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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
q-bio/0603037 | Herculano Martinho | Renata Andrade Bitar, Herculano da Silva Martinho, Carlos Julio Tierra
Criollo, Leandra Naira Zambelli Ramalho, Mario Mourao Netto, Airton Abrahao
Martin | Biochemical analysis of human breast tissues using FT-Raman spectroscopy | 29 pages, 9 figures. accepted Journal of Biomedical Optics | null | 10.1117/1.2363362 | null | q-bio.TO q-bio.QM | null | In this work we employ the Fourier Transform Raman Spectroscopy to study
normal and tumoral human breast tissues, including several subtypes of cancers.
We analyzed 194 Raman spectra from breast tissues that were separated into 9
groups according to their corresponding histopathological diagnosis. The
assignment of t... | [
{
"created": "Fri, 31 Mar 2006 18:52:11 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Bitar",
"Renata Andrade",
""
],
[
"Martinho",
"Herculano da Silva",
""
],
[
"Criollo",
"Carlos Julio Tierra",
""
],
[
"Ramalho",
"Leandra Naira Zambelli",
""
],
[
"Netto",
"Mario Mourao",
""
],
[
"Martin",
"Airton Abrahao",
... | In this work we employ the Fourier Transform Raman Spectroscopy to study normal and tumoral human breast tissues, including several subtypes of cancers. We analyzed 194 Raman spectra from breast tissues that were separated into 9 groups according to their corresponding histopathological diagnosis. The assignment of the... |
1510.08965 | Boya Song | Linda Ma, Boya Song, Thomas Curran, Nhu Phong, Emilie Dressaire and
Marcus Roper | Defining individual size in the model filamentous fungus
$\textit{Neurospora crassa}$ | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is challenging to apply the tenets of individuality to filamentous fungi:
a fungal mycelium can contain millions of genetically diverse but totipotent
nuclei, each capable of founding new mycelia. Moreover a single mycelium can
potentially stretch over kilometers and it is unlikely that its distant parts
share res... | [
{
"created": "Fri, 30 Oct 2015 04:00:22 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Jan 2016 01:07:41 GMT",
"version": "v2"
}
] | 2016-01-06 | [
[
"Ma",
"Linda",
""
],
[
"Song",
"Boya",
""
],
[
"Curran",
"Thomas",
""
],
[
"Phong",
"Nhu",
""
],
[
"Dressaire",
"Emilie",
""
],
[
"Roper",
"Marcus",
""
]
] | It is challenging to apply the tenets of individuality to filamentous fungi: a fungal mycelium can contain millions of genetically diverse but totipotent nuclei, each capable of founding new mycelia. Moreover a single mycelium can potentially stretch over kilometers and it is unlikely that its distant parts share resou... |
1812.11405 | Andreea Beica | Andreea Beica, J\'er\^ome Feret, Tatjana Petrov | Tropical Abstraction of Biochemical Reaction Networks with Guarantees | null | null | null | null | q-bio.MN cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biochemical molecules interact through modification and binding reactions,
giving raise to a combinatorial number of possible biochemical species. The
time-dependent evolution of concentrations of the species is commonly described
by a system of coupled ordinary differential equations (ODEs). However, the
analysis of... | [
{
"created": "Sat, 29 Dec 2018 17:30:35 GMT",
"version": "v1"
},
{
"created": "Thu, 21 Mar 2019 09:56:13 GMT",
"version": "v2"
}
] | 2019-03-22 | [
[
"Beica",
"Andreea",
""
],
[
"Feret",
"Jérôme",
""
],
[
"Petrov",
"Tatjana",
""
]
] | Biochemical molecules interact through modification and binding reactions, giving raise to a combinatorial number of possible biochemical species. The time-dependent evolution of concentrations of the species is commonly described by a system of coupled ordinary differential equations (ODEs). However, the analysis of s... |
2305.13348 | Justin Eilertsen | Justin Eilertsen and Wylie Stroberg | On the role of eigenvalue disparity and coordinate transformations in
the reduction of the linear noise approximation | 9 Figures, 38 pages | null | null | null | q-bio.MN math.DS math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Eigenvalue disparity, also known as timescale separation, permits the
systematic reduction of deterministic models of enzyme kinetics. Geometric
singular perturbation theory, of which eigenvalue disparity is central,
provides a coordinate-free framework for deriving reduced mass action models in
the deterministic rea... | [
{
"created": "Mon, 22 May 2023 16:39:17 GMT",
"version": "v1"
}
] | 2023-05-24 | [
[
"Eilertsen",
"Justin",
""
],
[
"Stroberg",
"Wylie",
""
]
] | Eigenvalue disparity, also known as timescale separation, permits the systematic reduction of deterministic models of enzyme kinetics. Geometric singular perturbation theory, of which eigenvalue disparity is central, provides a coordinate-free framework for deriving reduced mass action models in the deterministic realm... |
q-bio/0505010 | Ted Hesselroth | Ted Hesselroth and Klaus Schulten | The Dynamics of Image Processing by Feature Maps in the Primary Visual
Cortex | 44 pages, 16 figures. For archival purposes | null | null | null | q-bio.NC q-bio.QM | null | The operational characteristics of a linear neural network image processing
system based on the brain's vision system are investigated. The final stage of
the network consists of edge detectors of various orienations arranged in a
feature map, corresponding to the primary visual cortex, or V1. The lateral
geniculate ... | [
{
"created": "Thu, 5 May 2005 16:58:44 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Hesselroth",
"Ted",
""
],
[
"Schulten",
"Klaus",
""
]
] | The operational characteristics of a linear neural network image processing system based on the brain's vision system are investigated. The final stage of the network consists of edge detectors of various orienations arranged in a feature map, corresponding to the primary visual cortex, or V1. The lateral geniculate nu... |
2005.03651 | Alessio Notari | Alessio Notari, Giorgio Torrieri | COVID-19 transmission risk factors | 42 pages, 31 figures, 32 tables. Principal Component Analysis added
in v2 | null | null | null | q-bio.QM physics.soc-ph q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze risk factors correlated with the initial transmission growth rate
of the recent COVID-19 pandemic in different countries. The number of cases
follows in its early stages an almost exponential expansion; we chose as a
starting point in each country the first day $d_i$ with 30 cases and we fitted
for 12 days... | [
{
"created": "Thu, 7 May 2020 17:57:58 GMT",
"version": "v1"
},
{
"created": "Mon, 10 May 2021 22:16:08 GMT",
"version": "v2"
}
] | 2021-05-12 | [
[
"Notari",
"Alessio",
""
],
[
"Torrieri",
"Giorgio",
""
]
] | We analyze risk factors correlated with the initial transmission growth rate of the recent COVID-19 pandemic in different countries. The number of cases follows in its early stages an almost exponential expansion; we chose as a starting point in each country the first day $d_i$ with 30 cases and we fitted for 12 days, ... |
1008.2314 | Talitha Washington | Ronald E. Mickens and Talitha M. Washington | A Note on an NSFD Scheme for a Mathematical Model of Respiratory Virus
Transmission | The final version will be published in Journal of Difference
Equations and Applications | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We construct a nonstandard finite difference (NSFD) scheme for an SIRS
mathematical model of respiratory virus transmission. This discretization is in
full compliance with the NSFD methodology as formulated by R. E. Mickens. By
use of an exact conservation law satisfied by the SIRS differential equations,
we are able... | [
{
"created": "Fri, 13 Aug 2010 13:36:23 GMT",
"version": "v1"
}
] | 2010-08-16 | [
[
"Mickens",
"Ronald E.",
""
],
[
"Washington",
"Talitha M.",
""
]
] | We construct a nonstandard finite difference (NSFD) scheme for an SIRS mathematical model of respiratory virus transmission. This discretization is in full compliance with the NSFD methodology as formulated by R. E. Mickens. By use of an exact conservation law satisfied by the SIRS differential equations, we are able t... |
0902.2120 | Anirban Banerji | Anirban Banerji | An algorithm to relate protein surface roughness with local geometry of
protein exterior shape | null | null | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Changes in the extent of local concavity along with changes in surface
roughness of binding sites of proteins have long been considered as useful
markers to identify functional sites of proteins. However, an algorithm that
describes the connection between the simultaneous changes of these important
parameters - elude... | [
{
"created": "Thu, 12 Feb 2009 14:27:52 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Nov 2011 05:21:53 GMT",
"version": "v2"
}
] | 2011-11-29 | [
[
"Banerji",
"Anirban",
""
]
] | Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the connection between the simultaneous changes of these important parameters - eludes ... |
2202.12185 | Attila Szolnoki | Breno F. de Oliveira and Attila Szolnoki | Competition among alliances of different sizes | 9 pages, 7 figures, accepted for publication in Chaos, Solitons and
Fractals | Chaos, Solitons and Fractals 157 (2022) 111940 | 10.1016/j.chaos.2022.111940 | null | q-bio.PE cond-mat.stat-mech physics.bio-ph physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | To understand the biodiversity of an ecosystem cannot be understood by solely
analyzing the pair relations of competing species. Instead, we should consider
multi-point interactions because the presence of a third party could change the
original microscopic outcome significantly. In this way an alliance may emerge
wh... | [
{
"created": "Thu, 24 Feb 2022 16:37:44 GMT",
"version": "v1"
}
] | 2022-03-01 | [
[
"de Oliveira",
"Breno F.",
""
],
[
"Szolnoki",
"Attila",
""
]
] | To understand the biodiversity of an ecosystem cannot be understood by solely analyzing the pair relations of competing species. Instead, we should consider multi-point interactions because the presence of a third party could change the original microscopic outcome significantly. In this way an alliance may emerge wher... |
2202.07533 | Luis Pedro Garc\'ia-Pintos | Luis Pedro Garc\'ia-Pintos | Limits on the Evolutionary Rates of Biological Traits | Close to the published version | null | 10.1038/s41598-024-61872-z | null | q-bio.PE cond-mat.stat-mech physics.bio-ph q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This paper focuses on the maximum speed at which biological evolution can
occur. I derive inequalities that limit the rate of evolutionary processes
driven by natural selection, mutations, or genetic drift. These \emph{rate
limits} link the variability in a population to evolutionary rates. In
particular, high varian... | [
{
"created": "Tue, 15 Feb 2022 16:05:37 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Feb 2022 01:27:55 GMT",
"version": "v2"
},
{
"created": "Tue, 18 Jul 2023 15:39:33 GMT",
"version": "v3"
},
{
"created": "Fri, 14 Jun 2024 16:23:15 GMT",
"version": "v4"
}
] | 2024-06-17 | [
[
"García-Pintos",
"Luis Pedro",
""
]
] | This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These \emph{rate limits} link the variability in a population to evolutionary rates. In particular, high variance... |
1709.01116 | Dimitrios Adamos Dr | Fotis Kalaganis (1), Dimitrios A. Adamos (2 and 3), Nikos Laskaris (1
and 3) ((1) AIIA Lab, Department of Informatics, Aristotle University of
Thessaloniki, (2) School of Music Studies, Aristotle University of
Thessaloniki, (3) Neuroinformatics GRoup, Aristotle University of
Thessaloniki) | Musical NeuroPicks: a consumer-grade BCI for on-demand music streaming
services | null | Neurocomputing 2017 | null | null | q-bio.NC cs.CY cs.HC cs.MM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigated the possibility of using a machine-learning scheme in
conjunction with commercial wearable EEG-devices for translating listener's
subjective experience of music into scores that can be used in popular
on-demand music streaming services. Our study resulted into two variants,
differing in terms of perfo... | [
{
"created": "Mon, 4 Sep 2017 18:55:35 GMT",
"version": "v1"
}
] | 2017-09-06 | [
[
"Kalaganis",
"Fotis",
"",
"2 and 3"
],
[
"Adamos",
"Dimitrios A.",
"",
"2 and 3"
],
[
"Laskaris",
"Nikos",
"",
"1\n and 3"
]
] | We investigated the possibility of using a machine-learning scheme in conjunction with commercial wearable EEG-devices for translating listener's subjective experience of music into scores that can be used in popular on-demand music streaming services. Our study resulted into two variants, differing in terms of perform... |
0902.1941 | Francesco Piazza | Lorenzo Bongini, Francesco Piazza, Lapo Casetti and Paolo De Los Rios | Vibrational entropy and the structural organization of proteins | 12 pages, 8 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we analyze the vibrational spectra of a large ensemble of
non-homologous protein structures by means of a novel tool, that we coin the
Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the
intrinsic heterogeneity of force constants displayed by protein arrangements
and also incorp... | [
{
"created": "Wed, 11 Feb 2009 16:56:02 GMT",
"version": "v1"
}
] | 2009-02-12 | [
[
"Bongini",
"Lorenzo",
""
],
[
"Piazza",
"Francesco",
""
],
[
"Casetti",
"Lapo",
""
],
[
"Rios",
"Paolo De Los",
""
]
] | In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin the Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force constants displayed by protein arrangements and also incorpor... |
1112.2317 | Christopher L. Henley | Christopher L. Henley | Possible origins of macroscopic left-right asymmetry in organisms | 42 pages, 6 figures, resubmitted to J. Stat. Phys. special issue.
Major rewrite, rearranged sections/subsections, new Fig 3 + 6, new physics in
Sec 2.4 and 3.4.1, added Sec 5 and subsections of Sec 4 | null | 10.1007/s10955-012-0520-z | null | q-bio.SC q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | I consider the microscopic mechanisms by which a particular left-right (L/R)
asymmetry is generated at the organism level from the microscopic handedness of
cytoskeletal molecules. In light of a fundamental symmetry principle, the
typical pattern-formation mechanisms of diffusion plus regulation cannot
implement the ... | [
{
"created": "Sun, 11 Dec 2011 03:57:16 GMT",
"version": "v1"
},
{
"created": "Thu, 3 May 2012 01:36:21 GMT",
"version": "v2"
}
] | 2015-06-03 | [
[
"Henley",
"Christopher L.",
""
]
] | I consider the microscopic mechanisms by which a particular left-right (L/R) asymmetry is generated at the organism level from the microscopic handedness of cytoskeletal molecules. In light of a fundamental symmetry principle, the typical pattern-formation mechanisms of diffusion plus regulation cannot implement the "r... |
q-bio/0505016 | Dietrich Stauffer | Klaus Rohde and Dietrich Stauffer | Simulation of geographical trends in Chowdhury ecosystem model | 13 pages including 8 figures | null | null | null | q-bio.PE | null | A computer simulation based on individual births and deaths gives a
biodiversity increasing from cold to warm climates, in agreement with reality.
