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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
q-bio/0410032 | Paul van der Schoot | P. van der Schoot and R. Bruinsma | Electrostatics and the Assembly of an RNA Virus | 41 pages, 4 figures | null | 10.1103/PhysRevE.71.061928 | null | q-bio.BM q-bio.SC | null | Electrostatic interactions play a central role in the assembly of
single-stranded RNA viruses. Under physiological conditions of salinity and
acidity, virus capsid assembly requires the presence of genomic material that
is oppositely charged to the core proteins. In this paper we apply basic
polymer physics and stati... | [
{
"created": "Wed, 27 Oct 2004 20:02:04 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"van der Schoot",
"P.",
""
],
[
"Bruinsma",
"R.",
""
]
] | Electrostatic interactions play a central role in the assembly of single-stranded RNA viruses. Under physiological conditions of salinity and acidity, virus capsid assembly requires the presence of genomic material that is oppositely charged to the core proteins. In this paper we apply basic polymer physics and statist... |
2207.00584 | Siyuan Shan | Vishal Athreya Baskaran, Jolene Ranek, Siyuan Shan, Natalie Stanley,
Junier B. Oliva | Distribution-based Sketching of Single-Cell Samples | Accepted by ACM-BCB 2022 | null | 10.1145/3535508.3545539 | null | q-bio.QM cs.LG | http://creativecommons.org/publicdomain/zero/1.0/ | Modern high-throughput single-cell immune profiling technologies, such as
flow and mass cytometry and single-cell RNA sequencing can readily measure the
expression of a large number of protein or gene features across the millions of
cells in a multi-patient cohort. While bioinformatics approaches can be used to
link ... | [
{
"created": "Thu, 30 Jun 2022 19:43:06 GMT",
"version": "v1"
}
] | 2022-07-05 | [
[
"Baskaran",
"Vishal Athreya",
""
],
[
"Ranek",
"Jolene",
""
],
[
"Shan",
"Siyuan",
""
],
[
"Stanley",
"Natalie",
""
],
[
"Oliva",
"Junier B.",
""
]
] | Modern high-throughput single-cell immune profiling technologies, such as flow and mass cytometry and single-cell RNA sequencing can readily measure the expression of a large number of protein or gene features across the millions of cells in a multi-patient cohort. While bioinformatics approaches can be used to link im... |
2403.03234 | Yair Schiff | Yair Schiff, Chia-Hsiang Kao, Aaron Gokaslan, Tri Dao, Albert Gu, and
Volodymyr Kuleshov | Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling | ICML 2024; Code to reproduce our experiments is available at
https://github.com/kuleshov-group/caduceus | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by/4.0/ | Large-scale sequence modeling has sparked rapid advances that now extend into
biology and genomics. However, modeling genomic sequences introduces challenges
such as the need to model long-range token interactions, the effects of
upstream and downstream regions of the genome, and the reverse complementarity
(RC) of D... | [
{
"created": "Tue, 5 Mar 2024 01:42:51 GMT",
"version": "v1"
},
{
"created": "Wed, 5 Jun 2024 21:02:37 GMT",
"version": "v2"
}
] | 2024-06-07 | [
[
"Schiff",
"Yair",
""
],
[
"Kao",
"Chia-Hsiang",
""
],
[
"Gokaslan",
"Aaron",
""
],
[
"Dao",
"Tri",
""
],
[
"Gu",
"Albert",
""
],
[
"Kuleshov",
"Volodymyr",
""
]
] | Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA... |
1810.06844 | Kristina Wicke | Mareike Fischer and Michelle Galla and Lina Herbst and Yangjing Long
and Kristina Wicke | Classes of treebased networks | 45 pages, 26 figures | null | null | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, so-called treebased phylogenetic networks have gained considerable
interest in the literature, where a treebased network is a network that can be
constructed from a phylogenetic tree, called the base tree, by adding
additional edges. The main aim of this manuscript is to provide some sufficient
criteria for... | [
{
"created": "Tue, 16 Oct 2018 07:22:35 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Oct 2018 10:11:33 GMT",
"version": "v2"
},
{
"created": "Fri, 16 Aug 2019 14:03:08 GMT",
"version": "v3"
},
{
"created": "Wed, 27 Nov 2019 08:32:38 GMT",
"version": "v4"
}
] | 2019-11-28 | [
[
"Fischer",
"Mareike",
""
],
[
"Galla",
"Michelle",
""
],
[
"Herbst",
"Lina",
""
],
[
"Long",
"Yangjing",
""
],
[
"Wicke",
"Kristina",
""
]
] | Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional edges. The main aim of this manuscript is to provide some sufficient criteria for t... |
1703.05755 | Guillermo Abramson | Laila D. Kazimierski, Marcelo N. Kuperman, Horacio S. Wio and
Guillermo Abramson | Waves of seed propagation induced by delayed animal dispersion | Accepted in Journal of Theoretical Biology | null | 10.1016/j.jtbi.2017.09.030 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study a model of seed dispersal that considers the inclusion of an animal
disperser moving diffusively, feeding on fruits and transporting the seeds,
which are later deposited and capable of germination. The dynamics depends on
several population parameters of growth, decay, harvesting, transport,
digestion and ge... | [
{
"created": "Thu, 16 Mar 2017 17:56:39 GMT",
"version": "v1"
},
{
"created": "Mon, 2 Oct 2017 12:58:13 GMT",
"version": "v2"
}
] | 2017-10-03 | [
[
"Kazimierski",
"Laila D.",
""
],
[
"Kuperman",
"Marcelo N.",
""
],
[
"Wio",
"Horacio S.",
""
],
[
"Abramson",
"Guillermo",
""
]
] | We study a model of seed dispersal that considers the inclusion of an animal disperser moving diffusively, feeding on fruits and transporting the seeds, which are later deposited and capable of germination. The dynamics depends on several population parameters of growth, decay, harvesting, transport, digestion and germ... |
1912.03934 | Lionel Gil | Dora Matzakos-Karvouniari, Bruno Cessac and L. Gil | Noise driven broadening of the neural synchronisation transition in
stage II retinal waves | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Based on a biophysical model of retinal Starburst Amacrine Cell (SAC)
\cite{karvouniari-gil-etal:19} we analyse here the dynamics of retinal waves,
arising during the visual system development. Waves are induced by spontaneous
bursting of SACs and their coupling via acetycholine. We show that, despite the
acetylcholi... | [
{
"created": "Mon, 9 Dec 2019 09:58:51 GMT",
"version": "v1"
}
] | 2019-12-10 | [
[
"Matzakos-Karvouniari",
"Dora",
""
],
[
"Cessac",
"Bruno",
""
],
[
"Gil",
"L.",
""
]
] | Based on a biophysical model of retinal Starburst Amacrine Cell (SAC) \cite{karvouniari-gil-etal:19} we analyse here the dynamics of retinal waves, arising during the visual system development. Waves are induced by spontaneous bursting of SACs and their coupling via acetycholine. We show that, despite the acetylcholine... |
1301.6931 | Marco M\"oller | Marco M\"oller and Barbara Drossel | Scaling laws in critical random Boolean networks with general in- and
out-degree distributions | null | null | 10.1103/PhysRevE.87.052106 | null | q-bio.MN cond-mat.stat-mech physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We evaluate analytically and numerically the size of the frozen core and
various scaling laws for critical Boolean networks that have a power-law in-
and/or out-degree distribution. To this purpose, we generalize an efficient
method that has previously been used for conventional random Boolean networks
and for networ... | [
{
"created": "Tue, 29 Jan 2013 14:32:55 GMT",
"version": "v1"
}
] | 2015-06-12 | [
[
"Möller",
"Marco",
""
],
[
"Drossel",
"Barbara",
""
]
] | We evaluate analytically and numerically the size of the frozen core and various scaling laws for critical Boolean networks that have a power-law in- and/or out-degree distribution. To this purpose, we generalize an efficient method that has previously been used for conventional random Boolean networks and for networks... |
2310.15194 | Jie Ruan | Shiang Hu, Jie Ruan, Juan Hou, Pedro Antonio Valdes-Sosa, Zhao Lv | How do the resting EEG preprocessing states affect the outcomes of
postprocessing? | null | null | null | null | q-bio.NC cs.HC eess.SP q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Plenty of artifact removal tools and pipelines have been developed to correct
the EEG recordings and discover the values below the waveforms. Without visual
inspection from the experts, it is susceptible to derive improper preprocessing
states, like the insufficient preprocessed EEG (IPE), and the excessive
preproces... | [
{
"created": "Sun, 22 Oct 2023 08:08:46 GMT",
"version": "v1"
},
{
"created": "Tue, 12 Dec 2023 14:53:48 GMT",
"version": "v2"
}
] | 2023-12-13 | [
[
"Hu",
"Shiang",
""
],
[
"Ruan",
"Jie",
""
],
[
"Hou",
"Juan",
""
],
[
"Valdes-Sosa",
"Pedro Antonio",
""
],
[
"Lv",
"Zhao",
""
]
] | Plenty of artifact removal tools and pipelines have been developed to correct the EEG recordings and discover the values below the waveforms. Without visual inspection from the experts, it is susceptible to derive improper preprocessing states, like the insufficient preprocessed EEG (IPE), and the excessive preprocesse... |
1105.2362 | Liaofu Luo | Liaofu Luo | Protein Photo-folding and Quantum Folding Theory | 17 pages, 1 figure | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The rates of protein folding with photon absorption or emission and the cross
section of photon -protein inelastic scattering are calculated from the quantum
folding theory by use of standard field-theoretical method. All these protein
photo-folding processes are compared with common protein folding without
interacti... | [
{
"created": "Thu, 12 May 2011 03:18:55 GMT",
"version": "v1"
}
] | 2011-05-13 | [
[
"Luo",
"Liaofu",
""
]
] | The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein photo-folding processes are compared with common protein folding without interaction... |
1503.07796 | Joachim Krug | Stefan Nowak and Joachim Krug | Analysis of adaptive walks on NK fitness landscapes with different
interaction schemes | 29 pages, 9 figures | J. Stat. Mech. (2015) P06014 | 10.1088/1742-5468/2015/06/P06014 | null | q-bio.PE cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fitness landscapes are genotype to fitness mappings commonly used in
evolutionary biology and computer science which are closely related to spin
glass models. In this paper, we study the NK model for fitness landscapes where
the interaction scheme between genes can be explicitly defined. The focus is on
how this sche... | [
{
"created": "Thu, 26 Mar 2015 17:24:20 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Jun 2015 10:36:25 GMT",
"version": "v2"
}
] | 2015-06-12 | [
[
"Nowak",
"Stefan",
""
],
[
"Krug",
"Joachim",
""
]
] | Fitness landscapes are genotype to fitness mappings commonly used in evolutionary biology and computer science which are closely related to spin glass models. In this paper, we study the NK model for fitness landscapes where the interaction scheme between genes can be explicitly defined. The focus is on how this scheme... |
1207.2242 | Claus Metzner | F. Stadler, C. Metzner, J. Steinwachs, B. Fabry | Inhomogeneous ensembles of correlated random walkers | null | null | null | null | q-bio.QM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Discrete time random walks, in which a step of random sign but constant
length $\delta x$ is performed after each time interval $\delta t$, are widely
used models for stochastic processes. In the case of a correlated random walk,
the next step has the same sign as the previous one with a probability $q \neq
1/2$. We ... | [
{
"created": "Tue, 10 Jul 2012 06:58:58 GMT",
"version": "v1"
}
] | 2012-07-11 | [
[
"Stadler",
"F.",
""
],
[
"Metzner",
"C.",
""
],
[
"Steinwachs",
"J.",
""
],
[
"Fabry",
"B.",
""
]
] | Discrete time random walks, in which a step of random sign but constant length $\delta x$ is performed after each time interval $\delta t$, are widely used models for stochastic processes. In the case of a correlated random walk, the next step has the same sign as the previous one with a probability $q \neq 1/2$. We ex... |
1612.07425 | Petter Holme | Petter Holme, Nelly Litvak | Cost-efficient vaccination protocols for network epidemiology | null | null | 10.1371/journal.pcbi.1005696 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate methods to vaccinate contact networks -- i.e. removing nodes
in such a way that disease spreading is hindered as much as possible -- with
respect to their cost-efficiency. Any real implementation of such protocols
would come with costs related both to the vaccination itself, and gathering of
informatio... | [
{
"created": "Thu, 22 Dec 2016 03:07:34 GMT",
"version": "v1"
},
{
"created": "Sat, 20 May 2017 05:10:34 GMT",
"version": "v2"
}
] | 2017-11-01 | [
[
"Holme",
"Petter",
""
],
[
"Litvak",
"Nelly",
""
]
] | We investigate methods to vaccinate contact networks -- i.e. removing nodes in such a way that disease spreading is hindered as much as possible -- with respect to their cost-efficiency. Any real implementation of such protocols would come with costs related both to the vaccination itself, and gathering of information ... |
0708.0426 | Patricia Faisca | Rui D.M. Travasso, M.M. Telo da Gama and P.F.N. Faisca | Pathways to folding, nucleation events and native geometry | Accepted in J. Chem. Phys | null | 10.1063/1.2777150 | null | q-bio.BM | null | We perform extensive Monte Carlo simulations of a lattice model and the Go
potential to investigate the existence of folding pathways at the level of
contact cluster formation for two native structures with markedly different
geometries. Our analysis of folding pathways revealed a common underlying
folding mechanism,... | [
{
"created": "Thu, 2 Aug 2007 21:35:18 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Travasso",
"Rui D. M.",
""
],
[
"da Gama",
"M. M. Telo",
""
],
[
"Faisca",
"P. F. N.",
""
]
] | We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries. Our analysis of folding pathways revealed a common underlying folding mechanism, b... |
1911.11840 | Mahsa Yazdani | Mahsa Yazdani and Omid Tavakoli | The Effect of Salt Shock on Growth and Pigment Accumulation of
Dunaliella Salina | null | The 5th International Symposium on Biological Engineering and
Natural Sciences, August 14-16, 2017, Osaka, Japan | null | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dunaliella Salina is a halotolerant microalga with great pharmaceutical and
industrial potential, which commonly exists in hypersaline environments.
