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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1807.06203 | Ding Zhou | E. Kelly Buchanan, Ian Kinsella, Ding Zhou, Rong Zhu, Pengcheng Zhou,
Felipe Gerhard, John Ferrante, Ying Ma, Sharon Kim, Mohammed Shaik, Yajie
Liang, Rongwen Lu, Jacob Reimer, Paul Fahey, Taliah Muhammad, Graham Dempsey,
Elizabeth Hillman, Na Ji, Andreas Tolias, Liam Paninski | Penalized matrix decomposition for denoising, compression, and improved
demixing of functional imaging data | 36 pages, 18 figures | null | null | null | q-bio.NC stat.ML | http://creativecommons.org/licenses/by-sa/4.0/ | Calcium imaging has revolutionized systems neuroscience, providing the
ability to image large neural populations with single-cell resolution. The
resulting datasets are quite large, which has presented a barrier to routine
open sharing of this data, slowing progress in reproducible research. State of
the art methods ... | [
{
"created": "Tue, 17 Jul 2018 04:00:07 GMT",
"version": "v1"
}
] | 2018-07-18 | [
[
"Buchanan",
"E. Kelly",
""
],
[
"Kinsella",
"Ian",
""
],
[
"Zhou",
"Ding",
""
],
[
"Zhu",
"Rong",
""
],
[
"Zhou",
"Pengcheng",
""
],
[
"Gerhard",
"Felipe",
""
],
[
"Ferrante",
"John",
""
],
[
"Ma",
... | Calcium imaging has revolutionized systems neuroscience, providing the ability to image large neural populations with single-cell resolution. The resulting datasets are quite large, which has presented a barrier to routine open sharing of this data, slowing progress in reproducible research. State of the art methods fo... |
2103.08143 | Olga Lukyanova | Oleg Nikitin and Olga Lukyanova and Alex Kunin | Constrained plasticity reserve as a natural way to control frequency and
weights in spiking neural networks | 24 pages, 10 figures | null | null | null | q-bio.NC cs.AI cs.LG cs.NE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Biological neurons have adaptive nature and perform complex computations
involving the filtering of redundant information. However, most common neural
cell models, including biologically plausible, such as Hodgkin-Huxley or
Izhikevich, do not possess predictive dynamics on a single-cell level.
Moreover, the modern ru... | [
{
"created": "Mon, 15 Mar 2021 05:22:14 GMT",
"version": "v1"
},
{
"created": "Sun, 20 Jun 2021 10:56:05 GMT",
"version": "v2"
}
] | 2021-06-22 | [
[
"Nikitin",
"Oleg",
""
],
[
"Lukyanova",
"Olga",
""
],
[
"Kunin",
"Alex",
""
]
] | Biological neurons have adaptive nature and perform complex computations involving the filtering of redundant information. However, most common neural cell models, including biologically plausible, such as Hodgkin-Huxley or Izhikevich, do not possess predictive dynamics on a single-cell level. Moreover, the modern rule... |
1504.02927 | Michael Paulin | Michael G. Paulin | The Origin of Inference: Ediacaran Ecology and the Evolution of Bayesian
Brains | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The evolution of spiking neurons and nervous systems in the late Ediacaran
period simultaneously with the evolution of carnivores around 550 million years
ago can be explained by the need for accurately timed decisions under an
imminent threat of being eaten. A simple model shows that threshold triggering
devices, sp... | [
{
"created": "Sun, 12 Apr 2015 02:23:17 GMT",
"version": "v1"
}
] | 2015-04-14 | [
[
"Paulin",
"Michael G.",
""
]
] | The evolution of spiking neurons and nervous systems in the late Ediacaran period simultaneously with the evolution of carnivores around 550 million years ago can be explained by the need for accurately timed decisions under an imminent threat of being eaten. A simple model shows that threshold triggering devices, spik... |
1511.06431 | Nathan Baker | Chase P. Dowling, Elizabeth Jurrus, Sylvia Johnson, Nathan A. Baker | An ISA-Tab specification for protein titration data exchange | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Data curation presents a challenge to all scientific disciplines to ensure
public availability and reproducibility of experimental data. Standards for
data preservation and exchange are central to addressing this challenge: the
Investigation-Study-Assay Tabular (ISA-Tab) project has developed a widely used
template f... | [
{
"created": "Thu, 19 Nov 2015 22:45:50 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Feb 2016 00:46:47 GMT",
"version": "v2"
}
] | 2016-02-16 | [
[
"Dowling",
"Chase P.",
""
],
[
"Jurrus",
"Elizabeth",
""
],
[
"Johnson",
"Sylvia",
""
],
[
"Baker",
"Nathan A.",
""
]
] | Data curation presents a challenge to all scientific disciplines to ensure public availability and reproducibility of experimental data. Standards for data preservation and exchange are central to addressing this challenge: the Investigation-Study-Assay Tabular (ISA-Tab) project has developed a widely used template for... |
q-bio/0412041 | Jacek Miekisz | Dominik Kaminski, Jacek Miekisz, Marcin Zaborowski | Stochastic stability in three-player games | 18 pages | null | null | null | q-bio.PE | null | Animal behavior and evolution can often be described by game-theoretic
models. Although in many situations, the number of players is very large, their
strategic interactions are usually decomposed into a sum of two-player games.
Only recently evolutionarily stable strategies were defined for multi-player
games and th... | [
{
"created": "Wed, 22 Dec 2004 13:18:35 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Kaminski",
"Dominik",
""
],
[
"Miekisz",
"Jacek",
""
],
[
"Zaborowski",
"Marcin",
""
]
] | Animal behavior and evolution can often be described by game-theoretic models. Although in many situations, the number of players is very large, their strategic interactions are usually decomposed into a sum of two-player games. Only recently evolutionarily stable strategies were defined for multi-player games and thei... |
1406.6826 | Sarada Seetharaman | Sarada Seetharaman and Kavita Jain | Length of adaptive walk on uncorrelated and correlated fitness
landscapes | To appear in Phys. Rev. E | Phys. Rev. E 90, 032703 (2014) | 10.1103/PhysRevE.90.032703 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the adaptation dynamics of an asexual population that walks
uphill on a rugged fitness landscape which is endowed with large number of
local fitness peaks. We work in a parameter regime where only those mutants
that are single mutation away are accessible, as a result of which the
population eventually ge... | [
{
"created": "Thu, 26 Jun 2014 09:51:35 GMT",
"version": "v1"
},
{
"created": "Tue, 19 Aug 2014 06:21:34 GMT",
"version": "v2"
}
] | 2016-01-13 | [
[
"Seetharaman",
"Sarada",
""
],
[
"Jain",
"Kavita",
""
]
] | We consider the adaptation dynamics of an asexual population that walks uphill on a rugged fitness landscape which is endowed with large number of local fitness peaks. We work in a parameter regime where only those mutants that are single mutation away are accessible, as a result of which the population eventually gets... |
1307.8026 | Jared Simpson | Jared T. Simpson | Exploring Genome Characteristics and Sequence Quality Without a
Reference | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The de novo assembly of large, complex genomes is a significant challenge
with currently available DNA sequencing technology. While many de novo assembly
software packages are available, comparatively little attention has been paid
to assisting the user with the assembly. This paper addresses the practical
aspects of... | [
{
"created": "Tue, 30 Jul 2013 15:55:09 GMT",
"version": "v1"
}
] | 2013-07-31 | [
[
"Simpson",
"Jared T.",
""
]
] | The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to assisting the user with the assembly. This paper addresses the practical aspects of d... |
2102.05937 | Mihalis Kavousanakis | I. Lampropoulos and M. Kavousanakis | Assessment of intra-tumor heterogeneity in a two-dimensional vascular
tumor growth model | null | null | null | null | q-bio.PE | http://creativecommons.org/publicdomain/zero/1.0/ | We present a two-dimensional continuum model of tumor growth, which treats
the tissue as a composition of six distinct fluid phases; their dynamics are
governed by the equations of mass and momentum conservation. Our model divides
the cancer cells phase into two sub-phases depending on their maturity state.
The same ... | [
{
"created": "Thu, 11 Feb 2021 10:54:40 GMT",
"version": "v1"
}
] | 2021-02-12 | [
[
"Lampropoulos",
"I.",
""
],
[
"Kavousanakis",
"M.",
""
]
] | We present a two-dimensional continuum model of tumor growth, which treats the tissue as a composition of six distinct fluid phases; their dynamics are governed by the equations of mass and momentum conservation. Our model divides the cancer cells phase into two sub-phases depending on their maturity state. The same ap... |
1002.2595 | Wiet de Ronde | Wiet de Ronde, Filipe Tostevin and Pieter Rein ten Wolde | The effect of feedback on the fidelity of information transmission of
time-varying signals | Article 17 pages, S1: 12 pages | Phys. Rev. E 82, 031914 (2010) | 10.1103/PhysRevE.82.031914 | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Living cells are continually exposed to environmental signals that vary in
time. These signals are detected and processed by biochemical networks, which
are often highly stochastic. To understand how cells cope with a fluctuating
environment, we therefore have to understand how reliably biochemical networks
can trans... | [
{
"created": "Fri, 12 Feb 2010 16:51:56 GMT",
"version": "v1"
}
] | 2012-06-01 | [
[
"de Ronde",
"Wiet",
""
],
[
"Tostevin",
"Filipe",
""
],
[
"Wolde",
"Pieter Rein ten",
""
]
] | Living cells are continually exposed to environmental signals that vary in time. These signals are detected and processed by biochemical networks, which are often highly stochastic. To understand how cells cope with a fluctuating environment, we therefore have to understand how reliably biochemical networks can transmi... |
2209.13529 | Islem Rekik | Ece Cinar, Sinem Elif Haseki, Alaa Bessadok and Islem Rekik | Deep Cross-Modality and Resolution Graph Integration for Universal Brain
Connectivity Mapping and Augmentation | null | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The connectional brain template (CBT) captures the shared traits across all
individuals of a given population of brain connectomes, thereby acting as a
fingerprint. Estimating a CBT from a population where brain graphs are derived
from diverse neuroimaging modalities (e.g., functional and structural) and at
different... | [
{
"created": "Tue, 13 Sep 2022 14:04:12 GMT",
"version": "v1"
}
] | 2022-09-28 | [
[
"Cinar",
"Ece",
""
],
[
"Haseki",
"Sinem Elif",
""
],
[
"Bessadok",
"Alaa",
""
],
[
"Rekik",
"Islem",
""
]
] | The connectional brain template (CBT) captures the shared traits across all individuals of a given population of brain connectomes, thereby acting as a fingerprint. Estimating a CBT from a population where brain graphs are derived from diverse neuroimaging modalities (e.g., functional and structural) and at different r... |
2005.06286 | Matjaz Perc | Subhas Khajanchi, Kankan Sarkar, Jayanta Mondal | Dynamics of the COVID-19 pandemic in India | null | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | Understanding the dynamics of the COVID-19 pandemic is crucial for improved
control and social distancing strategies. To that effect, we have employed the
susceptible-exposed-infectious-recovered model, refined by contact tracing and
hospitalization data from Indian provinces Kerala, Delhi, Maharashtra, and West
Beng... | [
{
"created": "Wed, 13 May 2020 12:35:58 GMT",
"version": "v1"
},
{
"created": "Tue, 12 Jan 2021 17:52:54 GMT",
"version": "v2"
}
] | 2021-01-13 | [
[
"Khajanchi",
"Subhas",
""
],
[
"Sarkar",
"Kankan",
""
],
[
"Mondal",
"Jayanta",
""
]
] | Understanding the dynamics of the COVID-19 pandemic is crucial for improved control and social distancing strategies. To that effect, we have employed the susceptible-exposed-infectious-recovered model, refined by contact tracing and hospitalization data from Indian provinces Kerala, Delhi, Maharashtra, and West Bengal... |
2408.06750 | Ari Rappoport | Ari Rappoport | A CRH Theory of Autism Spectrum Disorder | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | This paper presents a complete theory of autism spectrum disorder (ASD),
explaining its etiology, symptoms, and pathology. The core cause of ASD is
excessive stress-induced postnatal release of corticotropin-releasing hormone
(CRH). CRH competes with urocortins for binding to the CRH2 receptor, impairing
their essent... | [
{
"created": "Tue, 13 Aug 2024 09:17:22 GMT",
"version": "v1"
}
] | 2024-08-14 | [
[
"Rappoport",
"Ari",
""
]
] | This paper presents a complete theory of autism spectrum disorder (ASD), explaining its etiology, symptoms, and pathology. The core cause of ASD is excessive stress-induced postnatal release of corticotropin-releasing hormone (CRH). CRH competes with urocortins for binding to the CRH2 receptor, impairing their essentia... |
1607.04886 | Marc Howard | Marc W. Howard and Karthik H. Shankar | Neural scaling laws for an uncertain world | null | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Autonomous neural systems must efficiently process information in a wide
range of novel environments, which may have very different statistical
properties. We consider the problem of how to optimally distribute receptors
along a one-dimensional continuum consistent with the following design
principles. First, neural ... | [
{
"created": "Sun, 17 Jul 2016 15:59:50 GMT",
"version": "v1"
},
{
"created": "Mon, 3 Apr 2017 04:13:42 GMT",
"version": "v2"
}
] | 2017-04-04 | [
[
"Howard",
"Marc W.",
""
],
[
"Shankar",
"Karthik H.",
""
]
] | Autonomous neural systems must efficiently process information in a wide range of novel environments, which may have very different statistical properties. We consider the problem of how to optimally distribute receptors along a one-dimensional continuum consistent with the following design principles. First, neural re... |
1010.3539 | Luca Peliti | Ginestra Bianconi, Davide Fichera, Silvio Franz and Luca Peliti | Modeling microevolution in a changing environment: The evolving
quasispecies and the Diluted Champion Process | 15 pages, 12 figures. Figures redrawn, some additional clarifications
in the text. To appear in Journal of Statistical Mechanics: Theory and
Experiment | J. Stat. Mech. (2011) P08022 | 10.1088/1742-5468/2011/08/P08022 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Several pathogens use evolvability as a survival strategy against acquired
immunity of the host. Despite their high variability in time, some of them
exhibit quite low variability within the population at any given time, a
somehow paradoxical behavior often called the evolving quasispecies. In this
paper we introduce... | [
{
"created": "Mon, 18 Oct 2010 09:59:01 GMT",
"version": "v1"
},
{
"created": "Mon, 9 May 2011 08:36:06 GMT",
"version": "v2"
},
{
"created": "Wed, 27 Jul 2011 08:55:37 GMT",
"version": "v3"
}
] | 2011-08-31 | [
[
"Bianconi",
"Ginestra",
""
],
[
"Fichera",
"Davide",
""
],
[
"Franz",
"Silvio",
""
],
[
"Peliti",
"Luca",
""
]
] | Several pathogens use evolvability as a survival strategy against acquired immunity of the host. Despite their high variability in time, some of them exhibit quite low variability within the population at any given time, a somehow paradoxical behavior often called the evolving quasispecies. In this paper we introduce a... |
1809.04069 | Ruobing Wang | Zhiyuan Ma, Ping Wang, Zehui Gao, Ruobing Wang, Koroush Khalighi | Estimate the Warfarin Dose by Ensemble of Machine Learning Algorithms | other authors do not agree to submit to arxiv | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Warfarin dosing remains challenging due to narrow therapeutic index and
highly individual variability. Incorrect warfarin dosing is associated with
devastating adverse events. Remarkable efforts have been made to develop the
machine learning based warfarin dosing algorithms incorporating clinical
factors and genetic ... | [
{
"created": "Mon, 10 Sep 2018 22:18:37 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Sep 2018 14:36:49 GMT",
"version": "v2"
}
] | 2018-09-14 | [
[
"Ma",
"Zhiyuan",
""
],
[
"Wang",
"Ping",
""
],
[
"Gao",
"Zehui",
""
],
[
"Wang",
"Ruobing",
""
],
[
"Khalighi",
"Koroush",
""
]
] | Warfarin dosing remains challenging due to narrow therapeutic index and highly individual variability. Incorrect warfarin dosing is associated with devastating adverse events. Remarkable efforts have been made to develop the machine learning based warfarin dosing algorithms incorporating clinical factors and genetic va... |
2101.11724 | Tatjana Skrbic | Tatjana \v{S}krbi\'c, Amos Maritan, Achille Giacometti and Jayanth R.
