz",
""
],
[
"Eyras",
"Eduardo",
""
]
] | The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora o... |
1508.02085 | Toan T. Nguyen | Toan T. Nguyen | Grand-canonical simulation of DNA condensation with two salts, affect of
divalent counterion size | Final revision, published online at J. Chem. Phys. arXiv admin note:
text overlap with arXiv:0912.3595 | J. Chem. Phys., 144 (2016) 065102 | 10.1063/1.4940312 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The problem of DNA$-$DNA interaction mediated by divalent counterions is
studied using a generalized Grand-canonical Monte-Carlo simulation for a system
of two salts. The effect of the divalent counterion size on the condensation
behavior of the DNA bundle is investigated. Experimentally, it is known that
multivalent... | [
{
"created": "Sun, 9 Aug 2015 21:00:45 GMT",
"version": "v1"
},
{
"created": "Fri, 28 Aug 2015 04:43:44 GMT",
"version": "v2"
},
{
"created": "Sat, 13 Feb 2016 03:41:40 GMT",
"version": "v3"
}
] | 2016-02-19 | [
[
"Nguyen",
"Toan T.",
""
]
] | The problem of DNA$-$DNA interaction mediated by divalent counterions is studied using a generalized Grand-canonical Monte-Carlo simulation for a system of two salts. The effect of the divalent counterion size on the condensation behavior of the DNA bundle is investigated. Experimentally, it is known that multivalent c... |
1408.5007 | Krzysztof Bartoszek | Krzysztof Bartoszek and Serik Sagitov | A Consistent Estimator of the Evolutionary Rate | null | Journal of Theoretical Biology 371:69-78, 2015 | 10.1016/j.jtbi.2015.01.019 | null | q-bio.PE math.PR q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a branching particle system where particles reproduce according
to the pure birth Yule process with the birth rate L, conditioned on the
observed number of particles to be equal n. Particles are assumed to move
independently on the real line according to the Brownian motion with the local
variance s2. In ... | [
{
"created": "Thu, 21 Aug 2014 14:08:47 GMT",
"version": "v1"
}
] | 2020-11-23 | [
[
"Bartoszek",
"Krzysztof",
""
],
[
"Sagitov",
"Serik",
""
]
] | We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate L, conditioned on the observed number of particles to be equal n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance s2. In th... |
1810.03687 | Xiao-Jun Tian | Xiao-Jun Tian, Dong Zhou, Haiyan Fu, Rong Zhang, Xiaojie Wang, Sui
Huang, Youhua Liu, Jianhua Xing | Sequential Wnt Agonist then Antagonist Treatment Accelerates Tissue
Repair and Minimizes Fibrosis | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tissue fibrosis compromises organ function and occurs as a potential
long-term outcome in response to acute tissue injuries. Currently, lack of
mechanistic understanding prevents effective prevention and treatment of the
progression from acute injury to fibrosis. Here, we combined quantitative
experimental studies wi... | [
{
"created": "Mon, 8 Oct 2018 20:19:43 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Mar 2019 15:06:07 GMT",
"version": "v2"
},
{
"created": "Thu, 4 Jul 2019 16:23:48 GMT",
"version": "v3"
}
] | 2019-07-05 | [
[
"Tian",
"Xiao-Jun",
""
],
[
"Zhou",
"Dong",
""
],
[
"Fu",
"Haiyan",
""
],
[
"Zhang",
"Rong",
""
],
[
"Wang",
"Xiaojie",
""
],
[
"Huang",
"Sui",
""
],
[
"Liu",
"Youhua",
""
],
[
"Xing",
"Jianhua"... | Tissue fibrosis compromises organ function and occurs as a potential long-term outcome in response to acute tissue injuries. Currently, lack of mechanistic understanding prevents effective prevention and treatment of the progression from acute injury to fibrosis. Here, we combined quantitative experimental studies with... |
1504.00120 | Andrew Teschendorff | Andrew E. Teschendorff and Christopher R. S. Banerji and Simone
Severini and Reimer Kuehn and Peter Sollich | Increased signaling entropy in cancer requires the scale-free property
of protein interaction networks | 20 pages, 5 figures. In Press in Sci Rep 2015 | Scientific Reports (2015) 5, 9646 | 10.1038/srep09646 | null | q-bio.MN q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/3.0/ | One of the key characteristics of cancer cells is an increased phenotypic
plasticity, driven by underlying genetic and epigenetic perturbations. However,
at a systems-level it is unclear how these perturbations give rise to the
observed increased plasticity. Elucidating such systems-level principles is key
for an imp... | [
{
"created": "Wed, 1 Apr 2015 06:50:41 GMT",
"version": "v1"
}
] | 2015-04-30 | [
[
"Teschendorff",
"Andrew E.",
""
],
[
"Banerji",
"Christopher R. S.",
""
],
[
"Severini",
"Simone",
""
],
[
"Kuehn",
"Reimer",
""
],
[
"Sollich",
"Peter",
""
]
] | One of the key characteristics of cancer cells is an increased phenotypic plasticity, driven by underlying genetic and epigenetic perturbations. However, at a systems-level it is unclear how these perturbations give rise to the observed increased plasticity. Elucidating such systems-level principles is key for an impro... |
2011.08081 | Morteza Nattagh Najafi | M. Rahimi-Majd, M. A. Seifi, L. de Arcangelis, M. N. Najafi | On the role of anaxonic local neurons in the crossover to continuously
varying exponents for avalanche activity | null | Phys. Rev. E 103, 042402 (2021) | 10.1103/PhysRevE.103.042402 | null | q-bio.NC cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Local anaxonic neurons with graded potential release are important
ingredients of nervous systems, present in the olfactory bulb system of
mammalians, in the human visual system, as well as in arthropods and nematodes.
We develop a neuronal network model including both axonic and anaxonic neurons
and monitor the acti... | [
{
"created": "Mon, 16 Nov 2020 16:27:29 GMT",
"version": "v1"
}
] | 2021-04-14 | [
[
"Rahimi-Majd",
"M.",
""
],
[
"Seifi",
"M. A.",
""
],
[
"de Arcangelis",
"L.",
""
],
[
"Najafi",
"M. N.",
""
]
] | Local anaxonic neurons with graded potential release are important ingredients of nervous systems, present in the olfactory bulb system of mammalians, in the human visual system, as well as in arthropods and nematodes. We develop a neuronal network model including both axonic and anaxonic neurons and monitor the activi... |
2211.08673 | Thomas Harris | Thomas Harris, Nicholas Geard, Cameron Zachreson | Correlation of viral loads in disease transmission chains could bias
early estimates of the reproduction number | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Early estimates of the transmission properties of a newly emerged pathogen
are critical to an effective public health response, and are often based on
limited outbreak data. Here, we use simulations to investigate a potential
source of bias in such estimates, arising from correlations between the viral
load of cases ... | [
{
"created": "Wed, 16 Nov 2022 04:59:56 GMT",
"version": "v1"
}
] | 2022-11-17 | [
[
"Harris",
"Thomas",
""
],
[
"Geard",
"Nicholas",
""
],
[
"Zachreson",
"Cameron",
""
]
] | Early estimates of the transmission properties of a newly emerged pathogen are critical to an effective public health response, and are often based on limited outbreak data. Here, we use simulations to investigate a potential source of bias in such estimates, arising from correlations between the viral load of cases in... |
2210.09574 | Shuqiang Huang | Shuqiang Huang, Cuiyu Tan, Jinzhen Zheng, Zhugu Huang, Zhihong Li,
Ziyin Lv, Wanru Chen | Integrative Pan-Cancer Analysis of RNMT: a Potential Prognostic and
Immunological Biomarker | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: RNA guanine-7 methyltransferase (RNMT) is one of the main
regulators of N7-methylguanosine, and the deregulation of RNMT correlated with
tumor development and immune metabolism. However, the specific function of RNMT
in pan-cancer remains unclear.
Methods: RNMT expression in different cancers was analyz... | [
{
"created": "Tue, 18 Oct 2022 04:07:32 GMT",
"version": "v1"
},
{
"created": "Thu, 21 Mar 2024 11:04:21 GMT",
"version": "v2"
}
] | 2024-03-22 | [
[
"Huang",
"Shuqiang",
""
],
[
"Tan",
"Cuiyu",
""
],
[
"Zheng",
"Jinzhen",
""
],
[
"Huang",
"Zhugu",
""
],
[
"Li",
"Zhihong",
""
],
[
"Lv",
"Ziyin",
""
],
[
"Chen",
"Wanru",
""
]
] | Background: RNA guanine-7 methyltransferase (RNMT) is one of the main regulators of N7-methylguanosine, and the deregulation of RNMT correlated with tumor development and immune metabolism. However, the specific function of RNMT in pan-cancer remains unclear. Methods: RNMT expression in different cancers was analyzed u... |
2104.05989 | Swapna Sasi | Mahak Kothari, Swapna Sasi, Jun Chen, Elham Zareian, Basabdatta Sen
Bhattacharya | Bayesian Optimisation for a Biologically Inspired Population Neural
Network | 7 pages, 7 figures | null | null | null | q-bio.QM cs.NE q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We have used Bayesian Optimisation (BO) to find hyper-parameters in an
existing biologically plausible population neural network. The 8-dimensional
optimal hyper-parameter combination should be such that the network dynamics
simulate the resting state alpha rhythm (8 - 13 Hz rhythms in brain signals).
