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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2308.07122 | Jose Fontanari | Jos\'e F. Fontanari, Viviane M. de Oliveira and Paulo R. A. Campos | Evolving division of labor in a response threshold model | null | Ecological Complexity 58 (2024) 101083 | 10.1016/j.ecocom.2024.101083 | null | q-bio.PE nlin.AO nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The response threshold model explains the emergence of division of labor
(i.e., task specialization) in an unstructured population by assuming that the
individuals have different propensities to work on different tasks. The
incentive to attend to a particular task increases when the task is left
unattended and decrea... | [
{
"created": "Mon, 14 Aug 2023 13:07:37 GMT",
"version": "v1"
}
] | 2024-04-29 | [
[
"Fontanari",
"José F.",
""
],
[
"de Oliveira",
"Viviane M.",
""
],
[
"Campos",
"Paulo R. A.",
""
]
] | The response threshold model explains the emergence of division of labor (i.e., task specialization) in an unstructured population by assuming that the individuals have different propensities to work on different tasks. The incentive to attend to a particular task increases when the task is left unattended and decrease... |
2210.12991 | Emilio Dorigatti | Ingo Ziegler, Bolei Ma, Ercong Nie, Bernd Bischl, David R\"ugamer,
Benjamin Schubert, Emilio Dorigatti | What cleaves? Is proteasomal cleavage prediction reaching a ceiling? | 15 pages, 1 figure | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | Epitope vaccines are a promising direction to enable precision treatment for
cancer, autoimmune diseases, and allergies. Effectively designing such vaccines
requires accurate prediction of proteasomal cleavage in order to ensure that
the epitopes in the vaccine are presented to T cells by the major
histocompatibility... | [
{
"created": "Mon, 24 Oct 2022 07:26:55 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Oct 2022 10:15:59 GMT",
"version": "v2"
}
] | 2022-10-26 | [
[
"Ziegler",
"Ingo",
""
],
[
"Ma",
"Bolei",
""
],
[
"Nie",
"Ercong",
""
],
[
"Bischl",
"Bernd",
""
],
[
"Rügamer",
"David",
""
],
[
"Schubert",
"Benjamin",
""
],
[
"Dorigatti",
"Emilio",
""
]
] | Epitope vaccines are a promising direction to enable precision treatment for cancer, autoimmune diseases, and allergies. Effectively designing such vaccines requires accurate prediction of proteasomal cleavage in order to ensure that the epitopes in the vaccine are presented to T cells by the major histocompatibility c... |
1810.13162 | Federica Bubba | Federica Bubba (LJLL), Camille Pouchol, Nathalie Ferrand (INSERM),
Guillaume Vidal (CRPP), Luis Almeida (LJLL), Beno{\i}t Perthame (LJLL),
Mich\`ele Sabbah (D\'epartement Oncologie - H\'ematologie) | A chemotaxis-based explanation of spheroid formation in 3D cultures of
breast cancer cells | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Three-dimensional cultures of cells are gaining popularity as an in vitro
improvement over 2D Petri dishes. In many such experiments, cells have been
found to organize in aggregates. We present new results of three-dimensional in
vitro cultures of breast cancer cells exhibiting patterns. Understanding their
formation... | [
{
"created": "Wed, 31 Oct 2018 08:53:30 GMT",
"version": "v1"
}
] | 2018-11-01 | [
[
"Bubba",
"Federica",
"",
"LJLL"
],
[
"Pouchol",
"Camille",
"",
"INSERM"
],
[
"Ferrand",
"Nathalie",
"",
"INSERM"
],
[
"Vidal",
"Guillaume",
"",
"CRPP"
],
[
"Almeida",
"Luis",
"",
"LJLL"
],
[
"Perthame",
"Be... | Three-dimensional cultures of cells are gaining popularity as an in vitro improvement over 2D Petri dishes. In many such experiments, cells have been found to organize in aggregates. We present new results of three-dimensional in vitro cultures of breast cancer cells exhibiting patterns. Understanding their formation i... |
1711.09273 | Stuart Hagler | Stuart Hagler | A General Optimal Control Model of Human Movement Patterns II: Rapid,
Targeted Hand Movements (Fitts Law) | 25 pages, 2 figures | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rapid, targeted hand movements exhibit a regular movement pattern described
by Fitts law. We develop a model of these movements in which this movement
pattern results from an optimal control model describing rapid hand movements
and a utility model describing the speed/accuracy trade-off between moving the
hand rapid... | [
{
"created": "Sat, 25 Nov 2017 18:59:40 GMT",
"version": "v1"
},
{
"created": "Sun, 9 Dec 2018 20:46:51 GMT",
"version": "v2"
}
] | 2018-12-11 | [
[
"Hagler",
"Stuart",
""
]
] | Rapid, targeted hand movements exhibit a regular movement pattern described by Fitts law. We develop a model of these movements in which this movement pattern results from an optimal control model describing rapid hand movements and a utility model describing the speed/accuracy trade-off between moving the hand rapidly... |
1807.07825 | {\L}ukasz Mioduszewski MSc | {\L}ukasz Mioduszewski and Marek Cieplak | Disordered peptide chains in an {\alpha}-C-based coarse-grained model | 20 pages, 9 figures, 2 tables. Published in PCCP, 2018, 20,
19057-19070 | Physical Chemistry Chemical Physics, 2018, 20, 19057-19070 | 10.1039/C8CP03309A | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We construct a one-bead-per-residue coarse-grained dynamical model to
describe intrinsically disordered proteins at significantly longer timescales
than in the all-atom models. In this model, inter-residue contacts form and
disappear during the course of the time evolution. The contacts may arise
between the sidechai... | [
{
"created": "Fri, 20 Jul 2018 13:05:34 GMT",
"version": "v1"
}
] | 2018-07-23 | [
[
"Mioduszewski",
"Łukasz",
""
],
[
"Cieplak",
"Marek",
""
]
] | We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during the course of the time evolution. The contacts may arise between the sidechains... |
1812.09414 | Tilo Schwalger | Valentin Schmutz, Wulfram Gerstner and Tilo Schwalger | Mesoscopic population equations for spiking neural networks with
synaptic short-term plasticity | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Coarse-graining microscopic models of biological neural networks to obtain
mesoscopic models of neural activities is an essential step towards multi-scale
models of the brain. Here, we extend a recent theory for mesoscopic population
dynamics with static synapses to the case of dynamic synapses exhibiting
short-term ... | [
{
"created": "Fri, 21 Dec 2018 23:36:11 GMT",
"version": "v1"
}
] | 2018-12-27 | [
[
"Schmutz",
"Valentin",
""
],
[
"Gerstner",
"Wulfram",
""
],
[
"Schwalger",
"Tilo",
""
]
] | Coarse-graining microscopic models of biological neural networks to obtain mesoscopic models of neural activities is an essential step towards multi-scale models of the brain. Here, we extend a recent theory for mesoscopic population dynamics with static synapses to the case of dynamic synapses exhibiting short-term pl... |
1003.1993 | Andre X. C. N. Valente | Andr\'e X. C. N. Valente, Jorge A. B. Sousa, Tiago F. Outeiro, Lino
Ferreira | A stem-cell ageing hypothesis on the origin of Parkinson's disease | null | null | null | null | q-bio.CB q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A transcriptome-wide blood expression dataset of Parkinson's disease (PD)
patients and controls was analyzed under the hypothesis-rich mathematical
framework. The analysis pointed towards differential expression in blood cells
in many of the processes known or predicted to be disrupted in PD. We suggest
that circulat... | [
{
"created": "Mon, 8 Mar 2010 19:56:30 GMT",