Banavar | Local sequence-structure relationships in proteins | 32 pages, 13 figures, 3 tables, 8 supplementary information pages;
Accepted for publication in Protein Science | null | null | null | q-bio.BM cond-mat.soft cond-mat.stat-mech physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We seek to understand the interplay between amino acid sequence and local
structure in proteins. Are some amino acids unique in their ability to fit
harmoniously into certain local structures? What is the role of sequence in
sculpting the putative native state folds from myriad possible conformations?
In order to add... | [
{
"created": "Wed, 27 Jan 2021 22:26:16 GMT",
"version": "v1"
}
] | 2021-01-29 | [
[
"Škrbić",
"Tatjana",
""
],
[
"Maritan",
"Amos",
""
],
[
"Giacometti",
"Achille",
""
],
[
"Banavar",
"Jayanth R.",
""
]
] | We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the putative native state folds from myriad possible conformations? In order to addre... |
1511.04340 | Jean-Marc Luck | J.M. Luck and A. Mehta | Universality in survivor distributions: Characterising the winners of
competitive dynamics | 12 pages, 6 figures, 2 tables | Phys. Rev. E 92, 052810 (2015) | 10.1103/PhysRevE.92.052810 | null | q-bio.QM cond-mat.stat-mech nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the survivor distributions of a spatially extended model of
competitive dynamics in different geometries. The model consists of a
deterministic dynamical system of individual agents at specified nodes, which
might or might not survive the predatory dynamics: all stochasticity is brought
in by the initi... | [
{
"created": "Fri, 13 Nov 2015 20:21:58 GMT",
"version": "v1"
}
] | 2015-11-24 | [
[
"Luck",
"J. M.",
""
],
[
"Mehta",
"A.",
""
]
] | We investigate the survivor distributions of a spatially extended model of competitive dynamics in different geometries. The model consists of a deterministic dynamical system of individual agents at specified nodes, which might or might not survive the predatory dynamics: all stochasticity is brought in by the initial... |
2009.07103 | Aditya Singh | Aditya Singh, Akram Mohammed, Lokesh Chinthala, Rishikesan
Kamaleswaran | Machine learning predicts early onset of fever from continuous
physiological data of critically ill patients | null | null | null | null | q-bio.QM cs.LG stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fever can provide valuable information for diagnosis and prognosis of various
diseases such as pneumonia, dengue, sepsis, etc., therefore, predicting fever
early can help in the effectiveness of treatment options and expediting the
treatment process. This study aims to develop novel algorithms that can
accurately pre... | [
{
"created": "Mon, 14 Sep 2020 09:16:09 GMT",
"version": "v1"
}
] | 2020-09-16 | [
[
"Singh",
"Aditya",
""
],
[
"Mohammed",
"Akram",
""
],
[
"Chinthala",
"Lokesh",
""
],
[
"Kamaleswaran",
"Rishikesan",
""
]
] | Fever can provide valuable information for diagnosis and prognosis of various diseases such as pneumonia, dengue, sepsis, etc., therefore, predicting fever early can help in the effectiveness of treatment options and expediting the treatment process. This study aims to develop novel algorithms that can accurately predi... |
1102.2146 | Rub\'en J. Requejo | Rub\'en J. Requejo and Juan Camacho | Coexistence of cooperators and defectors in well mixed populations
mediated by limiting resources | 9 pages, 7 figures | Phys. Rev. Lett. 108, 038701 (2012) | 10.1103/PhysRevLett.108.038701 | null | q-bio.PE stat.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Traditionally, resource limitation in evolutionary game theory is assumed
just to impose a constant population size. Here we show that resource
limitations may generate dynamical payoffs able to alter an original prisoner's
dilemma, and to allow for the stable coexistence between unconditional
cooperators and defecto... | [
{
"created": "Thu, 10 Feb 2011 15:34:27 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Sep 2011 03:37:29 GMT",
"version": "v2"
},
{
"created": "Thu, 25 Oct 2012 18:48:26 GMT",
"version": "v3"
}
] | 2012-10-26 | [
[
"Requejo",
"Rubén J.",
""
],
[
"Camacho",
"Juan",
""
]
] | Traditionally, resource limitation in evolutionary game theory is assumed just to impose a constant population size. Here we show that resource limitations may generate dynamical payoffs able to alter an original prisoner's dilemma, and to allow for the stable coexistence between unconditional cooperators and defectors... |
1303.5848 | Michael Stumpf | Angelique Ale, Paul Kirk, Michael P.P. Stumpf | A general moment expansion method for stochastic kinetic models | 13 pages, 7 figures, 2 tables | null | 10.1063/1.4802475 | null | q-bio.MN cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Moment approximation methods are gaining increasing attention for their use
in the approximation of the stochastic kinetics of chemical reaction systems.
In this paper we derive a general moment expansion method for any type of
propensities and which allows expansion up to any number of moments. For some
chemical rea... | [
{
"created": "Sat, 23 Mar 2013 14:06:29 GMT",
"version": "v1"
}
] | 2015-06-15 | [
[
"Ale",
"Angelique",
""
],
[
"Kirk",
"Paul",
""
],
[
"Stumpf",
"Michael P. P.",
""
]
] | Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities and which allows expansion up to any number of moments. For some chemical react... |
0707.0764 | Branko Dragovich | Branko Dragovich and Alexandra Dragovich | p-Adic Degeneracy of the Genetic Code | 11 pages, 1 table. Published in the Proceedings of '4th Summer School
in Modern Mathematcal Physics', September 2006, Belgrade (Serbia) | SFIN XX A1 (2007) 179-188 | null | null | q-bio.GN cs.IT math.IT physics.bio-ph | null | Degeneracy of the genetic code is a biological way to minimize effects of the
undesirable mutation changes. Degeneration has a natural description on the
5-adic space of 64 codons $\mathcal{C}_5 (64) = \{n_0 + n_1 5 + n_2 5^2
: n_i = 1, 2, 3, 4 \} ,$ where $n_i$ are digits related to nucleotides as
follows: C = 1, ... | [
{
"created": "Thu, 5 Jul 2007 11:40:53 GMT",
"version": "v1"
}
] | 2007-07-16 | [
[
"Dragovich",
"Branko",
""
],
[
"Dragovich",
"Alexandra",
""
]
] | Degeneracy of the genetic code is a biological way to minimize effects of the undesirable mutation changes. Degeneration has a natural description on the 5-adic space of 64 codons $\mathcal{C}_5 (64) = \{n_0 + n_1 5 + n_2 5^2 : n_i = 1, 2, 3, 4 \} ,$ where $n_i$ are digits related to nucleotides as follows: C = 1, A = ... |
2008.06034 | Tom Zhao | Tom Y. Zhao and Neelesh A. Patankar | Tetracycline as an inhibitor to the coronavirus SARS-CoV-2 | null | J Cell Biochem (2021) 1-8 | 10.1002/jcb.29909 | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The coronavirus SARS-CoV-2 remains an extant threat against public health on
a global scale. Cell infection begins when the spike protein of SARS-CoV-2
binds with the cell receptor, angiotensin-converting enzyme 2 (ACE2). Here, we
address the role of Tetracycline as an inhibitor for the receptor-binding
domain (RBD) ... | [
{
"created": "Thu, 13 Aug 2020 17:46:46 GMT",
"version": "v1"
}
] | 2021-02-24 | [
[
"Zhao",
"Tom Y.",
""
],
[
"Patankar",
"Neelesh A.",
""
]
] | The coronavirus SARS-CoV-2 remains an extant threat against public health on a global scale. Cell infection begins when the spike protein of SARS-CoV-2 binds with the cell receptor, angiotensin-converting enzyme 2 (ACE2). Here, we address the role of Tetracycline as an inhibitor for the receptor-binding domain (RBD) of... |
q-bio/0402007 | Jeremy Sumner | J. G. Sumner and P. D. Jarvis (University of Tasmania) | Entanglement Invariants and Phylogenetic Branching | 21 pages, 3 Figures. Accepted for publication in Journal of
Mathematical Biology | null | null | UTAS-PHYS-04-01 | q-bio.PE | null | It is possible to consider stochastic models of sequence evolution in
phylogenetics in the context of a dynamical tensor description inspired from
physics. Approaching the problem in this framework allows for the well
developed methods of mathematical physics to be exploited in the biological
arena. We present the te... | [
{
"created": "Wed, 4 Feb 2004 00:01:08 GMT",
"version": "v1"
},
{
"created": "Tue, 10 Feb 2004 03:23:54 GMT",
"version": "v2"
},
{
"created": "Mon, 19 Jul 2004 10:05:21 GMT",
"version": "v3"
},
{
"created": "Tue, 30 Nov 2004 11:10:58 GMT",
"version": "v4"
}
] | 2007-05-23 | [
[
"Sumner",
"J. G.",
"",
"University of Tasmania"
],
[
"Jarvis",
"P. D.",
"",
"University of Tasmania"
]
] | It is possible to consider stochastic models of sequence evolution in phylogenetics in the context of a dynamical tensor description inspired from physics. Approaching the problem in this framework allows for the well developed methods of mathematical physics to be exploited in the biological arena. We present the tens... |
2402.12943 | Giuseppe Gaeta | Giuseppe Gaeta | On some dynamical features of the complete Moran model for neutral
evolution in the presence of mutations | 22 pages, 8 figures | Open Communications in Nonlinear Mathematical Physics, Volume 4
(March 26, 2024) ocnmp:13104 | 10.46298/ocnmp.13104 | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a version of the classical Moran model, in which mutations are
taken into account; the possibility of mutations was introduced by Moran in his
seminal paper, but it is more often overlooked in discussing the Moran model.