Each combinatio... | [
{
"created": "Tue, 13 Apr 2021 07:48:42 GMT",
"version": "v1"
}
] | 2021-04-14 | [
[
"Kothari",
"Mahak",
""
],
[
"Sasi",
"Swapna",
""
],
[
"Chen",
"Jun",
""
],
[
"Zareian",
"Elham",
""
],
[
"Bhattacharya",
"Basabdatta Sen",
""
]
] | We have used Bayesian Optimisation (BO) to find hyper-parameters in an existing biologically plausible population neural network. The 8-dimensional optimal hyper-parameter combination should be such that the network dynamics simulate the resting state alpha rhythm (8 - 13 Hz rhythms in brain signals). Each combination ... |
q-bio/0509011 | Uwe Grimm | Michael Baake (Bielefeld), Uwe Grimm (Milton Keynes) and Harald
Jockusch (Bielefeld) | Freely forming groups: Trying to be rare | 8 pages with 1 figure; final version | The ANZIAM Journal 48 (2006) 1-10 | null | null | q-bio.PE math.DS | null | A simple weakly frequency dependent model for the dynamics of a population
with a finite number of types is proposed, based upon an advantage of being
rare. In the infinite population limit, this model gives rise to a non-smooth
dynamical system that reaches its globally stable equilibrium in finite time.
This dynami... | [
{
"created": "Fri, 9 Sep 2005 16:02:06 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Sep 2005 08:49:18 GMT",
"version": "v2"
},
{
"created": "Mon, 26 Jun 2006 12:31:02 GMT",
"version": "v3"
},
{
"created": "Fri, 29 Sep 2006 14:41:57 GMT",
"version": "v4"
}
] | 2007-05-23 | [
[
"Baake",
"Michael",
"",
"Bielefeld"
],
[
"Grimm",
"Uwe",
"",
"Milton Keynes"
],
[
"Jockusch",
"Harald",
"",
"Bielefeld"
]
] | A simple weakly frequency dependent model for the dynamics of a population with a finite number of types is proposed, based upon an advantage of being rare. In the infinite population limit, this model gives rise to a non-smooth dynamical system that reaches its globally stable equilibrium in finite time. This dynamica... |
0704.3619 | Marcus Kaiser | Luciano da F Costa, Marcus Kaiser, Claus C Hilgetag | Predicting the connectivity of primate cortical networks from
topological and spatial node properties | null | BMC Systems Biology 2007, 1:16 | 10.1186/1752-0509-1-16 | null | q-bio.NC physics.soc-ph | null | The organization of the connectivity between mammalian cortical areas has
become a major subject of study, because of its important role in scaffolding
the macroscopic aspects of animal behavior and intelligence. In this study we
present a computational reconstruction approach to the problem of network
organization, ... | [
{
"created": "Thu, 26 Apr 2007 20:13:58 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Costa",
"Luciano da F",
""
],
[
"Kaiser",
"Marcus",
""
],
[
"Hilgetag",
"Claus C",
""
]
] | The organization of the connectivity between mammalian cortical areas has become a major subject of study, because of its important role in scaffolding the macroscopic aspects of animal behavior and intelligence. In this study we present a computational reconstruction approach to the problem of network organization, by... |
1910.04100 | Thomas Sturm | Dima Grigoriev, Alexandru Iosif, Hamid Rahkooy, Thomas Sturm, Andreas
Weber | Efficiently and Effectively Recognizing Toricity of Steady State
Varieties | We made the presentation clearer and fixed many small flaws and
typos. A database with our computations is now available as ancillary file | Math. Comput. Sci., 15(2):199-232, Jun 2021 | 10.1007/s11786-020-00479-9 | null | q-bio.MN cs.SC math.AG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the problem of testing whether the points in a complex or real
variety with non-zero coordinates form a multiplicative group or, more
generally, a coset of a multiplicative group. For the coset case, we study the
notion of shifted toric varieties which generalizes the notion of toric
varieties. This requi... | [
{
"created": "Wed, 9 Oct 2019 16:25:58 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Apr 2020 07:40:47 GMT",
"version": "v2"
}
] | 2021-07-06 | [
[
"Grigoriev",
"Dima",
""
],
[
"Iosif",
"Alexandru",
""
],
[
"Rahkooy",
"Hamid",
""
],
[
"Sturm",
"Thomas",
""
],
[
"Weber",
"Andreas",
""
]
] | We consider the problem of testing whether the points in a complex or real variety with non-zero coordinates form a multiplicative group or, more generally, a coset of a multiplicative group. For the coset case, we study the notion of shifted toric varieties which generalizes the notion of toric varieties. This require... |
0905.0991 | Tom Michoel | Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen
Marchal | Comparative analysis of module-based versus direct methods for
reverse-engineering transcriptional regulatory networks | 13 pages, 1 table, 6 figures + 6 pages supplementary information (1
table, 5 figures) | BMC Systems Biology 2009, 3:49 | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have compared a recently developed module-based algorithm LeMoNe for
reverse-engineering transcriptional regulatory networks to a mutual information
based direct algorithm CLR, using benchmark expression data and databases of
known transcriptional regulatory interactions for Escherichia coli and
Saccharomyces cere... | [
{
"created": "Thu, 7 May 2009 10:39:44 GMT",
"version": "v1"
}
] | 2009-05-08 | [
[
"Michoel",
"Tom",
""
],
[
"De Smet",
"Riet",
""
],
[
"Joshi",
"Anagha",
""
],
[
"Van de Peer",
"Yves",
""
],
[
"Marchal",
"Kathleen",
""
]
] | We have compared a recently developed module-based algorithm LeMoNe for reverse-engineering transcriptional regulatory networks to a mutual information based direct algorithm CLR, using benchmark expression data and databases of known transcriptional regulatory interactions for Escherichia coli and Saccharomyces cerevi... |
2305.03925 | Wei Xie | Hua Zheng, Wei Xie, Paul Whitford, Ailun Wang, Chunsheng Fang, Wandi
Xu | Structure-Function Dynamics Hybrid Modeling: RNA Degradation | 12 pages, 5 figures | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | RNA structure and functional dynamics play fundamental roles in controlling
biological systems. Molecular dynamics simulation, which can characterize
interactions at an atomistic level, can advance the understanding on new drug
discovery, manufacturing, and delivery mechanisms. However, it is
computationally unattain... | [
{
"created": "Sat, 6 May 2023 04:40:48 GMT",
"version": "v1"
},
{
"created": "Wed, 10 May 2023 01:47:01 GMT",
"version": "v2"
},
{
"created": "Sun, 18 Jun 2023 00:25:36 GMT",
"version": "v3"
}
] | 2023-06-21 | [
[
"Zheng",
"Hua",
""
],
[
"Xie",
"Wei",
""
],
[
"Whitford",
"Paul",
""
],
[
"Wang",
"Ailun",
""
],
[
"Fang",
"Chunsheng",
""
],
[
"Xu",
"Wandi",
""
]
] | RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery, manufacturing, and delivery mechanisms. However, it is computationally unattainab... |
0811.3716 | Jonathan Doye | Gabriel Villar, Alex W. Wilber, Alex J. Williamson, Parvinder Thiara,
Jonathan P.K. Doye, Ard A. Louis, Mara N. Jochum, Anna C.F. Lewis and
Emmanuel D. Levy | The self-assembly and evolution of homomeric protein complexes | 4 pages, 4 figures | Phys. Rev. Lett. 102, 118106 (2009) | 10.1103/PhysRevLett.102.118106 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a simple "patchy particle" model to study the thermodynamics and
dynamics of self-assembly of homomeric protein complexes. Our calculations
allow us to rationalize recent results for dihedral complexes. Namely, why
evolution of such complexes naturally takes the system into a region of
interaction space ... | [
{
"created": "Sat, 22 Nov 2008 23:05:05 GMT",
"version": "v1"
}
] | 2009-10-07 | [
[
"Villar",
"Gabriel",
""
],
[
"Wilber",
"Alex W.",
""
],
[
"Williamson",
"Alex J.",
""
],
[
"Thiara",
"Parvinder",
""
],
[
"Doye",
"Jonathan P. K.",
""
],
[
"Louis",
"Ard A.",
""
],
[
"Jochum",
"Mara N.",
""... | We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of such complexes naturally takes the system into a region of interaction space wh... |
1301.0004 | Ignacio Gallo | Ignacio Gallo | Population genetics of gene function | 30 pages, 6 figures | null | 10.1007/s11538-013-9841-6 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper shows that differentiating the lifetimes of two phenotypes
independently from their fertility can lead to a qualitative change in the
equilibrium of a population: since survival and reproduction are distinct
functional aspects of an organism, this observation contributes to extend the
population-genetical ... | [
{
"created": "Sun, 30 Dec 2012 08:05:19 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Jan 2013 17:29:26 GMT",