"version": "v1"
},
{
"created": "Sat, 27 Mar 2010 23:44:27 GMT",
"version": "v2"
}
] | 2010-03-30 | [
[
"Valente",
"André X. C. N.",
""
],
[
"Sousa",
"Jorge A. B.",
""
],
[
"Outeiro",
"Tiago F.",
""
],
[
"Ferreira",
"Lino",
""
]
] | A transcriptome-wide blood expression dataset of Parkinson's disease (PD) patients and controls was analyzed under the hypothesis-rich mathematical framework. The analysis pointed towards differential expression in blood cells in many of the processes known or predicted to be disrupted in PD. We suggest that circulatin... |
2404.00365 | Malay Banerjee | Samiran Ghosh, Malay Banerjee, Vitaly Volpert | An age-distributed immuno-epidemiological model with information-based
vaccination decision | null | null | null | null | q-bio.PE math.DS | http://creativecommons.org/licenses/by/4.0/ | A new age-distributed immuno-epidemiological model with information-based
vaccine uptake suggested in this work represents a system of
integro-differential equations for the numbers of susceptible individuals,
infected individuals, vaccinated individuals and recovered individuals. This
model describes the influence o... | [
{
"created": "Sat, 30 Mar 2024 13:35:52 GMT",
"version": "v1"
}
] | 2024-04-02 | [
[
"Ghosh",
"Samiran",
""
],
[
"Banerjee",
"Malay",
""
],
[
"Volpert",
"Vitaly",
""
]
] | A new age-distributed immuno-epidemiological model with information-based vaccine uptake suggested in this work represents a system of integro-differential equations for the numbers of susceptible individuals, infected individuals, vaccinated individuals and recovered individuals. This model describes the influence of ... |
1709.04702 | Krzysztof Bartoszek | Krzysztof Bartoszek | Trait evolution with jumps: illusionary normality | http://kkzmbm.mimuw.edu.pl/?pageId=4&sprawId=23 | Proceedings of the XXIII National Conference on Applications of
Mathematics in Biology and Medicine. 2017, pp. 23-28 | null | null | q-bio.PE math.PR stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic comparative methods for real-valued traits usually make use of
stochastic process whose trajectories are continuous. This is despite
biological intuition that evolution is rather punctuated than gradual. On the
other hand, there has been a number of recent proposals of evolutionary models
with jump compo... | [
{
"created": "Thu, 14 Sep 2017 11:14:07 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Sep 2017 09:02:41 GMT",
"version": "v2"
}
] | 2017-09-25 | [
[
"Bartoszek",
"Krzysztof",
""
]
] | Phylogenetic comparative methods for real-valued traits usually make use of stochastic process whose trajectories are continuous. This is despite biological intuition that evolution is rather punctuated than gradual. On the other hand, there has been a number of recent proposals of evolutionary models with jump compone... |
1601.00987 | Sarah Muldoon | Sarah Feldt Muldoon, Fabio Pasqualetti, Shi Gu, Matthew Cieslak, Scott
T. Grafton, Jean M. Vettel, and Danielle S. Bassett | Stimulation-based control of dynamic brain networks | 54 pages, 10 figures, includes Supplementary Information | null | null | null | q-bio.NC cs.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ability to modulate brain states using targeted stimulation is
increasingly being employed to treat neurological disorders and to enhance
human performance. Despite the growing interest in brain stimulation as a form
of neuromodulation, much remains unknown about the network-level impact of
these focal perturbati... | [
{
"created": "Tue, 5 Jan 2016 21:33:24 GMT",
"version": "v1"
}
] | 2016-01-07 | [
[
"Muldoon",
"Sarah Feldt",
""
],
[
"Pasqualetti",
"Fabio",
""
],
[
"Gu",
"Shi",
""
],
[
"Cieslak",
"Matthew",
""
],
[
"Grafton",
"Scott T.",
""
],
[
"Vettel",
"Jean M.",
""
],
[
"Bassett",
"Danielle S.",
""
... | The ability to modulate brain states using targeted stimulation is increasingly being employed to treat neurological disorders and to enhance human performance. Despite the growing interest in brain stimulation as a form of neuromodulation, much remains unknown about the network-level impact of these focal perturbation... |
2206.00495 | Eleonora Vercesi | Stefano Gualandi and Giuseppe Toscani and Eleonora Vercesi | A kinetic description of the body size distributions of species | null | null | null | null | q-bio.PE cs.MA | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In this paper, by resorting to classical methods of statistical mechanics, we
build a kinetic model able to reproduce the observed statistical weight
distribution of many diverse species. The kinetic description of the time
variations of the weight distribution is based on elementary interactions that
describe in a q... | [
{
"created": "Wed, 1 Jun 2022 13:49:58 GMT",
"version": "v1"
}
] | 2022-06-02 | [
[
"Gualandi",
"Stefano",
""
],
[
"Toscani",
"Giuseppe",
""
],
[
"Vercesi",
"Eleonora",
""
]
] | In this paper, by resorting to classical methods of statistical mechanics, we build a kinetic model able to reproduce the observed statistical weight distribution of many diverse species. The kinetic description of the time variations of the weight distribution is based on elementary interactions that describe in a qua... |
1012.5887 | Peter Waddell | Peter J. Waddell, Ishita Khan, Xi Tan, and Sunghwan Yoo | A Unified Framework for Trees, Multi-Dimensional Scaling and Planar
Graphs | 14 pages, 4 figure and 1 table | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Least squares trees, multi-dimensional scaling and Neighbor Nets are all
different and popular ways of visualizing multi-dimensional data. The method of
flexi-Weighted Least Squares (fWLS) is a powerful method of fitting
phylogenetic trees, when the exact form of errors is unknown. Here, both
polynomial and exponenti... | [
{
"created": "Wed, 29 Dec 2010 08:33:00 GMT",
"version": "v1"
}
] | 2010-12-30 | [
[
"Waddell",
"Peter J.",
""
],
[
"Khan",
"Ishita",
""
],
[
"Tan",
"Xi",
""
],
[
"Yoo",
"Sunghwan",
""
]
] | Least squares trees, multi-dimensional scaling and Neighbor Nets are all different and popular ways of visualizing multi-dimensional data. The method of flexi-Weighted Least Squares (fWLS) is a powerful method of fitting phylogenetic trees, when the exact form of errors is unknown. Here, both polynomial and exponential... |
1507.08367 | Marisa Eisenberg | Jeremy P D'Silva, Marisa C. Eisenberg | Modeling Spatial Invasion of Ebola in West Africa | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The 2014-2015 Ebola Virus Disease (EVD) epidemic in West Africa was the
largest ever recorded, representing a fundamental shift in Ebola epidemiology
with unprecedented spatiotemporal complexity. We developed spatial transmission
models using a gravity-model framework to explain spatiotemporal dynamics of
EVD in West... | [
{
"created": "Thu, 30 Jul 2015 03:40:25 GMT",
"version": "v1"
},
{
"created": "Wed, 25 May 2016 14:19:25 GMT",
"version": "v2"
}
] | 2016-05-26 | [
[
"D'Silva",
"Jeremy P",
""
],
[
"Eisenberg",
"Marisa C.",
""
]
] | The 2014-2015 Ebola Virus Disease (EVD) epidemic in West Africa was the largest ever recorded, representing a fundamental shift in Ebola epidemiology with unprecedented spatiotemporal complexity. We developed spatial transmission models using a gravity-model framework to explain spatiotemporal dynamics of EVD in West A... |
2303.06194 | Ghazwan Hasan | Qutaiba Shuaib Al-Nema, Ghazwan Qasim Hasan, Omar Abdulazeez Alhamd | A high yield method for protoplast isolation and ease detection of rol B
and C genes in the hairy roots of cauliflflower (Brassica oleracea L.)