For this model, fixation is prevented by mutation, and we have an ergodic
Markov proce... | [
{
"created": "Tue, 20 Feb 2024 11:57:12 GMT",
"version": "v1"
},
{
"created": "Sat, 23 Mar 2024 13:48:15 GMT",
"version": "v2"
}
] | 2024-08-07 | [
[
"Gaeta",
"Giuseppe",
""
]
] | We present a version of the classical Moran model, in which mutations are taken into account; the possibility of mutations was introduced by Moran in his seminal paper, but it is more often overlooked in discussing the Moran model. For this model, fixation is prevented by mutation, and we have an ergodic Markov process... |
1009.6164 | Elife Bagci | Elife Zerrin Bagci, Sercan Murat Sen, Mehmet Cihan Camurdan | Analysis of a Mathematical Model of Apoptosis: Individual Differences
and Malfunction in Programmed Cell Death | null | null | null | null | q-bio.MN q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Apoptosis is an important area of research because of its role in keeping a
mature multicellular organism's number of cells constant hence, ensuring that
the organism does not have cell accumulation that may transform into cancer
with additional hallmarks. Firstly, we have carried out sensitivity analysis on
an exist... | [
{
"created": "Thu, 30 Sep 2010 15:11:01 GMT",
"version": "v1"
}
] | 2010-10-01 | [
[
"Bagci",
"Elife Zerrin",
""
],
[
"Sen",
"Sercan Murat",
""
],
[
"Camurdan",
"Mehmet Cihan",
""
]
] | Apoptosis is an important area of research because of its role in keeping a mature multicellular organism's number of cells constant hence, ensuring that the organism does not have cell accumulation that may transform into cancer with additional hallmarks. Firstly, we have carried out sensitivity analysis on an existin... |
q-bio/0512017 | Martyn Amos | Martyn Amos, David A. Hodgson and Alan Gibbons | Bacterial self-organisation and computation | Submitted to the International Journal of Unconventional Computing | null | null | null | q-bio.CB | null | In this article we highlight chemotaxis (cellular movement) as a rich source
of potential engineering applications and computational models, highlighting
current research and possible future work. We first give a brief description of
the biological mechanism, before describing recent work on modelling it in
silico. W... | [
{
"created": "Thu, 8 Dec 2005 11:28:46 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Amos",
"Martyn",
""
],
[
"Hodgson",
"David A.",
""
],
[
"Gibbons",
"Alan",
""
]
] | In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the biological mechanism, before describing recent work on modelling it in silico. We ... |
2012.11508 | Tanja Slotte | Juanita Guti\'errez-Valencia, William Hughes, Emma L. Berdan, Tanja
Slotte | The genomic architecture and evolutionary fates of supergenes | null | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Supergenes are genomic regions containing sets of tightly linked loci that
control multi-trait phenotypic polymorphisms under balancing selection. Recent
advances in genomics have uncovered significant variation in both the genomic
architecture as well as the mode of origin of supergenes across diverse
organismal sys... | [
{
"created": "Mon, 21 Dec 2020 17:26:07 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Mar 2021 09:23:58 GMT",
"version": "v2"
}
] | 2021-03-16 | [
[
"Gutiérrez-Valencia",
"Juanita",
""
],
[
"Hughes",
"William",
""
],
[
"Berdan",
"Emma L.",
""
],
[
"Slotte",
"Tanja",
""
]
] | Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic architecture as well as the mode of origin of supergenes across diverse organismal syste... |
1307.7831 | Aaron Darling | Nicolas Wieseke, Matthias Bernt, and Martin Middendorf | Unifying Parsimonious Tree Reconciliation | Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013) | null | null | null | q-bio.QM cs.CE cs.DS q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolution is a process that is influenced by various environmental factors,
e.g. the interactions between different species, genes, and biogeographical
properties. Hence, it is interesting to study the combined evolutionary history
of multiple species, their genes, and the environment they live in. A common
approach ... | [
{
"created": "Tue, 30 Jul 2013 05:47:27 GMT",
"version": "v1"
}
] | 2013-08-02 | [
[
"Wieseke",
"Nicolas",
""
],
[
"Bernt",
"Matthias",
""
],
[
"Middendorf",
"Martin",
""
]
] | Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to... |
2303.17402 | Mona Nourbakhsh | Mona Nourbakhsh (1), Kristine Degn (1), Astrid Saksager (1), Matteo
Tiberti (2), Elena Papaleo (1 and 2) ((1) Cancer Systems Biology, Section for
Bioinformatics, Department of Health and Technology, Technical University of
Denmark, 2800, Lyngby, Denmark, (2) Cancer Structural Biology, Danish Cancer
Society Rese... | Prediction of cancer driver genes and mutations: the potential of
integrative computational frameworks | 35 pages, 7 figures | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The vast amount of sequencing data presently available allow the scientific
community to explore a range of genetic variables that may drive and progress
cancer. A myriad of predictive tools has been proposed, allowing researchers
and clinicians to compare and prioritize driver genes and mutations and their
relative ... | [
{
"created": "Thu, 30 Mar 2023 14:17:55 GMT",
"version": "v1"
}
] | 2023-03-31 | [
[
"Nourbakhsh",
"Mona",
"",
"1 and 2"
],
[
"Degn",
"Kristine",
"",
"1 and 2"
],
[
"Saksager",
"Astrid",
"",
"1 and 2"
],
[
"Tiberti",
"Matteo",
"",
"1 and 2"
],
[
"Papaleo",
"Elena",
"",
"1 and 2"
]
] | The vast amount of sequencing data presently available allow the scientific community to explore a range of genetic variables that may drive and progress cancer. A myriad of predictive tools has been proposed, allowing researchers and clinicians to compare and prioritize driver genes and mutations and their relative pa... |
2104.07053 | Gr\'egoire Sergeant-Perthuis | David Rudrauf, Gr\'egoire Sergeant-Perthuis, Yvain Tisserand, Teerawat
Monnor, Olivier Belli | Combining the Projective Consciousness Model and Virtual Humans to
assess ToM capacity in Virtual Reality: a proof-of-concept | null | null | null | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Relating explicit psychological mechanisms and observable behaviours is a
central aim of psychological and behavioural science. We implemented the
principles of the Projective Consciousness Model into artificial agents
embodied as virtual humans, as a proof-of-concept for a methodological
framework aimed at simulatin... | [
{
"created": "Fri, 2 Apr 2021 23:55:39 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Sep 2021 17:13:44 GMT",
"version": "v2"
}
] | 2021-09-10 | [
[
"Rudrauf",
"David",
""
],
[
"Sergeant-Perthuis",
"Grégoire",
""
],
[
"Tisserand",
"Yvain",
""
],
[
"Monnor",
"Teerawat",
""
],
[
"Belli",
"Olivier",
""
]
] | Relating explicit psychological mechanisms and observable behaviours is a central aim of psychological and behavioural science. We implemented the principles of the Projective Consciousness Model into artificial agents embodied as virtual humans, as a proof-of-concept for a methodological framework aimed at simulating ... |
0706.1852 | Erik Aurell | Maria Werner, LiZhe Zhu, Erik Aurell | Cooperative action in eukaryotic gene regulation: physical properties of
a viral example | 7 pages, 6 figures, 1 table | null | 10.1103/PhysRevE.76.061909 | null | q-bio.SC cond-mat.soft q-bio.MN | null | The Epstein-Barr virus (EBV) infects more than 90% of the human population,
and is the cause of several both serious and mild diseases. It is a
tumorivirus, and has been widely studied as a model system for gene
(de)regulation in human. A central feature of the EBV life cycle is its ability
to persist in human B cell... | [
{
"created": "Wed, 13 Jun 2007 09:14:29 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Werner",
"Maria",
""
],
[
"Zhu",
"LiZhe",
""
],
[
"Aurell",
"Erik",
""
]
] | The Epstein-Barr virus (EBV) infects more than 90% of the human population, and is the cause of several both serious and mild diseases. It is a tumorivirus, and has been widely studied as a model system for gene (de)regulation in human. A central feature of the EBV life cycle is its ability to persist in human B cells ... |
0705.4635 | Thierry Emonet | Thierry Emonet and Philippe Cluzel | Relationship between cellular response and behavioral variability in
bacterial chemotaxis | 15 pages, 4 figures, Supporting information available here
http://cluzel.uchicago.edu/data/emonet/arxiv_070531_supp.pdf | null | 10.1073/pnas.0705463105 | null | q-bio.MN q-bio.CB q-bio.OT | null | Bacterial chemotaxis in Escherichia coli is a canonical system for the study
of signal transduction. A remarkable feature of this system is the coexistence
of precise adaptation in population with large fluctuating cellular behavior in
single cells (Korobkova et al. 2004, Nature, 428, 574). Using a stochastic
model, ... | [
{
"created": "Thu, 31 May 2007 16:05:09 GMT",
"version": "v1"
}
] | 2019-08-19 | [
[
"Emonet",
"Thierry",
""
],
[
"Cluzel",
"Philippe",
""
]
] | Bacterial chemotaxis in Escherichia coli is a canonical system for the study of signal transduction. A remarkable feature of this system is the coexistence of precise adaptation in population with large fluctuating cellular behavior in single cells (Korobkova et al. 2004, Nature, 428, 574). Using a stochastic model, we... |
1503.02904 | Martino Trassinelli | Martino Trassinelli (INSP) | Energy cost and optimisation in breath-hold diving | null | J. Theor. Biol. 396, 42-52 (2016) | 10.1016/j.jtbi.2016.02.009 | null | q-bio.QM physics.bio-ph physics.flu-dyn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a new model for calculating locomotion costs in breath-hold
divers. Starting from basic mechanics principles, we calculate the work that
the diver must provide through propulsion to counterbalance the action of drag,
the buoyant force and weight during immersion. Compared to those in previous
studies, the ... | [
{
"created": "Tue, 10 Mar 2015 13:52:29 GMT",
"version": "v1"
},
{
"created": "Wed, 11 Mar 2015 14:55:16 GMT",
"version": "v2"
},
{
"created": "Tue, 22 Dec 2015 09:39:31 GMT",
"version": "v3"
},
{
"created": "Tue, 19 Jan 2016 12:40:27 GMT",
"version": "v4"
}
] | 2024-01-30 | [
[
"Trassinelli",
"Martino",
"",
"INSP"
]
] | We present a new model for calculating locomotion costs in breath-hold divers. Starting from basic mechanics principles, we calculate the work that the diver must provide through propulsion to counterbalance the action of drag, the buoyant force and weight during immersion. Compared to those in previous studies, the mo... |
1811.05371 | Ching-Hao Wang | Ching-Hao Wang, Caleb J. Bashor, and Pankaj Mehta | The strength of protein-protein interactions controls the information
capacity and dynamical response of signaling networks | 13+10 pages, 5+9 figures, Supplemental Information included | null | null | null | q-bio.MN cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Eukaryotic cells transmit information by signaling through complex networks
of interacting proteins. Here we develop a theoretical and computational
framework that relates the biophysics of protein-protein interactions (PPIs)
within a signaling network to its information processing properties. To do so,
we generalize... | [
{
"created": "Tue, 13 Nov 2018 15:46:48 GMT",
"version": "v1"
},
{
"created": "Fri, 23 Nov 2018 17:40:55 GMT",
"version": "v2"
}
] | 2018-11-26 | [
[
"Wang",
"Ching-Hao",
""
],
[
"Bashor",
"Caleb J.",
""
],
[
"Mehta",
"Pankaj",
""
]
] | Eukaryotic cells transmit information by signaling through complex networks of interacting proteins. Here we develop a theoretical and computational framework that relates the biophysics of protein-protein interactions (PPIs) within a signaling network to its information processing properties. To do so, we generalize s... |
q-bio/0509037 | Mikl\'os Cs\H{u}r\"os | Mikl\'os Cs\H{u}r\"os, Istv\'an Mikl\'os | A probabilistic model for gene content evolution with duplication, loss,
and horizontal transfer | null | null | 10.1007/11732990_18 | null | q-bio.PE q-bio.QM | null | We introduce a Markov model for the evolution of a gene family along a
phylogeny. The model includes parameters for the rates of horizontal gene
transfer, gene duplication, and gene loss, in addition to branch lengths in the
phylogeny. The likelihood for the changes in the size of a gene family across
different organ... | [
{
"created": "Tue, 27 Sep 2005 14:17:53 GMT",
"version": "v1"
}
] | 2016-09-08 | [
[
"Csűrös",
"Miklós",
""
],
[
"Miklós",
"István",
""
]
] | We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organis... |
1302.4574 | Anirban Banerji | Anirban Banerji | Structural and evolutionary tunnels of pairwise residue-interaction
symmetries connect different structural classes of proteins | 23 pages, 5 Tables, 1 Figure | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Studying all non-redundant proteins in 76 most-commonly found structural
domains, the present work attempts to decipher latent patterns that
characterize acceptable and unacceptable symmetries in residue-residue
interactions in functional proteins. We report that cutting across the
structural classes, a select set of... | [
{
"created": "Tue, 19 Feb 2013 10:53:32 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Aug 2013 04:41:19 GMT",
"version": "v2"
}
] | 2013-08-23 | [
[
"Banerji",
"Anirban",
""
]
] | Studying all non-redundant proteins in 76 most-commonly found structural domains, the present work attempts to decipher latent patterns that characterize acceptable and unacceptable symmetries in residue-residue interactions in functional proteins. We report that cutting across the structural classes, a select set of p... |
1210.3378 | Simon Mochrie | S. G. J. Mochrie, A. H. Mack, D. J. Schlingman, R. Collins, M.
Kamenetska, and L. Regan | Unwinding and rewinding the nucleosome inner turn: Force dependence of
the kinetic rate constants | null | null | 10.1103/PhysRevE.87.012710 | null | q-bio.BM cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A simple model for the force-dependent unwinding and rewinding rates of the
nucleosome inner turn is constructed and quantitatively compared to the results
of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)].