Moreover, it is the best commercial source of beta-carotene (which has high
anti-oxidant properties) in comparison to other microalgae. In this study, we
investigated gr... | [
{
"created": "Tue, 26 Nov 2019 21:31:09 GMT",
"version": "v1"
}
] | 2019-11-28 | [
[
"Yazdani",
"Mahsa",
""
],
[
"Tavakoli",
"Omid",
""
]
] | Dunaliella Salina is a halotolerant microalga with great pharmaceutical and industrial potential, which commonly exists in hypersaline environments. Moreover, it is the best commercial source of beta-carotene (which has high anti-oxidant properties) in comparison to other microalgae. In this study, we investigated grow... |
q-bio/0608010 | Chunguang Li | Chunguang Li, Luonan Chen, Kazuyuki Aihara | Transient Resetting: A Novel Mechanism for Synchrony and Its Biological
Examples | 17 pages, 7 figures | PLoS Computational Biology 2 (8): e103, 2006 | 10.1371/journal.pcbi.0020103 | null | q-bio.MN nlin.CD | null | The study of synchronization in biological systems is essential for the
understanding of the rhythmic phenomena of living organisms at both molecular
and cellular levels. In this paper, by using simple dynamical systems theory,
we present a novel mechanism, named transient resetting, for the
synchronization of uncoup... | [
{
"created": "Fri, 4 Aug 2006 03:02:30 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Li",
"Chunguang",
""
],
[
"Chen",
"Luonan",
""
],
[
"Aihara",
"Kazuyuki",
""
]
] | The study of synchronization in biological systems is essential for the understanding of the rhythmic phenomena of living organisms at both molecular and cellular levels. In this paper, by using simple dynamical systems theory, we present a novel mechanism, named transient resetting, for the synchronization of uncouple... |
2206.12240 | Sirui Liu | Sirui Liu, Jun Zhang, Haotian Chu, Min Wang, Boxin Xue, Ningxi Ni,
Jialiang Yu, Yuhao Xie, Zhenyu Chen, Mengyun Chen, Yuan Liu, Piya Patra, Fan
Xu, Jie Chen, Zidong Wang, Lijiang Yang, Fan Yu, Lei Chen, Yi Qin Gao | PSP: Million-level Protein Sequence Dataset for Protein Structure
Prediction | null | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Proteins are essential component of human life and their structures are
important for function and mechanism analysis. Recent work has shown the
potential of AI-driven methods for protein structure prediction. However, the
development of new models is restricted by the lack of dataset and benchmark
training procedure... | [
{
"created": "Fri, 24 Jun 2022 14:08:44 GMT",
"version": "v1"
}
] | 2022-06-27 | [
[
"Liu",
"Sirui",
""
],
[
"Zhang",
"Jun",
""
],
[
"Chu",
"Haotian",
""
],
[
"Wang",
"Min",
""
],
[
"Xue",
"Boxin",
""
],
[
"Ni",
"Ningxi",
""
],
[
"Yu",
"Jialiang",
""
],
[
"Xie",
"Yuhao",
""
... | Proteins are essential component of human life and their structures are important for function and mechanism analysis. Recent work has shown the potential of AI-driven methods for protein structure prediction. However, the development of new models is restricted by the lack of dataset and benchmark training procedure. ... |
1304.0479 | Wendy Ingram | Wendy Marie Ingram, Leeanne M Goodrich, Ellen A Robey, Michael B Eisen | Mice Infected with Low-virulence Strains of Toxoplasma gondii Lose their
Innate Aversion to Cat Urine, Even after Extensive Parasite Clearance | 14 pages, 3 figures | null | 10.1371/journal.pone.0075246 | null | q-bio.TO q-bio.NC | http://creativecommons.org/licenses/by/3.0/ | Toxoplasma gondii chronic infection in rodent secondary hosts has been
reported to lead to a loss of innate, hard-wired fear toward cats, its primary
host. However the generality of this response across T. gondii strains and the
underlying mechanism for this pathogen mediated behavioral change remain
unknown. To begi... | [
{
"created": "Mon, 1 Apr 2013 20:53:18 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Jul 2013 21:08:20 GMT",
"version": "v2"
}
] | 2014-03-05 | [
[
"Ingram",
"Wendy Marie",
""
],
[
"Goodrich",
"Leeanne M",
""
],
[
"Robey",
"Ellen A",
""
],
[
"Eisen",
"Michael B",
""
]
] | Toxoplasma gondii chronic infection in rodent secondary hosts has been reported to lead to a loss of innate, hard-wired fear toward cats, its primary host. However the generality of this response across T. gondii strains and the underlying mechanism for this pathogen mediated behavioral change remain unknown. To begin ... |
1603.02414 | Christos Skiadas H | Christos H Skiadas | The Health-Mortality Approach in Estimating the Healthy Life Years Lost
Compared to the Global Burden of Disease Studies and Applications | 26 pages, 11 figures, 6 tables. arXiv admin note: substantial text
overlap with arXiv:1510.07346 | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a series of methods and models in order to explore the Global
Burden of Disease Study and the provided healthy life expectancy HALE estimates
from the World Health Organization WHO based on the mortality mx of a
population provided in a classical life table and a mortality diagram. Our
estimates are compar... | [
{
"created": "Tue, 8 Mar 2016 08:31:51 GMT",
"version": "v1"
}
] | 2016-03-09 | [
[
"Skiadas",
"Christos H",
""
]
] | We propose a series of methods and models in order to explore the Global Burden of Disease Study and the provided healthy life expectancy HALE estimates from the World Health Organization WHO based on the mortality mx of a population provided in a classical life table and a mortality diagram. Our estimates are compared... |
2306.13429 | Leonardo Novelli | Leonardo Novelli, Karl Friston, Adeel Razi | Spectral Dynamic Causal Modelling: A Didactic Introduction and its
Relationship with Functional Connectivity | null | null | null | null | q-bio.NC cs.CE | http://creativecommons.org/licenses/by/4.0/ | We present a didactic introduction to spectral Dynamic Causal Modelling
(DCM), a Bayesian state-space modelling approach used to infer effective
connectivity from non-invasive neuroimaging data. Spectral DCM is currently the
most widely applied DCM variant for resting-state functional MRI analysis. Our
aim is to expl... | [
{
"created": "Fri, 23 Jun 2023 10:46:39 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Sep 2023 02:24:23 GMT",
"version": "v2"
}
] | 2023-09-07 | [
[
"Novelli",
"Leonardo",
""
],
[
"Friston",
"Karl",
""
],
[
"Razi",
"Adeel",
""
]
] | We present a didactic introduction to spectral Dynamic Causal Modelling (DCM), a Bayesian state-space modelling approach used to infer effective connectivity from non-invasive neuroimaging data. Spectral DCM is currently the most widely applied DCM variant for resting-state functional MRI analysis. Our aim is to explai... |
1711.07258 | Marie-Constance Corsi | Marie-Constance Corsi, Mario Chavez, Denis Schwartz, Laurent
Hugueville, Ankit N. Khambhati, Danielle S. Bassett, Fabrizio De Vico Fallani | Integrating EEG and MEG signals to improve motor imagery classification
in brain-computer interfaces | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a fusion approach that combines features from simultaneously
recorded electroencephalographic (EEG) and magnetoencephalographic (MEG)
signals to improve classification performances in motor imagery-based
brain-computer interfaces (BCIs). We applied our approach to a group of 15
healthy subjects and found a... | [
{
"created": "Mon, 20 Nov 2017 11:30:15 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Mar 2018 13:27:13 GMT",
"version": "v2"
}
] | 2018-03-28 | [
[
"Corsi",
"Marie-Constance",
""
],
[
"Chavez",
"Mario",
""
],
[
"Schwartz",
"Denis",
""
],
[
"Hugueville",
"Laurent",
""
],
[
"Khambhati",
"Ankit N.",
""
],
[
"Bassett",
"Danielle S.",
""
],
[
"Fallani",
"Fabriz... | We propose a fusion approach that combines features from simultaneously recorded electroencephalographic (EEG) and magnetoencephalographic (MEG) signals to improve classification performances in motor imagery-based brain-computer interfaces (BCIs). We applied our approach to a group of 15 healthy subjects and found a s... |
0910.4077 | Marcin Zag\'orski | Z. Burda, A. Krzywicki, O. C. Martin, M. Zagorski | Sparse essential interactions in model networks of gene regulation | 9 pages, 5 figures | null | null | null | q-bio.MN cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene regulatory networks typically have low in-degrees, whereby any given
gene is regulated by few of the genes in the network. What mechanisms might be
responsible for these low in-degrees? Starting with an accepted framework of
the binding of transcription factors to DNA, we consider a simple model of gene
regulato... | [
{
"created": "Wed, 21 Oct 2009 12:58:49 GMT",
"version": "v1"
}
] | 2009-10-22 | [
[
"Burda",
"Z.",
""
],
[
"Krzywicki",
"A.",
""
],
[
"Martin",
"O. C.",
""
],
[
"Zagorski",
"M.",
""
]
] | Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the binding of transcription factors to DNA, we consider a simple model of gene regulatory... |
1711.11161 | Pedro M. F. Pereira | Pedro M. F. Pereira | Can Complex Collective Behaviour Be Generated Through Randomness, Memory
and a Pinch of Luck? | null | null | null | null | q-bio.PE nlin.CG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Machine Learning techniques have been used to teach computer programs how to
play games as complicated as Chess and Go. These were achieved using powerful
tools such as Neural Networks and Parallel Computing on Supercomputers. In this
paper, we define a model of populational growth and evolution based on the idea
of ... | [
{
"created": "Wed, 29 Nov 2017 23:56:29 GMT",
"version": "v1"
}
] | 2017-12-01 | [
[
"Pereira",
"Pedro M. F.",
""
]
] | Machine Learning techniques have been used to teach computer programs how to play games as complicated as Chess and Go. These were achieved using powerful tools such as Neural Networks and Parallel Computing on Supercomputers. In this paper, we define a model of populational growth and evolution based on the idea of Re... |
1008.1063 | Attila Szolnoki | Gyorgy Szabo, Attila Szolnoki, Melinda Varga, Livia Hanusovszky | Ordering in spatial evolutionary games for pairwise collective strategy
updates | 9 pages, 6 figures; accepted for publication in Physical Review E | Physical Review E 82 (2010) 026110 | 10.1103/PhysRevE.82.026110 | null | q-bio.PE cond-mat.stat-mech physics.bio-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolutionary $2 \times 2$ games are studied with players located on a square
lattice. During the evolution the randomly chosen neighboring players try to
maximize their collective income by adopting a random strategy pair with a
probability dependent on the difference of their summed payoffs between the
final and ini... | [
{
"created": "Thu, 5 Aug 2010 20:01:31 GMT",
"version": "v1"
}
] | 2010-08-23 | [
[
"Szabo",
"Gyorgy",
""
],
[
"Szolnoki",
"Attila",
""
],
[
"Varga",
"Melinda",
""
],
[
"Hanusovszky",
"Livia",
""
]
] | Evolutionary $2 \times 2$ games are studied with players located on a square lattice. During the evolution the randomly chosen neighboring players try to maximize their collective income by adopting a random strategy pair with a probability dependent on the difference of their summed payoffs between the final and initi... |
1609.04316 | Carlo Nicolini | Carlo Nicolini, C\'ecile Bordier, Angelo Bifone | Community detection in weighted brain connectivity networks beyond the
resolution limit | 27 pages with 6 figures and 1 table. Conference version for CCS2016 | null | null | null | q-bio.NC physics.soc-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Graph theory provides a powerful framework to investigate brain functional
connectivity networks and their modular organization. However, most graph-based
methods suffer from a fundamental resolution limit that may have affected
previous studies and prevented detection of modules, or communities, that are
smaller tha... | [
{
"created": "Wed, 14 Sep 2016 15:36:49 GMT",
"version": "v1"
}
] | 2016-09-15 | [
[
"Nicolini",
"Carlo",
""
],
[
"Bordier",
"Cécile",
""
],
[
"Bifone",
"Angelo",
""
]
] | Graph theory provides a powerful framework to investigate brain functional connectivity networks and their modular organization. However, most graph-based methods suffer from a fundamental resolution limit that may have affected previous studies and prevented detection of modules, or communities, that are smaller than ... |
1809.09450 | Alican Ozkan | Alican Ozkan, Neda Ghousifam, P. Jack Hoopes, Marissa Nichole Rylander | In Vitro Vascularized Liver and Tumor Tissue Microenvironments on a Chip
for Dynamic Determination of Nanoparticle Transport and Toxicity | 42 pages, 10 figures, 1 table | null | null | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper presents the development of a vascularized breast tumor and
healthy or tumorigenic liver microenvironments-on-a-chip connected in series.