"version": "v2"
},
{
"created": "Tue, 22 Jan 2013 15:13:07 GMT",
"version": "v3"
},
{
"created": "Thu, 24 Jan 2013 06:24:43 GMT",
"version": "v4"
},
{
"c... | 2013-05-22 | [
[
"Gallo",
"Ignacio",
""
]
] | This paper shows that differentiating the lifetimes of two phenotypes independently from their fertility can lead to a qualitative change in the equilibrium of a population: since survival and reproduction are distinct functional aspects of an organism, this observation contributes to extend the population-genetical ch... |
2404.04086 | Patricia Lamirande | Patricia Lamirande, Eamonn A. Gaffney, Michael Gertz, Philip K. Maini,
Jessica R. Crawshaw, Antonello Caruso | A first passage model of intravitreal drug delivery and residence time,
in relation to ocular geometry, individual variability, and injection
location | null | null | null | null | q-bio.QM math.AP | http://creativecommons.org/licenses/by/4.0/ | Purpose: Standard of care for various retinal diseases involves recurrent
intravitreal injections. This motivates mathematical modelling efforts to
identify influential factors for drug residence time, aiming to minimise
administration frequency. We sought to describe the vitreal diffusion of
therapeutics in nonclini... | [
{
"created": "Fri, 5 Apr 2024 13:21:48 GMT",
"version": "v1"
}
] | 2024-04-08 | [
[
"Lamirande",
"Patricia",
""
],
[
"Gaffney",
"Eamonn A.",
""
],
[
"Gertz",
"Michael",
""
],
[
"Maini",
"Philip K.",
""
],
[
"Crawshaw",
"Jessica R.",
""
],
[
"Caruso",
"Antonello",
""
]
] | Purpose: Standard of care for various retinal diseases involves recurrent intravitreal injections. This motivates mathematical modelling efforts to identify influential factors for drug residence time, aiming to minimise administration frequency. We sought to describe the vitreal diffusion of therapeutics in nonclinica... |
1901.10005 | Thomas Gaudelet | Thomas Gaudelet, Noel Malod-Dognin, Jon Sanchez-Valle, Vera Pancaldi,
Alfonso Valencia and Natasa Przulj | Unveiling new disease, pathway, and gene associations via multi-scale
neural networks | 16 pages | PLOS ONE, 15(4), p.e0231059 (2020) | 10.1371/journal.pone.0231059 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Diseases involve complex processes and modifications to the cellular
machinery. The gene expression profile of the affected cells contains
characteristic patterns linked to a disease. Hence, biological knowledge
pertaining to a disease can be derived from a patient cell's profile, improving
our diagnosis ability, as ... | [
{
"created": "Mon, 28 Jan 2019 21:17:57 GMT",
"version": "v1"
},
{
"created": "Sat, 11 May 2019 11:36:44 GMT",
"version": "v2"
},
{
"created": "Fri, 10 Apr 2020 07:53:13 GMT",
"version": "v3"
}
] | 2020-04-13 | [
[
"Gaudelet",
"Thomas",
""
],
[
"Malod-Dognin",
"Noel",
""
],
[
"Sanchez-Valle",
"Jon",
""
],
[
"Pancaldi",
"Vera",
""
],
[
"Valencia",
"Alfonso",
""
],
[
"Przulj",
"Natasa",
""
]
] | Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can be derived from a patient cell's profile, improving our diagnosis ability, as we... |
2301.02286 | Yury Garcia | Yury E. Garcia, Shu-Wei Chou-Chen, Luis A. Barboza, Maria L.
Daza-Torres, J. Cricelio Montesinos-Lopez, Paola Vasquez, Juan G. Calvo,
Miriam Nuno, and Fabio Sanchez | Common patterns between dengue cases, climate, and local environmental
variables in Costa Rica: A Wavelet Approach | 21 pages, 15 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Throughout history, prevention and control of dengue transmission have
challenged public health authorities worldwide. In the last decades, the
interaction of multiple factors, such as environmental and climate variability,
has influenced increments in incidence and geographical spread of the virus. In
Costa Rica, a ... | [
{
"created": "Tue, 3 Jan 2023 22:08:46 GMT",
"version": "v1"
}
] | 2023-01-09 | [
[
"Garcia",
"Yury E.",
""
],
[
"Chou-Chen",
"Shu-Wei",
""
],
[
"Barboza",
"Luis A.",
""
],
[
"Daza-Torres",
"Maria L.",
""
],
[
"Montesinos-Lopez",
"J. Cricelio",
""
],
[
"Vasquez",
"Paola",
""
],
[
"Calvo",
"Jua... | Throughout history, prevention and control of dengue transmission have challenged public health authorities worldwide. In the last decades, the interaction of multiple factors, such as environmental and climate variability, has influenced increments in incidence and geographical spread of the virus. In Costa Rica, a co... |
1605.08740 | Elizabeth Lee | Elizabeth C. Lee, Jason M. Asher, Sandra Goldlust, John D. Kraemer,
Andrew B. Lawson, and Shweta Bansal | Mind the scales: Harnessing spatial big data for infectious disease
surveillance and inference | 12 pages, 1 figure | null | null | null | q-bio.PE physics.soc-ph stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spatial big data have the "velocity," "volume," and "variety" of big data
sources and additional geographic information about the record. Digital data
sources, such as medical claims, mobile phone call data records, and geo-tagged
tweets, have entered infectious disease epidemiology as novel sources of data
to comple... | [
{
"created": "Fri, 27 May 2016 18:17:20 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Jun 2016 02:39:04 GMT",
"version": "v2"
},
{
"created": "Fri, 26 Aug 2016 20:31:56 GMT",
"version": "v3"
}
] | 2016-08-30 | [
[
"Lee",
"Elizabeth C.",
""
],
[
"Asher",
"Jason M.",
""
],
[
"Goldlust",
"Sandra",
""
],
[
"Kraemer",
"John D.",
""
],
[
"Lawson",
"Andrew B.",
""
],
[
"Bansal",
"Shweta",
""
]
] | Spatial big data have the "velocity," "volume," and "variety" of big data sources and additional geographic information about the record. Digital data sources, such as medical claims, mobile phone call data records, and geo-tagged tweets, have entered infectious disease epidemiology as novel sources of data to compleme... |
0808.2231 | Brian Gin | Brian C. Gin, Juan P. Garrahan and Phillip L. Geissler | The limited role of non-native contacts in folding pathways of a lattice
protein | 11 pages, 4 figures | J Mol Biol. 2009 Oct 9;392(5):1303-14. | 10.1016/j.jmb.2009.06.058 | null | q-bio.BM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Models of protein energetics which neglect interactions between amino acids
that are not adjacent in the native state, such as the Go model, encode or
underlie many influential ideas on protein folding. Implicit in this
simplification is a crucial assumption that has never been critically evaluated
in a broad context... | [
{
"created": "Sat, 16 Aug 2008 02:31:02 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Jan 2009 22:42:18 GMT",
"version": "v2"
}
] | 2009-10-08 | [
[
"Gin",
"Brian C.",
""
],
[
"Garrahan",
"Juan P.",
""
],
[
"Geissler",
"Phillip L.",
""
]
] | Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a crucial assumption that has never been critically evaluated in a broad context: ... |
2107.03220 | Yanqiao Zhu | Yanqiao Zhu, Hejie Cui, Lifang He, Lichao Sun, Carl Yang | Joint Embedding of Structural and Functional Brain Networks with Graph
Neural Networks for Mental Illness Diagnosis | Formal version accepted to IEEE EMBC 2022; previously presented at
ICML 2021 Workshop on Computational Approaches to Mental Health (no
proceedings) | null | null | null | q-bio.NC cs.LG physics.med-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multimodal brain networks characterize complex connectivities among different
brain regions from both structural and functional aspects and provide a new
means for mental disease analysis. Recently, Graph Neural Networks (GNNs) have
become a de facto model for analyzing graph-structured data. However, how to
employ G... | [
{
"created": "Wed, 7 Jul 2021 13:49:57 GMT",
"version": "v1"
},
{
"created": "Tue, 24 May 2022 17:04:23 GMT",
"version": "v2"
}
] | 2022-05-25 | [
[
"Zhu",
"Yanqiao",
""
],
[
"Cui",
"Hejie",
""
],
[
"He",
"Lifang",
""
],
[
"Sun",
"Lichao",
""
],
[
"Yang",
"Carl",
""
]
] | Multimodal brain networks characterize complex connectivities among different brain regions from both structural and functional aspects and provide a new means for mental disease analysis. Recently, Graph Neural Networks (GNNs) have become a de facto model for analyzing graph-structured data. However, how to employ GNN... |
2208.14102 | Medhavi Vishwakarma | Sindhu M, Medhavi Vishwakarma | Role of heterogeneity in dictating tumorigenesis in epithelial tissues | null | null | null | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | Biological systems across various length and time scales are noisy, including
