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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1802.04488 | Guillaume Le Treut | Guillaume Le Treut, Fran\c{c}ois K\'ep\`es, Henri Orland | A polymer model for the quantitative reconstruction of 3d chromosome
architecture from Hi-C and GAM data | 76 pages, 43 figures | Biophysical Journal 115, 2286-2294, December 18, 2018 | 10.1016/j.bpj.2018.10.032 | null | q-bio.QM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is widely believed that the folding of the chromosome in the nucleus has a
major effect on genetic expression. For example co-regulated genes in several
species have been shown to colocalize in space despite being far away on the
DNA sequence. In this manuscript, we present a new method to model the
three-dimensio... | [
{
"created": "Tue, 13 Feb 2018 07:23:17 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Apr 2020 06:55:21 GMT",
"version": "v2"
}
] | 2020-04-29 | [
[
"Treut",
"Guillaume Le",
""
],
[
"Képès",
"François",
""
],
[
"Orland",
"Henri",
""
]
] | It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA sequence. In this manuscript, we present a new method to model the three-dimensiona... |
0705.2704 | Danielle Rojas-Rousse | Auguste Ndoutoume, Danielle Rousse (IRBII), Roland Allemand | Rythmes d'activit\'e locomotrice chez deux insectes parasito\"ides
sympatriques : Eupelmus orientalis et Eupelmus vuilleti (Hym\'enopt\`ere,
Eupelmidae) | null | Comptes Rendus Biologies 329 (2006) 476-482 | null | null | q-bio.PE | null | With an automatic image analysis device, we studied the temporal distribution
of the locomotor activity of E. orientalis and E. vuilleti during 24 h, and
over several days to know whether the activity rhythms of these two Eupelmidae
play a role in their competitive interactions. The analysis of locomotor
activity rhy... | [
{
"created": "Fri, 18 May 2007 14:36:08 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Ndoutoume",
"Auguste",
"",
"IRBII"
],
[
"Rousse",
"Danielle",
"",
"IRBII"
],
[
"Allemand",
"Roland",
""
]
] | With an automatic image analysis device, we studied the temporal distribution of the locomotor activity of E. orientalis and E. vuilleti during 24 h, and over several days to know whether the activity rhythms of these two Eupelmidae play a role in their competitive interactions. The analysis of locomotor activity rhyth... |
1701.02599 | Vaibhav Wasnik | Vaibhav Wasnik | Issues in data expansion in understanding criticality in biological
systems | 6 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | At the point of a second order phase transition also termed as a critical
point, systems display long range order and their macroscopic behaviors are
independent of the microscopic details making up the system. Due to these
properties, it has long been speculated that biological systems that show
similar behavior des... | [
{
"created": "Tue, 10 Jan 2017 14:06:21 GMT",
"version": "v1"
},
{
"created": "Mon, 17 Jul 2017 08:55:17 GMT",
"version": "v2"
}
] | 2017-07-18 | [
[
"Wasnik",
"Vaibhav",
""
]
] | At the point of a second order phase transition also termed as a critical point, systems display long range order and their macroscopic behaviors are independent of the microscopic details making up the system. Due to these properties, it has long been speculated that biological systems that show similar behavior despi... |
0708.2061 | Eduardo Candelario-Jalil | E. Candelario-Jalil, S. M. Al-Dalain, R. Castillo, G. Martinez, O. S.
Fernandez | Selective vulnerability to kainate-induced oxidative damage in different
rat brain regions | null | Journal of Applied Toxicology 21(5): 403-407 (2001) | null | null | q-bio.TO | null | Some markers of oxidative injury were measured in different rat brain areas
(hippocampus, cerebral cortex, striatum, hypothalamus, amygdala/piriform cortex
and cerebellum) after the systemic administration of an excitotoxic dose of
kainic acid (KA, 9 mg kg(-1) i.p.) at two different sampling times (24 and 48
h). Kain... | [
{
"created": "Wed, 15 Aug 2007 15:31:13 GMT",
"version": "v1"
}
] | 2007-08-16 | [
[
"Candelario-Jalil",
"E.",
""
],
[
"Al-Dalain",
"S. M.",
""
],
[
"Castillo",
"R.",
""
],
[
"Martinez",
"G.",
""
],
[
"Fernandez",
"O. S.",
""
]
] | Some markers of oxidative injury were measured in different rat brain areas (hippocampus, cerebral cortex, striatum, hypothalamus, amygdala/piriform cortex and cerebellum) after the systemic administration of an excitotoxic dose of kainic acid (KA, 9 mg kg(-1) i.p.) at two different sampling times (24 and 48 h). Kainic... |
q-bio/0601026 | Jie Liang | Xiang Li and Jie Liang | Knowledge-based energy functions for computational studies of proteins | 57 pages, 6 figures. To be published in a book by Springer | null | 10.1007/978-0-387-68372-0_3 | null | q-bio.BM | null | This chapter discusses theoretical framework and methods for developing
knowledge-based potential functions essential for protein structure prediction,
protein-protein interaction, and protein sequence design. We discuss in some
details about the Miyazawa-Jernigan contact statistical potential,
distance-dependent sta... | [
{
"created": "Thu, 19 Jan 2006 05:40:23 GMT",
"version": "v1"
}
] | 2015-06-26 | [
[
"Li",
"Xiang",
""
],
[
"Liang",
"Jie",
""
]
] | This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent stati... |
1607.03957 | Aleksandra Walczak | Jonathan Desponds, Huy Tran, Teresa Ferraro, Tanguy Lucas, Carmina
Perez Romero, Aurelien Guillou, Cecile Fradin, Mathieu Coppey, Nathalie
Dostatni, and Aleksandra M. Walczak | Precision of readout at the hunchback gene: analyzing short
transcription time traces in living fly embryos | null | null | 10.1371/journal.pcbi.1005256 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The simultaneous expression of the hunchback gene in the numerous nuclei of
the developing fly embryo gives us a unique opportunity to study how
transcription is regulated in living organisms. A recently developed MS2-MCP
technique for imaging nascent messenger RNA in living Drosophila embryos allows
us to quantify t... | [
{
"created": "Wed, 13 Jul 2016 23:23:49 GMT",
"version": "v1"
},
{
"created": "Sun, 20 Nov 2016 22:12:42 GMT",
"version": "v2"
}
] | 2017-02-08 | [
[
"Desponds",
"Jonathan",
""
],
[
"Tran",
"Huy",
""
],
[
"Ferraro",
"Teresa",
""
],
[
"Lucas",
"Tanguy",
""
],
[
"Romero",
"Carmina Perez",
""
],
[
"Guillou",
"Aurelien",
""
],
[
"Fradin",
"Cecile",
""
],
... | The simultaneous expression of the hunchback gene in the numerous nuclei of the developing fly embryo gives us a unique opportunity to study how transcription is regulated in living organisms. A recently developed MS2-MCP technique for imaging nascent messenger RNA in living Drosophila embryos allows us to quantify the... |
2306.12448 | Glen Pridham | Glen Pridham and Andrew D. Rutenberg | Network dynamical stability analysis reveals key "mallostatic" natural
variables that erode homeostasis and drive age-related decline of health | 42 pages including supplmenetal | Sci Rep 13, 22140 (2023) | 10.1038/s41598-023-49129-7 | null | q-bio.OT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Using longitudinal study data, we dynamically model how aging affects
homeostasis in both mice and humans. We operationalize homeostasis as a
multivariate mean-reverting stochastic process. We hypothesize that biomarkers
have stable equilibrium values, but that deviations from equilibrium of each
biomarker affects ot... | [
{
"created": "Tue, 20 Jun 2023 19:02:51 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Oct 2023 14:17:52 GMT",
"version": "v2"
}
] | 2023-12-14 | [
[
"Pridham",
"Glen",
""
],
[
"Rutenberg",
"Andrew D.",
""
]
] | Using longitudinal study data, we dynamically model how aging affects homeostasis in both mice and humans. We operationalize homeostasis as a multivariate mean-reverting stochastic process. We hypothesize that biomarkers have stable equilibrium values, but that deviations from equilibrium of each biomarker affects othe... |
2103.03722 | Vittorio Lippi | Mustafa Emre Ak\c{c}ay, Vittorio Lippi, Thomas Mergner | Visual Modulation of Human Responses to Support Surface Translation | null | Frontiers in Human Neuroscience 15 (2021) 98 | 10.3389/fnhum.2021.615200 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Vision is known to improve human postural responses to external
perturbations. This study investigates the role of vision for the responses to
continuous pseudorandom support surface translations in the body sagittal plane
in three visual conditions: with the eyes closed (EC), in stroboscopic
illumination (EO/SI; onl... | [
{
"created": "Fri, 5 Mar 2021 14:52:19 GMT",
"version": "v1"
}
] | 2021-03-08 | [
[
"Akçay",
"Mustafa Emre",
""
],
[
"Lippi",
"Vittorio",
""
],
[
"Mergner",
"Thomas",
""
]
] | Vision is known to improve human postural responses to external perturbations. This study investigates the role of vision for the responses to continuous pseudorandom support surface translations in the body sagittal plane in three visual conditions: with the eyes closed (EC), in stroboscopic illumination (EO/SI; only ... |
2312.02193 | Petr Slepicka | Jana Pryjmakova, Daniel Grossberger, Anna Kutova, Barbora Vokata,
Miroslav Slouf, Petr Slepicka, Jakub Siegel | A new promising material for biological applications: multi-level
physical modification of AgNPs-decorated PEEK | null | null | null | null | q-bio.OT physics.med-ph | http://creativecommons.org/licenses/by/4.0/ | In the case of polymer medical devices, the surface design plays a crucial
role in contact with human tissue. The use of AgNPs as antibacterial agents is
well known; however, their anchoring into the polymer surface can still be
investigated. This work describes the change in surface morphology and
behaviour in the b... | [
{
"created": "Sat, 2 Dec 2023 08:44:13 GMT",
"version": "v1"
}
] | 2023-12-06 | [
[
"Pryjmakova",
"Jana",
""
],
[
"Grossberger",
"Daniel",
""
],
[
"Kutova",
"Anna",
""
],
[
"Vokata",
"Barbora",
""
],
[
"Slouf",
"Miroslav",
""
],
[
"Slepicka",
"Petr",
""
],
[
"Siegel",
"Jakub",
""
]
] | In the case of polymer medical devices, the surface design plays a crucial role in contact with human tissue. The use of AgNPs as antibacterial agents is well known; however, their anchoring into the polymer surface can still be investigated. This work describes the change in surface morphology and behaviour in the bio... |
2407.16215 | Tsuyoshi Tatsukawa | Tsuyoshi Tatsukawa and Jun-nosuke Teramae | Energy-information trade-off makes the cortical critical power law the
optimal coding | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stimulus responses of cortical neurons exhibit the critical power law, where
the covariance eigenspectrum follows the power law with the exponent just at
the edge of differentiability of the neural manifold. This criticality is
conjectured to balance the expressivity and robustness of neural codes, because
a non-diff... | [
{
"created": "Tue, 23 Jul 2024 06:44:45 GMT",
"version": "v1"
}
] | 2024-07-24 | [
[
"Tatsukawa",
"Tsuyoshi",
""
],
[
"Teramae",
"Jun-nosuke",
""
]
] | Stimulus responses of cortical neurons exhibit the critical power law, where the covariance eigenspectrum follows the power law with the exponent just at the edge of differentiability of the neural manifold. This criticality is conjectured to balance the expressivity and robustness of neural codes, because a non-differ... |
q-bio/0407019 | Reza Ejtehadi | M. R. Ejtehadi (1 and 2), S. P. Avall (1) and S. S. Plotkin (1) ((1)
Univ. of British Columbia, Canada, (2) Sharif Univ. of Tech., Iran) | Three-body Interactions Improve the Prediction of Rate and Mechanism in
Protein Folding Models | 9 pages, 2 tables and 5 figures | null | 10.1073/pnas.0403486101 | null | q-bio.QM cond-mat.soft physics.bio-ph q-bio.BM | null | Here we study the effects of many-body interactions on rate and mechanism in
protein folding, using the results of molecular dynamics simulations on
numerous coarse-grained C-alpha-model single-domain proteins. After adding
three-body interactions explicitly as a perturbation to a Go-like Hamiltonian
with native pair... | [
{
"created": "Wed, 14 Jul 2004 19:28:38 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Ejtehadi",
"M. R.",
"",
"1 and 2"
],
[
"Avall",
"S. P.",
""
],
[
"Plotkin",
"S. S.",
""
]
] | Here we study the effects of many-body interactions on rate and mechanism in protein folding, using the results of molecular dynamics simulations on numerous coarse-grained C-alpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Go-like Hamiltonian with native pair-w... |
1805.06795 | Igor P. Omelyan | Igor Omelyan and Yuri Kozitsky | Spatially inhomogeneous population dynamics: beyond the mean field
approximation | 7 pages, 4 figures | null | 10.1088/1751-8121/ab2808 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a novel method for numerical modeling of spatially inhomogeneous
moment dynamics of populations with nonlocal dispersal and competition in
continuous space. It is based on analytically solvable decompositions of the
time evolution operator for a coupled set of master equations. This has allowed
us -- for t... | [
{
"created": "Thu, 17 May 2018 14:18:24 GMT",
"version": "v1"
},
{
"created": "Fri, 27 Jul 2018 15:09:06 GMT",
"version": "v2"
},
{
"created": "Mon, 6 Aug 2018 14:41:04 GMT",
"version": "v3"
},
{
"created": "Tue, 4 Dec 2018 13:32:09 GMT",
"version": "v4"
}
] | 2019-07-24 | [
[
"Omelyan",
"Igor",
""
],
[
"Kozitsky",
"Yuri",
""
]
] | We propose a novel method for numerical modeling of spatially inhomogeneous moment dynamics of populations with nonlocal dispersal and competition in continuous space. It is based on analytically solvable decompositions of the time evolution operator for a coupled set of master equations. This has allowed us -- for the... |
1310.3011 | Liane Gabora | Liane Gabora and Nancy Holmes | Dark Side of Creativity - Dangling from a Tassel on the Fabric of
Socially Constructed Reality: Reflections on the Creative Writing Process | 22 pages. Gabora, L., & Holmes, N. (2010). In (A. Cropley, D.