This is the first description of a vascularized multi tissue-on-a-chip
microenvironment for modeling cancerous breast and cancerous/healthy liver
microenvironments, to a... | [
{
"created": "Tue, 25 Sep 2018 13:02:54 GMT",
"version": "v1"
},
{
"created": "Wed, 28 Nov 2018 03:05:35 GMT",
"version": "v2"
}
] | 2018-11-29 | [
[
"Ozkan",
"Alican",
""
],
[
"Ghousifam",
"Neda",
""
],
[
"Hoopes",
"P. Jack",
""
],
[
"Rylander",
"Marissa Nichole",
""
]
] | This paper presents the development of a vascularized breast tumor and healthy or tumorigenic liver microenvironments-on-a-chip connected in series. This is the first description of a vascularized multi tissue-on-a-chip microenvironment for modeling cancerous breast and cancerous/healthy liver microenvironments, to all... |
2403.13851 | Lucas B\"ottcher | Lucas B\"ottcher, Luis L. Fonseca, Reinhard C. Laubenbacher | Control of Medical Digital Twins with Artificial Neural Networks | 13 pages, 5 figures | null | null | null | q-bio.QM cs.LG cs.SY eess.SY math.DS math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The objective of personalized medicine is to tailor interventions to an
individual patient's unique characteristics. A key technology for this purpose
involves medical digital twins, computational models of human biology that can
be personalized and dynamically updated to incorporate patient-specific data
collected o... | [
{
"created": "Mon, 18 Mar 2024 19:30:46 GMT",
"version": "v1"
}
] | 2024-03-22 | [
[
"Böttcher",
"Lucas",
""
],
[
"Fonseca",
"Luis L.",
""
],
[
"Laubenbacher",
"Reinhard C.",
""
]
] | The objective of personalized medicine is to tailor interventions to an individual patient's unique characteristics. A key technology for this purpose involves medical digital twins, computational models of human biology that can be personalized and dynamically updated to incorporate patient-specific data collected ove... |
1304.8045 | Buhm Han | Buhm Han, Jae Hoon Sul, Eleazar Eskin, Paul I. W. de Bakker, Soumya
Raychaudhuri | A general framework for meta-analyzing dependent studies with
overlapping subjects in association mapping | 1/17/14: Minor text changes | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Meta-analysis of genome-wide association studies is increasingly popular and
many meta-analytic methods have been recently proposed. A majority of
meta-analytic methods combine information from multiple studies by assuming
that studies are independent since individuals collected in one study are
unlikely to be collec... | [
{
"created": "Tue, 30 Apr 2013 16:01:14 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Oct 2013 21:53:36 GMT",
"version": "v2"
},
{
"created": "Fri, 17 Jan 2014 17:59:19 GMT",
"version": "v3"
}
] | 2014-01-20 | [
[
"Han",
"Buhm",
""
],
[
"Sul",
"Jae Hoon",
""
],
[
"Eskin",
"Eleazar",
""
],
[
"de Bakker",
"Paul I. W.",
""
],
[
"Raychaudhuri",
"Soumya",
""
]
] | Meta-analysis of genome-wide association studies is increasingly popular and many meta-analytic methods have been recently proposed. A majority of meta-analytic methods combine information from multiple studies by assuming that studies are independent since individuals collected in one study are unlikely to be collecte... |
2002.00245 | Mandev Gill | Mandev S. Gill, Philippe Lemey, Marc A. Suchard, Andrew Rambaut, Guy
Baele | Online Bayesian phylodynamic inference in BEAST with application to
epidemic reconstruction | 20 pages, 3 figures | null | null | null | q-bio.PE stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reconstructing pathogen dynamics from genetic data as they become available
during an outbreak or epidemic represents an important statistical scenario in
which observations arrive sequentially in time and one is interested in
performing inference in an 'online' fashion. Widely-used Bayesian phylogenetic
inference pa... | [
{
"created": "Sat, 1 Feb 2020 17:30:59 GMT",
"version": "v1"
}
] | 2020-02-04 | [
[
"Gill",
"Mandev S.",
""
],
[
"Lemey",
"Philippe",
""
],
[
"Suchard",
"Marc A.",
""
],
[
"Rambaut",
"Andrew",
""
],
[
"Baele",
"Guy",
""
]
] | Reconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive sequentially in time and one is interested in performing inference in an 'online' fashion. Widely-used Bayesian phylogenetic inference pack... |
1912.10489 | Tai Sing Lee | Siming Yan, Xuyang Fang, Bowen Xiao, Harold Rockwell, Yimeng Zhang,
Tai Sing Lee | Recurrent Feedback Improves Feedforward Representations in Deep Neural
Networks | 10 pages, 5 figures | null | null | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The abundant recurrent horizontal and feedback connections in the primate
visual cortex are thought to play an important role in bringing global and
semantic contextual information to early visual areas during perceptual
inference, helping to resolve local ambiguity and fill in missing details. In
this study, we find... | [
{
"created": "Sun, 22 Dec 2019 17:40:19 GMT",
"version": "v1"
}
] | 2019-12-24 | [
[
"Yan",
"Siming",
""
],
[
"Fang",
"Xuyang",
""
],
[
"Xiao",
"Bowen",
""
],
[
"Rockwell",
"Harold",
""
],
[
"Zhang",
"Yimeng",
""
],
[
"Lee",
"Tai Sing",
""
]
] | The abundant recurrent horizontal and feedback connections in the primate visual cortex are thought to play an important role in bringing global and semantic contextual information to early visual areas during perceptual inference, helping to resolve local ambiguity and fill in missing details. In this study, we find t... |
2003.00328 | Gerhard Mayer | Gerhard Mayer | Mass spectrometry for semi-experimental protein structure determination
and modeling | 28 pages | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The structure of proteins is essential for its function. The determination of
protein structures is possible by experimental or predicted by computational
methods, but also a combination of both approaches is possible. Here, first an
overview about experimental structure determination methods with their pros and
cons... | [
{
"created": "Sat, 29 Feb 2020 18:43:09 GMT",
"version": "v1"
}
] | 2020-03-03 | [
[
"Mayer",
"Gerhard",
""
]
] | The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an overview about experimental structure determination methods with their pros and cons i... |
2307.11033 | Roberto Corral L\'opez | Roberto Corral L\'opez and Samir Suweis and Sandro Azaele and Miguel
A. Mu\~noz | Stochastic trade-offs and the emergence of diversification in E. coli
evolution experiments | null | null | null | null | q-bio.PE physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Laboratory experiments with bacterial colonies, under well-controlled
conditions often lead to evolutionary diversification, where at least two
ecotypes emerge from an initially monomorphic population. Empirical evidence
suggests that such "evolutionary branching" occurs stochastically, even under
fixed and stable co... | [
{
"created": "Thu, 20 Jul 2023 17:08:05 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Jul 2024 06:19:04 GMT",
"version": "v2"
}
] | 2024-07-24 | [
[
"López",
"Roberto Corral",
""
],
[
"Suweis",
"Samir",
""
],
[
"Azaele",
"Sandro",
""
],
[
"Muñoz",
"Miguel A.",
""
]
] | Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such "evolutionary branching" occurs stochastically, even under fixed and stable cond... |
1312.5492 | Shinya Kuroda | Takuya Koumura, Hidetoshi Urakubo, Kaoru Ohashi, Masashi Fujii and
Shinya Kuroda | Stochasticity in Ca$^{2+}$ increase in spines enables robust and
sensitive information coding | 47 pages, 4 figures, 8 supplementary figures | null | 10.1371/journal.pone.0099040 | null | q-bio.MN q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A dendritic spine is a very small structure (~0.1 {\mu}m$^3$) of a neuron
that processes input timing information. Why are spines so small? Here, we
provide functional reasons; the size of spines is optimal for information
coding. Spines code input timing information by the probability of Ca$^{2+}$
increases, which m... | [
{
"created": "Thu, 19 Dec 2013 11:49:19 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Feb 2014 11:55:53 GMT",
"version": "v2"
}
] | 2014-06-18 | [
[
"Koumura",
"Takuya",
""
],
[
"Urakubo",
"Hidetoshi",
""
],
[
"Ohashi",
"Kaoru",
""
],
[
"Fujii",
"Masashi",
""
],
[
"Kuroda",
"Shinya",
""
]
] | A dendritic spine is a very small structure (~0.1 {\mu}m$^3$) of a neuron that processes input timing information. Why are spines so small? Here, we provide functional reasons; the size of spines is optimal for information coding. Spines code input timing information by the probability of Ca$^{2+}$ increases, which mak... |
2305.01580 | Li Kai | Li Kai, Li Ning, Zhang Wei, Gao Ming | Molecular design method based on novel molecular representation and
variational auto-encoder | 13 pages, 7 figures, conference: NIAI | 4th International Conference on Natural Language Processing,
Information Retrieval and AI (NIAI 2023), Volume 13, Number 03, February
2023, pp. 23-35, 2023. CS & IT - CSCP 2023 | 10.5121/csit.2023.130303 | null | q-bio.BM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Based on the traditional VAE, a novel neural network model is presented, with
the latest molecular representation, SELFIES, to improve the effect of
generating new molecules. In this model, multi-layer convolutional network and
Fisher information are added to the original encoding layer to learn the data
characterist... | [
{
"created": "Mon, 20 Feb 2023 05:11:53 GMT",
"version": "v1"
}
] | 2023-05-03 | [
[
"Kai",
"Li",
""
],
[
"Ning",
"Li",
""
],
[
"Wei",
"Zhang",
""
],
[
"Ming",
"Gao",
""
]
] | Based on the traditional VAE, a novel neural network model is presented, with the latest molecular representation, SELFIES, to improve the effect of generating new molecules. In this model, multi-layer convolutional network and Fisher information are added to the original encoding layer to learn the data characteristic... |
1606.03235 | Pablo Villegas G\'ongora | Pablo Villegas, Jos\'e Ruiz-Franco, Jorge Hidalgo, Miguel A. Mu\~noz | Intrinsic noise and deviations from criticality in Boolean
gene-regulatory networks | 14 pages, 6 figures and 1 table. Submitted to Scientific Reports | Scientific Reports 6, 34743 (2016) | 10.1038/srep34743 | null | q-bio.MN cond-mat.dis-nn nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene regulatory networks can be successfully modeled as Boolean networks. A
much discussed hypothesis says that such model networks reproduce empirical
findings the best if they are tuned to operate at criticality, i.e. at the
borderline between their ordered and disordered phases. Critical networks have
been argued ... | [
{
"created": "Fri, 10 Jun 2016 09:06:11 GMT",
"version": "v1"
}
] | 2016-10-12 | [
[
"Villegas",
"Pablo",
""
],
[
"Ruiz-Franco",
"José",
""
],
[
"Hidalgo",
"Jorge",
""
],
[
"Muñoz",
"Miguel A.",
""
]
] | Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline between their ordered and disordered phases. Critical networks have been argued to... |
0911.1843 | Cecile Fauvelot | Cecile Fauvelot (COREUS), Francesca Bertozzi (CIRSA), Federica
Costantini (CIRSA), Laura Airoldi (CIRSA), Marco Abbiati (CIRSA) | Lower genetic diversity in the limpet Patella caerulea on urban coastal
structures compared to natural rocky habitats | null | Marine Biology 156 (2009) 2313 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human-made structures are increasingly found in marine coastal habitats. The
aim of the present study was to explore whether urban coastal structures can
affect the genetic variation of hard-bottom species. We conducted a population
genetic analysis on the limpet Patella caerulea sampled in both natural and
artificia... | [
{
"created": "Tue, 10 Nov 2009 07:16:54 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Fauvelot",
"Cecile",
"",
"COREUS"
],
[
"Bertozzi",
"Francesca",
"",
"CIRSA"
],
[
"Costantini",
"Federica",
"",
"CIRSA"
],
[
"Airoldi",
"Laura",
"",
"CIRSA"
],
[
"Abbiati",
"Marco",
"",
"CIRSA"
]
] | Human-made structures are increasingly found in marine coastal habitats. The aim of the present study was to explore whether urban coastal structures can affect the genetic variation of hard-bottom species. We conducted a population genetic analysis on the limpet Patella caerulea sampled in both natural and artificial ... |
2109.11985 | Matt Holzer | Ashley Armbruster, Matt Holzer, Noah Roselli, Lena Underwood | Epidemic spreading on complex networks as front propagation into an
unstable state | null | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study epidemic arrival times in meta-population disease models through the
lens of front propagation into unstable states. We demonstrate that several
features of invasion fronts in the PDE context are also relevant to the network
case. We show that the susceptible-infected-recovered model on a network is
linearly... | [
{
"created": "Fri, 24 Sep 2021 14:17:44 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Oct 2022 17:41:02 GMT",
"version": "v2"
}
] | 2022-10-19 | [
[
"Armbruster",
"Ashley",
""
],
[
"Holzer",
"Matt",
""
],
[
"Roselli",
"Noah",
""
],
[
"Underwood",
"Lena",
""
]
] | We study epidemic arrival times in meta-population disease models through the lens of front propagation into unstable states. We demonstrate that several features of invasion fronts in the PDE context are also relevant to the network case. We show that the susceptible-infected-recovered model on a network is linearly d... |
1704.08851 | Sebastian Weichwald | Sebastian Weichwald and Moritz Grosse-Wentrup | The right tool for the right question --- beyond the encoding versus
decoding dichotomy | preprint | null | null | null | q-bio.NC stat.AP stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There are two major questions that neuroimaging studies attempt to answer:
First, how are sensory stimuli represented in the brain (which we term the
stimulus-based setting)? And, second, how does the brain generate cognition
(termed the response-based setting)? There has been a lively debate in the
neuroimaging comm... | [
{
"created": "Fri, 28 Apr 2017 08:56:47 GMT",
"version": "v1"
}
] | 2017-05-01 | [
[
"Weichwald",
"Sebastian",
""
],
[
"Grosse-Wentrup",
"Moritz",
""
]
] | There are two major questions that neuroimaging studies attempt to answer: First, how are sensory stimuli represented in the brain (which we term the stimulus-based setting)? And, second, how does the brain generate cognition (termed the response-based setting)? There has been a lively debate in the neuroimaging commun... |
1808.04458 | Mohammadsadegh Ghiasi | Mohammad S. Ghiasi, Jason E. Chen, Edward K. Rodriguez, Ashkan Vaziri,
Ara Nazarian | Computational Modeling of the Effects of Inflammatory Response and
Granulation Tissue Properties on Human Bone Fracture Healing | 25 Pages, 7 Figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bone healing process includes four phases: inflammatory response, soft callus
formation, hard callus development, and remodeling. Mechanobiological models
have been used to investigate the role of various mechanical and biological
factors on the bone healing. However, the initial phase of healing, which
includes the ... | [