Complexity of foodwebs increases with time and at a higher rate at low
latitudes, and there is a higher rate of species creation at low latitudes.
Keeping many niches empt... | [
{
"created": "Mon, 9 May 2005 13:57:29 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Rohde",
"Klaus",
""
],
[
"Stauffer",
"Dietrich",
""
]
] | A computer simulation based on individual births and deaths gives a biodiversity increasing from cold to warm climates, in agreement with reality. Complexity of foodwebs increases with time and at a higher rate at low latitudes, and there is a higher rate of species creation at low latitudes. Keeping many niches empty ... |
1909.11943 | Maksims Fiosins | Jelena Fiosina, Maksims Fiosins, Stefan Bonn | Deep Learning and Random Forest-Based Augmentation of sRNA Expression
Profiles | null | Lecture Notes in Computer Science, 11490 (2019) | 10.1007/978-3-030-20242-2_14 | null | q-bio.GN cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The lack of well-structured annotations in a growing amount of RNA expression
data complicates data interoperability and reusability. Commonly - used text
mining methods extract annotations from existing unstructured data descriptions
and often provide inaccurate output that requires manual curation. Automatic
data-b... | [
{
"created": "Thu, 26 Sep 2019 07:10:03 GMT",
"version": "v1"
}
] | 2019-09-27 | [
[
"Fiosina",
"Jelena",
""
],
[
"Fiosins",
"Maksims",
""
],
[
"Bonn",
"Stefan",
""
]
] | The lack of well-structured annotations in a growing amount of RNA expression data complicates data interoperability and reusability. Commonly - used text mining methods extract annotations from existing unstructured data descriptions and often provide inaccurate output that requires manual curation. Automatic data-bas... |
2101.04183 | Peter Thompson | Peter R. Thompson, Andrew E. Derocher, Mark A. Edwards, Mark A. Lewis | Detecting seasonal episodic-like spatiotemporal memory patterns using
animal movement modelling | 23 pages, including title and abstract; 4 tables; 3 figures; one
Appendix containing 2 additional tables and 1 additional figure | null | 10.1111/2041-210X.13743 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | 1. Spatial memory plays a role in the way animals perceive their
environments, resulting in memory-informed movement patterns that are
observable to ecologists. Developing mathematical techniques to understand how
animals use memory in their environments allows for an increased understanding
of animal cognition. 2. H... | [
{
"created": "Mon, 11 Jan 2021 20:46:35 GMT",
"version": "v1"
},
{
"created": "Tue, 15 Feb 2022 21:09:01 GMT",
"version": "v2"
}
] | 2022-02-17 | [
[
"Thompson",
"Peter R.",
""
],
[
"Derocher",
"Andrew E.",
""
],
[
"Edwards",
"Mark A.",
""
],
[
"Lewis",
"Mark A.",
""
]
] | 1. Spatial memory plays a role in the way animals perceive their environments, resulting in memory-informed movement patterns that are observable to ecologists. Developing mathematical techniques to understand how animals use memory in their environments allows for an increased understanding of animal cognition. 2. Her... |
2103.04246 | Alvin Chan | Alvin Chan, Anna Korsakova, Yew-Soon Ong, Fernaldo Richtia Winnerdy,
Kah Wai Lim, Anh Tuan Phan | RNA Alternative Splicing Prediction with Discrete Compositional Energy
Network | ACM CHIL 2021 Camera-Ready | null | null | null | q-bio.GN cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | A single gene can encode for different protein versions through a process
called alternative splicing. Since proteins play major roles in cellular
functions, aberrant splicing profiles can result in a variety of diseases,
including cancers. Alternative splicing is determined by the gene's primary
sequence and other r... | [
{
"created": "Sun, 7 Mar 2021 03:15:10 GMT",
"version": "v1"
}
] | 2021-03-09 | [
[
"Chan",
"Alvin",
""
],
[
"Korsakova",
"Anna",
""
],
[
"Ong",
"Yew-Soon",
""
],
[
"Winnerdy",
"Fernaldo Richtia",
""
],
[
"Lim",
"Kah Wai",
""
],
[
"Phan",
"Anh Tuan",
""
]
] | A single gene can encode for different protein versions through a process called alternative splicing. Since proteins play major roles in cellular functions, aberrant splicing profiles can result in a variety of diseases, including cancers. Alternative splicing is determined by the gene's primary sequence and other reg... |
1911.08121 | Nina Miolane | Nina Miolane, Fr\'ed\'eric Poitevin, Yee-Ting Li, Susan Holmes | Estimation of Orientation and Camera Parameters from Cryo-Electron
Microscopy Images with Variational Autoencoders and Generative Adversarial
Networks | null | null | null | null | q-bio.QM cs.CV eess.IV stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cryo-electron microscopy (cryo-EM) is capable of producing reconstructed 3D
images of biomolecules at near-atomic resolution. As such, it represents one of
the most promising imaging techniques in structural biology. However, raw
cryo-EM images are only highly corrupted - noisy and band-pass filtered - 2D
projections... | [
{
"created": "Tue, 19 Nov 2019 07:04:43 GMT",
"version": "v1"
},
{
"created": "Sun, 23 May 2021 19:11:06 GMT",
"version": "v2"
}
] | 2021-05-25 | [
[
"Miolane",
"Nina",
""
],
[
"Poitevin",
"Frédéric",
""
],
[
"Li",
"Yee-Ting",
""
],
[
"Holmes",
"Susan",
""
]
] | Cryo-electron microscopy (cryo-EM) is capable of producing reconstructed 3D images of biomolecules at near-atomic resolution. As such, it represents one of the most promising imaging techniques in structural biology. However, raw cryo-EM images are only highly corrupted - noisy and band-pass filtered - 2D projections o... |
q-bio/0605009 | Stefan Braunewell | Stefan Braunewell and Stefan Bornholdt | Superstability of the yeast cell cycle dynamics: Ensuring causality in
the presence of biochemical stochasticity | 6 pages, 4 figures, 1 table | null | null | null | q-bio.MN | null | Gene regulatory dynamics is governed by molecular processes and therefore
exhibits an inherent stochasticity. However, for the survival of an organism it
is a strict necessity that this intrinsic noise does not prevent robust
functioning of the system. It is still an open question how dynamical stability
is achieved ... | [
{
"created": "Fri, 5 May 2006 09:33:36 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Braunewell",
"Stefan",
""
],
[
"Bornholdt",
"Stefan",
""
]
] | Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of the system. It is still an open question how dynamical stability is achieved in... |
1905.10916 | Sepehr Ehsani | Sepehr Ehsani | The challenges of purely mechanistic models in biology and the minimum
need for a 'mechanism-plus-X' framework | 38 pages, 3 figures | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Ever since the advent of molecular biology in the 1970s, mechanical models
have become the dogma in the field, where a "true" understanding of any subject
is equated to a mechanistic description. This has been to the detriment of the
biomedical sciences, where, barring some exceptions, notable new feats of
understand... | [
{
"created": "Mon, 27 May 2019 00:56:00 GMT",
"version": "v1"
}
] | 2019-05-28 | [
[
"Ehsani",
"Sepehr",
""
]
] | Ever since the advent of molecular biology in the 1970s, mechanical models have become the dogma in the field, where a "true" understanding of any subject is equated to a mechanistic description. This has been to the detriment of the biomedical sciences, where, barring some exceptions, notable new feats of understandin... |
2403.05044 | Eddy Kwessi | Eddy Kwessi | Information Theory in a Darwinian Evolution Population Dynamics Model | null | null | null | null | q-bio.PE cs.IT math.DS math.IT math.ST stat.TH | http://creativecommons.org/licenses/by/4.0/ | Using information theory, we propose an estimation method for traits
parameters in a Darwinian evolution model for species with on trait or multiple
traits. We use the Fisher's information to obtain the errors on the estimation
for one species with one or multiple traits. We perform simulations to
illustrate the meth... | [
{
"created": "Fri, 8 Mar 2024 04:39:05 GMT",
"version": "v1"
}
] | 2024-03-11 | [
[
"Kwessi",
"Eddy",
""
]
] | Using information theory, we propose an estimation method for traits parameters in a Darwinian evolution model for species with on trait or multiple traits. We use the Fisher's information to obtain the errors on the estimation for one species with one or multiple traits. We perform simulations to illustrate the method... |
2112.01318 | Jiahui Chen | Jiahui Chen, Rui Wang, Nancy Benovich Gilby and Guo-Wei Wei | Omicron (B.1.1.529): Infectivity, vaccine breakthrough, and antibody
resistance | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
variant Omicron (B.1.1.529) has ushered panic responses around the world due to
its contagious and vaccine escape mutations. The essential infectivity and
antibody resistance of the SARS-CoV-2 variant are determined by its mutations
on the spike ... | [
{
"created": "Wed, 1 Dec 2021 14:29:48 GMT",
"version": "v1"
}
] | 2021-12-03 | [
[
"Chen",
"Jiahui",
""
],
[
"Wang",
"Rui",
""
],
[
"Gilby",
"Nancy Benovich",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has ushered panic responses around the world due to its contagious and vaccine escape mutations. The essential infectivity and antibody resistance of the SARS-CoV-2 variant are determined by its mutations on the spike (S... |
2212.12034 | Alexandria Volkening | Electa Cleveland, Angela Zhu, Bjorn Sandstede, and Alexandria
Volkening | Quantifying different modeling frameworks using topological data
analysis: a case study with zebrafish patterns | null | null | null | null | q-bio.CB math.DS | http://creativecommons.org/licenses/by/4.0/ | Mathematical models come in many forms across biological applications. In the
case of complex, spatial dynamics and pattern formation, stochastic models also
face two main challenges: pattern data is largely qualitative, and model
realizations may vary significantly. Together these issues make it difficult to
relate ... | [
{
"created": "Thu, 22 Dec 2022 20:54:32 GMT",
"version": "v1"
}
] | 2022-12-26 | [
[
"Cleveland",
"Electa",
""
],
[
"Zhu",
"Angela",
""
],
[
"Sandstede",
"Bjorn",
""
],
[
"Volkening",
"Alexandria",
""
]
] | Mathematical models come in many forms across biological applications. In the case of complex, spatial dynamics and pattern formation, stochastic models also face two main challenges: pattern data is largely qualitative, and model realizations may vary significantly. Together these issues make it difficult to relate mo... |
2408.07222 | Marek Mutwil | Rohan Shawn Sunil, Shan Chun Lim, Manoj Itharajula, Marek Mutwil | The gene function prediction challenge: large language models and
knowledge graphs to the rescue | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Elucidating gene function is one of the ultimate goals of plant science.