Cropley, J. Kaufman, & M. Runco, Eds.) The Dark Side of Creativity (pp.
277-296). Cambridge UK: Cambridge University Press | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This chapter begins with an investigation into experiences of depression,
alienation, and self-abuse amongst the highly creative. After this journey to
the dark side, it may be uplifting to see that Mother Nature may have a few
tricks up her sleeve to minimize the extent to which we succumb to the negative
aspects of... | [
{
"created": "Fri, 11 Oct 2013 03:07:06 GMT",
"version": "v1"
}
] | 2013-10-14 | [
[
"Gabora",
"Liane",
""
],
[
"Holmes",
"Nancy",
""
]
] | This chapter begins with an investigation into experiences of depression, alienation, and self-abuse amongst the highly creative. After this journey to the dark side, it may be uplifting to see that Mother Nature may have a few tricks up her sleeve to minimize the extent to which we succumb to the negative aspects of c... |
2310.12070 | Alexander Lewanski | Alexander L. Lewanski and Michael C. Grundler and Gideon S. Bradburd | The era of the ARG: an empiricist's guide to ancestral recombination
graphs | 34 pages, 3 figures, 3 tables | null | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | In the presence of recombination, the evolutionary relationships between a
set of sampled genomes cannot be described by a single genealogical tree.
Instead, the genomes are related by a complex, interwoven collection of
genealogies formalized in a structure called an ancestral recombination graph
(ARG). An ARG exten... | [
{
"created": "Wed, 18 Oct 2023 16:04:51 GMT",
"version": "v1"
}
] | 2023-10-19 | [
[
"Lewanski",
"Alexander L.",
""
],
[
"Grundler",
"Michael C.",
""
],
[
"Bradburd",
"Gideon S.",
""
]
] | In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies formalized in a structure called an ancestral recombination graph (ARG). An ARG extensi... |
2307.10833 | Vyacheslav Yukalov | V.I. Yukalov | Selected Topics of Social Physics: Nonequilibrium Systems | Review, 60 pages | Physics 5 (2023) 704--751 | null | null | q-bio.PE physics.bio-ph physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | This review article is the second part of the project ``Selected Topics of
Social Physics". The first part has been devoted to equilibrium systems. The
present part considers nonequilibrium systems. The style of the paper combines
the features of a tutorial and a review, which, from one side, makes it easy to
read fo... | [
{
"created": "Thu, 20 Jul 2023 12:53:02 GMT",
"version": "v1"
}
] | 2023-07-22 | [
[
"Yukalov",
"V. I.",
""
]
] | This review article is the second part of the project ``Selected Topics of Social Physics". The first part has been devoted to equilibrium systems. The present part considers nonequilibrium systems. The style of the paper combines the features of a tutorial and a review, which, from one side, makes it easy to read for ... |
q-bio/0606001 | Georgy Karev | Georgy P. Karev | On Mathematical Theory of Selection: Discrete-Time Models | 8 pages, 3 figures; submitted to International Conference on Complex
Systems 2006 | null | null | null | q-bio.PE q-bio.QM | null | Mathematical theory of selection systems is developed for a wide class of
dynamical models of inhomogeneous populations with discrete time. The Price
equation and its particular case, the Fisher Fundamental theorem of natural
selection (FTNS), are well known general results of the theory. It is known
that the Price e... | [
{
"created": "Thu, 1 Jun 2006 16:13:28 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Karev",
"Georgy P.",
""
]
] | Mathematical theory of selection systems is developed for a wide class of dynamical models of inhomogeneous populations with discrete time. The Price equation and its particular case, the Fisher Fundamental theorem of natural selection (FTNS), are well known general results of the theory. It is known that the Price equ... |
2207.00821 | Min Li | Huimin Zhu, Renyi Zhou, Jing Tang, Min Li | PGMG: A Pharmacophore-Guided Deep Learning Approach for Bioactive
Molecular Generation | null | null | null | null | q-bio.BM cs.LG q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The rational design of novel molecules with desired bioactivity is a critical
but challenging task in drug discovery, especially when treating a novel target
family or understudied targets. Here, we propose PGMG, a pharmacophore-guided
deep learning approach for bioactivate molecule generation. Through the
guidance o... | [
{
"created": "Sat, 2 Jul 2022 12:31:17 GMT",
"version": "v1"
}
] | 2022-07-05 | [
[
"Zhu",
"Huimin",
""
],
[
"Zhou",
"Renyi",
""
],
[
"Tang",
"Jing",
""
],
[
"Li",
"Min",
""
]
] | The rational design of novel molecules with desired bioactivity is a critical but challenging task in drug discovery, especially when treating a novel target family or understudied targets. Here, we propose PGMG, a pharmacophore-guided deep learning approach for bioactivate molecule generation. Through the guidance of ... |
1410.3301 | Joseph Crawford | Yihan Sun, Joseph Crawford, Jie Tang, Tijana Milenkovi\'c | Simultaneous Optimization of Both Node and Edge Conservation in Network
Alignment via WAVE | 12 pages, 4 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Network alignment can be used to transfer functional knowledge between
conserved regions of different networks. Typically, existing methods use a node
cost function (NCF) to compute similarity between nodes in different networks
and an alignment strategy (AS) to find high-scoring alignments with respect to
the total ... | [
{
"created": "Mon, 13 Oct 2014 13:38:30 GMT",
"version": "v1"
}
] | 2014-10-14 | [
[
"Sun",
"Yihan",
""
],
[
"Crawford",
"Joseph",
""
],
[
"Tang",
"Jie",
""
],
[
"Milenković",
"Tijana",
""
]
] | Network alignment can be used to transfer functional knowledge between conserved regions of different networks. Typically, existing methods use a node cost function (NCF) to compute similarity between nodes in different networks and an alignment strategy (AS) to find high-scoring alignments with respect to the total NC... |
2012.10197 | Mihaela Delcea | Ina Buchholz, Felix Nagel, Annelie Klein, Preshit R. Wagh, Ujjwal M.
Mahajan, Andreas Greinacher, Markus M. Lerch, Julia Mayerle, Mihaela Delcea | The impact of physiological stress conditions on protein structure and
trypsin inhibition of serine protease inhibitor Kazal type 1 (SPINK1) and its
N34S variant | null | null | 10.1016/j.bbapap.2019.140281 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the most common mutations in the serine protease inhibitor Kazal type
1 (SPINK1) gene is the N34S variant which is strongly associated with chronic
pancreatitis. Although it is assumed that N34S mutation constitutes a high-risk
factor, the underlying pathologic mechanism is still unknown. In the present
study,... | [
{
"created": "Fri, 18 Dec 2020 12:43:35 GMT",
"version": "v1"
}
] | 2020-12-21 | [
[
"Buchholz",
"Ina",
""
],
[
"Nagel",
"Felix",
""
],
[
"Klein",
"Annelie",
""
],
[
"Wagh",
"Preshit R.",
""
],
[
"Mahajan",
"Ujjwal M.",
""
],
[
"Greinacher",
"Andreas",
""
],
[
"Lerch",
"Markus M.",
""
],
... | One of the most common mutations in the serine protease inhibitor Kazal type 1 (SPINK1) gene is the N34S variant which is strongly associated with chronic pancreatitis. Although it is assumed that N34S mutation constitutes a high-risk factor, the underlying pathologic mechanism is still unknown. In the present study, w... |
0907.4907 | Chandrasekar Kuppusamy | Jane H. Sheeba, V. K. Chandrasekar and M. Lakshmanan | Event--related desynchronization in diffusively coupled oscillator
models | Accepted in Physical Review Letters | null | 10.1103/PhysRevLett.103.074101 | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We seek explanation for the neurophysiological phenomenon of event related
desynchronization (ERD) by using models of diffusively coupled nonlinear
oscillators. We demonstrate that when the strength of the event is sufficient,
ERD is found to emerge and the accomplishment of a behavioral/functional task
is determined... | [
{
"created": "Tue, 28 Jul 2009 12:59:53 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Sheeba",
"Jane H.",
""
],
[
"Chandrasekar",
"V. K.",
""
],
[
"Lakshmanan",
"M.",
""
]
] | We seek explanation for the neurophysiological phenomenon of event related desynchronization (ERD) by using models of diffusively coupled nonlinear oscillators. We demonstrate that when the strength of the event is sufficient, ERD is found to emerge and the accomplishment of a behavioral/functional task is determined b... |
2304.02697 | Zehua Zeng | Zehua Zeng and Hongwu Du | Revolutionizing Single Cell Analysis: The Power of Large Language Models
for Cell Type Annotation | 5 pages, 1 figures | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In recent years, single cell RNA sequencing has become a widely used
technique to study cellular diversity and function. However, accurately
annotating cell types from single cell data has been a challenging task, as it
requires extensive knowledge of cell biology and gene function. The emergence
of large language mo... | [
{
"created": "Wed, 5 Apr 2023 18:45:54 GMT",
"version": "v1"
}
] | 2023-04-07 | [
[
"Zeng",
"Zehua",
""
],
[
"Du",
"Hongwu",
""
]
] | In recent years, single cell RNA sequencing has become a widely used technique to study cellular diversity and function. However, accurately annotating cell types from single cell data has been a challenging task, as it requires extensive knowledge of cell biology and gene function. The emergence of large language mode... |
2102.09729 | Tijl Grootswagers | Tijl Grootswagers, Amanda K Robinson | Overfitting the literature to one set of stimuli and data | null | Front. Hum. Neurosci. 15:682661 (2021) | 10.3389/fnhum.2021.682661 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The fast-growing field of Computational Cognitive Neuroscience is on track to
meet its first crisis. A large number of papers in this nascent field are
developing and testing novel analysis methods using the same stimuli and
neuroimaging datasets. Publication bias and confirmatory exploration will
result in overfitti... | [
{
"created": "Fri, 19 Feb 2021 04:06:39 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Feb 2021 00:44:36 GMT",
"version": "v2"
}
] | 2021-07-09 | [
[
"Grootswagers",
"Tijl",
""
],
[
"Robinson",
"Amanda K",
""
]
] | The fast-growing field of Computational Cognitive Neuroscience is on track to meet its first crisis. A large number of papers in this nascent field are developing and testing novel analysis methods using the same stimuli and neuroimaging datasets. Publication bias and confirmatory exploration will result in overfitting... |
1907.09551 | Stuart Newman | Stuart A. Newman | Cell differentiation: what have we learned in 50 years? | null | null | null | null | q-bio.TO q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | I revisit two theories of cell differentiation in multicellular organisms
published a half-century ago, Stuart Kauffman's global gene regulatory dynamics
(GGRD) model and Roy Britten's and Eric Davidson's modular gene regulatory
network (MGRN) model, in light of newer knowledge of mechanisms of gene
regulation in the... | [
{
"created": "Mon, 22 Jul 2019 20:10:19 GMT",
"version": "v1"
},
{
"created": "Fri, 6 Sep 2019 20:08:20 GMT",
"version": "v2"
}
] | 2019-09-10 | [
[
"Newman",
"Stuart A.",
""
]
] | I revisit two theories of cell differentiation in multicellular organisms published a half-century ago, Stuart Kauffman's global gene regulatory dynamics (GGRD) model and Roy Britten's and Eric Davidson's modular gene regulatory network (MGRN) model, in light of newer knowledge of mechanisms of gene regulation in the m... |
2010.01591 | Richard Betzel | Richard Betzel | Network neuroscience and the connectomics revolution | 24 pages, 5 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Connectomics and network neuroscience offer quantitative scientific
frameworks for modeling and analyzing networks of structurally and functionally
interacting neurons, neuronal populations, and macroscopic brain areas. This
shift in perspective and emphasis on distributed brain function has provided
fundamental insi... | [
{
"created": "Sun, 4 Oct 2020 14:36:03 GMT",
"version": "v1"
}
] | 2020-10-06 | [
[
"Betzel",
"Richard",
""
]
] | Connectomics and network neuroscience offer quantitative scientific frameworks for modeling and analyzing networks of structurally and functionally interacting neurons, neuronal populations, and macroscopic brain areas. This shift in perspective and emphasis on distributed brain function has provided fundamental insigh... |
1602.05887 | Gianna Vivaldo | Gianna Vivaldo, Elisa Masi, Camilla Pandolfi, Stefano Mancuso, Guido
Caldarelli | Networks of plants: how to measure similarity in vegetable species | 18 pages, 6 figures, 7 tables, 1 section of Supplementary Material | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite the common misconception of nearly static organisms, plants do
interact continuously with the environment and with each other. It is fair to
assume that during their evolution they developed particular features to
overcome problems and to exploit possibilities from environment. In this paper
we introduce vari... | [
{
"created": "Thu, 18 Feb 2016 17:40:48 GMT",
"version": "v1"
}
] | 2016-02-19 | [
[
"Vivaldo",
"Gianna",
""
],
[
"Masi",
"Elisa",
""
],
[
"Pandolfi",
"Camilla",
""
],
[
"Mancuso",
"Stefano",
""
],
[
"Caldarelli",
"Guido",
""
]
] | Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems and to exploit possibilities from environment. In this paper we introduce variou... |
2004.14829 | Korbinian Schreiber | K. Schreiber, T. C. Wunderlich, C. Pehle, M. A. Petrovici, J.
