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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1210.0362 | Leo van Iersel | Leo van Iersel and Vincent Moulton | Trinets encode tree-child and level-2 phylogenetic networks | null | null | null | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic networks generalize evolutionary trees, and are commonly used to
represent evolutionary histories of species that undergo reticulate
evolutionary processes such as hybridization, recombination and lateral gene
transfer. Recently, there has been great interest in trying to develop methods
to construct roo... | [
{
"created": "Mon, 1 Oct 2012 12:14:50 GMT",
"version": "v1"
}
] | 2012-10-02 | [
[
"van Iersel",
"Leo",
""
],
[
"Moulton",
"Vincent",
""
]
] | Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct roote... |
1111.2998 | David Lukatsky | Itamar Sela and David B. Lukatsky | DNA sequence correlations shape nonspecific transcription factor-DNA
binding affinity | null | Biophys. J. 101(1), 160-166 (2011) | 10.1016/j.bpj.2011.04.037 | null | q-bio.BM q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcription factors (TFs) are regulatory proteins that bind DNA in promoter
regions of the genome and either promote or repress gene expression. Here we
predict analytically that enhanced homo-oligonucleotide sequence correlations,
such as poly(dA:dT) and poly(dC:dG) tracts, statistically enhance non-specific
TF-DN... | [
{
"created": "Sun, 13 Nov 2011 09:13:51 GMT",
"version": "v1"
}
] | 2011-11-15 | [
[
"Sela",
"Itamar",
""
],
[
"Lukatsky",
"David B.",
""
]
] | Transcription factors (TFs) are regulatory proteins that bind DNA in promoter regions of the genome and either promote or repress gene expression. Here we predict analytically that enhanced homo-oligonucleotide sequence correlations, such as poly(dA:dT) and poly(dC:dG) tracts, statistically enhance non-specific TF-DNA ... |
1309.0833 | Ron Nielsen | Ron W Nielsen aka Jan Nurzynski | Growth of human population in Australia, 1000-10,000 years BP | 8 pages, 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Close analysis of the published interpretation of the number of rock-shelter
sites in Australia provides further evidence that there was no intensification
in the growth of human population between 1000 and 10,000 years BP. An
alternative way of determining the time-dependent distribution of the size of
human populat... | [
{
"created": "Tue, 3 Sep 2013 20:25:55 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Oct 2013 02:06:13 GMT",
"version": "v2"
}
] | 2013-10-22 | [
[
"Nurzynski",
"Ron W Nielsen aka Jan",
""
]
] | Close analysis of the published interpretation of the number of rock-shelter sites in Australia provides further evidence that there was no intensification in the growth of human population between 1000 and 10,000 years BP. An alternative way of determining the time-dependent distribution of the size of human populatio... |
1007.4124 | Tsvi Tlusty | Tsvi Tlusty | A simple model for the evolution of molecular codes driven by the
interplay of accuracy, diversity and cost | Keywords: molecular codes, rate-distortion theory, biological
information channels, stochastic maps, genetic code, genetic networks | Tsvi Tlusty 2008 Phys. Biol. 5 016001 | 10.1088/1478-3975/5/1/016001 | null | q-bio.QM cs.IT math.IT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular codes translate information written in one type of molecules into
another molecular language. We introduce a simple model that treats molecular
codes as noisy information channels. An optimal code is a channel that conveys
information accurately and efficiently while keeping down the impact of errors.
The e... | [
{
"created": "Fri, 23 Jul 2010 13:20:35 GMT",
"version": "v1"
}
] | 2010-07-26 | [
[
"Tlusty",
"Tsvi",
""
]
] | Molecular codes translate information written in one type of molecules into another molecular language. We introduce a simple model that treats molecular codes as noisy information channels. An optimal code is a channel that conveys information accurately and efficiently while keeping down the impact of errors. The equ... |
1205.3739 | Ivan Santamaria-Holek | J. Lopez Alamilla, I. Santamaria-Holek | Reconstructing the free-energy landscape associated to molecular motors
processivity | To appear in Biophysical Chemistry, 12 pgs, 8 figures | null | null | null | q-bio.SC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a biochemical model providing the kinetic and energetic
descriptions of the processivity dynamics of kinesin and dinein molecular
motors. Our approach is a modified version of a well known model describing
kinesin dynamics and considers the presence of a competitive inhibition
reaction by ADP. We first rec... | [
{
"created": "Wed, 16 May 2012 17:24:43 GMT",
"version": "v1"
}
] | 2012-05-17 | [
[
"Alamilla",
"J. Lopez",
""
],
[
"Santamaria-Holek",
"I.",
""
]
] | We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and considers the presence of a competitive inhibition reaction by ADP. We first recon... |
1808.05002 | Arkady Zgonnikov | Takashi Suzuki, Ihor Lubashevsky, Arkady Zgonnikov | Complexity of human response delay in intermittent control: The case of
virtual stick balancing | 12 pages, 5 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Response delay is an inherent and essential part of human actions. In the
context of human balance control, the response delay is traditionally modeled
using the formalism of delay-differential equations, which adopts the
approximation of fixed delay. However, experimental studies revealing
substantial variability, a... | [
{
"created": "Wed, 15 Aug 2018 09:01:10 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Aug 2018 11:49:00 GMT",
"version": "v2"
}
] | 2018-08-22 | [
[
"Suzuki",
"Takashi",
""
],
[
"Lubashevsky",
"Ihor",
""
],
[
"Zgonnikov",
"Arkady",
""
]
] | Response delay is an inherent and essential part of human actions. In the context of human balance control, the response delay is traditionally modeled using the formalism of delay-differential equations, which adopts the approximation of fixed delay. However, experimental studies revealing substantial variability, ada... |
1204.0574 | Hamidreza Namazi Dr. | Karthik Seetharaman, Hamidreza Namazi, Vladimir V.Kulish | Phase lagging model of brain response to external stimuli - modeling of
single action potential | 19 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we detail a phase lagging model of brain response to external
stimuli. The model is derived using the basic laws of physics like conservation
of energy law. This model eliminates the paradox of instantaneous propagation
of the action potential in the brain. The solution of this model is then
presented. ... | [
{
"created": "Tue, 3 Apr 2012 02:20:09 GMT",
"version": "v1"
}
] | 2012-05-21 | [
[
"Seetharaman",
"Karthik",
""
],
[
"Namazi",
"Hamidreza",
""
],
[
"Kulish",
"Vladimir V.",
""
]
] | In this paper we detail a phase lagging model of brain response to external stimuli. The model is derived using the basic laws of physics like conservation of energy law. This model eliminates the paradox of instantaneous propagation of the action potential in the brain. The solution of this model is then presented. Th... |
1808.00868 | Candy Abboud | Candy Abboud, Olivier Bonnefon, Eric Parent, Samuel Soubeyrand | Dating and localizing an invasion from post-introduction data and a
coupled reaction-diffusion-absorption model | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Invasion of new territories by alien organisms is of primary concern for
environmental and health agencies and has been a core topic in mathematical
modeling, in particular in the intents of reconstructing the past dynamics of
the alien organisms and predicting their future spatial extents. Partial
differential equat... | [
{
"created": "Wed, 1 Aug 2018 16:21:36 GMT",
"version": "v1"
}
] | 2018-08-03 | [
[
"Abboud",
"Candy",
""
],
[
"Bonnefon",
"Olivier",
""
],
[
"Parent",
"Eric",
""
],
[
"Soubeyrand",
"Samuel",
""
]
] | Invasion of new territories by alien organisms is of primary concern for environmental and health agencies and has been a core topic in mathematical modeling, in particular in the intents of reconstructing the past dynamics of the alien organisms and predicting their future spatial extents. Partial differential equatio... |
1007.1383 | Anna Mummert | Bonita Lawrence and Anna Mummert and Charles Somerville | A Model of the Number of Antibiotic Resistant Bacteria in Rivers | 18 pages, 5 figures, 2 tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The large reservoir of antibiotic resistant bacteria in raw and treated water
supplies is a matter of public health concern. Currently, the National
Antimicrobial Resistance Monitoring Systems, a collaborative effort of the
Centers for Disease Control, the US Department of Agriculture, and the US Food
and Drug Admini... | [
{
"created": "Thu, 8 Jul 2010 14:06:26 GMT",
"version": "v1"
}
] | 2010-07-09 | [
[
"Lawrence",
"Bonita",
""
],
[
"Mummert",
"Anna",
""
],
[
"Somerville",
"Charles",
""
]
] | The large reservoir of antibiotic resistant bacteria in raw and treated water supplies is a matter of public health concern. Currently, the National Antimicrobial Resistance Monitoring Systems, a collaborative effort of the Centers for Disease Control, the US Department of Agriculture, and the US Food and Drug Administ... |
1310.2357 | Rodrigo Aldecoa | Rodrigo Aldecoa and Ignacio Mar\'in | SurpriseMe: an integrated tool for network community structure
characterization using Surprise maximization | 6 pages | Bioinformatics 30, 1041 (2014) | 10.1093/bioinformatics/btt741 | null | q-bio.MN cs.SI physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Detecting communities, densely connected groups may contribute to unravel the
underlying relationships among the units present in diverse biological networks
(e.g., interactome, coexpression networks, ecological networks, etc.). We
recently showed that communities can be very precisely characterized by
maximizing Sur... | [
{
"created": "Wed, 9 Oct 2013 05:44:11 GMT",
"version": "v1"
}
] | 2014-04-11 | [
[
"Aldecoa",
"Rodrigo",
""
],
[
"Marín",
"Ignacio",
""
]
] | Detecting communities, densely connected groups may contribute to unravel the underlying relationships among the units present in diverse biological networks (e.g., interactome, coexpression networks, ecological networks, etc.). We recently showed that communities can be very precisely characterized by maximizing Surpr... |
1711.02454 | Dave Thirumalai | Ngo Min Toan and D. Thirumalai | Forced-rupture of Cell-Adhesion Complexes Reveals abrupt switch between
two Brittle States | 29 pages, 6 figures, Submitted to J. Chem. Phys | null | 10.1063/1.5011056 | null | q-bio.BM cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cell adhesion complexes (CACs), which are activated by ligand binding, play
key roles in many cellular functions ranging from cell cycle regulation to
mediation of cell extracellular matrix adhesion. Inspired by single molecule
pulling experiments on leukocyte function-associated antigen-1 (LFA-1),
expressed in T-cel... | [
{
"created": "Tue, 7 Nov 2017 13:28:48 GMT",
"version": "v1"
}
] | 2018-04-04 | [
[
"Toan",
"Ngo Min",
""
],
[
"Thirumalai",
"D.",
""
]
] | Cell adhesion complexes (CACs), which are activated by ligand binding, play key roles in many cellular functions ranging from cell cycle regulation to mediation of cell extracellular matrix adhesion. Inspired by single molecule pulling experiments on leukocyte function-associated antigen-1 (LFA-1), expressed in T-cells... |
1604.01317 | Michael Sadovsky | Sergey Tsarev, Michael Sadovsky | New Error Tolerant Method to Search Long Repeats in Symbol Sequences | 13 pages, 4 figures | null | null | null | q-bio.GN cs.DS cs.IT math.IT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A new method to identify all sufficiently long repeating substrings in one or
several symbol sequences is proposed. The method is based on a specific gauge
applied to symbol sequences that guarantees identification of the repeating
substrings. It allows the matching of substrings to contain a given level of
errors. T... | [
{
"created": "Tue, 5 Apr 2016 16:18:33 GMT",
"version": "v1"
}
] | 2016-04-07 | [
[
"Tsarev",
"Sergey",
""
],
[
"Sadovsky",
"Michael",
""
]
] | A new method to identify all sufficiently long repeating substrings in one or several symbol sequences is proposed. The method is based on a specific gauge applied to symbol sequences that guarantees identification of the repeating substrings. It allows the matching of substrings to contain a given level of errors. The... |
1511.03559 | Jorge Hidalgo | Jorge Hidalgo, Rafael Rubio de Casas and Miguel A. Munoz | Environmental unpredictability and inbreeding depression select for
mixed dispersal syndromes | 15 pages, 8 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mixed dispersal syndromes have historically been regarded as bet-hedging
mechanisms that enhance survival in unpredictable environments, ensuring that
some propagules stay in the maternal environment while others can potentially
colonize new sites. However, this entails paying the costs of both dispersal
and non-disp... | [
{
"created": "Wed, 11 Nov 2015 16:34:48 GMT",
"version": "v1"
}
] | 2015-11-12 | [
[
"Hidalgo",
"Jorge",
""
],
[
"de Casas",
"Rafael Rubio",
""
],
[
"Munoz",
"Miguel A.",
""
]
] | Mixed dispersal syndromes have historically been regarded as bet-hedging mechanisms that enhance survival in unpredictable environments, ensuring that some propagules stay in the maternal environment while others can potentially colonize new sites. However, this entails paying the costs of both dispersal and non-disper... |
1304.6952 | Jay Newby | Jay M. Newby, Paul C. Bressloff, James P. Keener | Breakdown of fast-slow analysis in an excitable system with channel
noise | null | null | 10.1103/PhysRevLett.111.128101 | null | q-bio.NC cond-mat.stat-mech q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a stochastic version of an excitable system based on the
