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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1203.6465 | Viktor Wixler | Sergey V. Chesnokov, Lina G. Chesnokov and Viktor Wixler | Phenomenon of irreducible genetic markers for TATAAA motifs in human
chromosome 1 | 17 pages including 1 Figure and 6 Tables | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is well known that the general transcription factors (GTF) specifically
recognize correct TATA boxes, distinguishing them from many others. Employing
the principles of determinacy analysis (mathematical theory of rules) we
analyzed a fragment of human chromosome 1 DNA sequence and identified specific
genetic marke... | [
{
"created": "Thu, 29 Mar 2012 08:21:44 GMT",
"version": "v1"
}
] | 2012-03-30 | [
[
"Chesnokov",
"Sergey V.",
""
],
[
"Chesnokov",
"Lina G.",
""
],
[
"Wixler",
"Viktor",
""
]
] | It is well known that the general transcription factors (GTF) specifically recognize correct TATA boxes, distinguishing them from many others. Employing the principles of determinacy analysis (mathematical theory of rules) we analyzed a fragment of human chromosome 1 DNA sequence and identified specific genetic markers... |
1609.04649 | Joana Grah | Joana Sarah Grah, Jennifer Alison Harrington, Siang Boon Koh, Jeremy
Andrew Pike, Alexander Schreiner, Martin Burger, Carola-Bibiane Sch\"onlieb,
Stefanie Reichelt | Mathematical Imaging Methods for Mitosis Analysis in Live-Cell Phase
Contrast Microscopy | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we propose a workflow to detect and track mitotic cells in
time-lapse microscopy image sequences. In order to avoid the requirement for
cell lines expressing fluorescent markers and the associated phototoxicity,
phase contrast microscopy is often preferred over fluorescence microscopy in
live-cell imagi... | [
{
"created": "Wed, 14 Sep 2016 16:38:04 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Sep 2016 10:10:55 GMT",
"version": "v2"
},
{
"created": "Fri, 10 Feb 2017 11:50:01 GMT",
"version": "v3"
}
] | 2017-02-13 | [
[
"Grah",
"Joana Sarah",
""
],
[
"Harrington",
"Jennifer Alison",
""
],
[
"Koh",
"Siang Boon",
""
],
[
"Pike",
"Jeremy Andrew",
""
],
[
"Schreiner",
"Alexander",
""
],
[
"Burger",
"Martin",
""
],
[
"Schönlieb",
"... | In this paper we propose a workflow to detect and track mitotic cells in time-lapse microscopy image sequences. In order to avoid the requirement for cell lines expressing fluorescent markers and the associated phototoxicity, phase contrast microscopy is often preferred over fluorescence microscopy in live-cell imaging... |
1801.09589 | Chendi Wang | Chendi Wang, Rafeef Abugharbieh | Coactivated Clique Based Multisource Overlapping Brain Subnetwork
Extraction | 18 pages, 5 figures | null | null | null | q-bio.NC cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Subnetwork extraction using community detection methods is commonly used to
study the brain's modular structure. Recent studies indicated that certain
brain regions are known to interact with multiple subnetworks. However, most
existing methods are mainly for non-overlapping subnetwork extraction. In this
paper, we p... | [
{
"created": "Fri, 26 Jan 2018 18:56:23 GMT",
"version": "v1"
}
] | 2018-01-30 | [
[
"Wang",
"Chendi",
""
],
[
"Abugharbieh",
"Rafeef",
""
]
] | Subnetwork extraction using community detection methods is commonly used to study the brain's modular structure. Recent studies indicated that certain brain regions are known to interact with multiple subnetworks. However, most existing methods are mainly for non-overlapping subnetwork extraction. In this paper, we pre... |
2009.08378 | Timo C. Wunderlich | Timo C. Wunderlich, Christian Pehle | Event-Based Backpropagation can compute Exact Gradients for Spiking
Neural Networks | null | null | 10.1038/s41598-021-91786-z | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spiking neural networks combine analog computation with event-based
communication using discrete spikes. While the impressive advances of deep
learning are enabled by training non-spiking artificial neural networks using
the backpropagation algorithm, applying this algorithm to spiking networks was
previously hindere... | [
{
"created": "Thu, 17 Sep 2020 15:45:00 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Sep 2020 15:59:39 GMT",
"version": "v2"
},
{
"created": "Mon, 31 May 2021 18:00:07 GMT",
"version": "v3"
}
] | 2021-06-22 | [
[
"Wunderlich",
"Timo C.",
""
],
[
"Pehle",
"Christian",
""
]
] | Spiking neural networks combine analog computation with event-based communication using discrete spikes. While the impressive advances of deep learning are enabled by training non-spiking artificial neural networks using the backpropagation algorithm, applying this algorithm to spiking networks was previously hindered ... |
2304.02198 | Bowen Jing | Bowen Jing, Ezra Erives, Peter Pao-Huang, Gabriele Corso, Bonnie
Berger, Tommi Jaakkola | EigenFold: Generative Protein Structure Prediction with Diffusion Models | ICLR MLDD workshop 2023 | null | null | null | q-bio.BM cs.LG physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein structure prediction has reached revolutionary levels of accuracy on
single structures, yet distributional modeling paradigms are needed to capture
the conformational ensembles and flexibility that underlie biological function.
Towards this goal, we develop EigenFold, a diffusion generative modeling
framework... | [
{
"created": "Wed, 5 Apr 2023 02:46:13 GMT",
"version": "v1"
}
] | 2023-04-06 | [
[
"Jing",
"Bowen",
""
],
[
"Erives",
"Ezra",
""
],
[
"Pao-Huang",
"Peter",
""
],
[
"Corso",
"Gabriele",
""
],
[
"Berger",
"Bonnie",
""
],
[
"Jaakkola",
"Tommi",
""
]
] | Protein structure prediction has reached revolutionary levels of accuracy on single structures, yet distributional modeling paradigms are needed to capture the conformational ensembles and flexibility that underlie biological function. Towards this goal, we develop EigenFold, a diffusion generative modeling framework f... |
2208.04275 | Maxwell J. D. Ramstead | Maxwell J. D Ramstead | One person's modus ponens...: Comment on "The Markov blanket trick: On
the scope of the free energy principle and active inference" by Raja and
colleagues (2021) | null | null | 10.1016/j.plrev.2022.11.001 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this comment on "The Markov blanket trick: On the scope of the free energy
principle and active inference" by Raja and colleagues (2021) in Physics of
Life Reviews, I argue that the argument presented by the authors is valid;
however, I claim that the argument contains a flawed premise, which undermines
their conc... | [
{
"created": "Mon, 8 Aug 2022 17:14:47 GMT",
"version": "v1"
}
] | 2022-11-30 | [
[
"Ramstead",
"Maxwell J. D",
""
]
] | In this comment on "The Markov blanket trick: On the scope of the free energy principle and active inference" by Raja and colleagues (2021) in Physics of Life Reviews, I argue that the argument presented by the authors is valid; however, I claim that the argument contains a flawed premise, which undermines their conclu... |
1902.02463 | Mike Steel Prof. | Kristina Wicke and Mike Steel | Combinatorial properties of phylogenetic diversity indices | 31 pages, 7 figures | null | null | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic diversity indices provide a formal way to apportion
'evolutionary heritage' across species. Two natural diversity indices are Fair
Proportion (FP) and Equal Splits (ES). FP is also called 'evolutionary
distinctiveness' and, for rooted trees, is identical to the Shapley Value (SV),
which arises from coope... | [
{
"created": "Thu, 7 Feb 2019 03:45:34 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Jul 2019 08:56:21 GMT",
"version": "v2"
},
{
"created": "Wed, 2 Oct 2019 20:39:58 GMT",
"version": "v3"
}
] | 2019-10-04 | [
[
"Wicke",
"Kristina",
""
],
[
"Steel",
"Mike",
""
]
] | Phylogenetic diversity indices provide a formal way to apportion 'evolutionary heritage' across species. Two natural diversity indices are Fair Proportion (FP) and Equal Splits (ES). FP is also called 'evolutionary distinctiveness' and, for rooted trees, is identical to the Shapley Value (SV), which arises from coopera... |
1106.3035 | Chuan Xue | Chuan Xue and Elena O. Budrene and Hans G. Othmer | Radial and spiral stream formation in Proteus mirabilis | null | null | 10.1371/journal.pcbi.1002332 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The enteric bacterium Proteus mirabilis, which is a pathogen that forms
biofilms in vivo, can swarm over hard surfaces and form concentric ring
patterns in colonies. Colony formation involves two distinct cell types:
swarmer cells that dominate near the surface and the leading edge, and swimmer
cells that prefer a le... | [
{
"created": "Wed, 15 Jun 2011 17:41:32 GMT",
"version": "v1"
},
{
"created": "Fri, 17 Jun 2011 21:45:55 GMT",
"version": "v2"
}
] | 2015-05-28 | [
[
"Xue",
"Chuan",
""
],
[
"Budrene",
"Elena O.",
""
],
[
"Othmer",
"Hans G.",
""
]
] | The enteric bacterium Proteus mirabilis, which is a pathogen that forms biofilms in vivo, can swarm over hard surfaces and form concentric ring patterns in colonies. Colony formation involves two distinct cell types: swarmer cells that dominate near the surface and the leading edge, and swimmer cells that prefer a less... |
1510.08729 | Gabriel Silva | Gabriel A. Silva | The prevalence of small world networks explained by modeling the
competing dynamics of local signaling events in geometric networks | Updated version of the paper | null | null | null | q-bio.MN math.DS physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Networks are ubiquitous throughout science and engineering. A number of
methods, including some from our own group, have explored how one goes about
computing or predicting the dynamics of networks given information about
internal models of individual nodes and network connectivity, possibly with
additional informati... | [
{
"created": "Fri, 9 Oct 2015 06:50:08 GMT",
"version": "v1"
},
{
"created": "Thu, 3 Mar 2016 18:11:27 GMT",
"version": "v2"
},
{
"created": "Thu, 12 May 2016 23:20:21 GMT",
"version": "v3"
},
{
"created": "Fri, 12 May 2017 03:22:27 GMT",
"version": "v4"
},
{
"cre... | 2017-11-06 | [
[
"Silva",
"Gabriel A.",
""
]
] | Networks are ubiquitous throughout science and engineering. A number of methods, including some from our own group, have explored how one goes about computing or predicting the dynamics of networks given information about internal models of individual nodes and network connectivity, possibly with additional information... |
0708.3599 | Siebe van Albada | Siebe B. van Albada and Pieter Rein ten Wolde | Enzyme localization can drastically affect signal amplification in
signal transduction pathways | PLoS Comp Biol, in press. 32 pages including 6 figures and supporting
information | null | 10.1371/journal.pcbi.0030195.eor | null | q-bio.MN | null | Push-pull networks are ubiquitous in signal transduction pathways in both
prokaryotic and eukaryotic cells. They allow cells to strongly amplify signals
via the mechanism of zero-order ultrasensitivity. In a push-pull network, two
antagonistic enzymes control the activity of a protein by covalent
modification. These ... | [
{
"created": "Mon, 27 Aug 2007 14:40:17 GMT",
"version": "v1"
}
] | 2007-08-28 | [
[
"van Albada",
"Siebe B.",
""
],
[
"Wolde",
"Pieter Rein ten",
""
]
] | Push-pull networks are ubiquitous in signal transduction pathways in both prokaryotic and eukaryotic cells. They allow cells to strongly amplify signals via the mechanism of zero-order ultrasensitivity. In a push-pull network, two antagonistic enzymes control the activity of a protein by covalent modification. These en... |
1507.00368 | Piotr S{\l}owi\'nski | Piotr S{\l}owi\'nski, Chao Zhai, Francesco Alderisio, Robin Salesse,
Mathieu Gueugnon, Ludovic Marin, Benoit G. Bardy, Mario di Bernardo, and
Krasimira Tsaneva-Atanasova | Dynamic similarity promotes interpersonal coordination in joint-action | null | J. R. Soc. Interface 2016, 13, 20151093 | 10.1098/rsif.2015.1093 | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human movement has been studied for decades and dynamic laws of motion that
are common to all humans have been derived. Yet, every individual moves
