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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0706.2126 | Thierry Cachat | Eugene Asarin (LIAFA), Thierry Cachat (LIAFA), Alexander Seliverstov
(IITP), Tayssir Touili (LIAFA), Vassily Lyubetsky (IITP) | Attenuation Regulation as a Term Rewriting System | to appear | Proceedings of the Second International Conference on Algebraic
Biology (06/07/2007) 12 | null | null | q-bio.QM | null | The classical attenuation regulation of gene expression in bacteria is
considered. We propose to represent the secondary RNA structure in the leader
region of a gene or an operon by a term, and we give a probabilistic term
rewriting system modeling the whole process of such a regulation.
| [
{
"created": "Thu, 14 Jun 2007 13:59:59 GMT",
"version": "v1"
}
] | 2007-06-15 | [
[
"Asarin",
"Eugene",
"",
"LIAFA"
],
[
"Cachat",
"Thierry",
"",
"LIAFA"
],
[
"Seliverstov",
"Alexander",
"",
"IITP"
],
[
"Touili",
"Tayssir",
"",
"LIAFA"
],
[
"Lyubetsky",
"Vassily",
"",
"IITP"
]
] | The classical attenuation regulation of gene expression in bacteria is considered. We propose to represent the secondary RNA structure in the leader region of a gene or an operon by a term, and we give a probabilistic term rewriting system modeling the whole process of such a regulation. |
1403.2574 | Sven Bilke | Yevgeniy Gindin, Manuel S. Valenzuela, Mirit I. Aladjem, Paul S.
Meltzer and Sven Bilke | A chromatin structure based model accurately predicts DNA replication
timing in human cells | null | null | null | null | q-bio.SC q-bio.GN | http://creativecommons.org/licenses/publicdomain/ | The metazoan genome is replicated in precise cell lineage specific temporal
order. However, the mechanism controlling this orchestrated process is poorly
understood as no molecular mechanisms have been identified that actively
regulate the firing sequence of genome replication. Here we develop a
mechanistic model of ... | [
{
"created": "Tue, 11 Mar 2014 13:41:52 GMT",
"version": "v1"
}
] | 2014-03-12 | [
[
"Gindin",
"Yevgeniy",
""
],
[
"Valenzuela",
"Manuel S.",
""
],
[
"Aladjem",
"Mirit I.",
""
],
[
"Meltzer",
"Paul S.",
""
],
[
"Bilke",
"Sven",
""
]
] | The metazoan genome is replicated in precise cell lineage specific temporal order. However, the mechanism controlling this orchestrated process is poorly understood as no molecular mechanisms have been identified that actively regulate the firing sequence of genome replication. Here we develop a mechanistic model of ge... |
1105.5764 | Andrey Shabalin | Andrey A. Shabalin | Matrix eQTL: Ultra fast eQTL analysis via large matrix operations | 9 pages, 1 figure | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Expression quantitative trait loci (eQTL) mapping aims to determine genomic
regions that regulate gene transcription. Expression QTL is used to study the
regulatory structure of normal tissues and to search for genetic factors in
complex diseases such as cancer, diabetes, and cystic fibrosis. A modern eQTL
dataset co... | [
{
"created": "Sun, 29 May 2011 07:16:12 GMT",
"version": "v1"
}
] | 2011-05-31 | [
[
"Shabalin",
"Andrey A.",
""
]
] | Expression quantitative trait loci (eQTL) mapping aims to determine genomic regions that regulate gene transcription. Expression QTL is used to study the regulatory structure of normal tissues and to search for genetic factors in complex diseases such as cancer, diabetes, and cystic fibrosis. A modern eQTL dataset cont... |
1202.0405 | Federico Felizzi | Federico Felizzi, Jerome Galtier, Georgios Fengos, Dagmar Iber | Spatial organization of proteomes: A low-rank approximation | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the problem of signal transduction via a descriptive analysis
of the spatial organization of the complement of proteins exerting a certain
function within a cellular compartment. We propose a scheme to assign a
numerical value to individual proteins in a protein interaction network by
means of a simple... | [
{
"created": "Thu, 2 Feb 2012 10:51:23 GMT",
"version": "v1"
}
] | 2012-02-03 | [
[
"Felizzi",
"Federico",
""
],
[
"Galtier",
"Jerome",
""
],
[
"Fengos",
"Georgios",
""
],
[
"Iber",
"Dagmar",
""
]
] | We investigate the problem of signal transduction via a descriptive analysis of the spatial organization of the complement of proteins exerting a certain function within a cellular compartment. We propose a scheme to assign a numerical value to individual proteins in a protein interaction network by means of a simple o... |
1606.04354 | Alberto Pezzotta | Alberto Pezzotta, Matteo Adorisio, Antonio Celani | From Conformational Spread to Allosteric and Cooperative models of E.
coli flagellar motor | 22 pages, 10 figures; new version with appendix | null | 10.1088/1742-5468/aa569e | null | q-bio.QM physics.bio-ph q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Escherichia coli swims using flagella activated by rotary motors. The
direction of rotation of the motors is indirectly regulated by the binding of a
single messenger protein. The conformational spread model has been shown to
accurately describe the equilibrium properties as well as the dynamics of the
flagellar moto... | [
{
"created": "Tue, 14 Jun 2016 13:40:17 GMT",
"version": "v1"
},
{
"created": "Mon, 18 Jul 2016 10:15:04 GMT",
"version": "v2"
},
{
"created": "Thu, 29 Sep 2016 12:43:06 GMT",
"version": "v3"
}
] | 2017-03-08 | [
[
"Pezzotta",
"Alberto",
""
],
[
"Adorisio",
"Matteo",
""
],
[
"Celani",
"Antonio",
""
]
] | Escherichia coli swims using flagella activated by rotary motors. The direction of rotation of the motors is indirectly regulated by the binding of a single messenger protein. The conformational spread model has been shown to accurately describe the equilibrium properties as well as the dynamics of the flagellar motor.... |
2002.08891 | Maxwell Bertolero Dr | Maxwell A. Bertolero, Dustin Moraczewski, Adam Thomas, and Danielle S.
Bassett | Deep Neural Networks Carve the Brain at its Joints | null | null | null | null | q-bio.NC physics.data-an q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How an individual's unique brain connectivity determines that individual's
cognition, behavior, and risk for pathology is a fundamental question in basic
and clinical neuroscience. In seeking answers, many have turned to machine
learning, with some noting the particular promise of deep neural networks in
modelling co... | [
{
"created": "Thu, 20 Feb 2020 17:37:53 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Sep 2020 15:09:51 GMT",
"version": "v2"
}
] | 2023-12-08 | [
[
"Bertolero",
"Maxwell A.",
""
],
[
"Moraczewski",
"Dustin",
""
],
[
"Thomas",
"Adam",
""
],
[
"Bassett",
"Danielle S.",
""
]
] | How an individual's unique brain connectivity determines that individual's cognition, behavior, and risk for pathology is a fundamental question in basic and clinical neuroscience. In seeking answers, many have turned to machine learning, with some noting the particular promise of deep neural networks in modelling comp... |
2012.06112 | Swapna Sasi Mrs | Pranav Mahajan, Advait Rane, Swapna Sasi, Basabdatta Sen Bhattacharya | Quantifying Synchronization in a Biologically Inspired Neural Network | 13 pages | null | null | null | q-bio.QM q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We present a collated set of algorithms to obtain objective measures of
synchronisation in brain time-series data. The algorithms are implemented in
MATLAB; we refer to our collated set of 'tools' as SyncBox. Our motivation for
SyncBox is to understand the underlying dynamics in an existing population
neural network,... | [
{
"created": "Fri, 11 Dec 2020 04:08:15 GMT",
"version": "v1"
}
] | 2020-12-14 | [
[
"Mahajan",
"Pranav",
""
],
[
"Rane",
"Advait",
""
],
[
"Sasi",
"Swapna",
""
],
[
"Bhattacharya",
"Basabdatta Sen",
""
]
] | We present a collated set of algorithms to obtain objective measures of synchronisation in brain time-series data. The algorithms are implemented in MATLAB; we refer to our collated set of 'tools' as SyncBox. Our motivation for SyncBox is to understand the underlying dynamics in an existing population neural network, c... |
2312.14732 | Mariona Torrens Fontanals | Mariona Torrens-Fontanals, Panagiotis Tourlas, Stefan Doerr, Gianni De
Fabritiis | PlayMolecule Viewer: a toolkit for the visualization of molecules and
other data | 10 pages, 4 figures, submitted to the Journal of Chemical Information
and Modeling | null | 10.1021/acs.jcim.3c01776 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | PlayMolecule Viewer is a web-based data visualization toolkit designed to
streamline the exploration of data resulting from structural bioinformatics or
computer-aided drug design efforts. By harnessing state-of-the-art web
technologies such as WebAssembly, PlayMolecule Viewer integrates powerful
Python libraries dir... | [
{
"created": "Fri, 22 Dec 2023 14:40:18 GMT",
"version": "v1"
}
] | 2024-01-31 | [
[
"Torrens-Fontanals",
"Mariona",
""
],
[
"Tourlas",
"Panagiotis",
""
],
[
"Doerr",
"Stefan",
""
],
[
"De Fabritiis",
"Gianni",
""
]
] | PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies such as WebAssembly, PlayMolecule Viewer integrates powerful Python libraries direc... |
1706.02451 | Wutu Lin | Tiger W. Lin, Anup Das, Giri P. Krishnan, Maxim Bazhenov, Terrence J.
Sejnowski | Differential Covariance: A New Class of Methods to Estimate Sparse
Connectivity from Neural Recordings | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With our ability to record more neurons simultaneously, making sense of these
data is a challenge. Functional connectivity is one popular way to study the
relationship between multiple neural signals. Correlation-based methods are a
set of currently well-used techniques for functional connectivity estimation.
However... | [
{
"created": "Thu, 8 Jun 2017 04:54:27 GMT",
"version": "v1"
}
] | 2017-06-09 | [
[
"Lin",
"Tiger W.",
""
],
[
"Das",
"Anup",
""
],
[
"Krishnan",
"Giri P.",
""
],
[
"Bazhenov",
"Maxim",
""
],
[
"Sejnowski",
"Terrence J.",
""
]
] | With our ability to record more neurons simultaneously, making sense of these data is a challenge. Functional connectivity is one popular way to study the relationship between multiple neural signals. Correlation-based methods are a set of currently well-used techniques for functional connectivity estimation. However, ... |
1802.10207 | Girik Malik | Girik Malik, Anirban Banerji, Maksim Kouza, Irina A. Buhimschi,
Andrzej Kloczkowski | Deciphering general characteristics of residues constituting allosteric
communication paths | 29 pages, 4 figures, 5 tables | null | null | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Considering all the PDB annotated allosteric proteins (from ASD - AlloSteric
Database) belonging to four different classes (kinases, nuclear receptors,
peptidases and transcription factors), this work has attempted to decipher
certain consistent patterns present in the residues constituting the allosteric
communicati... | [
{
"created": "Tue, 27 Feb 2018 23:21:21 GMT",
"version": "v1"
}
] | 2018-03-01 | [
[
"Malik",
"Girik",
""
],
[
"Banerji",
"Anirban",
""
],
[
"Kouza",
"Maksim",
""
],
[
"Buhimschi",
"Irina A.",
""
],
[
"Kloczkowski",
"Andrzej",
""
]
] | Considering all the PDB annotated allosteric proteins (from ASD - AlloSteric Database) belonging to four different classes (kinases, nuclear receptors, peptidases and transcription factors), this work has attempted to decipher certain consistent patterns present in the residues constituting the allosteric communication... |
2009.09422 | Alfredo Braunstein | Antoine Baker, Indaco Biazzo, Alfredo Braunstein, Giovanni Catania,
Luca Dall'Asta, Alessandro Ingrosso, Florent Krzakala, Fabio Mazza, Marc
M\'ezard, Anna Paola Muntoni, Maria Refinetti, Stefano Sarao Mannelli, Lenka
Zdeborov\'a | Epidemic mitigation by statistical inference from contact tracing data | 21 pages, 7 figures | PNAS 2021 Vol. 118 No. 32 e2106548118 | 10.1073/pnas.2106548118 | null | q-bio.PE cond-mat.stat-mech cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Contact-tracing is an essential tool in order to mitigate the impact of
pandemic such as the COVID-19. In order to achieve efficient and scalable
contact-tracing in real time, digital devices can play an important role. While
a lot of attention has been paid to analyzing the privacy and ethical risks of
the associate... | [
{
"created": "Sun, 20 Sep 2020 12:24:45 GMT",
"version": "v1"
}
] | 2021-07-29 | [
[
"Baker",
"Antoine",
""
],
[
"Biazzo",
"Indaco",
""
],
[
"Braunstein",
"Alfredo",
""
],
[
"Catania",
"Giovanni",
""
],
[
"Dall'Asta",
"Luca",
""
],
[
"Ingrosso",
"Alessandro",
""
],
[
"Krzakala",
"Florent",
... | Contact-tracing is an essential tool in order to mitigate the impact of pandemic such as the COVID-19. In order to achieve efficient and scalable contact-tracing in real time, digital devices can play an important role. While a lot of attention has been paid to analyzing the privacy and ethical risks of the associated ... |
1302.2047 | Sim-Hui Tee | Sim-Hui Tee | In Silico Analysis of Tandem Repeats in GIF of Gastric Parietal Cells | Submitted to Journal of Biomedical Engineering Research | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tandem repeats are ubiquitous in the genome of organisms and their mutated
forms play a vital role in pathogenesis. In this study, tandem repeats in
Gastric Intrinsic Factor (GIF) of gastric parietal cells have been investigated
using an in silico approach. Six types of the nucleotide tandem repeat motifs
have been i... | [
{
"created": "Fri, 8 Feb 2013 14:31:34 GMT",
"version": "v1"
}
] | 2013-02-11 | [
[
"Tee",
"Sim-Hui",
""
]
] | Tandem repeats are ubiquitous in the genome of organisms and their mutated forms play a vital role in pathogenesis. In this study, tandem repeats in Gastric Intrinsic Factor (GIF) of gastric parietal cells have been investigated using an in silico approach. Six types of the nucleotide tandem repeat motifs have been inv... |
1504.04543 | Michael GB Blum | Nicolas Duforet-Frebourg, Keurcien Luu, Guillaume Laval, Eric Bazin,
Michael G.B. Blum | Detecting genomic signatures of natural selection with principal
component analysis: application to the 1000 Genomes data | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To characterize natural selection, various analytical methods for detecting
candidate genomic regions have been developed. We propose to perform
genome-wide scans of natural selection using principal component analysis. We
show that the common Fst index of genetic differentiation between populations
can be viewed as ... | [
{
"created": "Wed, 8 Apr 2015 13:49:11 GMT",
"version": "v1"
},
{
"created": "Thu, 21 May 2015 16:39:24 GMT",
"version": "v2"
},
{
"created": "Thu, 24 Sep 2015 08:36:43 GMT",
"version": "v3"
},
{
"created": "Tue, 29 Sep 2015 08:20:39 GMT",
"version": "v4"
},
{
"cr... | 2015-11-19 | [
[
"Duforet-Frebourg",
"Nicolas",
""
],
[
"Luu",
"Keurcien",
""
],
[
"Laval",
"Guillaume",
""
],
[
"Bazin",
"Eric",
""
],
[
"Blum",
"Michael G. B.",
""
]
] | To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis. We show that the common Fst index of genetic differentiation between populations can be viewed as a ... |
2103.13156 | Cecilia Berardo | Cecilia Berardo and Stefan Geritz | Coevolution of the reckless prey and the patient predator | 22 pages, 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The war of attrition in game theory is a model of a stand-off situation
between two opponents where the winner is determined by its persistence. We
model a stand-off between a predator and a prey when the prey is hiding and the
predator is waiting for the prey to come out from its refuge, or when the two
are locked i... | [
{
"created": "Wed, 24 Mar 2021 12:57:43 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Aug 2021 18:20:27 GMT",
"version": "v2"
}
] | 2021-08-19 | [
[
"Berardo",
"Cecilia",
""
],
[
"Geritz",
"Stefan",
""
]
] | The war of attrition in game theory is a model of a stand-off situation between two opponents where the winner is determined by its persistence. We model a stand-off between a predator and a prey when the prey is hiding and the predator is waiting for the prey to come out from its refuge, or when the two are locked in ... |
1102.5694 | Iain Johnston | Iain G. Johnston, Sebastian A. Ahnert, Jonathan P. K. Doye and Ard A.