Morris-Lecar model of a neuron, in which the noise originates from stochastic
Sodium and Potassium ion channels opening and closing. One can analyze neural
excitability in the deterministic model by using a separation of time scales
involving a fast... | [
{
"created": "Thu, 25 Apr 2013 16:11:33 GMT",
"version": "v1"
},
{
"created": "Fri, 30 Aug 2013 21:09:59 GMT",
"version": "v2"
}
] | 2015-06-15 | [
[
"Newby",
"Jay M.",
""
],
[
"Bressloff",
"Paul C.",
""
],
[
"Keener",
"James P.",
""
]
] | We consider a stochastic version of an excitable system based on the Morris-Lecar model of a neuron, in which the noise originates from stochastic Sodium and Potassium ion channels opening and closing. One can analyze neural excitability in the deterministic model by using a separation of time scales involving a fast v... |
1007.4098 | Sudip Kundu | Dhriti Sengupta and Sudip Kundu | Protein contact networks at different length scales and role of
hydrophobic, hydrophilic and charged residues in protein's structural
organisation | null | null | null | null | q-bio.BM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The three dimensional structure of a protein is an outcome of the
interactions of its constituent amino acids in 3D space. Considering the amino
acids as nodes and the interactions among them as edges we have constructed and
analyzed protein contact networks at different length scales, long and
short-range. While lon... | [
{
"created": "Fri, 23 Jul 2010 10:52:44 GMT",
"version": "v1"
}
] | 2010-07-26 | [
[
"Sengupta",
"Dhriti",
""
],
[
"Kundu",
"Sudip",
""
]
] | The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed protein contact networks at different length scales, long and short-range. While long ... |
1011.2605 | Sergei Nechaev | S.K. Nechaev, M.V. Tamm, O.V. Valba | Sequence matching algorithms and pairing of noncoding RNAs | 23 pages, 14 figures | null | null | null | q-bio.QM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A new statistical method of alignment of two heteropolymers which can form
hierarchical cloverleaf-like secondary structures is proposed. This offers a
new constructive algorithm for quantitative determination of binding free
energy of two noncoding RNAs with arbitrary primary sequences. The alignment of
ncRNAs diffe... | [
{
"created": "Thu, 11 Nov 2010 10:26:42 GMT",
"version": "v1"
}
] | 2010-11-12 | [
[
"Nechaev",
"S. K.",
""
],
[
"Tamm",
"M. V.",
""
],
[
"Valba",
"O. V.",
""
]
] | A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two noncoding RNAs with arbitrary primary sequences. The alignment of ncRNAs differs... |
2310.07543 | Jonathan D. Victor | Jonathan D. Victor, Guillermo Aguilar, Suniyya A. Waraich | Ordinal Characterization of Similarity Judgments | Body: 44 pages; 6 figures; 3 appendices | null | null | null | q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Characterizing judgments of similarity within a perceptual or semantic
domain, and making inferences about the underlying structure of this domain
from these judgments, has an increasingly important role in cognitive and
systems neuroscience. We present a new framework for this purpose that makes
very limited assumpt... | [
{
"created": "Wed, 11 Oct 2023 14:47:51 GMT",
"version": "v1"
}
] | 2023-10-12 | [
[
"Victor",
"Jonathan D.",
""
],
[
"Aguilar",
"Guillermo",
""
],
[
"Waraich",
"Suniyya A.",
""
]
] | Characterizing judgments of similarity within a perceptual or semantic domain, and making inferences about the underlying structure of this domain from these judgments, has an increasingly important role in cognitive and systems neuroscience. We present a new framework for this purpose that makes very limited assumptio... |
1309.6479 | Jannik Vollmer | Jannik Vollmer, Denis Menshykau, Dagmar Iber | Simulating Organogenesis in COMSOL: Cell-based Signaling Models | 6 pages, 3 Figures, Proceedings of COMSOL Conference 2013 | null | null | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most models of biological pattern formation are simulated on continuous
domains even though cells are discrete objects that provide internal boundaries
to the diffusion of regulatory components. In our previous papers on simulating
organogenesis in COMSOL (Germann et al COMSOL Conf Procedings 2011; Menshykau
and Iber... | [
{
"created": "Wed, 25 Sep 2013 12:23:41 GMT",
"version": "v1"
}
] | 2013-09-26 | [
[
"Vollmer",
"Jannik",
""
],
[
"Menshykau",
"Denis",
""
],
[
"Iber",
"Dagmar",
""
]
] | Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating organogenesis in COMSOL (Germann et al COMSOL Conf Procedings 2011; Menshykau and Iber, ... |
2307.01602 | Csenge Petak | Csenge Petak, Lapo Frati, Melissa H. Pespeni, Nick Cheney | Coping with seasons: evolutionary dynamics of gene networks in a
changing environment | Accepted at the Genetic and Evolutionary Computation Conference 2023
as a poster paper | null | 10.1145/3583133.3590744 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In environments that vary frequently and unpredictably, bet-hedgers can
overtake the population. Diversifying bet-hedgers have a diverse set of
offspring so that, no matter the conditions they find themselves in, at least
some offspring will have high fitness. In contrast, conservative bet-hedgers
have a set of offsp... | [
{
"created": "Tue, 4 Jul 2023 09:41:15 GMT",
"version": "v1"
}
] | 2023-07-06 | [
[
"Petak",
"Csenge",
""
],
[
"Frati",
"Lapo",
""
],
[
"Pespeni",
"Melissa H.",
""
],
[
"Cheney",
"Nick",
""
]
] | In environments that vary frequently and unpredictably, bet-hedgers can overtake the population. Diversifying bet-hedgers have a diverse set of offspring so that, no matter the conditions they find themselves in, at least some offspring will have high fitness. In contrast, conservative bet-hedgers have a set of offspri... |
1703.09637 | Joshua D. Salvi | Joshua D. Salvi, Daibhid O Maoileidigh, Brian A. Fabella, Melanie
Tobin, and A. J. Hudspeth | Control of a hair bundle's mechanosensory function by its mechanical
load | null | Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):E1000-9 | 10.1073/pnas.1501453112 | null | q-bio.NC physics.bio-ph q-bio.CB | http://creativecommons.org/publicdomain/zero/1.0/ | Hair cells, the sensory receptors of the internal ear, subserve different
functions in various receptor organs: they detect oscillatory stimuli in the
auditory system, but transduce constant and step stimuli in the vestibular and
lateral-line systems. We show that a hair cell's function can be controlled
experimental... | [
{
"created": "Tue, 28 Mar 2017 15:41:21 GMT",
"version": "v1"
}
] | 2017-03-29 | [
[
"Salvi",
"Joshua D.",
""
],
[
"Maoileidigh",
"Daibhid O",
""
],
[
"Fabella",
"Brian A.",
""
],
[
"Tobin",
"Melanie",
""
],
[
"Hudspeth",
"A. J.",
""
]
] | Hair cells, the sensory receptors of the internal ear, subserve different functions in various receptor organs: they detect oscillatory stimuli in the auditory system, but transduce constant and step stimuli in the vestibular and lateral-line systems. We show that a hair cell's function can be controlled experimentally... |
1406.0217 | Mike Steel Prof. | Mareike Fischer, Michelle Galla, Lina Herbst and Mike Steel | The most parsimonious tree for random data | 19 pages, 8 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Applying a method to reconstruct a phylogenetic tree from random data
provides a way to detect whether that method has an inherent bias towards
certain tree `shapes'. For maximum parsimony, applied to a sequence of random
2-state data, each possible binary phylogenetic tree has exactly the same
distribution for its p... | [
{
"created": "Sun, 1 Jun 2014 23:50:13 GMT",
"version": "v1"
}
] | 2014-06-03 | [
[
"Fischer",
"Mareike",
""
],
[
"Galla",
"Michelle",
""
],
[
"Herbst",
"Lina",
""
],
[
"Steel",
"Mike",
""
]
] | Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each possible binary phylogenetic tree has exactly the same distribution for its par... |
0806.4444 | Christian Korn | C. B. Korn and U. S. Schwarz | Mean encounter times for cell adhesion in hydrodynamic flow: analytical
progress by dimensional reduction | Reftex, postscript figures included | EPL 83:28007 (2008) | 10.1209/0295-5075/83/28007 | null | q-bio.CB physics.bio-ph q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For a cell moving in hydrodynamic flow above a wall, translational and
rotational degrees of freedom are coupled by the Stokes equation. In addition,
there is a close coupling of convection and diffusion due to the
position-dependent mobility. These couplings render calculation of the mean
encounter time between cell... | [
{
"created": "Fri, 27 Jun 2008 07:48:44 GMT",
"version": "v1"
}
] | 2008-07-14 | [
[
"Korn",
"C. B.",
""
],
[
"Schwarz",
"U. S.",
""
]
] | For a cell moving in hydrodynamic flow above a wall, translational and rotational degrees of freedom are coupled by the Stokes equation. In addition, there is a close coupling of convection and diffusion due to the position-dependent mobility. These couplings render calculation of the mean encounter time between cell s... |
1103.6276 | Stuart Borrett Stuart Borrett | Stuart R. Borrett, Michael A. Freeze, Andria K. Salas | Equivalence of the realized input and output oriented indirect effects
metrics in ecological network analysis | 13 pages, 1 figure, 1 table | Borrett, S.R., M.A. Freeze, and A.K. Salas. 2011. Equivalence of
the realized input and output oriented indirect effects metrics in Ecological
Network Analysis. Ecological Modelling 222(13): 2142-2148 | 10.1016/j.ecolmodel.2011.04.003 | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A new understanding of the consequences of how ecosystem elements are
interconnected is emerging from the development and application of Ecological
Network Analysis. The relative importance of indirect effects is central to
this understanding, and the ratio of indirect flow to direct flow (I/D) is one
indicator of th... | [
{
"created": "Thu, 31 Mar 2011 19:38:14 GMT",
"version": "v1"
}
] | 2011-11-28 | [
[
"Borrett",
"Stuart R.",
""
],
[
"Freeze",
"Michael A.",
""
],
[
"Salas",
"Andria K.",
""
]
] | A new understanding of the consequences of how ecosystem elements are interconnected is emerging from the development and application of Ecological Network Analysis. The relative importance of indirect effects is central to this understanding, and the ratio of indirect flow to direct flow (I/D) is one indicator of thei... |
1810.04269 | Isabel Irurzun Prof. | Isabel M. Irurzun, Magdalena M. Defeo, L. Garavaglia, Thomas Mailland,
E. E. Mola | Scaling behavior in the heart rate variability characteristics with age | 6 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we study the characteristics of the heart rate variability (HRV)
as a function of age and gender. The analyzed data include previous results
reported in the literature. The data obtained in this work expand the range of
age studied until now revealing new behaviors not reported before. We analyze
some me... | [
{
"created": "Wed, 5 Sep 2018 14:00:41 GMT",
"version": "v1"
}
] | 2018-10-11 | [
[
"Irurzun",
"Isabel M.",
""
],
[
"Defeo",
"Magdalena M.",
""
],
[
"Garavaglia",
"L.",
""
],
[
"Mailland",
"Thomas",
""
],
[
"Mola",
"E. E.",
""
]
] | In this work we study the characteristics of the heart rate variability (HRV) as a function of age and gender. The analyzed data include previous results reported in the literature. The data obtained in this work expand the range of age studied until now revealing new behaviors not reported before. We analyze some meas... |
2010.12706 | Deepak K. Agrawal | Deepak. K. Agrawal, Bradford J. Smith, Peter D. Sottile, and David J.
Albers | A damaged-informed lung model for ventilator waveforms | 22 pages, 7 figure, 1 table and Supplementary File | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The acute respiratory distress syndrome (ARDS) is characterized by the acute
development of diffuse alveolar damage (DAD) resulting in increased vascular
permeability and decreased alveolar gas exchange. Mechanical ventilation is a
potentially lifesaving intervention to improve oxygen exchange but has the
potential t... | [
{
"created": "Fri, 23 Oct 2020 23:23:31 GMT",
"version": "v1"
}
] | 2020-10-27 | [
[
"Agrawal",
"Deepak. K.",
""
],
[
"Smith",
"Bradford J.",
""
],
[
"Sottile",
"Peter D.",
""
],
[
"Albers",
"David J.",
""
]
] | The acute respiratory distress syndrome (ARDS) is characterized by the acute development of diffuse alveolar damage (DAD) resulting in increased vascular permeability and decreased alveolar gas exchange. Mechanical ventilation is a potentially lifesaving intervention to improve oxygen exchange but has the potential to ... |
1503.00183 | Romulus Breban | Samit Bhattacharyya, Chris Bauch, Romulus Breban | Role of word-of-mouth for programs of voluntary vaccination: A
game-theoretic approach | 10 pages, 2 figures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a model describing the synergetic feedback between word-of-mouth
(WoM) and epidemic dynamics controlled by voluntary vaccination. We combine a
game-theoretic model for the spread of WoM and a compartmental model describing
$SIR$ disease dynamics in the presence of a program of voluntary vaccination.
We eva... | [
{
"created": "Sat, 28 Feb 2015 21:33:41 GMT",
"version": "v1"
}
] | 2015-03-03 | [
[
"Bhattacharyya",
"Samit",
""
],
[
"Bauch",
"Chris",
""
],
[
"Breban",
"Romulus",
""
]
] | We propose a model describing the synergetic feedback between word-of-mouth (WoM) and epidemic dynamics controlled by voluntary vaccination. We combine a game-theoretic model for the spread of WoM and a compartmental model describing $SIR$ disease dynamics in the presence of a program of voluntary vaccination. We evalu... |
1604.06121 | Chathika Gunaratne | Chathika Gunaratne, Mustafa Ilhan Akbas, Ivan Garibay, Ozlem Ozmen | Evaluation of Zika Vector Control Strategies Using Agent-Based Modeling | 14 pages, 6 figures, 1 table, conference | null | null | null | q-bio.PE cs.MA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Aedes Aegypti is the vector of several deadly diseases, including Zika.