differently from everyone else (faster/slower, harder/smoother etc). We propose
here an index of such variability, namely an individual motor signature (IMS)
able to capt... | [
{
"created": "Wed, 1 Jul 2015 20:41:07 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Dec 2015 08:16:07 GMT",
"version": "v2"
}
] | 2016-03-24 | [
[
"Słowiński",
"Piotr",
""
],
[
"Zhai",
"Chao",
""
],
[
"Alderisio",
"Francesco",
""
],
[
"Salesse",
"Robin",
""
],
[
"Gueugnon",
"Mathieu",
""
],
[
"Marin",
"Ludovic",
""
],
[
"Bardy",
"Benoit G.",
""
],
... | Human movement has been studied for decades and dynamic laws of motion that are common to all humans have been derived. Yet, every individual moves differently from everyone else (faster/slower, harder/smoother etc). We propose here an index of such variability, namely an individual motor signature (IMS) able to captur... |
2303.12651 | Joshua Kaste | Joshua A.M. Kaste and Yair Shachar-Hill | Model Validation and Selection in Metabolic Flux Analysis and Flux
Balance Analysis | 23 pages, 2 figures, 1 table | null | null | null | q-bio.MN q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | 13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are
widely used to investigate the operation of biochemical networks in both
biological and biotechnological research. Both of these methods use metabolic
reaction network models of metabolism operating at steady state, so that
reaction rates (flux... | [
{
"created": "Wed, 22 Mar 2023 15:32:01 GMT",
"version": "v1"
}
] | 2023-03-23 | [
[
"Kaste",
"Joshua A. M.",
""
],
[
"Shachar-Hill",
"Yair",
""
]
] | 13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both of these methods use metabolic reaction network models of metabolism operating at steady state, so that reaction rates (fluxes... |
1503.08527 | Alexey Shipunov | Brandon Chrisman, Allison Rabe, Ranelle Ivens, Sarah Lopez, and Alexey
Shipunov | The ecological impact of flooding: a study of tree damage | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/publicdomain/ | The objective of this research was to identify factors affecting tree damage
in the historical Minot flood of 2011. We hypothesized that tree height,
identity, origin, and maximum water height affect in the severity of damage
sustained by a tree in a flood event. All these factors were significant but
highly interact... | [
{
"created": "Mon, 30 Mar 2015 03:21:01 GMT",
"version": "v1"
}
] | 2015-03-31 | [
[
"Chrisman",
"Brandon",
""
],
[
"Rabe",
"Allison",
""
],
[
"Ivens",
"Ranelle",
""
],
[
"Lopez",
"Sarah",
""
],
[
"Shipunov",
"Alexey",
""
]
] | The objective of this research was to identify factors affecting tree damage in the historical Minot flood of 2011. We hypothesized that tree height, identity, origin, and maximum water height affect in the severity of damage sustained by a tree in a flood event. All these factors were significant but highly interactiv... |
1702.00360 | Thomas Ouldridge | Thomas E. Ouldridge | The importance of thermodynamics for molecular systems, and the
importance of molecular systems for thermodynamics | To appear in Nat. Comput. Special issue for DNA22 | null | null | null | q-bio.MN cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Improved understanding of molecular systems has only emphasised the
sophistication of networks within the cell. Simultaneously, the advance of
nucleic acid nanotechnology, a platform within which reactions can be
exquisitely controlled, has made the development of artificial architectures
and devices possible. Vital ... | [
{
"created": "Wed, 1 Feb 2017 17:14:50 GMT",
"version": "v1"
},
{
"created": "Mon, 2 Oct 2017 17:02:05 GMT",
"version": "v2"
}
] | 2017-10-03 | [
[
"Ouldridge",
"Thomas E.",
""
]
] | Improved understanding of molecular systems has only emphasised the sophistication of networks within the cell. Simultaneously, the advance of nucleic acid nanotechnology, a platform within which reactions can be exquisitely controlled, has made the development of artificial architectures and devices possible. Vital to... |
2402.00207 | Lucas Machado Moschen | Lucas Machado Moschen, Mar\'ia Soledad Aronna | Optimal vaccination strategies on networks and in metropolitan areas | 29 pages, 23 figures | null | null | null | q-bio.PE math.OC q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | This study presents a mathematical model for optimal vaccination strategies
in interconnected metropolitan areas, considering commuting patterns. It is a
compartmental model with a vaccination rate for each city, acting as a control
function. The commuting patterns are incorporated through a weighted adjacency
matrix... | [
{
"created": "Wed, 31 Jan 2024 22:09:22 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Apr 2024 15:03:50 GMT",
"version": "v2"
}
] | 2024-04-29 | [
[
"Moschen",
"Lucas Machado",
""
],
[
"Aronna",
"María Soledad",
""
]
] | This study presents a mathematical model for optimal vaccination strategies in interconnected metropolitan areas, considering commuting patterns. It is a compartmental model with a vaccination rate for each city, acting as a control function. The commuting patterns are incorporated through a weighted adjacency matrix a... |
1002.1023 | Michael B\"orsch | Michael Boersch | Targeting cytochrome C oxidase in mitochondria with Pt(II)-porphyrins
for Photodynamic Therapy | 11 pages, 5 figures | null | 10.1117/12.841284 | null | q-bio.BM physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mitochondria are the power house of living cells, where the synthesis of the
chemical "energy currency" adenosine triphosphate (ATP) occurs. Oxidative
phosphorylation by a series of membrane protein complexes I to IV, that is, the
electron transport chain, is the source of the electrochemical potential
difference or ... | [
{
"created": "Thu, 4 Feb 2010 15:43:01 GMT",
"version": "v1"
}
] | 2015-05-18 | [
[
"Boersch",
"Michael",
""
]
] | Mitochondria are the power house of living cells, where the synthesis of the chemical "energy currency" adenosine triphosphate (ATP) occurs. Oxidative phosphorylation by a series of membrane protein complexes I to IV, that is, the electron transport chain, is the source of the electrochemical potential difference or pr... |
1801.01823 | Ulisse Ferrari | Ulisse Ferrari, Stephane Deny, Matthew Chalk, Gasper Tkacik, Olivier
Marre, Thierry Mora | Separating intrinsic interactions from extrinsic correlations in a
network of sensory neurons | null | Phys. Rev. E 98, 042410 (2018) | 10.1103/PhysRevE.98.042410 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Correlations in sensory neural networks have both extrinsic and intrinsic
origins. Extrinsic or stimulus correlations arise from shared inputs to the
network, and thus depend strongly on the stimulus ensemble. Intrinsic or noise
correlations reflect biophysical mechanisms of interactions between neurons,
which are ex... | [
{
"created": "Fri, 5 Jan 2018 16:36:56 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Feb 2018 15:54:44 GMT",
"version": "v2"
}
] | 2018-11-05 | [
[
"Ferrari",
"Ulisse",
""
],
[
"Deny",
"Stephane",
""
],
[
"Chalk",
"Matthew",
""
],
[
"Tkacik",
"Gasper",
""
],
[
"Marre",
"Olivier",
""
],
[
"Mora",
"Thierry",
""
]
] | Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network, and thus depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expe... |
2211.05658 | Mo Wang | Mo Wang, Kexin Lou, Zeming Liu, Pengfei Wei, Quanying Liu | Multi-objective optimization via evolutionary algorithm (MOVEA) for
high-definition transcranial electrical stimulation of the human brain | null | NeuroImage, Volume 280, 2020 | 10.1016/j.neuroimage.2023.120348 | null | q-bio.QM cs.NE q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Designing a transcranial electrical stimulation (TES) strategy requires
considering multiple objectives, such as intensity in the target area,
focality, stimulation depth, and avoidance zone, which are often mutually
exclusive. A computational framework for optimizing different strategies and
comparing trade-offs bet... | [
{
"created": "Thu, 10 Nov 2022 15:42:06 GMT",
"version": "v1"
},
{
"created": "Mon, 3 Apr 2023 19:55:07 GMT",
"version": "v2"
}
] | 2023-09-13 | [
[
"Wang",
"Mo",
""
],
[
"Lou",
"Kexin",
""
],
[
"Liu",
"Zeming",
""
],
[
"Wei",
"Pengfei",
""
],
[
"Liu",
"Quanying",
""
]
] | Designing a transcranial electrical stimulation (TES) strategy requires considering multiple objectives, such as intensity in the target area, focality, stimulation depth, and avoidance zone, which are often mutually exclusive. A computational framework for optimizing different strategies and comparing trade-offs betwe... |
q-bio/0703048 | Azi Lipshtat | Azi Lipshtat | An "All Possible Steps" Approach to the Accelerated Use of Gillespie's
Algorithm | Accepted for publication at the Journal of Chemical Physics. 19
pages, including 2 Tables and 4 Figures | null | 10.1063/1.2730507 | null | q-bio.QM physics.comp-ph | null | Many physical and biological processes are stochastic in nature.
Computational models and simulations of such processes are a mathematical and
computational challenge. The basic stochastic simulation algorithm was
published by D. Gillespie about three decades ago [D.T. Gillespie, J. Phys.
Chem. {\bf 81}, 2340, (1977)... | [
{
"created": "Thu, 22 Mar 2007 12:57:11 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Lipshtat",
"Azi",
""
]
] | Many physical and biological processes are stochastic in nature. Computational models and simulations of such processes are a mathematical and computational challenge. The basic stochastic simulation algorithm was published by D. Gillespie about three decades ago [D.T. Gillespie, J. Phys. Chem. {\bf 81}, 2340, (1977)].... |
2307.04052 | Tinglin Huang | Tinglin Huang, Ziniu Hu, Rex Ying | Learning to Group Auxiliary Datasets for Molecule | Accepted at NeurIPS 2023, Camera Ready Version | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The limited availability of annotations in small molecule datasets presents a
challenge to machine learning models. To address this, one common strategy is
to collaborate with additional auxiliary datasets. However, having more data
does not always guarantee improvements. Negative transfer can occur when the
knowledg... | [
{
"created": "Sat, 8 Jul 2023 22:02:22 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Nov 2023 23:03:35 GMT",
"version": "v2"
}
] | 2023-11-10 | [
[
"Huang",
"Tinglin",
""
],
[
"Hu",
"Ziniu",
""
],
[
"Ying",
"Rex",
""
]
] | The limited availability of annotations in small molecule datasets presents a challenge to machine learning models. To address this, one common strategy is to collaborate with additional auxiliary datasets. However, having more data does not always guarantee improvements. Negative transfer can occur when the knowledge ... |
1309.0936 | Namiko Mitarai | Namiko Mitarai and Steen Pedersen | Control of ribosome traffic by position-dependent choice of synonymous
codons | 12 pages, 6 Figures. This is an author-created, un-copyedited version
of an article accepted for publication in Physical Biology. IOP Publishing
Ltd is not responsible for any errors or omissions in this version of the
manuscript or any version derived from it | Phys. Biol. 10 (2013) 056011 | 10.1088/1478-3975/10/5/056011 | null | q-bio.SC q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Messenger RNA encodes a sequence of amino acids by using codons. For most
amino acids there are multiple synonymous codons that can encode the amino
acid. The translation speed can vary from one codon to another, thus there is
room for changing the ribosome speed while keeping the amino acid sequence and
hence the re... | [
{
"created": "Wed, 4 Sep 2013 08:05:06 GMT",
"version": "v1"
}
] | 2013-10-10 | [
[
"Mitarai",
"Namiko",
""
],
[
"Pedersen",
"Steen",
""
]
] | Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence the resu... |
2206.12997 | Corey Keller | Juha Gogulski, Jessica M. Ross, Austin Talbot, Christopher Cline,
Francesco L Donati, Saachi Munot, Naryeong Kim, Ciara Gibbs, Nikita Bastin,
Jessica Yang, Christopher B. Minasi, Manjima Sarkar, Jade Truong, Corey J
Keller | Personalized rTMS for Depression: A Review | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Personalized treatments are gaining momentum across all fields of medicine.