First, a coarse-grained model for the histone-DNA free energy landscape that
incorporat... | [
{
"created": "Thu, 11 Oct 2012 21:44:39 GMT",
"version": "v1"
},
{
"created": "Fri, 4 Jan 2013 16:13:41 GMT",
"version": "v2"
}
] | 2015-06-11 | [
[
"Mochrie",
"S. G. J.",
""
],
[
"Mack",
"A. H.",
""
],
[
"Schlingman",
"D. J.",
""
],
[
"Collins",
"R.",
""
],
[
"Kamenetska",
"M.",
""
],
[
"Regan",
"L.",
""
]
] | A simple model for the force-dependent unwinding and rewinding rates of the nucleosome inner turn is constructed and quantitatively compared to the results of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)]. First, a coarse-grained model for the histone-DNA free energy landscape that incorporates... |
1505.00351 | Sarine Babikian | Sarine Babikian, Francisco J. Valero-Cuevas, Eva Kanso | Slow Limb Movements Require Precise Control of Muscle Stiffness | null | null | null | null | q-bio.TO q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Slow and accurate finger and limb movements are essential to daily
activities, but their neural control and governing mechanics are relatively
unexplored. We consider neuromechanical systems where slow movements are
produced by neural commands that modulate muscle stiffness. This formulation
based on strain-energy eq... | [
{
"created": "Sat, 2 May 2015 16:32:34 GMT",
"version": "v1"
},
{
"created": "Tue, 5 May 2015 17:18:39 GMT",
"version": "v2"
}
] | 2015-05-06 | [
[
"Babikian",
"Sarine",
""
],
[
"Valero-Cuevas",
"Francisco J.",
""
],
[
"Kanso",
"Eva",
""
]
] | Slow and accurate finger and limb movements are essential to daily activities, but their neural control and governing mechanics are relatively unexplored. We consider neuromechanical systems where slow movements are produced by neural commands that modulate muscle stiffness. This formulation based on strain-energy equi... |
0802.1904 | Nicolas Vuillerme | Nicolas Vuillerme (TIMC), Cyril Burdet (LMAS), Brice Isableu (EA
4042), Sylvain Demetz (LMAS) | The magnitude of the effect of calf muscles fatigue on postural control
during bipedal quiet standing with vision depends on the eye-visual target
distance | null | Gait & Posture / Gait and Posture 24, 2 (2006) 169-72 | 10.1016/j.gaitpost.2005.07.011 | null | q-bio.NC | null | The purpose of the present experiment was to investigate whether, with
vision, the magnitude of the effect of calf muscles fatigue on postural control
during bipedal quiet standing depends on the eye-visual target distance. Twelve
young university students were asked to stand upright as immobile as possible
in three ... | [
{
"created": "Wed, 13 Feb 2008 20:12:20 GMT",
"version": "v1"
}
] | 2008-02-14 | [
[
"Vuillerme",
"Nicolas",
"",
"TIMC"
],
[
"Burdet",
"Cyril",
"",
"LMAS"
],
[
"Isableu",
"Brice",
"",
"EA\n 4042"
],
[
"Demetz",
"Sylvain",
"",
"LMAS"
]
] | The purpose of the present experiment was to investigate whether, with vision, the magnitude of the effect of calf muscles fatigue on postural control during bipedal quiet standing depends on the eye-visual target distance. Twelve young university students were asked to stand upright as immobile as possible in three vi... |
1703.01900 | Jipeng Qiang | Jipeng Qiang and Wei Ding and John Quackenbush and Ping Chen | Network-based Distance Metric with Application to Discover Disease
Subtypes in Cancer | null | null | null | null | q-bio.QM cs.IR q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While we once thought of cancer as single monolithic diseases affecting a
specific organ site, we now understand that there are many subtypes of cancer
defined by unique patterns of gene mutations. These gene mutational data, which
can be more reliably obtained than gene expression data, help to determine how
the sub... | [
{
"created": "Wed, 1 Mar 2017 02:09:50 GMT",
"version": "v1"
}
] | 2017-03-07 | [
[
"Qiang",
"Jipeng",
""
],
[
"Ding",
"Wei",
""
],
[
"Quackenbush",
"John",
""
],
[
"Chen",
"Ping",
""
]
] | While we once thought of cancer as single monolithic diseases affecting a specific organ site, we now understand that there are many subtypes of cancer defined by unique patterns of gene mutations. These gene mutational data, which can be more reliably obtained than gene expression data, help to determine how the subty... |
2401.06151 | Alex Morehead | Alex Morehead, Jeffrey Ruffolo, Aadyot Bhatnagar, Ali Madani | Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein
Complexes with SE(3)-Discrete Diffusion | 15 pages, 11 figures, presented at the NeurIPS 2023 Machine Learning
in Structural Biology (MLSB) workshop. Code available at
https://github.com/Profluent-Internships/MMDiff | null | null | null | q-bio.BM cs.AI cs.LG q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Generative models of macromolecules carry abundant and impactful implications
for industrial and biomedical efforts in protein engineering. However, existing
methods are currently limited to modeling protein structures or sequences,
independently or jointly, without regard to the interactions that commonly
occur betw... | [
{
"created": "Thu, 21 Dec 2023 05:53:33 GMT",
"version": "v1"
}
] | 2024-01-15 | [
[
"Morehead",
"Alex",
""
],
[
"Ruffolo",
"Jeffrey",
""
],
[
"Bhatnagar",
"Aadyot",
""
],
[
"Madani",
"Ali",
""
]
] | Generative models of macromolecules carry abundant and impactful implications for industrial and biomedical efforts in protein engineering. However, existing methods are currently limited to modeling protein structures or sequences, independently or jointly, without regard to the interactions that commonly occur betwee... |
2205.00054 | Zachary Jackson | Zachary Jackson, BingKan Xue | Heterogeneity of Interaction Strengths and Its Consequences on
Ecological Systems | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Ecosystems are formed by networks of species and their interactions.
Traditional models of such interactions assume a constant interaction strength
between a given pair of species. However, there is often significant trait
variation among individual organisms even within the same species, causing
heterogeneity in the... | [
{
"created": "Fri, 29 Apr 2022 19:28:24 GMT",
"version": "v1"
}
] | 2022-05-03 | [
[
"Jackson",
"Zachary",
""
],
[
"Xue",
"BingKan",
""
]
] | Ecosystems are formed by networks of species and their interactions. Traditional models of such interactions assume a constant interaction strength between a given pair of species. However, there is often significant trait variation among individual organisms even within the same species, causing heterogeneity in their... |
2310.07185 | Ankur Gupta | Benjamin M. Alessio, Ankur Gupta | The Ubiquity of Diffusiophoresis: Exploring Human Population Dynamics
While Including Concentration Gradient-Driven Advection | null | null | null | null | q-bio.PE cond-mat.soft physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Diffusiophoresis, which refers to the movement of entities driven by
gradients in the concentration of attractants, is observable in colloids and
chemotactic bacteria. We suggest that humans also exhibit diffusiophoresis when
they perceive concentration gradients in economic opportunities, social
connections, safety ... | [
{
"created": "Wed, 11 Oct 2023 04:23:46 GMT",
"version": "v1"
}
] | 2023-10-12 | [
[
"Alessio",
"Benjamin M.",
""
],
[
"Gupta",
"Ankur",
""
]
] | Diffusiophoresis, which refers to the movement of entities driven by gradients in the concentration of attractants, is observable in colloids and chemotactic bacteria. We suggest that humans also exhibit diffusiophoresis when they perceive concentration gradients in economic opportunities, social connections, safety fa... |
1111.3065 | Didier Sornette | Ivan Osorio, Alexey Lyubushin and Didier Sornette | Towards a Probabilistic Definition of Seizures | 17 pages with 4 figures | Epilepsy & Behavior 22, S18-S28 (2011) | 10.1016/j.yebeh.2011.09.009 | null | q-bio.NC physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This writing: a) Draws attention to the intricacies inherent to the pursuit
of a universal seizure definition even when powerful, well understood signal
analysis methods are utilized to this end; b) Identifies this aim as a
multi-objective optimization problem and discusses the advantages and
disadvantages of adoptin... | [
{
"created": "Sun, 13 Nov 2011 21:35:50 GMT",
"version": "v1"
}
] | 2011-11-15 | [
[
"Osorio",
"Ivan",
""
],
[
"Lyubushin",
"Alexey",
""
],
[
"Sornette",
"Didier",
""
]
] | This writing: a) Draws attention to the intricacies inherent to the pursuit of a universal seizure definition even when powerful, well understood signal analysis methods are utilized to this end; b) Identifies this aim as a multi-objective optimization problem and discusses the advantages and disadvantages of adopting ... |
2003.02340 | Emily Diller | Emily Diller and Jason Parker | Variation in correlation between prognosis and histologic feature based
on biopsy selection | 9 Pages, 2 figures, 1 table | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Glioblastoma multiform carries a dismal prognosis with poor response to gold
standard treatment. Innovative data analysis methods have been developed to
characterize tumor genomic expression with histologic features. In a clinical
setting, biopsy selection methods may be constrained by time and financial
burden to th... | [
{
"created": "Wed, 4 Mar 2020 21:35:14 GMT",
"version": "v1"
}
] | 2020-03-06 | [
[
"Diller",
"Emily",
""
],
[
"Parker",
"Jason",
""
]
] | Glioblastoma multiform carries a dismal prognosis with poor response to gold standard treatment. Innovative data analysis methods have been developed to characterize tumor genomic expression with histologic features. In a clinical setting, biopsy selection methods may be constrained by time and financial burden to the ... |
2010.12332 | Mohammad Reza Dayer | Mohammad Reza Dayer | Old Drugs for JAK-STAT Pathway Inhibition in COVID-19 | null | null | 10.13140/RG.2.2.33735.73122 | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | The pandemic threat of COVID-19 with more than 37 million cases in which
about 5 percent entering critical stage characterized by cytokine storm and
hyperinflammatory condition, the state more often leads to admission to
intensive care unit with rapid mortality. Janus kinase enzymes of Jak-1, Jak-2,
Jak-3, and Tyk2 s... | [
{
"created": "Fri, 23 Oct 2020 13:09:16 GMT",
"version": "v1"
}
] | 2020-10-26 | [
[
"Dayer",
"Mohammad Reza",
""
]
] | The pandemic threat of COVID-19 with more than 37 million cases in which about 5 percent entering critical stage characterized by cytokine storm and hyperinflammatory condition, the state more often leads to admission to intensive care unit with rapid mortality. Janus kinase enzymes of Jak-1, Jak-2, Jak-3, and Tyk2 see... |
1307.3426 | Carl Whitfield | Carl A. Whitfield, Davide Marenduzzo, Rapha\"el Voituriez and Rhoda J.
Hawkins | Active polar fluid flow in finite droplets | 9 pages, 5 figures + 4 appendices (15 pages total) | Eur. Phys. J. E, 37 2 (2014) 8 | 10.1140/epje/i2014-14008-3 | null | q-bio.CB cond-mat.soft q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a continuum level analytical model of a droplet of active
contractile fluid consisting of filaments and motors. We calculate the steady
state flows that result from a splayed polarisation of the filaments. We
account for the interaction with an arbitrary external medium by imposing a
viscous friction at th... | [
{
"created": "Fri, 12 Jul 2013 11:57:33 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Oct 2013 15:48:45 GMT",
"version": "v2"
},
{
"created": "Wed, 19 Feb 2014 11:58:48 GMT",
"version": "v3"
}
] | 2014-02-20 | [
[
"Whitfield",
"Carl A.",
""
],
[
"Marenduzzo",
"Davide",
""
],
[
"Voituriez",
"Raphaël",
""
],
[
"Hawkins",
"Rhoda J.",
""
]
] | We present a continuum level analytical model of a droplet of active contractile fluid consisting of filaments and motors. We calculate the steady state flows that result from a splayed polarisation of the filaments. We account for the interaction with an arbitrary external medium by imposing a viscous friction at the ... |
q-bio/0608018 | Emilio Hernandez-Garcia | E. Hernandez-Garcia, A. F. Rozenfeld, V. M. Eguiluz, S. Arnaud-Haond,
and C. M. Duarte | Clone size distributions in networks of genetic similarity | 17 pages, 4 figures. One figure improved and other minor changes. To
appear in Physica D | Physica D, 214, 166-173 (2006) | 10.1016/j.physd.2006.09.015 | null | q-bio.PE cond-mat.stat-mech q-bio.QM | null | We build networks of genetic similarity in which the nodes are organisms
sampled from biological populations. The procedure is illustrated by
constructing networks from genetic data of a marine clonal plant. An important
feature in the networks is the presence of clone subgraphs, i.e. sets of
organisms with identical... | [
{
"created": "Wed, 9 Aug 2006 14:17:24 GMT",
"version": "v1"
},
{
"created": "Sat, 23 Sep 2006 08:28:21 GMT",
"version": "v2"
}
] | 2008-01-23 | [
[
"Hernandez-Garcia",
"E.",
""
],
[
"Rozenfeld",
"A. F.",
""
],
[
"Eguiluz",
"V. M.",
""
],
[
"Arnaud-Haond",
"S.",
""
],
[
"Duarte",
"C. M.",
""
]
] | We build networks of genetic similarity in which the nodes are organisms sampled from biological populations. The procedure is illustrated by constructing networks from genetic data of a marine clonal plant. An important feature in the networks is the presence of clone subgraphs, i.e. sets of organisms with identical g... |
1505.06550 | Yang Li | Yang Li and XifengYan | MSPKmerCounter: A Fast and Memory Efficient Approach for K-mer Counting | null | null | null | null | q-bio.GN cs.CE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A major challenge in next-generation genome sequencing (NGS) is to assemble
massive overlapping short reads that are randomly sampled from DNA fragments.