Louis | Evolutionary Dynamics in a Simple Model of Self-Assembly | null | Phys. Rev. E 83, 066105 (2011) | 10.1103/PhysRevE.83.066105 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the evolutionary dynamics of an idealised model for the robust
self-assembly of two-dimensional structures called polyominoes. The model
includes rules that encode interactions between sets of square tiles that drive
the self-assembly process. The relationship between the model's rule set and
its resul... | [
{
"created": "Mon, 28 Feb 2011 15:53:08 GMT",
"version": "v1"
}
] | 2013-09-03 | [
[
"Johnston",
"Iain G.",
""
],
[
"Ahnert",
"Sebastian A.",
""
],
[
"Doye",
"Jonathan P. K.",
""
],
[
"Louis",
"Ard A.",
""
]
] | We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the self-assembly process. The relationship between the model's rule set and its resulti... |
2105.14284 | Samuel Fischer | Samuel M. Fischer, Pouria Ramazi, Sean Simmons, Mark S. Poesch, Mark
A. Lewis | Boosting propagule transport models with individual-specific data from
mobile apps | Keywords: Angler; Gravity Model; Invasives (Applied Ecology);
Modelling (Disease Ecology); Smartphone Apps; Survey Method; Vector; Whirling
Disease | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Management of invasive species and pathogens requires information about the
traffic of potential vectors. Such information is often taken from vector
traffic models fitted to survey data. Here, user-specific data collected via
mobile apps offer new opportunities to obtain more accurate estimates and to
analyze how ve... | [
{
"created": "Sat, 29 May 2021 12:37:57 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Nov 2021 20:01:37 GMT",
"version": "v2"
},
{
"created": "Tue, 13 Dec 2022 17:25:55 GMT",
"version": "v3"
}
] | 2022-12-14 | [
[
"Fischer",
"Samuel M.",
""
],
[
"Ramazi",
"Pouria",
""
],
[
"Simmons",
"Sean",
""
],
[
"Poesch",
"Mark S.",
""
],
[
"Lewis",
"Mark A.",
""
]
] | Management of invasive species and pathogens requires information about the traffic of potential vectors. Such information is often taken from vector traffic models fitted to survey data. Here, user-specific data collected via mobile apps offer new opportunities to obtain more accurate estimates and to analyze how vect... |
2007.09477 | Marcio Watanabe | Marcio Watanabe | Efficacy of Hydroxychloroquine as Prophylaxis for Covid-19 | 10 pages, 1 figure | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Limitations in the design of the experiment of Boulware et al[1] are
considered in Cohen[2]. They are not subject to correction but they are
reported for readers' consideration. However, they made an analysis for the
incidence based on Fisher's hypothesis test for means while they published
detailed time dependent da... | [
{
"created": "Sat, 18 Jul 2020 17:03:21 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Jul 2020 18:39:56 GMT",
"version": "v2"
}
] | 2020-07-23 | [
[
"Watanabe",
"Marcio",
""
]
] | Limitations in the design of the experiment of Boulware et al[1] are considered in Cohen[2]. They are not subject to correction but they are reported for readers' consideration. However, they made an analysis for the incidence based on Fisher's hypothesis test for means while they published detailed time dependent data... |
q-bio/0510027 | C. Soul\'e | C. Soul\'e (IHES) | Mathematical approaches to differentiation and gene regulation | To appear in Notes Comptes-Rendus Acad. Sc. Paris, Biologie | null | null | null | q-bio.MN | null | We consider some mathematical issues raised by the modelling of gene
networks. The expression of genes is governed by a complex set of regulations,
which is often described symbolically by interaction graphs. Once such a graph
has been established, there remains the difficult task to decide which
dynamical properties... | [
{
"created": "Fri, 14 Oct 2005 07:02:13 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Soulé",
"C.",
"",
"IHES"
]
] | We consider some mathematical issues raised by the modelling of gene networks. The expression of genes is governed by a complex set of regulations, which is often described symbolically by interaction graphs. Once such a graph has been established, there remains the difficult task to decide which dynamical properties o... |
1609.05151 | Sidney Redner | M. Chupeau, O. Benichou, S. Redner | Random Search with Memory in Patchy Media: Exploration-Exploitation
Tradeoff | 5 pages, 3 figures, plus 3 pages of supplemental material. V2: Final
manuscript to appear in PRE | Phys. Rev. E 95, 012157 (2017) | 10.1103/PhysRevE.95.012157 | null | q-bio.PE cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How to best exploit patchy resources? This long-standing question belongs to
the extensively studied class of explore/exploit problems that arise in a wide
range of situations, from animal foraging, to robotic exploration, and to human
decision processes. Despite its broad relevance, the issue of optimal
exploitation... | [
{
"created": "Fri, 16 Sep 2016 17:45:25 GMT",
"version": "v1"
},
{
"created": "Wed, 11 Jan 2017 23:42:36 GMT",
"version": "v2"
}
] | 2017-01-31 | [
[
"Chupeau",
"M.",
""
],
[
"Benichou",
"O.",
""
],
[
"Redner",
"S.",
""
]
] | How to best exploit patchy resources? This long-standing question belongs to the extensively studied class of explore/exploit problems that arise in a wide range of situations, from animal foraging, to robotic exploration, and to human decision processes. Despite its broad relevance, the issue of optimal exploitation h... |
0704.1885 | Jesse Bloom | Jesse D. Bloom, Zhongyi Lu, David Chen, Alpan Raval, Ophelia S.
Venturelli, and Frances H. Arnold | Evolution favors protein mutational robustness in sufficiently large
populations | null | BMC Biology 5:29 (2007) | 10.1186/1741-7007-5-29 | null | q-bio.PE q-bio.BM | null | BACKGROUND: An important question is whether evolution favors properties such
as mutational robustness or evolvability that do not directly benefit any
individual, but can influence the course of future evolution. Functionally
similar proteins can differ substantially in their robustness to mutations and
capacity to ... | [
{
"created": "Sat, 14 Apr 2007 19:42:13 GMT",
"version": "v1"
}
] | 2009-04-16 | [
[
"Bloom",
"Jesse D.",
""
],
[
"Lu",
"Zhongyi",
""
],
[
"Chen",
"David",
""
],
[
"Raval",
"Alpan",
""
],
[
"Venturelli",
"Ophelia S.",
""
],
[
"Arnold",
"Frances H.",
""
]
] | BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar proteins can differ substantially in their robustness to mutations and capacity to ev... |
1512.08660 | John Vandermeer | John Vandermeer and Doug Jackson | Spatial pattern and power function deviation in a cellular automata
model of an ant population | null | null | null | null | q-bio.PE nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A spatially explicit model previously developed to apply to a population of
arboreal nesting ants in southern Mexico is explored in detail, including
notions of criticality and robust criticality and expected power law
adjustment.
| [
{
"created": "Tue, 29 Dec 2015 11:44:44 GMT",
"version": "v1"
}
] | 2015-12-31 | [
[
"Vandermeer",
"John",
""
],
[
"Jackson",
"Doug",
""
]
] | A spatially explicit model previously developed to apply to a population of arboreal nesting ants in southern Mexico is explored in detail, including notions of criticality and robust criticality and expected power law adjustment. |
0712.3897 | Yuri A. Dabaghian | Yu. Dabaghian, A. G. Cohn, L. Frank | Topological Maps from Signals | posted by permission of ACM for personal use. The definitive version
was published in (ACMGIS .07, November 7-9, 2007, Seattle, WA) ISBN
978-1-59593-914-2/07/11. 11 pages, 4 figures | proceedings of the 15th ACM International Symposium ACM GIS 2007,
pp. 392-395 | null | null | q-bio.QM q-bio.NC | null | We discuss the task of reconstructing the topological map of an environment
based on the sequences of locations visited by a mobile agent -- this occurs in
systems neuroscience, where one runs into the task of reconstructing the global
topological map of the environment based on activation patterns of the place
codin... | [
{
"created": "Sun, 23 Dec 2007 06:00:20 GMT",
"version": "v1"
}
] | 2007-12-27 | [
[
"Dabaghian",
"Yu.",
""
],
[
"Cohn",
"A. G.",
""
],
[
"Frank",
"L.",
""
]
] | We discuss the task of reconstructing the topological map of an environment based on the sequences of locations visited by a mobile agent -- this occurs in systems neuroscience, where one runs into the task of reconstructing the global topological map of the environment based on activation patterns of the place coding ... |
1907.09738 | Linqing Feng | Linqing Feng, Jun Ho Song, Jiwon Kim, Soomin Jeong, Jin Sung Park,
Jinhyun Kim | Robust Nucleus Detection with Partially Labeled Exemplars | null | IEEE Access, vol. 7, pp. 162169-162178, 2019 | 10.1109/ACCESS.2019.2952098 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Quantitative analysis of cell nuclei in microscopic images is an essential
yet challenging source of biological and pathological information. The major
challenge is accurate detection and segmentation of densely packed nuclei in
images acquired under a variety of conditions. Mask R-CNN-based methods have
achieved sta... | [
{
"created": "Tue, 23 Jul 2019 07:53:22 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Aug 2019 09:34:26 GMT",
"version": "v2"
},
{
"created": "Wed, 13 Nov 2019 11:05:31 GMT",
"version": "v3"
}
] | 2019-11-14 | [
[
"Feng",
"Linqing",
""
],
[
"Song",
"Jun Ho",
""
],
[
"Kim",
"Jiwon",
""
],
[
"Jeong",
"Soomin",
""
],
[
"Park",
"Jin Sung",
""
],
[
"Kim",
"Jinhyun",
""
]
] | Quantitative analysis of cell nuclei in microscopic images is an essential yet challenging source of biological and pathological information. The major challenge is accurate detection and segmentation of densely packed nuclei in images acquired under a variety of conditions. Mask R-CNN-based methods have achieved state... |
1410.6364 | Andrea De Martino | Daniele De Martino, Fabrizio Capuani, Andrea De Martino | Inferring metabolic phenotypes from the exometabolome through a
thermodynamic variational principle | 10 pages, to appear in New J Phys (Special Issue) | New J. Phys. 16 (2014) 115018 | 10.1088/1367-2630/16/11/115018 | null | q-bio.MN cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Networks of biochemical reactions, like cellular metabolic networks, are kept
in non-equilibrium steady states by the exchange fluxes connecting them to the
environment. In most cases, feasible flux configurations can be derived from
minimal mass-balance assumptions upon prescribing in- and out-take fluxes. Here
we c... | [
{
"created": "Thu, 23 Oct 2014 13:44:14 GMT",
"version": "v1"
}
] | 2014-12-01 | [
[
"De Martino",
"Daniele",
""
],
[
"Capuani",
"Fabrizio",
""
],
[
"De Martino",
"Andrea",
""
]
] | Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from minimal mass-balance assumptions upon prescribing in- and out-take fluxes. Here we con... |
1804.08404 | Hartmut Grote | Hartmut Grote | Commentary: Intentional Observer Effects on Quantum Randomness: A
Bayesian Analysis Reveals Evidence Against Micro-Psychokinesis | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The paper titled `Intentional Observer Effects on Quantum Randomness: A