Effective and sustainable vector control measures must be deployed to keep A.
aegypti numbers under control. The distribution of A. Aegypti is subject to
spatial and climatic constraints. Using agent-based modeling, we model the
population dynami... | [
{
"created": "Wed, 20 Apr 2016 20:52:41 GMT",
"version": "v1"
},
{
"created": "Thu, 4 Aug 2016 18:11:18 GMT",
"version": "v2"
}
] | 2016-08-05 | [
[
"Gunaratne",
"Chathika",
""
],
[
"Akbas",
"Mustafa Ilhan",
""
],
[
"Garibay",
"Ivan",
""
],
[
"Ozmen",
"Ozlem",
""
]
] | Aedes Aegypti is the vector of several deadly diseases, including Zika. Effective and sustainable vector control measures must be deployed to keep A. aegypti numbers under control. The distribution of A. Aegypti is subject to spatial and climatic constraints. Using agent-based modeling, we model the population dynamics... |
2407.14556 | Ralph Lano P | Ralph P. Lano | Mechanical Self-replication | null | null | null | null | q-bio.OT cs.CL physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This study presents a theoretical model for a self-replicating mechanical
system inspired by biological processes within living cells and supported by
computer simulations. The model decomposes self-replication into core
components, each of which is executed by a single machine constructed from a
set of basic block t... | [
{
"created": "Thu, 18 Jul 2024 09:49:50 GMT",
"version": "v1"
}
] | 2024-07-23 | [
[
"Lano",
"Ralph P.",
""
]
] | This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of which is executed by a single machine constructed from a set of basic block typ... |
1906.08365 | Dushyant Sahoo | Dushyant Sahoo, Theodore D. Satterthwaite and Christos Davatzikos | Extraction of hierarchical functional connectivity components in human
brain using resting-state fMRI | null | null | 10.1109/TMI.2020.3042873 | null | q-bio.NC cs.LG eess.IV stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The study of hierarchy in networks of the human brain has been of significant
interest among the researchers as numerous studies have pointed out towards a
functional hierarchical organization of the human brain. This paper provides a
novel method for the extraction of hierarchical connectivity components in the
huma... | [
{
"created": "Wed, 19 Jun 2019 21:29:40 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Jun 2019 18:27:57 GMT",
"version": "v2"
},
{
"created": "Mon, 7 Dec 2020 17:24:32 GMT",
"version": "v3"
}
] | 2021-03-02 | [
[
"Sahoo",
"Dushyant",
""
],
[
"Satterthwaite",
"Theodore D.",
""
],
[
"Davatzikos",
"Christos",
""
]
] | The study of hierarchy in networks of the human brain has been of significant interest among the researchers as numerous studies have pointed out towards a functional hierarchical organization of the human brain. This paper provides a novel method for the extraction of hierarchical connectivity components in the human ... |
1205.0098 | Jiao Sy | Shuyun Jiao, and Ping Ao | Absorbing Phenomena and Escaping Time for Muller's Ratchet in Adaptive
Landscape | published in BMC Systems Biology Special Issues | BMC Systems Biology 2012, 6(Suppl 1):S10 | 10.1186/1752-0509-6-S1-S10 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: The accumulation of deleterious mutations of a population
directly contributes to the fate as to how long the population would exist, a
process often described as Muller's ratchet with the absorbing phenomenon. The
key to understand this absorbing phenomenon is to characterize the decaying
time of the fit... | [
{
"created": "Tue, 1 May 2012 06:55:54 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Aug 2012 03:31:45 GMT",
"version": "v2"
},
{
"created": "Sat, 8 Sep 2012 06:54:06 GMT",
"version": "v3"
}
] | 2012-09-11 | [
[
"Jiao",
"Shuyun",
""
],
[
"Ao",
"Ping",
""
]
] | Background: The accumulation of deleterious mutations of a population directly contributes to the fate as to how long the population would exist, a process often described as Muller's ratchet with the absorbing phenomenon. The key to understand this absorbing phenomenon is to characterize the decaying time of the fitte... |
2407.03380 | Srivathsan Badrinarayanan | Srivathsan Badrinarayanan, Chakradhar Guntuboina, Parisa Mollaei, Amir
Barati Farimani | Multi-Peptide: Multimodality Leveraged Language-Graph Learning of
Peptide Properties | null | null | null | null | q-bio.QM cs.AI cs.LG | http://creativecommons.org/publicdomain/zero/1.0/ | Peptides are essential in biological processes and therapeutics. In this
study, we introduce Multi-Peptide, an innovative approach that combines
transformer-based language models with Graph Neural Networks (GNNs) to predict
peptide properties. We combine PeptideBERT, a transformer model tailored for
peptide property ... | [
{
"created": "Tue, 2 Jul 2024 20:13:47 GMT",
"version": "v1"
}
] | 2024-07-08 | [
[
"Badrinarayanan",
"Srivathsan",
""
],
[
"Guntuboina",
"Chakradhar",
""
],
[
"Mollaei",
"Parisa",
""
],
[
"Farimani",
"Amir Barati",
""
]
] | Peptides are essential in biological processes and therapeutics. In this study, we introduce Multi-Peptide, an innovative approach that combines transformer-based language models with Graph Neural Networks (GNNs) to predict peptide properties. We combine PeptideBERT, a transformer model tailored for peptide property pr... |
1805.05597 | Francois Enault | Camille Loiseau, Victor Hatte, Charlotte Andrieu, Loic Barlet, Audric
Cologne, Romain De Oliveira, Lionel Ferrato-Berberian, H\'el\`ene Gardon
(LMGE), Damien Lauber, M\'elanie Molinier, St\'ephanie Monnerie, Kissi N
'Gou, Benjamin Penaud, Olivier Pereira, Justine Picarle, Amandine Septier,
Antoine Mahul, Jean-C... | PanGeneHome : A Web Interface to Analyze Microbial Pangenomes | null | Journal of Bioinformatics, Computational and Systems Biology,
Elyns Group, 2017 | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | PanGeneHome is a web server dedicated to the analysis of available microbial
pangenomes. For any prokaryotic taxon with at least three sequenced genomes,
PanGeneHome provides (i) conservation level of genes, (ii) pangenome and
core-genome curves, estimated pangenome size and other metrics, (iii)
dendrograms based on ... | [
{
"created": "Tue, 15 May 2018 07:08:13 GMT",
"version": "v1"
}
] | 2018-05-16 | [
[
"Loiseau",
"Camille",
"",
"LMGE"
],
[
"Hatte",
"Victor",
"",
"LMGE"
],
[
"Andrieu",
"Charlotte",
"",
"LMGE"
],
[
"Barlet",
"Loic",
"",
"LMGE"
],
[
"Cologne",
"Audric",
"",
"LMGE"
],
[
"De Oliveira",
"Romain... | PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. For any prokaryotic taxon with at least three sequenced genomes, PanGeneHome provides (i) conservation level of genes, (ii) pangenome and core-genome curves, estimated pangenome size and other metrics, (iii) dendrograms based on ge... |
1711.05351 | Vanessa Haverd | Vanessa Haverd, Benjamin Smith, Lars Nieradzik, Peter R. Briggs,
William Woodgate, Cathy M. Trudinger, Josep G. Canadell | A new version of the CABLE land surface model, incorporating land-use
change, woody vegetation demography and a novel optimisation-based approach
to plant coordination of photosynthesis | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | CABLE is a land surface model (LSM) that can be applied stand-alone, as well
as providing for land surface-atmosphere exchange within the Australian
Community Climate and Earth System Simulator (ACCESS). We describe critical new
developments that extend the applicability of CABLE for regional and global
carbon-climat... | [
{
"created": "Tue, 14 Nov 2017 23:13:44 GMT",
"version": "v1"
}
] | 2017-11-16 | [
[
"Haverd",
"Vanessa",
""
],
[
"Smith",
"Benjamin",
""
],
[
"Nieradzik",
"Lars",
""
],
[
"Briggs",
"Peter R.",
""
],
[
"Woodgate",
"William",
""
],
[
"Trudinger",
"Cathy M.",
""
],
[
"Canadell",
"Josep G.",
"... | CABLE is a land surface model (LSM) that can be applied stand-alone, as well as providing for land surface-atmosphere exchange within the Australian Community Climate and Earth System Simulator (ACCESS). We describe critical new developments that extend the applicability of CABLE for regional and global carbon-climate ... |
1003.5535 | Max Little | Max A. Little and Nick S. Jones | Sparse bayesian step-filtering for high-throughput analysis of molecular
machine dynamics | 4 pages, link to code available from author's website. | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nature has evolved many molecular machines such as kinesin, myosin, and the
rotary flagellar motor powered by an ion current from the mitochondria. Direct
observation of the step-like motion of these machines with time series from
novel experimental assays has recently become possible. These time series are
corrupted... | [
{
"created": "Mon, 29 Mar 2010 13:22:37 GMT",
"version": "v1"
}
] | 2010-03-30 | [
[
"Little",
"Max A.",
""
],
[
"Jones",
"Nick S.",
""
]
] | Nature has evolved many molecular machines such as kinesin, myosin, and the rotary flagellar motor powered by an ion current from the mitochondria. Direct observation of the step-like motion of these machines with time series from novel experimental assays has recently become possible. These time series are corrupted b... |
1405.2373 | David Sivak | David A. Sivak and Matt Thomson | Environmental statistics and optimal regulation | 21 pages, 7 figures | PLoS Comp Bio 10(9), e1003826, 2014 | 10.1016/j.bpj.2014.11.1999 | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Any organism is embedded in an environment that changes over time. The
timescale for and statistics of environmental change, the precision with which
the organism can detect its environment, and the costs and benefits of
particular protein expression levels all will affect the suitability of
different strategies-such... | [
{
"created": "Sat, 10 May 2014 01:12:47 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Aug 2014 23:40:30 GMT",
"version": "v2"
}
] | 2023-07-19 | [
[
"Sivak",
"David A.",
""
],
[
"Thomson",
"Matt",
""
]
] | Any organism is embedded in an environment that changes over time. The timescale for and statistics of environmental change, the precision with which the organism can detect its environment, and the costs and benefits of particular protein expression levels all will affect the suitability of different strategies-such a... |
q-bio/0501008 | Binder Hans | Hans Binder, Stephan Preibisch, Toralf Kirsten | Base pair interactions and hybridization isotherms of matched and
mismatched oligonucleotide probes on microarrays | 32 pages, 12 figures, 3 tables | null | null | null | q-bio.BM | null | The lack of specificity in microarray experiments due to non-specific
hybridization raises a serious problem for the analysis of microarray data
because the residual chemical background intensity is not related to the
expression degree of the gene of interest. We analyzed the concentration
dependence of the signal in... | [
{
"created": "Thu, 6 Jan 2005 16:35:04 GMT",
"version": "v1"
},
{
"created": "Wed, 11 May 2005 20:22:52 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Binder",
"Hans",
""
],
[
"Preibisch",
"Stephan",
""
],
[
"Kirsten",
"Toralf",
""
]
] | The lack of specificity in microarray experiments due to non-specific hybridization raises a serious problem for the analysis of microarray data because the residual chemical background intensity is not related to the expression degree of the gene of interest. We analyzed the concentration dependence of the signal inte... |
2311.12045 | Lauren Sanders | Kevin Li, Danko Nikoli\'c, Vjekoslav Nikoli\'c, Davor Andri\'c, Lauren
M. Sanders, Sylvain V. Costes | Using Guided Transfer Learning to Predispose AI Agent to Learn
Efficiently from Small RNA-sequencing Datasets | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Given the increasing availability of RNA-seq data and its complex and
heterogeneous nature, there has been growing interest in applying AI/machine
learning methodologies to work with such data modalities. However, because
omics data is characterized by high dimensionality and low sample size (HDLSS),
current attempts... | [
{
"created": "Fri, 17 Nov 2023 22:47:46 GMT",
"version": "v1"
}
] | 2023-11-22 | [
[
"Li",
"Kevin",
""
],
[
"Nikolić",
"Danko",
""
],
[
"Nikolić",
"Vjekoslav",
""
],
[
"Andrić",
"Davor",
""
],
[
"Sanders",
"Lauren M.",
""
],
[
"Costes",
"Sylvain V.",
""
]
] | Given the increasing availability of RNA-seq data and its complex and heterogeneous nature, there has been growing interest in applying AI/machine learning methodologies to work with such data modalities. However, because omics data is characterized by high dimensionality and low sample size (HDLSS), current attempts a... |
2103.02163 | Zhaoxia Yu | Tong Shen, Gyorgy Lur, Xiangmin Xu, Zhaoxia Yu | To Deconvolve, or Not to Deconvolve: Inferences of Neuronal Activities
using Calcium Imaging Data | null | null | null | null | q-bio.NC stat.AP | http://creativecommons.org/licenses/by-nc-nd/4.0/ | With the increasing popularity of calcium imaging data in neuroscience
research, methods for analyzing calcium trace data are critical to address
various questions. The observed calcium traces are either analyzed directly or
deconvolved to spike trains to infer neuronal activities. When both approaches
are applicable... | [
{
"created": "Wed, 3 Mar 2021 03:57:18 GMT",
"version": "v1"
}
] | 2021-03-04 | [
[
"Shen",
"Tong",
""
],
[
"Lur",
"Gyorgy",
""
],
[
"Xu",
"Xiangmin",
""
],
[
"Yu",
"Zhaoxia",
""
]
] | With the increasing popularity of calcium imaging data in neuroscience research, methods for analyzing calcium trace data are critical to address various questions. The observed calcium traces are either analyzed directly or deconvolved to spike trains to infer neuronal activities. When both approaches are applicable, ... |
q-bio/0401033 | Lior Pachter | Lior Pachter, Bernd Sturmfels | Parametric Inference for Biological Sequence Analysis | 15 pages, 4 figures. See also companion paper "Tropical Geometry of
Statistical Models" (q-bio.QM/0311009) | null | 10.1073/pnas.0406011101 | null | q-bio.GN cs.LG math.ST stat.TH | null | One of the major successes in computational biology has been the unification,
using the graphical model formalism, of a multitude of algorithms for
annotating and comparing biological sequences. Graphical models that have been
applied towards these problems include hidden Markov models for annotation,
tree models for... | [
{
"created": "Mon, 26 Jan 2004 03:50:03 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Pachter",
"Lior",
""
],
[
"Sturmfels",
"Bernd",
""
]
] | One of the major successes in computational biology has been the unification, using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied towards these problems include hidden Markov models for annotation, tree models for p... |
2303.00394 | Sebastien Lambert | S\'ebastien Lambert (IHAP), Billy Bauzile (IHAP), Am\'elie Mugnier