To complete assembling, one needs to finish a fundamental task in many leading
assembly algorithms: counting the number of occurrences of k-mers (length-k
substring... | [
{
"created": "Mon, 25 May 2015 07:21:56 GMT",
"version": "v1"
}
] | 2015-05-26 | [
[
"Li",
"Yang",
""
],
[
"XifengYan",
"",
""
]
] | A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading assembly algorithms: counting the number of occurrences of k-mers (length-k substrings ... |
1906.02863 | Qi Zhao | Qi Zhao, Lingli Zhang, Chun Shen, Jie Zhang, Jianfeng Feng | Double Generalized Linear Model Reveals Those with High Intelligence are
More Similar in Cortical Thickness | null | null | null | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most studies indicate that intelligence (g) is positively correlated with
cortical thickness. However, the interindividual variability of cortical
thickness has not been taken into account. In this study, we aimed to identify
the association between intelligence and cortical thickness in adolescents from
both the gro... | [
{
"created": "Fri, 7 Jun 2019 02:11:21 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Nov 2019 10:34:16 GMT",
"version": "v2"
}
] | 2019-11-25 | [
[
"Zhao",
"Qi",
""
],
[
"Zhang",
"Lingli",
""
],
[
"Shen",
"Chun",
""
],
[
"Zhang",
"Jie",
""
],
[
"Feng",
"Jianfeng",
""
]
] | Most studies indicate that intelligence (g) is positively correlated with cortical thickness. However, the interindividual variability of cortical thickness has not been taken into account. In this study, we aimed to identify the association between intelligence and cortical thickness in adolescents from both the group... |
2310.03186 | Xaq Pitkow | Rajkumar Vasudeva Raju, Zhe Li, Scott Linderman, Xaq Pitkow | Inferring Inference | 26 pages, 4 figures and 1 supplementary figure | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | Patterns of microcircuitry suggest that the brain has an array of repeated
canonical computational units. Yet neural representations are distributed, so
the relevant computations may only be related indirectly to single-neuron
transformations. It thus remains an open challenge how to define canonical
distributed comp... | [
{
"created": "Wed, 4 Oct 2023 22:12:11 GMT",
"version": "v1"
},
{
"created": "Fri, 6 Oct 2023 19:14:54 GMT",
"version": "v2"
},
{
"created": "Fri, 13 Oct 2023 22:04:12 GMT",
"version": "v3"
}
] | 2023-10-17 | [
[
"Raju",
"Rajkumar Vasudeva",
""
],
[
"Li",
"Zhe",
""
],
[
"Linderman",
"Scott",
""
],
[
"Pitkow",
"Xaq",
""
]
] | Patterns of microcircuitry suggest that the brain has an array of repeated canonical computational units. Yet neural representations are distributed, so the relevant computations may only be related indirectly to single-neuron transformations. It thus remains an open challenge how to define canonical distributed comput... |
1512.01197 | Geza Odor | Michael T. Gastner and G\'eza \'Odor | The topology of large Open Connectome networks for the human brain | 14 pages, 6 figures, accepted version in Scientific Reports | Scientific Reports 6 (2016) 27249 | 10.1038/srep27249 | null | q-bio.NC cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The structural human connectome (i.e.\ the network of fiber connections in
the brain) can be analyzed at ever finer spatial resolution thanks to advances
in neuroimaging. Here we analyze several large data sets for the human brain
network made available by the Open Connectome Project. We apply statistical
model selec... | [
{
"created": "Thu, 3 Dec 2015 19:13:54 GMT",
"version": "v1"
},
{
"created": "Fri, 13 May 2016 12:42:43 GMT",
"version": "v2"
}
] | 2016-06-08 | [
[
"Gastner",
"Michael T.",
""
],
[
"Ódor",
"Géza",
""
]
] | The structural human connectome (i.e.\ the network of fiber connections in the brain) can be analyzed at ever finer spatial resolution thanks to advances in neuroimaging. Here we analyze several large data sets for the human brain network made available by the Open Connectome Project. We apply statistical model selecti... |
0706.2077 | Michael Sadovsky | Michael G.Sadovsky, Julia A.Putintzeva | Codon Usage Bias Measured Through Entropy Approach | 15 pages, 1 figure | null | null | null | q-bio.GN | null | Codon usage bias measure is defined through the mutual entropy calculation of
real codon frequency distribution against the quasi-equilibrium one. This
latter is defined in three manners: (1) the frequency of synonymous codons is
supposed to be equal (i.e., the arithmetic mean of their frequencies); (2) it
coincides ... | [
{
"created": "Thu, 14 Jun 2007 10:07:48 GMT",
"version": "v1"
}
] | 2007-06-15 | [
[
"Sadovsky",
"Michael G.",
""
],
[
"Putintzeva",
"Julia A.",
""
]
] | Codon usage bias measure is defined through the mutual entropy calculation of real codon frequency distribution against the quasi-equilibrium one. This latter is defined in three manners: (1) the frequency of synonymous codons is supposed to be equal (i.e., the arithmetic mean of their frequencies); (2) it coincides to... |
1506.08683 | Oskar Hallatschek Dr. | Oskar Hallatschek and Lukas Geyrhofer | Collective Fluctuations in models of adaptation | null | null | null | null | q-bio.PE cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dynamics of adaptation is difficult to predict because it is highly
stochastic even in large populations. The uncertainty emerges from number
fluctuations, called genetic drift, arising in the small number of particularly
fit individuals of the population. Random genetic drift in this evolutionary
vanguard also l... | [
{
"created": "Mon, 29 Jun 2015 15:35:40 GMT",
"version": "v1"
}
] | 2015-06-30 | [
[
"Hallatschek",
"Oskar",
""
],
[
"Geyrhofer",
"Lukas",
""
]
] | The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit individuals of the population. Random genetic drift in this evolutionary vanguard also lim... |
q-bio/0504016 | Kunihiko Kaneko | Kunihiko Kaneko | On Recursive Production and Evolvabilty of Cells: Catalytic Reaction
Network Approach | 46 pages 28 figures | Adv Chem. Phys 130 (2005) 543-598 | null | null | q-bio.MN cond-mat.stat-mech nlin.AO physics.bio-ph q-bio.CB | null | To unveil the logic of cell from a level of chemical reaction dynamics, we
need to clarify how ensemble of chemicals can autonomously produce the set of
chemical, without assuming a specific external control echanism. A cell
consists of a huge number of chemical species that catalyze each other. Often
the number of e... | [
{
"created": "Tue, 12 Apr 2005 02:02:44 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Kaneko",
"Kunihiko",
""
]
] | To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a huge number of chemical species that catalyze each other. Often the number of eac... |
0711.2208 | Jacob Bock Axelsen | Jacob Bock Axelsen, Sebastian Bernhardsson, Kim Sneppen | One Hub-One Process: A Tool Based View on Regulatory Network Topology | 18 pages, 3 figures, 5 supplementary figures | BMC Systems Biology 2008, 2:25 | 10.1186/1752-0509-2-25 | null | q-bio.MN cond-mat.soft | null | The relationship between the regulatory design and the functionality of
molecular networks is a key issue in biology. Modules and motifs have been
associated to various cellular processes, thereby providing anecdotal evidence
for performance based localization on molecular networks. To quantify
structure-function rel... | [
{
"created": "Wed, 14 Nov 2007 14:16:39 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Nov 2007 15:02:23 GMT",
"version": "v2"
}
] | 2008-03-04 | [
[
"Axelsen",
"Jacob Bock",
""
],
[
"Bernhardsson",
"Sebastian",
""
],
[
"Sneppen",
"Kim",
""
]
] | The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for performance based localization on molecular networks. To quantify structure-function relat... |
1611.06065 | Maude Pupin | Qassim Esmaeel, Maude Pupin (CRIStAL, BONSAI), Nam Phuong Kieu,
Gabrielle Chataign\'e, Max B\'echet, Jovana Deravel, Fran\c{c}ois Krier,
Monica H\"ofte, Philippe Jacques, Val\'erie Lecl\`ere (CRIStAL, BONSAI) | Burkholderia genome mining for nonribosomal peptide synthetases reveals
a great potential for novel siderophores and lipopeptides synthesis | null | MicrobiologyOpen, 2016, 5 (3), pp.512 - 526 | 10.1002/mbo3.347 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Burkholderia is an important genus encompassing a variety of species,
including pathogenic strains as well as strains that promote plant growth. We
have carried out a global strategy, which combined two complementary
approaches. The first one is genome guided with deep analysis of genome
sequences and the second one ... | [
{
"created": "Fri, 18 Nov 2016 13:28:43 GMT",
"version": "v1"
}
] | 2016-11-21 | [
[
"Esmaeel",
"Qassim",
"",
"CRIStAL, BONSAI"
],
[
"Pupin",
"Maude",
"",
"CRIStAL, BONSAI"
],
[
"Kieu",
"Nam Phuong",
"",
"CRIStAL, BONSAI"
],
[
"Chataigné",
"Gabrielle",
"",
"CRIStAL, BONSAI"
],
[
"Béchet",
"Max",
"",
"C... | Burkholderia is an important genus encompassing a variety of species, including pathogenic strains as well as strains that promote plant growth. We have carried out a global strategy, which combined two complementary approaches. The first one is genome guided with deep analysis of genome sequences and the second one is... |
q-bio/0605013 | Kate Sugden Ms | K. E. P. Sugden, M. R. Evans, W. C. K. Poon, N. D. Read | A model of hyphal tip growth involving microtubule-based transport | 5 pages, 5 figures | Phys. Rev. E 75, 031909 (2007) | 10.1103/PhysRevE.75.031909 | null | q-bio.SC cond-mat.stat-mech | null | We propose a simple model for mass transport within a fungal hypha and its
subsequent growth. Inspired by the role of microtubule-transported vesicles, we
embody the internal dynamics of mass inside a hypha with mutually excluding
particles progressing stochastically along a growing one-dimensional lattice.
The conne... | [
{
"created": "Tue, 9 May 2006 10:46:42 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Mar 2007 16:08:06 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Sugden",
"K. E. P.",
""
],
[
"Evans",
"M. R.",
""
],
[
"Poon",
"W. C. K.",
""
],
[
"Read",
"N. D.",
""
]
] | We propose a simple model for mass transport within a fungal hypha and its subsequent growth. Inspired by the role of microtubule-transported vesicles, we embody the internal dynamics of mass inside a hypha with mutually excluding particles progressing stochastically along a growing one-dimensional lattice. The connect... |
1310.0507 | Sepehr Ehsani | Sepehr Ehsani | Correlative-causative structures and the 'pericause': an analysis of
causation and a model based on cellular biology | 7 pages, 4 figures | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The advent of molecular biology has led to the identification of definitive
causative factors for a number of diseases, most of which are monogenic. Causes
for most common diseases across the population, however, seem elusive and
cannot be pinpointed to a limited number of genes or genetic pathways. This
realization ... | [
{
"created": "Tue, 1 Oct 2013 22:22:02 GMT",
"version": "v1"
}
] | 2013-10-03 | [
[
"Ehsani",
"Sepehr",
""
]
] | The advent of molecular biology has led to the identification of definitive causative factors for a number of diseases, most of which are monogenic. Causes for most common diseases across the population, however, seem elusive and cannot be pinpointed to a limited number of genes or genetic pathways. This realization ha... |
1712.08336 | Shankha Sanyal | Sayan Nag, Shankha Sanyal, Archi Banerjee, Ranjan Sengupta and Dipak
Ghosh | Music of Brain and Music on Brain: A Novel EEG Sonification approach | 6 pages, 4 figures; Presented in the International Symposium on
Frontiers of Research in speech and Music (FRSM)-2017, held at NIT, Rourkela
in 15-16 December 2017 | null | null | null | q-bio.NC cs.SD eess.AS physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Can we hear the sound of our brain? Is there any technique which can enable
us to hear the neuro-electrical impulses originating from the different lobes
of brain? The answer to all these questions is YES. In this paper we present a
novel method with which we can sonify the Electroencephalogram (EEG) data
recorded in... | [
{
"created": "Fri, 22 Dec 2017 08:30:47 GMT",
"version": "v1"
}
] | 2017-12-25 | [
[
"Nag",
"Sayan",
""
],
[
"Sanyal",
"Shankha",
""
],
[
"Banerjee",
"Archi",
""
],
[
"Sengupta",
"Ranjan",
""
],
[
"Ghosh",
"Dipak",
""
]
] | Can we hear the sound of our brain? Is there any technique which can enable us to hear the neuro-electrical impulses originating from the different lobes of brain? The answer to all these questions is YES. In this paper we present a novel method with which we can sonify the Electroencephalogram (EEG) data recorded in r... |
1905.10834 | Neil Oxtoby | Neil P. Oxtoby, Fabio S. Ferreira, Agoston Mihalik, Tong Wu, Mikael
Brudfors, Hongxiang Lin, Anita Rau, Stefano B. Blumberg, Maria Robu, Cemre
Zor, Maira Tariq, Maria Del Mar Estarellas Garcia, Baris Kanber, Daniil I.
Nikitichev, Janaina Mourao-Miranda | ABCD Neurocognitive Prediction Challenge 2019: Predicting individual
residual fluid intelligence scores from cortical grey matter morphology | 8 pages plus references, 3 figures, 2 tables. Submission to the ABCD
Neurocognitive Prediction Challenge at MICCAI 2019 | null | null | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We predicted residual fluid intelligence scores from T1-weighted MRI data
available as part of the ABCD NP Challenge 2019, using morphological similarity
of grey-matter regions across the cortex. Individual structural covariance
networks (SCN) were abstracted into graph-theory metrics averaged over nodes
across the b... | [
{
"created": "Sun, 26 May 2019 16:38:28 GMT",
"version": "v1"
}
] | 2019-05-28 | [
[
"Oxtoby",
"Neil P.",
""
],
[
"Ferreira",
"Fabio S.",
""
],
[
"Mihalik",
"Agoston",
""
],
[
"Wu",
"Tong",
""
],
[
"Brudfors",
"Mikael",
""
],
[
"Lin",
"Hongxiang",
""
],
[
"Rau",
"Anita",
""
],
[
"Bl... | We predicted residual fluid intelligence scores from T1-weighted MRI data available as part of the ABCD NP Challenge 2019, using morphological similarity of grey-matter regions across the cortex. Individual structural covariance networks (SCN) were abstracted into graph-theory metrics averaged over nodes across the bra... |
1705.08324 | Helen Liedtke | H.Liedtke, A.T. McBride, S. Sivarasu, S. Roche | Computational simulation of bone remodelling post reverse total shoulder
arthroplasty | null | null | null | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bone is a living material. It adapts, in an optimal sense, to loading by
changing its density and trabeculae architecture - a process termed
remodelling. Implanted orthopaedic devices can significantly alter the loading
on the surrounding bone, which can have a detrimental impact on bone ingrowth
that is critical to ... | [
{
"created": "Tue, 11 Apr 2017 09:38:15 GMT",
"version": "v1"
}
] | 2017-05-24 | [
[
"Liedtke",
"H.",
""
],
[
"McBride",
"A. T.",
""
],
[
"Sivarasu",
"S.",
""
],
[
"Roche",
"S.",
""
]
] | Bone is a living material. It adapts, in an optimal sense, to loading by changing its density and trabeculae architecture - a process termed remodelling. Implanted orthopaedic devices can significantly alter the loading on the surrounding bone, which can have a detrimental impact on bone ingrowth that is critical to en... |
2006.04176 | Zafeirios Fountas PhD | Zafeirios Fountas, Noor Sajid, Pedro A.M. Mediano, Karl Friston | Deep active inference agents using Monte-Carlo methods | To appear in NeurIPS 2020 | null | null | null | q-bio.NC cs.AI stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Active inference is a Bayesian framework for understanding biological
intelligence. The underlying theory brings together perception and action under
one single imperative: minimizing free energy. However, despite its theoretical