tissues. Why are biological tissues inherently chaotic? Does heterogeneity play
a role in determining the physiology and pathology of tissues? How do physical
and biochemical heterogeneity crosstalk to dictate tissue function? In this
revie... | [
{
"created": "Tue, 30 Aug 2022 09:35:30 GMT",
"version": "v1"
},
{
"created": "Sun, 18 Sep 2022 15:28:45 GMT",
"version": "v2"
},
{
"created": "Thu, 29 Sep 2022 12:13:54 GMT",
"version": "v3"
}
] | 2022-09-30 | [
[
"M",
"Sindhu",
""
],
[
"Vishwakarma",
"Medhavi",
""
]
] | Biological systems across various length and time scales are noisy, including tissues. Why are biological tissues inherently chaotic? Does heterogeneity play a role in determining the physiology and pathology of tissues? How do physical and biochemical heterogeneity crosstalk to dictate tissue function? In this review,... |
1908.05120 | Alexandre de Brevern | Tarun Narwani (BIGR), Catherine Etchebest (BIGR), Pierrick Craveur
(BIGR), Sylvain L\'eonard (DSIMB, BIGR), Joseph Rebehmed (LAU, BIGR),
Narayanaswamy Srinivasan, Aur\'elie Bornot (DSIMB), Jean-Christophe Gelly
(BIGR), Alexandre de Brevern (BIGR) | In silico prediction of protein flexibility with local structure
approach | null | Biochimie, Elsevier, 2019, 165, pp.150-155 | 10.1016/j.biochi.2019.07.025 | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Flexibility is an intrinsic essential feature of protein structures, directly
linked to their functions. To this day, most of the prediction methods use the
crystallographic data (namely B-factors) as the only indicator of protein's
inner flexibility and predicts them as rigid or flexible.PredyFlexy stands
differentl... | [
{
"created": "Wed, 14 Aug 2019 13:40:51 GMT",
"version": "v1"
}
] | 2019-08-15 | [
[
"Narwani",
"Tarun",
"",
"BIGR"
],
[
"Etchebest",
"Catherine",
"",
"BIGR"
],
[
"Craveur",
"Pierrick",
"",
"BIGR"
],
[
"Léonard",
"Sylvain",
"",
"DSIMB, BIGR"
],
[
"Rebehmed",
"Joseph",
"",
"LAU, BIGR"
],
[
"Srin... | Flexibility is an intrinsic essential feature of protein structures, directly linked to their functions. To this day, most of the prediction methods use the crystallographic data (namely B-factors) as the only indicator of protein's inner flexibility and predicts them as rigid or flexible.PredyFlexy stands differently ... |
2312.05956 | Kohitij Kar | Kohitij Kar, and James J DiCarlo | The Quest for an Integrated Set of Neural Mechanisms Underlying Object
Recognition in Primates | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Visual object recognition -- the behavioral ability to rapidly and accurately
categorize many visually encountered objects -- is core to primate cognition.
This behavioral capability is algorithmically impressive because of the myriad
identity-preserving viewpoints and scenes that dramatically change the visual
image... | [
{
"created": "Sun, 10 Dec 2023 17:58:08 GMT",
"version": "v1"
}
] | 2023-12-12 | [
[
"Kar",
"Kohitij",
""
],
[
"DiCarlo",
"James J",
""
]
] | Visual object recognition -- the behavioral ability to rapidly and accurately categorize many visually encountered objects -- is core to primate cognition. This behavioral capability is algorithmically impressive because of the myriad identity-preserving viewpoints and scenes that dramatically change the visual image p... |
1310.4598 | Alexey Mazur K | Alexey K. Mazur and Mounir Maaloum | DNA flexibility on short length scales probed by atomic force microscopy | 5 pages, 5 figures; to appear in PRL | Phys. Rev. Lett. (2014) 112,068104 | 10.1103/PhysRevLett.112.068104 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Unusually high bending flexibility has been recently reported for DNA on
short length scales. We use atomic force microscopy (AFM) in solution to obtain
a direct estimate of DNA bending statistics for scales down to one helical
turn. It appears that DNA behaves as a Gaussian chain and is well described by
the worm-li... | [
{
"created": "Thu, 17 Oct 2013 07:30:29 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Jan 2014 17:44:42 GMT",
"version": "v2"
}
] | 2014-07-22 | [
[
"Mazur",
"Alexey K.",
""
],
[
"Maaloum",
"Mounir",
""
]
] | Unusually high bending flexibility has been recently reported for DNA on short length scales. We use atomic force microscopy (AFM) in solution to obtain a direct estimate of DNA bending statistics for scales down to one helical turn. It appears that DNA behaves as a Gaussian chain and is well described by the worm-like... |
1403.6328 | Simone Pigolotti | Giuseppe Bianco, Patrizio Mariani, Andre W. Visser, Maria Grazia
Mazzocchi, and Simone Pigolotti | Analysis of self-overlap reveals trade-offs in plankton swimming
trajectories | 9 pages, 5 figures, submitted | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Movement is a fundamental behaviour of organisms that brings about beneficial
encounters with resources and mates, but at the same time exposes the organism
to dangerous encounters with predators. The movement patterns adopted by
organisms should reflect a balance between these contrasting processes. This
trade-off c... | [
{
"created": "Tue, 25 Mar 2014 12:49:38 GMT",
"version": "v1"
}
] | 2014-03-26 | [
[
"Bianco",
"Giuseppe",
""
],
[
"Mariani",
"Patrizio",
""
],
[
"Visser",
"Andre W.",
""
],
[
"Mazzocchi",
"Maria Grazia",
""
],
[
"Pigolotti",
"Simone",
""
]
] | Movement is a fundamental behaviour of organisms that brings about beneficial encounters with resources and mates, but at the same time exposes the organism to dangerous encounters with predators. The movement patterns adopted by organisms should reflect a balance between these contrasting processes. This trade-off can... |
0807.0247 | Catherine Beauchemin | Amy L. Bauer, Catherine A.A. Beauchemin, and Alan S. Perelson | Agent-Based Modeling of Host-Pathogen Systems: The Successes and
Challenges | LaTeX, 12 pages, 1 EPS figure, uses document class REVTeX 4, and
packages hyperref, xspace, graphics, amsmath, verbatim, and SIunits | Information Sciences, Volume 179, Issue 10, 29 April 2009, Pages
1379-1389 | 10.1016/j.ins.2008.11.012 | null | q-bio.CB q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Agent-based models have been employed to describe numerous processes in
immunology. Simulations based on these types of models have been used to
enhance our understanding of immunology and disease pathology. We review
various agent-based models relevant to host-pathogen systems and discuss their
contributions to our ... | [
{
"created": "Tue, 1 Jul 2008 22:01:21 GMT",
"version": "v1"
}
] | 2017-12-05 | [
[
"Bauer",
"Amy L.",
""
],
[
"Beauchemin",
"Catherine A. A.",
""
],
[
"Perelson",
"Alan S.",
""
]
] | Agent-based models have been employed to describe numerous processes in immunology. Simulations based on these types of models have been used to enhance our understanding of immunology and disease pathology. We review various agent-based models relevant to host-pathogen systems and discuss their contributions to our un... |
1612.09268 | Sidarta Ribeiro | Natalia Bezerra Mota, Sylvia Pinheiro, Mariano Sigman, Diego Fernandez
Slezak, Guillermo Cecchi, Mauro Copelli, Sidarta Ribeiro | The ontogeny of discourse structure mimics the development of literature | Natalia Bezerra Mota and Sylvia Pinheiro: Equal contribution Sidarta
Ribeiro and Mauro Copelli: Corresponding authors | null | null | null | q-bio.NC cs.CL physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Discourse varies with age, education, psychiatric state and historical epoch,
but the ontogenetic and cultural dynamics of discourse structure remain to be
quantitatively characterized. To this end we investigated word graphs obtained
from verbal reports of 200 subjects ages 2-58, and 676 literary texts spanning
~5,0... | [
{
"created": "Tue, 27 Dec 2016 21:58:42 GMT",
"version": "v1"
}
] | 2016-12-30 | [
[
"Mota",
"Natalia Bezerra",
""
],
[
"Pinheiro",
"Sylvia",
""
],
[
"Sigman",
"Mariano",
""
],
[
"Slezak",
"Diego Fernandez",
""
],
[
"Cecchi",
"Guillermo",
""
],
[
"Copelli",
"Mauro",
""
],
[
"Ribeiro",
"Sidarta"... | Discourse varies with age, education, psychiatric state and historical epoch, but the ontogenetic and cultural dynamics of discourse structure remain to be quantitatively characterized. To this end we investigated word graphs obtained from verbal reports of 200 subjects ages 2-58, and 676 literary texts spanning ~5,000... |
2203.04695 | Shengchao Liu | Shengchao Liu, Meng Qu, Zuobai Zhang, Huiyu Cai, Jian Tang | Structured Multi-task Learning for Molecular Property Prediction | null | null | null | null | q-bio.BM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multi-task learning for molecular property prediction is becoming