Precision medicine can be applied to neuromodulatory techniques, where focused
brain stimulation treatments such as repetitive transcranial magnetic
stimulation (rTMS) are used to modulate brain circuits and alleviate clinical
symptoms. rTMS ... | [
{
"created": "Mon, 27 Jun 2022 00:04:07 GMT",
"version": "v1"
}
] | 2022-07-20 | [
[
"Gogulski",
"Juha",
""
],
[
"Ross",
"Jessica M.",
""
],
[
"Talbot",
"Austin",
""
],
[
"Cline",
"Christopher",
""
],
[
"Donati",
"Francesco L",
""
],
[
"Munot",
"Saachi",
""
],
[
"Kim",
"Naryeong",
""
],
... | Personalized treatments are gaining momentum across all fields of medicine. Precision medicine can be applied to neuromodulatory techniques, where focused brain stimulation treatments such as repetitive transcranial magnetic stimulation (rTMS) are used to modulate brain circuits and alleviate clinical symptoms. rTMS is... |
2105.06036 | Americo Cunha Jr | Eber Dantas, Michel Tosin, Americo Cunha Jr | Calibration of a SEIR-SEI epidemic model to describe the Zika virus
outbreak in Brazil | null | Applied Mathematics and Computation, vol. 338, pp. 249-259, 2018 | 10.1016/j.amc.2018.06.024 | null | q-bio.PE cs.NA math.DS math.NA math.OC stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multiple instances of Zika virus epidemic have been reported around the world
in the last two decades, turning the related illness into an international
concern. In this context the use of mathematical models for epidemics is of
great importance, since they are useful tools to study the underlying outbreak
numbers an... | [
{
"created": "Thu, 13 May 2021 01:51:20 GMT",
"version": "v1"
}
] | 2021-05-14 | [
[
"Dantas",
"Eber",
""
],
[
"Tosin",
"Michel",
""
],
[
"Cunha",
"Americo",
"Jr"
]
] | Multiple instances of Zika virus epidemic have been reported around the world in the last two decades, turning the related illness into an international concern. In this context the use of mathematical models for epidemics is of great importance, since they are useful tools to study the underlying outbreak numbers and ... |
q-bio/0501018 | Peter F. Arndt | Peter F. Arndt and Terence Hwa | Identification and Measurement of Neighbor Dependent Nucleotide
Substitution Processes | 15 pages, 3 figures | null | null | null | q-bio.GN | null | The presence of neighbor dependencies generated a specific pattern of
dinucleotide frequencies in all organisms. Especially, the
CpG-methylation-deamination process is the predominant substitution process in
vertebrates and needs to be incorporated into a more realistic model for
nucleotide substitutions. Based on a ... | [
{
"created": "Thu, 13 Jan 2005 12:22:47 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Arndt",
"Peter F.",
""
],
[
"Hwa",
"Terence",
""
]
] | The presence of neighbor dependencies generated a specific pattern of dinucleotide frequencies in all organisms. Especially, the CpG-methylation-deamination process is the predominant substitution process in vertebrates and needs to be incorporated into a more realistic model for nucleotide substitutions. Based on a ge... |
1902.10168 | Leonardo Pellegrina | Leonardo Pellegrina, Cinzia Pizzi, Fabio Vandin | Fast Approximation of Frequent $k$-mers and Applications to Metagenomics | Accepted for RECOMB 2019 | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Estimating the abundances of all $k$-mers in a set of biological sequences is
a fundamental and challenging problem with many applications in biological
analysis. While several methods have been designed for the exact or approximate
solution of this problem, they all require to process the entire dataset, that
can be... | [
{
"created": "Tue, 26 Feb 2019 19:09:05 GMT",
"version": "v1"
}
] | 2019-02-28 | [
[
"Pellegrina",
"Leonardo",
""
],
[
"Pizzi",
"Cinzia",
""
],
[
"Vandin",
"Fabio",
""
]
] | Estimating the abundances of all $k$-mers in a set of biological sequences is a fundamental and challenging problem with many applications in biological analysis. While several methods have been designed for the exact or approximate solution of this problem, they all require to process the entire dataset, that can be e... |
2309.13565 | Joydeb Gomasta Mr. | Hasina Sultana, Sharmila Rani Mallick, Jahidul Hassan, Joydeb Gomasta,
Md. Humayun Kabir, Md. Sakibul Alam Sakib, Mahmuda Hossen, Muhammad Mustakim
Billah, Emrul Kayesh | Nutritional composition and bioactive compounds of mini watermelon
genotypes in Bangladesh | 22 pages, 6 tables, 3 figures | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Given the present rising trends in changing lifestyle and consumption
patterns, watermelon production has shifted from big to small-sized fruits
having desirable quality attributes. Hence, analyses of fruit quality traits of
mini watermelon are crucial to develop improved cultivars with enhanced
nutritional compositi... | [
{
"created": "Sun, 24 Sep 2023 06:43:00 GMT",
"version": "v1"
}
] | 2023-09-26 | [
[
"Sultana",
"Hasina",
""
],
[
"Mallick",
"Sharmila Rani",
""
],
[
"Hassan",
"Jahidul",
""
],
[
"Gomasta",
"Joydeb",
""
],
[
"Kabir",
"Md. Humayun",
""
],
[
"Sakib",
"Md. Sakibul Alam",
""
],
[
"Hossen",
"Mahmuda... | Given the present rising trends in changing lifestyle and consumption patterns, watermelon production has shifted from big to small-sized fruits having desirable quality attributes. Hence, analyses of fruit quality traits of mini watermelon are crucial to develop improved cultivars with enhanced nutritional composition... |
1403.7104 | Brian Williams Dr | Brian Williams | Elimination of HIV in South Africa through expanded access to
antiretroviral therapy: Cautions, caveats and the importance of parsimony | Two pages. One figure embedded in text | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a recent article Hontelez and colleagues investigate the prospects for
elimination of HIV in South Africa through expanded access to antiretroviral
therapy (ART) using STDSIM, a micro-simulation model. One of the first
published models to suggest that expanded access to ART could lead to the
elimination of HIV, re... | [
{
"created": "Wed, 26 Mar 2014 04:45:57 GMT",
"version": "v1"
}
] | 2014-03-28 | [
[
"Williams",
"Brian",
""
]
] | In a recent article Hontelez and colleagues investigate the prospects for elimination of HIV in South Africa through expanded access to antiretroviral therapy (ART) using STDSIM, a micro-simulation model. One of the first published models to suggest that expanded access to ART could lead to the elimination of HIV, refe... |
1812.00105 | Ehtibar Dzhafarov | Victor H. Cervantes and Ehtibar N. Dzhafarov | True Contextuality in a Psychophysical Experiment | version 2 is a minor revision | null | null | null | q-bio.NC math.PR quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent crowdsourcing experiments have shown that true contextuality of the
kind found in quantum mechanics can also be present in human behavior. In these
experiments simple human choices were aggregated over large numbers of
respondents, with each respondent dealing with a single context (set of
questions asked). In... | [
{
"created": "Sat, 1 Dec 2018 00:28:10 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Feb 2019 22:15:31 GMT",
"version": "v2"
}
] | 2019-02-26 | [
[
"Cervantes",
"Victor H.",
""
],
[
"Dzhafarov",
"Ehtibar N.",
""
]
] | Recent crowdsourcing experiments have shown that true contextuality of the kind found in quantum mechanics can also be present in human behavior. In these experiments simple human choices were aggregated over large numbers of respondents, with each respondent dealing with a single context (set of questions asked). In t... |
1206.5904 | Dipjyoti Das | Dipjyoti Das and Dibyendu Das and Ashok Prasad | Giant number fluctuations in microbial ecologies | 18 pages, 5 figures | Journal Theoretical Biology, Vol. 308, pp. 96-104 (2012) | 10.1016/j.jtbi.2012.05.030 | null | q-bio.PE cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Statistical fluctuations in population sizes of microbes may be quite large
depending on the nature of their underlying stochastic dynamics. For example,
the variance of the population size of a microbe undergoing a pure birth
process with unlimited resources is proportional to the square of its mean. We
refer to suc... | [
{
"created": "Tue, 26 Jun 2012 07:46:12 GMT",
"version": "v1"
}
] | 2012-06-27 | [
[
"Das",
"Dipjyoti",
""
],
[
"Das",
"Dibyendu",
""
],
[
"Prasad",
"Ashok",
""
]
] | Statistical fluctuations in population sizes of microbes may be quite large depending on the nature of their underlying stochastic dynamics. For example, the variance of the population size of a microbe undergoing a pure birth process with unlimited resources is proportional to the square of its mean. We refer to such ... |
1404.5010 | Benedict Paten | Benedict Paten, Adam Novak and David Haussler | Mapping to a Reference Genome Structure | 25 pages | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To support comparative genomics, population genetics, and medical genetics,
we propose that a reference genome should come with a scheme for mapping each
base in any DNA string to a position in that reference genome. We refer to a
collection of one or more reference genomes and a scheme for mapping to their
positions... | [
{
"created": "Sun, 20 Apr 2014 04:48:24 GMT",
"version": "v1"
}
] | 2014-04-22 | [
[
"Paten",
"Benedict",
""
],
[
"Novak",
"Adam",
""
],
[
"Haussler",
"David",
""
]
] | To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a collection of one or more reference genomes and a scheme for mapping to their positions a... |
2009.04519 | Laura Schaposnik | Vishaal Ram, Laura P. Schaposnik, Nikos Konstantinou, Eliz Volkan,
Marietta Papadatou-Pastou, Banu Manav, Domicele Jonauskaite, Christine Mohr | Extrapolating continuous color emotions through deep learning | To appear in Physical Review R. (8 pages, 13 figures) | Physical Review RESEARCH 2, 033350 (2020) | 10.1103/PhysRevResearch.2.033350 | null | q-bio.QM cs.LG physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | By means of an experimental dataset, we use deep learning to implement an RGB
extrapolation of emotions associated to color, and do a mathematical study of
the results obtained through this neural network. In particular, we see that
males typically associate a given emotion with darker colors while females with
brigh... | [
{
"created": "Wed, 5 Aug 2020 02:08:29 GMT",
"version": "v1"
}
] | 2022-10-18 | [
[
"Ram",
"Vishaal",
""
],
[
"Schaposnik",
"Laura P.",
""
],
[
"Konstantinou",
"Nikos",
""
],
[
"Volkan",
"Eliz",
""
],
[
"Papadatou-Pastou",
"Marietta",
""
],
[
"Manav",
"Banu",
""
],
[
"Jonauskaite",
"Domicele",... | By means of an experimental dataset, we use deep learning to implement an RGB extrapolation of emotions associated to color, and do a mathematical study of the results obtained through this neural network. In particular, we see that males typically associate a given emotion with darker colors while females with brighte... |
1808.08662 | Luay Nakhleh | R.A.L. Elworth, H.A. Ogilvie, J. Zhu, L. Nakhleh | Advances in Computational Methods for Phylogenetic Networks in the
Presence of Hybridization | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Phylogenetic networks extend phylogenetic trees to allow for modeling
reticulate evolutionary processes such as hybridization. They take the shape of
a rooted, directed, acyclic graph, and when parameterized with evolutionary
parameters, such as divergence times and population sizes, they form a
generative process of... | [
{
"created": "Mon, 27 Aug 2018 01:46:06 GMT",
"version": "v1"
}
] | 2018-08-28 | [
[
"Elworth",
"R. A. L.",
""
],
[
"Ogilvie",
"H. A.",
""
],
[
"Zhu",
"J.",
""
],
[
"Nakhleh",
"L.",
""
]
] | Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters, such as divergence times and population sizes, they form a generative process of m... |
1401.2897 | Andrei Khrennikov Yu | Masanari Asano, Takahisa Hashimoto, Andrei Khrennikov, Masanori Ohya,
Yoshiharu Tanaka | Violation of contextual generalization of the Leggett-Garg inequality
for recognition of ambiguous figures | Presented at the conference Quantum Interactions 14, University of
Leicester, July 2014; submitted to Physica Scripta, IOP; new version contains
discussions on Bell and contextuality, marginal selectivity,
Kolmogorovization of contextual data | Phys. Scr. T 163 (2014) 014006 | 10.1088/0031-8949/2014/T163/014006 | null | q-bio.NC math.PR math.ST quant-ph stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We interpret the Leggett-Garg (LG) inequality as a kind of contextual
probabilistic inequality in which one combines data collected in experiments
performed for three different contexts. In the original version of the
inequality these contexts have the temporal nature and they are given by three
pairs of instances of... | [
{
"created": "Fri, 10 Jan 2014 09:33:13 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Jan 2014 18:16:15 GMT",
"version": "v2"
},
{
"created": "Fri, 2 May 2014 14:01:00 GMT",
"version": "v3"
}
] | 2015-06-18 | [
[
"Asano",
"Masanari",
""
],
[
"Hashimoto",
"Takahisa",
""
],
[
"Khrennikov",
"Andrei",
""
],
[
"Ohya",
"Masanori",
""
],
[
"Tanaka",
"Yoshiharu",
""
]
] | We interpret the Leggett-Garg (LG) inequality as a kind of contextual probabilistic inequality in which one combines data collected in experiments performed for three different contexts. In the original version of the inequality these contexts have the temporal nature and they are given by three pairs of instances of t... |
1204.2822 | Elena Shchekinova Y | E. Shchekinova, M. G. J. L\"oder, M. Boersma, K. H. Wiltshire | The Effect of Differentiation of Prey Community on Stable Coexistence in
a Three-Species Food--Web Model | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Food webs with intraguild predation (IGP) are widespread in natural habitats.
Their adaptation and resilience behaviour is principal for understanding
restructuring of ecological communities. In spite of the importance of IGP food
webs their behaviour even for the simplest 3-species systems has not been fully
explore... | [
{
"created": "Thu, 12 Apr 2012 08:24:21 GMT",
"version": "v1"
}
] | 2012-04-16 | [
[
"Shchekinova",
"E.",
""
],
[
"Löder",
"M. G. J.",
""
],
[
"Boersma",
"M.",
""
],
[
"Wiltshire",
"K. H.",
""
]
] | Food webs with intraguild predation (IGP) are widespread in natural habitats. Their adaptation and resilience behaviour is principal for understanding restructuring of ecological communities. In spite of the importance of IGP food webs their behaviour even for the simplest 3-species systems has not been fully explored.... |
1011.0322 | Mauro Mobilia | Michael Assaf, Mauro Mobilia | Fixation of a Deleterious Allele under Mutation Pressure and Finite
Selection Intensity | 26 pages, 5 figures. Accepted by the Journal of Theoretical Biology | J. Theor. Biol. 275, 93-103 (2011) | 10.1016/j.jtbi.2011.01.025 | null | q-bio.PE cond-mat.stat-mech nlin.AO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The mean fixation time of a deleterious mutant allele is studied beyond the
diffusion approximation. As in Kimura's classical work [M. Kimura, Proc. Natl.
Acad. Sci. U.S.A. Vol.77, 522 (1980)], that was motivated by the problem of
fixation in the presence of amorphic or hypermorphic mutations, we consider a
diallelic... | [
{
"created": "Mon, 1 Nov 2010 14:02:54 GMT",
"version": "v1"
},
{
"created": "Wed, 19 Jan 2011 11:52:53 GMT",
"version": "v2"
}
] | 2011-02-22 | [
[
"Assaf",
"Michael",
""
],
[
"Mobilia",
"Mauro",
""
]
] | The mean fixation time of a deleterious mutant allele is studied beyond the diffusion approximation. As in Kimura's classical work [M. Kimura, Proc. Natl. Acad. Sci. U.S.A. Vol.77, 522 (1980)], that was motivated by the problem of fixation in the presence of amorphic or hypermorphic mutations, we consider a diallelic m... |
1408.6694 | Erik Volz | Erik M. Volz and Simon DW Frost | Sampling through time and phylodynamic inference with coalescent and
birth-death models | Submitted | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many population genetic models have been developed for the purpose of
inferring population size and growth rates from random samples of genetic data.
We examine two popular approaches to this problem, the coalescent and the
birth-death-sampling model, in the context of estimating population size and
birth rates in a ... | [
{
"created": "Thu, 28 Aug 2014 12:13:37 GMT",
"version": "v1"
}
] | 2014-08-29 | [
[
"Volz",
"Erik M.",
""
],
[
"Frost",
"Simon DW",
""
]
] | Many population genetic models have been developed for the purpose of inferring population size and growth rates from random samples of genetic data. We examine two popular approaches to this problem, the coalescent and the birth-death-sampling model, in the context of estimating population size and birth rates in a po... |
2006.04684 | Ali Salari | Ali Salari, Gregory Kiar, Lindsay Lewis, Alan C. Evans, Tristan
Glatard | File-based localization of numerical perturbations in data analysis
pipelines | 10 pages, 6 figures, 2 tables | null | null | null | q-bio.QM eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Data analysis pipelines are known to be impacted by computational conditions,
presumably due to the creation and propagation of numerical errors. While this
process could play a major role in the current reproducibility crisis, the
precise causes of such instabilities and the path along which they propagate in
pipeli... | [
{
"created": "Wed, 3 Jun 2020 19:11:40 GMT",
"version": "v1"
},
{
"created": "Tue, 29 Sep 2020 01:00:09 GMT",
"version": "v2"
}
] | 2020-09-30 | [
[
"Salari",
"Ali",
""
],
[
"Kiar",
"Gregory",
""
],
[
"Lewis",
"Lindsay",
""
],
[
"Evans",
"Alan C.",
""
],
[
"Glatard",
"Tristan",
""
]
] | Data analysis pipelines are known to be impacted by computational conditions, presumably due to the creation and propagation of numerical errors. While this process could play a major role in the current reproducibility crisis, the precise causes of such instabilities and the path along which they propagate in pipeline... |
q-bio/0505054 | Sagi Snir | Benny Chor, Michael D. Hendy and Sagi Snir | Maximum Likelihood Jukes-Cantor Triplets: Analytic Solutions | null | null | null | null | q-bio.PE | null | Complex systems of polynomial equations have to be set up and solved
algebraically in order to obtain analytic solutions for maximum likelihood on
phylogenetic trees. This has restricted the types of systems previously
resolved to the simplest models - three and four taxa under a molecular clock,
with just two state ... | [
{
"created": "Fri, 27 May 2005 18:09:56 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Chor",
"Benny",
""
],
[
"Hendy",
"Michael D.",
""
],
[
"Snir",
"Sagi",
""
]
] | Complex systems of polynomial equations have to be set up and solved algebraically in order to obtain analytic solutions for maximum likelihood on phylogenetic trees. This has restricted the types of systems previously resolved to the simplest models - three and four taxa under a molecular clock, with just two state ch... |
1604.08921 | Artur Fassoni | Artur C. Fassoni and Hyun M. Yang | An ecological resilience perspective on cancer: insights from a toy
model | null | null | null | null | q-bio.PE math.DS q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we propose an ecological resilience point of view on cancer.