{
"created": "Mon, 13 Aug 2018 20:37:01 GMT",
"version": "v1"
}
] | 2018-08-15 | [
[
"Ghiasi",
"Mohammad S.",
""
],
[
"Chen",
"Jason E.",
""
],
[
"Rodriguez",
"Edward K.",
""
],
[
"Vaziri",
"Ashkan",
""
],
[
"Nazarian",
"Ara",
""
]
] | Bone healing process includes four phases: inflammatory response, soft callus formation, hard callus development, and remodeling. Mechanobiological models have been used to investigate the role of various mechanical and biological factors on the bone healing. However, the initial phase of healing, which includes the in... |
1803.10044 | Roland L. Knorr | Roland L. Knorr, Jan Steinkuehler and Rumiana Dimova | Micron-sized domains in quasi single-component giant vesicles | null | null | null | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Giant unilamellar vesicles (GUVs), are a convenient tool to study
membrane-bound processes using optical microscopy. An increasing number of
studies highlights the potential of these model membranes when addressing
questions in membrane biophysics and cell biology. Among them, phase
transitions and domain formation, ... | [
{
"created": "Tue, 27 Mar 2018 12:38:46 GMT",
"version": "v1"
},
{
"created": "Mon, 25 Jun 2018 19:17:10 GMT",
"version": "v2"
}
] | 2018-06-27 | [
[
"Knorr",
"Roland L.",
""
],
[
"Steinkuehler",
"Jan",
""
],
[
"Dimova",
"Rumiana",
""
]
] | Giant unilamellar vesicles (GUVs), are a convenient tool to study membrane-bound processes using optical microscopy. An increasing number of studies highlights the potential of these model membranes when addressing questions in membrane biophysics and cell biology. Among them, phase transitions and domain formation, dy... |
1307.7861 | Aaron Darling | Michal N\'an\'asi, Tom\'a\v{s} Vina\v{r}, and Bro\v{n}a Brejov\'a | Probabilistic Approaches to Alignment with Tandem Repeats | Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013) | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a simple tractable pair hidden Markov model for pairwise sequence
alignment that accounts for the presence of short tandem repeats. Using the
framework of gain functions, we design several optimization criteria for
decoding this model and describe the resulting decoding algorithms, ranging
from the traditi... | [
{
"created": "Tue, 30 Jul 2013 08:02:34 GMT",
"version": "v1"
}
] | 2013-07-31 | [
[
"Nánási",
"Michal",
""
],
[
"Vinař",
"Tomáš",
""
],
[
"Brejová",
"Broňa",
""
]
] | We propose a simple tractable pair hidden Markov model for pairwise sequence alignment that accounts for the presence of short tandem repeats. Using the framework of gain functions, we design several optimization criteria for decoding this model and describe the resulting decoding algorithms, ranging from the tradition... |
2212.07638 | Muhammad Anwari Leksono | Muhammad Anwari Leksono and Ayu Purwarianti | Sequential Labelling and DNABERT For Splice Site Prediction in Homo
Sapiens DNA | revision 1, 5 figures, 3 tables | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genome sequencing technology has improved significantly in few last years and
resulted in abundance genetic data. Artificial intelligence has been employed
to analyze genetic data in response to its sheer size and variability. Gene
prediction on single DNA has been conducted using various deep learning
architectures ... | [
{
"created": "Thu, 15 Dec 2022 07:18:36 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Mar 2023 11:41:59 GMT",
"version": "v2"
}
] | 2023-03-17 | [
[
"Leksono",
"Muhammad Anwari",
""
],
[
"Purwarianti",
"Ayu",
""
]
] | Genome sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene prediction on single DNA has been conducted using various deep learning architectures to... |
1403.5686 | Haris Vikalo | Xiaohu Shen, Manohar Shamaiah, and Haris Vikalo | Iterative Learning for Reference-Guided DNA Sequence Assembly from Short
Reads: Algorithms and Limits of Performance | Submitted to IEEE Transactions on Signal Processing | null | 10.1109/TSP.2014.2333564 | null | q-bio.GN cs.CE cs.IT math.IT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent emergence of next-generation DNA sequencing technology has enabled
acquisition of genetic information at unprecedented scales. In order to
determine the genetic blueprint of an organism, sequencing platforms typically
employ so-called shotgun sequencing strategy to oversample the target genome
with a library o... | [
{
"created": "Sat, 22 Mar 2014 16:59:53 GMT",
"version": "v1"
}
] | 2015-06-19 | [
[
"Shen",
"Xiaohu",
""
],
[
"Shamaiah",
"Manohar",
""
],
[
"Vikalo",
"Haris",
""
]
] | Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ so-called shotgun sequencing strategy to oversample the target genome with a library of ... |
2001.11972 | Shawn Gu | Shawn Gu and Tijana Milenkovic | Data-driven biological network alignment that uses topological,
sequence, and functional information | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many proteins remain functionally unannotated. Sequence alignment (SA)
uncovers missing annotations by transferring functional knowledge between
species' sequence-conserved regions. Because SA is imperfect, network alignment
(NA) complements SA by transferring functional knowledge between conserved
biological network... | [
{
"created": "Fri, 31 Jan 2020 17:43:13 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Jun 2020 19:36:28 GMT",
"version": "v2"
}
] | 2020-06-16 | [
[
"Gu",
"Shawn",
""
],
[
"Milenkovic",
"Tijana",
""
]
] | Many proteins remain functionally unannotated. Sequence alignment (SA) uncovers missing annotations by transferring functional knowledge between species' sequence-conserved regions. Because SA is imperfect, network alignment (NA) complements SA by transferring functional knowledge between conserved biological network, ... |
2311.17755 | Franck Andre | Juan Gonz\'alez-Cuevas, Ricardo Arg\"uello, Marcos Florentin, Franck
M. Andr\'e (METSY), Lluis Mir (IGR, METSY) | Experimental and Theoretical Brownian Dynamics Analysis of Ion Transport
During Cellular Electroporation of E. coli Bacteria | Annals of Biomedical Engineering, 2023 | null | 10.1007/s10439-023-03353-4 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Escherichia coli bacterium is a rod-shaped organism composed of a complex
double membrane structure. Knowledge of electric field driven ion transport
through both membranes and the evolution of their induced permeabilization has
important applications in biomedical engineering, delivery of genes and
antibacterial age... | [
{
"created": "Wed, 29 Nov 2023 15:57:32 GMT",
"version": "v1"
}
] | 2023-11-30 | [
[
"González-Cuevas",
"Juan",
"",
"METSY"
],
[
"Argüello",
"Ricardo",
"",
"METSY"
],
[
"Florentin",
"Marcos",
"",
"METSY"
],
[
"André",
"Franck M.",
"",
"METSY"
],
[
"Mir",
"Lluis",
"",
"IGR, METSY"
]
] | Escherichia coli bacterium is a rod-shaped organism composed of a complex double membrane structure. Knowledge of electric field driven ion transport through both membranes and the evolution of their induced permeabilization has important applications in biomedical engineering, delivery of genes and antibacterial agent... |
1407.5503 | Ellen Baake | Corinna Ernst and Ellen Baake | Rare event simulation in immune biology: Models of negative selection in
T-cell maturation | 13 pages, 5 figures; accepted for 10th International Workshop on Rare
Event Simulation, Amsterdam, Aug. 27-29, 2014 | null | null | null | q-bio.CB math.PR q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a probabilistic T-cell model that includes negative selection and
takes contrasting models of tissue-restricted antigen (TRA) expression in the
thymus into account. We start from the basic model of van den Berg, Rand, and
Burroughs (2001) and include negative selection via individual-based T-cell
modelling... | [
{
"created": "Mon, 21 Jul 2014 14:16:06 GMT",
"version": "v1"
}
] | 2014-07-22 | [
[
"Ernst",
"Corinna",
""
],
[
"Baake",
"Ellen",
""
]
] | We present a probabilistic T-cell model that includes negative selection and takes contrasting models of tissue-restricted antigen (TRA) expression in the thymus into account. We start from the basic model of van den Berg, Rand, and Burroughs (2001) and include negative selection via individual-based T-cell modelling, ... |
1607.00483 | Vaibhav Madhok | Vaibhav Madhok | Quasi-Species in High Dimensional Spaces | Ideas on high dimensionality geometry, concentration of measure and
quasi-species evolution. Work in progress | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show that, under certain assumptions, the fitness of almost all
quasi-species becomes independent of mutational probabilities and the initial
frequency distributions of the sequences in high dimensional sequence spaces.
This result is the consequence of the concentration of measure on a high
dimensional hyperspher... | [
{
"created": "Sat, 2 Jul 2016 09:32:50 GMT",
"version": "v1"
}
] | 2016-07-05 | [
[
"Madhok",
"Vaibhav",
""
]
] | We show that, under certain assumptions, the fitness of almost all quasi-species becomes independent of mutational probabilities and the initial frequency distributions of the sequences in high dimensional sequence spaces. This result is the consequence of the concentration of measure on a high dimensional hypersphere ... |
1811.03177 | Younhun Kim | Younhun Kim, Frederic Koehler, Ankur Moitra, Elchanan Mossel and
Govind Ramnarayan | How Many Subpopulations is Too Many? Exponential Lower Bounds for
Inferring Population Histories | 38 pages, Appeared in RECOMB 2019 | null | null | null | q-bio.PE math.ST q-bio.QM stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reconstruction of population histories is a central problem in population
genetics. Existing coalescent-based methods, like the seminal work of Li and
Durbin (Nature, 2011), attempt to solve this problem using sequence data but
have no rigorous guarantees. Determining the amount of data needed to correctly
reconstruc... | [
{
"created": "Wed, 7 Nov 2018 23:00:15 GMT",
"version": "v1"
},
{
"created": "Wed, 8 May 2019 15:24:19 GMT",
"version": "v2"
}
] | 2020-05-11 | [
[
"Kim",
"Younhun",
""
],
[
"Koehler",
"Frederic",
""
],
[
"Moitra",
"Ankur",
""
],
[
"Mossel",
"Elchanan",
""
],
[
"Ramnarayan",
"Govind",
""
]
] | Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no rigorous guarantees. Determining the amount of data needed to correctly reconstruct ... |
1204.5999 | Michael Deem | Dirk M. Lorenz, Alice Jeng, and Michael W. Deem | The Emergence of Modularity in Biological Systems | 54 pages, 25 figures | Physics of Life Reviews, 8 (2011) 129-160 | 10.1016/j.plrev.2011.02.003 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this review, we discuss modularity and hierarchy in biological systems. We
review examples from protein structure, genetics, and biological networks of
modular partitioning of the geometry of biological space. We review theories to
explain modular organization of biology, with a focus on explaining how biology
may... | [
{
"created": "Thu, 26 Apr 2012 18:45:00 GMT",
"version": "v1"
}
] | 2015-06-04 | [
[
"Lorenz",
"Dirk M.",
""
],
[
"Jeng",
"Alice",
""
],
[
"Deem",
"Michael W.",
""
]
] | In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may s... |
2401.10211 | Zhengyi Li | Zhengyi Li, Menglu Li, Lida Zhu, Wen Zhang | Improving PTM Site Prediction by Coupling of Multi-Granularity Structure
and Multi-Scale Sequence Representation | null | null | null | null | q-bio.QM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein post-translational modification (PTM) site prediction is a
fundamental task in bioinformatics. Several computational methods have been
developed to predict PTM sites. However, existing methods ignore the structure
information and merely utilize protein sequences. Furthermore, designing a more
fine-grained str... | [
{
"created": "Thu, 4 Jan 2024 20:49:32 GMT",
"version": "v1"
}
] | 2024-01-19 | [
[
"Li",
"Zhengyi",
""
],
[
"Li",
"Menglu",
""
],
[
"Zhu",
"Lida",
""
],
[
"Zhang",
"Wen",
""
]
] | Protein post-translational modification (PTM) site prediction is a fundamental task in bioinformatics. Several computational methods have been developed to predict PTM sites. However, existing methods ignore the structure information and merely utilize protein sequences. Furthermore, designing a more fine-grained struc... |
2109.00364 | Florian Franke | Florian Franke, Sebatian Aland, Hans-Joachim B\"ohme, Anja
Voss-B\"ohme, Steffen Lange | Is cell segregation like oil and water: asymptotic versus transitory
regime | 41 pages, 11+11 figures, 1+1 table | PLoS Computational Biology, September 2022 | 10.1371/journal.pcbi.1010460 | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | Segregation of different cell types is a crucial process for the pattern
formation in tissues, in particular during embryogenesis. Since the involved
cell interactions are complex and difficult to measure individually in
experiments, mathematical modelling plays an increasingly important role to
unravel the mechanism... | [
{
"created": "Wed, 1 Sep 2021 12:59:52 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Oct 2021 06:04:19 GMT",
"version": "v2"
},
{
"created": "Wed, 13 Apr 2022 09:31:25 GMT",
"version": "v3"
},
{
"created": "Fri, 22 Jul 2022 08:25:09 GMT",
"version": "v4"
}
] | 2022-09-21 | [
[
"Franke",
"Florian",
""
],
[
"Aland",
"Sebatian",
""
],
[
"Böhme",
"Hans-Joachim",
""
],
[
"Voss-Böhme",
"Anja",
""
],
[
"Lange",
"Steffen",
""
]
] | Segregation of different cell types is a crucial process for the pattern formation in tissues, in particular during embryogenesis. Since the involved cell interactions are complex and difficult to measure individually in experiments, mathematical modelling plays an increasingly important role to unravel the mechanisms ... |
2403.11517 | Haibao Wang | Haibao Wang, Jun Kai Ho, Fan L. Cheng, Shuntaro C. Aoki, Yusuke
Muraki, Misato Tanaka and Yukiyasu Kamitani | Inter-individual and inter-site neural code conversion without shared
stimuli | null | null | null | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inter-individual variability in fine-grained functional brain organization
poses challenges for scalable data analysis and modeling. Functional alignment
techniques can help mitigate these individual differences but typically require
paired brain data with the same stimuli between individuals, which is often
unavaila... | [
{
"created": "Mon, 18 Mar 2024 07:10:52 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Aug 2024 11:16:16 GMT",
"version": "v2"
}
] | 2024-08-02 | [
[
"Wang",
"Haibao",
""
],
[
"Ho",
"Jun Kai",
""
],
[
"Cheng",
"Fan L.",
""
],
[
"Aoki",
"Shuntaro C.",
""
],
[
"Muraki",
"Yusuke",
""
],
[
"Tanaka",
"Misato",
""
],
[
"Kamitani",
"Yukiyasu",
""
]
] | Inter-individual variability in fine-grained functional brain organization poses challenges for scalable data analysis and modeling. Functional alignment techniques can help mitigate these individual differences but typically require paired brain data with the same stimuli between individuals, which is often unavailabl... |
1908.04875 | Casey Fleeter | Casey M. Fleeter, Gianluca Geraci, Daniele E. Schiavazzi, Andrew M.