increasingly important in drug discovery. However, in contrast to other
domains, the performance of multi-task learning in drug discovery is still not
satisfying as the number of labeled data for each task is too limited, which
calls for additional dat... | [
{
"created": "Tue, 22 Feb 2022 20:31:23 GMT",
"version": "v1"
},
{
"created": "Thu, 6 Oct 2022 03:21:41 GMT",
"version": "v2"
}
] | 2022-10-07 | [
[
"Liu",
"Shengchao",
""
],
[
"Qu",
"Meng",
""
],
[
"Zhang",
"Zuobai",
""
],
[
"Cai",
"Huiyu",
""
],
[
"Tang",
"Jian",
""
]
] | Multi-task learning for molecular property prediction is becoming increasingly important in drug discovery. However, in contrast to other domains, the performance of multi-task learning in drug discovery is still not satisfying as the number of labeled data for each task is too limited, which calls for additional data ... |
0705.3473 | Alex Barnett | A. H. Barnett and P. R. Moorcroft | Analytic steady-state space use patterns and rapid computations in
mechanistic home range analysis | 14 pages, 7 figures, submit to J. Math. Biol | null | null | null | q-bio.QM | null | Mechanistic home range models are important tools in modeling animal dynamics
in spatially-complex environments. We introduce a class of stochastic models
for animal movement in a habitat of varying preference. Such models interpolate
between spatially-implicit resource selection analysis (RSA) and
advection-diffusio... | [
{
"created": "Wed, 23 May 2007 21:53:04 GMT",
"version": "v1"
}
] | 2007-05-25 | [
[
"Barnett",
"A. H.",
""
],
[
"Moorcroft",
"P. R.",
""
]
] | Mechanistic home range models are important tools in modeling animal dynamics in spatially-complex environments. We introduce a class of stochastic models for animal movement in a habitat of varying preference. Such models interpolate between spatially-implicit resource selection analysis (RSA) and advection-diffusion ... |
1909.12653 | Mauricio Barahona | Maxwell Hodges, Mauricio Barahona and Sophia N. Yaliraki | Allostery and cooperativity in multimeric proteins: bond-to-bond
propensities in ATCase | 17 pages, 7 figures | Scientific Reports, volume 8, Article number: 11079 (2018) | 10.1038/s41598-018-27992-z | null | q-bio.QM physics.bio-ph physics.chem-ph q-bio.BM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with
six active sites that exhibits allostery: its catalytic rate is modulated by
the binding of various substrates at distal points from the active sites. A
recently developed method, bond-to-bond propensity analysis, has proven capable
of predict... | [
{
"created": "Fri, 27 Sep 2019 12:37:49 GMT",
"version": "v1"
}
] | 2019-09-30 | [
[
"Hodges",
"Maxwell",
""
],
[
"Barahona",
"Mauricio",
""
],
[
"Yaliraki",
"Sophia N.",
""
]
] | Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with six active sites that exhibits allostery: its catalytic rate is modulated by the binding of various substrates at distal points from the active sites. A recently developed method, bond-to-bond propensity analysis, has proven capable of predictin... |
1707.00027 | Nathan Baker | Elizabeth Jurrus, Dave Engel, Keith Star, Kyle Monson, Juan Brandi,
Lisa E. Felberg, David H. Brookes, Leighton Wilson, Jiahui Chen, Karina
Liles, Minju Chun, Peter Li, David W. Gohara, Todd Dolinsky, Robert Konecny,
David R. Koes, Jens Erik Nielsen, Teresa Head-Gordon, Weihua Geng, Robert
Krasny, Guo Wei Wei, ... | Improvements to the APBS biomolecular solvation software suite | null | null | 10.1002/pro.3280 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages
that has provided impact in the study of a broad range of chemical, biological,
and biomedical applications. APBS addresses three key technology challenges for
unde... | [
{
"created": "Fri, 30 Jun 2017 19:09:01 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Aug 2017 21:24:37 GMT",
"version": "v2"
}
] | 2017-12-29 | [
[
"Jurrus",
"Elizabeth",
""
],
[
"Engel",
"Dave",
""
],
[
"Star",
"Keith",
""
],
[
"Monson",
"Kyle",
""
],
[
"Brandi",
"Juan",
""
],
[
"Felberg",
"Lisa E.",
""
],
[
"Brookes",
"David H.",
""
],
[
"Wil... | The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for unders... |
2004.00834 | Claus Vogl | Claus Vogl, Sandra Peer | Inference of population genetic parameters with a biallelic mutation
drift model using the coalescent, diffusion with orthogonal polynomials, and
the Moran model | 26 pages, 2 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In population genetics, extant samples are usually used for inference of past
population genetic forces. With the Kingman coalescent and the backward
diffusion equation, inference of the marginal likelihood proceeds from an
extant sample backward in time. Conditional on an extant sample, the Moran
model can also be u... | [
{
"created": "Thu, 2 Apr 2020 06:26:53 GMT",
"version": "v1"
}
] | 2020-04-03 | [
[
"Vogl",
"Claus",
""
],
[
"Peer",
"Sandra",
""
]
] | In population genetics, extant samples are usually used for inference of past population genetic forces. With the Kingman coalescent and the backward diffusion equation, inference of the marginal likelihood proceeds from an extant sample backward in time. Conditional on an extant sample, the Moran model can also be use... |
1608.04700 | Antoine Zambelli | Antoine Zambelli | A Data-Driven Approach to Estimating the Number of Clusters in
Hierarchical Clustering | 6 pages, 7 figures, 12 tables | null | null | null | q-bio.QM cs.LG stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose two new methods for estimating the number of clusters in a
hierarchical clustering framework in the hopes of creating a fully automated
process with no human intervention. The methods are completely data-driven and
require no input from the researcher, and as such are fully automated. They are
quite easy t... | [
{
"created": "Tue, 16 Aug 2016 18:35:09 GMT",
"version": "v1"
}
] | 2016-08-17 | [
[
"Zambelli",
"Antoine",
""
]
] | We propose two new methods for estimating the number of clusters in a hierarchical clustering framework in the hopes of creating a fully automated process with no human intervention. The methods are completely data-driven and require no input from the researcher, and as such are fully automated. They are quite easy to ... |
2112.14500 | Mar\'ia Vallet-Regi | Elena Alvarez, Manuel Estevez, Carla Jimenez-Jimenez, Montserrat
Colilla, Isabel Izquierdo-Barba, Blanca Gonzalez, Maria Vallet-Regi | A versatile multicomponent mesoporous silica nanosystem with dual
antimicrobial and osteogenic effects | 27 pages, 8 figures | Acta Biomaterialia 136 (2021) 570 to 581 | 10.1016/j.actbio.2021.09.027 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In this manuscript, we propose a simple and versatile methodology to design
nanosystems based on biocompatible and multicomponent mesoporous silica
nanoparticles (MSNs) for infection management. This strategy relies on the
combination of antibiotic molecules and antimicrobial metal ions into the same
nanosystem, affo... | [
{
"created": "Wed, 29 Dec 2021 11:12:33 GMT",
"version": "v1"
}
] | 2021-12-30 | [
[
"Alvarez",
"Elena",
""
],
[
"Estevez",
"Manuel",
""
],
[
"Jimenez-Jimenez",
"Carla",
""
],
[
"Colilla",
"Montserrat",
""
],
[
"Izquierdo-Barba",
"Isabel",
""
],
[
"Gonzalez",
"Blanca",
""
],
[
"Vallet-Regi",
"M... | In this manuscript, we propose a simple and versatile methodology to design nanosystems based on biocompatible and multicomponent mesoporous silica nanoparticles (MSNs) for infection management. This strategy relies on the combination of antibiotic molecules and antimicrobial metal ions into the same nanosystem, afford... |
2303.13996 | Steven Salzberg | Paulo Amaral, Silvia Carbonell-Sala, Francisco M. De La Vega, Tiago
Faial, Adam Frankish, Thomas Gingeras, Roderic Guigo, Jennifer L Harrow,
Artemis G. Hatzigeorgiou, Rory Johnson, Terence D. Murphy, Mihaela Pertea,
Kim D. Pruitt, Shashikant Pujar, Hazuki Takahashi, Igor Ulitsky, Ales
Varabyou, Christine A. Wel... | The status of the human gene catalogue | 14 pages | null | null | null | q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Scientists have been trying to identify all of the genes in the human genome
since the initial draft of the genome was published in 2001. Over the
intervening years, much progress has been made in identifying protein-coding
genes, and the estimated number has shrunk to fewer than 20,000, although the