This view is based on the analysis of a simple ODE model for the interactions
between cancer and normal cells. The model presents two regimes for tumor
growth. In the first, cancer arises due to three reasons: a partial corruption
of the funct... | [
{
"created": "Fri, 29 Apr 2016 17:43:41 GMT",
"version": "v1"
},
{
"created": "Wed, 31 Aug 2016 19:37:47 GMT",
"version": "v2"
}
] | 2016-09-01 | [
[
"Fassoni",
"Artur C.",
""
],
[
"Yang",
"Hyun M.",
""
]
] | In this paper we propose an ecological resilience point of view on cancer. This view is based on the analysis of a simple ODE model for the interactions between cancer and normal cells. The model presents two regimes for tumor growth. In the first, cancer arises due to three reasons: a partial corruption of the functio... |
q-bio/0501025 | Fabio De Blasio | Birgitte Freiesleben De Blasio, Fabio Vittorio De Blasio | Dynamics of competing species in a model of adaptive radiations and
macroevolution | null | null | null | null | q-bio.PE | null | We present a simple model of adaptive radiations in evolution based on
species competition. Competition is found to promote species divergence and
branching, and to dampen the net species production. In the model simulations,
high taxonomic diversification and branching take place during the beginning of
the radiatio... | [
{
"created": "Tue, 18 Jan 2005 19:15:19 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"De Blasio",
"Birgitte Freiesleben",
""
],
[
"De Blasio",
"Fabio Vittorio",
""
]
] | We present a simple model of adaptive radiations in evolution based on species competition. Competition is found to promote species divergence and branching, and to dampen the net species production. In the model simulations, high taxonomic diversification and branching take place during the beginning of the radiation.... |
2206.09398 | Alexis Thual | Alexis Thual, Huy Tran, Tatiana Zemskova, Nicolas Courty, R\'emi
Flamary, Stanislas Dehaene, Bertrand Thirion | Aligning individual brains with Fused Unbalanced Gromov-Wasserstein | null | Advances in Neural Information Processing Systems, 35 (2022)
21792-21804 | null | null | q-bio.NC stat.ML | http://creativecommons.org/licenses/by/4.0/ | Individual brains vary in both anatomy and functional organization, even
within a given species. Inter-individual variability is a major impediment when
trying to draw generalizable conclusions from neuroimaging data collected on
groups of subjects. Current co-registration procedures rely on limited data,
and thus le... | [
{
"created": "Sun, 19 Jun 2022 13:06:11 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Nov 2022 16:38:23 GMT",
"version": "v2"
},
{
"created": "Tue, 22 Aug 2023 23:02:57 GMT",
"version": "v3"
}
] | 2023-09-28 | [
[
"Thual",
"Alexis",
""
],
[
"Tran",
"Huy",
""
],
[
"Zemskova",
"Tatiana",
""
],
[
"Courty",
"Nicolas",
""
],
[
"Flamary",
"Rémi",
""
],
[
"Dehaene",
"Stanislas",
""
],
[
"Thirion",
"Bertrand",
""
]
] | Individual brains vary in both anatomy and functional organization, even within a given species. Inter-individual variability is a major impediment when trying to draw generalizable conclusions from neuroimaging data collected on groups of subjects. Current co-registration procedures rely on limited data, and thus lead... |
1509.02450 | Olivier Rivoire | S\'ebastien Boyer, Dipanwita Biswas, Ananda Kumar Soshee, Natale
Scaramozzino, Cl\'ement Nizak, Olivier Rivoire | Hierarchy and extremes in selections from pools of randomized proteins | null | null | 10.1073/pnas.1517813113 | null | q-bio.PE q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Variation and selection are the core principles of Darwinian evolution, yet
quantitatively relating the diversity of a population to its capacity to
respond to selection is challenging. Here, we examine this problem at a
molecular level in the context of populations of partially randomized proteins
selected for bindi... | [
{
"created": "Tue, 8 Sep 2015 17:14:46 GMT",
"version": "v1"
}
] | 2016-04-27 | [
[
"Boyer",
"Sébastien",
""
],
[
"Biswas",
"Dipanwita",
""
],
[
"Soshee",
"Ananda Kumar",
""
],
[
"Scaramozzino",
"Natale",
""
],
[
"Nizak",
"Clément",
""
],
[
"Rivoire",
"Olivier",
""
]
] | Variation and selection are the core principles of Darwinian evolution, yet quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in the context of populations of partially randomized proteins selected for binding... |
2008.04172 | Sara Hamis | Sara J Hamis, Fiona R Macfarlane | A single-cell mathematical model of SARS-CoV-2 induced pyroptosis and
the effects of anti-inflammatory intervention | 35 pages including the appendix, 9 figures in the main manuscript,
Supporting Information (PDF) included | null | null | null | q-bio.SC | http://creativecommons.org/licenses/by/4.0/ | Pyroptosis is an inflammatory mode of cell death that can contribute to the
cytokine storm associated with severe cases of coronavirus disease 2019
(COVID-19). The formation of the NLRP3 inflammasome is central to pyroptosis,
which may be induced by severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2). Inflam... | [
{
"created": "Mon, 10 Aug 2020 14:51:34 GMT",
"version": "v1"
},
{
"created": "Wed, 2 Dec 2020 22:13:25 GMT",
"version": "v2"
},
{
"created": "Tue, 23 Mar 2021 15:37:33 GMT",
"version": "v3"
},
{
"created": "Mon, 29 Mar 2021 14:26:51 GMT",
"version": "v4"
}
] | 2021-03-30 | [
[
"Hamis",
"Sara J",
""
],
[
"Macfarlane",
"Fiona R",
""
]
] | Pyroptosis is an inflammatory mode of cell death that can contribute to the cytokine storm associated with severe cases of coronavirus disease 2019 (COVID-19). The formation of the NLRP3 inflammasome is central to pyroptosis, which may be induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Inflamma... |
1305.5369 | Daniel Remondini | G. Menichetti, G. Bianconi, E. Giampieri, G. Castellani, D. Remondini | Network Entropy measures applied to different systemic perturbations of
cell basal state | NOTE: includes supplementary material | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We characterize different cell states, related to cancer and ageing
phenotypes, by a measure of entropy of network ensembles, integrating gene
expression values and protein interaction networks. The entropy measure
estimates the parameter space available to the network ensemble, that can be
interpreted as the level o... | [
{
"created": "Thu, 23 May 2013 10:29:30 GMT",
"version": "v1"
}
] | 2013-05-24 | [
[
"Menichetti",
"G.",
""
],
[
"Bianconi",
"G.",
""
],
[
"Giampieri",
"E.",
""
],
[
"Castellani",
"G.",
""
],
[
"Remondini",
"D.",
""
]
] | We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter space available to the network ensemble, that can be interpreted as the level of ... |
1109.1108 | Marco Chierici | Marco Chierici and Giuseppe Jurman and Marco Roncador and Cesare
Furlanello | Single-base mismatch profiles for NGS samples | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Within the preprocessing pipeline of a Next Generation Sequencing sample, its
set of Single-Base Mismatches is one of the first outcomes, together with the
number of correctly aligned reads. The union of these two sets provides a 4x4
matrix (called Single Base Indicator, SBI in what follows) representing a
blueprint ... | [
{
"created": "Tue, 6 Sep 2011 08:25:14 GMT",
"version": "v1"
}
] | 2011-09-07 | [
[
"Chierici",
"Marco",
""
],
[
"Jurman",
"Giuseppe",
""
],
[
"Roncador",
"Marco",
""
],
[
"Furlanello",
"Cesare",
""
]
] | Within the preprocessing pipeline of a Next Generation Sequencing sample, its set of Single-Base Mismatches is one of the first outcomes, together with the number of correctly aligned reads. The union of these two sets provides a 4x4 matrix (called Single Base Indicator, SBI in what follows) representing a blueprint of... |
1611.06834 | Laurent Perrinet | Cesar Ravello (CINV), Maria-Jose Escobar, Adrian Palacios (CINV),
Laurent Perrinet (INT) | Differential response of the retinal neural code with respect to the
sparseness of natural images | arXiv admin note: substantial text overlap with arXiv:1702.02485 | null | 10.5281/zenodo.5823016 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Natural images follow statistics inherited by the structure of our physical
(visual) environment. In particular, a prominent facet of this structure is
that images can be described by a relatively sparse number of features. To
investigate the role of this sparseness in the efficiency of the neural code,
we designed a... | [
{
"created": "Mon, 21 Nov 2016 15:28:16 GMT",
"version": "v1"
},
{
"created": "Wed, 5 Jan 2022 19:53:44 GMT",
"version": "v2"
}
] | 2022-01-07 | [
[
"Ravello",
"Cesar",
"",
"CINV"
],
[
"Escobar",
"Maria-Jose",
"",
"CINV"
],
[
"Palacios",
"Adrian",
"",
"CINV"
],
[
"Perrinet",
"Laurent",
"",
"INT"
]
] | Natural images follow statistics inherited by the structure of our physical (visual) environment. In particular, a prominent facet of this structure is that images can be described by a relatively sparse number of features. To investigate the role of this sparseness in the efficiency of the neural code, we designed a n... |
q-bio/0401041 | Thorsten Poeschel | Thorsten Poeschel, Cornelius Froemmel, Christoph Gille | Online tool for the discrimination of equi-distributions | 12 pages, 8 figures | BMC Bioinformatics, Vol. 4, 580 (2003) | null | null | q-bio.GN cond-mat.stat-mech | null | For many applications one wishes to decide whether a certain set of numbers
originates from an equiprobability distribution or whether they are unequally
distributed. Distributions of relative frequencies may deviate significantly
from the corresponding probability distributions due to finite sample effects.