Despite this, only ~15% of all genes in the model plant Arabidopsis thaliana
have comprehensively experimentally verified functions. While bioinformatical
gene function prediction approaches can guide biologists in their experimental
efforts, ne... | [
{
"created": "Tue, 13 Aug 2024 22:39:21 GMT",
"version": "v1"
}
] | 2024-08-15 | [
[
"Sunil",
"Rohan Shawn",
""
],
[
"Lim",
"Shan Chun",
""
],
[
"Itharajula",
"Manoj",
""
],
[
"Mutwil",
"Marek",
""
]
] | Elucidating gene function is one of the ultimate goals of plant science. Despite this, only ~15% of all genes in the model plant Arabidopsis thaliana have comprehensively experimentally verified functions. While bioinformatical gene function prediction approaches can guide biologists in their experimental efforts, neit... |
2111.10530 | Manuel Baltieri Dr | Manuel Baltieri and Takuya Isomura | Kalman filters as the steady-state solution of gradient descent on
variational free energy | null | null | null | null | q-bio.NC cs.SY eess.SY math.OC math.ST stat.TH | http://creativecommons.org/licenses/by-sa/4.0/ | The Kalman filter is an algorithm for the estimation of hidden variables in
dynamical systems under linear Gauss-Markov assumptions with widespread
applications across different fields. Recently, its Bayesian interpretation has
received a growing amount of attention especially in neuroscience, robotics and
machine le... | [
{
"created": "Sat, 20 Nov 2021 07:23:02 GMT",
"version": "v1"
}
] | 2021-11-23 | [
[
"Baltieri",
"Manuel",
""
],
[
"Isomura",
"Takuya",
""
]
] | The Kalman filter is an algorithm for the estimation of hidden variables in dynamical systems under linear Gauss-Markov assumptions with widespread applications across different fields. Recently, its Bayesian interpretation has received a growing amount of attention especially in neuroscience, robotics and machine lear... |
q-bio/0606018 | Wentian Li | Wentian Li, Young Ju Suh, Jingshan Zhang | Does Logarithm Transformation of Microarray Data Affect Ranking Order of
Differentially Expressed Genes? | submitted to IEEE/EMBS Conference'06 | null | 10.1109/IEMBS.2006.260896 | null | q-bio.QM | null | A common practice in microarray analysis is to transform the microarray raw
data (light intensity) by a logarithmic transformation, and the justification
for this transformation is to make the distribution more symmetric and
Gaussian-like. Since this transformation is not universally practiced in all
microarray analy... | [
{
"created": "Wed, 14 Jun 2006 20:45:25 GMT",
"version": "v1"
}
] | 2016-11-17 | [
[
"Li",
"Wentian",
""
],
[
"Suh",
"Young Ju",
""
],
[
"Zhang",
"Jingshan",
""
]
] | A common practice in microarray analysis is to transform the microarray raw data (light intensity) by a logarithmic transformation, and the justification for this transformation is to make the distribution more symmetric and Gaussian-like. Since this transformation is not universally practiced in all microarray analysi... |
2301.12221 | Luigi Frunzo | F. Russo, A. Tenore, M.R. Mattei, L. Frunzo | Multiscale modelling of heavy metals adsorption on algal-bacterial
photogranules | 43 pages, 18 figures, preprint version | null | null | null | q-bio.CB physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A multiscale mathematical model describing the genesis and ecology of
algal-bacterial photogranules and the metals biosorption on their solid matrix
within a sequencing batch reactor (SBR) is presented. The granular biofilm is
modelled as a spherical free boundary domain with radial symmetry and a
vanishing initial v... | [
{
"created": "Sat, 28 Jan 2023 15:02:17 GMT",
"version": "v1"
}
] | 2023-01-31 | [
[
"Russo",
"F.",
""
],
[
"Tenore",
"A.",
""
],
[
"Mattei",
"M. R.",
""
],
[
"Frunzo",
"L.",
""
]
] | A multiscale mathematical model describing the genesis and ecology of algal-bacterial photogranules and the metals biosorption on their solid matrix within a sequencing batch reactor (SBR) is presented. The granular biofilm is modelled as a spherical free boundary domain with radial symmetry and a vanishing initial val... |
1301.6360 | Tomasz Rutkowski | M. Chang, N. Nishikawa, Z.R. Struzik, K. Mori, S. Makino, D. Mandic,
and T.M. Rutkowski | Comparison of P300 Responses in Auditory, Visual and Audiovisual Spatial
Speller BCI Paradigms | Proceedings of the Fifth International Brain-Computer Interface
Meeting 2013, 2 pages, 1 figure | null | 10.3217/978-3-85125-260-6-156 | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The aim of this study is to provide a comprehensive test of three spatial
speller settings, for the auditory, visual, and audiovisual paradigms. For
rigour, the study is conducted with 16 BCI-na\"ive subjects in an experimental
set-up based on five Japanese hiragana characters. Auditory P300 responses give
encouragin... | [
{
"created": "Sun, 27 Jan 2013 14:44:23 GMT",
"version": "v1"
},
{
"created": "Sun, 12 May 2013 06:39:06 GMT",
"version": "v2"
}
] | 2013-05-14 | [
[
"Chang",
"M.",
""
],
[
"Nishikawa",
"N.",
""
],
[
"Struzik",
"Z. R.",
""
],
[
"Mori",
"K.",
""
],
[
"Makino",
"S.",
""
],
[
"Mandic",
"D.",
""
],
[
"Rutkowski",
"T. M.",
""
]
] | The aim of this study is to provide a comprehensive test of three spatial speller settings, for the auditory, visual, and audiovisual paradigms. For rigour, the study is conducted with 16 BCI-na\"ive subjects in an experimental set-up based on five Japanese hiragana characters. Auditory P300 responses give encouragingl... |
2310.16004 | Frederik Van Daele | Frederik Van Daele, Olivier Honnay, Hanne De Kort | Habitat fragmentation reshapes genomic footprints of selection in a
forest herb | 26 pages, 5 figures | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the combined effects of climate change and habitat
fragmentation on the adaptive potential of plant populations is essential for
devising effective conservation strategies. This is particularly important
where mating system variation impacts the evolutionary consequences of habitat
fragmentation. Here w... | [
{
"created": "Tue, 24 Oct 2023 16:57:38 GMT",
"version": "v1"
}
] | 2023-10-25 | [
[
"Van Daele",
"Frederik",
""
],
[
"Honnay",
"Olivier",
""
],
[
"De Kort",
"Hanne",
""
]
] | Understanding the combined effects of climate change and habitat fragmentation on the adaptive potential of plant populations is essential for devising effective conservation strategies. This is particularly important where mating system variation impacts the evolutionary consequences of habitat fragmentation. Here we ... |
1510.00696 | Lior Pachter | Harold Pimentel, John G. Conboy, and Lior Pachter | Keep Me Around: Intron Retention Detection and Analysis | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a tool, keep me around (kma), a suite of python scripts and an R
package that finds retained introns in RNA-Seq experiments and incorporates
biological replicates to reduce the number of false positives when detecting
retention events. kma uses the results of existing quantification tools that
probabilisti... | [
{
"created": "Fri, 2 Oct 2015 19:20:20 GMT",
"version": "v1"
}
] | 2015-10-05 | [
[
"Pimentel",
"Harold",
""
],
[
"Conboy",
"John G.",
""
],
[
"Pachter",
"Lior",
""
]
] | We present a tool, keep me around (kma), a suite of python scripts and an R package that finds retained introns in RNA-Seq experiments and incorporates biological replicates to reduce the number of false positives when detecting retention events. kma uses the results of existing quantification tools that probabilistica... |
0905.4629 | Johan Elf | Paul Sjoberg, Otto G Berg and Johan Elf | Taking the reaction-diffusion master equation to the microscopic limit | null | null | null | null | q-bio.QM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The reaction-diffusion master equation (RDME) is commonly used to model
processes where both the spatial and stochastic nature of chemical reactions
need to be considered. We show that the RDME in many cases is inconsistent with
a microscopic description of diffusion limited chemical reactions and that this
will resu... | [
{
"created": "Thu, 28 May 2009 12:18:30 GMT",
"version": "v1"
}
] | 2009-05-29 | [
[
"Sjoberg",
"Paul",
""
],
[
"Berg",
"Otto G",
""
],
[
"Elf",
"Johan",
""
]
] | The reaction-diffusion master equation (RDME) is commonly used to model processes where both the spatial and stochastic nature of chemical reactions need to be considered. We show that the RDME in many cases is inconsistent with a microscopic description of diffusion limited chemical reactions and that this will result... |
0810.3280 | Oleksii Kuchaiev | Oleksii Kuchaiev, Tijana Milenkovic, Vesna Memisevic, Wayne Hayes,
Natasa Przulj | Topological network alignment uncovers biological function and phylogeny | Algorithm explained in more details. Additional analysis added | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sequence comparison and alignment has had an enormous impact on our
understanding of evolution, biology, and disease. Comparison and alignment of
biological networks will likely have a similar impact. Existing network
alignments use information external to the networks, such as sequence, because
no good algorithm for... | [
{
"created": "Sat, 18 Oct 2008 00:49:44 GMT",
"version": "v1"
},
{
"created": "Sat, 14 Mar 2009 00:00:59 GMT",
"version": "v2"
},
{
"created": "Fri, 14 Aug 2009 20:30:35 GMT",
"version": "v3"
},
{
"created": "Wed, 7 Oct 2009 23:50:54 GMT",
"version": "v4"
}
] | 2009-10-08 | [
[
"Kuchaiev",
"Oleksii",
""
],
[
"Milenkovic",
"Tijana",
""
],
[
"Memisevic",
"Vesna",
""
],
[
"Hayes",
"Wayne",
""
],
[
"Przulj",
"Natasa",
""
]
] | Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for p... |
2403.12995 | Siyu Long | Kangjie Zheng (equal contribution), Siyu Long (equal contribution),
Tianyu Lu, Junwei Yang, Xinyu Dai, Ming Zhang, Zaiqing Nie, Wei-Ying Ma, Hao
Zhou | ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular
Modeling | ICML2024 camera-ready, update some experimental results, add github
url, fix some typos | null | null | null | q-bio.BM cs.CE cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Protein language models have demonstrated significant potential in the field
of protein engineering. However, current protein language models primarily
operate at the residue scale, which limits their ability to provide information
at the atom level. This limitation prevents us from fully exploiting the
capabilities ... | [
{
"created": "Tue, 5 Mar 2024 13:35:41 GMT",
"version": "v1"
},
{
"created": "Thu, 16 May 2024 08:21:11 GMT",
"version": "v2"
},
{
"created": "Fri, 31 May 2024 07:28:40 GMT",
"version": "v3"
},
{
"created": "Thu, 13 Jun 2024 02:29:34 GMT",
"version": "v4"
}
] | 2024-06-14 | [
[
"Zheng",
"Kangjie",
"",
"equal contribution"
],
[
"Long",
"Siyu",
"",
"equal contribution"
],
[
"Lu",
"Tianyu",
""
],
[
"Yang",
"Junwei",
""
],
[
"Dai",
"Xinyu",
""
],
[
"Zhang",
"Ming",
""
],
[
"Nie",
... | Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the atom level. This limitation prevents us from fully exploiting the capabilities of... |
1209.4603 | Jianhua Xing | Ping Wang, Chaoming Song, Hang Zhang, Zhanghan Wu, Jianhua Xing | Global Epigenetic State Network Governs Cellular Pluripotent
Reprogramming and Transdifferentiation | 18 pages,4 figures, 2 tables | Interface Focus 4(3):20130068 (2014) | 10.1098/?rsfs.2013.0068 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How do mammalian cells that share the same genome exist in notably distinct
phenotypes, exhibiting differences in morphology, gene expression patterns, and
epigenetic chromatin statuses? Furthermore how do cells of different phenotypes
differentiate reproducibly from a single fertilized egg? These fundamental
questio... | [
{
"created": "Thu, 20 Sep 2012 18:39:25 GMT",
"version": "v1"
}
] | 2014-04-29 | [
[
"Wang",
"Ping",
""
],
[
"Song",
"Chaoming",
""
],
[
"Zhang",
"Hang",
""
],
[
"Wu",
"Zhanghan",
""
],
[
"Xing",
"Jianhua",
""
]
] | How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes differentiate reproducibly from a single fertilized egg? These fundamental questions... |
1103.5150 | Mohamed I Shehata | M.I.Shehata | On stability in dynamical Prisoner's dilemma game with non-uniform
interaction rates | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stability of evolutionary dynamics of non-repeated Prisoner's Dilemma game
with non-uniform interaction rates [1], via benefit and cost dilemma is studied
. Moreover, the stability condition (b+c/b-c)2 < r1r3 is derived in case of
coexistence between cooperators and defectors .If r1,r3 -> infinity cooperation
is the ... | [
{
"created": "Sat, 26 Mar 2011 19:48:13 GMT",
"version": "v1"
}
] | 2011-03-29 | [
[
"Shehata",
"M. I.",
""
]
] | Stability of evolutionary dynamics of non-repeated Prisoner's Dilemma game with non-uniform interaction rates [1], via benefit and cost dilemma is studied . Moreover, the stability condition (b+c/b-c)2 < r1r3 is derived in case of coexistence between cooperators and defectors .If r1,r3 -> infinity cooperation is the do... |
2004.11325 | Sahar Rahbar | Sahar Rahbar | Mathematical and Preclinical Investigation of Respiratory Sinus
Arrhythmia Effects on Cardiac Output | null | null | null | null | q-bio.TO math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Respiratory sinus arrhythmia (RSA) is heart rate variability in synchrony
with respiration although its functional significance not clear. The loss of
sinus arrhythmia may indicate underlying heart failure or disease; therefore,
there would be a great advantage of knowing how it works and affects the
cardio-respirato... | [
{
"created": "Thu, 23 Apr 2020 17:19:44 GMT",
"version": "v1"
}
] | 2020-04-24 | [
[
"Rahbar",
"Sahar",
""
]
] | Respiratory sinus arrhythmia (RSA) is heart rate variability in synchrony with respiration although its functional significance not clear. The loss of sinus arrhythmia may indicate underlying heart failure or disease; therefore, there would be a great advantage of knowing how it works and affects the cardio-respiratory... |
2401.16220 | Alexey Ovchinnikov | Yosef Berman, Joshua Forrest, Matthew Grote, Alexey Ovchinnikov, and
Sonia Rueda | Symbolic-numeric algorithm for parameter estimation in discrete-time
models with $\exp$ | null | null | null | null | q-bio.QM cs.SC cs.SY eess.SY math.AC math.DS | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Determining unknown parameter values in dynamic models is crucial for
accurate analysis of the dynamics across the different scientific disciplines.
Discrete-time dynamic models are widely used to model biological processes, but
it is often difficult to determine these parameters. In this paper, we propose
a robust s... | [
{
"created": "Mon, 29 Jan 2024 15:19:16 GMT",
"version": "v1"
}
] | 2024-01-30 | [
[
"Berman",
"Yosef",
""
],
[
"Forrest",
"Joshua",
""
],
[
"Grote",
"Matthew",
""
],
[
"Ovchinnikov",
"Alexey",
""
],
[
"Rueda",
"Sonia",
""
]
] | Determining unknown parameter values in dynamic models is crucial for accurate analysis of the dynamics across the different scientific disciplines. Discrete-time dynamic models are widely used to model biological processes, but it is often difficult to determine these parameters. In this paper, we propose a robust sym... |
1405.1314 | Pooja Chandrashekar | Pooja Chandrashekar | Mathematically Modeling the GPe/STN Neuronal Cluster to Account for
Parkinsonian Tremor and Developing a Novel Method to Accurately Diagnose
Parkinson's Disease Using Speech Measurements and an Artificial Neural
Network | 13 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Parkinsons disease (PD) is a debilitating motor system disorder characterized
by progressive loss of movement, tremors, and speech slurring. PD is due to the
loss of dopamine-producing brain cells, and symptoms only worsen over time,
making early detection and diagnosis of the disease key to effective management
and ... | [
{
"created": "Tue, 6 May 2014 15:28:38 GMT",
"version": "v1"
}
] | 2014-05-07 | [
[
"Chandrashekar",
"Pooja",
""
]
] | Parkinsons disease (PD) is a debilitating motor system disorder characterized by progressive loss of movement, tremors, and speech slurring. PD is due to the loss of dopamine-producing brain cells, and symptoms only worsen over time, making early detection and diagnosis of the disease key to effective management and tr... |
1707.06524 | Denis Horv\'ath | Denis Horvath, Branislav Brutovsky | Toward understanding of the role of reversibility of phenotypic
switching in the evolution of resistance to therapy | 24 pages, 1 table, 8 figures | null | 10.1016/j.physleta.2018.03.052 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reversibility of state transitions is intensively studied topic in many
scientific disciplines over many years. In cell biology, it plays an important
role in epigenetic variation of phenotypes, known as phenotypic plasticity.