Schemmel, and K. Meier | Closed-loop experiments on the BrainScaleS-2 architecture | Neuro-inspired Computational Elements Workshop (NICE 2020). arXiv
admin note: text overlap with arXiv:1912.12980 | null | 10.1145/3381755.3381776 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The evolution of biological brains has always been contingent on their
embodiment within their respective environments, in which survival required
appropriate navigation and manipulation skills. Studying such interactions thus
represents an important aspect of computational neuroscience and, by extension,
a topic of ... | [
{
"created": "Wed, 29 Apr 2020 12:15:24 GMT",
"version": "v1"
}
] | 2020-05-01 | [
[
"Schreiber",
"K.",
""
],
[
"Wunderlich",
"T. C.",
""
],
[
"Pehle",
"C.",
""
],
[
"Petrovici",
"M. A.",
""
],
[
"Schemmel",
"J.",
""
],
[
"Meier",
"K.",
""
]
] | The evolution of biological brains has always been contingent on their embodiment within their respective environments, in which survival required appropriate navigation and manipulation skills. Studying such interactions thus represents an important aspect of computational neuroscience and, by extension, a topic of in... |
2303.01579 | Wolfram M\"obius | Thomas Tunstall, Tim Rogers, Wolfram M\"obius | Assisted percolation of slow-spreading mutants in heterogeneous
environments | null | null | null | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Environmental heterogeneity can drive genetic heterogeneity in expanding
populations; mutant strains may emerge that trade overall growth rate for an
improved ability to survive in patches that are hostile to the wild type. This
evolutionary dynamic is of practical importance when seeking to prevent the
emergence of ... | [
{
"created": "Thu, 2 Mar 2023 21:13:52 GMT",
"version": "v1"
}
] | 2023-03-06 | [
[
"Tunstall",
"Thomas",
""
],
[
"Rogers",
"Tim",
""
],
[
"Möbius",
"Wolfram",
""
]
] | Environmental heterogeneity can drive genetic heterogeneity in expanding populations; mutant strains may emerge that trade overall growth rate for an improved ability to survive in patches that are hostile to the wild type. This evolutionary dynamic is of practical importance when seeking to prevent the emergence of da... |
1711.04870 | Adam Noel | Adam Noel and Yuting Fang and Nan Yang and Dimitrios Makrakis and
Andrew W. Eckford | Using Game Theory for Real-Time Behavioural Dynamics in Microscopic
Populations with Noisy Signalling | 10 pages, 10 figures, 1 table. Submitted for publication | null | null | null | q-bio.CB cs.IT math.IT physics.bio-ph q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper introduces the application of game theory to understand noisy
real-time signalling and the resulting behavioural dynamics in microscopic
populations such as bacteria and other cells. It presents a bridge between the
fields of molecular communication and microscopic game theory. Molecular
communication uses... | [
{
"created": "Mon, 13 Nov 2017 21:54:49 GMT",
"version": "v1"
},
{
"created": "Wed, 16 May 2018 13:07:20 GMT",
"version": "v2"
},
{
"created": "Mon, 4 Feb 2019 23:09:02 GMT",
"version": "v3"
}
] | 2019-02-06 | [
[
"Noel",
"Adam",
""
],
[
"Fang",
"Yuting",
""
],
[
"Yang",
"Nan",
""
],
[
"Makrakis",
"Dimitrios",
""
],
[
"Eckford",
"Andrew W.",
""
]
] | This paper introduces the application of game theory to understand noisy real-time signalling and the resulting behavioural dynamics in microscopic populations such as bacteria and other cells. It presents a bridge between the fields of molecular communication and microscopic game theory. Molecular communication uses c... |
0809.1968 | Quan-Xing Liu | Quan-Xing Liu, Rong-Hua Wang and Zhen Jin | Persistence, extinction and spatio-temporal synchronization of SIRS
cellular automata models | 12pages | J. Stat. Mech. (2009) P07007 | 10.1088/1742-5468/2009/07/P07007 | null | q-bio.PE nlin.CG nlin.PS physics.soc-ph q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spatially explicit models have been widely used in today's mathematical
ecology and epidemiology to study persistence and extinction of populations as
well as their spatial patterns. Here we extend the earlier work--static
dispersal between neighbouring individuals to mobility of individuals as well
as multi-patches ... | [
{
"created": "Thu, 11 Sep 2008 12:05:25 GMT",
"version": "v1"
}
] | 2009-07-01 | [
[
"Liu",
"Quan-Xing",
""
],
[
"Wang",
"Rong-Hua",
""
],
[
"Jin",
"Zhen",
""
]
] | Spatially explicit models have been widely used in today's mathematical ecology and epidemiology to study persistence and extinction of populations as well as their spatial patterns. Here we extend the earlier work--static dispersal between neighbouring individuals to mobility of individuals as well as multi-patches en... |
0910.3226 | Filippo Posta | Filippo Posta, Tom Chou | A mathematical model of intercellular signaling during epithelial wound
healing | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent experiments in epithelial wound healing have demonstrated the
necessity of Mitogen-activated protein kinase (MAPK) for coordinated cell
movement after damage. This MAPK activity is characterized by two wave-like
phenomena. One MAPK "wave" that originates immediately after injury, propagates
deep into the cell ... | [
{
"created": "Fri, 16 Oct 2009 20:50:28 GMT",
"version": "v1"
}
] | 2009-10-20 | [
[
"Posta",
"Filippo",
""
],
[
"Chou",
"Tom",
""
]
] | Recent experiments in epithelial wound healing have demonstrated the necessity of Mitogen-activated protein kinase (MAPK) for coordinated cell movement after damage. This MAPK activity is characterized by two wave-like phenomena. One MAPK "wave" that originates immediately after injury, propagates deep into the cell la... |
2211.08527 | Robin Gutzen | Robin Gutzen, Giulia De Bonis, Chiara De Luca, Elena Pastorelli,
Cristiano Capone, Anna Letizia Allegra Mascaro, Francesco Resta, Arnau
Manasanch, Francesco Saverio Pavone, Maria V. Sanchez-Vives, Maurizio Mattia,
Sonja Gr\"un, Pier Stanislao Paolucci, Michael Denker | Comparing apples to apples -- Using a modular and adaptable analysis
pipeline to compare slow cerebral rhythms across heterogeneous datasets | null | null | 10.1016/j.crmeth.2023.100681 | null | q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Neuroscience is moving towards a more integrative discipline, where
understanding brain function requires consolidating the accumulated evidence
seen across experiments, species, and measurement techniques. A remaining
challenge on that path is integrating such heterogeneous data into analysis
workflows such that con... | [
{
"created": "Tue, 15 Nov 2022 21:54:40 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Feb 2023 17:03:16 GMT",
"version": "v2"
}
] | 2024-01-09 | [
[
"Gutzen",
"Robin",
""
],
[
"De Bonis",
"Giulia",
""
],
[
"De Luca",
"Chiara",
""
],
[
"Pastorelli",
"Elena",
""
],
[
"Capone",
"Cristiano",
""
],
[
"Mascaro",
"Anna Letizia Allegra",
""
],
[
"Resta",
"Francesco... | Neuroscience is moving towards a more integrative discipline, where understanding brain function requires consolidating the accumulated evidence seen across experiments, species, and measurement techniques. A remaining challenge on that path is integrating such heterogeneous data into analysis workflows such that consi... |
1708.08560 | David K. Lubensky | Jeremy Hadidjojo and David K. Lubensky | Spontaneous Chiral Symmetry Breaking in Planar Polarized Epithelia | null | null | null | null | q-bio.TO physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most animal body plans have some degree of left-right asymmetry. This
chirality at the tissue and organ level is often assumed to originate from the
intrinsic handedness of biological molecules. How this handedness might be
transferred from molecules to tissues during development, however, is not well
understood. Her... | [
{
"created": "Mon, 28 Aug 2017 23:38:19 GMT",
"version": "v1"
}
] | 2017-08-30 | [
[
"Hadidjojo",
"Jeremy",
""
],
[
"Lubensky",
"David K.",
""
]
] | Most animal body plans have some degree of left-right asymmetry. This chirality at the tissue and organ level is often assumed to originate from the intrinsic handedness of biological molecules. How this handedness might be transferred from molecules to tissues during development, however, is not well understood. Here ... |
1808.03359 | Ekkehard Ullner | Antonio Politi, Ekkehard Ullner, and Alessandro Torcini | Collective irregular dynamics in balanced networks of leaky
integrate-and-fire neurons | 12 pages, 13 figures | Eur. Phys. J. Special Topics 227, 1185 (2018) | 10.1140/epjst/e2018-00079-7 | null | q-bio.NC cond-mat.dis-nn nlin.AO nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We extensively explore networks of weakly unbalanced, leaky
integrate-and-fire (LIF) neurons for different coupling strength, connectivity,
and by varying the degree of refractoriness, as well as the delay in the spike
transmission. We find that the neural network does not only exhibit a
microscopic (single-neuron) s... | [
{
"created": "Thu, 9 Aug 2018 22:03:32 GMT",
"version": "v1"
}
] | 2018-12-14 | [
[
"Politi",
"Antonio",
""
],
[
"Ullner",
"Ekkehard",
""
],
[
"Torcini",
"Alessandro",
""
]
] | We extensively explore networks of weakly unbalanced, leaky integrate-and-fire (LIF) neurons for different coupling strength, connectivity, and by varying the degree of refractoriness, as well as the delay in the spike transmission. We find that the neural network does not only exhibit a microscopic (single-neuron) sto... |
1510.03194 | Jicun Wang-Michelitsch | Jicun Wang-Michelitsch, Thomas M. Michelitsch | The high osmotic pressure in a lens fiber as a driving force for the
development of senile cortical cataract | 8 pages, figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In lens cataract, the clouding change in lens leads to a decline of
transparency of part of the lens. There are three types of senile cataract:
cortical cataract, nuclear cataract, and posterior/anterior sub-capsular
cataract. The most common senile cataract is cortical cataract. For
understanding cortical cataract, ... | [
{
"created": "Mon, 12 Oct 2015 09:23:09 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Feb 2018 11:07:55 GMT",
"version": "v2"
}
] | 2018-02-06 | [
[
"Wang-Michelitsch",
"Jicun",
""
],
[
"Michelitsch",
"Thomas M.",
""
]
] | In lens cataract, the clouding change in lens leads to a decline of transparency of part of the lens. There are three types of senile cataract: cortical cataract, nuclear cataract, and posterior/anterior sub-capsular cataract. The most common senile cataract is cortical cataract. For understanding cortical cataract, th... |
2405.05091 | Rudy Arthur | Rudy Arthur, Arwen E. Nicholson and Nathan J. Mayne | What doesn't kill Gaia makes her stronger | 12 pages, 7 figures | null | null | null | q-bio.PE astro-ph.EP physics.pop-ph | http://creativecommons.org/licenses/by/4.0/ | Life on Earth has experienced numerous upheavals over its approximately 4
billion year history. In previous work we have discussed how interruptions to
stability lead, on average, to increases in habitability over time, a tendency
we called Entropic Gaia. Here we continue this exploration, working with the
Tangled Na... | [
{
"created": "Wed, 8 May 2024 14:40:45 GMT",
"version": "v1"
}
] | 2024-05-09 | [
[
"Arthur",
"Rudy",
""
],
[
"Nicholson",
"Arwen E.",
""
],
[
"Mayne",
"Nathan J.",
""
]
] | Life on Earth has experienced numerous upheavals over its approximately 4 billion year history. In previous work we have discussed how interruptions to stability lead, on average, to increases in habitability over time, a tendency we called Entropic Gaia. Here we continue this exploration, working with the Tangled Natu... |
2305.18370 | Saurabh Sihag | Saurabh Sihag, Gonzalo Mateos, Corey McMillan, Alejandro Ribeiro | Explainable Brain Age Prediction using coVariance Neural Networks | Camera ready version for NeurIPS 2023. arXiv admin note: substantial
text overlap with arXiv:2305.01807 | null | null | null | q-bio.QM cs.LG stat.AP | http://creativecommons.org/licenses/by/4.0/ | In computational neuroscience, there has been an increased interest in
developing machine learning algorithms that leverage brain imaging data to
provide estimates of "brain age" for an individual. Importantly, the
discordance between brain age and chronological age (referred to as "brain age
gap") can capture accele... | [
{
"created": "Sat, 27 May 2023 22:28:25 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Sep 2023 23:03:07 GMT",
"version": "v2"
},
{
"created": "Fri, 27 Oct 2023 17:21:37 GMT",
"version": "v3"
}
] | 2023-10-30 | [
[
"Sihag",
"Saurabh",
""
],
[
"Mateos",
"Gonzalo",
""
],
[
"McMillan",
"Corey",
""
],
[
"Ribeiro",
"Alejandro",
""
]
] | In computational neuroscience, there has been an increased interest in developing machine learning algorithms that leverage brain imaging data to provide estimates of "brain age" for an individual. Importantly, the discordance between brain age and chronological age (referred to as "brain age gap") can capture accelera... |
1610.08227 | Franz Chouly | Marine Bruneau (LMB), Thierry Mottet, Serge Moulin, Ma\"el Kerbiriou
(LMB), Franz Chouly (LMB), St\'ephane Chretien (NPL), Christophe Guyeux | A clustering tool for nucleotide sequences using Laplacian Eigenmaps and
Gaussian Mixture Models | null | null | null | null | q-bio.QM math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a new procedure for clustering nucleotide sequences based on the
"Laplacian Eigenmaps" and Gaussian Mixture modelling. This proposal is then
applied to a set of 100 DNA sequences from the mitochondrially encoded NADH
dehydrogenase 3 (ND3) gene of a collection of Platyhelminthes and Nematoda
species. The re... | [
{
"created": "Wed, 26 Oct 2016 08:43:58 GMT",
"version": "v1"
}
] | 2016-10-27 | [
[
"Bruneau",
"Marine",
"",
"LMB"
],
[
"Mottet",
"Thierry",
"",
"LMB"
],
[
"Moulin",
"Serge",
"",
"LMB"
],
[
"Kerbiriou",
"Maël",
"",
"LMB"
],
[
"Chouly",
"Franz",
"",
"LMB"
],
[
"Chretien",
"Stéphane",
""... | We propose a new procedure for clustering nucleotide sequences based on the "Laplacian Eigenmaps" and Gaussian Mixture modelling. This proposal is then applied to a set of 100 DNA sequences from the mitochondrially encoded NADH dehydrogenase 3 (ND3) gene of a collection of Platyhelminthes and Nematoda species. The resu... |
1608.02038 | Eran Elhaik | Ranajit Das, Paul Wexler, Mehdi Pirooznia, and Eran Elhaik | Responding to an enquiry concerning the geographic population structure
(GPS) approach and the origin of Ashkenazic Jews - a reply to Flegontov et al | 32 pages, 2 figures, 2 tables | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Recently, we investigated the geographical origins of Ashkenazic Jews (AJs)
and their native language Yiddish by applying a biogeographical tool, the
Geographic Population Structure (GPS), to a cohort of 367 exclusively
Yiddish-speaking and multilingual AJs genotyped on the Genochip microarray. GPS
localized most AJs... | [
{
"created": "Fri, 5 Aug 2016 22:54:34 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Aug 2016 12:09:23 GMT",
"version": "v2"
}
] | 2016-08-18 | [
[
"Das",
"Ranajit",
""
],
[
"Wexler",
"Paul",
""
],
[
"Pirooznia",
"Mehdi",
""
],
[
"Elhaik",
"Eran",
""
]
] | Recently, we investigated the geographical origins of Ashkenazic Jews (AJs) and their native language Yiddish by applying a biogeographical tool, the Geographic Population Structure (GPS), to a cohort of 367 exclusively Yiddish-speaking and multilingual AJs genotyped on the Genochip microarray. GPS localized most AJs a... |
2004.13452 | Sebasti\'an Contreras | Sebastian Contreras, H. Andres Villavicencio, David Medina-Ortiz, Juan
Pablo Biron-Lattes, Alvaro Olivera-Nappa | A multi-group SEIRA model for the spread of COVID-19 among heterogeneous
populations | null | Chaos Solitons Fractals 136 (2020) 109925 | 10.1016/j.chaos.2020.109925 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The outbreak and propagation of COVID-19 have posed a considerable challenge
to modern society. In particular, the different restrictive actions taken by
governments to prevent the spread of the virus have changed the way humans