Hence, i... | [
{
"created": "Wed, 28 Jan 2004 14:06:57 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Poeschel",
"Thorsten",
""
],
[
"Froemmel",
"Cornelius",
""
],
[
"Gille",
"Christoph",
""
]
] | For many applications one wishes to decide whether a certain set of numbers originates from an equiprobability distribution or whether they are unequally distributed. Distributions of relative frequencies may deviate significantly from the corresponding probability distributions due to finite sample effects. Hence, it ... |
2004.03806 | Dweipayan Goswami Dr. | Priyashi Rao, Arpit Shukla, Paritosh Parmar, Dweipayan Goswami | Proposing a fungal metabolite-Flaviolin as a potential inhibitor of
3CLpro of novel coronavirus SARS-CoV2 using docking and molecular dynamics | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here after performing docking and molecular dynamics of various small
molecules derived as a secondary metabolite from fungi, we propose Flaviolin to
act as potent inhibitor of 3-chymotrypsin (3C) like protease (3CLpro) of noval
corona virus SARS-CoV2 responsible for pandemic condition caused by coronavirus
disease 2... | [
{
"created": "Wed, 8 Apr 2020 04:37:03 GMT",
"version": "v1"
}
] | 2020-04-09 | [
[
"Rao",
"Priyashi",
""
],
[
"Shukla",
"Arpit",
""
],
[
"Parmar",
"Paritosh",
""
],
[
"Goswami",
"Dweipayan",
""
]
] | Here after performing docking and molecular dynamics of various small molecules derived as a secondary metabolite from fungi, we propose Flaviolin to act as potent inhibitor of 3-chymotrypsin (3C) like protease (3CLpro) of noval corona virus SARS-CoV2 responsible for pandemic condition caused by coronavirus disease 201... |
0908.0339 | Robert Hilborn | Robert C. Hilborn and Jessie D. Erwin | Stochastic Coherence in an Oscillatory Gene Circuit Model | null | J. Theor. Biology 253 (2008) 349 | 10.1016/j.jtbi.2008.03.012 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show that noise-induced oscillations in a gene circuit model display
stochastic coherence, that is, a maximum in the regularity of the oscillations
as a function of noise amplitude. The effect is manifest as a system-size
effect in a purely stochastic molecular reaction description of the circuit
dynamics. We comp... | [
{
"created": "Mon, 3 Aug 2009 20:18:43 GMT",
"version": "v1"
}
] | 2009-08-05 | [
[
"Hilborn",
"Robert C.",
""
],
[
"Erwin",
"Jessie D.",
""
]
] | We show that noise-induced oscillations in a gene circuit model display stochastic coherence, that is, a maximum in the regularity of the oscillations as a function of noise amplitude. The effect is manifest as a system-size effect in a purely stochastic molecular reaction description of the circuit dynamics. We compar... |
2309.02343 | Stefan Schuster | Stefan Schuster and Tatjana Malycheva | Enumeration of saturated and unsaturated substituted N-heterocycles | 11 pages, 4 figures | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Mathematical and computational approaches in chemistry and biochemistry fill
a gap in respect to the analysis of the physicochemical features of compounds
and their functionality and provide an overview of known as well as yet
unknown, but hypothetically possible structures. Nitrogen containing
heterocycles such as a... | [
{
"created": "Tue, 5 Sep 2023 15:59:41 GMT",
"version": "v1"
}
] | 2023-09-06 | [
[
"Schuster",
"Stefan",
""
],
[
"Malycheva",
"Tatjana",
""
]
] | Mathematical and computational approaches in chemistry and biochemistry fill a gap in respect to the analysis of the physicochemical features of compounds and their functionality and provide an overview of known as well as yet unknown, but hypothetically possible structures. Nitrogen containing heterocycles such as azi... |
1706.03839 | Aya Kabbara | Aya Kabbara, Mahmoud Hassan, Mohamad Khalil, Wassim El Falou, Hassan
Eid | A scalp-EEG network-based analysis of Alzheimer's disease patients at
rest | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most brain disorders including Alzheimer's disease (AD) are related to
alterations in the normal brain network organization and function. Exploring
these network alterations using non-invasive and easy to use technique is a
topic of great interest. In this paper, we collected EEG resting-state data
from AD patients a... | [
{
"created": "Mon, 12 Jun 2017 20:27:48 GMT",
"version": "v1"
}
] | 2017-06-14 | [
[
"Kabbara",
"Aya",
""
],
[
"Hassan",
"Mahmoud",
""
],
[
"Khalil",
"Mohamad",
""
],
[
"Falou",
"Wassim El",
""
],
[
"Eid",
"Hassan",
""
]
] | Most brain disorders including Alzheimer's disease (AD) are related to alterations in the normal brain network organization and function. Exploring these network alterations using non-invasive and easy to use technique is a topic of great interest. In this paper, we collected EEG resting-state data from AD patients and... |
2306.11965 | Nima Dehghani | Nima Dehghani | Symmetry's Edge in Cortical Dynamics: Multiscale Dynamics of Ensemble
Excitation and Inhibition | null | null | null | null | q-bio.NC cond-mat.dis-nn nlin.AO physics.bio-ph | http://creativecommons.org/licenses/by-sa/4.0/ | Creating a quantitative theory for the cortex poses several challenges and
raises numerous questions. For instance, what are the significant scales of the
system? Are they micro, meso or macroscopic? What are the relevant
interactions? Are they pairwise, higher order or mean-field? And what are the
control parameters... | [
{
"created": "Wed, 21 Jun 2023 01:38:42 GMT",
"version": "v1"
},
{
"created": "Thu, 4 Jan 2024 23:32:12 GMT",
"version": "v2"
},
{
"created": "Thu, 4 Jul 2024 17:33:21 GMT",
"version": "v3"
}
] | 2024-07-08 | [
[
"Dehghani",
"Nima",
""
]
] | Creating a quantitative theory for the cortex poses several challenges and raises numerous questions. For instance, what are the significant scales of the system? Are they micro, meso or macroscopic? What are the relevant interactions? Are they pairwise, higher order or mean-field? And what are the control parameters? ... |
q-bio/0604004 | Giuseppe Gaeta | G. Gaeta | Solitons in Yakushevich-like models of DNA dynamics with improved
intrapair potential | null | J. Nonlin. Math. Phys. 14 (2007), 57-81 | 10.2991/jnmp.2007.14.1.6 | null | q-bio.BM | null | The Yakushevich (Y) model provides a very simple pictures of DNA torsion
dynamics, yet yields remarkably correct predictions on certain physical
characteristics of the dynamics. In the standard Y model, the interaction
between bases of a pair is modelled by a harmonic potential, which becomes
anharmonic when describe... | [
{
"created": "Tue, 4 Apr 2006 13:33:08 GMT",
"version": "v1"
}
] | 2015-06-26 | [
[
"Gaeta",
"G.",
""
]
] | The Yakushevich (Y) model provides a very simple pictures of DNA torsion dynamics, yet yields remarkably correct predictions on certain physical characteristics of the dynamics. In the standard Y model, the interaction between bases of a pair is modelled by a harmonic potential, which becomes anharmonic when described ... |
2210.13564 | Alfonso Nieto-Castanon | Alfonso Nieto-Castanon | Preparing fMRI Data for Statistical Analysis | null | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This chapter describes several procedures used to prepare fMRI data for
statistical analyses. It includes the description of common preprocessing
steps, such as spatial realignment, coregistration, and spatial normalization,
aimed at the spatial alignment of all fMRI data within- and between- subjects,
as well as sev... | [
{
"created": "Mon, 24 Oct 2022 19:38:45 GMT",
"version": "v1"
}
] | 2022-10-26 | [
[
"Nieto-Castanon",
"Alfonso",
""
]
] | This chapter describes several procedures used to prepare fMRI data for statistical analyses. It includes the description of common preprocessing steps, such as spatial realignment, coregistration, and spatial normalization, aimed at the spatial alignment of all fMRI data within- and between- subjects, as well as sever... |
1802.05539 | Irina Kareva | Irina Kareva | Using mathematical modeling to ask meaningful biological questions
through combination of bifurcation analysis and population heterogeneity | 26 pages, 9 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Classical approaches to analyzing dynamical systems, including bifurcation
analysis, can provide invaluable insights into underlying structure of a
mathematical model, and the spectrum of all possible dynamical behaviors.
However, these models frequently fail to take into account population
heterogeneity, which, whil... | [
{
"created": "Thu, 15 Feb 2018 14:15:30 GMT",
"version": "v1"
}
] | 2018-02-16 | [
[
"Kareva",
"Irina",
""
]
] | Classical approaches to analyzing dynamical systems, including bifurcation analysis, can provide invaluable insights into underlying structure of a mathematical model, and the spectrum of all possible dynamical behaviors. However, these models frequently fail to take into account population heterogeneity, which, while ... |
1209.0312 | Spyros Papageorgiou Dr | Spyros Papageorgiou | An explanation of unexpected Hoxd expressions in mutant mice | 11 pages, 2 figures | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Hox gene collinearity enigma has often been approached using models based
on biomolecular mechanisms. The biophysical model, is an alternative approach,
speculating that collinearity is caused by physical forces pulling the Hox
clusters from a territory where they are inactive to a distinct spatial domain
where t... | [
{
"created": "Mon, 3 Sep 2012 11:41:06 GMT",
"version": "v1"
}
] | 2012-09-04 | [
[
"Papageorgiou",
"Spyros",
""
]
] | The Hox gene collinearity enigma has often been approached using models based on biomolecular mechanisms. The biophysical model, is an alternative approach, speculating that collinearity is caused by physical forces pulling the Hox clusters from a territory where they are inactive to a distinct spatial domain where the... |
2110.04892 | Eitan Asher Mr. | Eitan E. Asher, Maya Slovik, Rae Mitelman, Hagai Bergman, Shlomo
Havlin and Shay Moshel | Local Field Potential Journey into the Basal Ganglia | null | null | null | null | q-bio.NC physics.data-an | http://creativecommons.org/licenses/by/4.0/ | Local Field potential (LFP) in the basal ganglia (BG) nuclei in the brain
have attracted much research and clinical interest. However, the origin of this
signal is still under debate throughout the last decades. The question is
whether it is a local subthreshold phenomenon, synaptic input to neurons or it
is a flow o... | [
{
"created": "Sun, 10 Oct 2021 20:17:53 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Dec 2021 14:29:34 GMT",
"version": "v2"
},
{
"created": "Wed, 16 Feb 2022 11:17:18 GMT",
"version": "v3"
},
{
"created": "Wed, 19 Oct 2022 05:59:11 GMT",
"version": "v4"
}
] | 2022-10-20 | [
[
"Asher",
"Eitan E.",
""
],
[
"Slovik",
"Maya",
""
],
[
"Mitelman",
"Rae",
""
],
[
"Bergman",
"Hagai",
""
],
[
"Havlin",
"Shlomo",
""
],
[
"Moshel",
"Shay",
""
]
] | Local Field potential (LFP) in the basal ganglia (BG) nuclei in the brain have attracted much research and clinical interest. However, the origin of this signal is still under debate throughout the last decades. The question is whether it is a local subthreshold phenomenon, synaptic input to neurons or it is a flow of ... |
1905.12570 | James Yearsley | James M Yearsley and Jonathan J Halliwell | Contextuality in Human Decision Making in the Presence of Direct
Influences: A Comment on Basieva et al. (2019) | 5 pages. V2: Substantial Revisions | null | null | null | q-bio.NC quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a recent paper Basieva, Cervantes, Dzhafarov, and Khrennikov (2019)
presented a series of experiments which they claimed show evidence for
contextuality in human judgments. This was based on a set of modified Bell-like
inequalities designed to rule out effects caused by signalling. In this comment
we show that it ... | [
{
"created": "Tue, 7 May 2019 14:19:59 GMT",
"version": "v1"
},
{
"created": "Fri, 11 Oct 2019 12:16:36 GMT",
"version": "v2"
}
] | 2019-10-14 | [
[
"Yearsley",
"James M",
""
],
[
"Halliwell",
"Jonathan J",
""
]
] | In a recent paper Basieva, Cervantes, Dzhafarov, and Khrennikov (2019) presented a series of experiments which they claimed show evidence for contextuality in human judgments. This was based on a set of modified Bell-like inequalities designed to rule out effects caused by signalling. In this comment we show that it is... |
1611.05137 | Takahiro Ezaki | Takahiro Ezaki, Takamitsu Watanabe, Masayuki Ohzeki, Naoki Masuda | Energy landscape analysis of neuroimaging data | 22 pages, 4 figures, 1 table | Phil. Trans. R. Soc. A 375, 20160287 (2017) | 10.1098/rsta.2016.0287 | null | q-bio.NC cond-mat.stat-mech physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Computational neuroscience models have been used for understanding neural
dynamics in the brain and how they may be altered when physiological or other
conditions change. We review and develop a data-driven approach to neuroimaging
data called the energy landscape analysis. The methods are rooted in
statistical physi... | [
{
"created": "Wed, 16 Nov 2016 04:17:12 GMT",
"version": "v1"
},
{
"created": "Thu, 25 May 2017 14:01:27 GMT",
"version": "v2"
}
] | 2017-05-26 | [
[
"Ezaki",
"Takahiro",
""
],
[
"Watanabe",
"Takamitsu",
""
],
[
"Ohzeki",
"Masayuki",
""
],
[
"Masuda",
"Naoki",
""
]
] | Computational neuroscience models have been used for understanding neural dynamics in the brain and how they may be altered when physiological or other conditions change. We review and develop a data-driven approach to neuroimaging data called the energy landscape analysis. The methods are rooted in statistical physics... |
1305.3544 | Florian Hartig | Florian Hartig and Carsten F. Dormann | Does "model-free" forecasting really outperform the "true" model? A
reply to Perretti et al | Letter submitted to PNAS, with additional supplementary information.
R code included in the latex source | Proceedings of the National Academy of Sciences, 110, E3975, 2013 | 10.1073/pnas.1308603110 | null | q-bio.PE nlin.CD stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Estimating population models from uncertain observations is an important
problem in ecology. Perretti et al. observed that standard Bayesian state-space
solutions to this problem may provide biased parameter estimates when the
underlying dynamics are chaotic. Consequently, forecasts based on these
estimates showed po... | [
{
"created": "Wed, 15 May 2013 17:01:13 GMT",
"version": "v1"
}
] | 2013-10-28 | [
[
"Hartig",
"Florian",
""
],
[
"Dormann",
"Carsten F.",
""
]
] | Estimating population models from uncertain observations is an important problem in ecology. Perretti et al. observed that standard Bayesian state-space solutions to this problem may provide biased parameter estimates when the underlying dynamics are chaotic. Consequently, forecasts based on these estimates showed poor... |
2104.01589 | Guy Katriel | Guy Katriel | Dispersal-induced growth in a time-periodic environment | null | J. Math. Biol. 85, 24 (2022) | 10.1007/s00285-022-01791-7 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dispersal-induced growth (DIG) occurs when two populations with time-varying
growth rates, each of which, when isolated, would become extinct, are able to
persist and grow exponentially when dispersal among the two populations is
present. This work provides a mathematical exploration of this surprising
phenomenon, in... | [
{
"created": "Sun, 4 Apr 2021 11:29:53 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Apr 2021 14:52:42 GMT",
"version": "v2"
},
{
"created": "Sat, 10 Jul 2021 05:02:07 GMT",
"version": "v3"
},
{
"created": "Thu, 28 Apr 2022 05:14:08 GMT",
"version": "v4"
}
] | 2022-08-31 | [
[
"Katriel",
"Guy",
""
]
] | Dispersal-induced growth (DIG) occurs when two populations with time-varying growth rates, each of which, when isolated, would become extinct, are able to persist and grow exponentially when dispersal among the two populations is present. This work provides a mathematical exploration of this surprising phenomenon, in t... |
q-bio/0703001 | Sidney Redner | T. Antal, P. L. Krapivsky, S. Redner, M. Mailman, B. Chakraborty | Dynamics of Microtubule Growth and Catastrophe | 12 pages, 6 figures, 2-column revtex4; version 2: published version
for PRE; contains various small changes in response to referee comments | Phys. Rev. E 76, 041907 (2007) | 10.1103/PhysRevE.76.041907 | null | q-bio.QM cond-mat.stat-mech physics.bio-ph q-bio.BM | null | We investigate a simple model of microtubule dynamics in which a microtubule
evolves by: (i) attachment of guanosine triphosphate (GTP) to its end at rate
lambda, (ii) GTP converting irreversibly to guanosine diphosphate (GDP) at rate
1, and (iii) detachment of GDP from the end of a microtubule at rate mu. As a
funct... | [
{
"created": "Thu, 1 Mar 2007 19:41:08 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Apr 2008 23:55:13 GMT",
"version": "v2"
}
] | 2008-04-23 | [
[
"Antal",
"T.",
""
],
[
"Krapivsky",
"P. L.",
""
],
[
"Redner",
"S.",
""
],
[
"Mailman",
"M.",
""
],
[
"Chakraborty",
"B.",
""
]
] | We investigate a simple model of microtubule dynamics in which a microtubule evolves by: (i) attachment of guanosine triphosphate (GTP) to its end at rate lambda, (ii) GTP converting irreversibly to guanosine diphosphate (GDP) at rate 1, and (iii) detachment of GDP from the end of a microtubule at rate mu. As a functio... |
1502.02442 | Angelika Manhart | Angelika Manhart, Christian Schmeiser, Nikolaos Sfakianakis, Dietmar
Oelz | An Extended Filament Based Lamellipodium Model Produces Various Moving
Cell Shapes in the Presence of Chemotactic Signals | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Filament Based Lamellipodium Model (FBLM) is a two-phase two-dimensional
continuum model, describing the dynamcis of two interacting families of locally
parallel actin filaments (C.Schmeiser and D.Oelz, How do cells move?