More interestingly, the cell state reversibility is probably crucial in the
adaptation of p... | [
{
"created": "Thu, 20 Jul 2017 14:14:12 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Nov 2017 06:20:03 GMT",
"version": "v2"
},
{
"created": "Fri, 30 Mar 2018 03:24:38 GMT",
"version": "v3"
}
] | 2018-05-23 | [
[
"Horvath",
"Denis",
""
],
[
"Brutovsky",
"Branislav",
""
]
] | Reversibility of state transitions is intensively studied topic in many scientific disciplines over many years. In cell biology, it plays an important role in epigenetic variation of phenotypes, known as phenotypic plasticity. More interestingly, the cell state reversibility is probably crucial in the adaptation of pop... |
2204.02527 | Moo K. Chung | Soumya Das, D. Vijay Anand, Moo K. Chung | Topological Data Analysis of Human Brain Networks Through Order
Statistics | null | null | 10.1371/journal.pone.0276419 | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Understanding the common topological characteristics of the human brain
network across a population is central to understanding brain functions. The
abstraction of human connectome as a graph has been pivotal in gaining insights
on the topological properties of the brain network. The development of
group-level statis... | [
{
"created": "Wed, 6 Apr 2022 00:33:45 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Aug 2022 01:24:17 GMT",
"version": "v2"
},
{
"created": "Thu, 13 Oct 2022 06:07:20 GMT",
"version": "v3"
}
] | 2023-04-26 | [
[
"Das",
"Soumya",
""
],
[
"Anand",
"D. Vijay",
""
],
[
"Chung",
"Moo K.",
""
]
] | Understanding the common topological characteristics of the human brain network across a population is central to understanding brain functions. The abstraction of human connectome as a graph has been pivotal in gaining insights on the topological properties of the brain network. The development of group-level statisti... |
1404.4073 | Ido Kanter | Amir Goldental, Shoshana Guberman, Roni Vardi and Ido Kanter | Computational paradigm for dynamic logic-gates in neuronal activity | 32 pages, 14 figures, 1 table | Front. Comput. Neurosci. 8:52. (2014) | 10.3389/fncom.2014.00052 | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In 1943 McCulloch and Pitts suggested that the brain is composed of reliable
logic-gates similar to the logic at the core of today's computers. This
framework had a limited impact on neuroscience, since neurons exhibit far
richer dynamics. Here we propose a new experimentally corroborated paradigm in
which the truth ... | [
{
"created": "Tue, 15 Apr 2014 20:41:21 GMT",
"version": "v1"
}
] | 2014-05-06 | [
[
"Goldental",
"Amir",
""
],
[
"Guberman",
"Shoshana",
""
],
[
"Vardi",
"Roni",
""
],
[
"Kanter",
"Ido",
""
]
] | In 1943 McCulloch and Pitts suggested that the brain is composed of reliable logic-gates similar to the logic at the core of today's computers. This framework had a limited impact on neuroscience, since neurons exhibit far richer dynamics. Here we propose a new experimentally corroborated paradigm in which the truth ta... |
2212.00273 | Maywan Hariono | Maywan Hariono, Irwan Hidayat, Ipang Djunarko, Jeffry Julianus, Fadi
G. Saqallah, Muhammad Hidhir Khawory, Nurul Hanim Salin, Habibah Abdul Wahab | Carica papaya Leaf Extract Inhibits SARS-CoV-2 Main Proteases but not
Human TMPRSS2: An In-vitro and In-silico Study | 28 pages, 7 figures, 2 tables | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Carica papaya (CP) leaf is long known for its traditional pharmacological
effects against dengue virus and malaria. Therefore, CP could also be a
potential solution for the treatment of other infectious diseases, such as
coronavirus. In this study, we evaluate the potential effect of the ethanolic
CP leaf extract in ... | [
{
"created": "Thu, 1 Dec 2022 04:33:28 GMT",
"version": "v1"
}
] | 2022-12-02 | [
[
"Hariono",
"Maywan",
""
],
[
"Hidayat",
"Irwan",
""
],
[
"Djunarko",
"Ipang",
""
],
[
"Julianus",
"Jeffry",
""
],
[
"Saqallah",
"Fadi G.",
""
],
[
"Khawory",
"Muhammad Hidhir",
""
],
[
"Salin",
"Nurul Hanim",
... | Carica papaya (CP) leaf is long known for its traditional pharmacological effects against dengue virus and malaria. Therefore, CP could also be a potential solution for the treatment of other infectious diseases, such as coronavirus. In this study, we evaluate the potential effect of the ethanolic CP leaf extract in in... |
1808.08842 | Mussa Quareshy | Mussa Quareshy, Justyna Prusinska, Martin Kieffer, Kosuke Fukui,
Alonso J. Pardal, Silke Lehmann, Patrick Schafer, Charo I. del Genio, Stefan
Kepinski, Kenichiro Hayashi, Andrew Marsh, Richard M. Napier | The tetrazole analogue of the auxin indole-3-acetic acid binds
preferentially to TIR1 and not AFB5 | ACS Chemical Biology, 2018 | null | 10.1021/acschembio.8b00527 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Auxin is considered one of the cardinal hormones in plant growth and
development. It regulates a wide range of processes throughout the plant.
Synthetic auxins exploit the auxin-signalling pathway and are valuable as
herbicidal agrochemicals. Currently, despite a diversity of chemical scaffolds
all synthetic auxins h... | [
{
"created": "Mon, 27 Aug 2018 13:40:56 GMT",
"version": "v1"
}
] | 2018-08-28 | [
[
"Quareshy",
"Mussa",
""
],
[
"Prusinska",
"Justyna",
""
],
[
"Kieffer",
"Martin",
""
],
[
"Fukui",
"Kosuke",
""
],
[
"Pardal",
"Alonso J.",
""
],
[
"Lehmann",
"Silke",
""
],
[
"Schafer",
"Patrick",
""
],
... | Auxin is considered one of the cardinal hormones in plant growth and development. It regulates a wide range of processes throughout the plant. Synthetic auxins exploit the auxin-signalling pathway and are valuable as herbicidal agrochemicals. Currently, despite a diversity of chemical scaffolds all synthetic auxins hav... |
2404.15318 | James Ruffle | James K Ruffle, Samia Mohinta, Kelly Pegoretti Baruteau, Rebekah
Rajiah, Faith Lee, Sebastian Brandner, Parashkev Nachev, Harpreet Hyare | VASARI-auto: equitable, efficient, and economical featurisation of
glioma MRI | 28 pages, 6 figures, 1 table | null | null | null | q-bio.QM cs.CV q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | The VASARI MRI feature set is a quantitative system designed to standardise
glioma imaging descriptions. Though effective, deriving VASARI is
time-consuming and seldom used in clinical practice. This is a problem that
machine learning could plausibly automate. Using glioma data from 1172
patients, we developed VASARI... | [
{
"created": "Wed, 3 Apr 2024 13:33:07 GMT",
"version": "v1"
}
] | 2024-04-25 | [
[
"Ruffle",
"James K",
""
],
[
"Mohinta",
"Samia",
""
],
[
"Baruteau",
"Kelly Pegoretti",
""
],
[
"Rajiah",
"Rebekah",
""
],
[
"Lee",
"Faith",
""
],
[
"Brandner",
"Sebastian",
""
],
[
"Nachev",
"Parashkev",
"... | The VASARI MRI feature set is a quantitative system designed to standardise glioma imaging descriptions. Though effective, deriving VASARI is time-consuming and seldom used in clinical practice. This is a problem that machine learning could plausibly automate. Using glioma data from 1172 patients, we developed VASARI-a... |
1310.3465 | Martin Voracek | Martin Voracek | No effects of androgen receptor gene CAG and GGC repeat polymorphisms on
digit ratio (2D:4D): Meta-analysis | null | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objectives: A series of meta-analyses assessed whether differentially
efficacious variants (CAG and GGC repeat-length polymorphisms) of the human
androgen receptor gene are associated with digit ratio (2D:4D), a widely
investigated putative pointer to prenatal androgen action. Methods: Extensive
literature search str... | [
{
"created": "Sun, 13 Oct 2013 10:35:26 GMT",
"version": "v1"
}
] | 2013-10-15 | [
[
"Voracek",
"Martin",
""
]
] | Objectives: A series of meta-analyses assessed whether differentially efficacious variants (CAG and GGC repeat-length polymorphisms) of the human androgen receptor gene are associated with digit ratio (2D:4D), a widely investigated putative pointer to prenatal androgen action. Methods: Extensive literature search strat... |
2308.09941 | Tom Chou | Yue Wang, Blerta Shtylla, Tom Chou | Order-of-mutation effects on cancer progression: models for
myeloproliferative neoplasm | 22 pp, 7 figures. arXiv admin note: text overlap with
arXiv:2302.07955 | null | null | null | q-bio.MN q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We develop a modeling framework for cancer progression that distinguishes the
order of two possible mutations. Recent observations and information on
myeloproliferative neoplasms are analyzed within our framework. In some
patients with myeloproliferative neoplasms, two genetic mutations can be found,
JAK2 V617F and T... | [
{
"created": "Sat, 19 Aug 2023 08:21:56 GMT",
"version": "v1"
}
] | 2023-08-22 | [
[
"Wang",
"Yue",
""
],
[
"Shtylla",
"Blerta",
""
],
[
"Chou",
"Tom",
""
]
] | We develop a modeling framework for cancer progression that distinguishes the order of two possible mutations. Recent observations and information on myeloproliferative neoplasms are analyzed within our framework. In some patients with myeloproliferative neoplasms, two genetic mutations can be found, JAK2 V617F and TET... |
1308.2277 | Simon Childs | S.J. Childs | An Improved Temporal Formulation of Pupal Transpiration in Glossina | 33 pages, 27 figures, 3 tables. arXiv admin note: text overlap with
arXiv:0901.2470 | Mathematical Biosciences, 262: 214-229, 2015 | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The temporal aspect of a model of pupal dehydration is improved upon. The
observed dependence of pupal transpiration on time is attributed to an
alternation between two, essential modes, for which the deposition of a thin,
pupal skin inside the puparium and its subsequent demise are thought to be
responsible. For eac... | [
{
"created": "Sat, 10 Aug 2013 05:14:22 GMT",
"version": "v1"
},
{
"created": "Fri, 9 May 2014 19:11:14 GMT",
"version": "v2"
},
{
"created": "Tue, 19 May 2015 14:59:27 GMT",
"version": "v3"
}
] | 2015-05-20 | [
[
"Childs",
"S. J.",
""
]
] | The temporal aspect of a model of pupal dehydration is improved upon. The observed dependence of pupal transpiration on time is attributed to an alternation between two, essential modes, for which the deposition of a thin, pupal skin inside the puparium and its subsequent demise are thought to be responsible. For each ... |
2303.06951 | Frederic Lavancier | Lisa Balsollier (Nantes Univ), Fr\'ed\'eric Lavancier (Nantes Univ),
Jean Salamero, Charles Kervrann | A generative model to synthetize spatio-temporal dynamics of
biomolecules in cells | null | null | null | null | q-bio.SC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Generators of space-time dynamics in bioimaging have become essential to
build ground truth datasets for image processing algorithm evaluation such as
biomolecule detectors and trackers, as well as to generate training datasets
for deep learning algorithms. In this contribution, we leverage a stochastic
model, called... | [
{
"created": "Mon, 13 Mar 2023 09:43:48 GMT",
"version": "v1"
}
] | 2023-03-14 | [
[
"Balsollier",
"Lisa",
"",
"Nantes Univ"
],
[
"Lavancier",
"Frédéric",
"",
"Nantes Univ"
],
[
"Salamero",
"Jean",
""
],
[
"Kervrann",
"Charles",
""
]
] | Generators of space-time dynamics in bioimaging have become essential to build ground truth datasets for image processing algorithm evaluation such as biomolecule detectors and trackers, as well as to generate training datasets for deep learning algorithms. In this contribution, we leverage a stochastic model, called b... |
2109.06691 | Niko Komin | Niko Komin, Alexander Skupin | How to address cellular heterogeneity by distribution biology | null | Current Opinion in Systems Biology, Volume 3, June 2017, Pages
154-160 | 10.1016/j.coisb.2017.05.010 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Cellular heterogeneity is an immanent property of biological systems that
covers very different aspects of life ranging from genetic diversity to
cell-to-cell variability driven by stochastic molecular interactions, and noise
induced cell differentiation. Here, we review recent developments in
characterizing cellular... | [
{
"created": "Mon, 13 Sep 2021 16:46:58 GMT",
"version": "v1"
}
] | 2021-09-15 | [
[
"Komin",
"Niko",
""
],
[
"Skupin",
"Alexander",
""
]
] | Cellular heterogeneity is an immanent property of biological systems that covers very different aspects of life ranging from genetic diversity to cell-to-cell variability driven by stochastic molecular interactions, and noise induced cell differentiation. Here, we review recent developments in characterizing cellular h... |
1708.09264 | Brian Munsky | Zachary Fox and Brian Munsky | Stochasticity or Noise in Biochemical Reactions | Submitted for inclusion in the textbook Quantitative Biology: Theory,
Computational Methods and Examples of Models, edited by Brian Munsky, Lev S.
Tsimring, and William S. Hlavacek, to be published by MIT Press | null | null | null | q-bio.QM q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Heterogeneity in gene expression across isogenic cell populations can give
rise to phenotypic diversity, even when cells are in homogenous environments.