interact and conceive interaction. Due to geographical, behavioral, or economic
factors, ... | [
{
"created": "Tue, 28 Apr 2020 12:11:50 GMT",
"version": "v1"
}
] | 2021-10-05 | [
[
"Contreras",
"Sebastian",
""
],
[
"Villavicencio",
"H. Andres",
""
],
[
"Medina-Ortiz",
"David",
""
],
[
"Biron-Lattes",
"Juan Pablo",
""
],
[
"Olivera-Nappa",
"Alvaro",
""
]
] | The outbreak and propagation of COVID-19 have posed a considerable challenge to modern society. In particular, the different restrictive actions taken by governments to prevent the spread of the virus have changed the way humans interact and conceive interaction. Due to geographical, behavioral, or economic factors, di... |
1209.1371 | Ralph Brinks | Ralph Brinks | On the age-, time- and migration dependent dynamics of diseases | 13 pages, 4 figures | null | null | null | q-bio.PE q-bio.QM stat.ME stat.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper generalizes a previously published differential equation that
describes the relation between the age-specific incidence, remission, and
mortality of a disease with its prevalence. The underlying model is a simple
compartment model with three states (illness-death model). In contrast to the
former work, mig... | [
{
"created": "Thu, 6 Sep 2012 19:04:35 GMT",
"version": "v1"
}
] | 2012-09-07 | [
[
"Brinks",
"Ralph",
""
]
] | This paper generalizes a previously published differential equation that describes the relation between the age-specific incidence, remission, and mortality of a disease with its prevalence. The underlying model is a simple compartment model with three states (illness-death model). In contrast to the former work, migra... |
2202.01316 | Massimiliano Esposito | Artur Wachtel, Riccardo Rao, Massimiliano Esposito | Free-Energy Transduction in Chemical Reaction Networks: from Enzymes to
Metabolism | 17 pages, 17 figues, (v2: IV.A.3 & IV.C modified, VI expanded) | null | 10.1063/5.0091035 | null | q-bio.MN cond-mat.stat-mech physics.chem-ph | http://creativecommons.org/licenses/by/4.0/ | We provide a rigorous definition of free-energy transduction and its
efficiency in arbitrary -- linear or nonlinear -- open chemical reaction
networks (CRNs) operating at steady state. Our method is based on the knowledge
of the stoichiometric matrix and of the chemostatted species (i.e. the species
maintained at con... | [
{
"created": "Wed, 2 Feb 2022 22:41:30 GMT",
"version": "v1"
},
{
"created": "Mon, 13 Jun 2022 21:16:55 GMT",
"version": "v2"
}
] | 2022-06-15 | [
[
"Wachtel",
"Artur",
""
],
[
"Rao",
"Riccardo",
""
],
[
"Esposito",
"Massimiliano",
""
]
] | We provide a rigorous definition of free-energy transduction and its efficiency in arbitrary -- linear or nonlinear -- open chemical reaction networks (CRNs) operating at steady state. Our method is based on the knowledge of the stoichiometric matrix and of the chemostatted species (i.e. the species maintained at const... |
2101.10617 | Lingbin Bian | Lingbin Bian, Tiangang Cui, B.T. Thomas Yeo, Alex Fornito, Adeel Razi
and Jonathan Keith | Identification of brain states, transitions, and communities using
functional MRI | null | null | null | null | q-bio.NC stat.ML | http://creativecommons.org/licenses/by/4.0/ | Brain function relies on a precisely coordinated and dynamic balance between
the functional integration and segregation of distinct neural systems.
Characterizing the way in which neural systems reconfigure their interactions
to give rise to distinct but hidden brain states remains an open challenge. In
this paper, w... | [
{
"created": "Tue, 26 Jan 2021 08:10:00 GMT",
"version": "v1"
}
] | 2021-01-28 | [
[
"Bian",
"Lingbin",
""
],
[
"Cui",
"Tiangang",
""
],
[
"Yeo",
"B. T. Thomas",
""
],
[
"Fornito",
"Alex",
""
],
[
"Razi",
"Adeel",
""
],
[
"Keith",
"Jonathan",
""
]
] | Brain function relies on a precisely coordinated and dynamic balance between the functional integration and segregation of distinct neural systems. Characterizing the way in which neural systems reconfigure their interactions to give rise to distinct but hidden brain states remains an open challenge. In this paper, we ... |
1404.2487 | Liya Wang | Liya Wang, Lincoln Stein, and Doreen Ware | The relationships among GC content, nucleosome occupancy, and exon size | 26 pages, 9 figures | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The average size of internal translated exons, ranging from 120 to 165 nt
across metazoans, is approximately the size of the typical mononucleosome (147
nt). Genome-wide study has also shown that nucleosome occupancy is
significantly higher in exons than in introns, which might indicate that the
evolution of exon siz... | [
{
"created": "Wed, 9 Apr 2014 13:51:52 GMT",
"version": "v1"
},
{
"created": "Tue, 27 May 2014 20:23:26 GMT",
"version": "v2"
}
] | 2014-05-29 | [
[
"Wang",
"Liya",
""
],
[
"Stein",
"Lincoln",
""
],
[
"Ware",
"Doreen",
""
]
] | The average size of internal translated exons, ranging from 120 to 165 nt across metazoans, is approximately the size of the typical mononucleosome (147 nt). Genome-wide study has also shown that nucleosome occupancy is significantly higher in exons than in introns, which might indicate that the evolution of exon size ... |
2407.05226 | Hong Qin | Hong Qin | The Emergent Aging Model: Aging as an Emergent Property of Biological
Systems | 10 pages, 2 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Based on the study of cellular aging using the single-cell model organism of
budding yeast and corroborated by other studies, we propose the Emergent Aging
Model (EAM). EAM hypothesizes that aging is an emergent property of complex
biological systems, exemplified by biological networks such as gene networks.
An emerg... | [
{
"created": "Sun, 7 Jul 2024 01:19:22 GMT",
"version": "v1"
}
] | 2024-07-09 | [
[
"Qin",
"Hong",
""
]
] | Based on the study of cellular aging using the single-cell model organism of budding yeast and corroborated by other studies, we propose the Emergent Aging Model (EAM). EAM hypothesizes that aging is an emergent property of complex biological systems, exemplified by biological networks such as gene networks. An emergen... |
1411.0431 | Valmir Barbosa | Luciano Dyballa, Valmir C. Barbosa | Further insights into the interareal connectivity of a cortical network | null | Network Science 3 (2015), 526-550 | 10.1017/nws.2015.19 | null | q-bio.NC cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Over the past years, network science has proven invaluable as a means to
better understand many of the processes taking place in the brain. Recently,
interareal connectivity data of the macaque cortex was made available with
great richness of detail. We explore new aspects of this dataset, such as a
correlation betwe... | [
{
"created": "Mon, 3 Nov 2014 11:22:27 GMT",
"version": "v1"
}
] | 2022-09-02 | [
[
"Dyballa",
"Luciano",
""
],
[
"Barbosa",
"Valmir C.",
""
]
] | Over the past years, network science has proven invaluable as a means to better understand many of the processes taking place in the brain. Recently, interareal connectivity data of the macaque cortex was made available with great richness of detail. We explore new aspects of this dataset, such as a correlation between... |
1807.00701 | Adam Kleczkowski | Adam Kleczkowski, Andrew Bate, Michael Redenti and Nick Hanley | Weakest-link control of invasive species: Impacts of memory, bounded
rationality and network structure in repeated cooperative games | 29 pages, 6 figures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The nature of dispersal of many invasive pests and pathogens in agricultural
and forestry makes it necessary to consider how the actions of one manager
affect neighbouring properties. In addition to the direct effects of a
potential spread of a pest and the resulting economic loss, there are also
indirect consequence... | [
{
"created": "Fri, 29 Jun 2018 16:22:02 GMT",
"version": "v1"
}
] | 2018-07-03 | [
[
"Kleczkowski",
"Adam",
""
],
[
"Bate",
"Andrew",
""
],
[
"Redenti",
"Michael",
""
],
[
"Hanley",
"Nick",
""
]
] | The nature of dispersal of many invasive pests and pathogens in agricultural and forestry makes it necessary to consider how the actions of one manager affect neighbouring properties. In addition to the direct effects of a potential spread of a pest and the resulting economic loss, there are also indirect consequences ... |
2001.06093 | Mareike Fischer | Mareike Fischer, Michelle Galla and Kristina Wicke | Non-binary universal tree-based networks | arXiv admin note: text overlap with arXiv:1810.06853 | null | null | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A tree-based network $N$ on $X$ is called universal if every phylogenetic
tree on $X$ is a base tree for $N$. Recently, binary universal tree-based
networks have attracted great attention in the literature and their existence
has been analyzed in various studies. In this note, we extend the analysis to
non-binary net... | [
{
"created": "Tue, 14 Jan 2020 08:34:40 GMT",
"version": "v1"
}
] | 2020-01-20 | [
[
"Fischer",
"Mareike",
""
],
[
"Galla",
"Michelle",
""
],
[
"Wicke",
"Kristina",
""
]
] | A tree-based network $N$ on $X$ is called universal if every phylogenetic tree on $X$ is a base tree for $N$. Recently, binary universal tree-based networks have attracted great attention in the literature and their existence has been analyzed in various studies. In this note, we extend the analysis to non-binary netwo... |
1007.0986 | Ilya M. Nemenman | Pradeep Bandaru, Mukesh Bansal, and Ilya Nemenman | Mass Conservation And Inference of Metabolic Networks from
High-throughput Mass Spectrometry Data | 18 pages | J Comput Biol, vol. 18 (2) pp. 147-54, 2011 | 10.1089/cmb.2010.0222 | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a step towards the metabolome-wide computational inference of
cellular metabolic reaction networks from metabolic profiling data, such as
mass spectrometry. The reconstruction is based on identification of irreducible
statistical interactions among the metabolite activities using the ARACNE
reverse-enginee... | [
{
"created": "Tue, 6 Jul 2010 19:52:39 GMT",
"version": "v1"
}
] | 2011-06-02 | [
[
"Bandaru",
"Pradeep",
""
],
[
"Bansal",
"Mukesh",
""
],
[
"Nemenman",
"Ilya",
""
]
] | We present a step towards the metabolome-wide computational inference of cellular metabolic reaction networks from metabolic profiling data, such as mass spectrometry. The reconstruction is based on identification of irreducible statistical interactions among the metabolite activities using the ARACNE reverse-engineeri... |
1809.04804 | Peter Kasson | Peter M. Kasson and Shantenu Jha | Adaptive ensemble simulations of biomolecules | Manuscript accepted for publication in Current Opinion in Structural
Biology | Current Opinion in Structural Biology 2018. 52:87-94 | 10.1016/j.sbi.2018.09.005 | null | q-bio.QM physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent advances in both theory and computational power have created
opportunities to simulate biomolecular processes more efficiently using
adaptive ensemble simulations. Ensemble simulations are now widely used to
compute a number of individual simulation trajectories and analyze statistics
across them. Adaptive ens... | [
{
"created": "Thu, 13 Sep 2018 07:08:18 GMT",
"version": "v1"
}
] | 2018-09-27 | [
[
"Kasson",
"Peter M.",
""
],
[
"Jha",
"Shantenu",
""
]
] | Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of individual simulation trajectories and analyze statistics across them. Adaptive ensem... |
1305.5413 | Carlos Gershenson | Nelson Fernandez and Carlos Gershenson | Measuring Complexity in an Aquatic Ecosystem | 6 pages, to be published in Proceedings of the CCBCOL 2013, 2nd
Colombian Computational Biology Congress, Springer | null | null | null | q-bio.PE nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We apply formal measures of emergence, self-organization, homeostasis,
autopoiesis and complexity to an aquatic ecosystem; in particular to the
physiochemical component of an Arctic lake. These measures are based on
information theory. Variables with an homogeneous distribution have higher
values of emergence, while ... | [
{
"created": "Wed, 22 May 2013 03:43:08 GMT",
"version": "v1"
}
] | 2013-05-24 | [
[
"Fernandez",
"Nelson",
""
],
[
"Gershenson",
"Carlos",
""
]
] | We apply formal measures of emergence, self-organization, homeostasis, autopoiesis and complexity to an aquatic ecosystem; in particular to the physiochemical component of an Arctic lake. These measures are based on information theory. Variables with an homogeneous distribution have higher values of emergence, while va... |
1307.0968 | Jose A. Cuesta | Susanna Manrubia and Jos\'e A. Cuesta | Evolution on neutral networks accelerates the ticking rate of the
molecular clock | 31 pages, 4 figures | Journal of the Royal Society Interface 102, 20141010 (2015) | 10.1098/rsif.2014.1010 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Large sets of genotypes give rise to the same phenotype because phenotypic
expression is highly redundant. Accordingly, a population can accept mutations
without altering its phenotype, as long as thegenotype mutates into another one
on the same set. By linking every pair of genotypes that are mutually
accessible thr... | [
{
"created": "Wed, 3 Jul 2013 11:15:09 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Sep 2014 20:47:30 GMT",
"version": "v2"
}
] | 2015-02-18 | [
[
"Manrubia",
"Susanna",
""
],
[
"Cuesta",
"José A.",
""
]
] | Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the same set. By linking every pair of genotypes that are mutually accessible throu... |
2104.08969 | Ethan Moyer | Ethan Moyer, Jeff Winchell, Isamu Isozaki, Yigit Alparslan, Mali
Halac, and Edward Kim | Functional Protein Structure Annotation Using a Deep Convolutional
Generative Adversarial Network | 4 pages, 1 figure, 1 table | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Identifying novel functional protein structures is at the heart of molecular
engineering and molecular biology, requiring an often computationally
exhaustive search. We introduce the use of a Deep Convolutional Generative
Adversarial Network (DCGAN) to classify protein structures based on their
functionality by encod... | [
{
"created": "Sun, 18 Apr 2021 22:18:52 GMT",
"version": "v1"
}
] | 2021-04-20 | [
[
"Moyer",
"Ethan",
""
],
[
"Winchell",
"Jeff",
""
],
[
"Isozaki",
"Isamu",
""
],
[
"Alparslan",
"Yigit",
""
],
[
"Halac",
"Mali",
""
],
[
"Kim",
"Edward",
""
]
] | Identifying novel functional protein structures is at the heart of molecular engineering and molecular biology, requiring an often computationally exhaustive search. We introduce the use of a Deep Convolutional Generative Adversarial Network (DCGAN) to classify protein structures based on their functionality by encodin... |
1705.07109 | Ya\u{g}mur G\"u\c{c}l\"ut\"urk | Ya\u{g}mur G\"u\c{c}l\"ut\"urk, Umut G\"u\c{c}l\"u, Katja Seeliger,
Sander Bosch, Rob van Lier, Marcel van Gerven | Deep adversarial neural decoding | Added appendix and updated figures | null | null | null | q-bio.NC cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here, we present a novel approach to solve the problem of reconstructing
perceived stimuli from brain responses by combining probabilistic inference
with deep learning. Our approach first inverts the linear transformation from
latent features to brain responses with maximum a posteriori estimation and
then inverts th... | [
{
"created": "Fri, 19 May 2017 17:43:01 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Jun 2017 13:15:25 GMT",
"version": "v2"
},
{
"created": "Thu, 15 Jun 2017 16:56:34 GMT",
"version": "v3"
}
] | 2017-06-16 | [
[
"Güçlütürk",
"Yağmur",
""
],
[
"Güçlü",
"Umut",
""
],
[
"Seeliger",
"Katja",
""
],
[
"Bosch",
"Sander",
""
],
[
"van Lier",
"Rob",
""
],
[
"van Gerven",
"Marcel",
""
]
] | Here, we present a novel approach to solve the problem of reconstructing perceived stimuli from brain responses by combining probabilistic inference with deep learning. Our approach first inverts the linear transformation from latent features to brain responses with maximum a posteriori estimation and then inverts the ... |
1401.5701 | Fabian Spill | Fabian Spill, Pilar Guerrero, Tomas Alarcon, Philip K. Maini, Helen M.