number of distin... | [
{
"created": "Fri, 24 Mar 2023 13:49:25 GMT",
"version": "v1"
}
] | 2023-03-27 | [
[
"Amaral",
"Paulo",
""
],
[
"Carbonell-Sala",
"Silvia",
""
],
[
"De La Vega",
"Francisco M.",
""
],
[
"Faial",
"Tiago",
""
],
[
"Frankish",
"Adam",
""
],
[
"Gingeras",
"Thomas",
""
],
[
"Guigo",
"Roderic",
"... | Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the estimated number has shrunk to fewer than 20,000, although the number of distinct... |
2102.11629 | Simon Martina-Perez | Simon Martina-Perez, Matthew J. Simpson, Ruth E. Baker | Bayesian uncertainty quantification for data-driven equation learning | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | Equation learning aims to infer differential equation models from data. While
a number of studies have shown that differential equation models can be
successfully identified when the data are sufficiently detailed and corrupted
with relatively small amounts of noise, the relationship between observation
noise and unc... | [
{
"created": "Tue, 23 Feb 2021 11:08:30 GMT",
"version": "v1"
},
{
"created": "Mon, 17 May 2021 16:06:44 GMT",
"version": "v2"
},
{
"created": "Mon, 7 Jun 2021 17:19:44 GMT",
"version": "v3"
},
{
"created": "Wed, 29 Sep 2021 16:46:41 GMT",
"version": "v4"
}
] | 2021-09-30 | [
[
"Martina-Perez",
"Simon",
""
],
[
"Simpson",
"Matthew J.",
""
],
[
"Baker",
"Ruth E.",
""
]
] | Equation learning aims to infer differential equation models from data. While a number of studies have shown that differential equation models can be successfully identified when the data are sufficiently detailed and corrupted with relatively small amounts of noise, the relationship between observation noise and uncer... |
1906.11365 | Eshan Mitra | Eshan D. Mitra, William S. Hlavacek | Parameter Estimation and Uncertainty Quantification for Systems Biology
Models | 23 pages, 1 figure, 1 table | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mathematical models can provide quantitative insight into immunoreceptor
signaling, but require parameterization and uncertainty quantification before
making reliable predictions. We review currently available methods and software
tools to address these problems. We consider gradient-based and gradient-free
methods f... | [
{
"created": "Wed, 26 Jun 2019 22:22:21 GMT",
"version": "v1"
}
] | 2019-06-28 | [
[
"Mitra",
"Eshan D.",
""
],
[
"Hlavacek",
"William S.",
""
]
] | Mathematical models can provide quantitative insight into immunoreceptor signaling, but require parameterization and uncertainty quantification before making reliable predictions. We review currently available methods and software tools to address these problems. We consider gradient-based and gradient-free methods for... |
2211.02829 | Arka Sanyal Mr | Adrita Chanda, Adrija Aich, Arka Sanyal, Anantika Chandra, Saumyadeep
Goswami | Current Landscape of Mesenchymal Stem Cell Therapy in COVID Induced
Acute Respiratory Distress Syndrome | 14 Pages, 6 Figures | Acta Scientific MICROBIOLOGY (ISSN: 2581-3226), Volume 5 Issue 8
August 2022 | 10.31080/ASMI.2022.05.1125 | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | The severe acute respiratory syndrome coronavirus 2 outbreak in Chinas Hubei
area in late 2019 has now created a global pandemic that has spread to over 150
countries. In most people, COVID 19 is a respiratory infection that produces
fever, cough, and shortness of breath. Patients with severe COVID 19 may
develop ARD... | [
{
"created": "Sat, 5 Nov 2022 06:54:42 GMT",
"version": "v1"
}
] | 2022-11-08 | [
[
"Chanda",
"Adrita",
""
],
[
"Aich",
"Adrija",
""
],
[
"Sanyal",
"Arka",
""
],
[
"Chandra",
"Anantika",
""
],
[
"Goswami",
"Saumyadeep",
""
]
] | The severe acute respiratory syndrome coronavirus 2 outbreak in Chinas Hubei area in late 2019 has now created a global pandemic that has spread to over 150 countries. In most people, COVID 19 is a respiratory infection that produces fever, cough, and shortness of breath. Patients with severe COVID 19 may develop ARDS.... |
q-bio/0611049 | David A. Kessler | David A. Kessler, Nadav M. Shnerb | Extinction Rates for Fluctuation-Induced Metastabilities : A Real-Space
WKB Approach | null | null | 10.1007/s10955-007-9312-2 | null | q-bio.PE | null | The extinction of a single species due to demographic stochasticity is
analyzed. The discrete nature of the individual agents and the Poissonian noise
related to the birth-death processes result in local extinction of a metastable
population, as the system hits the absorbing state. The Fokker-Planck
formulation of th... | [
{
"created": "Thu, 16 Nov 2006 21:10:16 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Kessler",
"David A.",
""
],
[
"Shnerb",
"Nadav M.",
""
]
] | The extinction of a single species due to demographic stochasticity is analyzed. The discrete nature of the individual agents and the Poissonian noise related to the birth-death processes result in local extinction of a metastable population, as the system hits the absorbing state. The Fokker-Planck formulation of that... |
2106.12405 | Kento Nakamura | Kento Nakamura and Tetsuya J. Kobayashi | Optimal sensing and control of run-and-tumble chemotaxis | 8 pages, 4 figures | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Run-and-tumble chemotaxis is one of the representative search strategies of
an odor source via sensing its spatial gradient. The optimal ways of sensing
and control in the run-and-tumble chemotaxis have been analyzed theoretically
to elucidate the efficiency of strategies implemented in organisms. However,
because of... | [
{
"created": "Wed, 23 Jun 2021 13:48:31 GMT",
"version": "v1"
}
] | 2021-06-24 | [
[
"Nakamura",
"Kento",
""
],
[
"Kobayashi",
"Tetsuya J.",
""
]
] | Run-and-tumble chemotaxis is one of the representative search strategies of an odor source via sensing its spatial gradient. The optimal ways of sensing and control in the run-and-tumble chemotaxis have been analyzed theoretically to elucidate the efficiency of strategies implemented in organisms. However, because of t... |
1301.3528 | Momiao Xiong | Momiao Xiong and Long Ma | An Efficient Sufficient Dimension Reduction Method for Identifying
Genetic Variants of Clinical Significance | null | null | null | null | q-bio.GN cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fast and cheaper next generation sequencing technologies will generate
unprecedentedly massive and highly-dimensional genomic and epigenomic variation
data. In the near future, a routine part of medical record will include the
sequenced genomes. A fundamental question is how to efficiently extract genomic
and epigeno... | [
{
"created": "Tue, 15 Jan 2013 23:19:14 GMT",
"version": "v1"
}
] | 2013-01-17 | [
[
"Xiong",
"Momiao",
""
],
[
"Ma",
"Long",
""
]
] | Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced genomes. A fundamental question is how to efficiently extract genomic and epigenomi... |
1104.2562 | Mareike Fischer | Mareike Fischer | Mathematical aspects of phylogenetic groves | 17 pages, 5 figures | null | null | null | q-bio.PE cs.DS math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The inference of new information on the relatedness of species by
phylogenetic trees based on DNA data is one of the main challenges of modern
biology. But despite all technological advances, DNA sequencing is still a
time-consuming and costly process. Therefore, decision criteria would be
desirable to decide a prior... | [
{
"created": "Wed, 13 Apr 2011 17:58:47 GMT",
"version": "v1"
}
] | 2015-03-19 | [
[
"Fischer",
"Mareike",
""
]
] | The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and costly process. Therefore, decision criteria would be desirable to decide a priori ... |
0905.2329 | Marco Morelli | Marco J. Morelli, Pieter Rein ten Wolde and Rosalind J. Allen | DNA looping provides stability and robustness to the bacteriophage
lambda switch | In press on PNAS. Single file contains supplementary info | null | 10.1073/pnas.0810399106 | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The bistable gene regulatory switch controlling the transition from lysogeny
to lysis in bacteriophage lambda presents a unique challenge to quantitative
modeling. Despite extensive characterization of this regulatory network, the
origin of the extreme stability of the lysogenic state remains unclear. We have
constru... | [
{
"created": "Thu, 14 May 2009 13:37:23 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Morelli",
"Marco J.",
""
],
[
"Wolde",
"Pieter Rein ten",
""
],
[
"Allen",
"Rosalind J.",
""
]