Bayesian Analysis Reveals Evidence Against Micro-Psychokinesis', published in
Frontiers of Psychology in March 2018, reports on a mind-matter experiment with
the main result of strong evidence against Micro-Psychokinesis. Despite this
conclusion,... | [
{
"created": "Thu, 5 Apr 2018 16:49:53 GMT",
"version": "v1"
}
] | 2018-04-24 | [
[
"Grote",
"Hartmut",
""
]
] | The paper titled `Intentional Observer Effects on Quantum Randomness: A Bayesian Analysis Reveals Evidence Against Micro-Psychokinesis', published in Frontiers of Psychology in March 2018, reports on a mind-matter experiment with the main result of strong evidence against Micro-Psychokinesis. Despite this conclusion, t... |
2408.06377 | Wenwen Min | Donghai Fang, Fangfang Zhu, Dongting Xie and Wenwen Min | Masked Graph Autoencoders with Contrastive Augmentation for Spatially
Resolved Transcriptomics Data | null | null | null | null | q-bio.GN cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With the rapid advancement of Spatial Resolved Transcriptomics (SRT)
technology, it is now possible to comprehensively measure gene transcription
while preserving the spatial context of tissues. Spatial domain identification
and gene denoising are key objectives in SRT data analysis. We propose a
Contrastively Augmen... | [
{
"created": "Fri, 9 Aug 2024 02:49:23 GMT",
"version": "v1"
}
] | 2024-08-14 | [
[
"Fang",
"Donghai",
""
],
[
"Zhu",
"Fangfang",
""
],
[
"Xie",
"Dongting",
""
],
[
"Min",
"Wenwen",
""
]
] | With the rapid advancement of Spatial Resolved Transcriptomics (SRT) technology, it is now possible to comprehensively measure gene transcription while preserving the spatial context of tissues. Spatial domain identification and gene denoising are key objectives in SRT data analysis. We propose a Contrastively Augmente... |
2201.04371 | Simon Labarthe | Guillaume Ravel (PLEIADE, BioGeCo), Michel Bergmann (MEMPHIS), Alain
Trubuil (MaIAGE), Julien Deschamps (MICALIS), Romain Briandet (MICALIS),
Simon Labarthe (PLEIADE, BioGeCo, MaIAGE) | Inferring characteristics of bacterial swimming in biofilm matrix from
time-lapse confocal laser scanning microscopy | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biofilms are spatially organized microorganism colonies embedded in a
self-produced matrix, conferring to the microbial community resistance to
environmental stresses. Motile bacteria have been observed swimming in the
matrix of pathogenic exogeneous host biofilms. This observation opened new
promising routes for del... | [
{
"created": "Wed, 12 Jan 2022 09:09:17 GMT",
"version": "v1"
},
{
"created": "Mon, 23 May 2022 08:19:17 GMT",
"version": "v2"
}
] | 2022-05-24 | [
[
"Ravel",
"Guillaume",
"",
"PLEIADE, BioGeCo"
],
[
"Bergmann",
"Michel",
"",
"MEMPHIS"
],
[
"Trubuil",
"Alain",
"",
"MaIAGE"
],
[
"Deschamps",
"Julien",
"",
"MICALIS"
],
[
"Briandet",
"Romain",
"",
"MICALIS"
],
[
... | Biofilms are spatially organized microorganism colonies embedded in a self-produced matrix, conferring to the microbial community resistance to environmental stresses. Motile bacteria have been observed swimming in the matrix of pathogenic exogeneous host biofilms. This observation opened new promising routes for delet... |
q-bio/0504032 | Chikara Furusawa | Chikara Furusawa and Kunihiko Kaneko | Evolutionary origin of power-laws in Biochemical Reaction Network;
embedding abundance distribution into topology | 11 pages, 3 figures | null | 10.1103/PhysRevE.73.011912 | null | q-bio.PE q-bio.MN | null | The evolutionary origin of universal statistics in biochemical reaction
network is studied, to explain the power-law distribution of reaction links and
the power-law distributions of chemical abundances. Using cell models with
catalytic reaction network, we find evidence that the power-law distribution in
abundances ... | [
{
"created": "Thu, 28 Apr 2005 07:13:55 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Furusawa",
"Chikara",
""
],
[
"Kaneko",
"Kunihiko",
""
]
] | The evolutionary origin of universal statistics in biochemical reaction network is studied, to explain the power-law distribution of reaction links and the power-law distributions of chemical abundances. Using cell models with catalytic reaction network, we find evidence that the power-law distribution in abundances of... |
2405.04920 | Nicola Dietler | Nicola Dietler, Alia Abbara, Subham Choudhury, Anne-Florence Bitbol | Impact of phylogeny on the inference of functional sectors from protein
sequence data | null | null | null | null | q-bio.PE physics.bio-ph q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Statistical analysis of multiple sequence alignments of homologous proteins
has revealed groups of coevolving amino acids called sectors. These groups of
amino-acid sites feature collective correlations in their amino-acid usage, and
they are associated to functional properties. Modeling showed that natural
selection... | [
{
"created": "Wed, 8 May 2024 09:42:08 GMT",
"version": "v1"
}
] | 2024-05-09 | [
[
"Dietler",
"Nicola",
""
],
[
"Abbara",
"Alia",
""
],
[
"Choudhury",
"Subham",
""
],
[
"Bitbol",
"Anne-Florence",
""
]
] | Statistical analysis of multiple sequence alignments of homologous proteins has revealed groups of coevolving amino acids called sectors. These groups of amino-acid sites feature collective correlations in their amino-acid usage, and they are associated to functional properties. Modeling showed that natural selection o... |
2309.17161 | Mark Van Der Wilk | Jacob Green, Cecilia Cabrera Diaz, Maximilian A. H. Jakobs, Andrea
Dimitracopoulos, Mark van der Wilk, Ryan D. Greenhalgh | Current Methods for Drug Property Prediction in the Real World | null | null | null | null | q-bio.BM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Predicting drug properties is key in drug discovery to enable de-risking of
assets before expensive clinical trials, and to find highly active compounds
faster. Interest from the Machine Learning community has led to the release of
a variety of benchmark datasets and proposed methods. However, it remains
unclear for ... | [
{
"created": "Tue, 25 Jul 2023 17:50:05 GMT",
"version": "v1"
}
] | 2023-10-02 | [
[
"Green",
"Jacob",
""
],
[
"Diaz",
"Cecilia Cabrera",
""
],
[
"Jakobs",
"Maximilian A. H.",
""
],
[
"Dimitracopoulos",
"Andrea",
""
],
[
"van der Wilk",
"Mark",
""
],
[
"Greenhalgh",
"Ryan D.",
""
]
] | Predicting drug properties is key in drug discovery to enable de-risking of assets before expensive clinical trials, and to find highly active compounds faster. Interest from the Machine Learning community has led to the release of a variety of benchmark datasets and proposed methods. However, it remains unclear for pr... |
1502.04307 | Peter O. Fedichev | D. Podolskiy, I. Molodtcov, A. Zenin, V. Kogan, L. I. Menshikov, Vadim
N. Gladyshev, Robert J. Shmookler Reis, and P. O. Fedichev | Critical dynamics of gene networks is a mechanism behind ageing and
Gompertz law | 22 pages, 9 figures | null | null | null | q-bio.MN physics.bio-ph q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although accumulation of molecular damage is suggested to be an important
molecular mechanism of aging, a quantitative link between the dynamics of
damage accumulation and mortality of species has so far remained elusive. To
address this question, we examine stability properties of a generic gene
regulatory network (... | [
{
"created": "Sun, 15 Feb 2015 12:41:44 GMT",
"version": "v1"
},
{
"created": "Wed, 23 Nov 2016 06:25:52 GMT",
"version": "v2"
}
] | 2016-11-24 | [
[
"Podolskiy",
"D.",
""
],
[
"Molodtcov",
"I.",
""
],
[
"Zenin",
"A.",
""
],
[
"Kogan",
"V.",
""
],
[
"Menshikov",
"L. I.",
""
],
[
"Gladyshev",
"Vadim N.",
""
],
[
"Reis",
"Robert J. Shmookler",
""
],
[
... | Although accumulation of molecular damage is suggested to be an important molecular mechanism of aging, a quantitative link between the dynamics of damage accumulation and mortality of species has so far remained elusive. To address this question, we examine stability properties of a generic gene regulatory network (GR... |
0801.4278 | Shu-Dong Zhang | Shu-Dong Zhang and Timothy W. Gant | A simple and robust method for connecting small-molecule drugs using
gene-expression signatures | 8 pages, 2 figures, and 2 tables; supplementary data supplied as a
ZIP file | BMC Bioinformatics 2008, 9:258 | 10.1186/1471-2105-9-258 | null | q-bio.QM q-bio.GN | null | Interaction of a drug or chemical with a biological system can result in a
gene-expression profile or signature characteristic of the event. Using a
suitably robust algorithm these signatures can potentially be used to connect
molecules with similar pharmacological or toxicological properties. The
Connectivity Map wa... | [
{
"created": "Mon, 28 Jan 2008 14:00:01 GMT",
"version": "v1"
}
] | 2008-06-02 | [
[
"Zhang",
"Shu-Dong",
""
],
[
"Gant",
"Timothy W.",
""
]
] | Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties. The Connectivity Map was ... |
1904.01847 | Tal Einav | Tal Einav, Rob Phillips | How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites
Affects Gene Expression | null | null | 10.1073/pnas.1905615116 | null | q-bio.SC | http://creativecommons.org/licenses/by/4.0/ | Although the key promoter elements necessary to drive transcription in
Escherichia coli have long been understood, we still cannot predict the
behavior of arbitrary novel promoters, hampering our ability to characterize
the myriad of sequenced regulatory architectures as well as to design novel
synthetic circuits. Th... | [
{
"created": "Wed, 3 Apr 2019 08:42:39 GMT",
"version": "v1"
}
] | 2022-10-12 | [
[
"Einav",
"Tal",
""
],
[
"Phillips",
"Rob",
""
]
] | Although the key promoter elements necessary to drive transcription in Escherichia coli have long been understood, we still cannot predict the behavior of arbitrary novel promoters, hampering our ability to characterize the myriad of sequenced regulatory architectures as well as to design novel synthetic circuits. This... |
1607.03955 | William Barendse PhD | Sean McWilliam, Peter M. Grewe, Rowan J. Bunch and William Barendse | A draft genome assembly of southern bluefin tuna Thunnus maccoyii | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tuna are large pelagic fish whose populations are close to panmixia. In
addition, they are threatened species, so it is important for the maintenance
and monitoring of genetic diversity that genetic information at a genome level
be obtained. Here we report the draft assembly of the southern bluefin tuna
genome and th... | [
{
"created": "Wed, 13 Jul 2016 23:20:06 GMT",
"version": "v1"
}
] | 2016-07-15 | [
[
"McWilliam",
"Sean",
""
],
[
"Grewe",
"Peter M.",
""
],
[
"Bunch",
"Rowan J.",
""
],
[
"Barendse",
"William",
""
]
] | Tuna are large pelagic fish whose populations are close to panmixia. In addition, they are threatened species, so it is important for the maintenance and monitoring of genetic diversity that genetic information at a genome level be obtained. Here we report the draft assembly of the southern bluefin tuna genome and the ... |
1301.0953 | Alex Volinsky | Alex A. Volinsky, Nikolai V. Gubarev, Galina M. Orlovskaya, Elena V.