Kahn, Alison L. Marsden | Multilevel and multifidelity uncertainty quantification for
cardiovascular hemodynamics | null | null | 10.1016/j.cma.2020.113030 | null | q-bio.QM physics.comp-ph stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Standard approaches for uncertainty quantification in cardiovascular modeling
pose challenges due to the large number of uncertain inputs and the significant
computational cost of realistic three-dimensional simulations. We propose an
efficient uncertainty quantification framework utilizing a multilevel
multifidelity... | [
{
"created": "Tue, 13 Aug 2019 22:10:47 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Apr 2020 23:44:26 GMT",
"version": "v2"
}
] | 2020-04-20 | [
[
"Fleeter",
"Casey M.",
""
],
[
"Geraci",
"Gianluca",
""
],
[
"Schiavazzi",
"Daniele E.",
""
],
[
"Kahn",
"Andrew M.",
""
],
[
"Marsden",
"Alison L.",
""
]
] | Standard approaches for uncertainty quantification in cardiovascular modeling pose challenges due to the large number of uncertain inputs and the significant computational cost of realistic three-dimensional simulations. We propose an efficient uncertainty quantification framework utilizing a multilevel multifidelity M... |
q-bio/0502037 | Jean-Pascal Pfister | Jean-Pascal Pfister, Taro Toyoizumi, David Barber, Wulfram Gerstner | Optimal Spike-Timing Dependent Plasticity for Precise Action Potential
Firing | 27 pages, 10 figures | null | null | null | q-bio.NC | null | In timing-based neural codes, neurons have to emit action potentials at
precise moments in time. We use a supervised learning paradigm to derive a
synaptic update rule that optimizes via gradient ascent the likelihood of
postsynaptic firing at one or several desired firing times. We find that the
optimal strategy of ... | [
{
"created": "Thu, 24 Feb 2005 16:28:38 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Pfister",
"Jean-Pascal",
""
],
[
"Toyoizumi",
"Taro",
""
],
[
"Barber",
"David",
""
],
[
"Gerstner",
"Wulfram",
""
]
] | In timing-based neural codes, neurons have to emit action potentials at precise moments in time. We use a supervised learning paradigm to derive a synaptic update rule that optimizes via gradient ascent the likelihood of postsynaptic firing at one or several desired firing times. We find that the optimal strategy of up... |
2208.00935 | Jia Qi Yip | Jia Qi Yip, Dianwen Ng, Bin Ma, Konstantin Pervushin, Eng Siong Chng | Amino Acid Classification in 2D NMR Spectra via Acoustic Signal
Embeddings | null | null | null | null | q-bio.QM eess.AS | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Nuclear Magnetic Resonance (NMR) is used in structural biology to
experimentally determine the structure of proteins, which is used in many areas
of biology and is an important part of drug development. Unfortunately, NMR
data can cost thousands of dollars per sample to collect and it can take a
specialist weeks to a... | [
{
"created": "Mon, 1 Aug 2022 15:36:22 GMT",
"version": "v1"
}
] | 2022-08-03 | [
[
"Yip",
"Jia Qi",
""
],
[
"Ng",
"Dianwen",
""
],
[
"Ma",
"Bin",
""
],
[
"Pervushin",
"Konstantin",
""
],
[
"Chng",
"Eng Siong",
""
]
] | Nuclear Magnetic Resonance (NMR) is used in structural biology to experimentally determine the structure of proteins, which is used in many areas of biology and is an important part of drug development. Unfortunately, NMR data can cost thousands of dollars per sample to collect and it can take a specialist weeks to ass... |
q-bio/0507041 | Jim Bashford | J.D. Bashford and P.D. Jarvis | A base pairing model of duplex formation I: Watson-Crick pairing
geometries | Latex file, 13 pages, no figures. Refereed draft of manuscript
submitted to Biopolymers | Biopolymers 78: 287-297, 2005 | 10.1002/bip.20282 | UTAS-PHYS-2004-05 | q-bio.BM | null | We present a base-pairing model of oligonuleotide duplex formation and show
in detail its equivalence to the Nearest-Neighbour dimer methods from fits to
free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids
containing only Watson Crick pairs. In this approach the connection between
rank-deficien... | [
{
"created": "Thu, 28 Jul 2005 04:37:03 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bashford",
"J. D.",
""
],
[
"Jarvis",
"P. D.",
""
]
] | We present a base-pairing model of oligonuleotide duplex formation and show in detail its equivalence to the Nearest-Neighbour dimer methods from fits to free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids containing only Watson Crick pairs. In this approach the connection between rank-deficient ... |
2005.02388 | Endre Cs\'oka | Endre Cs\'oka | Application-oriented mathematical algorithms for group testing | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have a large number of samples and we want to find the infected ones using
as few number of tests as possible. We can use group testing which tells about
a small group of people whether at least one of them is infected. Group testing
is particularly efficient if the infection rate is low. The goal of this
article ... | [
{
"created": "Tue, 5 May 2020 14:40:46 GMT",
"version": "v1"
}
] | 2020-05-07 | [
[
"Csóka",
"Endre",
""
]
] | We have a large number of samples and we want to find the infected ones using as few number of tests as possible. We can use group testing which tells about a small group of people whether at least one of them is infected. Group testing is particularly efficient if the infection rate is low. The goal of this article is... |
2402.10308 | Wouter-Jan Rappel | Timothy J Tyree, Patrick Murphy, Wouter-Jan Rappel | Annihilation dynamics during spiral defect chaos revealed by particle
models | 11 pages, 11 figures | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Pair-annihilation events are ubiquitous in a variety of spatially extended
systems and are often studied using computationally expensive simulations. Here
we develop an approach in which we simulate the pair-annihilation of spiral
wave tips in cardiac models using a computationally efficient particle model.
Spiral wa... | [
{
"created": "Thu, 15 Feb 2024 20:20:29 GMT",
"version": "v1"
}
] | 2024-02-19 | [
[
"Tyree",
"Timothy J",
""
],
[
"Murphy",
"Patrick",
""
],
[
"Rappel",
"Wouter-Jan",
""
]
] | Pair-annihilation events are ubiquitous in a variety of spatially extended systems and are often studied using computationally expensive simulations. Here we develop an approach in which we simulate the pair-annihilation of spiral wave tips in cardiac models using a computationally efficient particle model. Spiral wave... |
1710.00718 | Yannis Pantazis | Yannis Pantazis and Ioannis Tsamardinos | A Unified Approach for Sparse Dynamical System Inference from Temporal
Measurements | 13 pages, 3 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Temporal variations in biological systems and more generally in natural
sciences are typically modelled as a set of Ordinary, Partial, or Stochastic
Differential or Difference Equations. Algorithms for learning the structure and
the parameters of a dynamical system are distinguished based on whether time is
discrete ... | [
{
"created": "Mon, 2 Oct 2017 15:16:55 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Oct 2017 18:48:45 GMT",
"version": "v2"
},
{
"created": "Sat, 19 Jan 2019 21:25:01 GMT",
"version": "v3"
}
] | 2019-01-23 | [
[
"Pantazis",
"Yannis",
""
],
[
"Tsamardinos",
"Ioannis",
""
]
] | Temporal variations in biological systems and more generally in natural sciences are typically modelled as a set of Ordinary, Partial, or Stochastic Differential or Difference Equations. Algorithms for learning the structure and the parameters of a dynamical system are distinguished based on whether time is discrete or... |
0711.0715 | Swarnendu Tripathi | Swarnendu Tripathi and John J. Portman | Inherent flexibility and protein function: the open/closed
conformational transition of the N-terminal domain of calmodulin | 21 pages, 8 figures | J. Chem. Phys. 128, 205104 (2008) | 10.1063/1.2928634 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The key to understanding a protein's function often lies in its
conformational dynamics. We develop a coarse-grained variational model to
investigate the interplay between structural transitions, conformational
flexibility and function of N-terminal calmodulin (nCaM) domain. In this model,
two energy basins correspon... | [
{
"created": "Mon, 5 Nov 2007 18:29:14 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Jul 2008 17:13:30 GMT",
"version": "v2"
}
] | 2008-07-10 | [
[
"Tripathi",
"Swarnendu",
""
],
[
"Portman",
"John J.",
""
]
] | The key to understanding a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility and function of N-terminal calmodulin (nCaM) domain. In this model, two energy basins correspondi... |
1107.4104 | Jiapu Zhang | Jiapu Zhang, David Y. Gao, and Johh Yearwood | A novel canonical dual computational approach for prion AGAAAAGA amyloid
fibril molecular modeling | null | J Theor Biol 284 (1) 149-157 (2011); selected by Protein
Crystallography Newsletter Volume 3, No. 9, September 2011, Crystallography
Times; Prions Research Today Volume 7 Issue 7, July 2011, p.14; the 18th of
the Top 25 Hottest Articles (picked up from papers of Jul 2011 to Sept 2011
of J Theor Biol) | 10.1016/j.jtbi.2011.06.024 | null | q-bio.BM cs.CE math-ph math.MP math.OC | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Many experimental studies have shown that the prion AGAAAAGA palindrome
hydrophobic region (113-120) has amyloid fibril forming properties and plays an
important role in prion diseases. However, due to the unstable, noncrystalline
and insoluble nature of the amyloid fibril, to date structural information on
AGAAAAGA ... | [
{
"created": "Mon, 18 Jul 2011 23:20:34 GMT",
"version": "v1"
}
] | 2013-12-10 | [
[
"Zhang",
"Jiapu",
""
],
[
"Gao",
"David Y.",
""
],
[
"Yearwood",
"Johh",
""
]
] | Many experimental studies have shown that the prion AGAAAAGA palindrome hydrophobic region (113-120) has amyloid fibril forming properties and plays an important role in prion diseases. However, due to the unstable, noncrystalline and insoluble nature of the amyloid fibril, to date structural information on AGAAAAGA re... |
1912.00985 | Joana Fradinho | Joana Fradinho, Adrian Oehmen and Maria Reis | Improving polyhydroxyalkanoates production in phototrophic mixed
cultures by optimizing accumulator reactor operating conditions | 29 pages, 4 figures, 4 tables | null | 10.1016/j.ijbiomac.2018.12.270 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Polyhydroxyalkanoates (PHAs) production with phototrophic mixed cultures
(PMCs) has been recently proposed. These cultures can be selected under the
permanent presence of carbon and the PHA production can be enhanced in
subsequent accumulation steps. To optimize the PHA production in accumulator
reactors, this work e... | [
{
"created": "Mon, 2 Dec 2019 18:23:42 GMT",
"version": "v1"
}
] | 2019-12-03 | [
[
"Fradinho",
"Joana",
""
],
[
"Oehmen",
"Adrian",
""
],
[
"Reis",
"Maria",
""
]
] | Polyhydroxyalkanoates (PHAs) production with phototrophic mixed cultures (PMCs) has been recently proposed. These cultures can be selected under the permanent presence of carbon and the PHA production can be enhanced in subsequent accumulation steps. To optimize the PHA production in accumulator reactors, this work eva... |
2209.05688 | M. Ali Al-Radhawi | M. Ali Al-Radhawi, Shubham Tripathi, Yun Zhang, Eduardo D. Sontag, and
Herbert Levine | Epigenetic factor competition reshapes the EMT landscape | null | Proc Natl Acad Sci USA, 119:e2210844119, 2022 | 10.1073/pnas.2210844119 | null | q-bio.MN q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The emergence of and transitions between distinct phenotypes in isogenic
cells can be attributed to the intricate interplay of epigenetic marks,
external signals, and gene regulatory elements. These elements include
chromatin remodelers, histone modifiers, transcription factors, and regulatory
RNAs. Mathematical mode... | [
{
"created": "Tue, 13 Sep 2022 01:57:49 GMT",
"version": "v1"
}
] | 2022-10-19 | [
[
"Al-Radhawi",
"M. Ali",
""
],
[
"Tripathi",
"Shubham",
""
],
[
"Zhang",
"Yun",
""
],
[
"Sontag",
"Eduardo D.",
""
],
[
"Levine",
"Herbert",
""
]
] | The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models... |
1210.5348 | Erich Schmid | Erich W. Schmid and Wolfgang Fink | Operational Design Considerations for Retinal Prostheses | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Three critical improvements for present day and future retinal vision