] | The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage lambda presents a unique challenge to quantitative modeling. Despite extensive characterization of this regulatory network, the origin of the extreme stability of the lysogenic state remains unclear. We have construct... |
1609.07292 | David A. Kessler | David A. Kessler and Herbert Levine | Nonlinear self-adapting wave patterns | null | null | 10.1088/1367-2630/18/12/122001 | null | q-bio.SC nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a new type of traveling wave pattern, one that can adapt to the
size of physical system in which it is embedded. Such a system arises when the
initial state has an instability that extends down to zero wavevector,
connecting at that point to two symmetry modes of the underlying dynamical
system. The Min sy... | [
{
"created": "Fri, 23 Sep 2016 09:46:51 GMT",
"version": "v1"
}
] | 2017-01-04 | [
[
"Kessler",
"David A.",
""
],
[
"Levine",
"Herbert",
""
]
] | We propose a new type of traveling wave pattern, one that can adapt to the size of physical system in which it is embedded. Such a system arises when the initial state has an instability that extends down to zero wavevector, connecting at that point to two symmetry modes of the underlying dynamical system. The Min syst... |
1203.6231 | Maroussia Favre | Maroussia Favre and Didier Sornette | Strong gender differences in reproductive success variance, and the
times to the most recent common ancestors | null | Journal of Theoretical Biology 310, 43-54 (2012) | 10.1016/j.jtbi.2012.06.026 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Time To the Most Recent Common Ancestor (TMRCA) based on human
mitochondrial DNA (mtDNA) is estimated to be twice that based on the
non-recombining part of the Y chromosome (NRY). These TMRCAs have special
demographic implications because mtDNA is transmitted only from mother to
child, and NRY from father to son.... | [
{
"created": "Wed, 28 Mar 2012 11:26:13 GMT",
"version": "v1"
}
] | 2013-12-19 | [
[
"Favre",
"Maroussia",
""
],
[
"Sornette",
"Didier",
""
]
] | The Time To the Most Recent Common Ancestor (TMRCA) based on human mitochondrial DNA (mtDNA) is estimated to be twice that based on the non-recombining part of the Y chromosome (NRY). These TMRCAs have special demographic implications because mtDNA is transmitted only from mother to child, and NRY from father to son. T... |
0712.3900 | Damien Eveillard | J\'er\'emie Bourdon (LINA), Damien Eveillard (LINA), Samuel Gabillard
(LINA), Theo Merle (LINA, ENS Cachan) | Integrating heterogeneous knowledges for understanding biological
behaviors: a probabilistic approach | 10 pages | null | null | null | q-bio.QM | null | Despite recent molecular technique improvements, biological knowledge remains
incomplete. Reasoning on living systems hence implies to integrate
heterogeneous and partial informations. Although current investigations
successfully focus on qualitative behaviors of macromolecular networks, others
approaches show partia... | [
{
"created": "Sun, 23 Dec 2007 07:22:47 GMT",
"version": "v1"
}
] | 2009-09-29 | [
[
"Bourdon",
"Jérémie",
"",
"LINA"
],
[
"Eveillard",
"Damien",
"",
"LINA"
],
[
"Gabillard",
"Samuel",
"",
"LINA"
],
[
"Merle",
"Theo",
"",
"LINA, ENS Cachan"
]
] | Despite recent molecular technique improvements, biological knowledge remains incomplete. Reasoning on living systems hence implies to integrate heterogeneous and partial informations. Although current investigations successfully focus on qualitative behaviors of macromolecular networks, others approaches show partial ... |
1707.02614 | Daniel Hoffmann | Jean-No\"el Grad, Alba Gigante, Christoph Wilms, Jan Nikolaj Dybowski,
Ludwig Ohl, Christian Ottmann, Carsten Schmuck, and Daniel Hoffmann | Locating large flexible ligands on proteins | null | null | 10.1021/acs.jcim.7b00413 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many biologically important ligands of proteins are large, flexible, and
often charged molecules that bind to extended regions on the protein surface.
It is infeasible or expensive to locate such ligands on proteins with standard
methods such as docking or molecular dynamics (MD) simulation. The alternative
approach ... | [
{
"created": "Sun, 9 Jul 2017 18:25:52 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Jul 2017 16:24:03 GMT",
"version": "v2"
}
] | 2018-04-17 | [
[
"Grad",
"Jean-Noël",
""
],
[
"Gigante",
"Alba",
""
],
[
"Wilms",
"Christoph",
""
],
[
"Dybowski",
"Jan Nikolaj",
""
],
[
"Ohl",
"Ludwig",
""
],
[
"Ottmann",
"Christian",
""
],
[
"Schmuck",
"Carsten",
""
]... | Many biologically important ligands of proteins are large, flexible, and often charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods such as docking or molecular dynamics (MD) simulation. The alternative approach pr... |
1901.06286 | Alexander L\"uck | Charalampos Kyriakopoulos, Pascal Giehr, Alexander L\"uck, J\"orn
Walter, Verena Wolf | A Hybrid HMM Approach for the Dynamics of DNA Methylation | 15 pages, 5 figures, 2 tables | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The understanding of mechanisms that control epigenetic changes is an
important research area in modern functional biology. Epigenetic modifications
such as DNA methylation are in general very stable over many cell divisions.
DNA methylation can however be subject to specific and fast changes over a
short time scale ... | [
{
"created": "Fri, 18 Jan 2019 14:55:08 GMT",
"version": "v1"
}
] | 2019-01-21 | [
[
"Kyriakopoulos",
"Charalampos",
""
],
[
"Giehr",
"Pascal",
""
],
[
"Lück",
"Alexander",
""
],
[
"Walter",
"Jörn",
""
],
[
"Wolf",
"Verena",
""
]
] | The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA methylation can however be subject to specific and fast changes over a short time scale ev... |
1901.04053 | Tim Peterson | Sandeep Kumar, Timothy R. Peterson | Moonshots for aging | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | As the global population ages, there is increased interest in living longer
and improving one's quality of life in later years. However, studying aging -
the decline in body function - is expensive and time-consuming. And despite
research success to make model organisms live longer, there still aren't really
any feas... | [
{
"created": "Sun, 13 Jan 2019 20:10:39 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Apr 2019 20:47:12 GMT",
"version": "v2"
}
] | 2019-04-23 | [
[
"Kumar",
"Sandeep",
""
],
[
"Peterson",
"Timothy R.",
""
]
] | As the global population ages, there is increased interest in living longer and improving one's quality of life in later years. However, studying aging - the decline in body function - is expensive and time-consuming. And despite research success to make model organisms live longer, there still aren't really any feasib... |
2401.01632 | Jose A Capitan | Jose A. Capitan and David Alonso | Out-of-equlibrium inference of stochastic model parameters through
population data from generic consumer-resource dynamics | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Consumer-resource dynamics is central in determining biomass transport across
ecosystems. The assumptions of mass action, chemostatic conditions and
stationarity in stochastic feeding dynamics lead to Holling type II functional
responses, whose use is widespread in macroscopic models of population
dynamics. However, ... | [
{
"created": "Wed, 3 Jan 2024 09:07:10 GMT",
"version": "v1"
}
] | 2024-01-04 | [
[
"Capitan",
"Jose A.",
""
],
[
"Alonso",
"David",
""
]
] | Consumer-resource dynamics is central in determining biomass transport across ecosystems. The assumptions of mass action, chemostatic conditions and stationarity in stochastic feeding dynamics lead to Holling type II functional responses, whose use is widespread in macroscopic models of population dynamics. However, to... |
2402.00090 | Vishnu Menon | Akash K Rao, Vishnu K Menon, Arnav Bhavsar, Shubhajit Roy Chowdhury,
Ramsingh Negi, Varun Dutt | Classification of attention performance post-longitudinal tDCS via
functional connectivity and machine learning methods | 6 pages, to be presented in the IEEE 9th International Conference for
Convergence in Technology (I2CT),Pune, April 2024. arXiv admin note:
substantial text overlap with arXiv:2401.17700 | null | null | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Attention is the brain's mechanism for selectively processing specific
stimuli while filtering out irrelevant information. Characterizing changes in
attention following long-term interventions (such as transcranial direct