Marchenko | Human anaerobic intestinal "rope" parasites | null | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human intestinal helminths are described in this paper. They can be over a
meter long, with an irregular cylindrical shape, resembling a rope. These
anaerobic intestinal "rope" parasites differ significantly from other
well-known intestinal parasites. Rope parasites can leave human body with
enemas, and are often mis... | [
{
"created": "Sat, 5 Jan 2013 23:18:37 GMT",
"version": "v1"
}
] | 2013-01-08 | [
[
"Volinsky",
"Alex A.",
""
],
[
"Gubarev",
"Nikolai V.",
""
],
[
"Orlovskaya",
"Galina M.",
""
],
[
"Marchenko",
"Elena V.",
""
]
] | Human intestinal helminths are described in this paper. They can be over a meter long, with an irregular cylindrical shape, resembling a rope. These anaerobic intestinal "rope" parasites differ significantly from other well-known intestinal parasites. Rope parasites can leave human body with enemas, and are often mista... |
1307.3434 | Jacob Kuriyan | Jacob Kuriyan, Nathaniel Cobb | Forecasts of Cancer and Chronic Patients: Big Data Metrics of Population
Health | 26 pages, 6 figures and 6 tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chronic diseases and cancer account for over 75 percent of healthcare costs
in the US. Increased prevention services and improved primary care are thought
to decrease costs. Current models for detecting changes in the health of
populations are cumbersome and expensive, and are not sensitive in the short
term. In this... | [
{
"created": "Fri, 12 Jul 2013 12:25:24 GMT",
"version": "v1"
}
] | 2013-07-15 | [
[
"Kuriyan",
"Jacob",
""
],
[
"Cobb",
"Nathaniel",
""
]
] | Chronic diseases and cancer account for over 75 percent of healthcare costs in the US. Increased prevention services and improved primary care are thought to decrease costs. Current models for detecting changes in the health of populations are cumbersome and expensive, and are not sensitive in the short term. In this p... |
q-bio/0311021 | M. J. Gagen | Larry J. Croft, Martin J. Lercher, Michael J. Gagen, John S. Mattick | Is prokaryotic complexity limited by accelerated growth in regulatory
overhead? | 10 pages, 1 figure | null | null | null | q-bio.MN q-bio.GN | null | Increased biological complexity is generally associated with the addition of
new genetic information, which must be integrated into the existing regulatory
network that operates within the cell. General arguments on network control, as
well as several recent genomic observations, indicate that regulatory gene
number ... | [
{
"created": "Sat, 15 Nov 2003 09:15:54 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Croft",
"Larry J.",
""
],
[
"Lercher",
"Martin J.",
""
],
[
"Gagen",
"Michael J.",
""
],
[
"Mattick",
"John S.",
""
]
] | Increased biological complexity is generally associated with the addition of new genetic information, which must be integrated into the existing regulatory network that operates within the cell. General arguments on network control, as well as several recent genomic observations, indicate that regulatory gene number gr... |
2004.06107 | Vasiliy Leonenko | Vasiliy N. Leonenko | Analyzing the spatial distribution of acute coronary syndrome cases
using synthesized data on arterial hypertension prevalence | Accepted for publication in the ICCS 2020 proceedings (Springer
Lecture Notes in Computer Science series) | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the current study, the authors demonstrate the method aimed at analyzing
the distribution of acute coronary syndrome (ACS) cases in Saint Petersburg
using the synthetic population approach and a statistical model for arterial
hypertension prevalence. The cumulative number of emergency services calls in a
separate ... | [
{
"created": "Fri, 10 Apr 2020 19:47:02 GMT",
"version": "v1"
}
] | 2020-04-15 | [
[
"Leonenko",
"Vasiliy N.",
""
]
] | In the current study, the authors demonstrate the method aimed at analyzing the distribution of acute coronary syndrome (ACS) cases in Saint Petersburg using the synthetic population approach and a statistical model for arterial hypertension prevalence. The cumulative number of emergency services calls in a separate ge... |
2402.15186 | Yousong Peng | Yifan Wu, Yousong Peng | Ten computational challenges in human virome studies | 16 pages, 1 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | In recent years, substantial advancements have been achieved in understanding
the diversity of the human virome and its intricate roles in human health and
diseases. Despite this progress, the field of human virome research remains
nascent, primarily hindered by the absence of effective methods, particularly
in the d... | [
{
"created": "Fri, 23 Feb 2024 08:33:00 GMT",
"version": "v1"
}
] | 2024-02-26 | [
[
"Wu",
"Yifan",
""
],
[
"Peng",
"Yousong",
""
]
] | In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent, primarily hindered by the absence of effective methods, particularly in the dom... |
1407.0972 | Walter S. Lasecki | Mircea Davidescu, Iain Couzin | Transient Leadership and Collective Cell Movement in Early Diverged
Multicellular Animals | null | null | null | ci-2014/51 | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Collective motion of cells is critical to some of the most vital tasks
including wound healing, development, and immune response [Friedl and Gilmour
2009; Tokarski et al. 2012; Lee et al. 2012; Beltman et al. 2009], and is
common to many pathological processes including cancer cell invasion and
teratogenesis [Khalil ... | [
{
"created": "Mon, 30 Jun 2014 02:26:31 GMT",
"version": "v1"
}
] | 2014-07-04 | [
[
"Davidescu",
"Mircea",
""
],
[
"Couzin",
"Iain",
""
]
] | Collective motion of cells is critical to some of the most vital tasks including wound healing, development, and immune response [Friedl and Gilmour 2009; Tokarski et al. 2012; Lee et al. 2012; Beltman et al. 2009], and is common to many pathological processes including cancer cell invasion and teratogenesis [Khalil an... |
2310.01392 | Sangeeta Saha | Sangeeta Saha, Swadesh Pal and Roderick Melnik | The analysis of the impact of fear in the presence of additional food
and prey refuge with nonlocal predator-prey models | 26 pages, 28 figures | null | null | null | q-bio.PE math.DS | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In a predator-prey interaction, many factors are present that affect the
growth of the species, either positively or negatively. Fear of predation is
such a factor that causes psychological stress in a prey species, so their
overall growth starts to decline. In this work, a predator-prey model is
proposed where the p... | [
{
"created": "Mon, 2 Oct 2023 17:50:22 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Jun 2024 22:01:44 GMT",
"version": "v2"
}
] | 2024-06-18 | [
[
"Saha",
"Sangeeta",
""
],
[
"Pal",
"Swadesh",
""
],
[
"Melnik",
"Roderick",
""
]
] | In a predator-prey interaction, many factors are present that affect the growth of the species, either positively or negatively. Fear of predation is such a factor that causes psychological stress in a prey species, so their overall growth starts to decline. In this work, a predator-prey model is proposed where the pre... |
1403.7105 | Dur-e-Zehta Baig | Dur-e-Zehra Baig | Physiological Control of Human Heart Rate and Oxygen Consumption during
Rhythmic Exercises | null | null | null | null | q-bio.QM cs.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Physical exercise has significant benefits for humans in improving the health
and quality of their lives, by improving the functional performance of their
cardiovascular and respiratory systems. However, it is very important to
control the workload, e.g. the frequency of body movements, within the
capability of the i... | [
{
"created": "Sat, 15 Mar 2014 05:53:19 GMT",
"version": "v1"
}
] | 2014-03-28 | [
[
"Baig",
"Dur-e-Zehra",
""
]
] | Physical exercise has significant benefits for humans in improving the health and quality of their lives, by improving the functional performance of their cardiovascular and respiratory systems. However, it is very important to control the workload, e.g. the frequency of body movements, within the capability of the ind... |
1305.5363 | David Golan | David Golan and Saharon Rosset | Narrowing the gap on heritability of common disease by direct estimation
in case-control GWAS | main text: 30 pages, 4 figures. Supplementary text: 35 pages, 16
figures | null | null | null | q-bio.PE q-bio.QM stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the major developments in recent years in the search for missing
heritability of human phenotypes is the adoption of linear mixed-effects models
(LMMs) to estimate heritability due to genetic variants which are not
significantly associated with the phenotype. A variant of the LMM approach has
been adapted to c... | [
{
"created": "Thu, 23 May 2013 09:48:55 GMT",
"version": "v1"
},
{
"created": "Mon, 27 May 2013 10:46:32 GMT",
"version": "v2"
}
] | 2013-05-28 | [
[
"Golan",
"David",
""
],
[
"Rosset",
"Saharon",
""
]
] | One of the major developments in recent years in the search for missing heritability of human phenotypes is the adoption of linear mixed-effects models (LMMs) to estimate heritability due to genetic variants which are not significantly associated with the phenotype. A variant of the LMM approach has been adapted to cas... |
1501.01144 | Tomasz Rutkowski | Katsuhiko Hamada, Hiromu Mori, Hiroyuki Shinoda, and Tomasz M.
Rutkowski | Airborne Ultrasonic Tactile Display BCI | arXiv admin note: substantial text overlap with arXiv:1404.4184 | Brain-Computer Interface Research - A State-of-the-Art Summary 4.
SpringerBriefs in Electrical and Computer Engineering. 2015. p. 57-65 | 10.1007/978-3-319-25190-5_6 | null | q-bio.NC cs.HC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | This chapter presents results of our project, which studied whether
contactless and airborne ultrasonic tactile display (AUTD) stimuli delivered to
a user's palms could serve as a platform for a brain computer interface (BCI)
paradigm. We used six palm positions to evoke combined somatosensory brain
responses to impl... | [
{
"created": "Tue, 6 Jan 2015 10:58:27 GMT",
"version": "v1"
},
{
"created": "Sat, 2 Jan 2016 06:32:29 GMT",
"version": "v2"
}
] | 2016-01-05 | [
[
"Hamada",
"Katsuhiko",
""
],
[
"Mori",
"Hiromu",
""
],
[
"Shinoda",
"Hiroyuki",
""
],
[
"Rutkowski",
"Tomasz M.",
""
]
] | This chapter presents results of our project, which studied whether contactless and airborne ultrasonic tactile display (AUTD) stimuli delivered to a user's palms could serve as a platform for a brain computer interface (BCI) paradigm. We used six palm positions to evoke combined somatosensory brain responses to implem... |
2012.10687 | Nicola Vassena | Nicola Vassena | Sensitivity of metabolic networks: perturbing metabolite concentrations | null | null | null | null | q-bio.MN math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sensitivity studies the network response to perturbations. We consider local
perturbations of the concentrations of metabolites at an equilibrium. We
investigate the responses in the network, both of the metabolite concentrations
and of the reaction fluxes. Our approach is purely qualitative, rather than
quantitative... | [
{
"created": "Sat, 19 Dec 2020 13:47:06 GMT",
"version": "v1"
}
] | 2020-12-22 | [
[
"Vassena",
"Nicola",
""
]
] | Sensitivity studies the network response to perturbations. We consider local perturbations of the concentrations of metabolites at an equilibrium. We investigate the responses in the network, both of the metabolite concentrations and of the reaction fluxes. Our approach is purely qualitative, rather than quantitative. ... |
1010.2842 | Harold P. de Vladar | Harold P. de Vladar and Nick Barton | The statistical mechanics of a polygenic characterunder stabilizing
selection, mutation and drift | 35 pages, 8 figures | null | 10.1098/rsif.2010.0438 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | By exploiting an analogy between population genetics and statistical
mechanics, we study the evolution of a polygenic trait under stabilizing
selection, mutation, and genetic drift. This requires us to track only four
macroscopic variables, instead of the distribution of all the allele
frequencies that influence the ... | [
{
"created": "Thu, 14 Oct 2010 07:48:44 GMT",
"version": "v1"
}
] | 2010-11-18 | [
[
"de Vladar",
"Harold P.",
""
],
[
"Barton",
"Nick",
""
]
] | By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation, and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the tr... |
0902.0622 | Michael B\"orsch | A. Kovalev, N. Zarrabi, F. Werz, M. Boersch, Z. Ristic, H. Lill, D.
Bald, C. Tietz, J. Wrachtrup | Hidden Semi-Markov Models for Single-Molecule Conformational Dynamics | 23 pages, 11 figures | null | null | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The conformational kinetics of enzymes can be reliably revealed when they are
governed by Markovian dynamics. Hidden Markov Models (HMMs) are appropriate
especially in the case of conformational states that are hardly
distinguishable. However, the evolution of the conformational states of
proteins mostly shows non-Ma... | [
{
"created": "Tue, 3 Feb 2009 21:21:51 GMT",
"version": "v1"
}
] | 2009-02-05 | [
[
"Kovalev",
"A.",
""
],
[
"Zarrabi",
"N.",
""
],
[
"Werz",
"F.",
""
],
[
"Boersch",
"M.",
""
],
[
"Ristic",
"Z.",
""
],
[
"Lill",
"H.",
""
],
[
"Bald",
"D.",
""
],
[
"Tietz",
"C.",
""
],
... | The conformational kinetics of enzymes can be reliably revealed when they are governed by Markovian dynamics. Hidden Markov Models (HMMs) are appropriate especially in the case of conformational states that are hardly distinguishable. However, the evolution of the conformational states of proteins mostly shows non-Mark... |
1712.02150 | Abhishek Dey | Abhishek Dey, Kushal Chakrabarti, Krishan Kumar Gola and Shaunak Sen | A Kalman Filter Approach for Biomolecular Systems with Noise Covariance
Updating | 23 pages, 9 figures | null | null | null | q-bio.QM stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An important part of system modeling is determining parameter values,
particularly for biomolecular systems, where direct measurements of individual
parameters are typically hard. While Extended Kalman Filters have been used for
this purpose, the choice of the process noise covariance is generally unclear.
In this ch... | [
{
"created": "Wed, 6 Dec 2017 12:09:42 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Apr 2018 10:12:15 GMT",
"version": "v2"
},
{
"created": "Mon, 12 Nov 2018 15:34:11 GMT",
"version": "v3"
}
] | 2018-11-13 | [
[
"Dey",
"Abhishek",
""
],
[
"Chakrabarti",
"Kushal",
""
],
[
"Gola",
"Krishan Kumar",
""
],
[
"Sen",
"Shaunak",
""
]
] | An important part of system modeling is determining parameter values, particularly for biomolecular systems, where direct measurements of individual parameters are typically hard. While Extended Kalman Filters have been used for this purpose, the choice of the process noise covariance is generally unclear. In this chap... |
1408.0907 | Alfredo Braunstein | Fabrizio Altarelli, Alfredo Braunstein, Luca Dall'Asta, Alessandro
Ingrosso, Riccardo Zecchina | The zero-patient problem with noisy observations | null | J. Stat. Mech. (2014) P10016 | 10.1088/1742-5468/2014/10/P10016 | null | q-bio.PE cond-mat.stat-mech q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A Belief Propagation approach has been recently proposed for the zero-patient
problem in a SIR epidemics. The zero-patient problem consists in finding the
initial source of an epidemic outbreak given observations at a later time. In
this work, we study a harder but related inference problem, in which
observations are... | [
{
"created": "Tue, 5 Aug 2014 09:47:29 GMT",
"version": "v1"
}
] | 2015-07-10 | [
[
"Altarelli",
"Fabrizio",
""
],
[
"Braunstein",
"Alfredo",
""
],
[
"Dall'Asta",
"Luca",
""
],
[
"Ingrosso",
"Alessandro",
""
],
[
"Zecchina",
"Riccardo",
""
]
] | A Belief Propagation approach has been recently proposed for the zero-patient problem in a SIR epidemics. The zero-patient problem consists in finding the initial source of an epidemic outbreak given observations at a later time. In this work, we study a harder but related inference problem, in which observations are n... |
1312.3260 | James Lindesay | James Lindesay, Tshela E. Mason, William Hercules, and Georgia M.
Dunston | The Foundations of Genodynamics: The Development of Metrics for
Genomic-Environmental Interactions | 22 pages, 14 figures | null | null | null | q-bio.GN physics.bio-ph q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Single nucleotide polymorphisms (SNPs) represent an important type of dynamic
sites within the human genome. These common variants often locally correlate
into more complex multi-SNP haploblocks that are maintained throughout
generations in a stable population. The information encoded in the structure of
common SNPs ... | [
{
"created": "Wed, 11 Dec 2013 17:51:56 GMT",
"version": "v1"
}
] | 2013-12-12 | [
[
"Lindesay",
"James",
""
],
[
"Mason",
"Tshela E.",
""
],
[
"Hercules",
"William",
""
],
[
"Dunston",
"Georgia M.",
""
]
] | Single nucleotide polymorphisms (SNPs) represent an important type of dynamic sites within the human genome. These common variants often locally correlate into more complex multi-SNP haploblocks that are maintained throughout generations in a stable population. The information encoded in the structure of common SNPs an... |
2001.02436 | Joel Miller | Joel C. Miller and Tony TIng | EoN (Epidemics on Networks): a fast, flexible Python package for
simulation, analytic approximation, and analysis of epidemics on networks | This paper is available in a shorter form without examples at
https://joss.theoj.org/papers/10.21105/joss.01731.pdf | Journal of Open Source Software, 4(44), 1731 (2019) | 10.21105/joss.01731 | null | q-bio.QM physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We provide a description of the Epidemics on Networks (EoN) python package
designed for studying disease spread in static networks. The package consists
of over $100$ methods available for users to perform stochastic simulation of a
range of different processes including SIS and SIR disease, and generic simple
or com... | [
{
"created": "Wed, 8 Jan 2020 10:15:47 GMT",
"version": "v1"
},
{
"created": "Sat, 18 Jan 2020 15:11:17 GMT",
"version": "v2"
}
] | 2020-01-22 | [
[
"Miller",
"Joel C.",
""
],
[
"TIng",
"Tony",
""
]
] | We provide a description of the Epidemics on Networks (EoN) python package designed for studying disease spread in static networks. The package consists of over $100$ methods available for users to perform stochastic simulation of a range of different processes including SIS and SIR disease, and generic simple or comle... |
2403.01702 | Wenjia Shi | Wenjia Shi, Yao Ma, Peilin Hu, Mi Pang, Xiaona Huang, Yiting Dang,
Yuxin Xie, Danni Wu | Hill Function-based Model of Transcriptional Response: Impact of
Nonspecific Binding and RNAP Interactions | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hill function is one of the widely used gene transcription regulation models.