implants are proposed and discussed: (1) A time profile for the stimulation
current that leads predominantly to transverse stimulation of nerve cells; (2)
auxiliary electric currents for electric field shaping with a time profile
chosen such that t... | [
{
"created": "Fri, 19 Oct 2012 09:07:33 GMT",
"version": "v1"
}
] | 2012-10-22 | [
[
"Schmid",
"Erich W.",
""
],
[
"Fink",
"Wolfgang",
""
]
] | Three critical improvements for present day and future retinal vision implants are proposed and discussed: (1) A time profile for the stimulation current that leads predominantly to transverse stimulation of nerve cells; (2) auxiliary electric currents for electric field shaping with a time profile chosen such that the... |
2401.00102 | Phuc Nguyen | Phuc Nguyen, Rohit Arora, Elliot D. Hill, Jasper Braun, Alexandra
Morgan, Liza M. Quintana, Gabrielle Mazzoni, Ghee Rye Lee, Rima Arnaout, Ramy
Arnaout | $\textit{greylock}$: A Python Package for Measuring The Composition of
Complex Datasets | 42 pages, many figures. Many thanks to Ralf Bundschuh for help with
the submission process | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Machine-learning datasets are typically characterized by measuring their size
and class balance. However, there exists a richer and potentially more useful
set of measures, termed diversity measures, that incorporate elements'
frequencies and between-element similarities. Although these have been
available in the R a... | [
{
"created": "Fri, 29 Dec 2023 23:51:48 GMT",
"version": "v1"
}
] | 2024-01-02 | [
[
"Nguyen",
"Phuc",
""
],
[
"Arora",
"Rohit",
""
],
[
"Hill",
"Elliot D.",
""
],
[
"Braun",
"Jasper",
""
],
[
"Morgan",
"Alexandra",
""
],
[
"Quintana",
"Liza M.",
""
],
[
"Mazzoni",
"Gabrielle",
""
],
[
... | Machine-learning datasets are typically characterized by measuring their size and class balance. However, there exists a richer and potentially more useful set of measures, termed diversity measures, that incorporate elements' frequencies and between-element similarities. Although these have been available in the R and... |
2103.09563 | Werner M\"uller | Elham Yousefi and Werner G. M\"uller | Impact of the error structure on the design and analysis of enzyme
kinetic models | null | null | null | null | q-bio.MN stat.ME | http://creativecommons.org/licenses/by/4.0/ | The statistical analysis of enzyme kinetic reactions usually involves models
of the response functions which are well defined on the basis of
Michaelis-Menten type equations. The error structure however is often without
good reason assumed as additive Gaussian noise. This simple assumption may lead
to undesired prope... | [
{
"created": "Wed, 17 Mar 2021 10:59:23 GMT",
"version": "v1"
}
] | 2021-03-19 | [
[
"Yousefi",
"Elham",
""
],
[
"Müller",
"Werner G.",
""
]
] | The statistical analysis of enzyme kinetic reactions usually involves models of the response functions which are well defined on the basis of Michaelis-Menten type equations. The error structure however is often without good reason assumed as additive Gaussian noise. This simple assumption may lead to undesired propert... |
1712.00843 | Marinka Zitnik | Monica Agrawal, Marinka Zitnik, Jure Leskovec | Large-scale analysis of disease pathways in the human interactome | null | Pacific Symposium on Biocomputing 23:111-122(2018) | null | null | q-bio.MN cs.LG cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Discovering disease pathways, which can be defined as sets of proteins
associated with a given disease, is an important problem that has the potential
to provide clinically actionable insights for disease diagnosis, prognosis, and
treatment. Computational methods aid the discovery by relying on
protein-protein intera... | [
{
"created": "Sun, 3 Dec 2017 21:51:07 GMT",
"version": "v1"
}
] | 2017-12-05 | [
[
"Agrawal",
"Monica",
""
],
[
"Zitnik",
"Marinka",
""
],
[
"Leskovec",
"Jure",
""
]
] | Discovering disease pathways, which can be defined as sets of proteins associated with a given disease, is an important problem that has the potential to provide clinically actionable insights for disease diagnosis, prognosis, and treatment. Computational methods aid the discovery by relying on protein-protein interact... |
1611.08929 | Md Jahoor Alam | Md. Jahoor Alam | GnRH induced Phase Synchrony of Coupled Neurons | 9 pages, 3 figures | null | null | null | q-bio.MN q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gonadotropin-releasing hormone (GnRH) is reported to control mammalian
reproductive processes. GnRH a neurohormone which is pulsatile released into
the pituitary portal blood by hypothalamic GnRH neurons. In the present study,
the phase synchronization among a population of identical neurons subjected to
a pool of co... | [
{
"created": "Sun, 27 Nov 2016 22:43:24 GMT",
"version": "v1"
}
] | 2016-12-06 | [
[
"Alam",
"Md. Jahoor",
""
]
] | Gonadotropin-releasing hormone (GnRH) is reported to control mammalian reproductive processes. GnRH a neurohormone which is pulsatile released into the pituitary portal blood by hypothalamic GnRH neurons. In the present study, the phase synchronization among a population of identical neurons subjected to a pool of coup... |
2108.05848 | Ilan Gronau | Zehavit Leibovich and Ilan Gronau | Eliminating unwanted patterns with minimal interference | This research was done as part of Zehavit Leibovich's dissertation
for an M.Sc degree in Computer Science. Relevant code available at
https://github.com/zehavitc/EliminatingDNAPatterns.git | null | null | null | q-bio.BM cs.CE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Artificial synthesis of DNA molecules is an essential part of the study of
biological mechanisms. The design of a synthetic DNA molecule usually involves
many objectives. One of the important objectives is to eliminate short sequence
patterns that correspond to binding sites of restriction enzymes or
transcription fa... | [
{
"created": "Tue, 3 Aug 2021 19:51:43 GMT",
"version": "v1"
}
] | 2021-08-13 | [
[
"Leibovich",
"Zehavit",
""
],
[
"Gronau",
"Ilan",
""
]
] | Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence patterns that correspond to binding sites of restriction enzymes or transcription fact... |
2206.13345 | Weifeng Li | Zechen Wang, Liangzhen Zheng, Sheng Wang, Mingzhi Lin, Zhihao Wang,
Adams Wai-Kin Kong, Yuguang Mu, Yanjie Wei, Weifeng Li | A fully differentiable ligand pose optimization framework guided by deep
learning and traditional scoring functions | null | Brief Bioinform . 2023 Jan 19;24(1):bbac520 | 10.1093/bib/bbac520 | null | q-bio.QM q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The machine learning (ML) and deep learning (DL) techniques are widely
recognized to be powerful tools for virtual drug screening. The recently
reported ML- or DL-based scoring functions have shown exciting performance in
predicting protein-ligand binding affinities with fruitful application
prospects. However, the d... | [
{
"created": "Mon, 27 Jun 2022 14:49:40 GMT",
"version": "v1"
}
] | 2023-07-07 | [
[
"Wang",
"Zechen",
""
],
[
"Zheng",
"Liangzhen",
""
],
[
"Wang",
"Sheng",
""
],
[
"Lin",
"Mingzhi",
""
],
[
"Wang",
"Zhihao",
""
],
[
"Kong",
"Adams Wai-Kin",
""
],
[
"Mu",
"Yuguang",
""
],
[
"Wei",
... | The machine learning (ML) and deep learning (DL) techniques are widely recognized to be powerful tools for virtual drug screening. The recently reported ML- or DL-based scoring functions have shown exciting performance in predicting protein-ligand binding affinities with fruitful application prospects. However, the dif... |
2311.16946 | Jacob Durrant | Mayar Ahmed, Alex M. Maldonado, Jacob D. Durrant | From Byte to Bench to Bedside: Molecular Dynamics Simulations and Drug
Discovery | 15 pages including references, 0 figures | null | null | null | q-bio.QM q-bio.BM | http://creativecommons.org/licenses/by-sa/4.0/ | Molecular dynamics (MD) simulations and computer-aided drug design (CADD)
have advanced substantially over the past two decades, thanks to continuous
computer hardware and software improvements. Given these advancements, MD
simulations are poised to become even more powerful tools for investigating the
dynamic intera... | [
{
"created": "Tue, 28 Nov 2023 16:49:04 GMT",
"version": "v1"
}
] | 2023-11-29 | [
[
"Ahmed",
"Mayar",
""
],
[
"Maldonado",
"Alex M.",
""
],
[
"Durrant",
"Jacob D.",
""
]
] | Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer hardware and software improvements. Given these advancements, MD simulations are poised to become even more powerful tools for investigating the dynamic interact... |
1806.08454 | Dalit Engelhardt | Dalit Engelhardt and Eugene I. Shakhnovich | Mutation rate variability as a driving force in adaptive evolution | null | Phys. Rev. E 99, 022424 (2019) | 10.1103/PhysRevE.99.022424 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mutation rate is a key determinant of the pace as well as outcome of
evolution, and variability in this rate has been shown in different scenarios
to play a key role in evolutionary adaptation and resistance evolution under
stress caused by selective pressure. Here we investigate the dynamics of
resistance fixation i... | [
{
"created": "Thu, 21 Jun 2018 23:30:17 GMT",
"version": "v1"
},
{
"created": "Sun, 3 Feb 2019 17:30:17 GMT",
"version": "v2"
}
] | 2019-03-01 | [
[
"Engelhardt",
"Dalit",
""
],
[
"Shakhnovich",
"Eugene I.",
""
]
] | Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress caused by selective pressure. Here we investigate the dynamics of resistance fixation in ... |
2203.10867 | Emilio N.M. Cirillo | Claudio Durastanti and Emilio N.M. Cirillo and Ilaria De Benedictis
and Mario Ledda and Antonio Sciortino and Antonella Lisi and Annalisa
Convertino and Valentina Mussi | Statistical classification for Raman spectra of tumoral genomic DNA | null | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We exploit Surface-Enhanced Raman Scattering (SERS) to investigate aqueous
droplets of genomic DNA deposited onto silver-coated silicon nanowires and we
show that it is possible to efficiently discriminate between spectra of tumoral
and healthy cells. To assess the robustness of the proposed technique, we
develop two... | [
{
"created": "Mon, 21 Mar 2022 10:41:07 GMT",
"version": "v1"
}
] | 2022-03-22 | [
[
"Durastanti",
"Claudio",
""
],
[
"Cirillo",
"Emilio N. M.",
""
],
[
"De Benedictis",
"Ilaria",
""
],
[
"Ledda",
"Mario",
""
],
[
"Sciortino",
"Antonio",
""
],
[
"Lisi",
"Antonella",
""
],
[
"Convertino",
"Annal... | We exploit Surface-Enhanced Raman Scattering (SERS) to investigate aqueous droplets of genomic DNA deposited onto silver-coated silicon nanowires and we show that it is possible to efficiently discriminate between spectra of tumoral and healthy cells. To assess the robustness of the proposed technique, we develop two d... |
2301.03408 | Christine Ahrends | Christine Ahrends (1), Diego Vidaurre (1 and 2) ((1) Center of
Functionally Integrative Neuroscience, Department of Clinical Medicine,
Aarhus University, Denmark, (2) Department of Psychiatry, University of
Oxford, United Kingdom) | Dynamic Functional Connectivity | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Most generally, dynamic functional connectivity (FC) refers to the
non-instantaneous couplings across timeseries from a set of brain areas, here
as measured by fMRI. This is in contrast to static FC, which is defined as
purely instantaneous relations. In this chapter, we provide a hands-on
description of a non-exhaus... | [
{
"created": "Mon, 9 Jan 2023 15:04:12 GMT",
"version": "v1"
}
] | 2023-01-10 | [
[
"Ahrends",
"Christine",
"",
"1 and 2"
],
[
"Vidaurre",
"Diego",
"",
"1 and 2"
]
] | Most generally, dynamic functional connectivity (FC) refers to the non-instantaneous couplings across timeseries from a set of brain areas, here as measured by fMRI. This is in contrast to static FC, which is defined as purely instantaneous relations. In this chapter, we provide a hands-on description of a non-exhausti... |
1806.06412 | Yuri A. Dabaghian | Luca Perotti, Justin DeVito, Daniel Bessis, Yuri Dabaghian | Discrete structure of the brain rhythms | 17 pages, 9 figures | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuronal activity in the brain generates synchronous oscillations of the
Local Field Potential (LFP). The traditional analyses of the LFPs are based on
decomposing the signal into simpler components, such as sinusoidal harmonics.