inoculated with Agrobacterium rhizogenes | 6 pages, 3 figures, 5 tables | Vol 8, 2022, 415-420 | 10.33640/2405-609X.3255 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protoplasts represent a unique experimental system for the circulation and
formation of genetically modified plants. Here, protoplasts were isolated from
genetically modified hairy root tissues of Brassica oleracea L. induced by the
Agrobacterium rhizogenes strain (ATCC13332). The concentration of enzyme
solutions ut... | [
{
"created": "Fri, 10 Mar 2023 19:59:18 GMT",
"version": "v1"
}
] | 2023-03-14 | [
[
"Al-Nema",
"Qutaiba Shuaib",
""
],
[
"Hasan",
"Ghazwan Qasim",
""
],
[
"Alhamd",
"Omar Abdulazeez",
""
]
] | Protoplasts represent a unique experimental system for the circulation and formation of genetically modified plants. Here, protoplasts were isolated from genetically modified hairy root tissues of Brassica oleracea L. induced by the Agrobacterium rhizogenes strain (ATCC13332). The concentration of enzyme solutions util... |
1303.4401 | Andrea Velenich | Andrea Velenich and Jeff Gore | The strength of genetic interactions scales weakly with the mutational
effects | 11 pages, 6 figures + Supplementary Material | Genome Biology 2013, 14:R76 | 10.1186/gb-2013-14-7-r76 | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genetic interactions pervade every aspect of biology, from evolutionary
theory where they determine the accessibility of evolutionary paths, to
medicine where they contribute to complex genetic diseases. Until very
recently, studies on epistatic interactions have been based on a handful of
mutations, providing at bes... | [
{
"created": "Mon, 18 Mar 2013 20:01:04 GMT",
"version": "v1"
}
] | 2014-01-20 | [
[
"Velenich",
"Andrea",
""
],
[
"Gore",
"Jeff",
""
]
] | Genetic interactions pervade every aspect of biology, from evolutionary theory where they determine the accessibility of evolutionary paths, to medicine where they contribute to complex genetic diseases. Until very recently, studies on epistatic interactions have been based on a handful of mutations, providing at best ... |
2401.10009 | Haiping Huang | Junbin Qiu and Haiping Huang | An optimization-based equilibrium measure describes non-equilibrium
steady state dynamics: application to edge of chaos | 21 pages, 9 figures, revised version 2 | null | null | null | q-bio.NC cond-mat.stat-mech cs.NE | http://creativecommons.org/licenses/by/4.0/ | Understanding neural dynamics is a central topic in machine learning,
non-linear physics and neuroscience. However, the dynamics is non-linear,
stochastic and particularly non-gradient, i.e., the driving force can not be
written as gradient of a potential. These features make analytic studies very
challenging. The co... | [
{
"created": "Thu, 18 Jan 2024 14:25:32 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Jun 2024 06:29:08 GMT",
"version": "v2"
}
] | 2024-06-10 | [
[
"Qiu",
"Junbin",
""
],
[
"Huang",
"Haiping",
""
]
] | Understanding neural dynamics is a central topic in machine learning, non-linear physics and neuroscience. However, the dynamics is non-linear, stochastic and particularly non-gradient, i.e., the driving force can not be written as gradient of a potential. These features make analytic studies very challenging. The comm... |
2401.14442 | Talip Ucar | Talip Ucar, Aubin Ramon, Dino Oglic, Rebecca Croasdale-Wood, Tom
Diethe, Pietro Sormanni | Improving Antibody Humanness Prediction using Patent Data | ICML 2024, 14 pages, 6 figures, Code:
https://github.com/AstraZeneca/SelfPAD | null | null | null | q-bio.QM cs.LG stat.ML | http://creativecommons.org/licenses/by/4.0/ | We investigate the potential of patent data for improving the antibody
humanness prediction using a multi-stage, multi-loss training process.