Its attribute of fitting may result in a lack of an underlying physical
picture, yet the fitting parameters can provide information about biochemical
reactions, such as the number of transcription factors (TFs) and the binding
energy betwee... | [
{
"created": "Mon, 4 Mar 2024 03:32:56 GMT",
"version": "v1"
}
] | 2024-03-05 | [
[
"Shi",
"Wenjia",
""
],
[
"Ma",
"Yao",
""
],
[
"Hu",
"Peilin",
""
],
[
"Pang",
"Mi",
""
],
[
"Huang",
"Xiaona",
""
],
[
"Dang",
"Yiting",
""
],
[
"Xie",
"Yuxin",
""
],
[
"Wu",
"Danni",
""
]... | Hill function is one of the widely used gene transcription regulation models. Its attribute of fitting may result in a lack of an underlying physical picture, yet the fitting parameters can provide information about biochemical reactions, such as the number of transcription factors (TFs) and the binding energy between ... |
2402.11950 | Tadahaya Mizuno | Yasuhiro Yoshikai, Tadahaya Mizuno, Shumpei Nemoto, Hiroyuki Kusuhara | A novel molecule generative model of VAE combined with Transformer for
unseen structure generation | 23 pages, 9 figures | null | null | null | q-bio.BM cs.LG physics.chem-ph | http://creativecommons.org/licenses/by/4.0/ | Recently, molecule generation using deep learning has been actively
investigated in drug discovery. In this field, Transformer and VAE are widely
used as powerful models, but they are rarely used in combination due to
structural and performance mismatch of them. This study proposes a model that
combines these two mod... | [
{
"created": "Mon, 19 Feb 2024 08:46:04 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Apr 2024 08:51:55 GMT",
"version": "v2"
}
] | 2024-04-08 | [
[
"Yoshikai",
"Yasuhiro",
""
],
[
"Mizuno",
"Tadahaya",
""
],
[
"Nemoto",
"Shumpei",
""
],
[
"Kusuhara",
"Hiroyuki",
""
]
] | Recently, molecule generation using deep learning has been actively investigated in drug discovery. In this field, Transformer and VAE are widely used as powerful models, but they are rarely used in combination due to structural and performance mismatch of them. This study proposes a model that combines these two model... |
1405.5559 | Stanley Lazic | Stanley E. Lazic, Johannes Fuss, Peter Gass | Quantifying the behavioural relevance of hippocampal neurogenesis | To be published in PLoS ONE | null | 10.1371/journal.pone.0113855 | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Few studies that examine the neurogenesis--behaviour relationship formally
establish covariation between neurogenesis and behaviour or rule out competing
explanations. The behavioural relevance of neurogenesis might therefore be
overestimated if other mechanisms account for some, or even all, of the
experimental effe... | [
{
"created": "Wed, 21 May 2014 21:21:02 GMT",
"version": "v1"
},
{
"created": "Sun, 9 Nov 2014 18:35:29 GMT",
"version": "v2"
}
] | 2015-06-19 | [
[
"Lazic",
"Stanley E.",
""
],
[
"Fuss",
"Johannes",
""
],
[
"Gass",
"Peter",
""
]
] | Few studies that examine the neurogenesis--behaviour relationship formally establish covariation between neurogenesis and behaviour or rule out competing explanations. The behavioural relevance of neurogenesis might therefore be overestimated if other mechanisms account for some, or even all, of the experimental effect... |
1009.2095 | Benjamin Machta | Benjamin B. Machta, Stefanos Papanikolaou, James P. Sethna, Sarah L.
Veatch | A minimal model of plasma membrane heterogeneity requires coupling
cortical actin to criticality | 18 pages, 5 figures and 12 page Supplement (2 additional figures) | Biophysical Journal, Volume 100, Issue 7, 1668-1677, 2011 | 10.1016/j.bpj.2011.02.029 | null | q-bio.SC cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a minimal model of plasma membrane heterogeneity that combines
criticality with connectivity to cortical cytoskeleton. Our model is motivated
by recent observations of micron-sized critical fluctuations in plasma membrane
vesicles that are detached from their cortical cytoskeleton. We incorporate
criticali... | [
{
"created": "Fri, 10 Sep 2010 20:11:34 GMT",
"version": "v1"
}
] | 2012-03-13 | [
[
"Machta",
"Benjamin B.",
""
],
[
"Papanikolaou",
"Stefanos",
""
],
[
"Sethna",
"James P.",
""
],
[
"Veatch",
"Sarah L.",
""
]
] | We present a minimal model of plasma membrane heterogeneity that combines criticality with connectivity to cortical cytoskeleton. Our model is motivated by recent observations of micron-sized critical fluctuations in plasma membrane vesicles that are detached from their cortical cytoskeleton. We incorporate criticality... |
1510.01935 | Erik Yusko | Erik C. Yusko, Brandon R. Bruhn, Olivia Eggenberger, Jared
Houghtaling, Ryan C. Rollings, Nathan C. Walsh, Santoshi Nandivada, Mariya
Pindrus, Adam R. Hall, David Sept, Jiali Li, Devendra S. Kalonia, Michael
Mayer | Real-time shape approximation and 5-D fingerprinting of single proteins | null | null | 10.1038/nnano.2016.267 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work exploits the zeptoliter sensing volume of electrolyte-filled
nanopores to determine, simultaneously and in real time, the approximate shape,
volume, charge, rotational diffusion coefficient, and dipole moment of
individual proteins. We have developed the theory for a quantitative
understanding and analysis ... | [
{
"created": "Sat, 29 Aug 2015 20:04:10 GMT",
"version": "v1"
}
] | 2017-04-26 | [
[
"Yusko",
"Erik C.",
""
],
[
"Bruhn",
"Brandon R.",
""
],
[
"Eggenberger",
"Olivia",
""
],
[
"Houghtaling",
"Jared",
""
],
[
"Rollings",
"Ryan C.",
""
],
[
"Walsh",
"Nathan C.",
""
],
[
"Nandivada",
"Santoshi",
... | This work exploits the zeptoliter sensing volume of electrolyte-filled nanopores to determine, simultaneously and in real time, the approximate shape, volume, charge, rotational diffusion coefficient, and dipole moment of individual proteins. We have developed the theory for a quantitative understanding and analysis of... |
1602.05092 | Andrea Barreiro | Andrea K. Barreiro and J. Nathan Kutz and Eli Shlizerman | Symmetries constrain dynamics in a family of balanced neural networks | In review; submitted 1/21/2016 Revision submitted 9/24/16 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We examine a family of random firing-rate neural networks in which we enforce
the neurobiological constraint of Dale's Law --- each neuron makes either
excitatory or inhibitory connections onto its post-synaptic targets. We find
that this constrained system may be described as a perturbation from a system
with non-tr... | [
{
"created": "Tue, 16 Feb 2016 16:50:15 GMT",
"version": "v1"
},
{
"created": "Sat, 24 Sep 2016 22:06:12 GMT",
"version": "v2"
}
] | 2016-09-27 | [
[
"Barreiro",
"Andrea K.",
""
],
[
"Kutz",
"J. Nathan",
""
],
[
"Shlizerman",
"Eli",
""
]
] | We examine a family of random firing-rate neural networks in which we enforce the neurobiological constraint of Dale's Law --- each neuron makes either excitatory or inhibitory connections onto its post-synaptic targets. We find that this constrained system may be described as a perturbation from a system with non-triv... |
q-bio/0611053 | N. Jacq | L.-M. Birkholtz, O. Bastien (DRDC), G. Wells, D. Grando (DRDC), F.
Joubert, V. Kasam (LPC-Clermont), M. Zimmermann, P. Ortet (DEVM), N. Jacq
(LPC-Clermont), S. Roy (DRDC/Bim), M. Hoffmann-Apitius, V. Breton
(LPC-Clermont), A. I. Louw, E. Mar\'echal (DRDC) | Integration and mining of malaria molecular, functional and
pharmacological data: how far are we from a chemogenomic knowledge space? | 43 pages, 4 figures, to appear in Malaria Journal | Malaria Journal 5 (2006) 1-24 | 10.1186/1475-2875-5-110 | null | q-bio.QM cs.DC q-bio.GN | null | The organization and mining of malaria genomic and post-genomic data is
highly motivated by the necessity to predict and characterize new biological
targets and new drugs. Biological targets are sought in a biological space
designed from the genomic data from Plasmodium falciparum, but using also the
millions of geno... | [
{
"created": "Fri, 17 Nov 2006 10:24:23 GMT",
"version": "v1"
}
] | 2016-08-16 | [
[
"Birkholtz",
"L. -M.",
"",
"DRDC"
],
[
"Bastien",
"O.",
"",
"DRDC"
],
[
"Wells",
"G.",
"",
"DRDC"
],
[
"Grando",
"D.",
"",
"DRDC"
],
[
"Joubert",
"F.",
"",
"LPC-Clermont"
],
[
"Kasam",
"V.",
"",
"LP... | The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomi... |
q-bio/0601050 | Hiro-Sato Niwa | Hiro-Sato Niwa | Exploitation dynamics of fish stocks | 27 pages, 19 figures | Ecological Informatics 1 (2006) 87-99 | 10.1016/j.ecoinf.2005.10.002 | null | q-bio.PE cond-mat.stat-mech | null | I address the question of the fluctuations in fishery landings. Using the
fishery statistics time-series collected by the Food and Agriculture
Organization of the United Nations since the early 1950s, I here analyze
fishing activities and find two scaling features of capture fisheries
production: (i) the standard dev... | [
{
"created": "Tue, 31 Jan 2006 02:17:47 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Niwa",
"Hiro-Sato",
""
]
] | I address the question of the fluctuations in fishery landings. Using the fishery statistics time-series collected by the Food and Agriculture Organization of the United Nations since the early 1950s, I here analyze fishing activities and find two scaling features of capture fisheries production: (i) the standard devia... |
1302.3832 | Silvio Ferreira | Leticia R Paiva, Hallan S Silva, Silvio C Ferreira and Marcelo L
Martins | Multiscale model for the effects of adaptive immunity suppression on the
viral therapy of cancer | 14 pages, 4 figures | null | 10.1088/1478-3975/10/2/025005 | null | q-bio.TO physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Oncolytic virotherapy - the use of viruses that specifically kill tumor cells
- is an innovative and highly promising route for treating cancer. However, its
therapeutic outcomes are mainly impaired by the host immune response to the
viral infection. In the present work, we propose a multiscale mathematical
model to ... | [
{
"created": "Fri, 15 Feb 2013 18:20:51 GMT",
"version": "v1"
}
] | 2015-06-15 | [
[
"Paiva",
"Leticia R",
""
],
[
"Silva",
"Hallan S",
""
],
[
"Ferreira",
"Silvio C",
""
],
[
"Martins",
"Marcelo L",
""
]
] | Oncolytic virotherapy - the use of viruses that specifically kill tumor cells - is an innovative and highly promising route for treating cancer. However, its therapeutic outcomes are mainly impaired by the host immune response to the viral infection. In the present work, we propose a multiscale mathematical model to st... |
1701.07138 | Wiktor Mlynarski | Wiktor M{\l}ynarski, Josh H. McDermott | Learning Mid-Level Auditory Codes from Natural Sound Statistics | 38 pages, 12 figures | null | null | null | q-bio.NC cs.SD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Interaction with the world requires an organism to transform sensory signals
into representations in which behaviorally meaningful properties of the
environment are made explicit. These representations are derived through
cascades of neuronal processing stages in which neurons at each stage recode
the output of prece... | [
{
"created": "Wed, 25 Jan 2017 02:00:50 GMT",
"version": "v1"
},
{
"created": "Thu, 26 Jan 2017 16:34:43 GMT",
"version": "v2"
},
{
"created": "Fri, 27 Jan 2017 19:21:10 GMT",
"version": "v3"
},
{
"created": "Mon, 15 May 2017 21:39:01 GMT",
"version": "v4"
},
{
"c... | 2017-10-17 | [
[
"Młynarski",
"Wiktor",
""
],
[
"McDermott",
"Josh H.",
""
]
] | Interaction with the world requires an organism to transform sensory signals into representations in which behaviorally meaningful properties of the environment are made explicit. These representations are derived through cascades of neuronal processing stages in which neurons at each stage recode the output of precedi... |
1704.08945 | Saar Rahav | Ilana Bogod, Saar Rahav | Kinetic discrimination of a polymerase in the presence of obstacles | 16 pages, 4 figures | Phys. Rev. E, v95, 042408 (2017) | 10.1103/PhysRevE.95.042408 | null | q-bio.SC cond-mat.soft cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the causes of high fidelity of copying in biological systems is
kinetic discrimination. In this mechanism larger dissipation and copying
velocity result in improved copying accuracy. We consider a model of a
polymerase which simultaneously copies a single stranded RNA and opens a
single- to double-stranded jun... | [
{
"created": "Wed, 26 Apr 2017 12:32:04 GMT",
"version": "v1"
}
] | 2017-05-01 | [
[
"Bogod",
"Ilana",
""
],
[
"Rahav",
"Saar",
""
]
] | One of the causes of high fidelity of copying in biological systems is kinetic discrimination. In this mechanism larger dissipation and copying velocity result in improved copying accuracy. We consider a model of a polymerase which simultaneously copies a single stranded RNA and opens a single- to double-stranded junct... |
1911.02803 | Olivier Rivoire | Olivier Rivoire | Geometry and flexibility of optimal catalysts in a minimal elastic
network model | null | null | null | null | q-bio.BM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have a general knowledge of the principles by which catalysts accelerate
the rate of chemical reactions but no precise understanding of the geometrical
and physical constraints to which their design is subject. To analyze these
constraints, we introduce a minimal model of catalysis based on elastic
networks where ... | [
{
"created": "Thu, 7 Nov 2019 08:44:16 GMT",
"version": "v1"
}
] | 2019-11-11 | [
[
"Rivoire",
"Olivier",
""
]
] | We have a general knowledge of the principles by which catalysts accelerate the rate of chemical reactions but no precise understanding of the geometrical and physical constraints to which their design is subject. To analyze these constraints, we introduce a minimal model of catalysis based on elastic networks where th... |