However, a common drawback of such methods is that the decomposition primitives
are usua... | [
{
"created": "Sun, 17 Jun 2018 16:42:50 GMT",
"version": "v1"
}
] | 2018-06-19 | [
[
"Perotti",
"Luca",
""
],
[
"DeVito",
"Justin",
""
],
[
"Bessis",
"Daniel",
""
],
[
"Dabaghian",
"Yuri",
""
]
] | Neuronal activity in the brain generates synchronous oscillations of the Local Field Potential (LFP). The traditional analyses of the LFPs are based on decomposing the signal into simpler components, such as sinusoidal harmonics. However, a common drawback of such methods is that the decomposition primitives are usuall... |
1503.05440 | Lionel Roques | L. Roques, E. Walker, P. Franck, S. Soubeyrand, E. K. Klein | Using genetic data to estimate diffusion rates in heterogeneous
landscapes | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Having a precise knowledge of the dispersal ability of a population in a
heterogeneous environment is of critical importance in agroecology and
conservation biology as it can provide management tools to limit the effects of
pests or to increase the survival of endangered species. In this paper, we
propose a mechanist... | [
{
"created": "Wed, 18 Mar 2015 15:03:16 GMT",
"version": "v1"
}
] | 2015-03-19 | [
[
"Roques",
"L.",
""
],
[
"Walker",
"E.",
""
],
[
"Franck",
"P.",
""
],
[
"Soubeyrand",
"S.",
""
],
[
"Klein",
"E. K.",
""
]
] | Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic... |
1705.10854 | Larissa Albantakis | Larissa Albantakis | A Tale of Two Animats: What does it take to have goals? | This article is a contribution to the FQXi 2016-2017 essay contest
"Wandering Towards a Goal" | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | What does it take for a system, biological or not, to have goals? Here, this
question is approached in the context of in silico artificial evolution. By
examining the informational and causal properties of artificial organisms
('animats') controlled by small, adaptive neural networks (Markov Brains), this
essay discu... | [
{
"created": "Tue, 30 May 2017 20:19:17 GMT",
"version": "v1"
}
] | 2017-06-01 | [
[
"Albantakis",
"Larissa",
""
]
] | What does it take for a system, biological or not, to have goals? Here, this question is approached in the context of in silico artificial evolution. By examining the informational and causal properties of artificial organisms ('animats') controlled by small, adaptive neural networks (Markov Brains), this essay discuss... |
1611.01037 | Valery Kirzhner | Valery Kirzhner, Zeev Volkovich, Renata Avros and Katerina Korenblat | Analysis of Metagenome Composition by the Method of Random Primers | 18 pages, 4 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metagenome, a mixture of different genomes (as a rule, bacterial), represents
a pattern, and the analysis of its composition is, currently, one of the
challenging problems of bioinformatics. In the present study, the possibility
of evaluating metagenome composition by DNA-marker methods is investigated.
These methods... | [
{
"created": "Wed, 2 Nov 2016 18:43:14 GMT",
"version": "v1"
}
] | 2016-11-04 | [
[
"Kirzhner",
"Valery",
""
],
[
"Volkovich",
"Zeev",
""
],
[
"Avros",
"Renata",
""
],
[
"Korenblat",
"Katerina",
""
]
] | Metagenome, a mixture of different genomes (as a rule, bacterial), represents a pattern, and the analysis of its composition is, currently, one of the challenging problems of bioinformatics. In the present study, the possibility of evaluating metagenome composition by DNA-marker methods is investigated. These methods a... |
1603.01789 | Pu Tian | Shiyang Long and Pu Tian | Nonlinear backbone torsional pair correlations in proteins | 25 pages, 8 figures | Scientific Report, 6:34481, 2016 | 10.1038/srep34481 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein allostery requires dynamical structural correlations. Physical origin
of which, however, remain elusive despite intensive studies during last two
decades. Based on analysis of molecular dynamics (MD) simulation trajectories
for ten proteins with different sizes and folds, we found that nonlinear
backbone tors... | [
{
"created": "Sun, 6 Mar 2016 05:41:23 GMT",
"version": "v1"
},
{
"created": "Fri, 6 May 2016 02:55:23 GMT",
"version": "v2"
}
] | 2017-02-23 | [
[
"Long",
"Shiyang",
""
],
[
"Tian",
"Pu",
""
]
] | Protein allostery requires dynamical structural correlations. Physical origin of which, however, remain elusive despite intensive studies during last two decades. Based on analysis of molecular dynamics (MD) simulation trajectories for ten proteins with different sizes and folds, we found that nonlinear backbone torsio... |
1803.02136 | Krzysztof Bartoszek | Krzysztof Bartoszek | Limit distribution of the quartet balance index for Aldous's b>=0-model | null | Applicationes Mathematicae 47:29-44, 2020 | 10.4064/am2385-6-2019 | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper builds up on T. Martinez-Coronado, A. Mir, F. Rossello and G.
Valiente's work "A balance index for phylogenetic trees based on quartets",
introducing a new balance index for trees. We show here that this balance
index, in the case of Aldous's b>=0-model, convergences weakly to a
distribution that can be ch... | [
{
"created": "Tue, 6 Mar 2018 12:17:53 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Nov 2018 19:00:11 GMT",
"version": "v2"
},
{
"created": "Fri, 30 Aug 2019 06:26:37 GMT",
"version": "v3"
}
] | 2020-11-23 | [
[
"Bartoszek",
"Krzysztof",
""
]
] | This paper builds up on T. Martinez-Coronado, A. Mir, F. Rossello and G. Valiente's work "A balance index for phylogenetic trees based on quartets", introducing a new balance index for trees. We show here that this balance index, in the case of Aldous's b>=0-model, convergences weakly to a distribution that can be char... |
2405.06851 | Francesca Mignacco | Francesca Mignacco, Chi-Ning Chou, SueYeon Chung | Nonlinear classification of neural manifolds with contextual information | 5 pages, 5 figures | null | null | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech cs.NE stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding how neural systems efficiently process information through
distributed representations is a fundamental challenge at the interface of
neuroscience and machine learning. Recent approaches analyze the statistical
and geometrical attributes of neural representations as population-level
mechanistic descript... | [
{
"created": "Fri, 10 May 2024 23:37:31 GMT",
"version": "v1"
}
] | 2024-05-14 | [
[
"Mignacco",
"Francesca",
""
],
[
"Chou",
"Chi-Ning",
""
],
[
"Chung",
"SueYeon",
""
]
] | Understanding how neural systems efficiently process information through distributed representations is a fundamental challenge at the interface of neuroscience and machine learning. Recent approaches analyze the statistical and geometrical attributes of neural representations as population-level mechanistic descriptor... |
1509.06863 | Youdong Mao | Zhou Yu, Wei Li Wang, Luis R. Castillo-Menendez, Joseph Sodroski,
Youdong Mao | On the parameters affecting dual-target-function evaluation of
single-particle selection from cryo-electron micrographs | 62 pages, 11 figures. arXiv admin note: text overlap with
arXiv:1309.2618 | BMC Bioinformatics 2019; 20:169 | 10.1186/s12859-019-2714-8 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the analysis of frozen hydrated biomolecules by single-particle
cryo-electron microscopy, template-based particle picking by a target function
called fast local correlation (FLC) allows a large number of particle images to
be automatically picked from micrographs. A second, independent target function
based on max... | [
{
"created": "Wed, 23 Sep 2015 07:13:28 GMT",
"version": "v1"
}
] | 2019-04-16 | [
[
"Yu",
"Zhou",
""
],
[
"Wang",
"Wei Li",
""
],
[
"Castillo-Menendez",
"Luis R.",
""
],
[
"Sodroski",
"Joseph",
""
],
[
"Mao",
"Youdong",
""
]
] | In the analysis of frozen hydrated biomolecules by single-particle cryo-electron microscopy, template-based particle picking by a target function called fast local correlation (FLC) allows a large number of particle images to be automatically picked from micrographs. A second, independent target function based on maxim... |
1206.0973 | Uwe C. T\"auber | Ulrich Dobramysl and Uwe C. Tauber (Virginia Tech) | Environmental vs. demographic variability in two-species predator-prey
models | 5 pages, 4 figures included; to appear in Phys. Rev. Lett. (2013) | Phys. Rev. Lett. 110 (2013) 048105 | 10.1103/PhysRevLett.110.048105 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the competing effects and relative importance of intrinsic
demographic and environmental variability on the evolutionary dynamics of a
stochastic two-species Lotka-Volterra model by means of Monte Carlo simulations
on a two-dimensional lattice. Individuals are assigned inheritable predation
efficiencie... | [
{
"created": "Tue, 5 Jun 2012 15:59:50 GMT",
"version": "v1"
},
{
"created": "Fri, 28 Dec 2012 17:43:28 GMT",
"version": "v2"
}
] | 2013-01-28 | [
[
"Dobramysl",
"Ulrich",
"",
"Virginia Tech"
],
[
"Tauber",
"Uwe C.",
"",
"Virginia Tech"
]
] | We investigate the competing effects and relative importance of intrinsic demographic and environmental variability on the evolutionary dynamics of a stochastic two-species Lotka-Volterra model by means of Monte Carlo simulations on a two-dimensional lattice. Individuals are assigned inheritable predation efficiencies;... |
1605.03553 | Kieran Fox | Kieran C.R. Fox, Yoona Kang, Michael Lifshitz, Kalina Christoff | Increasing cognitive-emotional flexibility with meditation and hypnosis:
The cognitive neuroscience of de-automatization | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Meditation and hypnosis both aim to facilitate cognitive-emotional
flexibility, i.e., the "de-automatization" of thought and behavior. However,
little research or theory has addressed how internal thought patterns might
change after such interventions, even though alterations in the internal flow
of consciousness may... | [
{
"created": "Wed, 11 May 2016 19:06:35 GMT",
"version": "v1"
}
] | 2016-05-12 | [
[
"Fox",
"Kieran C. R.",
""
],
[
"Kang",
"Yoona",
""
],
[
"Lifshitz",
"Michael",
""
],
[
"Christoff",
"Kalina",
""
]
] | Meditation and hypnosis both aim to facilitate cognitive-emotional flexibility, i.e., the "de-automatization" of thought and behavior. However, little research or theory has addressed how internal thought patterns might change after such interventions, even though alterations in the internal flow of consciousness may p... |
2210.02183 | Fabiano L. Ribeiro | William Roberto Luiz S. Pereira and Fabiano L. Ribeiro | The metabolic origins of big size in aquatic mammals | null | null | null | null | q-bio.PE q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The group of large aquatic mammals has representatives being the largest
living beings on earth, surpassing the weight and size of dinosaurs. In this
paper, we present some empirical evidence and a mathematical model to argue
that fat accumulation in marine mammals triggers a series of metabolic events
that result in... | [
{
"created": "Tue, 4 Oct 2022 17:32:33 GMT",
"version": "v1"
}
] | 2022-10-06 | [
[
"Pereira",
"William Roberto Luiz S.",
""
],
[
"Ribeiro",
"Fabiano L.",
""
]
] | The group of large aquatic mammals has representatives being the largest living beings on earth, surpassing the weight and size of dinosaurs. In this paper, we present some empirical evidence and a mathematical model to argue that fat accumulation in marine mammals triggers a series of metabolic events that result in t... |
0710.1622 | Peter Csermely | Robin Palotai, Mate S. Szalay, Peter Csermely | Chaperones as integrators of cellular networks: Changes of cellular
integrity in stress and diseases | 13 pages, 3 figures, 1 glossary | IUBMB Life (2008) 60, 10-15 | 10.1002/iub.8 | null | q-bio.MN | null | Cellular networks undergo rearrangements during stress and diseases. In
un-stressed state the yeast protein-protein interaction network (interactome)
is highly compact, and the centrally organized modules have a large overlap.
During stress several original modules became more separated, and a number of
novel modules... | [
{
"created": "Mon, 8 Oct 2007 19:32:35 GMT",
"version": "v1"
},
{
"created": "Sat, 23 Feb 2008 20:16:18 GMT",
"version": "v2"
}
] | 2008-02-23 | [
[
"Palotai",
"Robin",
""
],
[
"Szalay",
"Mate S.",
""
],
[
"Csermely",
"Peter",
""
]
] | Cellular networks undergo rearrangements during stress and diseases. In un-stressed state the yeast protein-protein interaction network (interactome) is highly compact, and the centrally organized modules have a large overlap. During stress several original modules became more separated, and a number of novel modules a... |
1607.05398 | Ross McVinish | R.J.G. Lester and R. McVinish | What causes the increase in aggregation as a parasite moves up a food
chain? | This is a preprint. The definitive version has been published under
the title "Does moving up a food chain increase aggregation in parasites?" | Journal of the Royal Society Interface, 13 (2016) 20160102 | 10.1098/rsif.2016.0102 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | General laws in ecological parasitology are scarce. Here we evaluate data
published by over 100 authors to determine whether the number of hosts in a
life cycle is associated with the degree of aggregation of fish parasites at
different stages. Parasite species were grouped taxonomically to produce 20 or
more data po... | [
{
"created": "Tue, 19 Jul 2016 04:24:26 GMT",
"version": "v1"
}
] | 2016-07-20 | [
[
"Lester",
"R. J. G.",
""
],
[
"McVinish",
"R.",
""
]
] | General laws in ecological parasitology are scarce. Here we evaluate data published by over 100 authors to determine whether the number of hosts in a life cycle is associated with the degree of aggregation of fish parasites at different stages. Parasite species were grouped taxonomically to produce 20 or more data poin... |
1007.4461 | Tsvi Tlusty | Yonatan Savir, Elad Noor, Ron Milo and Tsvi Tlusty | Cross-species analysis traces adaptation of Rubisco towards optimality
in a low dimensional landscape | http://www.pnas.org/content/107/8/3475.short
http://www.ncbi.nlm.nih.gov/pubmed/20142476
http://www.weizmann.ac.il/complex/tlusty/papers/PNAS2010.pdf | PNAS February 23, 2010 vol. 107 no. 8 3475-3480 | 10.1073/pnas.0911663107 | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rubisco, probably the most abundant protein in the biosphere, performs an
essential part in the process of carbon fixation through photosynthesis thus
facilitating life on earth. Despite the significant effect that Rubisco has on
the fitness of plants and other photosynthetic organisms, this enzyme is known
to have a... | [
{
"created": "Mon, 26 Jul 2010 13:51:15 GMT",
"version": "v1"
}
] | 2010-07-27 | [
[
"Savir",
"Yonatan",
""
],
[
"Noor",
"Elad",
""
],
[
"Milo",
"Ron",
""
],
[
"Tlusty",
"Tsvi",
""
]
] | Rubisco, probably the most abundant protein in the biosphere, performs an essential part in the process of carbon fixation through photosynthesis thus facilitating life on earth. Despite the significant effect that Rubisco has on the fitness of plants and other photosynthetic organisms, this enzyme is known to have a r... |
1409.0675 | Felix Polyakov | Felix Polyakov | Affine differential geometry and smoothness maximization as tools for
identifying geometric movement primitives | The current version of the manuscript is result of significant
revision. It contains novel solutions, some formulations and explanations
have been corrected and in many parts of the text improved. The manuscript
now contains discussion about performance of the compromised motor control
system in the framework o... | null | null | null | q-bio.NC math.DG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuroscientific studies of drawing-like movements usually analyze neural
representation of either geometric (eg. direction, shape) or temporal (eg.