(NeoCare), Benoit Durand (ANSES), Timoth\'ee Vergne (IHAP), Mathilde C Paul
(IHAP) | A systematic review of mechanistic models used to study avian influenza
virus transmission and control | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The global spread of avian influenza A viruses in domestic birds is causing
dramatic economic and social losses. Various mechanistic models have been
developed in an attempt to better understand avian influenza transmission and
to evaluate the effectiveness of control measures. However, no comprehensive
review of the... | [
{
"created": "Wed, 1 Mar 2023 10:26:33 GMT",
"version": "v1"
}
] | 2023-03-02 | [
[
"Lambert",
"Sébastien",
"",
"IHAP"
],
[
"Bauzile",
"Billy",
"",
"IHAP"
],
[
"Mugnier",
"Amélie",
"",
"NeoCare"
],
[
"Durand",
"Benoit",
"",
"ANSES"
],
[
"Vergne",
"Timothée",
"",
"IHAP"
],
[
"Paul",
"Mathil... | The global spread of avian influenza A viruses in domestic birds is causing dramatic economic and social losses. Various mechanistic models have been developed in an attempt to better understand avian influenza transmission and to evaluate the effectiveness of control measures. However, no comprehensive review of the m... |
1910.03936 | Mohammed Alser | Mohammed H K Alser | Accelerating the Understanding of Life's Code Through Better Algorithms
and Hardware Design | null | null | null | null | q-bio.GN cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Calculating the similarities between a pair of genomic sequences is one of
the most fundamental computational steps in genomic analysis. This step --
called sequence alignment -- is the computational bottleneck because: (1) it is
implemented using quadratic-time dynamic programming algorithms and (2) the
majority of ... | [
{
"created": "Tue, 8 Oct 2019 15:52:53 GMT",
"version": "v1"
}
] | 2019-10-10 | [
[
"Alser",
"Mohammed H K",
""
]
] | Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is implemented using quadratic-time dynamic programming algorithms and (2) the majority of ca... |
1811.05088 | Alexei Goun | Zachary Quine, Alexei Goun, Herschel Rabitz | Suppression of the Spectral Cross Talk of Optogenetic Switching by
Stimulated Depletion Quenching. Theoretical Analysis | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Optogenetics is a rapidly growing field of biotechnology, potentially
allowing a deeper understanding and control of complex biological networks. The
major challenge is the multiplexed control of several optogenetic components in
the presence of significant spectral cross talk. We propose and demonstrate
through simu... | [
{
"created": "Tue, 13 Nov 2018 03:34:08 GMT",
"version": "v1"
}
] | 2018-11-14 | [
[
"Quine",
"Zachary",
""
],
[
"Goun",
"Alexei",
""
],
[
"Rabitz",
"Herschel",
""
]
] | Optogenetics is a rapidly growing field of biotechnology, potentially allowing a deeper understanding and control of complex biological networks. The major challenge is the multiplexed control of several optogenetic components in the presence of significant spectral cross talk. We propose and demonstrate through simula... |
1510.09138 | Axel Blau | Aurel Vasile Martiniuc, Victor Boco\c{s}-Bin\c{t}in\c{t}an, Rouhollah
Habibey, Asiyeh Golabchi, Alois Knoll, Axel Blau | Paired spiking robustly shapes spontaneous activity in neural networks
in vitro | 23 pages, 9 figures; 2 supplementary pages, 2 supplementary figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In vivo, neurons establish functional connections and preserve information
along their synaptic pathways from one information processing stage to the next
in a very efficient manner. Paired spiking (PS) enhancement plays a key role by
acting as a temporal filter that deletes less informative spikes. We analyzed
the s... | [
{
"created": "Fri, 30 Oct 2015 15:56:23 GMT",
"version": "v1"
}
] | 2015-11-02 | [
[
"Martiniuc",
"Aurel Vasile",
""
],
[
"Bocoş-Binţinţan",
"Victor",
""
],
[
"Habibey",
"Rouhollah",
""
],
[
"Golabchi",
"Asiyeh",
""
],
[
"Knoll",
"Alois",
""
],
[
"Blau",
"Axel",
""
]
] | In vivo, neurons establish functional connections and preserve information along their synaptic pathways from one information processing stage to the next in a very efficient manner. Paired spiking (PS) enhancement plays a key role by acting as a temporal filter that deletes less informative spikes. We analyzed the spo... |
1811.03674 | Serena Bradde | Serena Bradde and Thierry Mora and Aleksandra M. Walczak | Cost and benefits of CRISPR spacer acquisition | 5 figures, 10 pages | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | CRISPR-Cas mediated immunity in bacteria allows bacterial populations to
protect themselves against pathogens. However, it also exposes them to the
dangers of auto-immunity by developing protection that targets its own genome.
Using a simple model of the coupled dynamics of phage and bacterial
populations, we explore... | [
{
"created": "Thu, 8 Nov 2018 20:54:32 GMT",
"version": "v1"
}
] | 2018-11-12 | [
[
"Bradde",
"Serena",
""
],
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M.",
""
]
] | CRISPR-Cas mediated immunity in bacteria allows bacterial populations to protect themselves against pathogens. However, it also exposes them to the dangers of auto-immunity by developing protection that targets its own genome. Using a simple model of the coupled dynamics of phage and bacterial populations, we explore h... |
1610.00611 | Grzegorz Wojcik Prof. | Dominik S. Kufel, Grzegorz M. Wojcik | Analytical modelling of temperature effects on synapses | 14 pages, 11 figures | Kufel, D. S., & Wojcik, G. M. (2018). Analytical modelling of
temperature effects on an AMPA-type synapse. Journal of computational
neuroscience, 44(3), 379-391 | 10.1007/s10827-018-0684-x | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It was previously reported, that temperature may significantly influence
neural dynamics on different levels of brain modelling. Due to this fact, while
creating the model in computational neuroscience we would like to make it
scalable for wide-range of various brain temperatures. However currently,
because of a lack... | [
{
"created": "Mon, 3 Oct 2016 16:12:27 GMT",
"version": "v1"
}
] | 2018-08-30 | [
[
"Kufel",
"Dominik S.",
""
],
[
"Wojcik",
"Grzegorz M.",
""
]
] | It was previously reported, that temperature may significantly influence neural dynamics on different levels of brain modelling. Due to this fact, while creating the model in computational neuroscience we would like to make it scalable for wide-range of various brain temperatures. However currently, because of a lack o... |
1303.7006 | Bhavin Khatri | Bhavin S. Khatri and Richard A. Goldstein | Evolutionary stochastic dynamics of speciation and a simple
genotype-phenotype map for protein binding DNA | 5 pages, 2 figures | Journal of Theoretical Biology, 378 (2015), p56-64 | 10.1016/j.jtbi.2015.04.027 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Speciation is of fundamental importance to understanding the huge diversity
of life on Earth. In contrast to current phenomenological models, we develop a
biophysically motivated approach to study speciation involving the co-evolution
of protein binding DNA for two geographically isolated populations. Our results
pre... | [
{
"created": "Wed, 27 Mar 2013 23:32:59 GMT",
"version": "v1"
},
{
"created": "Sun, 12 May 2013 10:27:34 GMT",
"version": "v2"
}
] | 2015-05-18 | [
[
"Khatri",
"Bhavin S.",
""
],
[
"Goldstein",
"Richard A.",
""
]
] | Speciation is of fundamental importance to understanding the huge diversity of life on Earth. In contrast to current phenomenological models, we develop a biophysically motivated approach to study speciation involving the co-evolution of protein binding DNA for two geographically isolated populations. Our results predi... |
1411.2017 | Kristina Crona | Kristina Crona | Recombination and peak jumping | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We find an advantage of recombination for a category of complex fitness
landscapes. Recent studies of empirical fitness landscapes reveal complex gene
interactions and multiple peaks, and recombination can be a powerful mechanism
for escaping suboptimal peaks. However classical work on recombination largely
ignores t... | [
{
"created": "Fri, 7 Nov 2014 20:06:18 GMT",
"version": "v1"
}
] | 2014-11-10 | [
[
"Crona",
"Kristina",
""
]
] | We find an advantage of recombination for a category of complex fitness landscapes. Recent studies of empirical fitness landscapes reveal complex gene interactions and multiple peaks, and recombination can be a powerful mechanism for escaping suboptimal peaks. However classical work on recombination largely ignores the... |
2301.10850 | Mohammad Anwar Ul Alam | Mohammad Anwar Ul Alam, Aschalew Kassu, and Lamin Kassama | Effect of sonication time and surfactant concentration on improving the
bio-accessibility of lycopene synthesized in poly-lactic co-glycolic acid
nanoparticles | null | 2022 ASABE Annual International Meeting 2200474 | 10.13031/aim.202200474 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The use of biodegradable polymers simplifies the development of therapeutic
devices with regards to transient implants and three-dimensional platform
suitable for tissue engineering. Further advances have also occurred in the
controlled released mechanism of bioactive compounds encapsulated in
biodegradable polymers.... | [
{
"created": "Wed, 25 Jan 2023 22:18:44 GMT",
"version": "v1"
}
] | 2023-01-27 | [
[
"Alam",
"Mohammad Anwar Ul",
""
],
[
"Kassu",
"Aschalew",
""
],
[
"Kassama",
"Lamin",
""
]
] | The use of biodegradable polymers simplifies the development of therapeutic devices with regards to transient implants and three-dimensional platform suitable for tissue engineering. Further advances have also occurred in the controlled released mechanism of bioactive compounds encapsulated in biodegradable polymers. T... |
2204.09225 | Xiaowei Yu | Xiaowei Yu, Lu Zhang, Lin Zhao, Yanjun Lyu, Tianming Liu, Dajiang Zhu | Disentangling Spatial-Temporal Functional Brain Networks via
Twin-Transformers | full pages | null | null | null | q-bio.NC cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How to identify and characterize functional brain networks (BN) is
fundamental to gain system-level insights into the mechanisms of brain
organizational architecture. Current functional magnetic resonance (fMRI)
analysis highly relies on prior knowledge of specific patterns in either
spatial (e.g., resting-state netw... | [
{
"created": "Wed, 20 Apr 2022 04:57:53 GMT",
"version": "v1"
},
{
"created": "Sun, 26 Jun 2022 18:46:03 GMT",
"version": "v2"
}
] | 2022-06-28 | [
[
"Yu",
"Xiaowei",
""
],
[
"Zhang",
"Lu",
""
],
[
"Zhao",
"Lin",
""
],
[
"Lyu",
"Yanjun",
""
],
[
"Liu",
"Tianming",
""
],
[
"Zhu",
"Dajiang",
""
]
] | How to identify and characterize functional brain networks (BN) is fundamental to gain system-level insights into the mechanisms of brain organizational architecture. Current functional magnetic resonance (fMRI) analysis highly relies on prior knowledge of specific patterns in either spatial (e.g., resting-state networ... |
2012.05294 | Imelda Trejo | Imelda Trejo and Nicolas Hengartner | A modified Susceptible-Infected-Recovered model for observed
under-reported incidence data | null | null | null | null | q-bio.PE stat.AP stat.CO | http://creativecommons.org/licenses/by/4.0/ | Fitting Susceptible-Infected-Recovered (SIR) models to incidence data is
problematic when not all infected individuals are reported. Assuming an
underlying SIR model with general but known distribution for the time to
recovery, this paper derives the implied differential-integral equations for
observed incidence data... | [
{
"created": "Wed, 9 Dec 2020 20:05:49 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Aug 2021 18:39:39 GMT",
"version": "v2"
}
] | 2021-08-16 | [
[
"Trejo",
"Imelda",
""
],
[
"Hengartner",
"Nicolas",
""
]
] | Fitting Susceptible-Infected-Recovered (SIR) models to incidence data is problematic when not all infected individuals are reported. Assuming an underlying SIR model with general but known distribution for the time to recovery, this paper derives the implied differential-integral equations for observed incidence data w... |
q-bio/0509014 | Mathieu Bouville | Mathieu Bouville | Fermentation kinetics including product and substrate inhibitions plus
biomass death: a mathematical analysis | 4 pages, 4 figures | Biotechnology Letters 29(5), 737-741 (2007) | 10.1007/s10529-006-9296-z | null | q-bio.QM q-bio.PE | null | Fermentation is generally modelled by kinetic equations giving the time
evolutions for biomass, substrate, and product concentrations. Although these
equations can be solved analytically in simple cases if substrate/product
inhibition and biomass death are included, they are typically solved
numerically. We propose a... | [
{
"created": "Tue, 13 Sep 2005 15:58:08 GMT",
"version": "v1"
},
{
"created": "Sun, 9 Oct 2005 10:54:29 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Bouville",
"Mathieu",
""
]
] | Fermentation is generally modelled by kinetic equations giving the time evolutions for biomass, substrate, and product concentrations. Although these equations can be solved analytically in simple cases if substrate/product inhibition and biomass death are included, they are typically solved numerically. We propose an ... |
1803.09005 | Mathilde Badoual | Chlo\'e Gerin, Johan Pallud, Christophe Deroulers, Pascale Varlet,
Catherine Oppenheim, Fran\c{c}ois-Xavier Roux, Fabrice Chr\'etien, Stephen
Randy Thomas, Basile Grammaticos, Mathilde Badoual | Quantitative characterization of the imaging limits of diffuse low-grade
oligodendrogliomas | 19 pages, 1 table, 6 figures, 1 supplementary figure | Neuro Oncology 2013 Oct;15(10):1379-88 | 10.1093/neuonc/not072 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background : Supratentorial diffuse low-grade gliomas in adults extend beyond
maximal visible MRI-defined abnormalities, and a gap exists between the imaging
signal changes and the actual tumor margins. Direct quantitative comparisons
between imaging and histological analyses are lacking to date. However, they
are of... | [
{
"created": "Fri, 23 Mar 2018 22:49:04 GMT",
"version": "v1"
}
] | 2018-03-28 | [
[
"Gerin",
"Chloé",
""
],
[
"Pallud",
"Johan",
""
],
[
"Deroulers",
"Christophe",
""
],
[
"Varlet",
"Pascale",
""
],
[
"Oppenheim",
"Catherine",
""
],
[
"Roux",
"François-Xavier",
""
],
[
"Chrétien",
"Fabrice",
... | Background : Supratentorial diffuse low-grade gliomas in adults extend beyond maximal visible MRI-defined abnormalities, and a gap exists between the imaging signal changes and the actual tumor margins. Direct quantitative comparisons between imaging and histological analyses are lacking to date. However, they are of t... |
2201.04296 | Diego Martinez | J. Chacon, M. Pimentel, A. Pedroso, A. Ferreira, D. Martinez, C.