2404.17603 | Meshach Ndlovu | Meshach Ndlovu | Assessing biological control method on the progression of anaplasmosis
disease in dominant cattle species in the Matabeleland north province
Zimbabwe | null | null | null | null | q-bio.PE math.DS | http://creativecommons.org/licenses/by/4.0/ | This paper presents a compartmental model for the transmission dynamics of
Anaplasmosis in resource limited farmers cattle subjected to a biological
control method. The study seeks to evaluate the stability and control of cattle
herds dynamics relative to finite agitation. Anaplasmosis disease pose a major
threat in ... | [
{
"created": "Wed, 24 Apr 2024 18:40:32 GMT",
"version": "v1"
}
] | 2024-04-30 | [
[
"Ndlovu",
"Meshach",
""
]
] | This paper presents a compartmental model for the transmission dynamics of Anaplasmosis in resource limited farmers cattle subjected to a biological control method. The study seeks to evaluate the stability and control of cattle herds dynamics relative to finite agitation. Anaplasmosis disease pose a major threat in er... |
1305.7068 | Yann Ponty | Vladimir Reinharz, Yann Ponty (LIX, INRIA Saclay - Ile de France),
J\'er\^ome Waldisp\"uhl | Using structural and evolutionary information to detect and correct
pyrosequencing errors in non-coding RNAs | Extended version of RECOMB'13 | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Analysis of the sequence-structure relationship in RNA molecules are
essential to evolutionary studies but also to concrete applications such as
error-correction methodologies in sequencing technologies. The prohibitive
sizes of the mutational and conformational landscapes combined with the volume
of data to proceed ... | [
{
"created": "Thu, 30 May 2013 11:47:24 GMT",
"version": "v1"
}
] | 2013-05-31 | [
[
"Reinharz",
"Vladimir",
"",
"LIX, INRIA Saclay - Ile de France"
],
[
"Ponty",
"Yann",
"",
"LIX, INRIA Saclay - Ile de France"
],
[
"Waldispühl",
"Jérôme",
""
]
] | Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the mutational and conformational landscapes combined with the volume of data to proceed re... |
0902.0959 | Michael E. Wall | Michael E. Wall, David A. Markowitz, Judah L. Rosner, Robert G. Martin | Model of Transcriptional Activation by MarA in Escherichia coli | 30 pages, 2 figures | null | 10.1016/j.bpj.2009.12.397 | LA-UR-09-00238 | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have developed a mathematical model of transcriptional activation by MarA
in Escherichia coli, and used the model to analyze measurements of
MarA-dependent activity of the marRAB, sodA, and micF promoters in mar-rob-
cells. The model rationalizes an unexpected poor correlation between the
mid-point of in vivo prom... | [
{
"created": "Thu, 5 Feb 2009 18:59:55 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Wall",
"Michael E.",
""
],
[
"Markowitz",
"David A.",
""
],
[
"Rosner",
"Judah L.",
""
],
[
"Martin",
"Robert G.",
""
]
] | We have developed a mathematical model of transcriptional activation by MarA in Escherichia coli, and used the model to analyze measurements of MarA-dependent activity of the marRAB, sodA, and micF promoters in mar-rob- cells. The model rationalizes an unexpected poor correlation between the mid-point of in vivo promot... |
1106.6319 | Joel Miller | Joel C. Miller and Erik M. Volz | Edge-based compartmental modeling for epidemic spread Part II: Model
Selection and Hierarchies | null | Journal of Mathematical Biology October 2013, Volume 67, Issue 4,
pp 869-899 | 10.1007/s00285-012-0572-3 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the edge-based compartmental models for epidemic spread developed
in Part I. We show conditions under which simpler models may be substituted for
more detailed models, and in so doing we define a hierarchy of epidemic models.
In particular we provide conditions under which it is appropriate to use the
sta... | [
{
"created": "Thu, 30 Jun 2011 18:10:10 GMT",
"version": "v1"
}
] | 2015-09-03 | [
[
"Miller",
"Joel C.",
""
],
[
"Volz",
"Erik M.",
""
]
] | We consider the edge-based compartmental models for epidemic spread developed in Part I. We show conditions under which simpler models may be substituted for more detailed models, and in so doing we define a hierarchy of epidemic models. In particular we provide conditions under which it is appropriate to use the stand... |
2308.09086 | Lucian Chan | Lucian Chan and Marcel Verdonk and Carl Poelking | Embracing assay heterogeneity with neural processes for markedly
improved bioactivity predictions | null | null | null | null | q-bio.QM cs.LG q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Predicting the bioactivity of a ligand is one of the hardest and most
important challenges in computer-aided drug discovery. Despite years of data
collection and curation efforts by research organizations worldwide,
bioactivity data remains sparse and heterogeneous, thus hampering efforts to
build predictive models t... | [
{
"created": "Thu, 17 Aug 2023 16:26:58 GMT",
"version": "v1"
}
] | 2023-08-21 | [
[
"Chan",
"Lucian",
""
],
[
"Verdonk",
"Marcel",
""
],
[
"Poelking",
"Carl",
""
]
] | Predicting the bioactivity of a ligand is one of the hardest and most important challenges in computer-aided drug discovery. Despite years of data collection and curation efforts by research organizations worldwide, bioactivity data remains sparse and heterogeneous, thus hampering efforts to build predictive models tha... |
2007.02197 | Mar\'ia da Fonseca | Mar\'ia da Fonseca and In\'es Samengo | Statistical properties of color matching functions | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In trichromats, color vision entails the projection of an
infinite-dimensional space (the one containing all possible electromagnetic
power spectra) onto the 3-dimensional space that modulates the activity of the
three types of cones. This drastic reduction in dimensionality gives rise to
metamerism, that is, the per... | [
{
"created": "Sat, 4 Jul 2020 22:10:33 GMT",
"version": "v1"
},
{
"created": "Sat, 1 May 2021 18:34:08 GMT",
"version": "v2"
}
] | 2021-05-04 | [
[
"da Fonseca",
"María",
""
],
[
"Samengo",
"Inés",
""
]
] | In trichromats, color vision entails the projection of an infinite-dimensional space (the one containing all possible electromagnetic power spectra) onto the 3-dimensional space that modulates the activity of the three types of cones. This drastic reduction in dimensionality gives rise to metamerism, that is, the perce... |
1401.1168 | Carsten Maedler | Pritiraj Mohanty, Yu Chen, Xihua Wang, Mi K. Hong, Carol L. Rosenberg,
David T. Weaver, Shyamsunder Erramilli | Field Effect Transistor Nanosensor for Breast Cancer Diagnostics | null | Invited Review in Biosensors and Molecular Technologies for Cancer
Diagnostics, edited by K. H. Herold and A. Rasooly (CRC Press, 2012) | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Silicon nanochannel field effect transistor (FET) biosensors are one of the
most promising technologies in the development of highly sensitive and
label-free analyte detection for cancer diagnostics. With their exceptional
electrical properties and small dimensions, silicon nanochannels are ideally
suited for extraor... | [
{
"created": "Mon, 6 Jan 2014 19:05:45 GMT",
"version": "v1"
}
] | 2014-01-07 | [
[
"Mohanty",
"Pritiraj",
""
],
[
"Chen",
"Yu",
""
],
[
"Wang",
"Xihua",
""
],
[
"Hong",
"Mi K.",
""
],
[
"Rosenberg",
"Carol L.",
""
],
[
"Weaver",
"David T.",
""
],
[
"Erramilli",
"Shyamsunder",
""
]
] | Silicon nanochannel field effect transistor (FET) biosensors are one of the most promising technologies in the development of highly sensitive and label-free analyte detection for cancer diagnostics. With their exceptional electrical properties and small dimensions, silicon nanochannels are ideally suited for extraordi... |
1805.09084 | PierGianLuca Porta Mana | PierGianLuca Porta Mana, Vahid Rostami, Emiliano Torre, Yasser Roudi | Maximum-entropy and representative samples of neuronal activity: a
dilemma | 12 pages, 2 figures. V2: added references and updated contact details | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The present work shows that the maximum-entropy method can be applied to a
sample of neuronal recordings along two different routes: (1) apply to the
sample; or (2) apply to a larger, unsampled neuronal population from which the
sample is drawn, and then marginalize to the sample. These two routes give
inequivalent r... | [
{
"created": "Wed, 23 May 2018 12:17:49 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Oct 2020 16:49:02 GMT",
"version": "v2"
}
] | 2020-10-20 | [
[
"Mana",
"PierGianLuca Porta",
""
],
[
"Rostami",
"Vahid",
""
],
[
"Torre",
"Emiliano",
""
],
[
"Roudi",
"Yasser",
""
]
] | The present work shows that the maximum-entropy method can be applied to a sample of neuronal recordings along two different routes: (1) apply to the sample; or (2) apply to a larger, unsampled neuronal population from which the sample is drawn, and then marginalize to the sample. These two routes give inequivalent res... |
1508.06854 | Konstantinos Kouvaris | Kostas Kouvaris, Jeff Clune, Louis Kounios, Markus Brede, Richard A.
Watson | How Evolution Learns to Generalise: Principles of under-fitting,
over-fitting and induction in the evolution of developmental organisation | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the most intriguing questions in evolution is how organisms exhibit
suitable phenotypic variation to rapidly adapt in novel selective environments
which is crucial for evolvability. Recent work showed that when selective
environments vary in a systematic manner, it is possible that development can
constrain th... | [
{
"created": "Thu, 27 Aug 2015 13:37:00 GMT",
"version": "v1"
}
] | 2015-08-28 | [
[
"Kouvaris",
"Kostas",
""
],
[
"Clune",
"Jeff",
""
],
[
"Kounios",
"Louis",
""
],
[
"Brede",
"Markus",
""
],
[
"Watson",
"Richard A.",
""
]
] | One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments which is crucial for evolvability. Recent work showed that when selective environments vary in a systematic manner, it is possible that development can constrain the ... |
1411.6473 | Hsiu-Hau Lin | Tsung-Cheng Lu, Yi-Ko Chen, Hsiu-Hau Lin and Chun-Chung-Chen | Fluctuation-induced dissipation in evolutionary dynamics | 6 pages, 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biodiversity and extinction are central issues in evolution. Dynamical
balance among different species in ecosystems is often described by
deterministic replicator equations with moderate success. However, fluctuations
are inevitable, either caused by external environment or intrinsic random
competitions in finite po... | [
{
"created": "Mon, 24 Nov 2014 14:55:27 GMT",
"version": "v1"
}
] | 2014-11-25 | [
[
"Lu",
"Tsung-Cheng",
""
],
[
"Chen",
"Yi-Ko",
""
],
[
"Lin",
"Hsiu-Hau",
""
],
[
"Chun-Chung-Chen",
"",
""
]
] | Biodiversity and extinction are central issues in evolution. Dynamical balance among different species in ecosystems is often described by deterministic replicator equations with moderate success. However, fluctuations are inevitable, either caused by external environment or intrinsic random competitions in finite popu... |
2109.03115 | Simon Dahan | Simon Dahan, Logan Z. J. Williams, Daniel Rueckert, Emma C. Robinson | Improving Phenotype Prediction using Long-Range Spatio-Temporal Dynamics
of Functional Connectivity | MLCN 2021 | null | null | null | q-bio.NC cs.CV cs.LG eess.IV | http://creativecommons.org/licenses/by/4.0/ | The study of functional brain connectivity (FC) is important for
understanding the underlying mechanisms of many psychiatric disorders. Many
recent analyses adopt graph convolutional networks, to study non-linear
interactions between functionally-correlated states. However, although patterns
of brain activation are k... | [
{
"created": "Tue, 7 Sep 2021 14:23:34 GMT",
"version": "v1"
}
] | 2021-09-08 | [
[
"Dahan",
"Simon",
""
],
[
"Williams",
"Logan Z. J.",
""
],
[
"Rueckert",
"Daniel",
""
],
[
"Robinson",
"Emma C.",
""
]
] | The study of functional brain connectivity (FC) is important for understanding the underlying mechanisms of many psychiatric disorders. Many recent analyses adopt graph convolutional networks, to study non-linear interactions between functionally-correlated states. However, although patterns of brain activation are kno... |
2307.04397 | Mathieu Hemery | Mathieu Hemery, Fran\c{c}ois Fages | On Estimating Derivatives of Input Signals in Biochemistry | null | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The online estimation of the derivative of an input signal is widespread in
control theory and engineering. In the realm of chemical reaction networks
(CRN), this raises however a number of specific issues on the different ways to
achieve it. A CRN pattern for implementing a derivative block has already been
proposed... | [
{
"created": "Mon, 10 Jul 2023 07:59:24 GMT",
"version": "v1"
}
] | 2023-07-11 | [
[
"Hemery",
"Mathieu",
""
],
[
"Fages",
"François",
""
]
] | The online estimation of the derivative of an input signal is widespread in control theory and engineering. In the realm of chemical reaction networks (CRN), this raises however a number of specific issues on the different ways to achieve it. A CRN pattern for implementing a derivative block has already been proposed f... |
2001.11679 | Peter Csermely | P\'eter Csermely, Nina Kunsic, P\'eter Mendik, M\'ark Kerest\'ely,