This diversity arises from the discrete, stochastic nature of biochemical
reactions, which naturally arise due to the very small numbers of genes, RNA,
or protein mo... | [
{
"created": "Wed, 30 Aug 2017 13:38:59 GMT",
"version": "v1"
}
] | 2017-08-31 | [
[
"Fox",
"Zachary",
""
],
[
"Munsky",
"Brian",
""
]
] | Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions, which naturally arise due to the very small numbers of genes, RNA, or protein mole... |
1711.08927 | Tom Michoel | Pau Erola, Eric Bonnet, Tom Michoel | Learning differential module networks across multiple experimental
conditions | Minor revision; 19 pages, 5 figures; chapter for a forthcoming book
on gene regulatory network inference | Methods in Molecular Biology, vol 1883, pp 303-321 (2018) | 10.1007/978-1-4939-8882-2_13 | null | q-bio.QM q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Module network inference is a statistical method to reconstruct gene
regulatory networks, which uses probabilistic graphical models to learn modules
of coregulated genes and their upstream regulatory programs from genome-wide
gene expression and other omics data. Here we review the basic theory of module
network infe... | [
{
"created": "Fri, 24 Nov 2017 11:17:14 GMT",
"version": "v1"
},
{
"created": "Mon, 12 Feb 2018 10:45:57 GMT",
"version": "v2"
}
] | 2019-05-28 | [
[
"Erola",
"Pau",
""
],
[
"Bonnet",
"Eric",
""
],
[
"Michoel",
"Tom",
""
]
] | Module network inference is a statistical method to reconstruct gene regulatory networks, which uses probabilistic graphical models to learn modules of coregulated genes and their upstream regulatory programs from genome-wide gene expression and other omics data. Here we review the basic theory of module network infere... |
1309.5337 | Mengjie Chen | Mengjie Chen and Haifan Lin and Hongyu Zhao | Change Point Analysis of Histone Modifications Reveals Epigenetic Blocks
Linking to Physical Domains | 23 pages, 6 figures | null | null | null | q-bio.GN q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Histone modification is a vital epigenetic mechanism for transcriptional
control in eukaryotes. High-throughput techniques have enabled whole-genome
analysis of histone modifications in recent years. However, most studies assume
one combination of histone modification invariantly translates to one
transcriptional out... | [
{
"created": "Fri, 20 Sep 2013 17:52:18 GMT",
"version": "v1"
},
{
"created": "Fri, 9 May 2014 14:38:44 GMT",
"version": "v2"
}
] | 2014-05-12 | [
[
"Chen",
"Mengjie",
""
],
[
"Lin",
"Haifan",
""
],
[
"Zhao",
"Hongyu",
""
]
] | Histone modification is a vital epigenetic mechanism for transcriptional control in eukaryotes. High-throughput techniques have enabled whole-genome analysis of histone modifications in recent years. However, most studies assume one combination of histone modification invariantly translates to one transcriptional outpu... |
2210.00539 | Stephen Turner | Stephen D. Turner | KGP: An R Package with Metadata from the 1000 Genomes Project | 5 pages, 2 figures, 2 tables | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | The 1000 Genomes Project provides sequencing data on 3,202 samples from 26
populations spanning five continental regions with no access or use
restrictions. The kgp R package provides consistent and comprehensive metadata
about samples and populations in the 1000 Genomes Project and other population
sequencing data i... | [
{
"created": "Sun, 2 Oct 2022 14:42:26 GMT",
"version": "v1"
}
] | 2022-10-04 | [
[
"Turner",
"Stephen D.",
""
]
] | The 1000 Genomes Project provides sequencing data on 3,202 samples from 26 populations spanning five continental regions with no access or use restrictions. The kgp R package provides consistent and comprehensive metadata about samples and populations in the 1000 Genomes Project and other population sequencing data in ... |
2005.07269 | Ritam Guha Mr. | Ritam Guha, Anik Sengupta, Ankan Dutta | Sewage Pooling Test for SARS-CoV-2 | 8 pages, 4 figures | null | null | null | q-bio.OT cs.CY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | CoVID-19 is currently one of the biggest threats to mankind. To date, it is
the reason for infections of over 35 lakhs and the death of over 2 lakh human
beings. We propose a procedure to detect CoVID-19 affected localities using a
sewage mass testing and pooling mechanism which has gained ground in recent
times. The... | [
{
"created": "Wed, 13 May 2020 16:00:17 GMT",
"version": "v1"
}
] | 2020-05-18 | [
[
"Guha",
"Ritam",
""
],
[
"Sengupta",
"Anik",
""
],
[
"Dutta",
"Ankan",
""
]
] | CoVID-19 is currently one of the biggest threats to mankind. To date, it is the reason for infections of over 35 lakhs and the death of over 2 lakh human beings. We propose a procedure to detect CoVID-19 affected localities using a sewage mass testing and pooling mechanism which has gained ground in recent times. The p... |
1206.1017 | Mike Steel Prof. | Wim Hordijk and Mike Steel | Autocatalytic Sets Extended: Dynamics, Inhibition, and a Generalization | 24 pages, 6 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Autocatalytic sets are often considered a necessary (but not
sufficient) condition for the origin and early evolution of life. Although the
idea of autocatalytic sets was already conceived of many years ago, only
recently have they gained more interest, following advances in creating them
experimentally i... | [
{
"created": "Tue, 5 Jun 2012 18:28:54 GMT",
"version": "v1"
}
] | 2012-06-06 | [
[
"Hordijk",
"Wim",
""
],
[
"Steel",
"Mike",
""
]
] | Background: Autocatalytic sets are often considered a necessary (but not sufficient) condition for the origin and early evolution of life. Although the idea of autocatalytic sets was already conceived of many years ago, only recently have they gained more interest, following advances in creating them experimentally in ... |
q-bio/0505007 | Ernesto Estrada | Ernesto Estrada | Virtual Identification of Essential Proteins Within the Protein
Interaction Network of Yeast | 11 pages, 3 figures | null | 10.1002/pmic.200500209 | null | q-bio.MN | null | Topological analysis of large scale protein-protein interaction networks
(PINs) is important for understanding the organisational and functional
principles of individual proteins. The number of interactions that a protein
has in a PIN has been observed to be correlated with its indispensability.
Essential proteins ge... | [
{
"created": "Tue, 3 May 2005 21:38:51 GMT",
"version": "v1"
}
] | 2013-04-02 | [
[
"Estrada",
"Ernesto",
""
]
] | Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has been observed to be correlated with its indispensability. Essential proteins gene... |
1609.02141 | Antonino Sciarrino | Diego Cocurullo and Antonino Sciarrino | Correlations in Usage Frequencies and Shannon Entropy for Codons | 42 pages, 12 figures, 33 Tables | null | null | Dipartimento di Scienze Fisiche, Naples,Italy, DSF-Th-2/08-v2 | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The usage frequencies for codons belonging to quartets are analized, over the
whole exonic region, for 92 biological species. Correlation is put into
evidence, between the usage frequencies of synonymous codons with third
nucleotide A and C and between the usage frequencies of non synonymous codons,
belonging to suit... | [
{
"created": "Wed, 7 Sep 2016 19:03:09 GMT",
"version": "v1"
}
] | 2016-09-09 | [
[
"Cocurullo",
"Diego",
""
],
[
"Sciarrino",
"Antonino",
""
]
] | The usage frequencies for codons belonging to quartets are analized, over the whole exonic region, for 92 biological species. Correlation is put into evidence, between the usage frequencies of synonymous codons with third nucleotide A and C and between the usage frequencies of non synonymous codons, belonging to suitab... |
1512.07596 | Danielle Bassett | Zitong Zhang, Qawi K. Telesford, Chad Giusti, Kelvin O. Lim, Danielle
S. Bassett | Choosing Wavelet Methods, Filters, and Lengths for Functional Brain
Network Construction | working paper | null | 10.1371/journal.pone.0157243 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Wavelet methods are widely used to decompose fMRI, EEG, or MEG signals into
time series representing neurophysiological activity in fixed frequency bands.
Using these time series, one can estimate frequency-band specific functional
connectivity between sensors or regions of interest, and thereby construct
functional ... | [
{
"created": "Wed, 23 Dec 2015 19:25:08 GMT",
"version": "v1"
}
] | 2016-09-28 | [
[
"Zhang",
"Zitong",
""
],
[
"Telesford",
"Qawi K.",
""
],
[
"Giusti",
"Chad",
""
],
[
"Lim",
"Kelvin O.",
""
],
[
"Bassett",
"Danielle S.",
""
]
] | Wavelet methods are widely used to decompose fMRI, EEG, or MEG signals into time series representing neurophysiological activity in fixed frequency bands. Using these time series, one can estimate frequency-band specific functional connectivity between sensors or regions of interest, and thereby construct functional br... |
1702.03418 | Yanjun Wang Dr. | Zhi-Song lv, Chen-Ping Zhu, Pei Nie, Jing Zhao, Hui-Jie Yang, Yan-Jun
Wang, Chin-Kun Hu | Exponential distance distribution of connected neurons in simulations of
two-dimensional in vitro neural network development | null | null | null | null | q-bio.NC physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The distribution of the geometric distances of connected neurons is a
practical factor underlying neural networks in the brain. It can affect the
brain\'s dynamic properties at the ground level. Karbowski derived a power-law
decay distribution that has not yet been verified by experiment. In this work,
we check its v... | [
{
"created": "Sat, 11 Feb 2017 12:26:25 GMT",
"version": "v1"
}
] | 2017-02-14 | [
[
"lv",
"Zhi-Song",
""
],
[
"Zhu",
"Chen-Ping",
""
],
[
"Nie",
"Pei",
""
],
[
"Zhao",
"Jing",
""
],
[
"Yang",
"Hui-Jie",
""
],
[
"Wang",
"Yan-Jun",
""
],
[
"Hu",
"Chin-Kun",
""
]
] | The distribution of the geometric distances of connected neurons is a practical factor underlying neural networks in the brain. It can affect the brain\'s dynamic properties at the ground level. Karbowski derived a power-law decay distribution that has not yet been verified by experiment. In this work, we check its val... |
1509.03192 | J\'ozsef Z. Farkas | Jozsef Z. Farkas, Andrew Yu Morozov, E. G. Arashkevich, A. Nikishina | Revisiting the stability of spatially heterogeneous predator-prey
systems under eutrophication | 2 figures; appendices available on request. To appear in the Bulletin
of Mathematical Biology | Bulletin of Mathematical Biology, 77, (2015) 1886-1908 | 10.1007/s11538-015-0108-2 | null | q-bio.PE math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We employ partial integro-differential equations to model trophic interaction
in a spatially extended heterogeneous environment. Compared to classical
reaction-diffusion models, this framework allows us to more realistically
describe the situation where movement of individuals occurs on a faster time
scale than the d... | [
{
"created": "Thu, 10 Sep 2015 15:20:19 GMT",
"version": "v1"
}
] | 2019-03-06 | [
[
"Farkas",
"Jozsef Z.",
""
],
[
"Morozov",
"Andrew Yu",
""
],
[
"Arashkevich",
"E. G.",
""
],
[
"Nikishina",
"A.",
""
]
] | We employ partial integro-differential equations to model trophic interaction in a spatially extended heterogeneous environment. Compared to classical reaction-diffusion models, this framework allows us to more realistically describe the situation where movement of individuals occurs on a faster time scale than the dem... |
q-bio/0408009 | Ganesh Bagler | Ganesh Bagler and Somdatta Sinha | Network properties of protein structures | 5 pages, 7 postscript figures, Accepted for publication in Physica A | Physica A, 346/1-2 (2005) pp. 27-33 | 10.1016/j.physa.2004.08.046 | null | q-bio.MN q-bio.BM | null | Protein structures can be studied as complex networks of interacting amino
acids. We study proteins of different structural classes from the network
perspective. Our results indicate that proteins, regardless of their structural
class, show small-world network property. Various network parameters offer
insight into t... | [
{
"created": "Fri, 13 Aug 2004 20:05:39 GMT",
"version": "v1"
}
] | 2007-11-19 | [
[
"Bagler",
"Ganesh",
""
],
[
"Sinha",
"Somdatta",
""
]
] | Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show small-world network property. Various network parameters offer insight into the... |
2003.01324 | Liaofu Luo | Yang Gao, Tao Li, Liaofu Luo | Phylogenetic Study of 2019-nCoV by Using Alignment Free Method
(Evolutionary Bifurcation of Novel Coronavirus Mutants) | 14 pages;2 figures | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | The phylogenetic tree of SARS-CoV-2 (nCov-19) viruses is reconstructed
according to the similarity of genome sequences. The tree topology of
Betacoronavirus is remarkably consistent with biologist's systematics. Because
the tree construction contains enough information about virus mutants, it is
suitable to study the... | [
{
"created": "Tue, 3 Mar 2020 04:10:07 GMT",
"version": "v1"
},
{
"created": "Mon, 4 May 2020 03:55:09 GMT",
"version": "v2"
},
{
"created": "Fri, 28 Jan 2022 07:32:01 GMT",
"version": "v3"
}
] | 2022-01-31 | [
[
"Gao",
"Yang",
""
],
[
"Li",
"Tao",
""
],
[
"Luo",
"Liaofu",
""
]
] | The phylogenetic tree of SARS-CoV-2 (nCov-19) viruses is reconstructed according to the similarity of genome sequences. The tree topology of Betacoronavirus is remarkably consistent with biologist's systematics. Because the tree construction contains enough information about virus mutants, it is suitable to study the e... |
q-bio/0604021 | Jesus M. Cortes | J.J. Torres, J.M. Cortes, J. Marro | Instability of attractors in autoassociative networks with bioinspired
fast synaptic noise | 6 pages, 2 figures | LNCS 3512: 161-167, 2005 | null | null | q-bio.NC | null | We studied autoassociative networks in which synapses are noisy on a time
scale much shorter that the one for the neuron dynamics. In our model a
presynaptic noise causes postsynaptic depression as recently observed in
neurobiological systems. This results in a nonequilibrium condition in which
the network sensitivit... | [
{
"created": "Sun, 16 Apr 2006 22:02:28 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Torres",
"J. J.",
""
],
[
"Cortes",
"J. M.",
""
],
[
"Marro",
"J.",
""
]
] | We studied autoassociative networks in which synapses are noisy on a time scale much shorter that the one for the neuron dynamics. In our model a presynaptic noise causes postsynaptic depression as recently observed in neurobiological systems. This results in a nonequilibrium condition in which the network sensitivity ... |
1809.10866 | Philippe Marcq | V. Nier, G. Peyret, J. d'Alessandro, S. Ishihara, B. Ladoux and P.