Humanness serves as a proxy for the immunogenic response to antibody
therapeutics, one of the major causes of attrition in drug discovery and a
challenging obstacle for their u... | [
{
"created": "Thu, 25 Jan 2024 16:04:17 GMT",
"version": "v1"
},
{
"created": "Wed, 31 Jan 2024 07:12:52 GMT",
"version": "v2"
},
{
"created": "Sat, 8 Jun 2024 07:14:03 GMT",
"version": "v3"
}
] | 2024-06-11 | [
[
"Ucar",
"Talip",
""
],
[
"Ramon",
"Aubin",
""
],
[
"Oglic",
"Dino",
""
],
[
"Croasdale-Wood",
"Rebecca",
""
],
[
"Diethe",
"Tom",
""
],
[
"Sormanni",
"Pietro",
""
]
] | We investigate the potential of patent data for improving the antibody humanness prediction using a multi-stage, multi-loss training process. Humanness serves as a proxy for the immunogenic response to antibody therapeutics, one of the major causes of attrition in drug discovery and a challenging obstacle for their use... |
2003.14150 | Anis Koubaa | Anis Koubaa | Understanding the COVID19 Outbreak: A Comparative Data Analytics and
Study | RIOTU Lab Technical Report | null | null | RT-2020-01 | q-bio.PE cs.SI | http://creativecommons.org/licenses/by/4.0/ | The Coronavirus, also known as the COVID-19 virus, has emerged in Wuhan China
since late November 2019. Since that time, it has been spreading at large-scale
until today all around the world. It is currently recognized as the world's
most viral and severe epidemic spread in the last twenty years, as compared to
Ebola... | [
{
"created": "Sun, 29 Mar 2020 10:33:24 GMT",
"version": "v1"
}
] | 2020-04-01 | [
[
"Koubaa",
"Anis",
""
]
] | The Coronavirus, also known as the COVID-19 virus, has emerged in Wuhan China since late November 2019. Since that time, it has been spreading at large-scale until today all around the world. It is currently recognized as the world's most viral and severe epidemic spread in the last twenty years, as compared to Ebola 2... |
2309.06388 | Chunyan Ao | Chunyan Ao, Zhichao Xiao, Lixin Guan, Liang Yu | Computational Approaches for Predicting Drug-Disease Associations: A
Comprehensive Review | 34 page, 5 figures, 2 tables | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent decades, traditional drug research and development have been facing
challenges such as high cost, long timelines, and high risks. To address these
issues, many computational approaches have been suggested for predicting the
relationship between drugs and diseases through drug repositioning, aiming to
reduce... | [
{
"created": "Sun, 10 Sep 2023 11:34:29 GMT",
"version": "v1"
}
] | 2023-09-13 | [
[
"Ao",
"Chunyan",
""
],
[
"Xiao",
"Zhichao",
""
],
[
"Guan",
"Lixin",
""
],
[
"Yu",
"Liang",
""
]
] | In recent decades, traditional drug research and development have been facing challenges such as high cost, long timelines, and high risks. To address these issues, many computational approaches have been suggested for predicting the relationship between drugs and diseases through drug repositioning, aiming to reduce t... |
2406.05248 | Paul Taylor | Richard C. Reynolds, Daniel R. Glen, Gang Chen, Ziad S. Saad, Robert
W. Cox, Paul A. Taylor | Processing, evaluating and understanding FMRI data with afni_proc.py | 52 pages, 10 figures, 6 tables | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | FMRI data are noisy, complicated to acquire, and typically go through many
steps of processing before they are used in a study or clinical practice. Being
able to visualize and understand the data from the start through the completion
of processing, while being confident that each intermediate step was
successful, is... | [
{
"created": "Fri, 7 Jun 2024 20:14:52 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Jun 2024 02:20:54 GMT",
"version": "v2"
}
] | 2024-06-12 | [
[
"Reynolds",
"Richard C.",
""
],
[
"Glen",
"Daniel R.",
""
],
[
"Chen",
"Gang",
""
],
[
"Saad",
"Ziad S.",
""
],
[
"Cox",
"Robert W.",
""
],
[
"Taylor",
"Paul A.",
""
]
] | FMRI data are noisy, complicated to acquire, and typically go through many steps of processing before they are used in a study or clinical practice. Being able to visualize and understand the data from the start through the completion of processing, while being confident that each intermediate step was successful, is c... |
1204.0831 | Iaroslav Ispolatov | Michael Doebeli and Iaroslav Ispolatov | Symmetric competition as a general model for single-species adaptive
dynamics | 26 pages, 1 figure | J. Math. Biol. (2013) 67: 169 | 10.1007/s00285-012-0547-4 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Adaptive dynamics is a widely used framework for modeling long-term evolution
of continuous phenotypes. It is based on invasion fitness functions, which
determine selection gradients and the canonical equation of adaptive dynamics.
Even though the derivation of the adaptive dynamics from a given invasion
fitness func... | [
{
"created": "Tue, 3 Apr 2012 23:11:09 GMT",
"version": "v1"
}
] | 2017-02-07 | [
[
"Doebeli",
"Michael",
""
],
[
"Ispolatov",
"Iaroslav",
""
]
] | Adaptive dynamics is a widely used framework for modeling long-term evolution of continuous phenotypes. It is based on invasion fitness functions, which determine selection gradients and the canonical equation of adaptive dynamics. Even though the derivation of the adaptive dynamics from a given invasion fitness functi... |
1204.2255 | Tijana Milenkovic | Ryan W. Solava, Ryan P. Michaels, Tijana Milenkovic | Identifying edge clusters in networks via edge graphlet degree vectors
(edge-GDVs) and edge-GDV-similarities | null | null | null | null | q-bio.MN cs.DM cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inference of new biological knowledge, e.g., prediction of protein function,
from protein-protein interaction (PPI) networks has received attention in the
post-genomic era. A popular strategy has been to cluster the network into
functionally coherent groups of proteins and predict protein function from the
clusters. ... | [
{
"created": "Tue, 10 Apr 2012 19:32:06 GMT",
"version": "v1"
}
] | 2012-04-11 | [
[
"Solava",
"Ryan W.",
""
],
[
"Michaels",
"Ryan P.",
""
],
[
"Milenkovic",
"Tijana",
""
]
] | Inference of new biological knowledge, e.g., prediction of protein function, from protein-protein interaction (PPI) networks has received attention in the post-genomic era. A popular strategy has been to cluster the network into functionally coherent groups of proteins and predict protein function from the clusters. Tr... |
1305.1573 | Alexander Mathis | Alexander Mathis, Andreas V.M. Herz, Martin B. Stemmler | Multi-Scale Codes in the Nervous System: The Problem of Noise
Correlations and the Ambiguity of Periodic Scales | 11 pages, 9 figures | Phys. Rev. E 88, 022713 2013 | 10.1103/PhysRevE.88.022713 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Encoding information about continuous variables using noisy computational
units is a challenge; nonetheless, asymptotic theory shows that combining
multiple periodic scales for coding can be highly precise despite the
corrupting influence of noise (Mathis et al., Phys. Rev. Lett. 2012). Indeed,
cortex seems to use su... | [
{
"created": "Tue, 7 May 2013 16:24:41 GMT",
"version": "v1"
},
{
"created": "Tue, 28 May 2013 13:33:40 GMT",
"version": "v2"
}
] | 2013-08-22 | [
[
"Mathis",
"Alexander",
""
],
[
"Herz",
"Andreas V. M.",
""
],
[
"Stemmler",
"Martin B.",
""
]
] | Encoding information about continuous variables using noisy computational units is a challenge; nonetheless, asymptotic theory shows that combining multiple periodic scales for coding can be highly precise despite the corrupting influence of noise (Mathis et al., Phys. Rev. Lett. 2012). Indeed, cortex seems to use such... |
2106.04089 | David Clark | David G. Clark, L. F. Abbott, SueYeon Chung | Credit Assignment Through Broadcasting a Global Error Vector | 20 pages, 6 figures; expanded references and discussion | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Backpropagation (BP) uses detailed, unit-specific feedback to train deep