Teod\'ora Farag\'o, D\'aniel V. Veres, and P\'eter Tompa | Learning of signaling networks: molecular mechanisms | cover story of the 2020 April issue of Trends in Biochemical Sciences | Trends in Biochemical Sciences (2020) 45, 284-294 | 10.1016/j.tibs.2019.12.005 | null | q-bio.MN cs.NE nlin.AO physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular processes of neuronal learning have been well-described. However,
learning mechanisms of non-neuronal cells have not been fully understood at the
molecular level. Here, we discuss molecular mechanisms of cellular learning,
including conformational memory of intrinsically disordered proteins and
prions, sign... | [
{
"created": "Fri, 31 Jan 2020 07:15:43 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Mar 2020 09:18:48 GMT",
"version": "v2"
}
] | 2020-03-18 | [
[
"Csermely",
"Péter",
""
],
[
"Kunsic",
"Nina",
""
],
[
"Mendik",
"Péter",
""
],
[
"Kerestély",
"Márk",
""
],
[
"Faragó",
"Teodóra",
""
],
[
"Veres",
"Dániel V.",
""
],
[
"Tompa",
"Péter",
""
]
] | Molecular processes of neuronal learning have been well-described. However, learning mechanisms of non-neuronal cells have not been fully understood at the molecular level. Here, we discuss molecular mechanisms of cellular learning, including conformational memory of intrinsically disordered proteins and prions, signal... |
1410.8230 | Leandro Alonso | Leandro M. Alonso | Parameter estimation, nonlinearity and Occam's razor | null | Chaos 25, 033104 (2015) | 10.1063/1.4914452 | null | q-bio.QM nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nonlinear systems are capable of displaying complex behavior even if this is
the result of a small number of interacting time scales. A widely studied case
is when complex dynamics emerges out of a nonlinear system being forced by a
simple harmonic function. In order to identify if a recorded time series is the
resul... | [
{
"created": "Thu, 30 Oct 2014 02:26:35 GMT",
"version": "v1"
}
] | 2015-06-01 | [
[
"Alonso",
"Leandro M.",
""
]
] | Nonlinear systems are capable of displaying complex behavior even if this is the result of a small number of interacting time scales. A widely studied case is when complex dynamics emerges out of a nonlinear system being forced by a simple harmonic function. In order to identify if a recorded time series is the result ... |
1703.05471 | Patricio Maturana | Patricio Maturana, Brendon J. Brewer, Steffen Klaere, Remco Bouckaert | Model selection and parameter inference in phylogenetics using Nested
Sampling | 23 pages, 12 figures, 3 tables | null | 10.1093/sysbio/syy050 | null | q-bio.QM stat.CO | http://creativecommons.org/licenses/by/4.0/ | Bayesian inference methods rely on numerical algorithms for both model
selection and parameter inference. In general, these algorithms require a high
computational effort to yield reliable estimates. One of the major challenges
in phylogenetics is the estimation of the marginal likelihood. This quantity is
commonly u... | [
{
"created": "Thu, 16 Mar 2017 05:00:37 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Dec 2017 05:30:12 GMT",
"version": "v2"
},
{
"created": "Tue, 10 Apr 2018 05:22:48 GMT",
"version": "v3"
}
] | 2018-08-09 | [
[
"Maturana",
"Patricio",
""
],
[
"Brewer",
"Brendon J.",
""
],
[
"Klaere",
"Steffen",
""
],
[
"Bouckaert",
"Remco",
""
]
] | Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in phylogenetics is the estimation of the marginal likelihood. This quantity is commonly use... |
1902.01143 | Stefan Hammer | Stefan Hammer, Christian G\"unzel, Mario M\"orl, Sven Findei{\ss} | Evolving methods for rational de novo design of functional RNA molecules | Published at METHODS, Issue title: Chemical Biology of RNA, Guest
Editor: Michael Ryckelynck | null | 10.1016/j.ymeth.2019.04.022 | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Artificial RNA molecules with novel functionality have many applications in
synthetic biology, pharmacy and white biotechnology. The de novo design of such
devices using computational methods and prediction tools is a
resource-efficient alternative to experimental screening and selection
pipelines. In this review, we... | [
{
"created": "Mon, 4 Feb 2019 12:14:46 GMT",
"version": "v1"
},
{
"created": "Mon, 25 Mar 2019 10:42:39 GMT",
"version": "v2"
},
{
"created": "Fri, 26 Apr 2019 18:58:35 GMT",
"version": "v3"
},
{
"created": "Fri, 10 May 2019 07:53:48 GMT",
"version": "v4"
}
] | 2019-05-13 | [
[
"Hammer",
"Stefan",
""
],
[
"Günzel",
"Christian",
""
],
[
"Mörl",
"Mario",
""
],
[
"Findeiß",
"Sven",
""
]
] | Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient alternative to experimental screening and selection pipelines. In this review, we d... |
2007.08429 | Camile Bahi | Camile Bahi | 5-HT2A mediated plasticity as a target in major depression: a narrative
review connecting the dots from neurobiology to cognition and psychology | 27 pages, 9 figures | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As the world's first primary morbidity factor, depression has a considerable
impact on both an individual as well as a societal level. despite their
discovery several decades ago, classical antidepressants have been shown to
provide limited benefits against this condition. However, substances such as
ketamine and psy... | [
{
"created": "Thu, 16 Jul 2020 16:09:32 GMT",
"version": "v1"
}
] | 2020-07-17 | [
[
"Bahi",
"Camile",
""
]
] | As the world's first primary morbidity factor, depression has a considerable impact on both an individual as well as a societal level. despite their discovery several decades ago, classical antidepressants have been shown to provide limited benefits against this condition. However, substances such as ketamine and psych... |
1404.7281 | Tom Michoel | Sofie Demeyer, Tom Michoel | Graph-based data integration predicts long-range regulatory interactions
across the human genome | 19 pages, 7 figures, 2 tables + 12 pages supplementary material (4
figures, 7 tables) | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcriptional regulation of gene expression is one of the main processes
that affect cell diversification from a single set of genes. Regulatory
proteins often interact with DNA regions located distally from the
transcription start sites (TSS) of the genes. We developed a computational
method that combines open chr... | [
{
"created": "Tue, 29 Apr 2014 09:19:40 GMT",
"version": "v1"
}
] | 2014-04-30 | [
[
"Demeyer",
"Sofie",
""
],
[
"Michoel",
"Tom",
""
]
] | Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites (TSS) of the genes. We developed a computational method that combines open chrom... |
q-bio/0507011 | B. Roy Frieden | B. Roy Frieden and Robert A. Gatenby | Power laws of complex systems from Extreme physical information | null | null | 10.1103/PhysRevE.72.036101 | null | q-bio.CB | null | Many complex systems obey allometric, or power, laws y=Yx^{a}. Here y is the
measured value of some system attribute a, Y is a constant, and x is a
stochastic variable. Remarkably, for many living systems the exponent a is
limited to values +or- n/4, n=0,1,2... Here x is the mass of a randomly
selected creature in th... | [
{
"created": "Thu, 7 Jul 2005 20:57:29 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Frieden",
"B. Roy",
""
],
[
"Gatenby",
"Robert A.",
""
]
] | Many complex systems obey allometric, or power, laws y=Yx^{a}. Here y is the measured value of some system attribute a, Y is a constant, and x is a stochastic variable. Remarkably, for many living systems the exponent a is limited to values +or- n/4, n=0,1,2... Here x is the mass of a randomly selected creature in the ... |
0706.3735 | Jeremy Gunawardena | Matthew Thomson and Jeremy Gunawardena | Multi-bit information storage by multisite phosphorylation | 29 pages, 6 figures | null | null | null | q-bio.MN | null | Cells store information in DNA and in stable programs of gene expression,
which thereby implement forms of long-term cellular memory. Cells must also
possess short-term forms of information storage, implemented
post-translationally, to transduce and interpret external signals. CaMKII, for
instance, is thought to impl... | [
{
"created": "Tue, 26 Jun 2007 04:02:19 GMT",
"version": "v1"
}
] | 2007-06-27 | [
[
"Thomson",
"Matthew",
""
],
[
"Gunawardena",
"Jeremy",
""
]
] | Cells store information in DNA and in stable programs of gene expression, which thereby implement forms of long-term cellular memory. Cells must also possess short-term forms of information storage, implemented post-translationally, to transduce and interpret external signals. CaMKII, for instance, is thought to implem... |
q-bio/0410021 | Markus Porto | Markus Porto, H. Eduardo Roman, Michele Vendruscolo, and Ugo Bastolla | Prediction of site-specific amino acid distributions and limits of
divergent evolutionary changes in protein sequences | 9 pages, 4 figures, references added | Mol. Biol. Evol. 22, 630-638 (2005) (see also Editor's Erratum,
Mol. Biol. Evol. 22, 1156 (2005)) | null | null | q-bio.BM q-bio.PE | null | We derive an analytic expression for site-specific stationary distributions
of amino acids from the Structurally Constrained Neutral (SCN) model of protein
evolution with conservation of folding stability. The stationary distributions
that we obtain have a Boltzmann-like shape, and their effective temperature
paramet... | [
{
"created": "Tue, 19 Oct 2004 14:29:29 GMT",
"version": "v1"
},
{
"created": "Thu, 4 Nov 2004 18:05:13 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Porto",
"Markus",
""
],
[
"Roman",
"H. Eduardo",
""
],
[
"Vendruscolo",
"Michele",
""
],
[
"Bastolla",
"Ugo",
""
]
] | We derive an analytic expression for site-specific stationary distributions of amino acids from the Structurally Constrained Neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that we obtain have a Boltzmann-like shape, and their effective temperature parameter... |
1501.05003 | Sarthok Sircar | S. Sircar and A. J. Roberts | Ion mediated crosslink driven mucous swelling kinetics | 18 pages, 9 figures | null | null | null | q-bio.TO cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present an experimentally guided, multi-phasic, multi-species ionic gel
model to compare and make qualitative predictions on the rheology of mucus of
healthy individuals (Wild Type) versus those infected with Cystic Fibrosis. The
mixture theory consists of the mucus (polymer phase) and water (solvent phase)
as wel... | [
{
"created": "Tue, 20 Jan 2015 22:17:37 GMT",
"version": "v1"
}
] | 2015-01-22 | [
[
"Sircar",
"S.",
""
],
[
"Roberts",
"A. J.",
""
]
] | We present an experimentally guided, multi-phasic, multi-species ionic gel model to compare and make qualitative predictions on the rheology of mucus of healthy individuals (Wild Type) versus those infected with Cystic Fibrosis. The mixture theory consists of the mucus (polymer phase) and water (solvent phase) as well ... |
q-bio/0702023 | Brigitte Gaillard | H. Meunier (DEPE-Iphc), J.-B. Leca (DEPE-Iphc), J.-L. Deneubourg, O.
Petit (DEPE-Iphc) | Group movement decisions in capuchin monkeys : the utility of an
experimental study and a mathematical model to explore the relationship
between individual and collective behaviours | null | Behaviour 143 (2006) 1511-1527 | null | null | q-bio.PE | null | In primate groups, collective movements are typically described as processes
dependent on leadership mechanisms. However, in some species, decision-making
includes negotiations and distributed leadership. These facts suggest that
simple underlying processes may explain certain decision mechanisms during
collective mo... | [
{
"created": "Fri, 9 Feb 2007 15:15:34 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Meunier",
"H.",
"",
"DEPE-Iphc"
],
[
"Leca",
"J. -B.",
"",
"DEPE-Iphc"
],
[
"Deneubourg",
"J. -L.",
"",
"DEPE-Iphc"
],
[
"Petit",
"O.",
"",
"DEPE-Iphc"
]
] | In primate groups, collective movements are typically described as processes dependent on leadership mechanisms. However, in some species, decision-making includes negotiations and distributed leadership. These facts suggest that simple underlying processes may explain certain decision mechanisms during collective move... |
1601.04974 | Leo van Iersel | Laura Jetten and Leo van Iersel | Nonbinary tree-based phylogenetic networks | null | null | null | null | q-bio.PE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rooted phylogenetic networks are used to describe evolutionary histories that
contain non-treelike evolutionary events such as hybridization and horizontal
gene transfer. In some cases, such histories can be described by a phylogenetic
base-tree with additional linking arcs, which can for example represent gene
trans... | [
{
"created": "Tue, 19 Jan 2016 16:13:31 GMT",
"version": "v1"
},
{
"created": "Wed, 1 Jun 2016 08:11:59 GMT",
"version": "v2"
},
{
"created": "Fri, 30 Sep 2016 05:34:13 GMT",
"version": "v3"
}
] | 2016-10-03 | [
[
"Jetten",
"Laura",
""
],
[
"van Iersel",
"Leo",
""
]
] | Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example represent gene transfe... |
1009.4141 | Yi Huiguang | Huiguang Yi | CO-phylum: An Assembly-Free Phylogenomic Approach for Close Related
Organisms | 21 pages, 6 figures | Nucl. Acids Res. first published online January 18, 2013 | 10.1093/nar/gkt003 | null | q-bio.QM q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Phylogenomic approaches developed thus far are either too time-consuming or
lack a solid evolutionary basis. Moreover, no phylogenomic approach is capable
of constructing a tree directly from unassembled raw sequencing data. A new
phylogenomic method, CO-phylum, is developed to alleviate these flaws.