Byrne | Mesoscopic and continuum modelling of angiogenesis | 48 pages, 13 figures | Journal of Mathematical Biology February 2015, Volume 70, Issue 3,
pp 485-532 | 10.1007/s00285-014-0771-1 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Angiogenesis is the formation of new blood vessels from pre-existing ones in
response to chemical signals secreted by, for example, a wound or a tumour. In
this paper, we propose a mesoscopic lattice-based model of angiogenesis, in
which processes that include proliferation and cell movement are considered as
stochas... | [
{
"created": "Wed, 22 Jan 2014 15:15:28 GMT",
"version": "v1"
}
] | 2016-03-02 | [
[
"Spill",
"Fabian",
""
],
[
"Guerrero",
"Pilar",
""
],
[
"Alarcon",
"Tomas",
""
],
[
"Maini",
"Philip K.",
""
],
[
"Byrne",
"Helen M.",
""
]
] | Angiogenesis is the formation of new blood vessels from pre-existing ones in response to chemical signals secreted by, for example, a wound or a tumour. In this paper, we propose a mesoscopic lattice-based model of angiogenesis, in which processes that include proliferation and cell movement are considered as stochasti... |
2002.07732 | Breno de Oliveira Ferraz | D. Bazeia, M.V. de Moraes, B.F. de Oliveira | Model for clustering of living species | 7 pages, 10 figures | EPL, 129 (2020) 28002 | 10.1209/0295-5075/129/28002 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Clusters appear in nature in a diversity of contexts, involving distances as
long as the cosmological ones, and down to atoms and molecules and the very
small nuclear size. They also appear in several other scenarios, in particular
in biological systems as in ants, bees, birds, fishes, gnus and rats, for
instance. He... | [
{
"created": "Tue, 18 Feb 2020 17:02:06 GMT",
"version": "v1"
}
] | 2020-02-19 | [
[
"Bazeia",
"D.",
""
],
[
"de Moraes",
"M. V.",
""
],
[
"de Oliveira",
"B. F.",
""
]
] | Clusters appear in nature in a diversity of contexts, involving distances as long as the cosmological ones, and down to atoms and molecules and the very small nuclear size. They also appear in several other scenarios, in particular in biological systems as in ants, bees, birds, fishes, gnus and rats, for instance. Here... |
1803.01111 | Michael Assaf | Ohad Vilk and Michael Assaf | Population Extinction under Bursty Reproduction in a Time Modulated
Environment | 11 pages, 8 figures | Phys. Rev. E 97, 062114 (2018) | 10.1103/PhysRevE.97.062114 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years non-demographic variability has been shown to greatly affect
dynamics of stochastic populations. For example, non-demographic noise in the
form of a bursty reproduction process with an a-priori unknown burst size, or
environmental variability in the form of time-varying reaction rates, have been
separ... | [
{
"created": "Sat, 3 Mar 2018 06:01:22 GMT",
"version": "v1"
}
] | 2018-06-13 | [
[
"Vilk",
"Ohad",
""
],
[
"Assaf",
"Michael",
""
]
] | In recent years non-demographic variability has been shown to greatly affect dynamics of stochastic populations. For example, non-demographic noise in the form of a bursty reproduction process with an a-priori unknown burst size, or environmental variability in the form of time-varying reaction rates, have been separat... |
2108.02570 | Minhong Kim | Minhong Kim | Predicting Post-Concussion Syndrome Outcomes with Machine Learning | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, machine learning models are used to predict outcomes for
patients with persistent post-concussion syndrome (PCS). Patients had sustained
a concussion at an average of two to three months before the study. By
utilizing assessed data, the machine learning models aimed to predict whether
or not a patient ... | [
{
"created": "Wed, 4 Aug 2021 09:04:13 GMT",
"version": "v1"
}
] | 2021-08-06 | [
[
"Kim",
"Minhong",
""
]
] | In this paper, machine learning models are used to predict outcomes for patients with persistent post-concussion syndrome (PCS). Patients had sustained a concussion at an average of two to three months before the study. By utilizing assessed data, the machine learning models aimed to predict whether or not a patient wo... |
1802.05166 | Alexander Bershadskii | A. Bershadskii | Hamiltonian dynamics and distributed chaos in DNA | extended | null | null | null | q-bio.OT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is shown that distributed chaos, generated by Hamiltonian DNA dynamics
with spontaneously broken time translational symmetry, imprints itself on the
DNA sequence of Arabidopsis thaliana (a model plant for genetic sequencing and
mapping) and of the NRXN1 and BRCA2 human genes (as an example). The
base-stacking inte... | [
{
"created": "Wed, 14 Feb 2018 15:47:44 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Feb 2018 17:18:38 GMT",
"version": "v2"
},
{
"created": "Tue, 13 Mar 2018 17:10:45 GMT",
"version": "v3"
}
] | 2018-03-14 | [
[
"Bershadskii",
"A.",
""
]
] | It is shown that distributed chaos, generated by Hamiltonian DNA dynamics with spontaneously broken time translational symmetry, imprints itself on the DNA sequence of Arabidopsis thaliana (a model plant for genetic sequencing and mapping) and of the NRXN1 and BRCA2 human genes (as an example). The base-stacking intera... |
2005.14597 | Paulo Protachevicz | P R Protachevicz, M S Santos, E G Seifert, E C Gabrick, F S Borges, R
R Borges, J Trobia, J D Szezech Jr, K C Iarosz, I L Caldas, C G Antonopoulos,
Y Xu, R L Viana, A M Batista | Noise induces continuous and noncontinuous transitions in neuronal
interspike intervals range | null | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Noise appears in the brain due to various sources, such as ionic channel
fluctuations and synaptic events. They affect the activities of the brain and
influence neuron action potentials. Stochastic differential equations have been
used to model firing patterns of neurons subject to noise. In this work, we
consider pe... | [
{
"created": "Fri, 29 May 2020 14:28:30 GMT",
"version": "v1"
}
] | 2020-06-01 | [
[
"Protachevicz",
"P R",
""
],
[
"Santos",
"M S",
""
],
[
"Seifert",
"E G",
""
],
[
"Gabrick",
"E C",
""
],
[
"Borges",
"F S",
""
],
[
"Borges",
"R R",
""
],
[
"Trobia",
"J",
""
],
[
"Szezech",
"J... | Noise appears in the brain due to various sources, such as ionic channel fluctuations and synaptic events. They affect the activities of the brain and influence neuron action potentials. Stochastic differential equations have been used to model firing patterns of neurons subject to noise. In this work, we consider pert... |
2001.07822 | Michael Baker Ph.D. | Michael E. Baker and Yoshinao Katsu | Progesterone: An Enigmatic Ligand for the Mineralocorticoid Receptor | 17 pages, 5 figures | null | null | null | q-bio.MN q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The progesterone receptor (PR) mediates progesterone regulation of female
reproductive physiology, as well as gene transcription in non-reproductive
tissues, such as brain, bone, lung and vasculature, in both women and men. An
unusual property of progesterone is its high affinity for the mineralocorticoid
receptor (M... | [
{
"created": "Wed, 22 Jan 2020 00:08:17 GMT",
"version": "v1"
}
] | 2020-01-23 | [
[
"Baker",
"Michael E.",
""
],
[
"Katsu",
"Yoshinao",
""
]
] | The progesterone receptor (PR) mediates progesterone regulation of female reproductive physiology, as well as gene transcription in non-reproductive tissues, such as brain, bone, lung and vasculature, in both women and men. An unusual property of progesterone is its high affinity for the mineralocorticoid receptor (MR)... |
1807.00038 | Adilson Enio Motter | Reka Albert, John Baillieul, Adilson E. Motter | Introduction to the Special Issue on Approaches to Control Biological
and Biologically Inspired Networks | null | IEEE Trans. Control Netw. Syst. 5(2), 690-693 (2018) | 10.1109/TCNS.2018.2836303 | null | q-bio.MN cond-mat.dis-nn cs.SY math.OC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The emerging field at the intersection of quantitative biology, network
modeling, and control theory has enjoyed significant progress in recent years.