Marcq | Kalman inversion stress microscopy | 23 pages, 8 pages | Biophysical Journal 115, 1808-1816 (2018) | 10.1016/j.bpj.2018.09.013 | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although mechanical cues are crucial to tissue morphogenesis and development,
the tissue mechanical stress field remains poorly characterized. Given traction
force timelapse movies, as obtained by traction force microscopy of in vitro
cellular sheets, we show that the tissue stress field can be estimated by
Kalman fi... | [
{
"created": "Fri, 28 Sep 2018 06:04:31 GMT",
"version": "v1"
}
] | 2019-04-22 | [
[
"Nier",
"V.",
""
],
[
"Peyret",
"G.",
""
],
[
"d'Alessandro",
"J.",
""
],
[
"Ishihara",
"S.",
""
],
[
"Ladoux",
"B.",
""
],
[
"Marcq",
"P.",
""
]
] | Although mechanical cues are crucial to tissue morphogenesis and development, the tissue mechanical stress field remains poorly characterized. Given traction force timelapse movies, as obtained by traction force microscopy of in vitro cellular sheets, we show that the tissue stress field can be estimated by Kalman filt... |
1003.0199 | Mark Little Mark Peter Little | M.P. Little | Monocyte and T-lymphocyte trans-endothelial migration in relation to
cardiovascular disease: some alternative boundary conditions in a model
recently proposed by Little et al. (PLoS Comput Biol 2009 5(10) e1000539) | null | null | null | null | q-bio.CB q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a slight modification to the monocyte and T-lymphocyte boundary
conditions of Little et al. (PLoS Comput Biol 2009 5(10) e1000539) and derive
alternative parameter estimates. No changes to the results and conclusions of
the paper of Little et al. (PLoS Comput Biol 2009 5(10) e1000539) are implied.
| [
{
"created": "Sun, 28 Feb 2010 17:34:59 GMT",
"version": "v1"
}
] | 2010-03-02 | [
[
"Little",
"M. P.",
""
]
] | We consider a slight modification to the monocyte and T-lymphocyte boundary conditions of Little et al. (PLoS Comput Biol 2009 5(10) e1000539) and derive alternative parameter estimates. No changes to the results and conclusions of the paper of Little et al. (PLoS Comput Biol 2009 5(10) e1000539) are implied. |
2108.00047 | Andrew Tilman | Andrew R. Tilman, V\'itor V. Vasconcelos, Erol Ak\c{c}ay, Joshua B.
Plotkin | The evolution of forecasting for decision making in dynamic environments | revised ms; results unchanged | Collective Intelligence 2:4 (2023) 1-14 | 10.1177/26339137231221726 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Global change is reshaping ecosystems and societies. Strategic choices that
were best yesterday may be sub-optimal tomorrow; and environmental conditions
that were once taken for granted may soon cease to exist. In this setting, how
people choose behavioral strategies has important consequences for
environmental dyna... | [
{
"created": "Fri, 30 Jul 2021 19:12:36 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Aug 2022 17:02:23 GMT",
"version": "v2"
}
] | 2024-04-23 | [
[
"Tilman",
"Andrew R.",
""
],
[
"Vasconcelos",
"Vítor V.",
""
],
[
"Akçay",
"Erol",
""
],
[
"Plotkin",
"Joshua B.",
""
]
] | Global change is reshaping ecosystems and societies. Strategic choices that were best yesterday may be sub-optimal tomorrow; and environmental conditions that were once taken for granted may soon cease to exist. In this setting, how people choose behavioral strategies has important consequences for environmental dynami... |
0809.5225 | Abhinav Singh | Abhinav Singh, Hao Wang, Wendy Morrison and Howard Weiss | Modeling Fish Biomass Structure at Near Pristine Coral Reefs and
Degradation by Fishing | 24 pages, 4 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Until recently, the only examples of inverted biomass pyramids have been in
freshwater and marine planktonic communities. In 2002 and 2008 investigators
documented inverted biomass pyramids for nearly pristine coral reef ecosystems
within the NW Hawaiian islands and the Line Islands, where apex predator
abundance com... | [
{
"created": "Tue, 30 Sep 2008 16:16:03 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Oct 2008 03:43:39 GMT",
"version": "v2"
},
{
"created": "Thu, 30 Jul 2009 17:14:07 GMT",
"version": "v3"
}
] | 2009-07-30 | [
[
"Singh",
"Abhinav",
""
],
[
"Wang",
"Hao",
""
],
[
"Morrison",
"Wendy",
""
],
[
"Weiss",
"Howard",
""
]
] | Until recently, the only examples of inverted biomass pyramids have been in freshwater and marine planktonic communities. In 2002 and 2008 investigators documented inverted biomass pyramids for nearly pristine coral reef ecosystems within the NW Hawaiian islands and the Line Islands, where apex predator abundance compr... |
2105.07087 | Luis G. Morelli | Sol M. Fern\'andez Arancibia and Hern\'an E. Grecco and Luis G.
Morelli | Effective description of bistability and irreversibility in apoptosis | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Apoptosis is a mechanism of programmed cell death in which cells engage in a
controlled demolition and prepare to be digested without damaging their
environment. In normal conditions apoptosis is repressed, until it is
irreversibly induced by an appropriate signal. In adult organisms apoptosis is
a natural way to dis... | [
{
"created": "Fri, 14 May 2021 22:51:51 GMT",
"version": "v1"
}
] | 2021-05-18 | [
[
"Arancibia",
"Sol M. Fernández",
""
],
[
"Grecco",
"Hernán E.",
""
],
[
"Morelli",
"Luis G.",
""
]
] | Apoptosis is a mechanism of programmed cell death in which cells engage in a controlled demolition and prepare to be digested without damaging their environment. In normal conditions apoptosis is repressed, until it is irreversibly induced by an appropriate signal. In adult organisms apoptosis is a natural way to dispo... |
2301.01264 | Oleg Kogan | Niranjan Sarpangala, Brooke Randell, Ajay Gopinathan, Oleg Kogan | Tunable intracellular transport on converging microtubule morphologies | null | null | null | null | q-bio.CB cond-mat.stat-mech q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A common type of cytoskeletal morphology involves multiple converging
microbutubules with their minus ends collected and stabilized by a microtubule
organizing center (MTOC) in the interior of the cell. This arrangement enables
the ballistic transport of cargo bound to microtubules, both dynein mediated
transport tow... | [
{
"created": "Tue, 3 Jan 2023 18:06:46 GMT",
"version": "v1"
}
] | 2023-01-04 | [
[
"Sarpangala",
"Niranjan",
""
],
[
"Randell",
"Brooke",
""
],
[
"Gopinathan",
"Ajay",
""
],
[
"Kogan",
"Oleg",
""
]
] | A common type of cytoskeletal morphology involves multiple converging microbutubules with their minus ends collected and stabilized by a microtubule organizing center (MTOC) in the interior of the cell. This arrangement enables the ballistic transport of cargo bound to microtubules, both dynein mediated transport towar... |
2310.12979 | Jeffrey Ouyang-Zhang | Jeffrey Ouyang-Zhang, Daniel J. Diaz, Adam R. Klivans, Philipp
Kr\"ahenb\"uhl | Predicting a Protein's Stability under a Million Mutations | NeurIPS 2023. Code available at
https://github.com/jozhang97/MutateEverything | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Stabilizing proteins is a foundational step in protein engineering. However,
the evolutionary pressure of all extant proteins makes identifying the scarce
number of mutations that will improve thermodynamic stability challenging. Deep
learning has recently emerged as a powerful tool for identifying promising
mutation... | [
{
"created": "Thu, 19 Oct 2023 17:59:47 GMT",
"version": "v1"
},
{
"created": "Mon, 30 Oct 2023 19:45:12 GMT",
"version": "v2"
}
] | 2023-11-01 | [
[
"Ouyang-Zhang",
"Jeffrey",
""
],
[
"Diaz",
"Daniel J.",
""
],
[
"Klivans",
"Adam R.",
""
],
[
"Krähenbühl",
"Philipp",
""
]
] | Stabilizing proteins is a foundational step in protein engineering. However, the evolutionary pressure of all extant proteins makes identifying the scarce number of mutations that will improve thermodynamic stability challenging. Deep learning has recently emerged as a powerful tool for identifying promising mutations.... |
1202.6274 | Haidong Feng | Haidong Feng, Jin Wang | A new mechanism of development and differentiation through slow
binding/unbinding of regulatory proteins to the genes | 25 pages, 5 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the differentiation, a biological process from a multipotent
stem or progenitor state to a mature cell is critically important. We develop a
theoretical framework to quantify the underlying potential landscape and
biological paths for cell development and differentiation. We propose a new
mechanism of d... | [
{
"created": "Tue, 28 Feb 2012 16:30:52 GMT",
"version": "v1"
}
] | 2012-02-29 | [
[
"Feng",
"Haidong",
""
],
[
"Wang",
"Jin",
""
]
] | Understanding the differentiation, a biological process from a multipotent stem or progenitor state to a mature cell is critically important. We develop a theoretical framework to quantify the underlying potential landscape and biological paths for cell development and differentiation. We propose a new mechanism of dif... |
1002.1736 | Hamid Reza Chitsaz | Hamidreza Chitsaz | Prediction of RNA-RNA interaction structure by centroids in the
Boltzmann ensemble | null | null | null | null | q-bio.BM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | New high-throughput sequencing technologies have made it possible to pursue
the advent of genome-wide transcriptomics. That progress combined with the
recent discovery of regulatory non-coding RNAs (ncRNAs) has necessitated fast
and accurate algorithms to predict RNA-RNA interaction probability and
structure. Althoug... | [
{
"created": "Mon, 8 Feb 2010 23:20:58 GMT",
"version": "v1"
}
] | 2010-02-10 | [
[
"Chitsaz",
"Hamidreza",
""
]
] | New high-throughput sequencing technologies have made it possible to pursue the advent of genome-wide transcriptomics. That progress combined with the recent discovery of regulatory non-coding RNAs (ncRNAs) has necessitated fast and accurate algorithms to predict RNA-RNA interaction probability and structure. Although ... |
q-bio/0512015 | Walton Gutierrez | Walton R. Gutierrez | Distribution networks and the optimal form of the kidney and lung | 5 pages, 4 figures | null | null | null | q-bio.TO q-bio.QM | null | A model is proposed to minimize the total volume of the main distribution
networks of fluids in organs such as the kidney and the lung. A consequence of
the minimization analysis is that the optimal overall form of the organs is a
modified ellipsoid. The variational procedure implementing this minimization is
similar... | [
{
"created": "Wed, 7 Dec 2005 01:24:00 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Gutierrez",
"Walton R.",
""
]
] | A model is proposed to minimize the total volume of the main distribution networks of fluids in organs such as the kidney and the lung. A consequence of the minimization analysis is that the optimal overall form of the organs is a modified ellipsoid. The variational procedure implementing this minimization is similar t... |
1908.11374 | Brian Camley | Melissa H. Mai and Brian A. Camley | Hydrodynamic Effects on the Motility of Crawling Eukaryotic Cells | Note: four supplemental movies are provided | null | null | null | q-bio.CB cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Eukaryotic cell motility is crucial during development, wound healing, the
immune response, and cancer metastasis. Some eukaryotic cells can swim, but
cells more commonly adhere to and crawl along the extracellular matrix. We
study the relationship between hydrodynamics and adhesion that describe whether
a cell is sw... | [
{
"created": "Thu, 29 Aug 2019 16:04:19 GMT",
"version": "v1"
}
] | 2019-09-02 | [
[
"Mai",
"Melissa H.",
""
],
[
"Camley",
"Brian A.",
""
]
] | Eukaryotic cell motility is crucial during development, wound healing, the immune response, and cancer metastasis. Some eukaryotic cells can swim, but cells more commonly adhere to and crawl along the extracellular matrix. We study the relationship between hydrodynamics and adhesion that describe whether a cell is swim... |
1907.08230 | Thierry Mora | Thierry Mora, Aleksandra M. Walczak | How many different clonotypes do immune repertoires contain? | null | Current Opinion in Systems Biology 18, 104--110 (2019) | 10.1016/j.coisb.2019.10.001 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Immune repertoires rely on diversity of T-cell and B-cell receptors to
protect us against foreign threats. The ability to recognize a wide variety of
pathogens is linked to the number of different clonotypes expressed by an
individual. Out of the estimated $\sim 10^{12}$ different B and T cells in
humans, how many of... | [
{
"created": "Thu, 18 Jul 2019 18:23:22 GMT",
"version": "v1"
}
] | 2020-11-20 | [
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M.",
""
]
] | Immune repertoires rely on diversity of T-cell and B-cell receptors to protect us against foreign threats. The ability to recognize a wide variety of pathogens is linked to the number of different clonotypes expressed by an individual. Out of the estimated $\sim 10^{12}$ different B and T cells in humans, how many of t... |
2212.02868 | Attila Szolnoki | Attila Szolnoki and Matjaz Perc | Oppressed species can form a winning pair in a multi-species ecosystem | 10 pages, 8 figures | Appl. Math. Comput. 438 (2023) 127568 | 10.1016/j.amc.2022.127568 | null | q-bio.PE cond-mat.stat-mech cs.GT nlin.PS physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | The self-protection of alliances against external invaders is a key concept
behind the maintenance of biodiversity in the face of natural selection. But
since these alliances, which can be formed by different numbers of competitors,
can also compete against each other, it is important to identify their
strengths and ... | [
{
"created": "Tue, 6 Dec 2022 10:16:46 GMT",
"version": "v1"
}
] | 2022-12-07 | [
[
"Szolnoki",
"Attila",
""
],
[
"Perc",
"Matjaz",
""
]
] | The self-protection of alliances against external invaders is a key concept behind the maintenance of biodiversity in the face of natural selection. But since these alliances, which can be formed by different numbers of competitors, can also compete against each other, it is important to identify their strengths and we... |
1305.4264 | Simon Holbek | Simon Holbek, Kristian Moss Bendtsen, Jeppe Juul | Moderate stem cell telomere shortening rate postpones cancer onset in
stochastic model | null | null | 10.1103/PhysRevE.88.042706 | null | q-bio.CB physics.bio-ph q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mammalian cells are restricted from proliferating indefinitely. Telomeres at
the end of each chromosome are shortened at cell division and, when they reach
a critical length, the cell will enter permanent cell cycle arrest - a state
known as senescence. This mechanism is thought to be tumor suppressing, as it
helps p... | [
{
"created": "Sat, 18 May 2013 13:23:05 GMT",
"version": "v1"
}
] | 2015-06-16 | [
[
"Holbek",
"Simon",
""
],
[
"Bendtsen",
"Kristian Moss",
""
],
[
"Juul",
"Jeppe",
""
]
] | Mammalian cells are restricted from proliferating indefinitely. Telomeres at the end of each chromosome are shortened at cell division and, when they reach a critical length, the cell will enter permanent cell cycle arrest - a state known as senescence. This mechanism is thought to be tumor suppressing, as it helps pre... |
q-bio/0505019 | Henrik Jeldtoft Jensen | Daniel Lawson, Henrik Jeldtoft Jensen and Kunihiko Kaneko | Diversity as a product of interspecial interactions | 7 pages, 3 figures | null | null | null | q-bio.PE | null | We demonstrate diversification rather than optimisation for highly
interacting organisms in a well mixed biological system by means of a simple
model and reference to experiment, and find the cause to be the complex network