Mathematical modeling of cytoskeleton dynamics and cell migration. Cell
mechanics: from sing... | [
{
"created": "Mon, 9 Feb 2015 11:26:13 GMT",
"version": "v1"
}
] | 2015-02-10 | [
[
"Manhart",
"Angelika",
""
],
[
"Schmeiser",
"Christian",
""
],
[
"Sfakianakis",
"Nikolaos",
""
],
[
"Oelz",
"Dietmar",
""
]
] | The Filament Based Lamellipodium Model (FBLM) is a two-phase two-dimensional continuum model, describing the dynamcis of two interacting families of locally parallel actin filaments (C.Schmeiser and D.Oelz, How do cells move? Mathematical modeling of cytoskeleton dynamics and cell migration. Cell mechanics: from single... |
1405.7963 | Fabien Campillo | Coralie Fritsch (INRIA Sophia Antipolis, MISTEA, I3M), J\'er\^ome
Harmand (INRIA Sophia Antipolis, LBE), Fabien Campillo (INRIA Sophia
Antipolis, MISTEA) | A modeling approach of the chemostat | arXiv admin note: substantial text overlap with arXiv:1308.2411 | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Population dynamics and in particular microbial population dynamics, though
they are complex but also intrinsically discrete and random, are conventionally
represented as deterministic differential equations systems. We propose to
revisit this approach by complementing these classic formalisms by stochastic
formalism... | [
{
"created": "Fri, 30 May 2014 19:30:15 GMT",
"version": "v1"
}
] | 2014-06-02 | [
[
"Fritsch",
"Coralie",
"",
"INRIA Sophia Antipolis, MISTEA, I3M"
],
[
"Harmand",
"Jérôme",
"",
"INRIA Sophia Antipolis, LBE"
],
[
"Campillo",
"Fabien",
"",
"INRIA Sophia\n Antipolis, MISTEA"
]
] | Population dynamics and in particular microbial population dynamics, though they are complex but also intrinsically discrete and random, are conventionally represented as deterministic differential equations systems. We propose to revisit this approach by complementing these classic formalisms by stochastic formalisms ... |
1608.00108 | Roland Kr\"amer | Ulrich Warttinger, Christina Giese, Job Harenberg, Roland Kr\"amer | Direct quantification of brown algae-derived fucoidans in human plasma
by a fluorescent probe assay | article, 15 pages, 2 schemes, 3 figures, 3 tables | null | null | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fucoidan is a generic term for a class of fucose rich, structurally diverse
sulfated polysaccharides that are found in brown algae and other marine
organisms. Depending on the species from which the fucoidan is extracted, a
wide variety of biological activities including antitumor, antiinflammatory,
immune-modulating... | [
{
"created": "Sat, 30 Jul 2016 12:06:19 GMT",
"version": "v1"
}
] | 2016-08-02 | [
[
"Warttinger",
"Ulrich",
""
],
[
"Giese",
"Christina",
""
],
[
"Harenberg",
"Job",
""
],
[
"Krämer",
"Roland",
""
]
] | Fucoidan is a generic term for a class of fucose rich, structurally diverse sulfated polysaccharides that are found in brown algae and other marine organisms. Depending on the species from which the fucoidan is extracted, a wide variety of biological activities including antitumor, antiinflammatory, immune-modulating, ... |
2201.08714 | Shuwen Yang | Shuwen Yang, Tianyu Wen, Ziyao Li and Guojie Song | Equivalent Distance Geometry Error for Molecular Conformation Comparison | null | null | null | null | q-bio.BM cs.LG physics.chem-ph | http://creativecommons.org/licenses/by/4.0/ | Straight-forward conformation generation models, which generate 3-D
structures directly from input molecular graphs, play an important role in
various molecular tasks with machine learning, such as 3D-QSAR and virtual
screening in drug design. However, existing loss functions in these models
either cost overmuch time... | [
{
"created": "Sat, 13 Nov 2021 09:04:55 GMT",
"version": "v1"
},
{
"created": "Tue, 15 Mar 2022 04:39:32 GMT",
"version": "v2"
}
] | 2022-03-16 | [
[
"Yang",
"Shuwen",
""
],
[
"Wen",
"Tianyu",
""
],
[
"Li",
"Ziyao",
""
],
[
"Song",
"Guojie",
""
]
] | Straight-forward conformation generation models, which generate 3-D structures directly from input molecular graphs, play an important role in various molecular tasks with machine learning, such as 3D-QSAR and virtual screening in drug design. However, existing loss functions in these models either cost overmuch time o... |
2204.11843 | Yuanxiang Gao | Yuanxiang Gao | A Computational Theory of Learning Flexible Reward-Seeking Behavior with
Place Cells | 14 pages, 23 figures | null | null | null | q-bio.NC cs.AI cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An important open question in computational neuroscience is how various
spatially tuned neurons, such as place cells, are used to support the learning
of reward-seeking behavior of an animal. Existing computational models either
lack biological plausibility or fall short of behavioral flexibility when
environments ch... | [
{
"created": "Fri, 22 Apr 2022 16:06:44 GMT",
"version": "v1"
},
{
"created": "Tue, 17 May 2022 05:39:54 GMT",
"version": "v2"
}
] | 2022-05-18 | [
[
"Gao",
"Yuanxiang",
""
]
] | An important open question in computational neuroscience is how various spatially tuned neurons, such as place cells, are used to support the learning of reward-seeking behavior of an animal. Existing computational models either lack biological plausibility or fall short of behavioral flexibility when environments chan... |
2310.17226 | Francois Boue | Maja Napieraj (MMB), Annie Br\^ulet (MMB), Javier Perez, Fran\c{c}ois
Bou\'e (MMB), Evelyne Lutton | In situ digestion of canola protein gel observed by synchrotron X-Ray
Scattering | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We address the issue of structure changes of a canola protein gel (as a solid
food model) during gastrointestinal digestion. We present a method for
synchrotron Small-Angle X-ray Scattering analysis of the digestion of a gel in
a capillary. Scanning the capillary allows tracking the digestion under
diffusion of enzym... | [
{
"created": "Thu, 26 Oct 2023 08:24:15 GMT",
"version": "v1"
}
] | 2023-10-27 | [
[
"Napieraj",
"Maja",
"",
"MMB"
],
[
"Brûlet",
"Annie",
"",
"MMB"
],
[
"Perez",
"Javier",
"",
"MMB"
],
[
"Boué",
"François",
"",
"MMB"
],
[
"Lutton",
"Evelyne",
""
]
] | We address the issue of structure changes of a canola protein gel (as a solid food model) during gastrointestinal digestion. We present a method for synchrotron Small-Angle X-ray Scattering analysis of the digestion of a gel in a capillary. Scanning the capillary allows tracking the digestion under diffusion of enzymat... |
1309.2055 | Tomasz Rutkowski | Tomasz M. Rutkowski | Beyond visual P300 based brain-computer interfacing paradigms | 7 pages, 5 figures, Proceedings of the Third Postgraduate Consortium
International Workshop on Innovations in Information and Communication
Science and Technology, (E. Cooper, G. A. Kobzev, A. F. Uvarov, and V. V.
Kryssanov, eds.), (Tomsk, Russia), pp. 277-283, TUSUR and Ritsumeikan,
September 2-5, 2013. ISBN 9... | null | null | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The paper reviews and summarizes recent developments in spatial auditory and
tactile brain-computer interfacing neurotechology applications. It serves as
the latest developments summary in "non-visual" brain-computer interfacing
solutions presented in a tutorial delivered by the author at the IICST 2013
workshop. The... | [
{
"created": "Mon, 9 Sep 2013 07:18:17 GMT",
"version": "v1"
}
] | 2013-09-10 | [
[
"Rutkowski",
"Tomasz M.",
""
]
] | The paper reviews and summarizes recent developments in spatial auditory and tactile brain-computer interfacing neurotechology applications. It serves as the latest developments summary in "non-visual" brain-computer interfacing solutions presented in a tutorial delivered by the author at the IICST 2013 workshop. The n... |
1208.1604 | Sanzo Miyazawa | Sanzo Miyazawa | Inference of Co-Evolving Site Pairs: an Excellent Predictor of Contact
Residue Pairs in Protein 3D structures | 17 pages, 4 figures, and 4 tables with supplementary information of 5
figures | PLoS ONE 8(1): e54252, 2013 | 10.1371/journal.pone.0054252 | null | q-bio.BM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Residue-residue interactions that fold a protein into a unique
three-dimensional structure and make it play a specific function impose
structural and functional constraints on each residue site. Selective
constraints on residue sites are recorded in amino acid orders in homologous
sequences and also in the evolutiona... | [
{
"created": "Wed, 8 Aug 2012 07:50:05 GMT",
"version": "v1"
}
] | 2013-01-18 | [
[
"Miyazawa",
"Sanzo",
""
]
] | Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints on each residue site. Selective constraints on residue sites are recorded in amino acid orders in homologous sequences and also in the evolutionary... |
1110.6194 | Joseph Rusinko | Joe Rusinko, Brian Hipp | Invariant Based Quartet Puzzling | 9 pages 1 figure | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Traditional Quartet Puzzling algorithms use maximum likelihood methods to
reconstruct quartet trees, and a puzzling algorithm to combine these quartets
into a tree for the full collection of $n$ taxa. We propose a variation of
Quartet Puzzling in which the quartet trees are reconstructed using
biologically symmetric ... | [
{
"created": "Thu, 27 Oct 2011 20:27:58 GMT",
"version": "v1"
}
] | 2011-10-31 | [
[
"Rusinko",
"Joe",
""
],
[
"Hipp",
"Brian",
""
]
] | Traditional Quartet Puzzling algorithms use maximum likelihood methods to reconstruct quartet trees, and a puzzling algorithm to combine these quartets into a tree for the full collection of $n$ taxa. We propose a variation of Quartet Puzzling in which the quartet trees are reconstructed using biologically symmetric in... |
1309.3640 | Alain Barrat | Philippe Vanhems, Alain Barrat, Ciro Cattuto, Jean-Fran\c{c}ois
Pinton, Nagham Khanafer, Corinne R\'egis, Byeul-a Kim, Brigitte Comte,
Nicolas Voirin | Estimating Potential Infection Transmission Routes in Hospital Wards
Using Wearable Proximity Sensors | null | PLoS ONE 8(9): e73970 (2013) | 10.1371/journal.pone.0073970 | null | q-bio.QM physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Contacts between patients, patients and health care workers (HCWs) and among
HCWs represent one of the important routes of transmission of hospital-acquired
infections (HAI). A detailed description and quantification of contacts in
hospitals provides key information for HAIs epidemiology and for the design and
valida... | [
{
"created": "Sat, 14 Sep 2013 09:46:52 GMT",
"version": "v1"
}
] | 2013-09-17 | [
[
"Vanhems",
"Philippe",
""
],
[
"Barrat",
"Alain",
""
],
[
"Cattuto",
"Ciro",
""
],
[
"Pinton",
"Jean-François",
""
],
[
"Khanafer",
"Nagham",
""
],
[
"Régis",
"Corinne",
""
],
[
"Kim",
"Byeul-a",
""
],
... | Contacts between patients, patients and health care workers (HCWs) and among HCWs represent one of the important routes of transmission of hospital-acquired infections (HAI). A detailed description and quantification of contacts in hospitals provides key information for HAIs epidemiology and for the design and validati... |
2101.05546 | Sylvia N\"urnberg | Alexander Denker, Anastasia Steshina, Theresa Grooss, Frank Ueckert,
Sylvia N\"urnberg | Feature reduction for machine learning on molecular features: The
GeneScore | 11 pages, 9 figures, 4 tables | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We present the GeneScore, a concept of feature reduction for Machine Learning
analysis of biomedical data. Using expert knowledge, the GeneScore integrates
different molecular data types into a single score. We show that the GeneScore
is superior to a binary matrix in the classification of cancer entities from
SNV, I... | [
{
"created": "Thu, 14 Jan 2021 10:58:39 GMT",
"version": "v1"
}
] | 2021-01-15 | [
[
"Denker",
"Alexander",
""
],
[
"Steshina",
"Anastasia",
""
],
[
"Grooss",
"Theresa",
""
],
[
"Ueckert",
"Frank",
""
],
[
"Nürnberg",
"Sylvia",
""
]
] | We present the GeneScore, a concept of feature reduction for Machine Learning analysis of biomedical data. Using expert knowledge, the GeneScore integrates different molecular data types into a single score. We show that the GeneScore is superior to a binary matrix in the classification of cancer entities from SNV, Ind... |
0806.2181 | Lee Altenberg | Lee Altenberg | The Evolutionary Reduction Principle for Linear Variation in Genetic
Transmission | 22 pages, 1 figure | Bulletin of Mathematical Biology, Volume 71, Number 5, 1264-1284
(2009) | 10.1007/s11538-009-9401-2 | null | q-bio.PE math.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The evolution of genetic systems has been analyzed through the use of
modifier gene models, in which a neutral gene is posited to control the
transmission of other genes under selection. Analysis of modifier gene models
has found the manifestations of an "evolutionary reduction principle": in a
population near equili... | [
{
"created": "Fri, 13 Jun 2008 03:56:42 GMT",
"version": "v1"
}
] | 2013-02-04 | [
[
"Altenberg",
"Lee",
""
]
] | The evolution of genetic systems has been analyzed through the use of modifier gene models, in which a neutral gene is posited to control the transmission of other genes under selection. Analysis of modifier gene models has found the manifestations of an "evolutionary reduction principle": in a population near equilibr... |
1812.06234 | Yogatheesan Varatharajah | Yogatheesan Varatharajah, Brent Berry, Jan Cimbalnik, Vaclav Kremen,
Jamie Van Gompel, Matt Stead, Benjamin Brinkmann, Ravishankar Iyer, and
Gregory Worrell | Integrating Artificial Intelligence with Real-time Intracranial EEG
Monitoring to Automate Interictal Identification of Seizure Onset Zones in
Focal Epilepsy | 25 pages, Journal of neural engineering (2018) | null | 10.1088/1741-2552/aac960 | null | q-bio.NC cs.AI q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An ability to map seizure-generating brain tissue, i.e., the seizure onset
zone (SOZ), without recording actual seizures could reduce the duration of
invasive EEG monitoring for patients with drug-resistant epilepsy. A
widely-adopted practice in the literature is to compare the incidence
(events/time) of putative pat... | [
{
"created": "Sat, 15 Dec 2018 05:15:40 GMT",
"version": "v1"
}
] | 2018-12-18 | [
[
"Varatharajah",
"Yogatheesan",
""
],
[
"Berry",
"Brent",
""
],
[
"Cimbalnik",
"Jan",
""
],
[
"Kremen",
"Vaclav",
""
],
[
"Van Gompel",
"Jamie",
""
],
[
"Stead",
"Matt",
""
],
[
"Brinkmann",
"Benjamin",
""
... | An ability to map seizure-generating brain tissue, i.e., the seizure onset zone (SOZ), without recording actual seizures could reduce the duration of invasive EEG monitoring for patients with drug-resistant epilepsy. A widely-adopted practice in the literature is to compare the incidence (events/time) of putative patho... |
2010.12600 | William Lemaire | William Lemaire (1), Maher Benhouria (1), Konin Koua (1), Wei Tong