speed) features of trajectories rather than trajectory's representation as a
whole. This work is about empirically supported mathematical ideas behind
splitting and mergi... | [
{
"created": "Tue, 2 Sep 2014 11:50:34 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Oct 2014 18:51:10 GMT",
"version": "v2"
},
{
"created": "Mon, 29 Dec 2014 20:53:43 GMT",
"version": "v3"
},
{
"created": "Wed, 27 Jan 2016 20:47:11 GMT",
"version": "v4"
}
] | 2016-01-28 | [
[
"Polyakov",
"Felix",
""
]
] | Neuroscientific studies of drawing-like movements usually analyze neural representation of either geometric (eg. direction, shape) or temporal (eg. speed) features of trajectories rather than trajectory's representation as a whole. This work is about empirically supported mathematical ideas behind splitting and merging... |
1109.6231 | Jeremy Gunawardena | Jeremy Gunawardena | A linear elimination framework | 27 pages, 8 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Key insights in molecular biology, such as enzyme kinetics, protein allostery
and gene regulation emerged from quantitative analysis based on time-scale
separation, allowing internal complexity to be eliminated and resulting in the
well-known formulas of Michaelis-Menten, Monod-Wyman-Changeux and
Ackers-Johnson-Shea.... | [
{
"created": "Wed, 28 Sep 2011 15:04:51 GMT",
"version": "v1"
}
] | 2011-09-29 | [
[
"Gunawardena",
"Jeremy",
""
]
] | Key insights in molecular biology, such as enzyme kinetics, protein allostery and gene regulation emerged from quantitative analysis based on time-scale separation, allowing internal complexity to be eliminated and resulting in the well-known formulas of Michaelis-Menten, Monod-Wyman-Changeux and Ackers-Johnson-Shea. I... |
2406.17086 | Yifan Yang | Yifan Yang, Yutong Mao, Xufu Liu, Xiao Liu | BrainMAE: A Region-aware Self-supervised Learning Framework for Brain
Signals | 27 pages, 16 figures | null | null | null | q-bio.QM cs.LG q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The human brain is a complex, dynamic network, which is commonly studied
using functional magnetic resonance imaging (fMRI) and modeled as network of
Regions of interest (ROIs) for understanding various brain functions. Recent
studies utilize deep learning approaches to learn the brain network
representation based on... | [
{
"created": "Mon, 24 Jun 2024 19:16:24 GMT",
"version": "v1"
}
] | 2024-06-26 | [
[
"Yang",
"Yifan",
""
],
[
"Mao",
"Yutong",
""
],
[
"Liu",
"Xufu",
""
],
[
"Liu",
"Xiao",
""
]
] | The human brain is a complex, dynamic network, which is commonly studied using functional magnetic resonance imaging (fMRI) and modeled as network of Regions of interest (ROIs) for understanding various brain functions. Recent studies utilize deep learning approaches to learn the brain network representation based on f... |
2402.16854 | Divahar Sivanesan | Divahar Sivanesan | Attention Based Molecule Generation via Hierarchical Variational
Autoencoder | null | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Molecule generation is a task made very difficult by the complex ways in
which we represent molecules computationally. A common technique used in
molecular generative modeling is to use SMILES strings with recurrent neural
networks built into variational autoencoders - but these suffer from a myriad
of issues: vanish... | [
{
"created": "Thu, 18 Jan 2024 21:45:12 GMT",
"version": "v1"
}
] | 2024-02-28 | [
[
"Sivanesan",
"Divahar",
""
]
] | Molecule generation is a task made very difficult by the complex ways in which we represent molecules computationally. A common technique used in molecular generative modeling is to use SMILES strings with recurrent neural networks built into variational autoencoders - but these suffer from a myriad of issues: vanishin... |
1201.5211 | Alexei Ryabov | Alexei B. Ryabov | Phytoplankton competition in deep biomass maximum | 13 pages, 7 figures; Theoretical Ecology 2012 | null | 10.1007/s12080-012-0158-0 | null | q-bio.PE nlin.AO nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Resource competition in heterogeneous environments is still an unresolved
problem of theoretical ecology. In this article I analyze competition between
two phytoplankton species in a deep water column, where the distributions of
main resources (light and a limiting nutrient) have opposing gradients and
co-limitation ... | [
{
"created": "Wed, 25 Jan 2012 09:22:13 GMT",
"version": "v1"
}
] | 2012-01-26 | [
[
"Ryabov",
"Alexei B.",
""
]
] | Resource competition in heterogeneous environments is still an unresolved problem of theoretical ecology. In this article I analyze competition between two phytoplankton species in a deep water column, where the distributions of main resources (light and a limiting nutrient) have opposing gradients and co-limitation by... |
1004.4387 | Areejit Samal | Pierre-Yves Bourguignon, Areejit Samal, Fran\c{c}ois K\'ep\`es,
J\"urgen Jost, Olivier C. Martin | Challenges in experimental data integration within genome-scale
metabolic models | 5 pages | Algorithms for Molecular Biology, 5:20 (2010)
http://www.almob.org/content/5/1/20 | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A report of the meeting "Challenges in experimental data integration within
genome-scale metabolic models", Institut Henri Poincar\'e, Paris, October 10-11
2009, organized by the CNRS-MPG joint program in Systems Biology.
| [
{
"created": "Sun, 25 Apr 2010 22:41:35 GMT",
"version": "v1"
}
] | 2010-04-27 | [
[
"Bourguignon",
"Pierre-Yves",
""
],
[
"Samal",
"Areejit",
""
],
[
"Képès",
"François",
""
],
[
"Jost",
"Jürgen",
""
],
[
"Martin",
"Olivier C.",
""
]
] | A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincar\'e, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in Systems Biology. |
1304.1565 | Muhammad Asim Mubeen | Asim M. Mubeen, Kevin H. Knuth | Bayesian Odds-Ratio Filters: A Template-Based Method for Online
Detection of P300 Evoked Responses | 9 pages, 3 figures | null | null | null | q-bio.NC physics.med-ph stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Template-based signal detection most often relies on computing a correlation,
or a dot product, between an incoming data stream and a signal template. While
such a correlation results in an ongoing estimate of the magnitude of the
signal in the data stream, it does not directly indicate the presence or
absence of a s... | [
{
"created": "Thu, 4 Apr 2013 21:27:40 GMT",
"version": "v1"
}
] | 2013-04-08 | [
[
"Mubeen",
"Asim M.",
""
],
[
"Knuth",
"Kevin H.",
""
]
] | Template-based signal detection most often relies on computing a correlation, or a dot product, between an incoming data stream and a signal template. While such a correlation results in an ongoing estimate of the magnitude of the signal in the data stream, it does not directly indicate the presence or absence of a sig... |
2006.00115 | Daniel Moyer | Daniel Moyer, Greg Ver Steeg, Paul M. Thompson | Overview of Scanner Invariant Representations | Accepted as a short paper in MIDL 2020. In accordance with the MIDL
2020 Call for Papers, this short paper is an overview of an already published
work arXiv:1904.05375, and was submitted to MIDL in order to allow
presentation and discussion at the meeting | null | null | MIDL/2020/ExtendedAbstract/yqm9RD_XHT | q-bio.QM cs.CV cs.LG eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pooled imaging data from multiple sources is subject to bias from each
source. Studies that do not correct for these scanner/site biases at best lose
statistical power, and at worst leave spurious correlations in their data.
Estimation of the bias effects is non-trivial due to the paucity of data with
correspondence ... | [
{
"created": "Fri, 29 May 2020 22:56:47 GMT",
"version": "v1"
}
] | 2020-06-02 | [
[
"Moyer",
"Daniel",
""
],
[
"Steeg",
"Greg Ver",
""
],
[
"Thompson",
"Paul M.",
""
]
] | Pooled imaging data from multiple sources is subject to bias from each source. Studies that do not correct for these scanner/site biases at best lose statistical power, and at worst leave spurious correlations in their data. Estimation of the bias effects is non-trivial due to the paucity of data with correspondence ac... |
1612.07106 | Xerxes D. Arsiwalla | Xerxes D. Arsiwalla and Paul Verschure | The Global Dynamical Complexity of the Human Brain Network | 16 pages, 6 figures | null | 10.1007/s41109-016-0018-8 | null | q-bio.NC cs.IT math.DS math.IT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How much information do large brain networks integrate as a whole over the
sum of their parts? Can the dynamical complexity of such networks be globally
quantified in an information-theoretic way and be meaningfully coupled to brain
function? Recently, measures of dynamical complexity such as integrated
information h... | [
{
"created": "Wed, 21 Dec 2016 13:44:31 GMT",
"version": "v1"
}
] | 2016-12-22 | [
[
"Arsiwalla",
"Xerxes D.",
""
],
[
"Verschure",
"Paul",
""
]
] | How much information do large brain networks integrate as a whole over the sum of their parts? Can the dynamical complexity of such networks be globally quantified in an information-theoretic way and be meaningfully coupled to brain function? Recently, measures of dynamical complexity such as integrated information hav... |
1701.07061 | Diego Mateos | D. M. Mateos, R. Guevara Erra, R. Wennberg, J.L. Perez Velazquez | Measures of Entropy and Complexity in altered states of consciousness | 2 figures | null | null | null | q-bio.NC cond-mat.stat-mech | http://creativecommons.org/publicdomain/zero/1.0/ | Quantification of complexity in neurophysiological signals has been studied
using different methods, especially those from information or dynamical system
theory. These studies revealed the dependence on different states of
consciousness, particularly that wakefulness is characterized by larger
complexity of brain si... | [
{
"created": "Mon, 9 Jan 2017 20:10:15 GMT",
"version": "v1"
}
] | 2017-01-26 | [
[
"Mateos",
"D. M.",
""
],
[
"Erra",
"R. Guevara",
""
],
[
"Wennberg",
"R.",
""
],
[
"Velazquez",
"J. L. Perez",
""
]
] | Quantification of complexity in neurophysiological signals has been studied using different methods, especially those from information or dynamical system theory. These studies revealed the dependence on different states of consciousness, particularly that wakefulness is characterized by larger complexity of brain sign... |
1707.00180 | Melanie Weber | Melanie Weber, Johannes Stelzer, Emil Saucan, Alexander Naitsat,
Gabriele Lohmann and J\"urgen Jost | Curvature-based Methods for Brain Network Analysis | Under Review | null | null | null | q-bio.NC cs.DM cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human brain forms functional networks on all spatial scales. Modern fMRI
scanners allow to resolve functional brain data in high resolutions, allowing
to study large-scale networks that relate to cognitive processes. The analysis
of such networks forms a cornerstone of experimental neuroscience. Due to the
immens... | [
{
"created": "Sat, 1 Jul 2017 17:55:28 GMT",
"version": "v1"
},
{
"created": "Mon, 13 May 2019 16:03:12 GMT",
"version": "v2"
}
] | 2019-05-14 | [
[
"Weber",
"Melanie",
""
],
[
"Stelzer",
"Johannes",
""
],
[
"Saucan",
"Emil",
""
],
[
"Naitsat",
"Alexander",
""
],
[
"Lohmann",
"Gabriele",
""
],
[
"Jost",
"Jürgen",
""
]
] | The human brain forms functional networks on all spatial scales. Modern fMRI scanners allow to resolve functional brain data in high resolutions, allowing to study large-scale networks that relate to cognitive processes. The analysis of such networks forms a cornerstone of experimental neuroscience. Due to the immense ... |
2004.14767 | Helmut Hlavacs | Helmut Hlavacs | How Often Should People be Tested for Corona to Avoid a Shutdown? | Please comment | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Based on the well known SIR model, this paper develops a model for predicting
the number of necessary testings of asymptomatic persons in order to push Reff
below 1, thus suppressing an outbreak. The model considers R0, time for
obtaining a test result, and effect of population discipline. The outcome are
closed form... | [
{
"created": "Mon, 27 Apr 2020 17:59:47 GMT",
"version": "v1"
}
] | 2020-05-01 | [
[
"Hlavacs",
"Helmut",
""
]
] | Based on the well known SIR model, this paper develops a model for predicting the number of necessary testings of asymptomatic persons in order to push Reff below 1, thus suppressing an outbreak. The model considers R0, time for obtaining a test result, and effect of population discipline. The outcome are closed form e... |
1504.06574 | Heng Li | Heng Li | FermiKit: assembly-based variant calling for Illumina resequencing data | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Summary: FermiKit is a variant calling pipeline for Illumina data. It de novo
assembles short reads and then maps the assembly against a reference genome to
call SNPs, short insertions/deletions (INDELs) and structural variations (SVs).
FermiKit takes about one day to assemble 30-fold human whole-genome data on a
mod... | [
{
"created": "Fri, 24 Apr 2015 17:27:42 GMT",
"version": "v1"
}
] | 2015-04-27 | [
[
"Li",
"Heng",
""
]
] | Summary: FermiKit is a variant calling pipeline for Illumina data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions (INDELs) and structural variations (SVs). FermiKit takes about one day to assemble 30-fold human whole-genome data on a moder... |
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