Ruelas | In vitro evaluation of the effect of Ceftiofur Sodium and of a new
Gentamycin Sulfate formulation on the viability of Marek disease virus | in Spanish | Proceedings of the XX Latin American Poultry Congress. 2007. Porto
Alegre, Brazil | null | null | q-bio.OT | http://creativecommons.org/licenses/by-sa/4.0/ | The present study evaluated In vitro effect of gentamicin sulfate and
ceftiofur sodium on the viability of the Marek's disease virus. The titer of
cell associated turkey herpesvirus (HVT) vaccine was not appreciably reduced
when incubated with 50 mg/ml of gentamicin sulfate or ceftiofur sodium.
Statistic difference w... | [
{
"created": "Wed, 12 Jan 2022 04:38:41 GMT",
"version": "v1"
}
] | 2022-01-13 | [
[
"Chacon",
"J.",
""
],
[
"Pimentel",
"M.",
""
],
[
"Pedroso",
"A.",
""
],
[
"Ferreira",
"A.",
""
],
[
"Martinez",
"D.",
""
],
[
"Ruelas",
"C.",
""
]
] | The present study evaluated In vitro effect of gentamicin sulfate and ceftiofur sodium on the viability of the Marek's disease virus. The titer of cell associated turkey herpesvirus (HVT) vaccine was not appreciably reduced when incubated with 50 mg/ml of gentamicin sulfate or ceftiofur sodium. Statistic difference was... |
1712.08058 | Christian Dansereau | Christian Dansereau, Angela Tam, AmanPreet Badhwar, Sebastian Urchs,
Pierre Orban, Pedro Rosa-Neto, Pierre Bellec | A brain signature highly predictive of future progression to Alzheimer's
dementia | null | null | null | null | q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Early prognosis of Alzheimer's dementia is hard. Mild cognitive impairment
(MCI) typically precedes Alzheimer's dementia, yet only a fraction of MCI
individuals will progress to dementia, even when screened using biomarkers. We
propose here to identify a subset of individuals who share a common brain
signature highly... | [
{
"created": "Thu, 21 Dec 2017 16:26:48 GMT",
"version": "v1"
},
{
"created": "Fri, 2 Mar 2018 17:37:11 GMT",
"version": "v2"
}
] | 2018-03-05 | [
[
"Dansereau",
"Christian",
""
],
[
"Tam",
"Angela",
""
],
[
"Badhwar",
"AmanPreet",
""
],
[
"Urchs",
"Sebastian",
""
],
[
"Orban",
"Pierre",
""
],
[
"Rosa-Neto",
"Pedro",
""
],
[
"Bellec",
"Pierre",
""
]
] | Early prognosis of Alzheimer's dementia is hard. Mild cognitive impairment (MCI) typically precedes Alzheimer's dementia, yet only a fraction of MCI individuals will progress to dementia, even when screened using biomarkers. We propose here to identify a subset of individuals who share a common brain signature highly p... |
2308.02172 | Haotian Zhang | Haotian Zhang, Huifeng Zhao, Xujun Zhang, Qun Su, Hongyan Du, Chao
Shen, Zhe Wang, Dan Li, Peichen Pan, Guangyong Chen, Yu Kang, Chang-yu Hsieh,
Tingjun Hou | Delete: Deep Lead Optimization Enveloped in Protein Pocket through
Unified Deleting Strategies and a Structure-aware Network | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Drug discovery is a highly complicated process, and it is unfeasible to fully
commit it to the recently developed molecular generation methods. Deep
learning-based lead optimization takes expert knowledge as a starting point,
learning from numerous historical cases about how to modify the structure for
better drug-fo... | [
{
"created": "Fri, 4 Aug 2023 07:18:08 GMT",
"version": "v1"
}
] | 2023-08-07 | [
[
"Zhang",
"Haotian",
""
],
[
"Zhao",
"Huifeng",
""
],
[
"Zhang",
"Xujun",
""
],
[
"Su",
"Qun",
""
],
[
"Du",
"Hongyan",
""
],
[
"Shen",
"Chao",
""
],
[
"Wang",
"Zhe",
""
],
[
"Li",
"Dan",
""
... | Drug discovery is a highly complicated process, and it is unfeasible to fully commit it to the recently developed molecular generation methods. Deep learning-based lead optimization takes expert knowledge as a starting point, learning from numerous historical cases about how to modify the structure for better drug-form... |
1303.0402 | Mayya Miftakhova | V.V. Babenko, M.M. Miftakhova, D.V. Yavna | Organizational properties of second-order visual filters sensitive to
the orientation modulations | 4 pages, 3 figures; this is the English version of paper; it's
published in Russian | Babenko V.V., Miftakhova M.M., Yavna D.V. Organizational
properties of second-order visual filters sensitive to the orientation
modulations // Proceedings of 10th International Conference "Applied Optics",
St. Petersburg. P. 331-334. 2012 | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here we show psychophysical study of second-order visual mechanisms sensitive
to the orientation modulations. Selectivity to orientation, phase and spatial
frequency of modulation is measured. Bandwidths for phase (0,5{\pi}) and
orientation (33,75 deg) are defined, but there is no evidence for spatial
frequency selec... | [
{
"created": "Sat, 2 Mar 2013 16:50:14 GMT",
"version": "v1"
}
] | 2013-03-05 | [
[
"Babenko",
"V. V.",
""
],
[
"Miftakhova",
"M. M.",
""
],
[
"Yavna",
"D. V.",
""
]
] | Here we show psychophysical study of second-order visual mechanisms sensitive to the orientation modulations. Selectivity to orientation, phase and spatial frequency of modulation is measured. Bandwidths for phase (0,5{\pi}) and orientation (33,75 deg) are defined, but there is no evidence for spatial frequency selecti... |
1509.02745 | Klaus Jaffe Dr | Klaus Jaffe | Extended Inclusive Fitness Theory bridges Economics and Biology through
a common understanding of Social Synergy | Bioeconomics, Synergy, Complexity | SpringerPlus. 5(1) 1-19, 2016, 5:1092 | 10.1186/s40064-016-2750-z | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inclusive Fitness Theory (IFT) was proposed half a century ago by W.D.
Hamilton to explain the emergence and maintenance of cooperation between
individuals that allows the existence of society. Contemporary evolutionary
ecology identified several factors that increase inclusive fitness, in addition
to kin-selection, ... | [
{
"created": "Wed, 9 Sep 2015 12:18:00 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Nov 2015 19:26:28 GMT",
"version": "v2"
}
] | 2017-03-07 | [
[
"Jaffe",
"Klaus",
""
]
] | Inclusive Fitness Theory (IFT) was proposed half a century ago by W.D. Hamilton to explain the emergence and maintenance of cooperation between individuals that allows the existence of society. Contemporary evolutionary ecology identified several factors that increase inclusive fitness, in addition to kin-selection, su... |
2309.07082 | Bel\'en Valenzuela | Bel\'en Valenzuela | Landau model to illustrate the process of learning and unlearning of
nociplastic pain | null | null | null | null | q-bio.TO physics.soc-ph q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Recent advances in the comprehension of the consolidation of nociplastic pain
points to a complex nonconscious learnt process of threat perception.
Neurobiological education is emerging as a promising approach to unlearn
nociplastic pain supported by biopsychosocial tools (exposition to movement,
mindfulness, sharing... | [
{
"created": "Mon, 11 Sep 2023 11:08:13 GMT",
"version": "v1"
}
] | 2023-09-14 | [
[
"Valenzuela",
"Belén",
""
]
] | Recent advances in the comprehension of the consolidation of nociplastic pain points to a complex nonconscious learnt process of threat perception. Neurobiological education is emerging as a promising approach to unlearn nociplastic pain supported by biopsychosocial tools (exposition to movement, mindfulness, sharing g... |
1806.02171 | Davide Fiore | Davide Fiore and Agostino Guarino and Mario di Bernardo | Analysis and control of genetic toggle switches subject to periodic
multi-input stimulation | Preprint accepted for publication on L-CSS (First submission
31.05.2018, accepted 21.08.2018) | IEEE Control Systems Letters, vol. 3, no. 2, pp. 278-283, 2019 | 10.1109/LCSYS.2018.2868925 | null | q-bio.MN cs.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this letter, we analyze a genetic toggle switch recently studied in the
literature where the expression of two repressor proteins can be tuned by
controlling two different inputs, namely the concentration of two inducer
molecules in the growth medium of the cells. Specifically, we investigate the
dynamics of this ... | [
{
"created": "Wed, 6 Jun 2018 13:28:29 GMT",
"version": "v1"
},
{
"created": "Tue, 4 Sep 2018 08:17:21 GMT",
"version": "v2"
}
] | 2020-03-18 | [
[
"Fiore",
"Davide",
""
],
[
"Guarino",
"Agostino",
""
],
[
"di Bernardo",
"Mario",
""
]
] | In this letter, we analyze a genetic toggle switch recently studied in the literature where the expression of two repressor proteins can be tuned by controlling two different inputs, namely the concentration of two inducer molecules in the growth medium of the cells. Specifically, we investigate the dynamics of this sy... |
1912.00960 | Matteo Romandini | Matteo Romandini, Jacopo Crezzini, Eugenio Bortolini, Paolo Boscato,
Francesco Boschin, Lisa Carrera, Nicola Nannini, Antonio Tagliacozzo,
Gabriele Terlato, Simona Arrighi, Federica Badino, Carla Figus, Federico
Lugli, Giulia Marciani, Gregorio Oxilia, Adriana Moroni, Fabio Negrino, Marco
Peresani, Julien Riel-... | Macromammal and bird assemblages across the Late Middle to Upper
Palaeolithic transition in Italy: an extended zooarchaeological review | null | null | 10.1016/j.quaint.2019.11.008 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evidence of human activities during the Middle to Upper Palaeolithic
transition is well represented from rock_shelters, caves and open_air sites
across Italy. Over the past decade, both the revision of taphonomic processes
affecting archaeological faunal assemblages and new zooarchaeological studies
have allowed arch... | [
{
"created": "Mon, 2 Dec 2019 17:47:11 GMT",
"version": "v1"
},
{
"created": "Thu, 19 Dec 2019 18:20:26 GMT",
"version": "v2"
},
{
"created": "Thu, 2 Jan 2020 18:35:39 GMT",
"version": "v3"
}
] | 2020-01-03 | [
[
"Romandini",
"Matteo",
""
],
[
"Crezzini",
"Jacopo",
""
],
[
"Bortolini",
"Eugenio",
""
],
[
"Boscato",
"Paolo",
""
],
[
"Boschin",
"Francesco",
""
],
[
"Carrera",
"Lisa",
""
],
[
"Nannini",
"Nicola",
""
... | Evidence of human activities during the Middle to Upper Palaeolithic transition is well represented from rock_shelters, caves and open_air sites across Italy. Over the past decade, both the revision of taphonomic processes affecting archaeological faunal assemblages and new zooarchaeological studies have allowed archae... |
1806.07557 | Heyrim Cho | Heyrim Cho and Doron Levy | Modeling continuous levels of resistance to multidrug therapy in cancer | 42 pages | null | 10.1016/j.apm.2018.07.025 | null | q-bio.PE q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multidrug resistance consists of a series of genetic and epigenetic
alternations that involve multifactorial and complex processes, which are a
challenge to successful cancer treatments. Accompanied by advances in
biotechnology and high-dimensional data analysis techniques that are bringing
in new opportunities in mo... | [
{
"created": "Wed, 20 Jun 2018 05:22:16 GMT",
"version": "v1"
}
] | 2022-04-19 | [
[
"Cho",
"Heyrim",
""
],
[
"Levy",
"Doron",
""
]
] | Multidrug resistance consists of a series of genetic and epigenetic alternations that involve multifactorial and complex processes, which are a challenge to successful cancer treatments. Accompanied by advances in biotechnology and high-dimensional data analysis techniques that are bringing in new opportunities in mode... |
q-bio/0611029 | Angelika Studeny | P. Pfaffelhuber and A. Studeny | Approximating genealogies for partially linked neutral loci under a
selective sweep | 30 pages, 7 figures, submitted to Journal of Math. Biology | null | null | null | q-bio.PE math.PR | null | Consider a genetic locus carrying a strongly beneficial allele which has
recently fixed in a large population. As strongly beneficial alleles fix
quickly, sequence diversity at partially linked neutral loci is reduced. This
phenomenon is known as a selective sweep. The fixation of the beneficial allele
not only affec... | [
{
"created": "Wed, 8 Nov 2006 11:30:52 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Pfaffelhuber",
"P.",
""
],
[
"Studeny",
"A.",
""
]
] | Consider a genetic locus carrying a strongly beneficial allele which has recently fixed in a large population. As strongly beneficial alleles fix quickly, sequence diversity at partially linked neutral loci is reduced. This phenomenon is known as a selective sweep. The fixation of the beneficial allele not only affects... |
1902.03429 | Yu Zong Chen | Chu Qin, Ying Tan, Shang Ying Chen, Xian Zeng, Xingxing Qi, Tian Jin,
Huan Shi, Yiwei Wan, Yu Chen, Jingfeng Li, Weidong He, Yali Wang, Peng Zhang,
Feng Zhu, Hongping Zhao, Yuyang Jiang, Yuzong Chen | Clustering Bioactive Molecules in 3D Chemical Space with Unsupervised
Deep Learning | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Unsupervised clustering has broad applications in data stratification,
pattern investigation and new discovery beyond existing knowledge. In
particular, clustering of bioactive molecules facilitates chemical space
mapping, structure-activity studies, and drug discovery. These tasks,
conventionally conducted by simila... | [
{
"created": "Sat, 9 Feb 2019 14:31:09 GMT",
"version": "v1"
}
] | 2019-02-12 | [
[
"Qin",
"Chu",
""
],
[
"Tan",
"Ying",
""
],
[
"Chen",
"Shang Ying",
""
],
[
"Zeng",
"Xian",
""
],
[
"Qi",