neural networks (DNNs) with remarkable success. That biological neural circuits
appear to perform credit assignment, but cannot implement BP, implies the
existence of other powerful learning algorithms. Here, we explore the extent to
which a glo... | [
{
"created": "Tue, 8 Jun 2021 04:08:46 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Oct 2021 20:31:37 GMT",
"version": "v2"
}
] | 2021-11-01 | [
[
"Clark",
"David G.",
""
],
[
"Abbott",
"L. F.",
""
],
[
"Chung",
"SueYeon",
""
]
] | Backpropagation (BP) uses detailed, unit-specific feedback to train deep neural networks (DNNs) with remarkable success. That biological neural circuits appear to perform credit assignment, but cannot implement BP, implies the existence of other powerful learning algorithms. Here, we explore the extent to which a globa... |
q-bio/0702007 | Joel Miller | Joel C. Miller | Predicting the size and probability of epidemics in a population with
heterogeneous infectiousness and susceptibility | 5 pages, 3 figures. Submitted to Physical Review Letters | null | 10.1103/PhysRevE.76.010101 | LA-UR-06-8193 | q-bio.QM q-bio.PE | null | We analytically address disease outbreaks in large, random networks with
heterogeneous infectivity and susceptibility. The transmissibility $T_{uv}$
(the probability that infection of $u$ causes infection of $v$) depends on the
infectivity of $u$ and the susceptibility of $v$. Initially a single node is
infected, fol... | [
{
"created": "Tue, 6 Feb 2007 01:17:33 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Miller",
"Joel C.",
""
]
] | We analytically address disease outbreaks in large, random networks with heterogeneous infectivity and susceptibility. The transmissibility $T_{uv}$ (the probability that infection of $u$ causes infection of $v$) depends on the infectivity of $u$ and the susceptibility of $v$. Initially a single node is infected, follo... |
1708.01751 | Hector Zenil | Hector Zenil and Peter Minary | Training-free Measures Based on Algorithmic Probability Identify High
Nucleosome Occupancy in DNA Sequences | 8 pages main text (4 figures), 12 total with Supplementary (1 figure) | null | null | null | q-bio.QM cs.IT math.IT q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce and study a set of training-free methods of
information-theoretic and algorithmic complexity nature applied to DNA
sequences to identify their potential capabilities to determine nucleosomal
binding sites. We test our measures on well-studied genomic sequences of
different sizes drawn from different sour... | [
{
"created": "Sat, 5 Aug 2017 11:09:46 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Aug 2017 14:00:56 GMT",
"version": "v2"
},
{
"created": "Tue, 16 Oct 2018 20:29:14 GMT",
"version": "v3"
}
] | 2018-10-18 | [
[
"Zenil",
"Hector",
""
],
[
"Minary",
"Peter",
""
]
] | We introduce and study a set of training-free methods of information-theoretic and algorithmic complexity nature applied to DNA sequences to identify their potential capabilities to determine nucleosomal binding sites. We test our measures on well-studied genomic sequences of different sizes drawn from different source... |
1905.04224 | Minhaj Nur Alam | Minhaj Alam, David Le, Jennifer I. Lim, R.V.P. Chan, and Xincheng Yao | Supervised machine learning based multi-task artificial intelligence
classification of retinopathies | Supplemental material attached at the end | https://www.mdpi.com/2077-0383/8/6/872 | 10.3390/jcm8060872 | null | q-bio.QM eess.IV q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Artificial intelligence (AI) classification holds promise as a novel and
affordable screening tool for clinical management of ocular diseases. Rural and
underserved areas, which suffer from lack of access to experienced
ophthalmologists may particularly benefit from this technology. Quantitative
optical coherence tom... | [
{
"created": "Fri, 10 May 2019 15:47:31 GMT",
"version": "v1"
}
] | 2019-06-19 | [
[
"Alam",
"Minhaj",
""
],
[
"Le",
"David",
""
],
[
"Lim",
"Jennifer I.",
""
],
[
"Chan",
"R. V. P.",
""
],
[
"Yao",
"Xincheng",
""
]
] | Artificial intelligence (AI) classification holds promise as a novel and affordable screening tool for clinical management of ocular diseases. Rural and underserved areas, which suffer from lack of access to experienced ophthalmologists may particularly benefit from this technology. Quantitative optical coherence tomog... |
1604.02919 | Silvia Grigolon | Silvia Grigolon, Francesca Di Patti, Andrea De Martino, Enzo Marinari | Noise Processing by MicroRNA-Mediated Circuits: the Incoherent
Feed-Forward Loop, Revisited | 25 pages (Main Text and Supplementary Information), 5 figures | Heliyon 2 (2016) e00095 | 10.1016/j.heliyon.2016.e00095 | null | q-bio.MN cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The intrinsic stochasticity of gene expression is usually mitigated in higher
eukaryotes by post-transcriptional regulation channels that stabilise the
output layer, most notably protein levels. The discovery of small non-coding
RNAs (miRNAs) in specific motifs of the genetic regulatory network has led to
identifying... | [
{
"created": "Mon, 11 Apr 2016 12:42:53 GMT",
"version": "v1"
}
] | 2016-04-12 | [
[
"Grigolon",
"Silvia",
""
],
[
"Di Patti",
"Francesca",
""
],
[
"De Martino",
"Andrea",
""
],
[
"Marinari",
"Enzo",
""
]
] | The intrinsic stochasticity of gene expression is usually mitigated in higher eukaryotes by post-transcriptional regulation channels that stabilise the output layer, most notably protein levels. The discovery of small non-coding RNAs (miRNAs) in specific motifs of the genetic regulatory network has led to identifying n... |
1304.5404 | Corentin Briat Dr | Ankit Gupta, Corentin Briat and Mustafa Khammash | A scalable computational framework for establishing long-term behavior
of stochastic reaction networks | 31 pages, 9 figures | null | 10.1371/journal.pcbi.1003669 | null | q-bio.MN cs.SY math.OC math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reaction networks are systems in which the populations of a finite number of
species evolve through predefined interactions. Such networks are found as
modeling tools in many biological disciplines such as biochemistry, ecology,
epidemiology, immunology, systems biology and synthetic biology. It is now
well-establish... | [
{
"created": "Fri, 19 Apr 2013 12:59:26 GMT",
"version": "v1"
},
{
"created": "Mon, 4 Nov 2013 05:52:53 GMT",
"version": "v2"
},
{
"created": "Mon, 5 May 2014 14:27:13 GMT",
"version": "v3"
}
] | 2015-06-15 | [
[
"Gupta",
"Ankit",
""
],
[
"Briat",
"Corentin",
""
],
[
"Khammash",
"Mustafa",
""
]
] | Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology, epidemiology, immunology, systems biology and synthetic biology. It is now well-established... |
0711.0175 | Razvan Radulescu M.D. | Razvan Tudor Radulescu | The insulin-RB synapse in health and disease: cellular rocket science | 12 pages | null | null | null | q-bio.BM q-bio.SC | null | Time has come for a survey of our knowledge on the physical interaction
between the growth-promoting insulin molecule and retinoblastoma tumor
suppressor protein (RB). Theoretical and experimental observations over the
past 15 years reviewed here indicate that the insulin-RB dimer may represent an
essential molecular... | [
{
"created": "Thu, 1 Nov 2007 19:53:44 GMT",
"version": "v1"
}
] | 2007-11-02 | [
[
"Radulescu",
"Razvan Tudor",
""
]
] | Time has come for a survey of our knowledge on the physical interaction between the growth-promoting insulin molecule and retinoblastoma tumor suppressor protein (RB). Theoretical and experimental observations over the past 15 years reviewed here indicate that the insulin-RB dimer may represent an essential molecular c... |
1810.12062 | Max Falkenberg McGillivray | Max Falkenberg, Andrew J. Ford, Anthony C. Li, Alberto Ciacci,