current stimulation (tDCS)) has seldom been emphasized in the literature. To
classify attention ... | [
{
"created": "Wed, 31 Jan 2024 10:38:52 GMT",
"version": "v1"
}
] | 2024-02-02 | [
[
"Rao",
"Akash K",
""
],
[
"Menon",
"Vishnu K",
""
],
[
"Bhavsar",
"Arnav",
""
],
[
"Chowdhury",
"Shubhajit Roy",
""
],
[
"Negi",
"Ramsingh",
""
],
[
"Dutt",
"Varun",
""
]
] | Attention is the brain's mechanism for selectively processing specific stimuli while filtering out irrelevant information. Characterizing changes in attention following long-term interventions (such as transcranial direct current stimulation (tDCS)) has seldom been emphasized in the literature. To classify attention pe... |
1106.6210 | Kazuhiko Minami | Kazuhiko Minami | Equivalence between two-dimensional cell-sorting and one-dimensional
generalized random walk -- spin representations of generating operators | 32 pages | null | null | null | q-bio.CB cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The two-dimensional cell-sorting problem is found to be mathematically
equivalent to the one-dimensional random walk problem with pair creations and
annihilations, i.e. the adhesion probabilities in the cell-sorting model relate
analytically to the expectation values in the random walk problem. This is an
example dem... | [
{
"created": "Thu, 30 Jun 2011 12:51:23 GMT",
"version": "v1"
}
] | 2011-07-01 | [
[
"Minami",
"Kazuhiko",
""
]
] | The two-dimensional cell-sorting problem is found to be mathematically equivalent to the one-dimensional random walk problem with pair creations and annihilations, i.e. the adhesion probabilities in the cell-sorting model relate analytically to the expectation values in the random walk problem. This is an example demon... |
1207.0108 | Eckhard Schlemm | Eckhard Schlemm | Asymptotic fitness distribution in the Bak-Sneppen model of biological
evolution with four species | 10 pages, one figure; to appear in Journal of Statistical Physics | 2012, Journal of Statistical Physics, 148, pp 191-203 | 10.1007/s10955-012-0538-2 | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We suggest a new method to compute the asymptotic fitness distribution in the
Bak-Sneppen model of biological evolution. As applications we derive the full
asymptotic distribution in the four-species model, and give an explicit linear
recurrence relation for a set of coefficients determining the asymptotic
distributi... | [
{
"created": "Sat, 30 Jun 2012 15:18:29 GMT",
"version": "v1"
}
] | 2015-05-19 | [
[
"Schlemm",
"Eckhard",
""
]
] | We suggest a new method to compute the asymptotic fitness distribution in the Bak-Sneppen model of biological evolution. As applications we derive the full asymptotic distribution in the four-species model, and give an explicit linear recurrence relation for a set of coefficients determining the asymptotic distribution... |
1211.5807 | Pleuni Pennings | Pleuni S. Pennings | HIV drug resistance: problems and perspectives | Updated version, minor changes in text. Review paper. Submitted to:
Infectious Disease Reports
http://www.pagepress.org/journals/index.php/idr/index | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Access to combination antiretroviral treatment (ART) has improved greatly
over recent years. At the end of 2011, more than eight million HIV infected
people were receiving antiretroviral therapy in low-income and middle-income
countries. ART generally works well in keeping the virus suppressed and the
patient healthy... | [
{
"created": "Sun, 25 Nov 2012 21:00:17 GMT",
"version": "v1"
},
{
"created": "Wed, 23 Jan 2013 21:23:27 GMT",
"version": "v2"
}
] | 2013-01-25 | [
[
"Pennings",
"Pleuni S.",
""
]
] | Access to combination antiretroviral treatment (ART) has improved greatly over recent years. At the end of 2011, more than eight million HIV infected people were receiving antiretroviral therapy in low-income and middle-income countries. ART generally works well in keeping the virus suppressed and the patient healthy. ... |
2403.12684 | Matthijs Meijers | Matthijs Meijers, Denis Ruchnewitz, Jan Eberhardt, Malancha Karmakar,
Marta {\L}uksza, and Michael L\"assig | Concepts and methods for predicting viral evolution | 30 pages, 6 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The seasonal human influenza virus undergoes rapid evolution, leading to
significant changes in circulating viral strains from year to year. These
changes are typically driven by adaptive mutations, particularly in the
antigenic epitopes, the regions of the viral surface protein haemagglutinin
targeted by human antib... | [
{
"created": "Tue, 19 Mar 2024 12:39:37 GMT",
"version": "v1"
},
{
"created": "Thu, 2 May 2024 10:15:27 GMT",
"version": "v2"
}
] | 2024-05-03 | [
[
"Meijers",
"Matthijs",
""
],
[
"Ruchnewitz",
"Denis",
""
],
[
"Eberhardt",
"Jan",
""
],
[
"Karmakar",
"Malancha",
""
],
[
"Łuksza",
"Marta",
""
],
[
"Lässig",
"Michael",
""
]
] | The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibod... |
2401.08712 | Fariba Jafari Horestani | M. Mehdi Owrang O, Fariba Jafari Horestani, Ginger Schwarz | Survival Analysis of Young Triple-Negative Breast Cancer Patients | 31 Pages, 11 Figures, 7 Tables, Peer-reviewed article | null | null | null | q-bio.QM cs.LG stat.AP | http://creativecommons.org/publicdomain/zero/1.0/ | Breast cancer prognosis is crucial for effective treatment, with the disease
more common in women over 40 years old but rare under 40 years old, where less
than 5 percent of cases occur in the U.S. Studies indicate a worse prognosis in
younger women, which varies by ethnicity. Breast cancers are classified based
on r... | [
{
"created": "Mon, 15 Jan 2024 17:51:14 GMT",
"version": "v1"
}
] | 2024-01-18 | [
[
"O",
"M. Mehdi Owrang",
""
],
[
"Horestani",
"Fariba Jafari",
""
],
[
"Schwarz",
"Ginger",
""
]
] | Breast cancer prognosis is crucial for effective treatment, with the disease more common in women over 40 years old but rare under 40 years old, where less than 5 percent of cases occur in the U.S. Studies indicate a worse prognosis in younger women, which varies by ethnicity. Breast cancers are classified based on rec... |
q-bio/0403026 | Abhijnan Rej | Abhijnan Rej | A Dynamical Similarity Approach to the Foundations of Complexity and
Coordination in Multiscale Systems | latex2e, 35 pages, University Scholar Thesis (University of
Connecticut) | null | null | null | q-bio.NC q-bio.QM | null | I review a number of cognate issues that, taken together, pertain to the
creation of a non-reductionistic theory of multiscale coordination and present
one candidate theory based on the principle of dynamical similarity.
| [
{
"created": "Thu, 18 Mar 2004 18:05:06 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Rej",
"Abhijnan",
""
]
] | I review a number of cognate issues that, taken together, pertain to the creation of a non-reductionistic theory of multiscale coordination and present one candidate theory based on the principle of dynamical similarity. |
2109.10474 | Yuxiang Wu | Yuxiang Wu, Shang Wu, Xin Wang, Chengtian Lang, Quanshi Zhang, Quan
Wen, Tianqi Xu | Rapid detection and recognition of whole brain activity in a freely
behaving Caenorhabditis elegans | null | PLOS Computational Biology 18(10): e1010594, 2022 | 10.1371/journal.pcbi.1010594 | null | q-bio.QM cs.CV | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Advanced volumetric imaging methods and genetically encoded activity
indicators have permitted a comprehensive characterization of whole brain
activity at single neuron resolution in \textit{Caenorhabditis elegans}. The
constant motion and deformation of the nematode nervous system, however, impose
a great challenge ... | [
{
"created": "Wed, 22 Sep 2021 01:33:54 GMT",
"version": "v1"
},
{
"created": "Thu, 23 Sep 2021 07:16:01 GMT",
"version": "v2"
},
{
"created": "Mon, 17 Jan 2022 15:57:51 GMT",
"version": "v3"
},
{
"created": "Thu, 15 Sep 2022 09:13:11 GMT",
"version": "v4"
}
] | 2022-10-12 | [
[
"Wu",
"Yuxiang",
""
],
[
"Wu",
"Shang",
""
],
[
"Wang",
"Xin",
""
],
[
"Lang",
"Chengtian",
""
],
[
"Zhang",
"Quanshi",
""
],
[
"Wen",
"Quan",
""
],
[
"Xu",
"Tianqi",
""
]
] | Advanced volumetric imaging methods and genetically encoded activity indicators have permitted a comprehensive characterization of whole brain activity at single neuron resolution in \textit{Caenorhabditis elegans}. The constant motion and deformation of the nematode nervous system, however, impose a great challenge fo... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.