"Xingxing",
""
],
[
"Jin",
"Tian",
""
],
[
"Shi",
"Huan",
""
],
[
"Wan",
"Yiwei",
""
... | Unsupervised clustering has broad applications in data stratification, pattern investigation and new discovery beyond existing knowledge. In particular, clustering of bioactive molecules facilitates chemical space mapping, structure-activity studies, and drug discovery. These tasks, conventionally conducted by similari... |
2010.14385 | Sara Oliveira | Sara M Oliveira, Alice Gruppi, Marta V. Vieira, Gabriela M. Souza,
Ant\'onio A. Vicente, Jos\'e A.C. Teixeira, Pablo Fuci\~nos, Giorgia Spigno
and Lorenzo M. Pastrana | How additive manufacturing can boost the bioactivity of baked functional
foods | null | null | 10.1016/j.jfoodeng.2020.110394 | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The antioxidant activity of baked foods is of utmost interest when
envisioning enhancing their health benefits. Incorporating functional
ingredients is challenging since their bioactivity naturally declines during
baking. In this study, 3D food printing and design of experiments are employed
to clarify how the antiox... | [
{
"created": "Tue, 27 Oct 2020 15:49:30 GMT",
"version": "v1"
}
] | 2020-11-17 | [
[
"Oliveira",
"Sara M",
""
],
[
"Gruppi",
"Alice",
""
],
[
"Vieira",
"Marta V.",
""
],
[
"Souza",
"Gabriela M.",
""
],
[
"Vicente",
"António A.",
""
],
[
"Teixeira",
"José A. C.",
""
],
[
"Fuciños",
"Pablo",
... | The antioxidant activity of baked foods is of utmost interest when envisioning enhancing their health benefits. Incorporating functional ingredients is challenging since their bioactivity naturally declines during baking. In this study, 3D food printing and design of experiments are employed to clarify how the antioxid... |
1810.04910 | Annabelle Haudry | Annabelle Haudry, Stefan Laurent, Martin Kapun | Population genomics on the fly: recent advances in Drosophila | book chapter, 69 pages (ref included), 2 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Drosophila melanogaster, a small dipteran of African origin, represents one
of the best-studied model organisms. Early work in this system has uniquely
shed light on the basic principles of genetics and resulted in a versatile
collection of genetic tools that allow to uncover mechanistic links between
genotype and ph... | [
{
"created": "Thu, 11 Oct 2018 09:15:03 GMT",
"version": "v1"
}
] | 2018-10-12 | [
[
"Haudry",
"Annabelle",
""
],
[
"Laurent",
"Stefan",
""
],
[
"Kapun",
"Martin",
""
]
] | Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phen... |
1406.7185 | Marijn van Dongen | M.N. van Dongen and F.E. Hoebeek and S.K.E. Koekkoek and C.I. De Zeeuw
and W.A. Serdijn | Efficacy of high frequency switched-mode stimulation in activating
Purkinje cells | 13 pages, 8 figures | null | null | null | q-bio.NC q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper investigates the efficacy of high frequency switched-mode neural
stimulation. Instead of using a constant stimulation amplitude, the stimulus is
switched on and off repeatedly with a high frequency (up to 100kHz) duty cycled
signal. By means of tissue modeling that includes the dynamic properties of
both t... | [
{
"created": "Fri, 27 Jun 2014 14:04:03 GMT",
"version": "v1"
}
] | 2014-06-30 | [
[
"van Dongen",
"M. N.",
""
],
[
"Hoebeek",
"F. E.",
""
],
[
"Koekkoek",
"S. K. E.",
""
],
[
"De Zeeuw",
"C. I.",
""
],
[
"Serdijn",
"W. A.",
""
]
] | This paper investigates the efficacy of high frequency switched-mode neural stimulation. Instead of using a constant stimulation amplitude, the stimulus is switched on and off repeatedly with a high frequency (up to 100kHz) duty cycled signal. By means of tissue modeling that includes the dynamic properties of both the... |
1912.02964 | Jianyuan Deng | Jianyuan Deng, Fusheng Wang | An Informatics-based Approach to Identify Key Pharmacological Components
in Drug-Drug Interactions | Accepted to AMIA 2020 Informatics Summit | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Drug-drug interactions (DDI) can cause severe adverse drug reactions and pose
a major challenge to medication therapy. Recently, informatics-based approaches
are emerging for DDI studies. In this paper, we aim to identify key
pharmacological components in DDI based on large-scale data from DrugBank, a
comprehensive D... | [
{
"created": "Fri, 6 Dec 2019 03:20:38 GMT",
"version": "v1"
}
] | 2019-12-09 | [
[
"Deng",
"Jianyuan",
""
],
[
"Wang",
"Fusheng",
""
]
] | Drug-drug interactions (DDI) can cause severe adverse drug reactions and pose a major challenge to medication therapy. Recently, informatics-based approaches are emerging for DDI studies. In this paper, we aim to identify key pharmacological components in DDI based on large-scale data from DrugBank, a comprehensive DDI... |
1706.03836 | Christian Meisel | Christian Meisel, Andreas Klaus, Vladyslav V. Vyazovskiy and Dietmar
Plenz | The interplay between long- and short-range temporal correlations shapes
cortex dynamics across vigilance states | null | null | null | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Increasing evidence suggests that cortical dynamics during wake exhibits
long-range temporal correlations suitable to integrate inputs over extended
periods of time to increase the signal-to-noise ratio in decision-making and
working memory tasks. Accordingly, sleep has been suggested as a state
characterized by a br... | [
{
"created": "Mon, 12 Jun 2017 20:16:42 GMT",
"version": "v1"
}
] | 2017-06-14 | [
[
"Meisel",
"Christian",
""
],
[
"Klaus",
"Andreas",
""
],
[
"Vyazovskiy",
"Vladyslav V.",
""
],
[
"Plenz",
"Dietmar",
""
]
] | Increasing evidence suggests that cortical dynamics during wake exhibits long-range temporal correlations suitable to integrate inputs over extended periods of time to increase the signal-to-noise ratio in decision-making and working memory tasks. Accordingly, sleep has been suggested as a state characterized by a brea... |
1212.0504 | Michael Menden | Michael P. Menden, Francesco Iorio, Mathew Garnett, Ultan McDermott,
Cyril Benes, Pedro J. Ballester, Julio Saez-Rodriguez | Machine learning prediction of cancer cell sensitivity to drugs based on
genomic and chemical properties | 26 pages, 7 figures, including supplemental information, presented by
Michael Menden at the 5th annual RECOMB Conference on Regulatory and Systems
Genomics with DREAM Challenges; accepted in PLOS ONE | null | 10.1371/journal.pone.0061318 | null | q-bio.GN cs.CE cs.LG q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Predicting the response of a specific cancer to a therapy is a major goal in
modern oncology that should ultimately lead to a personalised treatment.
High-throughput screenings of potentially active compounds against a panel of
genomically heterogeneous cancer cell lines have unveiled multiple
relationships between g... | [
{
"created": "Mon, 3 Dec 2012 19:38:09 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Dec 2012 15:10:37 GMT",
"version": "v2"
},
{
"created": "Mon, 18 Mar 2013 18:07:47 GMT",
"version": "v3"
}
] | 2015-06-12 | [
[
"Menden",
"Michael P.",
""
],
[
"Iorio",
"Francesco",
""
],
[
"Garnett",
"Mathew",
""
],
[
"McDermott",
"Ultan",
""
],
[
"Benes",
"Cyril",
""
],
[
"Ballester",
"Pedro J.",
""
],
[
"Saez-Rodriguez",
"Julio",
... | Predicting the response of a specific cancer to a therapy is a major goal in modern oncology that should ultimately lead to a personalised treatment. High-throughput screenings of potentially active compounds against a panel of genomically heterogeneous cancer cell lines have unveiled multiple relationships between gen... |
1805.01011 | Ishtiaque Ahammad | Ishtiaque Ahammad | Identification of Key Proteins Involved in Axon Guidance Related
Disorders: A Systems Biology Approach | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Axon guidance is a crucial process for growth of the central and peripheral
nervous systems. In this study, 3 axon guidance related disorders, namely-
Duane Retraction Syndrome (DRS) , Horizontal Gaze Palsy with Progressive
Scoliosis (HGPPS) and Congenital fibrosis of the extraocular muscles type 3
(CFEOM3) were stud... | [
{
"created": "Tue, 17 Apr 2018 18:22:45 GMT",
"version": "v1"
}
] | 2018-05-04 | [
[
"Ahammad",
"Ishtiaque",
""
]
] | Axon guidance is a crucial process for growth of the central and peripheral nervous systems. In this study, 3 axon guidance related disorders, namely- Duane Retraction Syndrome (DRS) , Horizontal Gaze Palsy with Progressive Scoliosis (HGPPS) and Congenital fibrosis of the extraocular muscles type 3 (CFEOM3) were studie... |
1807.02126 | Kanika Bansal | Kanika Bansal, Javier O. Garcia, Steven H. Tompson, Timothy Verstynen,
Jean M. Vettel, and Sarah F. Muldoon | Cognitive chimera states in human brain networks | null | null | 10.1126/sciadv.aau8535 | null | q-bio.NC math.DS physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human brain is a complex dynamical system that gives rise to cognition
through spatiotemporal patterns of coherent and incoherent activity between
brain regions. As different regions dynamically interact to perform cognitive
tasks, variable patterns of partial synchrony can be observed, forming chimera
states. We... | [
{
"created": "Thu, 5 Jul 2018 18:03:19 GMT",
"version": "v1"
}
] | 2019-04-09 | [
[
"Bansal",
"Kanika",
""
],
[
"Garcia",
"Javier O.",
""
],
[
"Tompson",
"Steven H.",
""
],
[
"Verstynen",
"Timothy",
""
],
[
"Vettel",
"Jean M.",
""
],
[
"Muldoon",
"Sarah F.",
""
]
] | The human brain is a complex dynamical system that gives rise to cognition through spatiotemporal patterns of coherent and incoherent activity between brain regions. As different regions dynamically interact to perform cognitive tasks, variable patterns of partial synchrony can be observed, forming chimera states. We p... |
1301.6470 | Mike Steel Prof. | Elliott Sober and Mike Steel | Time and Knowability in Evolutionary Processes | 22 pages, 4 figures | Philos. sci. 81 (2014) 558-579 | 10.1086/677954 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Historical sciences like evolutionary biology reconstruct past events by
using the traces that the past has bequeathed to the present. The Markov Chain
Convergence Theorem and the Data Processing Inequality describe how the mutual
information between present and past is affected by how much time there is in
between. ... | [
{
"created": "Mon, 28 Jan 2013 08:23:42 GMT",
"version": "v1"
},
{
"created": "Fri, 1 Feb 2013 02:19:31 GMT",
"version": "v2"
}
] | 2023-06-22 | [
[
"Sober",
"Elliott",
""
],
[
"Steel",
"Mike",
""
]
] | Historical sciences like evolutionary biology reconstruct past events by using the traces that the past has bequeathed to the present. The Markov Chain Convergence Theorem and the Data Processing Inequality describe how the mutual information between present and past is affected by how much time there is in between. Th... |
2110.01191 | Fang Wu | Fang Wu, Dragomir Radev, Stan Z. Li | Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs | null | null | null | null | q-bio.QM cs.CE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Procuring expressive molecular representations underpins AI-driven molecule
design and scientific discovery. The research mainly focuses on atom-level
homogeneous molecular graphs, ignoring the rich information in subgraphs or
motifs. However, it has been widely accepted that substructures play a dominant
role in ide... | [
{
"created": "Mon, 4 Oct 2021 05:11:23 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Oct 2021 05:59:37 GMT",
"version": "v2"
},
{
"created": "Thu, 23 Dec 2021 03:17:08 GMT",
"version": "v3"
},
{
"created": "Sun, 15 May 2022 11:27:25 GMT",
"version": "v4"
},
{
"cre... | 2023-01-10 | [
[
"Wu",
"Fang",
""
],
[
"Radev",
"Dragomir",
""
],
[
"Li",
"Stan Z.",
""
]
] | Procuring expressive molecular representations underpins AI-driven molecule design and scientific discovery. The research mainly focuses on atom-level homogeneous molecular graphs, ignoring the rich information in subgraphs or motifs. However, it has been widely accepted that substructures play a dominant role in ident... |
q-bio/0509010 | Georgy Karev | Artem S. Novozhilov, Georgy P. Karev, and Eugene V. Koonin | Mathematical modeling of evolution of horizontally transferred genes | 36 pages, 7 figures; submitted to Mol. Biol. Evol | null | null | null | q-bio.GN q-bio.QM | null | We describe a stochastic birth-and-death model of evolution of horizontally
transferred genes in microbial populations. The model is a generalization of
the stochastic model described by Berg and Kurland and includes five
parameters: the rate of mutational inactivation, selection coefficient,
immigration rate (i.e., ... | [
{
"created": "Fri, 9 Sep 2005 15:16:24 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Novozhilov",
"Artem S.",
""
],
[
"Karev",
"Georgy P.",
""
],
[
"Koonin",
"Eugene V.",
""
]
] | We describe a stochastic birth-and-death model of evolution of horizontally transferred genes in microbial populations. The model is a generalization of the stochastic model described by Berg and Kurland and includes five parameters: the rate of mutational inactivation, selection coefficient, immigration rate (i.e., ra... |
2001.08349 | Satpreet Harcharan Singh | Satpreet H. Singh, Steven M. Peterson, Rajesh P. N. Rao, Bingni W.