Nicholas S. Peters, Kim Christensen | Unified Mechanism of Atrial Fibrillation in a Simple Model | null | Phys. Rev. E 100, 062406 (2019) | 10.1103/PhysRevE.100.062406 | null | q-bio.TO physics.med-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The mechanism of atrial fibrillation (AF) is poorly understood, resulting in
disappointing success rates of ablative treatment. Different mechanisms defined
largely by different atrial activation patterns have been proposed and,
arguably, this dispute has slowed the progress of AF research. Recent clinical
evidence s... | [
{
"created": "Mon, 29 Oct 2018 11:32:52 GMT",
"version": "v1"
}
] | 2020-01-27 | [
[
"Falkenberg",
"Max",
""
],
[
"Ford",
"Andrew J.",
""
],
[
"Li",
"Anthony C.",
""
],
[
"Ciacci",
"Alberto",
""
],
[
"Peters",
"Nicholas S.",
""
],
[
"Christensen",
"Kim",
""
]
] | The mechanism of atrial fibrillation (AF) is poorly understood, resulting in disappointing success rates of ablative treatment. Different mechanisms defined largely by different atrial activation patterns have been proposed and, arguably, this dispute has slowed the progress of AF research. Recent clinical evidence sug... |
1211.0104 | Suman Kumar Banik | Alok Kumar Maity, Arnab Bandyopadhyay, Sudip Chattopadhyay,
Jyotipratim Ray Chaudhuri, Ralf Metzler, Pinaki Chaudhury and Suman K Banik | Quantification of noise in the bifunctionality-induced
post-translational modification | Revised version, 7 pages, 5 figures | Phys Rev E 88 (2013) 032716 | 10.1103/PhysRevE.88.032716 | null | q-bio.SC physics.bio-ph q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a generic analytical scheme for the quantification of fluctuations
due to bifunctionality-induced signal transduction within the members of
bacterial two-component system. The proposed model takes into account
post-translational modifications in terms of elementary phosphotransfer
kinetics. Sources of fluc... | [
{
"created": "Thu, 1 Nov 2012 06:19:23 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Sep 2013 05:35:52 GMT",
"version": "v2"
}
] | 2013-10-02 | [
[
"Maity",
"Alok Kumar",
""
],
[
"Bandyopadhyay",
"Arnab",
""
],
[
"Chattopadhyay",
"Sudip",
""
],
[
"Chaudhuri",
"Jyotipratim Ray",
""
],
[
"Metzler",
"Ralf",
""
],
[
"Chaudhury",
"Pinaki",
""
],
[
"Banik",
"Sum... | We present a generic analytical scheme for the quantification of fluctuations due to bifunctionality-induced signal transduction within the members of bacterial two-component system. The proposed model takes into account post-translational modifications in terms of elementary phosphotransfer kinetics. Sources of fluctu... |
2212.02864 | Adnan Ferdous Ashrafi | Mehedi Hasan Sarkar, Adnan Ferdous Ashrafi | Genetic Sequence compression using Machine Learning and Arithmetic
Encoding Decoding Techniques | 6 page, 4 figures, 3 tables, accepted at ICCIT 2022 | 2022 25th International Conference on Computer and Information
Technology (ICCIT), 2022, pp. 1038-1043 | 10.1109/ICCIT57492.2022.10055899 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | We live in a period where bio-informatics is rapidly expanding, a significant
quantity of genomic data has been produced as a result of the advancement of
high-throughput genome sequencing technology, raising concerns about the costs
associated with data storage and transmission. The question of how to properly
compr... | [
{
"created": "Tue, 6 Dec 2022 10:15:31 GMT",
"version": "v1"
}
] | 2023-03-10 | [
[
"Sarkar",
"Mehedi Hasan",
""
],
[
"Ashrafi",
"Adnan Ferdous",
""
]
] | We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs associated with data storage and transmission. The question of how to properly compres... |
q-bio/0405007 | Andrea Pagnani | M. Leone and A. Pagnani | Predicting protein functions with message passing algorithms | 12 pages, 9 eps figures, 1 additional html table | Bioinformatics 21: 239-247 (2005). | 10.1093/bioinformatics/bth491 | null | q-bio.QM cond-mat.dis-nn | null | Motivation: In the last few years a growing interest in biology has been
shifting towards the problem of optimal information extraction from the huge
amount of data generated via large scale and high-throughput techniques. One of
the most relevant issues has recently become that of correctly and reliably
predicting t... | [
{
"created": "Fri, 7 May 2004 11:05:17 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Leone",
"M.",
""
],
[
"Pagnani",
"A.",
""
]
] | Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most relevant issues has recently become that of correctly and reliably predicting the... |
0901.3914 | Yoichiro Mori | Yoichiro Mori | From Three-Dimensional Electrophysiology to the Cable Model: an
Asymptotic Study | null | null | null | null | q-bio.NC physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cellular electrophysiology is often modeled using the cable equations. The
cable model can only be used when ionic concentration effects and three
dimensional geometry effects are negligible. The Poisson model, in which the
electrostatic potential satisfies the Poisson equation and the ionic
concentrations satisfy th... | [
{
"created": "Sun, 25 Jan 2009 18:34:09 GMT",
"version": "v1"
}
] | 2009-01-27 | [
[
"Mori",
"Yoichiro",
""
]
] | Cellular electrophysiology is often modeled using the cable equations. The cable model can only be used when ionic concentration effects and three dimensional geometry effects are negligible. The Poisson model, in which the electrostatic potential satisfies the Poisson equation and the ionic concentrations satisfy the ... |
2001.10351 | Ali Demirci | Ali Demirci, Ayse Peker Dobie, Ayse Humeyra Bilge, Semra Ahmetolan | Unexpected parameter ranges of the 2009 A(H1N1) epidemic for Istanbul
and the Netherlands | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The data of the 2009 A(H1N1) epidemic in Istanbul, Turkey is unique in terms
of the collected data, which include not only the hospitalization but also the
fatality information recorded during the pandemic. The analysis of this data
displayed an unexpected time shift between the hospital referrals and
fatalities. Thi... | [
{
"created": "Tue, 28 Jan 2020 14:26:02 GMT",
"version": "v1"
}
] | 2020-01-29 | [
[
"Demirci",
"Ali",
""
],
[
"Dobie",
"Ayse Peker",
""
],
[
"Bilge",
"Ayse Humeyra",
""
],
[
"Ahmetolan",
"Semra",
""
]
] | The data of the 2009 A(H1N1) epidemic in Istanbul, Turkey is unique in terms of the collected data, which include not only the hospitalization but also the fatality information recorded during the pandemic. The analysis of this data displayed an unexpected time shift between the hospital referrals and fatalities. This ... |
1212.5010 | Tomas Tokar | Tomas Tokar, Zdenko Turcan, Jozef Ulicny | Boolean network-based model of the Bcl-2 family mediated MOMP regulation | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mitochondrial outer membrane permeabilization (MOMP) is one of the most
important points, in majority of apoptotic signaling cascades. Decision
mechanism controlling whether the MOMP occurs or not, is formed by an interplay
between members of the Bcl-2 family. To understand the role of individual
members of this fami... | [
{
"created": "Thu, 20 Dec 2012 12:45:22 GMT",
"version": "v1"
}
] | 2012-12-21 | [
[
"Tokar",
"Tomas",
""
],
[
"Turcan",
"Zdenko",
""
],
[
"Ulicny",
"Jozef",
""
]
] | Mitochondrial outer membrane permeabilization (MOMP) is one of the most important points, in majority of apoptotic signaling cascades. Decision mechanism controlling whether the MOMP occurs or not, is formed by an interplay between members of the Bcl-2 family. To understand the role of individual members of this family... |
2102.08209 | Masoumeh Zareh | Masoumeh Zareh, Mohammad Hossein Manshaei, and Sayed Jalal Zahabi | Modeling the Hallucinating Brain: A Generative Adversarial Framework | null | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/publicdomain/zero/1.0/ | This paper looks into the modeling of hallucination in the human's brain.