CO-phylum can ge... | [
{
"created": "Tue, 21 Sep 2010 16:48:58 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Nov 2010 00:04:47 GMT",
"version": "v2"
},
{
"created": "Wed, 6 Apr 2011 14:26:03 GMT",
"version": "v3"
}
] | 2013-01-22 | [
[
"Yi",
"Huiguang",
""
]
] | Phylogenomic approaches developed thus far are either too time-consuming or lack a solid evolutionary basis. Moreover, no phylogenomic approach is capable of constructing a tree directly from unassembled raw sequencing data. A new phylogenomic method, CO-phylum, is developed to alleviate these flaws. CO-phylum can gene... |
1310.2210 | Siavash Ghavami | Siavash Ghavami, Olaf Wolkenhauer, Farshad Lahouti, Mukhtar Ullah,
Michael Linnebacher | Accounting for Randomness in Measurement and Sampling in Study of Cancer
Cell Population Dynamics | 41 pages, 9 figures,submitted to IET System Biology Journal | null | 10.1049/iet-syb.2013.0031 | null | q-bio.CB q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Studying the development of malignant tumours, it is important to know and
predict the proportions of different cell types in tissue samples. Knowing the
expected temporal evolution of the proportion of normal tissue cells, compared
to stem-like and non-stem like cancer cells, gives an indication about the
progressio... | [
{
"created": "Tue, 8 Oct 2013 18:13:09 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Jan 2014 10:09:25 GMT",
"version": "v2"
}
] | 2015-11-24 | [
[
"Ghavami",
"Siavash",
""
],
[
"Wolkenhauer",
"Olaf",
""
],
[
"Lahouti",
"Farshad",
""
],
[
"Ullah",
"Mukhtar",
""
],
[
"Linnebacher",
"Michael",
""
]
] | Studying the development of malignant tumours, it is important to know and predict the proportions of different cell types in tissue samples. Knowing the expected temporal evolution of the proportion of normal tissue cells, compared to stem-like and non-stem like cancer cells, gives an indication about the progression ... |
1608.01936 | Bernard Feldman | Bernard J. Feldman | Explanation for Cancer in Rats, Mice and Humans due to Cell Phone
Radiofrequency Radiation | Five pages, no figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Very recently, the National Toxicology Program reported a correlation between
exposure to whole body 900 MHz radiofrequency radiation and cancer in the
brains and hearts of Sprague Dawley male rats. This paper proposes the
following explanation for these results. The neurons around the rat's brain and
heart form clos... | [
{
"created": "Fri, 22 Jul 2016 16:02:00 GMT",
"version": "v1"
},
{
"created": "Mon, 17 Jul 2017 19:15:51 GMT",
"version": "v2"
},
{
"created": "Wed, 19 Jul 2017 13:38:51 GMT",
"version": "v3"
}
] | 2017-07-20 | [
[
"Feldman",
"Bernard J.",
""
]
] | Very recently, the National Toxicology Program reported a correlation between exposure to whole body 900 MHz radiofrequency radiation and cancer in the brains and hearts of Sprague Dawley male rats. This paper proposes the following explanation for these results. The neurons around the rat's brain and heart form closed... |
2103.12186 | Feng Fu | Kamran Kaveh and Feng Fu | Immune checkpoint therapy modeling of PD-1/PD-L1 blockades reveals
subtle difference in their response dynamics and potential synergy in
combination | null | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Immune checkpoint therapy is one of the most promising immunotherapeutic
methods that are likely able to give rise to durable treatment response for
various cancer types. Despite much progress in the past decade, there are still
critical open questions with particular regards to quantifying and predicting
the efficac... | [
{
"created": "Mon, 22 Mar 2021 21:28:26 GMT",
"version": "v1"
}
] | 2021-03-24 | [
[
"Kaveh",
"Kamran",
""
],
[
"Fu",
"Feng",
""
]
] | Immune checkpoint therapy is one of the most promising immunotherapeutic methods that are likely able to give rise to durable treatment response for various cancer types. Despite much progress in the past decade, there are still critical open questions with particular regards to quantifying and predicting the efficacy ... |
1906.09908 | Zhen Zhou | Zhen Zhou, Xiaobo Chen, Yu Zhang, Lishan Qiao, Renping Yu, Gang Pan,
Han Zhang, Dinggang Shen | Brain Network Construction and Classification Toolbox (BrainNetClass) | null | null | 10.1002/hbm.24979 | null | q-bio.NC cs.CV cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Brain functional network has become an increasingly used approach in
understanding brain functions and diseases. Many network construction methods
have been developed, whereas the majority of the studies still used static
pairwise Pearson's correlation-based functional connectivity. The goal of this
work is to introd... | [
{
"created": "Mon, 17 Jun 2019 18:19:18 GMT",
"version": "v1"
}
] | 2020-03-13 | [
[
"Zhou",
"Zhen",
""
],
[
"Chen",
"Xiaobo",
""
],
[
"Zhang",
"Yu",
""
],
[
"Qiao",
"Lishan",
""
],
[
"Yu",
"Renping",
""
],
[
"Pan",
"Gang",
""
],
[
"Zhang",
"Han",
""
],
[
"Shen",
"Dinggang",
... | Brain functional network has become an increasingly used approach in understanding brain functions and diseases. Many network construction methods have been developed, whereas the majority of the studies still used static pairwise Pearson's correlation-based functional connectivity. The goal of this work is to introduc... |
1810.00954 | Alexandru Hening | Alexandru Hening and Dang H. Nguyen | The competitive exclusion principle in stochastic environments | 26 pages, 4 figures, to appear in Journal of Mathematical Biology | Journal of Mathematical Biology, vol. 80,1323-1351(2020) | null | null | q-bio.PE math.DS math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In its simplest form, the competitive exclusion principle states that a
number of species competing for a smaller number of resources cannot coexist.
However, it has been observed empirically that in some settings it is possible
to have coexistence. One example is Hutchinson's `paradox of the plankton'.
This is an in... | [
{
"created": "Mon, 1 Oct 2018 20:05:23 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Sep 2019 01:03:40 GMT",
"version": "v2"
}
] | 2021-02-18 | [
[
"Hening",
"Alexandru",
""
],
[
"Nguyen",
"Dang H.",
""
]
] | In its simplest form, the competitive exclusion principle states that a number of species competing for a smaller number of resources cannot coexist. However, it has been observed empirically that in some settings it is possible to have coexistence. One example is Hutchinson's `paradox of the plankton'. This is an inst... |
1402.6971 | Ka-Kit Lam | Ka-Kit Lam, Asif Khalak, David Tse | Near-optimal Assembly for Shotgun Sequencing with Noisy Reads | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent work identified the fundamental limits on the information requirements
in terms of read length and coverage depth required for successful de novo
genome reconstruction from shotgun sequencing data, based on the idealistic
assumption of no errors in the reads (noiseless reads). In this work, we show
that even w... | [
{
"created": "Thu, 27 Feb 2014 16:58:26 GMT",
"version": "v1"
}
] | 2014-02-28 | [
[
"Lam",
"Ka-Kit",
""
],
[
"Khalak",
"Asif",
""
],
[
"Tse",
"David",
""
]
] | Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption of no errors in the reads (noiseless reads). In this work, we show that even whe... |
2406.18240 | Iv\'an Matas Gonzalez | Francisca Silva-Claver\'ia and Carmen Serrano and Iv\'an Matas and
Amalia Serrano and Tom\'as Toledo-Pastrana and David Moreno-Ram\'irez and
Bego\~na Acha | Concordance in basal cell carcinoma diagnosis. Building a proper ground
truth to train Artificial Intelligence tools | Manuscript word count: 3000, Number of figures: 2, Number of tables:
3 | null | null | null | q-bio.QM cs.CV cs.IR stat.ME | http://creativecommons.org/licenses/by/4.0/ | Background: The existence of different basal cell carcinoma (BCC) clinical
criteria cannot be objectively validated. An adequate ground-truth is needed to
train an artificial intelligence (AI) tool that explains the BCC diagnosis by
providing its dermoscopic features. Objectives: To determine the consensus
among derm... | [
{
"created": "Wed, 26 Jun 2024 10:44:48 GMT",
"version": "v1"
}
] | 2024-06-27 | [
[
"Silva-Clavería",
"Francisca",
""
],
[
"Serrano",
"Carmen",
""
],
[
"Matas",
"Iván",
""
],
[
"Serrano",
"Amalia",
""
],
[
"Toledo-Pastrana",
"Tomás",
""
],
[
"Moreno-Ramírez",
"David",
""
],
[
"Acha",
"Begoña",... | Background: The existence of different basal cell carcinoma (BCC) clinical criteria cannot be objectively validated. An adequate ground-truth is needed to train an artificial intelligence (AI) tool that explains the BCC diagnosis by providing its dermoscopic features. Objectives: To determine the consensus among dermat... |
1308.6028 | Caterina La Porta AM | Caterina A. M. La Porta, Stefano Zapperi, James P. Sethna | Senescent Cells in Growing Tumors: Population Dynamics and Cancer Stem
Cells | null | PLoS Comput Biol 8(1): e1002316, 2012 | 10.1371/journal.pcbi.1002316 | null | q-bio.TO q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tumors are defined by their intense proliferation, but sometimes cancer cells
turn senescent and stop replicating. In the stochastic cancer model in which
all cells are tumorigenic, senescence is seen as the result of random
mutations, suggesting that it could represent a barrier to tumor growth. In the
hierarchical ... | [
{
"created": "Wed, 28 Aug 2013 02:10:26 GMT",
"version": "v1"
}
] | 2013-08-29 | [
[
"La Porta",
"Caterina A. M.",
""
],
[
"Zapperi",
"Stefano",
""
],
[
"Sethna",
"James P.",
""
]
] | Tumors are defined by their intense proliferation, but sometimes cancer cells turn senescent and stop replicating. In the stochastic cancer model in which all cells are tumorigenic, senescence is seen as the result of random mutations, suggesting that it could represent a barrier to tumor growth. In the hierarchical ca... |
1509.06926 | Matthias Chung | Matthias Chung, Justin Krueger, and Mihai Pop | Robust Parameter Estimation for Biological Systems: A Study on the
Dynamics of Microbial Communities | null | null | null | null | q-bio.QM math.OC q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Interest in the study of in-host microbial communities has increased in
recent years due to our improved understanding of the communities' significant
role in host health. As a result, the ability to model these communities using
differential equations, for example, and analyze the results has become
increasingly rel... | [
{
"created": "Wed, 23 Sep 2015 11:24:50 GMT",
"version": "v1"
}
] | 2015-09-24 | [
[
"Chung",
"Matthias",
""
],
[
"Krueger",
"Justin",
""
],
[
"Pop",
"Mihai",
""
]
] | Interest in the study of in-host microbial communities has increased in recent years due to our improved understanding of the communities' significant role in host health. As a result, the ability to model these communities using differential equations, for example, and analyze the results has become increasingly relev... |
1803.00338 | Manuel Molano-Mazon | Manuel Molano-Mazon, Arno Onken, Eugenio Piasini, Stefano Panzeri | Synthesizing realistic neural population activity patterns using
Generative Adversarial Networks | Published as a conference paper at ICLR 2018 V2: minor changes in
supp. material | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ability to synthesize realistic patterns of neural activity is crucial
for studying neural information processing. Here we used the Generative
Adversarial Networks (GANs) framework to simulate the concerted activity of a
population of neurons. We adapted the Wasserstein-GAN variant to facilitate the
generation of... | [
{
"created": "Thu, 1 Mar 2018 12:30:22 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Apr 2018 08:26:53 GMT",
"version": "v2"
}
] | 2018-04-18 | [
[
"Molano-Mazon",
"Manuel",
""
],
[
"Onken",
"Arno",
""
],
[
"Piasini",
"Eugenio",
""
],
[
"Panzeri",
"Stefano",
""
]
] | The ability to synthesize realistic patterns of neural activity is crucial for studying neural information processing. Here we used the Generative Adversarial Networks (GANs) framework to simulate the concerted activity of a population of neurons. We adapted the Wasserstein-GAN variant to facilitate the generation of u... |
1606.02917 | Geir Halnes | Geir Halnes, Klas H. Pettersen, Leiv {\O}yehaug, Marie E. Rognes,
Gaute T. Einevoll | Astrocytic Ion Dynamics: Implications for Potassium Buffering and Liquid
Flow | 27 pages, 7 figures | M. De Pitt\`a and H. Berry (eds.), Computational Glioscience,
Springer Series in Computational Neuroscience, Springer Nature Switzerland AG
2019 | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We review modeling of astrocyte ion dynamics with a specific focus on the
implications of so-called spatial potassium buffering, where excess potassium
in the extracellular space (ECS) is transported away to prevent pathological
neural spiking. The recently introduced Kirchoff-Nernst-Planck (KNP) scheme for
modeling ... | [
{
"created": "Thu, 9 Jun 2016 11:41:49 GMT",
"version": "v1"
},
{
"created": "Thu, 25 Apr 2019 23:26:09 GMT",
"version": "v2"
},
{
"created": "Mon, 2 Dec 2019 14:50:57 GMT",
"version": "v3"
}
] | 2019-12-03 | [
[
"Halnes",
"Geir",
""
],
[
"Pettersen",
"Klas H.",
""
],
[
"Øyehaug",
"Leiv",
""
],
[
"Rognes",
"Marie E.",
""
],
[
"Einevoll",
"Gaute T.",
""
]
] | We review modeling of astrocyte ion dynamics with a specific focus on the implications of so-called spatial potassium buffering, where excess potassium in the extracellular space (ECS) is transported away to prevent pathological neural spiking. The recently introduced Kirchoff-Nernst-Planck (KNP) scheme for modeling io... |
2102.10538 | Zhenyu Han | Zhenyu Han, Fengli Xu, Yong Li, Tao Jiang, Depeng Jin, Jianhua Lu,
James A. Evans | Policy-Aware Mobility Model Explains the Growth of COVID-19 in Cities | null | null | null | null | q-bio.PE cs.CY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With the continued spread of coronavirus, the task of forecasting distinctive
COVID-19 growth curves in different cities, which remain inadequately explained
by standard epidemiological models, is critical for medical supply and
treatment. Predictions must take into account non-pharmaceutical interventions
to slow th... | [
{
"created": "Sun, 21 Feb 2021 07:39:17 GMT",
"version": "v1"
}
] | 2021-02-23 | [
[
"Han",
"Zhenyu",
""
],
[
"Xu",
"Fengli",
""
],
[
"Li",
"Yong",
""
],
[
"Jiang",
"Tao",
""
],
[
"Jin",
"Depeng",
""
],
[
"Lu",
"Jianhua",
""
],
[
"Evans",
"James A.",
""
]
] | With the continued spread of coronavirus, the task of forecasting distinctive COVID-19 growth curves in different cities, which remain inadequately explained by standard epidemiological models, is critical for medical supply and treatment. Predictions must take into account non-pharmaceutical interventions to slow the ... |
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