This Special Issue brings together a selection of papers on complementary
approaches to observe, identify, and control biological and biologically
inspired networks. T... | [
{
"created": "Thu, 28 Jun 2018 05:30:38 GMT",
"version": "v1"
}
] | 2018-07-10 | [
[
"Albert",
"Reka",
""
],
[
"Baillieul",
"John",
""
],
[
"Motter",
"Adilson E.",
""
]
] | The emerging field at the intersection of quantitative biology, network modeling, and control theory has enjoyed significant progress in recent years. This Special Issue brings together a selection of papers on complementary approaches to observe, identify, and control biological and biologically inspired networks. The... |
1012.5649 | Valmir Barbosa | Andre Nathan, Valmir C. Barbosa | Network algorithmics and the emergence of information integration in
cortical models | null | Physical Review E 84 (2011), 011904 | 10.1103/PhysRevE.84.011904 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An information-theoretic framework known as integrated information theory
(IIT) has been introduced recently for the study of the emergence of
consciousness in the brain [D. Balduzzi and G. Tononi, PLoS Comput. Biol. 4,
e1000091 (2008)]. IIT purports that this phenomenon is to be equated with the
generation of inform... | [
{
"created": "Mon, 27 Dec 2010 19:42:38 GMT",
"version": "v1"
}
] | 2011-07-11 | [
[
"Nathan",
"Andre",
""
],
[
"Barbosa",
"Valmir C.",
""
]
] | An information-theoretic framework known as integrated information theory (IIT) has been introduced recently for the study of the emergence of consciousness in the brain [D. Balduzzi and G. Tononi, PLoS Comput. Biol. 4, e1000091 (2008)]. IIT purports that this phenomenon is to be equated with the generation of informat... |
2002.01889 | Tatjana Petrov | Tatjana Petrov and Denis Repin | Automated Deep Abstractions for Stochastic Chemical Reaction Networks | null | null | null | null | q-bio.MN cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Predicting stochastic cellular dynamics as emerging from the mechanistic
models of molecular interactions is a long-standing challenge in systems
biology: low-level chemical reaction network (CRN) models give raise to a
highly-dimensional continuous-time Markov chain (CTMC) which is computationally
demanding and ofte... | [
{
"created": "Thu, 30 Jan 2020 13:49:58 GMT",
"version": "v1"
}
] | 2020-02-06 | [
[
"Petrov",
"Tatjana",
""
],
[
"Repin",
"Denis",
""
]
] | Predicting stochastic cellular dynamics as emerging from the mechanistic models of molecular interactions is a long-standing challenge in systems biology: low-level chemical reaction network (CRN) models give raise to a highly-dimensional continuous-time Markov chain (CTMC) which is computationally demanding and often ... |
1905.06973 | Yang Jiao | Yu Zheng and Hanqing Nan and Qihui Fan and Xiaochen Wang and Liyu Liu
and Ruchuan Liu and Fangfu Ye and Bo Sun and Yang Jiao | Modeling cell migration regulated by cell-ECM micromechanical coupling | 11 pages 11 figures | Phys. Rev. E 100, 043303 (2019) | 10.1103/PhysRevE.100.043303 | null | q-bio.CB cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cell migration in fibreous extracellular matrix (ECM) is crucial to many
physiological and pathological processes such as tissue regeneration, immune
response and cancer progression. During migration, individual cells can
generate active pulling forces via actin filament contraction, which are
transmitted to the ECM ... | [
{
"created": "Thu, 16 May 2019 18:03:48 GMT",
"version": "v1"
}
] | 2019-10-16 | [
[
"Zheng",
"Yu",
""
],
[
"Nan",
"Hanqing",
""
],
[
"Fan",
"Qihui",
""
],
[
"Wang",
"Xiaochen",
""
],
[
"Liu",
"Liyu",
""
],
[
"Liu",
"Ruchuan",
""
],
[
"Ye",
"Fangfu",
""
],
[
"Sun",
"Bo",
""
... | Cell migration in fibreous extracellular matrix (ECM) is crucial to many physiological and pathological processes such as tissue regeneration, immune response and cancer progression. During migration, individual cells can generate active pulling forces via actin filament contraction, which are transmitted to the ECM fi... |
1408.3101 | Sergio Verduzco-Flores | Sergio Verduzco-Flores | How stochastic synchrony could work in cerebellar Purkinje cells | 46 pages, 8 figures. Similar to a version submitted to the Journal of
Mathematical Neuroscience | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Simple spike synchrony between Purkinje cells projecting to a common neuron
in the deep cerebellar nucleus is emerging as an important factor in the
encoding of output information from cerebellar cortex. Stochastic
synchronization is a viable mechanism through which this synchrony could be
generated, but it has recei... | [
{
"created": "Wed, 13 Aug 2014 19:35:00 GMT",
"version": "v1"
}
] | 2014-08-14 | [
[
"Verduzco-Flores",
"Sergio",
""
]
] | Simple spike synchrony between Purkinje cells projecting to a common neuron in the deep cerebellar nucleus is emerging as an important factor in the encoding of output information from cerebellar cortex. Stochastic synchronization is a viable mechanism through which this synchrony could be generated, but it has receive... |
1808.08086 | Alberto Sorrentino | Gianvittorio Luria, Dunja Duran, Elisa Visani, Sara Sommariva, Fabio
Rotondi, Davide Rossi Sebastiano, Ferruccio Panzica, Michele Piana, Alberto
Sorrentino | Bayesian Multi--Dipole Modeling in the Frequency Domain | null | Journal of Neuroscience Methods Volume 312, 15 January 2019, Pages
27-36 | 10.1016/j.jneumeth.2018.11.007 | null | q-bio.QM stat.AP stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Magneto- and Electro-encephalography record the electromagnetic
field generated by neural currents with high temporal frequency and good
spatial resolution, and are therefore well suited for source localization in
the time and in the frequency domain. In particular, localization of the
generators of neura... | [
{
"created": "Fri, 24 Aug 2018 10:55:07 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Dec 2018 14:21:54 GMT",
"version": "v2"
}
] | 2018-12-14 | [
[
"Luria",
"Gianvittorio",
""
],
[
"Duran",
"Dunja",
""
],
[
"Visani",
"Elisa",
""
],
[
"Sommariva",
"Sara",
""
],
[
"Rotondi",
"Fabio",
""
],
[
"Sebastiano",
"Davide Rossi",
""
],
[
"Panzica",
"Ferruccio",
"... | Background: Magneto- and Electro-encephalography record the electromagnetic field generated by neural currents with high temporal frequency and good spatial resolution, and are therefore well suited for source localization in the time and in the frequency domain. In particular, localization of the generators of neural ... |
2211.10205 | Georgina Al-Badri Dr | Georgina Al-Badri, James B. Phillips, Rebecca J. Shipley, and Nicholas
C. Ovenden | Formation of vascular-like structures using a chemotaxis-driven
multiphase model | null | null | null | null | q-bio.CB | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We propose a continuum model for pattern formation, based on the multiphase
model framework, to explore in vitro cell patterning within an extracellular
matrix. We demonstrate that, within this framework, chemotaxis-driven cell
migration can lead to formation of cell clusters and vascular-like structures
in 1D and 2D... | [
{
"created": "Fri, 18 Nov 2022 12:50:56 GMT",
"version": "v1"
}
] | 2022-11-21 | [
[
"Al-Badri",
"Georgina",
""
],
[
"Phillips",
"James B.",
""
],
[
"Shipley",
"Rebecca J.",
""
],
[
"Ovenden",
"Nicholas C.",
""
]
] | We propose a continuum model for pattern formation, based on the multiphase model framework, to explore in vitro cell patterning within an extracellular matrix. We demonstrate that, within this framework, chemotaxis-driven cell migration can lead to formation of cell clusters and vascular-like structures in 1D and 2D r... |
q-bio/0602007 | Mika Yoshida | Mika Yoshida, Kinji Fuchikami and Tatsuya Uezu | Realization of features of immune response by dynamical system models
and a possible mechanism of memory of antigen invasion | 17 pages, 11 figures | null | null | null | q-bio.PE | null | Among features of real immune responses which occur when antigens invade a
body,there are two remarkable features. One is that the amount of antibodies
produced in the secondary invasion by the same antigens is more than 10 times
larger than that in the primary invasion. The other is that more effective
antibodies wh... | [
{
"created": "Tue, 7 Feb 2006 04:38:15 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Yoshida",
"Mika",
""
],
[
"Fuchikami",
"Kinji",
""
],
[
"Uezu",
"Tatsuya",
""
]
] | Among features of real immune responses which occur when antigens invade a body,there are two remarkable features. One is that the amount of antibodies produced in the secondary invasion by the same antigens is more than 10 times larger than that in the primary invasion. The other is that more effective antibodies whic... |
1711.02754 | Dionisio Bazeia | D. Bazeia, J. Menezes, B.F. de Oliveira, J.G.G.S. Ramos | Hamming distance and mobility behavior in generalized
rock-paper-scissors models | 7 pages, 9 figures. To appear in EPL | EPL 119 (2017) 58003 | 10.1209/0295-5075/119/58003 | null | q-bio.PE cond-mat.stat-mech nlin.CD physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work reports on two related investigations of stochastic simulations
which are widely used to study biodiversity and other related issues. We first
deal with the behavior of the Hamming distance under the increase of the number
of species and the size of the lattice, and then investigate how the mobility
of the ... | [
{
"created": "Tue, 7 Nov 2017 22:34:48 GMT",
"version": "v1"
}
] | 2017-11-29 | [
[
"Bazeia",
"D.",
""
],
[
"Menezes",
"J.",
""
],
[
"de Oliveira",
"B. F.",
""
],
[
"Ramos",
"J. G. G. S.",
""
]
] | This work reports on two related investigations of stochastic simulations which are widely used to study biodiversity and other related issues. We first deal with the behavior of the Hamming distance under the increase of the number of species and the size of the lattice, and then investigate how the mobility of the sp... |
2307.16182 | Chiara Balestra | Chiara Balestra, Carlo Maj, Emmanuel M\"uller, Andreas Mayr | Redundancy-aware unsupervised rankings for collections of gene sets | arXiv admin note: substantial text overlap with arXiv:2207.12184 | null | null | null | q-bio.QM cs.GT cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The biological roles of gene sets are used to group them into collections.
These collections are often characterized by being high-dimensional,
overlapping, and redundant families of sets, thus precluding a straightforward
interpretation and study of their content. Bioinformatics looked for solutions
to reduce their ... | [
{
"created": "Sun, 30 Jul 2023 09:39:42 GMT",
"version": "v1"
}
] | 2023-08-01 | [
[
"Balestra",
"Chiara",
""
],
[
"Maj",
"Carlo",
""
],
[
"Müller",
"Emmanuel",
""
],
[
"Mayr",
"Andreas",
""
]
] | The biological roles of gene sets are used to group them into collections. These collections are often characterized by being high-dimensional, overlapping, and redundant families of sets, thus precluding a straightforward interpretation and study of their content. Bioinformatics looked for solutions to reduce their di... |
1911.04447 | Tanvir Ferdousi | Tanvir Ferdousi, Sifat Afroj Moon, Adrian Self, and Caterina Scoglio | Generation of swine movement network and analysis of efficient
mitigation strategies for African swine fever virus | 19 pages, 8 figures, journal article (under review in PLOS ONE) | null | 10.1371/journal.pone.0225785 | null | q-bio.PE cs.SI q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Animal movement networks are essential in understanding and containing the
spread of infectious diseases in farming industries. Due to its confidential
nature, movement data for the US swine farming population is not readily
available. Hence, we propose a method to generate such networks from limited
data available i... | [
{
"created": "Mon, 11 Nov 2019 18:51:14 GMT",
"version": "v1"
}
] | 2020-07-01 | [
[
"Ferdousi",
"Tanvir",
""
],
[
"Moon",
"Sifat Afroj",
""
],
[
"Self",
"Adrian",
""
],
[
"Scoglio",
"Caterina",
""
]
] | Animal movement networks are essential in understanding and containing the spread of infectious diseases in farming industries. Due to its confidential nature, movement data for the US swine farming population is not readily available. Hence, we propose a method to generate such networks from limited data available in ... |
q-bio/0309031 | Jonathan D. Victor | Jonathan D. Victor and Keith P. Purpura | Metric-space analysis of spike trains: theory, algorithms, and
application | 16 Figures (not in this file). Originally submitted to the neuro-sys
archive which was never publicly announced (was 9810001) | Network 8, 127-164 (1997) | null | null | q-bio.NC q-bio.QM | null | We present the mathematical basis of a new approach to the analysis of
temporal coding. The foundation of the approach is the construction of several
families of novel distances (metrics) between neuronal impulse trains. In
contrast to most previous approaches to the analysis of temporal coding, the
present approach ... | [
{
"created": "Fri, 30 Oct 1998 22:20:10 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Victor",
"Jonathan D.",
""
],
[
"Purpura",
"Keith P.",
""
]
] | We present the mathematical basis of a new approach to the analysis of temporal coding. The foundation of the approach is the construction of several families of novel distances (metrics) between neuronal impulse trains. In contrast to most previous approaches to the analysis of temporal coding, the present approach do... |
2205.13363 | Santosh Pandey | Upender Kalwa, Christopher Legner, Elizabeth Wlezien, Gregory Tylka,
Santosh Pandey | New methods of removing debris and high-throughput counting of cyst
nematode eggs extracted from field soil | null | Plos One 2019 | 10.1371/journal.pone.0223386 | null | q-bio.QM eess.IV | http://creativecommons.org/licenses/by/4.0/ | The soybean cyst nematode (SCN), Heterodera glycines, is the most damaging
pathogen of soybeans in the United States. To assess the severity of nematode
infestations in the field, SCN egg population densities are determined. Cysts
(dead females) of the nematode must be extracted from soil samples and then
ground to e... | [
{
"created": "Wed, 25 May 2022 01:55:27 GMT",
"version": "v1"
}
] | 2022-05-27 | [
[
"Kalwa",
"Upender",
""
],
[
"Legner",
"Christopher",
""
],
[
"Wlezien",
"Elizabeth",
""
],
[
"Tylka",
"Gregory",
""
],
[
"Pandey",
"Santosh",
""
]
] | The soybean cyst nematode (SCN), Heterodera glycines, is the most damaging pathogen of soybeans in the United States. To assess the severity of nematode infestations in the field, SCN egg population densities are determined. Cysts (dead females) of the nematode must be extracted from soil samples and then ground to ext... |
2308.01452 | Phillip Wilson | Elliott Hughes, Miguel Moyers-Gonzalez, Rua Murray, Phillip L. Wilson | A Mathematically Robust Model of Exotic Pine Invasions | 36 pages, 9 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Invasive pine trees pose a threat to biodiversity in a variety of Southern
Hemisphere countries, but understanding of the dynamics of invasions and the
factors that retard or accelerate spread is limited. Here, we consider the past
models of wilding pine spread and develop a new model of pine invasion. We show
that m... | [
{
"created": "Wed, 2 Aug 2023 21:59:55 GMT",
"version": "v1"
}
] | 2023-08-04 | [
[
"Hughes",
"Elliott",
""
],
[
"Moyers-Gonzalez",
"Miguel",
""
],
[
"Murray",
"Rua",
""
],
[
"Wilson",
"Phillip L.",
""
]
] | Invasive pine trees pose a threat to biodiversity in a variety of Southern Hemisphere countries, but understanding of the dynamics of invasions and the factors that retard or accelerate spread is limited. Here, we consider the past models of wilding pine spread and develop a new model of pine invasion. We show that man... |
0705.0201 | Jesse Bloom | Jesse D Bloom, Philip A Romero, Zhongyi Lu, and Frances H Arnold | Neutral genetic drift can aid functional protein evolution | null | Biology Direct 2:17 (2007) | 10.1186/1745-6150-2-17 | null | q-bio.PE q-bio.BM | null | BACKGROUND: Many of the mutations accumulated by naturally evolving proteins
are neutral in the sense that they do not significantly alter a protein's
ability to perform its primary biological function. However, new protein
functions evolve when selection begins to favor other, "promiscuous" functions
that are incide... | [
{
"created": "Wed, 2 May 2007 05:02:10 GMT",
"version": "v1"
}
] | 2007-07-18 | [
[
"Bloom",
"Jesse D",
""
],
[
"Romero",
"Philip A",
""
],
[
"Lu",
"Zhongyi",
""
],
[
"Arnold",
"Frances H",
""
]
] | BACKGROUND: Many of the mutations accumulated by naturally evolving proteins are neutral in the sense that they do not significantly alter a protein's ability to perform its primary biological function. However, new protein functions evolve when selection begins to favor other, "promiscuous" functions that are incident... |
1811.02507 | Takashi Morita | Takashi Morita, Hiroki Koda | Superregular grammars do not provide additional explanatory power but
allow for a compact analysis of animal song | Accepted for publication by Royal Society Open Science | null | 10.1098/rsos.190139 | null | q-bio.NC cs.CL | http://creativecommons.org/licenses/by/4.0/ | A pervasive belief with regard to the differences between human language and
animal vocal sequences (song) is that they belong to different classes of
computational complexity, with animal song belonging to regular languages,
whereas human language is superregular. This argument, however, lacks empirical
evidence sin... | [
{
"created": "Mon, 5 Nov 2018 05:07:37 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Jun 2019 12:06:15 GMT",
"version": "v2"
}
] | 2020-11-03 | [
[
"Morita",
"Takashi",
""
],
[
"Koda",
"Hiroki",
""
]
] | A pervasive belief with regard to the differences between human language and animal vocal sequences (song) is that they belong to different classes of computational complexity, with animal song belonging to regular languages, whereas human language is superregular. This argument, however, lacks empirical evidence since... |
1204.3398 | Namiko Mitarai | Namiko Mitarai, Joachim Mathiesen, Kim Sneppen | Emergence of diversity in a model ecosystem | 7 pages, 6 figures. Accepted for publication in PRE. Typos corrected,
Fig.3A and Fig.6 updated | Phys. Rev. E 86, 011929 (2012) | 10.1103/PhysRevE.86.011929 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The biological requirements for an ecosystem to develop and maintain species
diversity are in general unknown. Here we consider a model ecosystem of sessile
and mutually excluding organisms competing for space [Mathiesen et al. Phys.