Hallucinations are known to be causally associated with some malfunctions
within the interaction of different areas of the brain involved in perception.
Focusing on visual hallucination and its underlying causes, we identify an
adversarial mech... | [
{
"created": "Tue, 9 Feb 2021 14:30:14 GMT",
"version": "v1"
}
] | 2021-02-17 | [
[
"Zareh",
"Masoumeh",
""
],
[
"Manshaei",
"Mohammad Hossein",
""
],
[
"Zahabi",
"Sayed Jalal",
""
]
] | This paper looks into the modeling of hallucination in the human's brain. Hallucinations are known to be causally associated with some malfunctions within the interaction of different areas of the brain involved in perception. Focusing on visual hallucination and its underlying causes, we identify an adversarial mechan... |
0910.2084 | Suman Kumar Banik | Suman K Banik, Andrew T Fenley and Rahul V Kulkarni | A model for signal transduction during quorum sensing in \emph{Vibrio
harveyi} | 18 pages, 5 figures, IOP style files included | Phys. Biol. 6 (2009) 046008 | 10.1088/1478-3975/6/4/046008 | null | q-bio.CB q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a framework for analyzing luminescence regulation during quorum
sensing in the bioluminescent bacterium \emph{Vibrio harveyi}. Using a
simplified model for signal transduction in the quorum sensing pathway, we
identify key dimensionless parameters that control the system's response. These
parameters are es... | [
{
"created": "Mon, 12 Oct 2009 05:37:45 GMT",
"version": "v1"
}
] | 2009-10-22 | [
[
"Banik",
"Suman K",
""
],
[
"Fenley",
"Andrew T",
""
],
[
"Kulkarni",
"Rahul V",
""
]
] | We present a framework for analyzing luminescence regulation during quorum sensing in the bioluminescent bacterium \emph{Vibrio harveyi}. Using a simplified model for signal transduction in the quorum sensing pathway, we identify key dimensionless parameters that control the system's response. These parameters are esti... |
1911.04374 | Laura-Jayne Gardiner | Laura-Jayne Gardiner, Anna Paola Carrieri, Jenny Wilshaw, Stephen
Checkley, Edward O Pyzer-Knapp and Ritesh Krishna | Combining human cell line transcriptome analysis and Bayesian inference
to build trustworthy machine learning models for prediction of animal
toxicity in drug development | Machine Learning for Health (ML4H) at NeurIPS 2019 - Extended
Abstract | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biomedical data, particularly in the field of genomics, has characteristics
which make it challenging for machine learning applications - it can be sparse,
high dimensional and noisy. Biomedical applications also present challenges to
model selection - whilst powerful, accurate predictions are necessary, they
alone a... | [
{
"created": "Mon, 11 Nov 2019 16:32:02 GMT",
"version": "v1"
},
{
"created": "Tue, 12 Nov 2019 14:06:44 GMT",
"version": "v2"
}
] | 2019-11-13 | [
[
"Gardiner",
"Laura-Jayne",
""
],
[
"Carrieri",
"Anna Paola",
""
],
[
"Wilshaw",
"Jenny",
""
],
[
"Checkley",
"Stephen",
""
],
[
"Pyzer-Knapp",
"Edward O",
""
],
[
"Krishna",
"Ritesh",
""
]
] | Biomedical data, particularly in the field of genomics, has characteristics which make it challenging for machine learning applications - it can be sparse, high dimensional and noisy. Biomedical applications also present challenges to model selection - whilst powerful, accurate predictions are necessary, they alone are... |
2009.11121 | Cecilia Jarne | C. Jarne, F A. G\'omez Albarrac\'in, M. Caruso | An algorithm to represent inbreeding trees | null | null | 10.1016/j.physa.2021.125894 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent work has proven the existence of extreme inbreeding in a European
ancestry sample taken from the contemporary UK population \cite{nature_01}.