utility in explaining intelligence, computational implementations have been
restricted t... | [
{
"created": "Sun, 7 Jun 2020 15:10:42 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Oct 2020 13:17:36 GMT",
"version": "v2"
}
] | 2020-10-23 | [
[
"Fountas",
"Zafeirios",
""
],
[
"Sajid",
"Noor",
""
],
[
"Mediano",
"Pedro A. M.",
""
],
[
"Friston",
"Karl",
""
]
] | Active inference is a Bayesian framework for understanding biological intelligence. The underlying theory brings together perception and action under one single imperative: minimizing free energy. However, despite its theoretical utility in explaining intelligence, computational implementations have been restricted to ... |
2104.12708 | Juan Jim\'enez-S\'anchez | V\'ictor M. P\'erez-Garc\'ia, Gabriel F. Calvo, Jes\'us J. Bosque,
Odelaisy Le\'on-Triana, Juan Jim\'enez, Juli\'an P\'erez-Beteta, Juan
Belmonte-Beitia, Manuel Valiente, Luc\'ia Zhu, Pedro Garc\'ia-G\'omez, Pilar
S\'anchez-G\'omez, Esther Hern\'andez-San Miguel, Rafael Hortig\"uela,
Youness Azimzade, David Mol... | Universal scaling laws rule explosive growth inhuman cancers | null | Nat.Phys. 16 (2020) 1232-1237 | 10.1038/s41567-020-0978-6 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Most physical and other natural systems are complex entities composed of a
large number of interacting individual elements. It is a surprising fact that
they often obey the so-called scaling laws relating an observable quantity with
a measure of the size of the system. Here we describe the discovery of
universal supe... | [
{
"created": "Thu, 22 Apr 2021 09:49:47 GMT",
"version": "v1"
}
] | 2021-04-27 | [
[
"Pérez-García",
"Víctor M.",
""
],
[
"Calvo",
"Gabriel F.",
""
],
[
"Bosque",
"Jesús J.",
""
],
[
"León-Triana",
"Odelaisy",
""
],
[
"Jiménez",
"Juan",
""
],
[
"Pérez-Beteta",
"Julián",
""
],
[
"Belmonte-Beitia",
... | Most physical and other natural systems are complex entities composed of a large number of interacting individual elements. It is a surprising fact that they often obey the so-called scaling laws relating an observable quantity with a measure of the size of the system. Here we describe the discovery of universal superl... |
0802.1668 | Andrea Cavagna | Andrea Cavagna, Irene Giardina, Alberto Orlandi, Giorgio Parisi,
Andrea Procaccini, Massimiliano Viale, Vladimir Zdravkovic | The STARFLAG handbook on collective animal behaviour: Part I, empirical
methods | To be published in Animal Behaviour | Animal Behaviour 76 (1), 217-236 (2008) | null | null | q-bio.QM cond-mat.stat-mech q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The most startling examples of collective animal behaviour are provided by
very large and cohesive groups moving in three dimensions. Paradigmatic
examples are bird flocks, fish schools and insect swarms. However, because of
the sheer technical difficulty of obtaining 3D data, empirical studies
conducted to date have... | [
{
"created": "Tue, 12 Feb 2008 15:34:13 GMT",
"version": "v1"
}
] | 2014-10-10 | [
[
"Cavagna",
"Andrea",
""
],
[
"Giardina",
"Irene",
""
],
[
"Orlandi",
"Alberto",
""
],
[
"Parisi",
"Giorgio",
""
],
[
"Procaccini",
"Andrea",
""
],
[
"Viale",
"Massimiliano",
""
],
[
"Zdravkovic",
"Vladimir",
... | The most startling examples of collective animal behaviour are provided by very large and cohesive groups moving in three dimensions. Paradigmatic examples are bird flocks, fish schools and insect swarms. However, because of the sheer technical difficulty of obtaining 3D data, empirical studies conducted to date have o... |
1306.2605 | Sayak Mukherjee | Sayak Mukherjee, Sang-Cheol Seok, Veronica J. Vieland, and Jayajit Das | Cell responses only partially shape cell-to-cell variations in protein
abundances in Escherichia coli chemotaxis | 51 Pages, 18 Figures | PNAS epub, October 28, 2013 | 10.1073/pnas.1311069110 | null | q-bio.CB cond-mat.stat-mech q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cell-to-cell variations in protein abundance in clonal cell populations are
ubiquitous in living systems. Since protein composition determines responses in
individual cells, it stands to reason that the variations themselves are
subject to selective pressures. But the functional role of these cell-to-cell
differences... | [
{
"created": "Tue, 11 Jun 2013 18:36:34 GMT",
"version": "v1"
},
{
"created": "Tue, 29 Oct 2013 20:23:18 GMT",
"version": "v2"
}
] | 2013-11-01 | [
[
"Mukherjee",
"Sayak",
""
],
[
"Seok",
"Sang-Cheol",
""
],
[
"Vieland",
"Veronica J.",
""
],
[
"Das",
"Jayajit",
""
]
] | Cell-to-cell variations in protein abundance in clonal cell populations are ubiquitous in living systems. Since protein composition determines responses in individual cells, it stands to reason that the variations themselves are subject to selective pressures. But the functional role of these cell-to-cell differences i... |
1907.13549 | Eugenio Buzzoni | Jochen Blath, Eugenio Buzzoni, Jere Koskela and Maite Wilke Berenguer | Statistical tools for seed bank detection | 33 pages, 25 figures | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this article, we derive statistical tools to analyze and distinguish the
patterns of genetic variability produced by classical and recent population
genetic models related to seed banks. In particular, we are concerned with
models described by the Kingman coalescent (K), models exhibiting so-called
weak seed banks... | [
{
"created": "Wed, 31 Jul 2019 15:16:48 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Sep 2019 14:00:02 GMT",
"version": "v2"
},
{
"created": "Thu, 9 Jan 2020 17:29:22 GMT",
"version": "v3"
}
] | 2020-01-10 | [
[
"Blath",
"Jochen",
""
],
[
"Buzzoni",
"Eugenio",
""
],
[
"Koskela",
"Jere",
""
],
[
"Berenguer",
"Maite Wilke",
""
]
] | In this article, we derive statistical tools to analyze and distinguish the patterns of genetic variability produced by classical and recent population genetic models related to seed banks. In particular, we are concerned with models described by the Kingman coalescent (K), models exhibiting so-called weak seed banks d... |
2203.07211 | Jong Woo Kim | Jong Woo Kim, Niels Krausch, Judit Aizpuru, Tilman Barz, Sergio Lucia,
Peter Neubauer, Mariano Nicolas Cruz Bournazou | Model predictive control and moving horizon estimation for adaptive
optimal bolus feeding in high-throughput cultivation of \textit{E. coli} | null | null | null | null | q-bio.QM cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We discuss the application of a nonlinear model predictive control (MPC) and
a moving horizon estimation (MHE) to achieve an optimal operation of \textit{E.
coli} fed-batch cultivations with intermittent bolus feeding. 24 parallel
experiments were considered in a high-throughput microbioreactor platform at a
10 mL sc... | [
{
"created": "Mon, 14 Mar 2022 15:53:11 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Feb 2023 05:40:43 GMT",
"version": "v2"
}
] | 2023-02-07 | [
[
"Kim",
"Jong Woo",
""
],
[
"Krausch",
"Niels",
""
],
[
"Aizpuru",
"Judit",
""
],
[
"Barz",
"Tilman",
""
],
[
"Lucia",
"Sergio",
""
],
[
"Neubauer",
"Peter",
""
],
[
"Bournazou",
"Mariano Nicolas Cruz",
""
... | We discuss the application of a nonlinear model predictive control (MPC) and a moving horizon estimation (MHE) to achieve an optimal operation of \textit{E. coli} fed-batch cultivations with intermittent bolus feeding. 24 parallel experiments were considered in a high-throughput microbioreactor platform at a 10 mL scal... |
q-bio/0401028 | Thomas Petermann | Thomas Petermann and Paolo De Los Rios | Cluster approximations for probabilistic systems: a new perspective of
epidemiological modelling | Submitted to J. Theor. Biol; 11 pages, 12 figures | J. Theor. Biol. 229, 1 (2004). | 10.1016/j.jtbi.2004.02.017 | null | q-bio.PE cond-mat.stat-mech q-bio.QM | null | Especially in lattice structured populations, homogeneous mixing represents
an inadequate assumption. Various improvements upon the ordinary pair
approximation based on a number of assumptions concerning the higher-order
correlations have been proposed. To find approaches that allow for a derivation
of their dynamics... | [
{
"created": "Wed, 21 Jan 2004 20:18:22 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Petermann",
"Thomas",
""
],
[
"Rios",
"Paolo De Los",
""
]
] | Especially in lattice structured populations, homogeneous mixing represents an inadequate assumption. Various improvements upon the ordinary pair approximation based on a number of assumptions concerning the higher-order correlations have been proposed. To find approaches that allow for a derivation of their dynamics r... |
1502.06900 | Brian Wandell | B. A. Wandell, A. Rokem, L. M. Perry, G. Schaefer, R. F. Dougherty | Data management to support reproducible research | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We describe the current state and future plans for a set of tools for
scientific data management (SDM) designed to support scientific transparency
and reproducible research. SDM has been in active use at our MRI Center for
more than two years. We designed the system to be used from the beginning of a
research project... | [
{
"created": "Sat, 21 Feb 2015 06:00:04 GMT",
"version": "v1"
}
] | 2015-02-25 | [
[
"Wandell",
"B. A.",
""
],
[
"Rokem",
"A.",
""
],
[
"Perry",
"L. M.",
""
],
[
"Schaefer",
"G.",
""
],
[
"Dougherty",
"R. F.",
""
]
] | We describe the current state and future plans for a set of tools for scientific data management (SDM) designed to support scientific transparency and reproducible research. SDM has been in active use at our MRI Center for more than two years. We designed the system to be used from the beginning of a research project, ... |
q-bio/0406034 | J. F. R. Archilla | D. Hennig, J. F. R. Archilla, and J. M. Romero | Modeling the thermal evolution of enzyme-created bubbles in DNA | 19 pages, 7 figures | Interface, 2(2):89-95, 2005 | 10.1098/rsif.2004.0024 | null | q-bio.BM nlin.PS | null | The formation of bubbles in nucleic acids (NAs) are fundamental in many
biological processes such as DNA replication, recombination, telomeres
formation, nucleotide excision repair, as well as RNA transcription and
splicing. These precesses are carried out by assembled complexes with enzymes
that separate selected re... | [
{
"created": "Wed, 16 Jun 2004 17:25:31 GMT",
"version": "v1"
},
{
"created": "Sat, 4 Dec 2004 01:21:40 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Hennig",
"D.",
""
],
[
"Archilla",
"J. F. R.",
""
],
[
"Romero",
"J. M.",
""
]
] | The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses are carried out by assembled complexes with enzymes that separate selected regi... |
2102.00836 | Eugene Terentjev M. | Neil Ibata and Eugene M. Terentjev | Why exercise builds muscles: Titin mechanosensing controls skeletal
muscle growth under load | null | null | 10.1016/j.bpj.2021.07.023 | null | q-bio.TO physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Muscles sense internally generated and externally applied forces, responding
to these in a coordinated hierarchical manner at different time scales. The
center of the basic unit of the muscle, the sarcomeric M-band, is perfectly
placed to sense the different types of load to which the muscle is subjected.
In particul... | [
{
"created": "Mon, 1 Feb 2021 13:49:33 GMT",
"version": "v1"
},
{
"created": "Wed, 5 May 2021 12:20:27 GMT",
"version": "v2"
}
] | 2021-09-22 | [
[
"Ibata",
"Neil",
""
],
[
"Terentjev",
"Eugene M.",
""
]
] | Muscles sense internally generated and externally applied forces, responding to these in a coordinated hierarchical manner at different time scales. The center of the basic unit of the muscle, the sarcomeric M-band, is perfectly placed to sense the different types of load to which the muscle is subjected. In particular... |
2112.13044 | Jessica Rogge | Mark R Baker, Elizabeth L Hawthorne, Jessica R Rogge | COVID 19: Open source model for rapid reduction of R to below 1 in high
R0 scenarios | 10 pages, 6 figures, in English | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present an open source model that allows quantitative prediction of the
effects of testing on the rate of spread of COVID-19 described by R, the
reproduction number, and on the degree of quarantine, isolation and lockdown
required to limit it. The paper uses the model to quantify the outcomes of
different test typ... | [
{
"created": "Fri, 24 Dec 2021 12:09:37 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Jan 2022 15:54:55 GMT",
"version": "v2"
},
{
"created": "Fri, 28 Jan 2022 17:32:38 GMT",
"version": "v3"
}
] | 2022-01-31 | [
[
"Baker",
"Mark R",
""
],
[
"Hawthorne",
"Elizabeth L",
""
],
[
"Rogge",
"Jessica R",
""
]
] | We present an open source model that allows quantitative prediction of the effects of testing on the rate of spread of COVID-19 described by R, the reproduction number, and on the degree of quarantine, isolation and lockdown required to limit it. The paper uses the model to quantify the outcomes of different test types... |
1602.05558 | Hyun Youk | Th\'eo Maire, Hyun Youk | Molecular-level tuning of cellular autonomy controls the collective
behaviors of cell populations | 75 pages in total, includes main text, graphical abstract, 5 main
figures, supplementary information, and 10 supplementary figures | Cell Systems 1:349-360 (November 2015) | 10.1016/j.cels.2015.10.012 | null | q-bio.MN nlin.CG nlin.PS physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A rigorous understanding of how multicellular behaviors arise from the
actions of single cells requires quantitative frameworks that bridge the gap
between genetic circuits, the arrangement of cells in space, and
population-level behaviors. Here, we provide such a framework for a ubiquitous
class of multicellular sys... | [
{
"created": "Wed, 17 Feb 2016 20:11:35 GMT",
"version": "v1"
}
] | 2016-02-18 | [
[
"Maire",
"Théo",
""
],
[
"Youk",
"Hyun",
""
]
] | A rigorous understanding of how multicellular behaviors arise from the actions of single cells requires quantitative frameworks that bridge the gap between genetic circuits, the arrangement of cells in space, and population-level behaviors. Here, we provide such a framework for a ubiquitous class of multicellular syste... |
2011.04738 | Jann-Long Chern | Bo-Cyuan Lin, Yen-Jia Chen, Yi-Cheng Hung, Chun-sheng Chen, Han-Chun
Wang and Jann-Long Chern | The Data Forecast in COVID-19 Model with Applications to US, South
Korea, Brazil, India, Russia and Italy | 15 Pages, 19 fugures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we firstly propose SQIARD and SIARD models to investigate the
transmission of COVID-19 with quarantine, infected and asymptomatic infected,
and discuss the relation between the respective basic reproduction number $R_0,
R_Q$ and the stability of the equilibrium points of model. Secondly, after
training... | [
{
"created": "Thu, 5 Nov 2020 14:41:04 GMT",
"version": "v1"
},
{
"created": "Sun, 13 Jun 2021 09:20:56 GMT",
"version": "v2"
}
] | 2021-06-15 | [
[
"Lin",
"Bo-Cyuan",
""
],
[
"Chen",
"Yen-Jia",
""
],
[
"Hung",
"Yi-Cheng",
""
],
[
"Chen",
"Chun-sheng",
""
],
[
"Wang",
"Han-Chun",
""
],
[
"Chern",
"Jann-Long",
""
]
] | In this paper, we firstly propose SQIARD and SIARD models to investigate the transmission of COVID-19 with quarantine, infected and asymptomatic infected, and discuss the relation between the respective basic reproduction number $R_0, R_Q$ and the stability of the equilibrium points of model. Secondly, after training t... |
1907.06171 | Kelin Xia | D Vijay Anand, Kelin Xia, Yuguang Mu | Weighted persistent homology for osmolyte molecular aggregation and
hydrogen-bonding network analysis | 19 pages,9 figures | null | null | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has long been observed that trimethylamin N-oxide (TMAO) and urea
demonstrate dramatically different properties in a protein folding process.