Brunton | Investigating naturalistic hand movements by behavior mining in
long-term video and neural recordings | null | null | null | null | q-bio.NC cs.CV eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent technological advances in brain recording and artificial intelligence
are propelling a new paradigm in neuroscience beyond the traditional controlled
experiment. Rather than focusing on cued, repeated trials, naturalistic
neuroscience studies neural processes underlying spontaneous behaviors
performed in uncon... | [
{
"created": "Thu, 23 Jan 2020 02:41:35 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Jun 2020 22:52:49 GMT",
"version": "v2"
}
] | 2020-06-23 | [
[
"Singh",
"Satpreet H.",
""
],
[
"Peterson",
"Steven M.",
""
],
[
"Rao",
"Rajesh P. N.",
""
],
[
"Brunton",
"Bingni W.",
""
]
] | Recent technological advances in brain recording and artificial intelligence are propelling a new paradigm in neuroscience beyond the traditional controlled experiment. Rather than focusing on cued, repeated trials, naturalistic neuroscience studies neural processes underlying spontaneous behaviors performed in unconst... |
1610.00077 | Sangeeta Bhatia | Sangeeta Bhatia, Pedro Feij\~ao, Andrew R. Francis | Position and content paradigms in genome rearrangements: the wild and
crazy world of permutations in genomics | null | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modellers of large scale genome rearrangement events, in which segments of
DNA are inverted, moved, swapped, or even inserted or deleted, have found a
natural syntax in the language of permutations. Despite this, there has been a
wide range of modelling choices, assumptions and interpretations that make
navigating th... | [
{
"created": "Sat, 1 Oct 2016 03:24:05 GMT",
"version": "v1"
}
] | 2016-10-04 | [
[
"Bhatia",
"Sangeeta",
""
],
[
"Feijão",
"Pedro",
""
],
[
"Francis",
"Andrew R.",
""
]
] | Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range of modelling choices, assumptions and interpretations that make navigating the ... |
1207.3563 | Joshua Chang | Joshua C. Chang and K.C. Brennan and Dongdong He and Huaxiong Huang
and Robert M. Miura and Phillip L. Wilson and Jonathan J. Wylie | A mathematical model of the metabolic and perfusion effects on cortical
spreading depression | 17 pages including 9 figures, accepted by PLoS One | PLoS ONE 8(8) (2013) | 10.1371/journal.pone.0070469 | null | q-bio.NC q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cortical spreading depression (CSD) is a slow-moving ionic and metabolic
disturbance that propagates in cortical brain tissue. In addition to massive
cellular depolarization, CSD also involves significant changes in perfusion and
metabolism -- aspects of CSD that had not been modeled and are important to
traumatic br... | [
{
"created": "Mon, 16 Jul 2012 02:28:23 GMT",
"version": "v1"
},
{
"created": "Sat, 15 Jun 2013 21:15:12 GMT",
"version": "v2"
}
] | 2020-06-05 | [
[
"Chang",
"Joshua C.",
""
],
[
"Brennan",
"K. C.",
""
],
[
"He",
"Dongdong",
""
],
[
"Huang",
"Huaxiong",
""
],
[
"Miura",
"Robert M.",
""
],
[
"Wilson",
"Phillip L.",
""
],
[
"Wylie",
"Jonathan J.",
""
]
... | Cortical spreading depression (CSD) is a slow-moving ionic and metabolic disturbance that propagates in cortical brain tissue. In addition to massive cellular depolarization, CSD also involves significant changes in perfusion and metabolism -- aspects of CSD that had not been modeled and are important to traumatic brai... |
1901.02483 | Yana Safonova | Yana Safonova and Pavel A. Pevzner | De novo inference of diversity genes and analysis of non-canonical
V(DD)J recombination in immunoglobulins | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The V(D)J recombination forms the immunoglobulin genes by joining the
variable (V), diversity (D), and joining (J) germline genes. Since variations
in germline genes have been linked to various diseases, personalized
immunogenomics aims at finding alleles of germline genes across various
patients. Although recent stu... | [
{
"created": "Tue, 8 Jan 2019 19:41:18 GMT",
"version": "v1"
}
] | 2019-01-10 | [
[
"Safonova",
"Yana",
""
],
[
"Pevzner",
"Pavel A.",
""
]
] | The V(D)J recombination forms the immunoglobulin genes by joining the variable (V), diversity (D), and joining (J) germline genes. Since variations in germline genes have been linked to various diseases, personalized immunogenomics aims at finding alleles of germline genes across various patients. Although recent studi... |
1304.4337 | Song Xu | Song Xu and Shuyun Jiao and Pengyao Jiang and Ping Ao | Two-timescale evolution on a singular landscape | arXiv admin note: text overlap with arXiv:1108.1484 | null | 10.1103/PhysRevE.89.012724 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Under the effect of strong genetic drift, it is highly probable to observe
gene fixation or gene loss in a population, shown by infinite peaks on a
coherently constructed potential energy landscape. It is then important to ask
what such singular peaks imply, with or without the effects of other biological
factors. We... | [
{
"created": "Tue, 16 Apr 2013 06:10:28 GMT",
"version": "v1"
}
] | 2015-06-15 | [
[
"Xu",
"Song",
""
],
[
"Jiao",
"Shuyun",
""
],
[
"Jiang",
"Pengyao",
""
],
[
"Ao",
"Ping",
""
]
] | Under the effect of strong genetic drift, it is highly probable to observe gene fixation or gene loss in a population, shown by infinite peaks on a coherently constructed potential energy landscape. It is then important to ask what such singular peaks imply, with or without the effects of other biological factors. We s... |
2004.04819 | Massimo Materassi Dr | Massimo Materassi | Some fractal thoughts about the COVID-19 infection outbreak | null | null | null | null | q-bio.PE math.DS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Some ideas are presented about the physical motivation of the apparent
capacity of generalized logistic equations to describe the outbreak of the
COVID-19 infection, and in general of quite many other epidemics. The main
focuses here are: the complex, possibly fractal, structure of the locus
describing the "contagion... | [
{
"created": "Wed, 8 Apr 2020 16:52:05 GMT",
"version": "v1"
}
] | 2020-04-13 | [
[
"Materassi",
"Massimo",
""
]
] | Some ideas are presented about the physical motivation of the apparent capacity of generalized logistic equations to describe the outbreak of the COVID-19 infection, and in general of quite many other epidemics. The main focuses here are: the complex, possibly fractal, structure of the locus describing the "contagion e... |
1605.07479 | Nadav M. Shnerb | Yael Fried, David A. Kessler and Nadav M. Shnerb | Communities as cliques | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | High-diversity assemblages are very common in nature, and yet the factors
allowing for the maintenance of biodiversity remain obscure. The competitive
exclusion principle and May's complexity-diversity puzzle both suggest that a
community can support only a small number of species, turning the spotlight at
the dynami... | [
{
"created": "Tue, 24 May 2016 14:31:31 GMT",
"version": "v1"
}
] | 2016-05-25 | [
[
"Fried",
"Yael",
""
],
[
"Kessler",
"David A.",
""
],
[
"Shnerb",
"Nadav M.",
""
]
] | High-diversity assemblages are very common in nature, and yet the factors allowing for the maintenance of biodiversity remain obscure. The competitive exclusion principle and May's complexity-diversity puzzle both suggest that a community can support only a small number of species, turning the spotlight at the dynamics... |
2007.08262 | Sayantari Ghosh | Priya Chakraborty, Sayantari Ghosh | Emergent Correlations in Gene Expression Dynamics as Footprints of
Resource Competition | 15 pages, 7 figures | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genetic circuits need a cellular environment to operate in, which naturally
couples the circuit function with the overall functionality of gene regulatory
network. To execute their functions all gene circuits draw resources in the
form of RNA polymerases, ribosomes, and tRNAs. Recent experiments pointed out
that the ... | [
{
"created": "Thu, 16 Jul 2020 11:24:45 GMT",
"version": "v1"
}
] | 2020-07-17 | [
[
"Chakraborty",
"Priya",
""
],
[
"Ghosh",
"Sayantari",
""
]
] | Genetic circuits need a cellular environment to operate in, which naturally couples the circuit function with the overall functionality of gene regulatory network. To execute their functions all gene circuits draw resources in the form of RNA polymerases, ribosomes, and tRNAs. Recent experiments pointed out that the ro... |
2305.19284 | J. C. Phillips | J. C. Phillips | Sequence Evolution, Structure and Dynamics of Transmembrane Proteins:
Rhodopsin | 11 pages, 5 figures, 1 table | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Rhodopsin is a G-protein coupled receptor found in retinal rod cells, where
it mediates monocrhromatic vision in dim light. It is one of the most studied
proteins with thousands of reviewed entries in Uniprot. It has seven
transmembrane segments, here examined for their hydrophobic character, and how
that has evolved... | [
{
"created": "Sun, 28 May 2023 14:56:03 GMT",
"version": "v1"
}
] | 2023-06-01 | [
[
"Phillips",
"J. C.",
""
]
] | Rhodopsin is a G-protein coupled receptor found in retinal rod cells, where it mediates monocrhromatic vision in dim light. It is one of the most studied proteins with thousands of reviewed entries in Uniprot. It has seven transmembrane segments, here examined for their hydrophobic character, and how that has evolved f... |
2201.08894 | Lei Xie | Ryan K. Tan, Yang Liu, Lei Xie | Reinforcement Learning for Personalized Drug Discovery and Design for
Complex Diseases: A Systems Pharmacology Perspective | 26 pages, 3 figure | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Many multi-genic systemic diseases such as neurological disorders,
inflammatory diseases, and the majority of cancers do not have effective
treatments yet. Reinforcement learning powered systems pharmacology is a
potentially effective approach to design personalized therapies for untreatable
complex diseases. In this... | [
{
"created": "Fri, 21 Jan 2022 21:29:46 GMT",
"version": "v1"
},
{
"created": "Sat, 19 Feb 2022 02:19:56 GMT",
"version": "v2"
},
{
"created": "Wed, 23 Feb 2022 19:45:33 GMT",
"version": "v3"
}
] | 2022-02-25 | [
[
"Tan",
"Ryan K.",
""
],
[
"Liu",
"Yang",
""
],
[
"Xie",
"Lei",
""
]
] | Many multi-genic systemic diseases such as neurological disorders, inflammatory diseases, and the majority of cancers do not have effective treatments yet. Reinforcement learning powered systems pharmacology is a potentially effective approach to design personalized therapies for untreatable complex diseases. In this s... |
q-bio/0505049 | Karsten Suhre | Karsten Suhre (IGS) | Gene & Genome Duplication in Acanthamoeba Polyphaga Mimivirus | null | null | null | null | q-bio.GN | null | Gene duplication is key to molecular evolution in all three domains of life
and may be the first step in the emergence of new gene function. It is a well
recognized feature in large DNA viruses, but has not been studied extensively
in the largest known virus to date, the recently discovered Acanthamoeba
Polyphaga Mim... | [
{
"created": "Wed, 25 May 2005 14:17:57 GMT",
"version": "v1"
},
{
"created": "Mon, 27 Jun 2005 14:27:37 GMT",
"version": "v2"
},
{
"created": "Tue, 19 Jul 2005 12:34:14 GMT",
"version": "v3"
}
] | 2007-05-23 | [
[
"Suhre",
"Karsten",
"",
"IGS"
]
] | Gene duplication is key to molecular evolution in all three domains of life and may be the first step in the emergence of new gene function. It is a well recognized feature in large DNA viruses, but has not been studied extensively in the largest known virus to date, the recently discovered Acanthamoeba Polyphaga Mimiv... |
1208.5673 | Alfred Bennun | Alfred Bennun | The dynamics of H-bonds of the hydration shells of ions, ATPase and
NE-activated adenylyl cyclase on the coupling of energy and signal
transduction | null | null | null | null | q-bio.OT q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Glycerol titration distinguished from free water the local hydration shell
involved in ATPase transition from active to inactive, with cooperativity for
water n=16. Rat brain cortex: NE-stimulated and its basal AC in the absence of
free Mg2+, allows a refractive state of AC with negative cooperativity for
MgATP and A... | [
{
"created": "Tue, 17 Jul 2012 22:01:58 GMT",
"version": "v1"
}
] | 2012-08-29 | [
[
"Bennun",
"Alfred",
""
]
] | Glycerol titration distinguished from free water the local hydration shell involved in ATPase transition from active to inactive, with cooperativity for water n=16. Rat brain cortex: NE-stimulated and its basal AC in the absence of free Mg2+, allows a refractive state of AC with negative cooperativity for MgATP and ATP... |
1609.02794 | Fabio Nikolay | Fabio Nikolay, Marius Pesavento, George Kritikos, Nassos Typas | Learning Directed-Acyclic-Graphs from Large-Scale Genomics Data | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we consider the problem of learning the
genetic-interaction-map, i.e., the topology of a directed acyclic graph (DAG)
of genetic interactions from noisy double knockout (DK) data. Based on a set of
well established biological interaction models we detect and classify the
interactions between genes. We p... | [
{
"created": "Fri, 9 Sep 2016 13:48:14 GMT",
"version": "v1"
}
] | 2016-09-12 | [
[
"Nikolay",
"Fabio",
""
],
[
"Pesavento",
"Marius",
""
],
[
"Kritikos",
"George",
""
],
[
"Typas",
"Nassos",
""
]
] | In this paper we consider the problem of learning the genetic-interaction-map, i.e., the topology of a directed acyclic graph (DAG) of genetic interactions from noisy double knockout (DK) data. Based on a set of well established biological interaction models we detect and classify the interactions between genes. We pro... |
1308.3690 | Michael Retsky | M.W. Retsky, R. Demicheli, W.J.M. Hrushesky, P. Forget, M. DeKock, I.