(2), Gabriel Martin-Hardy (1), Melanie Stamp (3), Kumaravelu Ganesan (3),
Louis-Philippe Gauthier (1), Marwan Besrour (1), Arman Ahnood (4), David John
Garrett (4), S\'ebastien Roy (1), Michael Ibbotson (2,5), Steven Prawer (3),
R\'ejean Fontain... | Feasibility Assessment of an Optically Powered Digital Retinal
Prosthesis Architecture for Retinal Ganglion Cell Stimulation | 11 pages, 13 figures | null | null | null | q-bio.NC cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Clinical trials previously demonstrated the notable capacity to elicit visual
percepts in blind patients affected with retinal diseases by electrically
stimulating the remaining neurons on the retina. However, these implants
restored very limited visual acuity and required transcutaneous cables
traversing the eyeball... | [
{
"created": "Fri, 23 Oct 2020 18:11:56 GMT",
"version": "v1"
},
{
"created": "Fri, 13 Oct 2023 14:23:52 GMT",
"version": "v2"
}
] | 2023-10-16 | [
[
"Lemaire",
"William",
""
],
[
"Benhouria",
"Maher",
""
],
[
"Koua",
"Konin",
""
],
[
"Tong",
"Wei",
""
],
[
"Martin-Hardy",
"Gabriel",
""
],
[
"Stamp",
"Melanie",
""
],
[
"Ganesan",
"Kumaravelu",
""
],
... | Clinical trials previously demonstrated the notable capacity to elicit visual percepts in blind patients affected with retinal diseases by electrically stimulating the remaining neurons on the retina. However, these implants restored very limited visual acuity and required transcutaneous cables traversing the eyeball, ... |
1902.11236 | Melisa B Maidana Capitan | Melisa Maidana Capit\'an, Nuria C\'ampora, Claudio Sebasti\'an,
Sigvard Silvia Kochen, In\'es Samengo | Time- and frequency-resolved covariance analysis for detection and
characterization of seizures from intracraneal EEG recordings | 21 pages, 4 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The amount of power in different frequency bands of the electroencephalogram
(EEG) carries information about the behavioral state of a subject. Hence,
neurologists treating epileptic patients monitor the temporal evolution of the
different bands. We propose a covariance-based method to detect and
characterize epilept... | [
{
"created": "Thu, 28 Feb 2019 17:35:43 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Jun 2020 18:43:45 GMT",
"version": "v2"
}
] | 2020-06-17 | [
[
"Capitán",
"Melisa Maidana",
""
],
[
"Cámpora",
"Nuria",
""
],
[
"Sebastián",
"Claudio",
""
],
[
"Kochen",
"Sigvard Silvia",
""
],
[
"Samengo",
"Inés",
""
]
] | The amount of power in different frequency bands of the electroencephalogram (EEG) carries information about the behavioral state of a subject. Hence, neurologists treating epileptic patients monitor the temporal evolution of the different bands. We propose a covariance-based method to detect and characterize epileptic... |
1712.05035 | Zvi Rosen | Zvi Rosen, Anand Bhaskar, Sebastien Roch, Yun S. Song | Geometry of the sample frequency spectrum and the perils of demographic
inference | 21 pages, 5 figures | null | null | null | q-bio.PE math.AG math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The sample frequency spectrum (SFS), which describes the distribution of
mutant alleles in a sample of DNA sequences, is a widely used summary statistic
in population genetics. The expected SFS has a strong dependence on the
historical population demography and this property is exploited by popular
statistical method... | [
{
"created": "Wed, 13 Dec 2017 22:52:21 GMT",
"version": "v1"
}
] | 2017-12-19 | [
[
"Rosen",
"Zvi",
""
],
[
"Bhaskar",
"Anand",
""
],
[
"Roch",
"Sebastien",
""
],
[
"Song",
"Yun S.",
""
]
] | The sample frequency spectrum (SFS), which describes the distribution of mutant alleles in a sample of DNA sequences, is a widely used summary statistic in population genetics. The expected SFS has a strong dependence on the historical population demography and this property is exploited by popular statistical methods ... |
0911.0814 | Wojciech Waga | Wojciech Waga, Marta Zawierta, Stanislaw Cebrat | Modelling the Evolution of Spatially Distributed Populations in the
Uniformly Changing Environment - Sympatric Speciation | 15 pages, 7 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have simulated the evolution of age structured populations whose
individuals represented by their diploid genomes were distributed on a square
lattice. The environmental conditions on the whole territory changed
simultaneously in the same way by switching on or off some requirements.
Mutations accumulated in the g... | [
{
"created": "Wed, 4 Nov 2009 13:13:21 GMT",
"version": "v1"
}
] | 2009-11-05 | [
[
"Waga",
"Wojciech",
""
],
[
"Zawierta",
"Marta",
""
],
[
"Cebrat",
"Stanislaw",
""
]
] | We have simulated the evolution of age structured populations whose individuals represented by their diploid genomes were distributed on a square lattice. The environmental conditions on the whole territory changed simultaneously in the same way by switching on or off some requirements. Mutations accumulated in the gen... |
1404.7529 | B. Roy Frieden | B.R. Frieden and R.A. Gatenby | Cell development obeys maximum Fisher information | 24 pages, 2 figures | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Eukaryotic cell development has been optimized by natural selection to obey
maximal intracellular flux of messenger proteins. This, in turn, implies
maximum Fisher information on angular position about a target nuclear pore
complex (NPR). The cell is simply modeled as spherical, with cell membrane (CM)
diameter 10 mi... | [
{
"created": "Tue, 29 Apr 2014 20:55:56 GMT",
"version": "v1"
}
] | 2014-05-01 | [
[
"Frieden",
"B. R.",
""
],
[
"Gatenby",
"R. A.",
""
]
] | Eukaryotic cell development has been optimized by natural selection to obey maximal intracellular flux of messenger proteins. This, in turn, implies maximum Fisher information on angular position about a target nuclear pore complex (NPR). The cell is simply modeled as spherical, with cell membrane (CM) diameter 10 micr... |
2301.02659 | Pouya Baniasadi | Pouya Baniasadi | Bayesian modelling of visual discrimination learning in mice | Unpublished Masters Project Report for research conducted at the
University of Cambridge (2020) | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The brain constantly turns large flows of sensory information into selective
representations of the environment. It, therefore, needs to learn to process
those sensory inputs that are most relevant for behaviour. It is not well
understood how learning changes neural circuits in visual and decision-making
brain areas ... | [
{
"created": "Tue, 15 Nov 2022 16:59:20 GMT",
"version": "v1"
}
] | 2023-01-10 | [
[
"Baniasadi",
"Pouya",
""
]
] | The brain constantly turns large flows of sensory information into selective representations of the environment. It, therefore, needs to learn to process those sensory inputs that are most relevant for behaviour. It is not well understood how learning changes neural circuits in visual and decision-making brain areas to... |
1812.04435 | Rosalind J Allen | Rosalind J Allen and Bartlomiej Waclaw | Bacterial growth: a statistical physicist's guide | null | null | 10.1088/1361-6633/aae546 | null | q-bio.CB q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bacterial growth presents many beautiful phenomena that pose new theoretical
challenges to statistical physicists, and are also amenable to laboratory
experimentation. This review provides some of the essential biological
background, discusses recent applications of statistical physics in this field,
and highlights t... | [
{
"created": "Tue, 11 Dec 2018 14:38:51 GMT",
"version": "v1"
}
] | 2018-12-19 | [
[
"Allen",
"Rosalind J",
""
],
[
"Waclaw",
"Bartlomiej",
""
]
] | Bacterial growth presents many beautiful phenomena that pose new theoretical challenges to statistical physicists, and are also amenable to laboratory experimentation. This review provides some of the essential biological background, discusses recent applications of statistical physics in this field, and highlights the... |
1003.3391 | Adilson Enio Motter | Adilson E. Motter | Improved Network Performance via Antagonism: From Synthetic Rescues to
Multi-drug Combinations | Online Open "Problems and Paradigms" article | A.E. Motter, BioEssays 32, 236 (2010) | 10.1002/bies.200900128 | null | q-bio.MN nlin.AO physics.soc-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent research shows that a faulty or sub-optimally operating metabolic
network can often be rescued by the targeted removal of enzyme-coding
genes--the exact opposite of what traditional gene therapy would suggest.
Predictions go as far as to assert that certain gene knockouts can restore the
growth of otherwise no... | [
{
"created": "Wed, 17 Mar 2010 15:13:45 GMT",
"version": "v1"
}
] | 2010-03-18 | [
[
"Motter",
"Adilson E.",
""
]
] | Recent research shows that a faulty or sub-optimally operating metabolic network can often be rescued by the targeted removal of enzyme-coding genes--the exact opposite of what traditional gene therapy would suggest. Predictions go as far as to assert that certain gene knockouts can restore the growth of otherwise nonv... |
1208.4660 | Yohei Kondo | Yohei Kondo, Kunihiko Kaneko, and Shuji Ishihara | Identifying dynamical systems with bifurcations from noisy partial
observation | 16 pages, 6 figures | null | 10.1103/PhysRevE.87.042716 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dynamical systems are used to model a variety of phenomena in which the
bifurcation structure is a fundamental characteristic. Here we propose a
statistical machine-learning approach to derive lowdimensional models that
automatically integrate information in noisy time-series data from partial
observations. The metho... | [
{
"created": "Thu, 23 Aug 2012 02:41:36 GMT",
"version": "v1"
}
] | 2015-06-11 | [
[
"Kondo",
"Yohei",
""
],
[
"Kaneko",
"Kunihiko",
""
],
[
"Ishihara",
"Shuji",
""
]
] | Dynamical systems are used to model a variety of phenomena in which the bifurcation structure is a fundamental characteristic. Here we propose a statistical machine-learning approach to derive lowdimensional models that automatically integrate information in noisy time-series data from partial observations. The method ... |
2006.10651 | Chris Antonopoulos Dr | Ian Cooper, Argha Mondal, Chris G. Antonopoulos | A SIR model assumption for the spread of COVID-19 in different
communities | 18 pages, 17 figures | null | 10.1016/j.chaos.2020.110057 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we study the effectiveness of the modelling approach on the
pandemic due to the spreading of the novel COVID-19 disease and develop a
susceptible-infected-removed (SIR) model that provides a theoretical framework
to investigate its spread within a community. Here, the model is based upon the
well-known... | [
{
"created": "Thu, 18 Jun 2020 16:22:23 GMT",
"version": "v1"
}
] | 2020-08-26 | [
[
"Cooper",
"Ian",
""
],
[
"Mondal",
"Argha",
""
],
[
"Antonopoulos",
"Chris G.",
""
]
] | In this paper, we study the effectiveness of the modelling approach on the pandemic due to the spreading of the novel COVID-19 disease and develop a susceptible-infected-removed (SIR) model that provides a theoretical framework to investigate its spread within a community. Here, the model is based upon the well-known s... |
2209.02063 | Daniel Cooney | Daniel B. Cooney, Simon A. Levin, Yoichiro Mori, Joshua B. Plotkin | Evolutionary Dynamics Within and Among Competing Groups | 48 pages, 8 figures | null | 10.1073/pnas.2216186120 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biological and social systems are structured at multiple scales, and the
incentives of individuals who interact in a group may diverge from the
collective incentive of the group as a whole. Mechanisms to resolve this
tension are responsible for profound transitions in evolutionary history,
including the origin of cel... | [
{
"created": "Mon, 5 Sep 2022 17:16:55 GMT",
"version": "v1"
}
] | 2023-05-31 | [
[
"Cooney",
"Daniel B.",
""
],
[
"Levin",
"Simon A.",
""
],
[
"Mori",
"Yoichiro",
""
],
[
"Plotkin",
"Joshua B.",
""
]
] | Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible for profound transitions in evolutionary history, including the origin of cellu... |
2402.16409 | Francesco Sannino | Stefan Hohenegger and Francesco Sannino | Renormalisation Group Methods for Effective Epidemiological Models | 36 pages, 19 figures | null | null | null | q-bio.PE hep-th stat.AP | http://creativecommons.org/licenses/by/4.0/ | Epidemiological models describe the spread of an infectious disease within a
population. They capture microscopic details on how the disease is passed on
among individuals in various different ways, while making predictions about the
state of the entirety of the population. However, the type and structure of the
spec... | [
{
"created": "Mon, 26 Feb 2024 09:05:13 GMT",
"version": "v1"
}
] | 2024-02-27 | [
[
"Hohenegger",
"Stefan",
""
],
[
"Sannino",
"Francesco",
""
]
] | Epidemiological models describe the spread of an infectious disease within a population. They capture microscopic details on how the disease is passed on among individuals in various different ways, while making predictions about the state of the entirety of the population. However, the type and structure of the specif... |
1805.07061 | Yu Terada | Yu Terada, Tomoyuki Obuchi, Takuya Isomura, Yoshiyuki Kabashima | Objective and efficient inference for couplings in neuronal networks | null | null | 10.1088/1742-5468/ab3219 | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inferring directional couplings from the spike data of networks is desired in
various scientific fields such as neuroscience. Here, we apply a recently
proposed objective procedure to the spike data obtained from the
Hodgkin--Huxley type models and in vitro neuronal networks cultured in a
circular structure. As a res... | [
{
"created": "Fri, 18 May 2018 06:19:37 GMT",
"version": "v1"
}
] | 2020-01-29 | [
[
"Terada",
"Yu",
""
],
[
"Obuchi",
"Tomoyuki",
""
],
[
"Isomura",
"Takuya",
""
],
[
"Kabashima",
"Yoshiyuki",
""
]
] | Inferring directional couplings from the spike data of networks is desired in various scientific fields such as neuroscience. Here, we apply a recently proposed objective procedure to the spike data obtained from the Hodgkin--Huxley type models and in vitro neuronal networks cultured in a circular structure. As a resul... |
2306.14329 | Somya Mehra | Somya Mehra, James M. McCaw, Peter G. Taylor | Superinfection and the hypnozoite reservoir for Plasmodium vivax: a
general framework | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Malaria is a parasitic disease, transmitted by mosquito vectors. Plasmodium
vivax presents particular challenges for disease control, in light of an
undetectable reservoir of latent parasites (hypnozoites) within the host liver.