of interactions formed, allowing species less well adapted to an environment to
flourish by co... | [
{
"created": "Tue, 10 May 2005 13:58:37 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Lawson",
"Daniel",
""
],
[
"Jensen",
"Henrik Jeldtoft",
""
],
[
"Kaneko",
"Kunihiko",
""
]
] | We demonstrate diversification rather than optimisation for highly interacting organisms in a well mixed biological system by means of a simple model and reference to experiment, and find the cause to be the complex network of interactions formed, allowing species less well adapted to an environment to flourish by co-i... |
2112.08126 | Maja Linke | Maja Linke, Michael Ramscar | Finding Structure in Silence: The Role of Pauses in Aligning Speaker
Expectations | 25 pages, 5 figures | null | null | null | q-bio.NC q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The intelligibility of speech relies on the ability of interlocutors to
dynamically align their expectations about the rates at which informative
changes in signals occur. Exactly how this is achieved remains an open
question. We propose that speaker alignment is supported by the statistical
structure of spoken signa... | [
{
"created": "Wed, 15 Dec 2021 13:56:51 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Mar 2022 07:42:40 GMT",
"version": "v2"
},
{
"created": "Wed, 2 Nov 2022 11:21:57 GMT",
"version": "v3"
}
] | 2022-11-03 | [
[
"Linke",
"Maja",
""
],
[
"Ramscar",
"Michael",
""
]
] | The intelligibility of speech relies on the ability of interlocutors to dynamically align their expectations about the rates at which informative changes in signals occur. Exactly how this is achieved remains an open question. We propose that speaker alignment is supported by the statistical structure of spoken signals... |
2212.03290 | Rastine Merat | Rastine Merat | The human antigen R as an actionable super-hub within the network of
cancer cell persistency and plasticity | 12 pages, 3 figures | Translational Oncology, Volume 35, 2023, 101722, ISSN 1936-5233 | 10.1016/j.tranon.2023.101722 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In this perspective article, a clinically inspired phenotype-driven
experimental approach is put forward to address the challenge of the adaptive
response of solid cancers to small-molecule targeted therapies. A list of
conditions is derived, including an experimental quantitative assessment of
cell plasticity and an... | [
{
"created": "Tue, 6 Dec 2022 19:46:10 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Jan 2023 11:47:09 GMT",
"version": "v2"
},
{
"created": "Sun, 26 Mar 2023 10:37:09 GMT",
"version": "v3"
},
{
"created": "Wed, 21 Jun 2023 10:03:14 GMT",
"version": "v4"
}
] | 2023-06-22 | [
[
"Merat",
"Rastine",
""
]
] | In this perspective article, a clinically inspired phenotype-driven experimental approach is put forward to address the challenge of the adaptive response of solid cancers to small-molecule targeted therapies. A list of conditions is derived, including an experimental quantitative assessment of cell plasticity and an i... |
1803.09231 | Peter Gawthrop | Peter J. Gawthrop and Edmund J. Crampin | Biomolecular System Energetics | Accepted for 13th International Conference on Bond Graph Modeling
(ICBGM 18), July 9-12, 2018, Bordeaux, France | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Efficient energy transduction is one driver of evolution; and thus
understanding biomolecular energy transduction is crucial to understanding
living organisms. As an energy-orientated modelling methodology, bond graphs
provide a useful approach to describing and modelling the efficiency of living
systems. This paper ... | [
{
"created": "Sun, 25 Mar 2018 11:02:14 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Jun 2018 07:31:13 GMT",
"version": "v2"
}
] | 2018-06-11 | [
[
"Gawthrop",
"Peter J.",
""
],
[
"Crampin",
"Edmund J.",
""
]
] | Efficient energy transduction is one driver of evolution; and thus understanding biomolecular energy transduction is crucial to understanding living organisms. As an energy-orientated modelling methodology, bond graphs provide a useful approach to describing and modelling the efficiency of living systems. This paper gi... |
1110.5091 | Debora Marks | Debora S. Marks, Lucy J. Colwell, Robert Sheridan, Thomas A. Hopf,
Andrea Pagnani, Riccardo Zecchina, Chris Sander | 3D Protein Structure Predicted from Sequence | Debora S Marks and Lucy J Colwell are joint first authors. Supplement
and Appendices at: http://cbio.mskcc.org/foldingproteins. Updated version
25-Oct-2011 with '3D' added to the title and corrections of details in the
methods section to make it compatible with derivation of equations in the
main text and in th... | null | null | null | q-bio.BM cs.CE physics.bio-ph physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The evolutionary trajectory of a protein through sequence space is
constrained by function and three-dimensional (3D) structure. Residues in
spatial proximity tend to co-evolve, yet attempts to invert the evolutionary
record to identify these constraints and use them to computationally fold
proteins have so far been ... | [
{
"created": "Sun, 23 Oct 2011 22:02:12 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Oct 2011 18:59:33 GMT",
"version": "v2"
}
] | 2015-03-13 | [
[
"Marks",
"Debora S.",
""
],
[
"Colwell",
"Lucy J.",
""
],
[
"Sheridan",
"Robert",
""
],
[
"Hopf",
"Thomas A.",
""
],
[
"Pagnani",
"Andrea",
""
],
[
"Zecchina",
"Riccardo",
""
],
[
"Sander",
"Chris",
""
]
... | The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify these constraints and use them to computationally fold proteins have so far been un... |
1909.11211 | I\~nigo Urteaga | Kathy Li, I\~nigo Urteaga, Chris H. Wiggins, Anna Druet, Amanda Shea,
Virginia J. Vitzthum, No\'emie Elhadad | Characterizing physiological and symptomatic variation in menstrual
cycles using self-tracked mobile health data | The Supplementary Information for this work, as well as the code
required for data pre-processing and producing results is available in
https://github.com/iurteaga/menstrual_cycle_analysis | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The menstrual cycle is a key indicator of overall health for women of
reproductive age. Previously, menstruation was primarily studied through survey
results; however, as menstrual tracking mobile apps become more widely adopted,
they provide an increasingly large, content-rich source of menstrual health
experiences ... | [
{
"created": "Tue, 24 Sep 2019 22:21:10 GMT",
"version": "v1"
},
{
"created": "Mon, 13 Apr 2020 23:41:29 GMT",
"version": "v2"
},
{
"created": "Thu, 14 May 2020 22:57:02 GMT",
"version": "v3"
}
] | 2020-05-18 | [
[
"Li",
"Kathy",
""
],
[
"Urteaga",
"Iñigo",
""
],
[
"Wiggins",
"Chris H.",
""
],
[
"Druet",
"Anna",
""
],
[
"Shea",
"Amanda",
""
],
[
"Vitzthum",
"Virginia J.",
""
],
[
"Elhadad",
"Noémie",
""
]
] | The menstrual cycle is a key indicator of overall health for women of reproductive age. Previously, menstruation was primarily studied through survey results; however, as menstrual tracking mobile apps become more widely adopted, they provide an increasingly large, content-rich source of menstrual health experiences an... |
1310.7662 | Emmanuelle Tognoli | Emmanuelle Tognoli and J. A. Scott Kelso | Spectral dissociation of lateralized pairs of brain rhythms | 6 pages, 2 figures | null | 10.1016/j.neures.2019.12.006 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Using high resolution spectral methods to uncover neuromarkers of social,
cognitive and behavioral function, we have found that hemi-lateralized pairs of
oscillations such as left and right occipital alpha, or left and right rolandic
mu dissociate spectrally. That is, they show a shifted frequency distribution,
with ... | [
{
"created": "Tue, 29 Oct 2013 02:07:17 GMT",
"version": "v1"
}
] | 2020-05-11 | [
[
"Tognoli",
"Emmanuelle",
""
],
[
"Kelso",
"J. A. Scott",
""
]
] | Using high resolution spectral methods to uncover neuromarkers of social, cognitive and behavioral function, we have found that hemi-lateralized pairs of oscillations such as left and right occipital alpha, or left and right rolandic mu dissociate spectrally. That is, they show a shifted frequency distribution, with on... |
2110.07873 | Lokesh Boominathan | Lokesh Boominathan, Xaq Pitkow | Phase transitions in when feedback is useful | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Sensory observations about the world are invariably ambiguous. Inference
about the world's latent variables is thus an important computation for the
brain. However, computational constraints limit the performance of these
computations. These constraints include energetic costs for neural activity and
noise on every c... | [
{
"created": "Fri, 15 Oct 2021 05:50:16 GMT",
"version": "v1"
},
{
"created": "Wed, 25 May 2022 17:25:12 GMT",
"version": "v2"
},
{
"created": "Tue, 11 Oct 2022 21:16:16 GMT",
"version": "v3"
}
] | 2022-10-13 | [
[
"Boominathan",
"Lokesh",
""
],
[
"Pitkow",
"Xaq",
""
]
] | Sensory observations about the world are invariably ambiguous. Inference about the world's latent variables is thus an important computation for the brain. However, computational constraints limit the performance of these computations. These constraints include energetic costs for neural activity and noise on every cha... |
2009.03272 | Vivek Subramanian | Vivek Subramanian, Joshua Khani | Graph Convolutional Networks Reveal Neural Connections Encoding
Prosthetic Sensation | null | null | null | null | q-bio.NC cs.LG q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Extracting stimulus features from neuronal ensembles is of great interest to
the development of neuroprosthetics that project sensory information directly
to the brain via electrical stimulation. Machine learning strategies that
optimize stimulation parameters as the subject learns to interpret the
artificial input c... | [
{
"created": "Sun, 23 Aug 2020 01:43:46 GMT",
"version": "v1"
}
] | 2020-09-08 | [
[
"Subramanian",
"Vivek",
""
],
[
"Khani",
"Joshua",
""
]
] | Extracting stimulus features from neuronal ensembles is of great interest to the development of neuroprosthetics that project sensory information directly to the brain via electrical stimulation. Machine learning strategies that optimize stimulation parameters as the subject learns to interpret the artificial input cou... |
0907.4935 | Simone Bianco | Simone Bianco, Leah B. Shaw | Asymmetry in the presence of migration stabilizes multistrain disease
outbreaks | 17 pages, 5 figures, 3 appendices. Submitted version | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the effect of migration between coupled populations, or patches, on
the stability properties of multistrain disease dynamics. The epidemic model
used in this work displays a Hopf bifurcation to oscillations in a single well
mixed population. It is shown numerically that migration between two
non-identical pa... | [
{
"created": "Tue, 28 Jul 2009 15:25:40 GMT",
"version": "v1"
}
] | 2009-07-29 | [
[
"Bianco",
"Simone",
""
],
[
"Shaw",
"Leah B.",
""
]
] | We study the effect of migration between coupled populations, or patches, on the stability properties of multistrain disease dynamics. The epidemic model used in this work displays a Hopf bifurcation to oscillations in a single well mixed population. It is shown numerically that migration between two non-identical patc... |
2203.11920 | Pavle Goldstein | Braslav Rabar, Keti Ni\v{z}eti\'c and Pavle Goldstein | A Clique-Based Method for Improving Motif Scanning Accuracy | 14 pages, plenty of figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | We present a new approach for improving motif scanning accuracy, based on
analysis of in-between similarity. Given a set of motifs obtained from a
scanning process, we construct an associated weighted graph. We also compute
the expected weight of an edge in such a graph. It turns out that restricting
results to the m... | [
{
"created": "Tue, 22 Mar 2022 17:41:08 GMT",
"version": "v1"
}
] | 2022-03-23 | [
[
"Rabar",
"Braslav",
""
],
[
"Nižetić",
"Keti",
""
],
[
"Goldstein",
"Pavle",
""
]
] | We present a new approach for improving motif scanning accuracy, based on analysis of in-between similarity. Given a set of motifs obtained from a scanning process, we construct an associated weighted graph. We also compute the expected weight of an edge in such a graph. It turns out that restricting results to the max... |
2206.03364 | Han Li | Han Li, Dan Zhao and Jianyang Zeng | KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular
Property Prediction | 11 pages, to appear in KDD 2022 research track | null | 10.1145/3534678.3539426 | null | q-bio.BM cs.AI cs.LG physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Designing accurate deep learning models for molecular property prediction
plays an increasingly essential role in drug and material discovery. Recently,
due to the scarcity of labeled molecules, self-supervised learning methods for
learning generalizable and transferable representations of molecular graphs
have attra... | [
{
"created": "Thu, 2 Jun 2022 08:22:14 GMT",
"version": "v1"
}
] | 2022-06-08 | [
[
"Li",
"Han",
""
],
[
"Zhao",
"Dan",
""
],
[
"Zeng",
"Jianyang",
""
]
] | Designing accurate deep learning models for molecular property prediction plays an increasingly essential role in drug and material discovery. Recently, due to the scarcity of labeled molecules, self-supervised learning methods for learning generalizable and transferable representations of molecular graphs have attract... |
1812.02478 | Jochen Braun | Stepan Aleshin, Gergo Ziman, Ilona Kovacs, Jochen Braun | Perceptual reversals in binocular rivalry: improved detection from OKN | 37 pages, 9 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When binocular rivalry is induced by opponent motion displays, perceptual
reversals are often associated with changed oculomotor behaviour (Frassle et
al., 2014; Fujiwara et al., 2017). Specifically, the direction of smooth
pursuit phases in optokinetic nystagmus (OKN) typically corresponds to the
direction of motion... | [
{
"created": "Thu, 6 Dec 2018 11:45:27 GMT",
"version": "v1"
}
] | 2018-12-07 | [
[
"Aleshin",
"Stepan",
""
],
[
"Ziman",
"Gergo",
""
],
[
"Kovacs",
"Ilona",
""
],
[
"Braun",
"Jochen",
""
]
] | When binocular rivalry is induced by opponent motion displays, perceptual reversals are often associated with changed oculomotor behaviour (Frassle et al., 2014; Fujiwara et al., 2017). Specifically, the direction of smooth pursuit phases in optokinetic nystagmus (OKN) typically corresponds to the direction of motion t... |
1207.7196 | Jo\~ao Sacramento | Jo\~ao Sacramento and Andreas Wichert | Binary Willshaw learning yields high synaptic capacity for long-term
familiarity memory | 20 pages, 4 figures | Biological Cybernetics, vol. 106, no. 2, pp. 123-133, 2012 | 10.1007/s00422-012-0488-4 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate from a computational perspective the efficiency of the
Willshaw synaptic update rule in the context of familiarity discrimination, a
binary-answer, memory-related task that has been linked through psychophysical
experiments with modified neural activity patterns in the prefrontal and
perirhinal cortex ... | [
{
"created": "Tue, 31 Jul 2012 09:42:31 GMT",
"version": "v1"
}
] | 2012-08-01 | [
[
"Sacramento",
"João",
""
],
[
"Wichert",
"Andreas",
""
]
] | We investigate from a computational perspective the efficiency of the Willshaw synaptic update rule in the context of familiarity discrimination, a binary-answer, memory-related task that has been linked through psychophysical experiments with modified neural activity patterns in the prefrontal and perirhinal cortex re... |
1906.10538 | Jared Vasil | Jared Vasil, Paul B. Badcock, Axel Constant, Karl Friston, Maxwell J.