Gukas, R.A. Rogers, M. Baum, V. Sukhatme, and J.S. Vaidya | Reduction of breast cancer relapses with perioperative non-steroidal
anti-inflammatory drugs: new findings and a review | 25 pages, 10 figures, in press; Current Medicinal Chemistry, May 2013 | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To explain a bimodal pattern of hazard of relapse among early stage breast
cancer patients identified in multiple databases, we proposed that late
relapses result from steady stochastic progressions from single dormant
malignant cells to avascular micrometastases and then on to growing deposits.
However in order to e... | [
{
"created": "Fri, 16 Aug 2013 18:40:21 GMT",
"version": "v1"
}
] | 2013-08-19 | [
[
"Retsky",
"M. W.",
""
],
[
"Demicheli",
"R.",
""
],
[
"Hrushesky",
"W. J. M.",
""
],
[
"Forget",
"P.",
""
],
[
"DeKock",
"M.",
""
],
[
"Gukas",
"I.",
""
],
[
"Rogers",
"R. A.",
""
],
[
"Baum",
"... | To explain a bimodal pattern of hazard of relapse among early stage breast cancer patients identified in multiple databases, we proposed that late relapses result from steady stochastic progressions from single dormant malignant cells to avascular micrometastases and then on to growing deposits. However in order to exp... |
0907.2043 | Carla Sofia Carvalho | Ekaterini Vourvouhaki and C. Sofia Carvalho | A Bayesian approach to the probability of coronary heart disease subject
to the --308 tumor necrosis factor-$\alpha$ SNP | 23 pages, 2 figures, version accepted for publication in J.Biosystems | null | 10.1016/j.biosystems.2011.03.010 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the correlation of the occurrence of coronary heart disease (CHD)
with the presence of the single-nucleotide polymorphism (SNP) at the -308
position of the tumor necrosis factor alpha (TNF-$\alpha$) gene. We also
consider the influence of the occurrence of type 2 diabetes (t2DM). Using
Bayesian inference, we... | [
{
"created": "Sun, 12 Jul 2009 14:01:32 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Mar 2010 16:22:57 GMT",
"version": "v2"
},
{
"created": "Thu, 5 May 2011 14:50:35 GMT",
"version": "v3"
}
] | 2011-05-06 | [
[
"Vourvouhaki",
"Ekaterini",
""
],
[
"Carvalho",
"C. Sofia",
""
]
] | We study the correlation of the occurrence of coronary heart disease (CHD) with the presence of the single-nucleotide polymorphism (SNP) at the -308 position of the tumor necrosis factor alpha (TNF-$\alpha$) gene. We also consider the influence of the occurrence of type 2 diabetes (t2DM). Using Bayesian inference, we f... |
1606.02837 | Nadav M. Shnerb | Matan Danino, Yahav Shem-Tov and Nadav M. Shnerb | Spatial neutral dynamics | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neutral models, in which individual agents with equal fitness undergo a
birth-death-mutation process, are very popular in population genetics and
community ecology. Usually these models are applied to populations and
communities with spatial structure, but the analytic results presented so far
are limited to well-mix... | [
{
"created": "Thu, 9 Jun 2016 06:58:57 GMT",
"version": "v1"
}
] | 2016-06-10 | [
[
"Danino",
"Matan",
""
],
[
"Shem-Tov",
"Yahav",
""
],
[
"Shnerb",
"Nadav M.",
""
]
] | Neutral models, in which individual agents with equal fitness undergo a birth-death-mutation process, are very popular in population genetics and community ecology. Usually these models are applied to populations and communities with spatial structure, but the analytic results presented so far are limited to well-mixed... |
1904.00117 | Jean Feng | Jean Feng, William S DeWitt III, Aaron McKenna, Noah Simon, Amy
Willis, Frederick A Matsen IV | Estimation of cell lineage trees by maximum-likelihood phylogenetics | null | null | null | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by/4.0/ | CRISPR technology has enabled large-scale cell lineage tracing for complex
multicellular organisms by mutating synthetic genomic barcodes during
organismal development. However, these sophisticated biological tools currently
use ad-hoc and outmoded computational methods to reconstruct the cell lineage
tree from the m... | [
{
"created": "Fri, 29 Mar 2019 23:27:36 GMT",
"version": "v1"
}
] | 2019-04-02 | [
[
"Feng",
"Jean",
""
],
[
"DeWitt",
"William S",
"III"
],
[
"McKenna",
"Aaron",
""
],
[
"Simon",
"Noah",
""
],
[
"Willis",
"Amy",
""
],
[
"Matsen",
"Frederick A",
"IV"
]
] | CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and outmoded computational methods to reconstruct the cell lineage tree from the mut... |
1601.07766 | Luca Puviani | Luca Puviani, Sidita Rama, Giorgio Vitetta | Prediction Errors Drive UCS Revaluation and not Classical Conditioning:
Evidence and Neurophysiological Consequences | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nowadays, the experimental study of emotional learning is commonly based on
classical conditioning paradigms and models, which have been thoroughly
investigated in the last century. On the contrary, limited attention has been
paid to the revaluation of an unconditioned stimulus (UCS), which, as
experimentally observe... | [
{
"created": "Thu, 28 Jan 2016 14:12:22 GMT",
"version": "v1"
}
] | 2016-01-29 | [
[
"Puviani",
"Luca",
""
],
[
"Rama",
"Sidita",
""
],
[
"Vitetta",
"Giorgio",
""
]
] | Nowadays, the experimental study of emotional learning is commonly based on classical conditioning paradigms and models, which have been thoroughly investigated in the last century. On the contrary, limited attention has been paid to the revaluation of an unconditioned stimulus (UCS), which, as experimentally observed ... |
1107.2330 | Andrea De Martino | Daniele De Martino, Matteo Figliuzzi, Andrea De Martino, Enzo Marinari | Computing fluxes and chemical potential distributions in biochemical
networks: energy balance analysis of the human red blood cell | 16 pages, 13 figures | null | null | null | q-bio.MN cond-mat.dis-nn cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The analysis of non-equilibrium steady states of biochemical reaction
networks relies on finding the configurations of fluxes and chemical potentials
satisfying stoichiometric (mass balance) and thermodynamic (energy balance)
constraints. Efficient methods to explore such states are crucial to predict
reaction direct... | [
{
"created": "Tue, 12 Jul 2011 15:43:19 GMT",
"version": "v1"
}
] | 2011-07-13 | [
[
"De Martino",
"Daniele",
""
],
[
"Figliuzzi",
"Matteo",
""
],
[
"De Martino",
"Andrea",
""
],
[
"Marinari",
"Enzo",
""
]
] | The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints. Efficient methods to explore such states are crucial to predict reaction directio... |
1602.08417 | Nicolas Gauvrit | Nicolas Gauvrit and Fabien Mathy | Mathematical transcription of the "Time-Based Resource Sharing" theory
of working memory | 21 pages, 5 figures, 1 table | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The time-based resource sharing (TBRS) model is a prominent model of working
memory that is both predictive and simple. The TBRS is the mainstream
decay-based model and the most susceptible to competition with
interference-based models. A connectionist implementation of the TBRS, the
TBRS*, has recently been develope... | [
{
"created": "Fri, 1 Jan 2016 16:05:53 GMT",
"version": "v1"
}
] | 2016-02-29 | [
[
"Gauvrit",
"Nicolas",
""
],
[
"Mathy",
"Fabien",
""
]
] | The time-based resource sharing (TBRS) model is a prominent model of working memory that is both predictive and simple. The TBRS is the mainstream decay-based model and the most susceptible to competition with interference-based models. A connectionist implementation of the TBRS, the TBRS*, has recently been developed.... |
1307.7385 | Bhaskar DasGupta | Reka Albert, Bhaskar DasGupta, Nasim Mobasheri | Some Perspectives on Network Modeling in Therapeutic Target Prediction | null | Biomedical Engineering and Computational Biology, 5, 17-24, 2013 | 10.4137/BECB.S10793 | null | q-bio.MN cs.CE cs.DM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Drug target identification is of significant commercial interest to
pharmaceutical companies, and there is a vast amount of research done related
to the topic of therapeutic target identification. Interdisciplinary research
in this area involves both the biological network community and the graph
algorithms community... | [
{
"created": "Sun, 28 Jul 2013 17:42:01 GMT",
"version": "v1"
}
] | 2013-07-30 | [
[
"Albert",
"Reka",
""
],
[
"DasGupta",
"Bhaskar",
""
],
[
"Mobasheri",
"Nasim",
""
]
] | Drug target identification is of significant commercial interest to pharmaceutical companies, and there is a vast amount of research done related to the topic of therapeutic target identification. Interdisciplinary research in this area involves both the biological network community and the graph algorithms community. ... |
1405.3310 | Jason Perlmutter | Jason D Perlmutter, Matthew R Perkett, Michael F Hagan | Pathways for virus assembly around nucleic acids | 24 pages, 12 figures | null | null | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the pathways by which viral capsid proteins assemble around
their genomes could identify key intermediates as potential drug targets. In
this work we use computer simulations to characterize assembly over a wide
range of capsid protein-protein interaction strengths and solution ionic
strengths. We find ... | [
{
"created": "Tue, 13 May 2014 21:22:11 GMT",
"version": "v1"
}
] | 2014-05-15 | [
[
"Perlmutter",
"Jason D",
""
],
[
"Perkett",
"Matthew R",
""
],
[
"Hagan",
"Michael F",
""
]
] | Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of capsid protein-protein interaction strengths and solution ionic strengths. We find th... |
1512.09133 | Tomas Ros | Tomas Ros, Paul Frewen, Jean Theberge, Rosemarie Kluetsch, Andreas
Mueller, Gian Candrian, Rakesh Jetly, Patrik Vuilleumier, Ruth Lanius | Neurofeedback Tunes Scale-Free Dynamics in Spontaneous Brain Activity | null | Cerebral Cortex (2016) | 10.1093/cercor/bhw285 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain oscillations exhibit long-range temporal correlations (LRTCs), which
reflect the regularity of their fluctuations: low values representing more
random (decorrelated) while high values more persistent (correlated) dynamics.
LRTCs constitute supporting evidence that the brain operates near criticality,
a state wh... | [
{
"created": "Wed, 30 Dec 2015 20:58:03 GMT",
"version": "v1"
},
{
"created": "Thu, 17 Mar 2016 09:16:18 GMT",
"version": "v2"
},
{
"created": "Fri, 2 Feb 2018 10:18:50 GMT",
"version": "v3"
}
] | 2018-02-05 | [
[
"Ros",
"Tomas",
""
],
[
"Frewen",
"Paul",
""
],
[
"Theberge",
"Jean",
""
],
[
"Kluetsch",
"Rosemarie",
""
],
[
"Mueller",
"Andreas",
""
],
[
"Candrian",
"Gian",
""
],
[
"Jetly",
"Rakesh",
""
],
[
"V... | Brain oscillations exhibit long-range temporal correlations (LRTCs), which reflect the regularity of their fluctuations: low values representing more random (decorrelated) while high values more persistent (correlated) dynamics. LRTCs constitute supporting evidence that the brain operates near criticality, a state wher... |
1707.00769 | Emilio Gallicchio | Emilio Gallicchio | Alchemical Response Parameters from an Analytical Model of Molecular
Binding | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a parameterized analytical model of alchemical molecular binding.
The model describes accurately the free energy profiles of linear
single-decoupling alchemical binding free energy calculations. The parameters
of the model, which are physically motivated, are obtained by fitting model
predictions to numeri... | [
{
"created": "Mon, 3 Jul 2017 22:00:33 GMT",
"version": "v1"
},
{
"created": "Wed, 5 Jul 2017 17:09:19 GMT",
"version": "v2"
}
] | 2017-07-06 | [
[
"Gallicchio",
"Emilio",
""
]
] | We present a parameterized analytical model of alchemical molecular binding. The model describes accurately the free energy profiles of linear single-decoupling alchemical binding free energy calculations. The parameters of the model, which are physically motivated, are obtained by fitting model predictions to numerica... |
1609.08213 | Chandan Singh | Chandan Singh, William B. Levy | Complexity Leads to Simplicity: A Consensus Layer V Pyramidal Neuron Can
Sustain Interpulse-Interval Coding | submitted to PLOS Computational Biology | Published in PLOS One 2017 | 10.1371/journal.pone.0180839 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In terms of the long-distance communication of a single neuron, interpulse
intervals (IPIs) are a possible alternative to rate and binary codes. As a
proxy for IPI, the time-to-spike (TTS) for a neuron can be found in the
biophysical and experimental literature. Using the current, consensus layer V
pyramidal neuron, ... | [
{
"created": "Mon, 26 Sep 2016 22:31:25 GMT",
"version": "v1"
}
] | 2019-01-15 | [
[
"Singh",
"Chandan",
""
],
[
"Levy",
"William B.",
""
]
] | In terms of the long-distance communication of a single neuron, interpulse intervals (IPIs) are a possible alternative to rate and binary codes. As a proxy for IPI, the time-to-spike (TTS) for a neuron can be found in the biophysical and experimental literature. Using the current, consensus layer V pyramidal neuron, th... |
2102.11667 | Larry Bull | Larry Bull | On Sexual Selection | arXiv admin note: substantial text overlap with arXiv:1808.03471,
arXiv:1903.07429, arXiv:1811.04073, arXiv:2004.10061 | null | null | null | q-bio.PE cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sexual selection is a fundamental aspect of evolution for all eukaryotic
organisms with mating types. This paper suggests intersexual selection is best
viewed as a mechanism to compensate for the unavoidable dynamics of coevolution
between sexes that emerge with isogamy. Using the NK model of fitness
landscapes, the ... | [
{
"created": "Tue, 23 Feb 2021 12:47:58 GMT",
"version": "v1"
}
] | 2021-02-24 | [
[
"Bull",
"Larry",
""
]
] | Sexual selection is a fundamental aspect of evolution for all eukaryotic organisms with mating types. This paper suggests intersexual selection is best viewed as a mechanism to compensate for the unavoidable dynamics of coevolution between sexes that emerge with isogamy. Using the NK model of fitness landscapes, the co... |
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