Even with the enormous theoretical and experimental research work of the two
osmolytes, various aspects of their underlying mechanisms still remain largely
elusive. In this ... | [
{
"created": "Sun, 14 Jul 2019 06:04:39 GMT",
"version": "v1"
}
] | 2019-07-16 | [
[
"Anand",
"D Vijay",
""
],
[
"Xia",
"Kelin",
""
],
[
"Mu",
"Yuguang",
""
]
] | It has long been observed that trimethylamin N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work of the two osmolytes, various aspects of their underlying mechanisms still remain largely elusive. In this pa... |
q-bio/0311016 | Rom\`an R. Zapatrin | Christopher Altman, Jaroslaw Pykacz, Roman Zapatrin | Superpositional Quantum Network Topologies | 10 pages, LaTeX2e | International Journal of Theoretical Physics, 43, 2029-2040 (2004) | 10.1023/B:IJTP.0000049008.51567.ec | null | q-bio.NC quant-ph | null | We introduce superposition-based quantum networks composed of (i) the
classical perceptron model of multilayered, feedforward neural networks and
(ii) the algebraic model of evolving reticular quantum structures as described
in quantum gravity. The main feature of this model is moving from particular
neural topologie... | [
{
"created": "Wed, 12 Nov 2003 10:37:32 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Mar 2004 11:46:59 GMT",
"version": "v2"
},
{
"created": "Fri, 30 Jul 2004 10:48:14 GMT",
"version": "v3"
}
] | 2009-11-10 | [
[
"Altman",
"Christopher",
""
],
[
"Pykacz",
"Jaroslaw",
""
],
[
"Zapatrin",
"Roman",
""
]
] | We introduce superposition-based quantum networks composed of (i) the classical perceptron model of multilayered, feedforward neural networks and (ii) the algebraic model of evolving reticular quantum structures as described in quantum gravity. The main feature of this model is moving from particular neural topologies ... |
1010.3537 | Moritz Deger | Moritz Helias, Moritz Deger, Stefan Rotter, Markus Diesmann | The perfect integrator driven by Poisson input and its approximation in
the diffusion limit | 7 pages, 3 figures, v2: corrected authors in reference | null | 10.3389/fnins.2011.00019 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this note we consider the perfect integrator driven by Poisson process
input. We derive its equilibrium and response properties and contrast them to
the approximations obtained by applying the diffusion approximation. In
particular, the probability density in the vicinity of the threshold differs,
which leads to a... | [
{
"created": "Mon, 18 Oct 2010 09:57:29 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Nov 2010 11:18:59 GMT",
"version": "v2"
}
] | 2022-05-18 | [
[
"Helias",
"Moritz",
""
],
[
"Deger",
"Moritz",
""
],
[
"Rotter",
"Stefan",
""
],
[
"Diesmann",
"Markus",
""
]
] | In this note we consider the perfect integrator driven by Poisson process input. We derive its equilibrium and response properties and contrast them to the approximations obtained by applying the diffusion approximation. In particular, the probability density in the vicinity of the threshold differs, which leads to alt... |
2006.06826 | Ian Leifer | Flaviano Morone, Ian Leifer, Hernan A. Makse | Fibration symmetries uncover the building blocks of biological networks | null | Proc Natl Acad Sci USA. 2020;117(15):83068314 | 10.1073/pnas.1914628117 | null | q-bio.MN physics.data-an q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A major ambition of systems science is to uncover the building blocks of any
biological network to decipher how cellular function emerges from their
interactions. Here, we introduce a graph representation of the information flow
in these networks as a set of input trees, one for each node, which contains
all pathways... | [
{
"created": "Wed, 10 Jun 2020 17:05:25 GMT",
"version": "v1"
}
] | 2020-06-15 | [
[
"Morone",
"Flaviano",
""
],
[
"Leifer",
"Ian",
""
],
[
"Makse",
"Hernan A.",
""
]
] | A major ambition of systems science is to uncover the building blocks of any biological network to decipher how cellular function emerges from their interactions. Here, we introduce a graph representation of the information flow in these networks as a set of input trees, one for each node, which contains all pathways a... |
q-bio/0408011 | Steven N. Evans | Steven N. Evans and Tandy Warnow | Unidentifiable divergence times in rates-across-sites models | 13 pages, update to include referee's comments, to appear in IEEE/ACM
Transactions on Computational Biology and Bioinformatics | null | null | U.C. Berkeley Department of Statistics Technical Report #668 | q-bio.PE q-bio.GN | null | The rates-across-sites assumption in phylogenetic inference posits that the
rate matrix governing the Markovian evolution of a character on an edge of the
putative phylogenetic tree is the product of a character-specific scale factor
and a rate matrix that is particular to that edge. Thus, evolution follows
basically... | [
{
"created": "Sun, 15 Aug 2004 20:19:37 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Nov 2004 14:20:24 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Evans",
"Steven N.",
""
],
[
"Warnow",
"Tandy",
""
]
] | The rates-across-sites assumption in phylogenetic inference posits that the rate matrix governing the Markovian evolution of a character on an edge of the putative phylogenetic tree is the product of a character-specific scale factor and a rate matrix that is particular to that edge. Thus, evolution follows basically t... |
2111.02930 | Markus Fleck | Markus Fleck and Noah Weber and Christopher Trummer | Decoupled coordinates for machine learning-based molecular fragment
linking | 16 pages, 5 Figures | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Recent developments in machine-learning based molecular fragment linking have
demonstrated the importance of informing the generation process with structural
information specifying the relative orientation of the fragments to be linked.
However, such structural information has not yet been provided in the form of a
c... | [
{
"created": "Mon, 1 Nov 2021 17:39:23 GMT",
"version": "v1"
}
] | 2021-11-05 | [
[
"Fleck",
"Markus",
""
],
[
"Weber",
"Noah",
""
],
[
"Trummer",
"Christopher",
""
]
] | Recent developments in machine-learning based molecular fragment linking have demonstrated the importance of informing the generation process with structural information specifying the relative orientation of the fragments to be linked. However, such structural information has not yet been provided in the form of a com... |
2111.14964 | Tatiana Yakushkina S. | Igor Samokhin, Tatiana Yakushkina, Dmitry Markin, Alexander S. Bratus | Fitness landscape adaptation in open replicator systems with
competition: application to cancer therapy | null | null | null | null | q-bio.PE cs.NA math.DS math.NA | http://creativecommons.org/licenses/by/4.0/ | This study focuses on open quasispecies systems with competition and death
flow, described by modified Eigen and Crow-Kimura models. We examine the
evolutionary adaptation process as a reaction to changes in rates. One of the
fundamental assumptions, which forms the basis of our mathematical model, is
the existence o... | [
{
"created": "Mon, 29 Nov 2021 21:17:49 GMT",
"version": "v1"
}
] | 2021-12-01 | [
[
"Samokhin",
"Igor",
""
],
[
"Yakushkina",
"Tatiana",
""
],
[
"Markin",
"Dmitry",
""
],
[
"Bratus",
"Alexander S.",
""
]
] | This study focuses on open quasispecies systems with competition and death flow, described by modified Eigen and Crow-Kimura models. We examine the evolutionary adaptation process as a reaction to changes in rates. One of the fundamental assumptions, which forms the basis of our mathematical model, is the existence of ... |
1303.0882 | Jeffrey Ross-Ibarra | David M. Wills, Clinton Whipple, Shohei Takuno, Lisa E. Kursel, Laura
M. Shannon, Jeffrey Ross-Ibarra, John F. Doebley | From Many, One: Genetic Control of Prolificacy during Maize
Domestication | null | PLoS Genetics 2013 9(6): e1003604 | 10.1371/journal.pgen.1003604 | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A reduction in number and an increase in size of inflorescences is a common
aspect of plant domestication. When maize was domesticated from teosinte, the
number and arrangement of ears changed dramatically. Teosinte has long lateral
branches that bear multiple small ears at their nodes and tassels at their
tips. Maiz... | [
{
"created": "Mon, 4 Mar 2013 22:35:20 GMT",
"version": "v1"
}
] | 2013-07-30 | [
[
"Wills",
"David M.",
""
],
[
"Whipple",
"Clinton",
""
],
[
"Takuno",
"Shohei",
""
],
[
"Kursel",
"Lisa E.",
""
],
[
"Shannon",
"Laura M.",
""
],
[
"Ross-Ibarra",
"Jeffrey",
""
],
[
"Doebley",
"John F.",
""
... | A reduction in number and an increase in size of inflorescences is a common aspect of plant domestication. When maize was domesticated from teosinte, the number and arrangement of ears changed dramatically. Teosinte has long lateral branches that bear multiple small ears at their nodes and tassels at their tips. Maize ... |
1706.07091 | Andrei D. Robu | Andrei D. Robu, Christoph Salge, Chrystopher L. Nehaniv and Daniel
Polani | Time as it could Be measured in Artificial Living Systems | Accepted at the European Conference on Artificial Life 2017, Lyon,
France | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Being able to measure time, whether directly or indirectly, is a significant
advantage for an organism. It permits it to predict regular events, and prepare
for them on time. Thus, clocks are ubiquitous in biology. In the present paper,
we consider the most minimal abstract pure clocks and investigate their
character... | [
{
"created": "Tue, 20 Jun 2017 15:55:47 GMT",
"version": "v1"
}
] | 2017-06-23 | [
[
"Robu",
"Andrei D.",
""
],
[
"Salge",
"Christoph",
""
],
[
"Nehaniv",
"Chrystopher L.",
""
],
[
"Polani",
"Daniel",
""
]
] | Being able to measure time, whether directly or indirectly, is a significant advantage for an organism. It permits it to predict regular events, and prepare for them on time. Thus, clocks are ubiquitous in biology. In the present paper, we consider the most minimal abstract pure clocks and investigate their characteris... |
1608.02027 | Nikolaus Kriegeskorte | Nikolaus Kriegeskorte, J\"orn Diedrichsen | Inferring brain-computational mechanisms with models of activity
measurements | 25 pages, 9 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | High-resolution functional imaging is providing increasingly rich
measurements of brain activity in animals and humans. A major challenge is to
leverage such data to gain insight into the brain's computational mechanisms.