D. Ramstead | A World unto Itself: Human Communication as Active Inference | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Work in developmental psychology suggests that humans are predisposed to
align their mental states with other individuals. This manifests principally in
cooperative communication, that is, intentional communication geared towards
aligning mental states. This viewpoint has received ample empirical support.
However, th... | [
{
"created": "Tue, 25 Jun 2019 13:58:36 GMT",
"version": "v1"
},
{
"created": "Sun, 23 Feb 2020 01:09:33 GMT",
"version": "v2"
}
] | 2020-02-25 | [
[
"Vasil",
"Jared",
""
],
[
"Badcock",
"Paul B.",
""
],
[
"Constant",
"Axel",
""
],
[
"Friston",
"Karl",
""
],
[
"Ramstead",
"Maxwell J. D.",
""
]
] | Work in developmental psychology suggests that humans are predisposed to align their mental states with other individuals. This manifests principally in cooperative communication, that is, intentional communication geared towards aligning mental states. This viewpoint has received ample empirical support. However, this... |
1308.4917 | Chad M. Topaz | Christa Nilsen, John Paige, Olivia Warner, Benjamin Mayhew, Ryan
Sutley, Matthew Lam, Andrew J. Bernoff, and Chad M. Topaz | Social aggregation in pea aphids: Experimental measurement and
stochastic modeling | 19 pages, 6 figures | null | 10.1371/journal.pone.0083343 | null | q-bio.QM nlin.AO q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An ongoing challenge in the mathematical modeling of biological aggregations
is to strengthen the connection between models and biological data by
quantifying the rules that individuals follow. We model aggregation of the pea
aphid, Acyrthosiphon pisum. Specifically, we conduct experiments to track the
motion of aphi... | [
{
"created": "Fri, 16 Aug 2013 19:18:25 GMT",
"version": "v1"
}
] | 2014-03-05 | [
[
"Nilsen",
"Christa",
""
],
[
"Paige",
"John",
""
],
[
"Warner",
"Olivia",
""
],
[
"Mayhew",
"Benjamin",
""
],
[
"Sutley",
"Ryan",
""
],
[
"Lam",
"Matthew",
""
],
[
"Bernoff",
"Andrew J.",
""
],
[
"T... | An ongoing challenge in the mathematical modeling of biological aggregations is to strengthen the connection between models and biological data by quantifying the rules that individuals follow. We model aggregation of the pea aphid, Acyrthosiphon pisum. Specifically, we conduct experiments to track the motion of aphids... |
2406.02618 | Mika\"el Simard | Mika\"el Simard, Zhuoyan Shen, Maria A. Hawkins, Charles-Antoine
Collins-Fekete | Immunocto: a massive immune cell database auto-generated for
histopathology | null | null | null | null | q-bio.QM cs.AI eess.IV | http://creativecommons.org/licenses/by/4.0/ | With the advent of novel cancer treatment options such as immunotherapy,
studying the tumour immune micro-environment is crucial to inform on prognosis
and understand response to therapeutic agents. A key approach to characterising
the tumour immune micro-environment may be through combining (1) digitised
microscopic... | [
{
"created": "Mon, 3 Jun 2024 17:03:58 GMT",
"version": "v1"
}
] | 2024-06-06 | [
[
"Simard",
"Mikaël",
""
],
[
"Shen",
"Zhuoyan",
""
],
[
"Hawkins",
"Maria A.",
""
],
[
"Collins-Fekete",
"Charles-Antoine",
""
]
] | With the advent of novel cancer treatment options such as immunotherapy, studying the tumour immune micro-environment is crucial to inform on prognosis and understand response to therapeutic agents. A key approach to characterising the tumour immune micro-environment may be through combining (1) digitised microscopic h... |
2112.10048 | Linxing Preston Jiang | Linxing Preston Jiang, Rajesh P. N. Rao | Predictive Coding Theories of Cortical Function | In Oxford Research Encyclopedia of Neuroscience (2022) | null | 10.1093/acrefore/9780190264086.013.328 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Predictive coding is a unifying framework for understanding perception,
action and neocortical organization. In predictive coding, different areas of
the neocortex implement a hierarchical generative model of the world that is
learned from sensory inputs. Cortical circuits are hypothesized to perform
Bayesian inferen... | [
{
"created": "Sun, 19 Dec 2021 03:14:38 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Apr 2023 01:45:33 GMT",
"version": "v2"
},
{
"created": "Fri, 19 May 2023 00:08:31 GMT",
"version": "v3"
}
] | 2023-05-22 | [
[
"Jiang",
"Linxing Preston",
""
],
[
"Rao",
"Rajesh P. N.",
""
]
] | Predictive coding is a unifying framework for understanding perception, action and neocortical organization. In predictive coding, different areas of the neocortex implement a hierarchical generative model of the world that is learned from sensory inputs. Cortical circuits are hypothesized to perform Bayesian inference... |
2402.06772 | Zixun Lan | Zixun Lan, Binjie Hong, Jiajun Zhu, Zuo Zeng, Zhenfu Liu, Limin Yu,
Fei Ma | Retrosynthesis Prediction via Search in (Hyper) Graph | null | null | null | null | q-bio.QM cs.AI cs.CE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Predicting reactants from a specified core product stands as a fundamental
challenge within organic synthesis, termed retrosynthesis prediction. Recently,
semi-template-based methods and graph-edits-based methods have achieved good
performance in terms of both interpretability and accuracy. However, due to
their mech... | [
{
"created": "Fri, 9 Feb 2024 20:25:45 GMT",
"version": "v1"
}
] | 2024-02-13 | [
[
"Lan",
"Zixun",
""
],
[
"Hong",
"Binjie",
""
],
[
"Zhu",
"Jiajun",
""
],
[
"Zeng",
"Zuo",
""
],
[
"Liu",
"Zhenfu",
""
],
[
"Yu",
"Limin",
""
],
[
"Ma",
"Fei",
""
]
] | Predicting reactants from a specified core product stands as a fundamental challenge within organic synthesis, termed retrosynthesis prediction. Recently, semi-template-based methods and graph-edits-based methods have achieved good performance in terms of both interpretability and accuracy. However, due to their mechan... |
2404.04299 | Anindita Nath Nath | Anindita Nath (1), Savannah Mwesigwa (1), Yulin Dai (1), Xiaoqian
Jiang (2) and Zhongming Zhao (1 and 3) ((1) Center for Precision Health,
McWilliams School of Biomedical Informatics, UT Health Houston, TX (2)
Department of Health Data Science and Artificial Intelligence, McWilliams
School of Biomedical Informa... | GENEVIC: GENetic data Exploration and Visualization via Intelligent
interactive Console | null | null | null | null | q-bio.QM cs.AI | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Summary: The vast generation of genetic data poses a significant challenge in
efficiently uncovering valuable knowledge. Introducing GENEVIC, an AI-driven
chat framework that tackles this challenge by bridging the gap between genetic
data generation and biomedical knowledge discovery. Leveraging generative AI,
notabl... | [
{
"created": "Thu, 4 Apr 2024 20:53:30 GMT",
"version": "v1"
}
] | 2024-04-09 | [
[
"Nath",
"Anindita",
"",
"1 and 3"
],
[
"Mwesigwa",
"Savannah",
"",
"1 and 3"
],
[
"Dai",
"Yulin",
"",
"1 and 3"
],
[
"Jiang",
"Xiaoqian",
"",
"1 and 3"
],
[
"Zhao",
"Zhongming",
"",
"1 and 3"
]
] | Summary: The vast generation of genetic data poses a significant challenge in efficiently uncovering valuable knowledge. Introducing GENEVIC, an AI-driven chat framework that tackles this challenge by bridging the gap between genetic data generation and biomedical knowledge discovery. Leveraging generative AI, notably ... |
1605.07266 | Pengcheng Zhou | Pengcheng Zhou, Shanna L. Resendez, Jose Rodriguez-Romaguera, Jessica
C. Jimenez, Shay Q. Neufeld, Garret D. Stuber, Rene Hen, Mazen A. Kheirbek,
Bernardo L. Sabatini, Robert E. Kass, Liam Paninski | Efficient and accurate extraction of in vivo calcium signals from
microendoscopic video data | The image has been compressed for meeting arXiv requirements. A pdf
version with higher resolution image can be downloaded here
https://zhoupc.github.io/data/zhou2016.pdf | null | null | null | q-bio.NC q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In vivo calcium imaging through microscopes has enabled deep brain imaging of
previously inaccessible neuronal populations within the brains of freely moving
subjects. However, microendoscopic data suffer from high levels of background
fluorescence as well as an increased potential for overlapping neuronal
signals. P... | [
{
"created": "Tue, 24 May 2016 02:35:09 GMT",
"version": "v1"
},
{
"created": "Thu, 25 May 2017 20:22:54 GMT",
"version": "v2"
}
] | 2017-05-29 | [
[
"Zhou",
"Pengcheng",
""
],
[
"Resendez",
"Shanna L.",
""
],
[
"Rodriguez-Romaguera",
"Jose",
""
],
[
"Jimenez",
"Jessica C.",
""
],
[
"Neufeld",
"Shay Q.",
""
],
[
"Stuber",
"Garret D.",
""
],
[
"Hen",
"Rene",
... | In vivo calcium imaging through microscopes has enabled deep brain imaging of previously inaccessible neuronal populations within the brains of freely moving subjects. However, microendoscopic data suffer from high levels of background fluorescence as well as an increased potential for overlapping neuronal signals. Pre... |
2305.05093 | Wang-Yu Tong | Wang-Yu Tong, De-Xiang Yong, Xin Xu, Cai-Hua Qiu, Yan Zhang, Xing-Wang
Yang, Ting-Ting Xia, Qing-Yang Liu, Su-Li Cao, Yan Sun and Xue Li | Prokaryotic genome editing based on the subtype I-B-Svi CRISPR-Cas
system | 113 pages, 10 figures, and 6 tables | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Type I CRISPR-Cas systems are the most common among six types of CRISPR-Cas
systems, however, non-self-targeting genome editing based on a single Cas3 of
type I CRISPR-Cas systems has not been reported. Here, we present the subtype
I-B-Svi CRISPR-Cas system (with three confirmed CRISPRs and a cas gene cluster)
and ge... | [
{
"created": "Mon, 8 May 2023 23:32:47 GMT",
"version": "v1"
}
] | 2023-05-10 | [
[
"Tong",
"Wang-Yu",
""
],
[
"Yong",
"De-Xiang",
""
],
[
"Xu",
"Xin",
""
],
[
"Qiu",
"Cai-Hua",
""
],
[
"Zhang",
"Yan",
""
],
[
"Yang",
"Xing-Wang",
""
],
[
"Xia",
"Ting-Ting",
""
],
[
"Liu",
"Qin... | Type I CRISPR-Cas systems are the most common among six types of CRISPR-Cas systems, however, non-self-targeting genome editing based on a single Cas3 of type I CRISPR-Cas systems has not been reported. Here, we present the subtype I-B-Svi CRISPR-Cas system (with three confirmed CRISPRs and a cas gene cluster) and geno... |
1208.2981 | Sivan Leviyang | Sivan Leviyang | Computational Inference Methods for HIV-1 Selective Sweeps Shaped by
Early Cytotoxic T-Lymphocyte Response | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we develop a stochastic model of acute HIV infection, based on
the well-known standard model, that allows us to simulate the complex mutation
pathways of HIV escape from multiple CTL responses. Under this model, we
describe two computational inference methods. In one, we use a Bayesian
approach to constr... | [
{
"created": "Tue, 14 Aug 2012 21:46:30 GMT",
"version": "v1"
}
] | 2012-08-16 | [
[
"Leviyang",
"Sivan",
""
]
] | In this work we develop a stochastic model of acute HIV infection, based on the well-known standard model, that allows us to simulate the complex mutation pathways of HIV escape from multiple CTL responses. Under this model, we describe two computational inference methods. In one, we use a Bayesian approach to construc... |
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