Superinfection, which is driven by temporally proximate mosquito inoculation
and/or hypno... | [
{
"created": "Sun, 25 Jun 2023 19:59:09 GMT",
"version": "v1"
}
] | 2023-06-27 | [
[
"Mehra",
"Somya",
""
],
[
"McCaw",
"James M.",
""
],
[
"Taylor",
"Peter G.",
""
]
] | Malaria is a parasitic disease, transmitted by mosquito vectors. Plasmodium vivax presents particular challenges for disease control, in light of an undetectable reservoir of latent parasites (hypnozoites) within the host liver. Superinfection, which is driven by temporally proximate mosquito inoculation and/or hypnozo... |
2011.14241 | David Winkler | Sakshi Piplani, Puneet Singh, David A. Winkler, Nikolai Petrovsky | Computationally repurposed drugs and natural products against RNA
dependent RNA polymerase as potential COVID-19 therapies | 38 pages plus supplementary, 11 figures | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | For fast development of COVID-19, it is only feasible to use drugs (off label
use) or approved natural products that are already registered or been assessed
for safety in previous human trials. These agents can be quickly assessed in
COVID-19 patients, as their safety and pharmacokinetics should already be well
under... | [
{
"created": "Sun, 29 Nov 2020 00:17:26 GMT",
"version": "v1"
}
] | 2020-12-01 | [
[
"Piplani",
"Sakshi",
""
],
[
"Singh",
"Puneet",
""
],
[
"Winkler",
"David A.",
""
],
[
"Petrovsky",
"Nikolai",
""
]
] | For fast development of COVID-19, it is only feasible to use drugs (off label use) or approved natural products that are already registered or been assessed for safety in previous human trials. These agents can be quickly assessed in COVID-19 patients, as their safety and pharmacokinetics should already be well underst... |
1711.04828 | Gregory Way | Gregory P. Way and Casey S. Greene | Evaluating deep variational autoencoders trained on pan-cancer gene
expression | 4 pages, 3 figures, 2 tables, NIPS 2017 | null | null | null | q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Cancer is a heterogeneous disease with diverse molecular etiologies and
outcomes. The Cancer Genome Atlas (TCGA) has released a large compendium of
over 10,000 tumors with RNA-seq gene expression measurements. Gene expression
captures the diverse molecular profiles of tumors and can be interrogated to
reveal differen... | [
{
"created": "Mon, 13 Nov 2017 20:11:26 GMT",
"version": "v1"
}
] | 2017-11-15 | [
[
"Way",
"Gregory P.",
""
],
[
"Greene",
"Casey S.",
""
]
] | Cancer is a heterogeneous disease with diverse molecular etiologies and outcomes. The Cancer Genome Atlas (TCGA) has released a large compendium of over 10,000 tumors with RNA-seq gene expression measurements. Gene expression captures the diverse molecular profiles of tumors and can be interrogated to reveal differenti... |
2208.01569 | Lyle Poley | Lyle Poley, Joseph W. Baron, Tobias Galla | Generalised Lotka-Volterra model with hierarchical interactions | 10 pages, 6 Figures | null | 10.1103/PhysRevE.107.024313 | null | q-bio.PE cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the analysis of complex ecosystems it is common to use random interaction
coefficients, often assumed to be such that all species are statistically
equivalent. In this work we relax this assumption by choosing interactions
according to the cascade model, which we incorporate into a generalised
Lotka-Volterra dynam... | [
{
"created": "Tue, 2 Aug 2022 16:16:50 GMT",
"version": "v1"
}
] | 2023-03-08 | [
[
"Poley",
"Lyle",
""
],
[
"Baron",
"Joseph W.",
""
],
[
"Galla",
"Tobias",
""
]
] | In the analysis of complex ecosystems it is common to use random interaction coefficients, often assumed to be such that all species are statistically equivalent. In this work we relax this assumption by choosing interactions according to the cascade model, which we incorporate into a generalised Lotka-Volterra dynamic... |
1612.04532 | Yong Chen | Yong Chen | Influence of cell-cell interactions on the population growth rate in a
tumor | 5 pages, 2 figures | Commun. Theor. Phys. 68, 798 (2017) | 10.1088/0253-6102/68/6/798 | null | q-bio.PE physics.bio-ph q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The understanding of the macroscopic phenomenological models of the
population growth at a microscopic level is important to predict the population
behaviors emerged from the interactions between the individuals. In this work
we consider the influence of the cell-cell interaction on the population growth
rate $R$ in ... | [
{
"created": "Wed, 14 Dec 2016 08:38:49 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Nov 2017 02:43:42 GMT",
"version": "v2"
}
] | 2017-11-23 | [
[
"Chen",
"Yong",
""
]
] | The understanding of the macroscopic phenomenological models of the population growth at a microscopic level is important to predict the population behaviors emerged from the interactions between the individuals. In this work we consider the influence of the cell-cell interaction on the population growth rate $R$ in a ... |
2402.10990 | Francesco Galimberti | Francesco Galimberti (1), Stephanie Bopp (1), Alessandro Carletti (1),
Rui Catarino (1), Martin Claverie (1), Pietro Florio (1), Alessio Ippolito
(2), Arwyn Jones (1), Flavio Marchetto (3), Michael Olvedy (1), Alberto
Pistocchi (1), Astrid Verhegghen (1), Marijn Van Der Velde (1), Diana Vieira
(1), Raphael d'An... | From parcels to people: development of a spatially explicit risk
indicator to monitor residential pesticide exposure in agricultural areas | 40 pages, 4 tables, 22 figures | null | null | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The increase in global pesticide use has mirrored the rising demand for food
over the last decades, resulting in a boost in crop yields. However, concerns
about the impact of pesticides on biodiversity, ecosystems, and human health,
especially for populations residing close to cultivated areas, are growing.
This stud... | [
{
"created": "Fri, 16 Feb 2024 12:05:21 GMT",
"version": "v1"
}
] | 2024-02-20 | [
[
"Galimberti",
"Francesco",
""
],
[
"Bopp",
"Stephanie",
""
],
[
"Carletti",
"Alessandro",
""
],
[
"Catarino",
"Rui",
""
],
[
"Claverie",
"Martin",
""
],
[
"Florio",
"Pietro",
""
],
[
"Ippolito",
"Alessio",
... | The increase in global pesticide use has mirrored the rising demand for food over the last decades, resulting in a boost in crop yields. However, concerns about the impact of pesticides on biodiversity, ecosystems, and human health, especially for populations residing close to cultivated areas, are growing. This study ... |
1803.01236 | Marcos Trevisan Dr. | Alan Taitz, Diego E Shalom, Marcos A Trevisan | Vocal effort modulates the motor planning of short speech structures | 17 pages, 3 figures | Phys. Rev. E 97, 052406 (2018) | 10.1103/PhysRevE.97.052406 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Speech requires programming the sequence of vocal gestures that produce the
sounds of words. Here we explored the timing of this program by asking our
participants to pronounce, as quickly as possible, a sequence of
consonant-consonant-vowel (CCV) structures appearing on screen. We measured the
delay between visual p... | [
{
"created": "Sat, 3 Mar 2018 20:45:33 GMT",
"version": "v1"
}
] | 2018-05-23 | [
[
"Taitz",
"Alan",
""
],
[
"Shalom",
"Diego E",
""
],
[
"Trevisan",
"Marcos A",
""
]
] | Speech requires programming the sequence of vocal gestures that produce the sounds of words. Here we explored the timing of this program by asking our participants to pronounce, as quickly as possible, a sequence of consonant-consonant-vowel (CCV) structures appearing on screen. We measured the delay between visual pre... |
1005.4342 | Iain Johnston | Sam F. Greenbury and Iain G. Johnston and Matthew A. Smith and
Jonathan P. K. Doye and Ard A. Louis | The effect of scale-free topology on the robustness and evolvability of
genetic regulatory networks | 16 pages, 15 figures | J. Theor. Biol. 267, 48-61 (2010) | 10.1016/j.jtbi.2010.08.006 | null | q-bio.PE q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate how scale-free (SF) and Erdos-Renyi (ER) topologies affect the
interplay between evolvability and robustness of model gene regulatory networks
with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006)
we find that networks with SFin topologies, that is SF topology for incoming
node... | [
{
"created": "Mon, 24 May 2010 14:49:37 GMT",
"version": "v1"
}
] | 2013-09-03 | [
[
"Greenbury",
"Sam F.",
""
],
[
"Johnston",
"Iain G.",
""
],
[
"Smith",
"Matthew A.",
""
],
[
"Doye",
"Jonathan P. K.",
""
],
[
"Louis",
"Ard A.",
""
]
] | We investigate how scale-free (SF) and Erdos-Renyi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SFin topologies, that is SF topology for incoming nodes ... |
1309.5458 | Tom McLeish FRS | Tom C B McLeish, Thomas L Rogers, Mark R Wilson | Allostery without conformation change: modelling protein dynamics at
multiple scales | 20 Pages, 8 figures | T. C. B. McLeish, T. L. Rodgers and M. R. Wilson, Phys. Biol., 10,
056004 (2013) | 10.1088/1478-3975/10/5/056004 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The original ideas of Cooper and Dryden, that allosteric signalling can be
induced between distant binding sites on proteins without any change in mean
structural conformation, has proved to be a remarkably prescient insight into
the rich structure of protein dynamics. It represents an alternative to the
celebrated M... | [
{
"created": "Sat, 21 Sep 2013 10:13:36 GMT",
"version": "v1"
}
] | 2013-09-24 | [
[
"McLeish",
"Tom C B",
""
],
[
"Rogers",
"Thomas L",
""
],
[
"Wilson",
"Mark R",
""
]
] | The original ideas of Cooper and Dryden, that allosteric signalling can be induced between distant binding sites on proteins without any change in mean structural conformation, has proved to be a remarkably prescient insight into the rich structure of protein dynamics. It represents an alternative to the celebrated Mon... |
1409.2182 | Garrett Evans | Garrett N. Evans | Convolution Metric for Neuron Membrane Potential Recordings | 31 pages, 4 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | I provide a convolution metric which takes neural membrane potential
recordings as arguments and compares their subthreshold features along with the
timing and number of spikes within them--summarizing differences in these with
a single "distance" between the recordings. Based on van Rossum's 2001 metric
for spike tr... | [
{
"created": "Mon, 8 Sep 2014 01:27:18 GMT",
"version": "v1"
}
] | 2014-09-09 | [
[
"Evans",
"Garrett N.",
""
]
] | I provide a convolution metric which takes neural membrane potential recordings as arguments and compares their subthreshold features along with the timing and number of spikes within them--summarizing differences in these with a single "distance" between the recordings. Based on van Rossum's 2001 metric for spike trai... |
0704.3948 | Alexey Mazur K | Alexey K. Mazur | The Worm-Like Chain Theory And Bending Of Short DNA | 4 pages, 3 figures, to appear in PRL | Phys. Rev. Lett. 98, 218102, 2007. | 10.1103/PhysRevLett.98.218102 | null | q-bio.BM cond-mat.soft physics.bio-ph | null | The probability distributions for bending angles in double helical DNA
obtained in all-atom molecular dynamics simulations are compared with
theoretical predictions. The computed distributions remarkably agree with the
worm-like chain theory for double helices of one helical turn and longer, and
qualitatively differ ... | [
{
"created": "Mon, 30 Apr 2007 14:24:59 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Mazur",
"Alexey K.",
""
]
] | The probability distributions for bending angles in double helical DNA obtained in all-atom molecular dynamics simulations are compared with theoretical predictions. The computed distributions remarkably agree with the worm-like chain theory for double helices of one helical turn and longer, and qualitatively differ fr... |
1308.1564 | Tibor Antal | Tibor Antal, P. L. Krapivsky, M. A. Nowak | Spatial evolution of tumors with successive driver mutations | 16 pages | null | null | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the spatial evolutionary dynamics of solid tumors as they obtain
additional driver mutations. We start with a cancer clone that expands
uniformly in three dimensions giving rise to a spherical shape. We assume that
cell division occurs on the surface of the growing tumor. Each cell division
has a chance to g... | [
{
"created": "Wed, 7 Aug 2013 13:19:26 GMT",
"version": "v1"
}
] | 2013-08-08 | [
[
"Antal",
"Tibor",
""
],
[
"Krapivsky",
"P. L.",
""
],
[
"Nowak",
"M. A.",
""
]
] | We study the spatial evolutionary dynamics of solid tumors as they obtain additional driver mutations. We start with a cancer clone that expands uniformly in three dimensions giving rise to a spherical shape. We assume that cell division occurs on the surface of the growing tumor. Each cell division has a chance to giv... |
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