Rev. Lett. 107, 188101 (2011)]. The competition is controlled by an interaction
netw... | [
{
"created": "Mon, 16 Apr 2012 08:27:03 GMT",
"version": "v1"
},
{
"created": "Mon, 16 Jul 2012 12:46:52 GMT",
"version": "v2"
},
{
"created": "Wed, 25 Jul 2012 07:46:12 GMT",
"version": "v3"
}
] | 2012-09-10 | [
[
"Mitarai",
"Namiko",
""
],
[
"Mathiesen",
"Joachim",
""
],
[
"Sneppen",
"Kim",
""
]
] | The biological requirements for an ecosystem to develop and maintain species diversity are in general unknown. Here we consider a model ecosystem of sessile and mutually excluding organisms competing for space [Mathiesen et al. Phys. Rev. Lett. 107, 188101 (2011)]. The competition is controlled by an interaction networ... |
q-bio/0507042 | Michael Baake | Evelyn Rost (Greifswald), Ralf Geske (Neubrandenburg), Michael Baake
(Bielefeld) | Signal analysis of impulse response functions in MR- and CT-measurements
of cerebral blood flow | 15 pages, 6 figures | J. Theor. Biol. 240 (2006) 451-458 | null | null | q-bio.TO | null | The impulse response function (IRF) of a localized bolus in cerebral blood
flow codes important information on the tissue type. It is indirectly
accessible both from MR- and CT-imaging methods, at least in principle. In
practice, however, noise and limited signal resolution render standard
deconvolution techniques al... | [
{
"created": "Thu, 28 Jul 2005 13:41:31 GMT",
"version": "v1"
}
] | 2014-09-30 | [
[
"Rost",
"Evelyn",
"",
"Greifswald"
],
[
"Geske",
"Ralf",
"",
"Neubrandenburg"
],
[
"Baake",
"Michael",
"",
"Bielefeld"
]
] | The impulse response function (IRF) of a localized bolus in cerebral blood flow codes important information on the tissue type. It is indirectly accessible both from MR- and CT-imaging methods, at least in principle. In practice, however, noise and limited signal resolution render standard deconvolution techniques almo... |
q-bio/0611013 | Zhao Jing | Zhao Jing, Tao Lin, Yu Hong, Luo Jian-Hua, Z. W. Cao, Li Yixue | Bow-tie topological features of metabolic networks and the functional
significance | 15 pages, 5 figures | Chinese Science Bulletin 2007, 52:1036 - 1045 | null | null | q-bio.MN | null | Exploring the structural topology of genome-based large-scale metabolic
network is essential for investigating possible relations between structure and
functionality. Visualization would be helpful for obtaining immediate
information about structural organization. In this work, metabolic networks of
75 organisms were... | [
{
"created": "Sat, 4 Nov 2006 02:15:44 GMT",
"version": "v1"
}
] | 2007-09-06 | [
[
"Jing",
"Zhao",
""
],
[
"Lin",
"Tao",
""
],
[
"Hong",
"Yu",
""
],
[
"Jian-Hua",
"Luo",
""
],
[
"Cao",
"Z. W.",
""
],
[
"Yixue",
"Li",
""
]
] | Exploring the structural topology of genome-based large-scale metabolic network is essential for investigating possible relations between structure and functionality. Visualization would be helpful for obtaining immediate information about structural organization. In this work, metabolic networks of 75 organisms were i... |
1408.4782 | Jaewook Joo | Jaewook Joo and Sanjeev Chauhan | Design principles of noise-induced oscillation in biochemical reaction
networks: II. coupled positive and negative feedback loops | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | According to the chemical reaction network theory, the topology of a certain
class of chemical reaction networks, regardless of the kinetic details, sets a
limit on the dynamical properties that a particular network can potentially
admit; the structure of a network predetermines the dynamic capacity of the
network. W... | [
{
"created": "Wed, 20 Aug 2014 19:49:07 GMT",
"version": "v1"
}
] | 2014-08-21 | [
[
"Joo",
"Jaewook",
""
],
[
"Chauhan",
"Sanjeev",
""
]
] | According to the chemical reaction network theory, the topology of a certain class of chemical reaction networks, regardless of the kinetic details, sets a limit on the dynamical properties that a particular network can potentially admit; the structure of a network predetermines the dynamic capacity of the network. We ... |
1809.06632 | William Grant | William P. Grant, Sebastian E. Ahnert | Modular decomposition of protein structure using community detection | 8 figures, 1 table, 11 pages | Journal of Complex Networks (2018), cny014 | 10.1093/comnet/cny014 | null | q-bio.BM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | As the number of solved protein structures increases, the opportunities for
meta-analysis of this dataset increase too. Protein structures are known to be
formed of domains; structural and functional subunits that are often repeated
across sets of proteins. These domains generally form compact, globular
regions, and ... | [
{
"created": "Tue, 18 Sep 2018 10:39:53 GMT",
"version": "v1"
}
] | 2018-09-19 | [
[
"Grant",
"William P.",
""
],
[
"Ahnert",
"Sebastian E.",
""
]
] | As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Protein structures are known to be formed of domains; structural and functional subunits that are often repeated across sets of proteins. These domains generally form compact, globular regions, and ar... |
2304.09225 | Zijin Gu | Zijin Gu, Keith Jamison, Mert R. Sabuncu and Amy Kuceyeski | Modulating human brain responses via optimal natural image selection and
synthetic image generation | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Understanding how human brains interpret and process information is
important. Here, we investigated the selectivity and inter-individual
differences in human brain responses to images via functional MRI. In our first
experiment, we found that images predicted to achieve maximal activations using
a group level encodi... | [
{
"created": "Tue, 18 Apr 2023 18:25:26 GMT",
"version": "v1"
}
] | 2023-04-20 | [
[
"Gu",
"Zijin",
""
],
[
"Jamison",
"Keith",
""
],
[
"Sabuncu",
"Mert R.",
""
],
[
"Kuceyeski",
"Amy",
""
]
] | Understanding how human brains interpret and process information is important. Here, we investigated the selectivity and inter-individual differences in human brain responses to images via functional MRI. In our first experiment, we found that images predicted to achieve maximal activations using a group level encoding... |
1206.3003 | Thierry Rabilloud | Thierry Rabilloud (LCBM) | The Whereabouts of 2D Gels in Quantitative Proteomics | null | Methods in Molecular Biology -Clifton then Totowa- 893 (2012)
25-35 | 10.1007/978-1-61779-885-6_2 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two-dimensional gel electrophoresis has been instrumental in the development
of proteomics. Although it is no longer the exclusive scheme used for
proteomics, its unique features make it a still highly valuable tool,
especially when multiple quantitative comparisons of samples must be made, and
even for large samples... | [
{
"created": "Thu, 14 Jun 2012 04:57:18 GMT",
"version": "v1"
}
] | 2012-06-15 | [
[
"Rabilloud",
"Thierry",
"",
"LCBM"
]
] | Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when multiple quantitative comparisons of samples must be made, and even for large samples s... |
2407.19059 | Andrea Radtke | Andrea J. Radtke (Lymphocyte Biology Section and Center for Advanced
Tissue Imaging, Laboratory of Immune System Biology, National Institute of
Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD,
USA), Ifeanyichukwu Anidi (Critical Care Medicine and Pulmonary Branch,
National Heart, Lu... | The IBEX Knowledge-Base: Achieving more together with open science | 8 pages, 1 figure, 9 references | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for
highly multiplexed imaging of diverse tissues. Based on open science
principles, we created the IBEX Knowledge-Base, a resource for reagents,
protocols and more, to empower innovation.
| [
{
"created": "Fri, 26 Jul 2024 19:35:20 GMT",
"version": "v1"
}
] | 2024-07-30 | [
[
"Radtke",
"Andrea J.",
"",
"Lymphocyte Biology Section and Center for Advanced\n Tissue Imaging, Laboratory of Immune System Biology, National Institute of\n Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD,\n USA"
],
[
"Anidi",
"Ifeanyichukwu",
"",
... | Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, protocols and more, to empower innovation. |
1710.06984 | Michael Meehan Dr | Michael T. Meehan, Daniel G. Cocks, Emma S. McBryde | Global stability of the multi-strain Kermack-McKendrick (renewal)
epidemic model | 8 pages | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We extend a recent investigation by Meehan et al. (2019) regarding the global
stability properties of the general Kermack-McKendrick (renewal) model to the
multi-strain case. We demonstrate that the basic reproduction number of each
strain $R_{0j}$ represents a sharp threshold parameter such that when $R_{0j}
\leq 1$... | [
{
"created": "Thu, 19 Oct 2017 02:03:50 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Jul 2019 04:02:49 GMT",
"version": "v2"
}
] | 2019-07-03 | [
[
"Meehan",
"Michael T.",
""
],
[
"Cocks",
"Daniel G.",
""
],
[
"McBryde",
"Emma S.",
""
]
] | We extend a recent investigation by Meehan et al. (2019) regarding the global stability properties of the general Kermack-McKendrick (renewal) model to the multi-strain case. We demonstrate that the basic reproduction number of each strain $R_{0j}$ represents a sharp threshold parameter such that when $R_{0j} \leq 1$ f... |
2104.02594 | Andrea De Martino | Anna Paola Muntoni, Alfredo Braunstein, Andrea Pagnani, Daniele De
Martino, Andrea De Martino | Relationship between fitness and heterogeneity in exponentially growing
microbial populations | 12+30 pages (includes Supporting Text) | null | 10.1016/j.bpj.2022.04.012 | null | q-bio.MN cond-mat.dis-nn cond-mat.stat-mech physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite major environmental and genetic differences, microbial metabolic
networks are known to generate consistent physiological outcomes across vastly
different organisms. This remarkable robustness suggests that, at least in
bacteria, metabolic activity may be guided by universal principles. The
constrained optimiz... | [
{
"created": "Tue, 6 Apr 2021 15:31:22 GMT",
"version": "v1"
},
{
"created": "Thu, 7 Apr 2022 08:35:42 GMT",
"version": "v2"
}
] | 2022-05-24 | [
[
"Muntoni",
"Anna Paola",
""
],
[
"Braunstein",
"Alfredo",
""
],
[
"Pagnani",
"Andrea",
""
],
[
"De Martino",
"Daniele",
""
],
[
"De Martino",
"Andrea",
""
]
] | Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria, metabolic activity may be guided by universal principles. The constrained optimizat... |
2209.10698 | R.K. Brojen Singh | Moirangthem Shubhakanta Singh, Mairembam Kelvin Singh and R.K. Brojen
Singh | Stochastic approach to study the properties of the complex patterns
observed in cytokine and T-cells interaction process | 14 pages, 1 figure | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Patterns in complex systems store hidden information of the system which is
needed to be explored. We present a simple model of cytokine and T-cells
interaction and studied the model within stochastic framework by constructing
Master equation of the system and solving it. The solved probability
distribution function ... | [
{
"created": "Wed, 21 Sep 2022 22:54:02 GMT",
"version": "v1"
}
] | 2022-09-23 | [
[
"Singh",
"Moirangthem Shubhakanta",
""
],
[
"Singh",
"Mairembam Kelvin",
""
],
[
"Singh",
"R. K. Brojen",
""
]
] | Patterns in complex systems store hidden information of the system which is needed to be explored. We present a simple model of cytokine and T-cells interaction and studied the model within stochastic framework by constructing Master equation of the system and solving it. The solved probability distribution function of... |
1907.12742 | Hilaria Mollica | Hilaria Mollica, Roberto Palomba, Rosita Primavera and Paolo Decuzzi | Two channel compartmentalized microfluidic chip for real time monitoring
of the metastatic cascade | null | null | 10.1021/acsbiomaterials.9b00697 | null | q-bio.CB q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metastases are the primary cause of death in cancer patients. Small animal
models are helping in dissecting some of key features in the metastatic
cascade. Yet, tools for systematically analyze the contribution of blood flow,
vascular permeability, inflammation, tissue architecture, and biochemical
stimuli are missin... | [
{
"created": "Tue, 30 Jul 2019 05:21:26 GMT",
"version": "v1"
}
] | 2019-07-31 | [
[
"Mollica",
"Hilaria",
""
],
[
"Palomba",
"Roberto",
""
],
[
"Primavera",
"Rosita",
""
],
[
"Decuzzi",
"Paolo",
""
]
] | Metastases are the primary cause of death in cancer patients. Small animal models are helping in dissecting some of key features in the metastatic cascade. Yet, tools for systematically analyze the contribution of blood flow, vascular permeability, inflammation, tissue architecture, and biochemical stimuli are missing.... |
q-bio/0410004 | Taguchi Y.-H. | Koji Matsumura and Y-h. Taguchi | Can Neural Networks Recognize Parts? | Submitted to J. Phys. Soc. Jpn | null | null | null | q-bio.NC | null | We have demonstrated neural networks can recognize parts by visual images.