The first step is to define candidate brain-computational models (BCMs) that
can perform the beh... | [
{
"created": "Fri, 5 Aug 2016 21:38:37 GMT",
"version": "v1"
}
] | 2016-08-09 | [
[
"Kriegeskorte",
"Nikolaus",
""
],
[
"Diedrichsen",
"Jörn",
""
]
] | High-resolution functional imaging is providing increasingly rich measurements of brain activity in animals and humans. A major challenge is to leverage such data to gain insight into the brain's computational mechanisms. The first step is to define candidate brain-computational models (BCMs) that can perform the behav... |
1704.00497 | Taoyang Wu | Vincent Moulton and Andreas Spillner and Taoyang Wu | UPGMA and the normalized equidistant minimum evolution problem | 29 pages, 8 figures | null | null | null | q-bio.PE cs.CC cs.DM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a widely used
clustering method. Here we show that UPGMA is a greedy heuristic for the
normalized equidistant minimum evolution (NEME) problem, that is, finding a
rooted tree that minimizes the minimum evolution score relative to the
dissimilarity matrix am... | [
{
"created": "Mon, 3 Apr 2017 09:38:33 GMT",
"version": "v1"
}
] | 2017-04-04 | [
[
"Moulton",
"Vincent",
""
],
[
"Spillner",
"Andreas",
""
],
[
"Wu",
"Taoyang",
""
]
] | UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a widely used clustering method. Here we show that UPGMA is a greedy heuristic for the normalized equidistant minimum evolution (NEME) problem, that is, finding a rooted tree that minimizes the minimum evolution score relative to the dissimilarity matrix amon... |
1906.09861 | Andrea De Martino | Jonathan Fiorentino, Andrea De Martino | Independent channels for miRNA biosynthesis ensure efficient static and
dynamic control in the regulation of the early stages of myogenesis | 16+eps pages | null | 10.1016/j.jtbi.2017.06.038 | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivated by recent experimental work, we define and study a deterministic
model of the complex miRNA-based regulatory circuit that putatively controls
the early stage of myogenesis in human. We aim in particular at a quantitative
understanding of (i) the roles played by the separate and independent miRNA
biosynthesi... | [
{
"created": "Mon, 24 Jun 2019 11:35:37 GMT",
"version": "v1"
}
] | 2019-06-25 | [
[
"Fiorentino",
"Jonathan",
""
],
[
"De Martino",
"Andrea",
""
]
] | Motivated by recent experimental work, we define and study a deterministic model of the complex miRNA-based regulatory circuit that putatively controls the early stage of myogenesis in human. We aim in particular at a quantitative understanding of (i) the roles played by the separate and independent miRNA biosynthesis ... |
1507.08269 | Lianchun Yu | Lianchun Yu, Longfei Wang, Fei Jia, Duojie Jia | Stimulus-Dependent Frequency Modulation of Information Transmission in
Neural Systems | 15 pages, 8 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural oscillations are universal phenomena and can be observed at different
levels of neural systems, from single neuron to macroscopic brain. The
frequency of those oscillations are related to the brain functions. However,
little is know about how the oscillating frequency of neural system affects
neural informatio... | [
{
"created": "Fri, 13 Feb 2015 07:02:48 GMT",
"version": "v1"
}
] | 2015-07-30 | [
[
"Yu",
"Lianchun",
""
],
[
"Wang",
"Longfei",
""
],
[
"Jia",
"Fei",
""
],
[
"Jia",
"Duojie",
""
]
] | Neural oscillations are universal phenomena and can be observed at different levels of neural systems, from single neuron to macroscopic brain. The frequency of those oscillations are related to the brain functions. However, little is know about how the oscillating frequency of neural system affects neural information ... |
q-bio/0511005 | Hong Qian | Hong Qian (Univ. of Washington) and Daniel A. Beard (Medical Collge of
Wisconsin) | Metabolic Futile Cycles and Their Functions: A Systems Analysis of
Energy and Control | 11 pages, 5 figures | IEE Proceedings - Systems Biology , Vol. 153, pp. 192-200 (2006) | 10.1049/ip-syb:20050086 | null | q-bio.SC q-bio.MN | null | It has long been hypothesized that futile cycles in cellular metabolism are
involved in the regulation of biochemical pathways. Following the work of
Newsholme and Crabtree, we develop a quantitative theory for this idea based on
open-system thermodynamics and metabolic control analysis. It is shown that the
{\it sto... | [
{
"created": "Fri, 4 Nov 2005 07:18:16 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Jun 2006 19:40:10 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Qian",
"Hong",
"",
"Univ. of Washington"
],
[
"Beard",
"Daniel A.",
"",
"Medical Collge of\n Wisconsin"
]
] | It has long been hypothesized that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, we develop a quantitative theory for this idea based on open-system thermodynamics and metabolic control analysis. It is shown that the {\it stoic... |
2003.12417 | Alessio Notari | Alessio Notari | Temperature dependence of COVID-19 transmission | 5 pages, 5 figures. Updated with improved analysis, leading to higher
significance. Analysis with extended dataset added | null | 10.1016/j.scitotenv.2020.144390 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The recent coronavirus pandemic follows in its early stages an almost
exponential growth, with the number of cases quite well fit in time by
$N(t)\propto e^{\alpha t}$, in many countries. We analyze the rate $\alpha$ for
each country, starting from a threshold of 30 total cases and using the next 12
days, capturing t... | [
{
"created": "Fri, 27 Mar 2020 13:47:43 GMT",
"version": "v1"
},
{
"created": "Tue, 31 Mar 2020 18:41:55 GMT",
"version": "v2"
},
{
"created": "Fri, 3 Apr 2020 15:20:22 GMT",
"version": "v3"
},
{
"created": "Wed, 22 Apr 2020 22:15:04 GMT",
"version": "v4"
}
] | 2020-12-22 | [
[
"Notari",
"Alessio",
""
]
] | The recent coronavirus pandemic follows in its early stages an almost exponential growth, with the number of cases quite well fit in time by $N(t)\propto e^{\alpha t}$, in many countries. We analyze the rate $\alpha$ for each country, starting from a threshold of 30 total cases and using the next 12 days, capturing thu... |
2306.10373 | Hina Shaheen | Hina Shaheen, Roderick Melnik, Sundeep Singh | Data-driven Stochastic Model for Quantifying the Interplay Between
Amyloid-beta and Calcium Levels in Alzheimer's Disease | 20 pages, 6 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The abnormal aggregation of extracellular amyloid-$\beta$ (A\beta) in senile
plaques resulting in calcium (Ca^{+2}) dyshomeostasis is one of the primary
symptoms of Alzheimer's disease (AD). Significant research efforts have been
devoted in the past to better understand the underlying molecular mechanisms
driving A\b... | [
{
"created": "Sat, 17 Jun 2023 15:13:38 GMT",
"version": "v1"
}
] | 2023-06-21 | [
[
"Shaheen",
"Hina",
""
],
[
"Melnik",
"Roderick",
""
],
[
"Singh",
"Sundeep",
""
]
] | The abnormal aggregation of extracellular amyloid-$\beta$ (A\beta) in senile plaques resulting in calcium (Ca^{+2}) dyshomeostasis is one of the primary symptoms of Alzheimer's disease (AD). Significant research efforts have been devoted in the past to better understand the underlying molecular mechanisms driving A\bet... |
1108.5657 | Vasily Ogryzko V | Arman Kulyyassov, Muhammad Shoaib, Andrei Pichugin, Patricia
Kannouche, Erlan Ramanculov, Marc Lipinski and Vasily Ogryzko | PUB-MS - a mass-spectrometry-based method to monitor protein-protein
proximity in vivo | 46 pages, 5 main Figures and 7 supplementary Figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The common techniques to study protein-protein proximity in vivo are not
well-adapted to the capabilities and the expertise of a standard proteomics
laboratory, typically based on the use of mass spectrometry. With the aim of
closing this gap, we have developed PUB-MS (for Proximity Utilizing
Biotinylation and Mass S... | [
{
"created": "Mon, 29 Aug 2011 17:10:27 GMT",
"version": "v1"
}
] | 2011-08-30 | [
[
"Kulyyassov",
"Arman",
""
],
[
"Shoaib",
"Muhammad",
""
],
[
"Pichugin",
"Andrei",
""
],
[
"Kannouche",
"Patricia",
""
],
[
"Ramanculov",
"Erlan",
""
],
[
"Lipinski",
"Marc",
""
],
[
"Ogryzko",
"Vasily",
""... | The common techniques to study protein-protein proximity in vivo are not well-adapted to the capabilities and the expertise of a standard proteomics laboratory, typically based on the use of mass spectrometry. With the aim of closing this gap, we have developed PUB-MS (for Proximity Utilizing Biotinylation and Mass Spe... |
2202.00143 | Henry Cousins | Henry Cousins, Taryn Hall, Yinglong Guo, Luke Tso, Kathy Tzy-Hwa
Tzeng, Le Cong, Russ Altman | Gene set proximity analysis: expanding gene set enrichment analysis
through learned geometric embeddings | 21 pages, 6 figures | null | 10.1093/bioinformatics/btac735 | null | q-bio.QM q-bio.GN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Gene set analysis methods rely on knowledge-based representations of genetic
interactions in the form of both gene set collections and protein-protein
interaction (PPI) networks. Explicit representations of genetic interactions
often fail to capture complex interdependencies among genes, limiting the
analytic power o... | [
{
"created": "Mon, 31 Jan 2022 23:11:26 GMT",
"version": "v1"
}
] | 2023-02-23 | [
[
"Cousins",
"Henry",
""
],
[
"Hall",
"Taryn",
""
],
[
"Guo",
"Yinglong",
""
],
[
"Tso",
"Luke",
""
],
[
"Tzeng",
"Kathy Tzy-Hwa",
""
],
[
"Cong",
"Le",
""
],
[
"Altman",
"Russ",
""
]
] | Gene set analysis methods rely on knowledge-based representations of genetic interactions in the form of both gene set collections and protein-protein interaction (PPI) networks. Explicit representations of genetic interactions often fail to capture complex interdependencies among genes, limiting the analytic power of ... |
1506.01033 | Adam Marblestone | Samuel G Rodriques, Adam H Marblestone, Max Mankin, Lowell Wood and
Edward S Boyden | Multiplexed Neural Recording Down a Single Optical Fiber via Optical
Reflectometry with Capacitive Signal Enhancement | null | null | 10.1117/1.JBO.21.5.057003 | null | q-bio.NC physics.optics | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a fiber-optic architecture for neural recording without contrast
agents, and study its properties theoretically. Our sensor design is inspired
by electrooptic modulators, which modulate the refractive index of a waveguide
by applying an electric field across an electrooptic core material, and allows
reco... | [
{
"created": "Tue, 2 Jun 2015 20:05:05 GMT",
"version": "v1"
}
] | 2020-02-04 | [
[
"Rodriques",
"Samuel G",
""
],
[
"Marblestone",
"Adam H",
""
],
[
"Mankin",
"Max",
""
],
[
"Wood",
"Lowell",
""
],
[
"Boyden",
"Edward S",
""
]
] | We introduce a fiber-optic architecture for neural recording without contrast agents, and study its properties theoretically. Our sensor design is inspired by electrooptic modulators, which modulate the refractive index of a waveguide by applying an electric field across an electrooptic core material, and allows record... |
2202.11752 | Raju Hazari | Raju Hazari and P Pal Chaudhuri | Analysis of Coronavirus Envelope Protein with Cellular Automata (CA)
Model | null | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The reason of significantly higher transmissibility of SARS Covid (2019
CoV-2) compared to SARS Covid (2003 CoV) and MERS Covid (2012 MERS) can be
attributed to mutations reported in structural proteins, and the role played by
non-structural proteins (nsps) and accessory proteins (ORFs) for viral
replication, assembl... | [
{
"created": "Sat, 15 Jan 2022 19:07:18 GMT",
"version": "v1"
}
] | 2022-02-25 | [
[
"Hazari",
"Raju",
""
],
[
"Chaudhuri",
"P Pal",
""
]
] | The reason of significantly higher transmissibility of SARS Covid (2019 CoV-2) compared to SARS Covid (2003 CoV) and MERS Covid (2012 MERS) can be attributed to mutations reported in structural proteins, and the role played by non-structural proteins (nsps) and accessory proteins (ORFs) for viral replication, assembly,... |
1207.5289 | Pabitra Pal Choudhury | Sk. Sarif Hassan, Pabitra Pal Choudhury, Antara Sengupta, Binayak
Sahu, Rojalin Mishra, Devendra Kumar Yadav, Saswatee Panda, Dharamveer
Pradhan, Shrusti Dash and Gourav Pradhan | A Quantitative Understanding of Human Sex Chromosomal Genes | null | null | null | null | q-bio.GN q-bio.PE | http://creativecommons.org/licenses/by/3.0/ | In the last few decades, the human allosomes are engrossed in an intensive
attention among researchers. The allosomes are now already been sequenced and
found there are about 2000 and 78 genes in human X and Y chromosomes
respectively. The hemizygosity of the human X chromosome in males exposes
recessive disease alle... | [
{
"created": "Mon, 23 Jul 2012 04:20:23 GMT",
"version": "v1"
},
{
"created": "Mon, 2 Dec 2013 04:13:18 GMT",
"version": "v2"
}
] | 2013-12-03 | [
[
"Hassan",
"Sk. Sarif",
""
],
[
"Choudhury",
"Pabitra Pal",
""
],
[
"Sengupta",
"Antara",
""
],
[
"Sahu",
"Binayak",
""
],
[
"Mishra",
"Rojalin",
""
],
[
"Yadav",
"Devendra Kumar",
""
],
[
"Panda",
"Saswatee",
... | In the last few decades, the human allosomes are engrossed in an intensive attention among researchers. The allosomes are now already been sequenced and found there are about 2000 and 78 genes in human X and Y chromosomes respectively. The hemizygosity of the human X chromosome in males exposes recessive disease allele... |
1708.05774 | Daniel Kepple | Daniel Kepple and Alexei Koulakov | Constructing an olfactory perceptual space and predicting percepts from
molecular structure | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Given the structure of a novel molecule, there is still no one who can
reliably predict what odor percept that molecule will evoke. The challenge
comes from both the difficulty in quantitatively characterizing molecular
structure, and the inadequacy of language to fully characterize olfactory
perception. Here, we pre... | [
{
"created": "Fri, 18 Aug 2017 21:56:53 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Jun 2018 20:50:17 GMT",
"version": "v2"
}
] | 2018-06-08 | [
[
"Kepple",
"Daniel",
""
],
[
"Koulakov",
"Alexei",
""
]
] | Given the structure of a novel molecule, there is still no one who can reliably predict what odor percept that molecule will evoke. The challenge comes from both the difficulty in quantitatively characterizing molecular structure, and the inadequacy of language to fully characterize olfactory perception. Here, we prese... |
2307.05606 | Erdi Kara | Erdi Kara, T. L. Jackson, Chartese Jones, Reginald L. McGee II,
Rockford Sison | Mathematical Modeling Insights into Improving CAR T cell Therapy for
Solid Tumors: Antigen Heterogeneity and Bystander Effects | null | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | As an adoptive cellular therapy, Chimeric Antigen Receptor T-cell (CAR
T-cell) therapy has shown remarkable success in hematological malignancies, but
only limited efficacy against solid tumors. Compared with blood cancers, solid
tumors present a unique set of challenges that ultimately neutralize the
function of CAR... | [
{
"created": "Mon, 10 Jul 2023 21:35:39 GMT",
"version": "v1"
}
] | 2023-07-13 | [
[
"Kara",
"Erdi",
""
],
[
"Jackson",
"T. L.",
""
],
[
"Jones",
"Chartese",
""
],
[
"McGee",
"Reginald L.",
"II"
],
[
"Sison",
"Rockford",
""
]
] | As an adoptive cellular therapy, Chimeric Antigen Receptor T-cell (CAR T-cell) therapy has shown remarkable success in hematological malignancies, but only limited efficacy against solid tumors. Compared with blood cancers, solid tumors present a unique set of challenges that ultimately neutralize the function of CAR T... |
1903.04353 | Pedro Lind | Jo\~ao Sequeira, Jorge Lou\c{c}\~a, Ant\'onio M. Mendes and Pedro G.
Lind | Transition from endemic behavior to eradication of malaria due to
combined drug therapies: an agent-model approach | 12 pages, 6 figures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce an agent-based model describing a
susceptible-infectious-susceptible (SIS) system of humans and mosquitoes to
predict malaria epidemiological scenarios in realistic biological conditions.
Emphasis is given to the transition from endemic behavior to eradication of
malaria transmission induced by combined ... | [
{
"created": "Fri, 8 Mar 2019 10:59:18 GMT",
"version": "v1"
}
] | 2019-03-12 | [
[
"Sequeira",
"João",
""
],
[
"Louçã",
"Jorge",
""
],
[
"Mendes",
"António M.",
""
],
[
"Lind",
"Pedro G.",
""
]
] | We introduce an agent-based model describing a susceptible-infectious-susceptible (SIS) system of humans and mosquitoes to predict malaria epidemiological scenarios in realistic biological conditions. Emphasis is given to the transition from endemic behavior to eradication of malaria transmission induced by combined dr... |
1210.3809 | John Barton | John Barton, Eduardo D. Sontag | The energy costs of biological insulators | 16 pages, 5 figures | null | 10.1016/j.bpj.2013.01.056 | null | q-bio.MN q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biochemical signaling pathways can be insulated from impedance and
competition effects through enzymatic "futile cycles" which consume energy,
typically in the form of ATP. We hypothesize that better insulation necessarily
requires higher energy consumption, and provide evidence, through the
computational analysis of... | [
{
"created": "Sun, 14 Oct 2012 16:23:33 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Oct 2012 16:11:27 GMT",
"version": "v2"
}
] | 2014-05-06 | [
[
"Barton",
"John",
""
],
[
"Sontag",
"Eduardo D.",
""
]
] | Biochemical signaling pathways can be insulated from impedance and competition effects through enzymatic "futile cycles" which consume energy, typically in the form of ATP. We hypothesize that better insulation necessarily requires higher energy consumption, and provide evidence, through the computational analysis of a... |
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