Input signals are gray scale photographs of objects consisting of some parts
and output signals are their shapes. By training neural networks by a few set
of images, without any supervision they become to be able to recognize the
boundary betw... | [
{
"created": "Mon, 4 Oct 2004 10:29:49 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Matsumura",
"Koji",
""
],
[
"Taguchi",
"Y-h.",
""
]
] | We have demonstrated neural networks can recognize parts by visual images. Input signals are gray scale photographs of objects consisting of some parts and output signals are their shapes. By training neural networks by a few set of images, without any supervision they become to be able to recognize the boundary betwee... |
1803.08440 | David Fisher | David N Fisher, Matthew Brachmann, Joseph B Burant | Complex dynamics and development of behavioural individuality | Version of manuscript following initial rejection and invitation to
resubmit from journal. Further revised version now published, see:
https://www.sciencedirect.com/science/article/pii/S0003347218300654 | null | 10.1016/j.anbehav.2018.02.015 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Behavioural differences may arise in the absence of genetic or environmental
variation. Chaotic dynamics may influence behavioural development, and so this
among-individual variation. We discuss methods and experimental designs to test
this idea. Ultimately, nonlinear and chaotic behavioural development may
explain m... | [
{
"created": "Thu, 22 Mar 2018 16:34:29 GMT",
"version": "v1"
}
] | 2018-03-23 | [
[
"Fisher",
"David N",
""
],
[
"Brachmann",
"Matthew",
""
],
[
"Burant",
"Joseph B",
""
]
] | Behavioural differences may arise in the absence of genetic or environmental variation. Chaotic dynamics may influence behavioural development, and so this among-individual variation. We discuss methods and experimental designs to test this idea. Ultimately, nonlinear and chaotic behavioural development may explain muc... |
1011.5737 | Juraj Stacho | Michel Habib and Juraj Stacho | Unique perfect phylogeny is NP-hard | null | null | null | null | q-bio.PE cs.CC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We answer, in the affirmative, the following question proposed by Mike Steel
as a $100 challenge: "Is the following problem NP-hard? Given a ternary
phylogenetic X-tree T and a collection Q of quartet subtrees on X, is T the
only tree that displays Q ?"
| [
{
"created": "Fri, 26 Nov 2010 09:36:03 GMT",
"version": "v1"
}
] | 2010-11-29 | [
[
"Habib",
"Michel",
""
],
[
"Stacho",
"Juraj",
""
]
] | We answer, in the affirmative, the following question proposed by Mike Steel as a $100 challenge: "Is the following problem NP-hard? Given a ternary phylogenetic X-tree T and a collection Q of quartet subtrees on X, is T the only tree that displays Q ?" |
1503.08992 | Changwang Zhang | Changwang Zhang, Shi Zhou, Elisabetta Groppelli, Pierre Pellegrino,
Ian Williams, Persephone Borrow, Benjamin M. Chain, Clare Jolly | Hybrid spreading mechanisms and T cell activation shape the dynamics of
HIV-1 infection | null | PLOS Computational Biology. 2015 Apr 2;11(4):e1004179 | 10.1371/journal.pcbi.1004179 | null | q-bio.PE cs.AI cs.CE physics.bio-ph q-bio.CB | http://creativecommons.org/licenses/by-nc-sa/3.0/ | HIV-1 can disseminate between susceptible cells by two mechanisms: cell-free
infection following fluid-phase diffusion of virions and by highly-efficient
direct cell-to-cell transmission at immune cell contacts. The contribution of
this hybrid spreading mechanism, which is also a characteristic of some
important comp... | [
{
"created": "Tue, 31 Mar 2015 10:14:54 GMT",
"version": "v1"
}
] | 2024-01-02 | [
[
"Zhang",
"Changwang",
""
],
[
"Zhou",
"Shi",
""
],
[
"Groppelli",
"Elisabetta",
""
],
[
"Pellegrino",
"Pierre",
""
],
[
"Williams",
"Ian",
""
],
[
"Borrow",
"Persephone",
""
],
[
"Chain",
"Benjamin M.",
""
... | HIV-1 can disseminate between susceptible cells by two mechanisms: cell-free infection following fluid-phase diffusion of virions and by highly-efficient direct cell-to-cell transmission at immune cell contacts. The contribution of this hybrid spreading mechanism, which is also a characteristic of some important comput... |
1406.4030 | Arne Traulsen | Bin Wu, Benedikt Bauer, Tobias Galla, and Arne Traulsen | When do microscopic assumptions determine the outcome in evolutionary
game dynamics? | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The modelling of evolutionary game dynamics in finite populations requires
microscopic processes that determine how strategies spread. The exact details
of these processes are often chosen without much further consideration.
Different types of microscopic models, including in particular fitness-based
selection rules ... | [
{
"created": "Mon, 16 Jun 2014 14:32:17 GMT",
"version": "v1"
}
] | 2014-06-17 | [
[
"Wu",
"Bin",
""
],
[
"Bauer",
"Benedikt",
""
],
[
"Galla",
"Tobias",
""
],
[
"Traulsen",
"Arne",
""
]
] | The modelling of evolutionary game dynamics in finite populations requires microscopic processes that determine how strategies spread. The exact details of these processes are often chosen without much further consideration. Different types of microscopic models, including in particular fitness-based selection rules an... |
1102.2634 | Philippe Desjardins-Proulx | Philippe Desjardins-Proulx and Dominique Gravel | How likely is speciation in neutral ecology ? | 7 pages, 3 figures | The American Naturalist 179(1):137-144, 2012 | 10.1086/663196 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Patterns of biodiversity predicted by the neutral theory rely on a simple
phenomenological model of speciation. To further investigate the effect of
speciation on neutral biodiversity, we analyze a spatially-explicit neutral
model based on population genetics. We define the metacommunity as a system of
populations ex... | [
{
"created": "Sun, 13 Feb 2011 20:02:31 GMT",
"version": "v1"
},
{
"created": "Sun, 20 Feb 2011 05:50:16 GMT",
"version": "v2"
},
{
"created": "Thu, 23 Jun 2011 09:21:29 GMT",
"version": "v3"
}
] | 2012-07-10 | [
[
"Desjardins-Proulx",
"Philippe",
""
],
[
"Gravel",
"Dominique",
""
]
] | Patterns of biodiversity predicted by the neutral theory rely on a simple phenomenological model of speciation. To further investigate the effect of speciation on neutral biodiversity, we analyze a spatially-explicit neutral model based on population genetics. We define the metacommunity as a system of populations exch... |
1910.09600 | Paul Bertin | Mohammad Hashir, Paul Bertin, Martin Weiss, Vincent Frappier, Theodore
J. Perkins, Genevi\`eve Boucher and Joseph Paul Cohen | Is graph-based feature selection of genes better than random? | Accepted to the Machine Learning in Computational Biology (MLCB)
meeting 2019. 7 pages. 4 figures. arXiv admin note: substantial text overlap
with arXiv:1905.02295 | null | null | null | q-bio.GN cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene interaction graphs aim to capture various relationships between genes
and represent decades of biology research. When trying to make predictions from
genomic data, those graphs could be used to overcome the curse of
dimensionality by making machine learning models sparser and more consistent
with biological comm... | [
{
"created": "Mon, 21 Oct 2019 18:51:25 GMT",
"version": "v1"
},
{
"created": "Tue, 19 Nov 2019 23:35:05 GMT",
"version": "v2"
},
{
"created": "Fri, 27 Dec 2019 17:43:20 GMT",
"version": "v3"
}
] | 2020-01-14 | [
[
"Hashir",
"Mohammad",
""
],
[
"Bertin",
"Paul",
""
],
[
"Weiss",
"Martin",
""
],
[
"Frappier",
"Vincent",
""
],
[
"Perkins",
"Theodore J.",
""
],
[
"Boucher",
"Geneviève",
""
],
[
"Cohen",
"Joseph Paul",
""... | Gene interaction graphs aim to capture various relationships between genes and represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality by making machine learning models sparser and more consistent with biological common... |
0811.3407 | Nicholas Chia | Nicholas Chia, Ido Golding, Nigel Goldenfeld | Lambda-prophage induction modeled as a cooperative failure mode of lytic
repression | added reference | null | 10.1103/PhysRevE.80.030901 | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze a system-level model for lytic repression of lambda-phage in E.
coli using reliability theory, showing that the repressor circuit comprises 4
redundant components whose failure mode is prophage induction. Our model
reflects the specific biochemical mechanisms involved in regulation, including
long-range co... | [
{
"created": "Thu, 20 Nov 2008 20:56:11 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Nov 2008 06:51:37 GMT",
"version": "v2"
},
{
"created": "Wed, 3 Dec 2008 08:07:58 GMT",
"version": "v3"
}
] | 2013-05-29 | [
[
"Chia",
"Nicholas",
""
],
[
"Golding",
"Ido",
""
],
[
"Goldenfeld",
"Nigel",
""
]
] | We analyze a system-level model for lytic repression of lambda-phage in E. coli using reliability theory, showing that the repressor circuit comprises 4 redundant components whose failure mode is prophage induction. Our model reflects the specific biochemical mechanisms involved in regulation, including long-range coop... |
2205.08308 | Alicia Shin | Alicia Shin | The Relationship Between Insulin Resistance Neutrophil to Lymphocyte
Ratio | 12 pages, 6 figures | null | null | null | q-bio.QM | http://creativecommons.org/publicdomain/zero/1.0/ | Aim: There is increasing interest in the role of chronic inflammation on
pathogenesis of various disease, and one of its markers, high NLR is associated
with various mortality and morbidity risk. Insulin resistance (IR) might be one
potential associate factors, as suggested in preclinical studies. However,
epidemiolo... | [
{
"created": "Fri, 13 May 2022 20:18:26 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Dec 2022 20:53:02 GMT",
"version": "v2"
}
] | 2022-12-29 | [
[
"Shin",
"Alicia",
""
]
] | Aim: There is increasing interest in the role of chronic inflammation on pathogenesis of various disease, and one of its markers, high NLR is associated with various mortality and morbidity risk. Insulin resistance (IR) might be one potential associate factors, as suggested in preclinical studies. However, epidemiologi... |
1007.3447 | Stephane Ghozzi | St\'ephane Ghozzi, J\'er\^ome Wong Ng, Didier Chatenay and J\'er\^ome
Robert | Inference of plasmid copy number mean and noise from single cell gene
expression data | 9 pages, 3 figures, 2 tables | Phys. Rev. E 82, 051916 (2010) | 10.1103/PhysRevE.82.051916 | null | q-bio.CB physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Plasmids are extra-chromosomal DNA molecules which code for their own
replication. We previously reported a setup using genes coding for fluorescent
proteins of two colors that allowed us, using a simple model, to extract the
plasmid copy number noise in a monoclonal population of bacteria [J. Wong Ng et
al., Phys. R... | [
{
"created": "Tue, 20 Jul 2010 15:25:12 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Nov 2010 09:55:24 GMT",
"version": "v2"
}
] | 2010-11-17 | [
[
"Ghozzi",
"Stéphane",
""
],
[
"Ng",
"Jérôme Wong",
""
],
[
"Chatenay",
"Didier",
""
],
[
"Robert",
"Jérôme",
""
]
] | Plasmids are extra-chromosomal DNA molecules which code for their own replication. We previously reported a setup using genes coding for fluorescent proteins of two colors that allowed us, using a simple model, to extract the plasmid copy number noise in a monoclonal population of bacteria [J. Wong Ng et al., Phys. Rev... |
2402.12383 | Idoia Berges | Idoia Berges, Jes\'us Berm\'udez, Arantza Illarramendi | Binding SNOMED-CT Terms to Archetype Elements: Establishing a Baseline
of Results | This document is the Accepted Manuscript version of a Published Work
that appeared in final form in Methods of Information in Medicine 54(1) :
45-49 (2015), copyright 2015 Schattauer. To access the final edited and
published work see https://doi.org/10.3414/me13-02-0022 | Methods of Information in Medicine 54(1) : 45-49 (2015) | 10.3414/me13-02-0022 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Introduction: This article is part of the Focus Theme of METHODS of
Information in Medicine on "Managing Interoperability and Complexity in Health
Systems". Background: The proliferation of archetypes as a means to represent
information of Electronic Health Records has raised the need of binding
terminological codes ... | [
{
"created": "Fri, 26 Jan 2024 15:13:34 GMT",
"version": "v1"
}
] | 2024-02-21 | [
[
"Berges",
"Idoia",
""
],
[
"Bermúdez",
"Jesús",
""
],
[
"Illarramendi",
"Arantza",
""
]
] | Introduction: This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". Background: The proliferation of archetypes as a means to represent information of Electronic Health Records has raised the need of binding terminological codes - ... |
1304.7109 | Manuel Sch\"olling | Manuel Sch\"olling and Rudolf Hanel | Reconstructing protein binding patterns from ChIP time-series | null | null | null | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation Gene transcription requires the orchestrated binding of various
proteins to the promoter of a gene. The binding times and binding order of
proteins allow to draw conclusions about the proteins' exact function in the
recruitment process. Time-resolved ChIP experiments are being used to analyze
the order of ... | [
{
"created": "Fri, 26 Apr 2013 09:51:04 GMT",
"version": "v1"
}
] | 2013-04-29 | [
[
"Schölling",
"Manuel",
""
],
[
"Hanel",
"Rudolf",
""
]
] | Motivation Gene transcription requires the orchestrated binding of various proteins to the promoter of a gene. The binding times and binding order of proteins allow to draw conclusions about the proteins' exact function in the recruitment process. Time-resolved ChIP experiments are being used to analyze the order of pr... |
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