This result brings our attention again to a math problem related to inbreeding
family trees and diversity. Groups with a finite number of individuals could
give a variet... | [
{
"created": "Mon, 21 Sep 2020 20:24:30 GMT",
"version": "v1"
},
{
"created": "Mon, 1 Feb 2021 14:21:41 GMT",
"version": "v2"
}
] | 2021-09-08 | [
[
"Jarne",
"C.",
""
],
[
"Albarracín",
"F A. Gómez",
""
],
[
"Caruso",
"M.",
""
]
] | Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees and diversity. Groups with a finite number of individuals could give a variety ... |
1612.02807 | Thierry Mora | Ulisse Ferrari, Tomoyuki Obuchi, Thierry Mora | Random versus maximum entropy models of neural population activity | null | Phys. Rev. E 95, 042321 (2017) | 10.1103/PhysRevE.95.042321 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The principle of maximum entropy provides a useful method for inferring
statistical mechanics models from observations in correlated systems, and is
widely used in a variety of fields where accurate data are available. While the
assumptions underlying maximum entropy are intuitive and appealing, its
adequacy for desc... | [
{
"created": "Thu, 8 Dec 2016 20:44:59 GMT",
"version": "v1"
}
] | 2017-06-02 | [
[
"Ferrari",
"Ulisse",
""
],
[
"Obuchi",
"Tomoyuki",
""
],
[
"Mora",
"Thierry",
""
]
] | The principle of maximum entropy provides a useful method for inferring statistical mechanics models from observations in correlated systems, and is widely used in a variety of fields where accurate data are available. While the assumptions underlying maximum entropy are intuitive and appealing, its adequacy for descri... |
1509.05904 | Shai Carmi | Shai Carmi, James Xue, and Itsik Pe'er | A note on the distribution of admixture segment lengths and ancestry
proportions under pulse and two-wave admixture models | 12 pages, 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Admixed populations are formed by the merging of two or more ancestral
populations, and the ancestry of each locus in an admixed genome derives from
either source. Consider a simple "pulse" admixture model, where populations A
and B merged t generations ago without subsequent gene flow. We derive the
distribution of ... | [
{
"created": "Sat, 19 Sep 2015 15:42:53 GMT",
"version": "v1"
}
] | 2015-09-22 | [
[
"Carmi",
"Shai",
""
],
[
"Xue",
"James",
""
],
[
"Pe'er",
"Itsik",
""
]
] | Admixed populations are formed by the merging of two or more ancestral populations, and the ancestry of each locus in an admixed genome derives from either source. Consider a simple "pulse" admixture model, where populations A and B merged t generations ago without subsequent gene flow. We derive the distribution of th... |
1311.2435 | Jo\~ao Batista | Jo\~ao Barroso-Batista, Ana Sousa, Marta Louren\c{c}o, Marie-Louise
Bergman, Jocelyne Demengeot, Karina B. Xavier and Isabel Gordo | The first steps of adaptation of Escherichia coli to the gut are
dominated by soft sweeps | 46 pages with figures (5 in the main text, 4 in supplementary
materials) and tables (7 in supplementary materials). Submitted to PLOS
Genetics | PLoS Genet 10(3): e1004182 (2014) | 10.1371/journal.pgen.1004182 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/3.0/ | The accumulation of adaptive mutations is essential for survival in novel
environments. However, in clonal populations with a high mutational supply, the
power of natural selection is expected to be limited. This is due to clonal
interference - the competition of clones carrying different beneficial
mutations - which... | [
{
"created": "Mon, 11 Nov 2013 13:24:52 GMT",
"version": "v1"
}
] | 2014-04-04 | [
[
"Barroso-Batista",
"João",
""
],
[
"Sousa",
"Ana",
""
],
[
"Lourenço",
"Marta",
""
],
[
"Bergman",
"Marie-Louise",
""
],
[
"Demengeot",
"Jocelyne",
""
],
[
"Xavier",
"Karina B.",
""
],
[
"Gordo",
"Isabel",
... | The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal interference - the competition of clones carrying different beneficial mutations - which l... |
1112.1393 | Sara Walker | Marcelo Gleiser, Bradley J. Nelson and Sara Imari Walker | Chiral Polymerization in Open Systems From Chiral-Selective Reaction
Rates | 15 pages, 6 figures, accepted for publication in Origins of Life and
Evolution of Biospheres | null | 10.1007/s11084-012-9274-5 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the possibility that prebiotic homochirality can be achieved
exclusively through chiral-selective reaction rate parameters without any other
explicit mechanism for chiral bias. Specifically, we examine an open network of
polymerization reactions, where the reaction rates can have chiral-selective
value... | [
{
"created": "Tue, 6 Dec 2011 20:20:13 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Mar 2012 07:04:08 GMT",
"version": "v2"
},
{
"created": "Thu, 26 Apr 2012 17:24:47 GMT",
"version": "v3"
}
] | 2015-06-03 | [
[
"Gleiser",
"Marcelo",
""
],
[
"Nelson",
"Bradley J.",
""
],
[
"Walker",
"Sara Imari",
""
]
] | We investigate the possibility that prebiotic homochirality can be achieved exclusively through chiral-selective reaction rate parameters without any other explicit mechanism for chiral bias. Specifically, we examine an open network of polymerization reactions, where the reaction rates can have chiral-selective values.... |
1702.07038 | Isabel Gauthier Isabel Gauthier | Isabel Gauthier | The Quest for the FFA led to the Expertise Account of its Specialization | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This article is written in response to a Progressions article by Kanwisher in
the Journal of Neuroscience, The Quest for the FFA and Where It Led (Kanwisher,
2017). I reflect on the extensive research program dedicated to the study of
how and why perceptual expertise explains the many ways that faces are special,
a r... | [
{
"created": "Wed, 22 Feb 2017 23:11:00 GMT",
"version": "v1"
}
] | 2017-02-24 | [
[
"Gauthier",
"Isabel",
""
]
] | This article is written in response to a Progressions article by Kanwisher in the Journal of Neuroscience, The Quest for the FFA and Where It Led (Kanwisher, 2017). I reflect on the extensive research program dedicated to the study of how and why perceptual expertise explains the many ways that faces are special, a res... |
1504.00043 | Sattar Taheri-Araghi | Suckjoon Jun and Sattar Taheri-Araghi | Cell-size maintenance: universal strategy revealed | null | Trends in Microbiology, Vol. 23, No. 1, 4-6, 2015 | 10.1016/j.tim.2014.12.001 | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How cells maintain a stable size has fascinated scientists since the
beginning of modern biology, but has remained largely mysterious. Recently,
however, the ability to analyze single bacteria in real time has provided new,
important quantitative insights into this long-standing question in cell
biology.
| [
{
"created": "Tue, 31 Mar 2015 21:13:06 GMT",
"version": "v1"
}
] | 2015-04-02 | [
[
"Jun",
"Suckjoon",
""
],
[
"Taheri-Araghi",
"Sattar",
""
]
] | How cells maintain a stable size has fascinated scientists since the beginning of modern biology, but has remained largely mysterious. Recently, however, the ability to analyze single bacteria in real time has provided new, important quantitative insights into this long-standing question in cell biology. |
1508.05707 | Lucilla de Arcangelis | Vittorio Capano, Hans J. Herrmann and Lucilla de Arcangelis | Optimal percentage of inhibitory synapses in multi-task learning | 5 pages, 5 figures | SCIENTIFIC REPORTS vol 5 page 9895 (2015) | 10.1038/srep09895 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Performing more tasks in parallel is a typical feature of complex brains.
These are characterized by the coexistence of excitatory and inhibitory
synapses, whose percentage in mammals is measured to have a typical value of
20-30\%. Here we investigate parallel learning of more Boolean rules in
neuronal networks. We f... | [
{
"created": "Mon, 24 Aug 2015 07:27:05 GMT",
"version": "v1"
}
] | 2015-08-25 | [
[
"Capano",
"Vittorio",
""
],
[
"Herrmann",
"Hans J.",
""
],
[
"de Arcangelis",
"Lucilla",
""
]
] | Performing more tasks in parallel is a typical feature of complex brains. These are characterized by the coexistence of excitatory and inhibitory synapses, whose percentage in mammals is measured to have a typical value of 20-30\%. Here we investigate parallel learning of more Boolean rules in neuronal networks. We fin... |
1807.00668 | Andrew McMurry | Andrew J McMurry (1), Richen Zhang (1), Alex Foxman (2), Lawrence
Reiter, (2) Ronny Schnel (2), DeLeys Brandman (1) ((1) Medal, Inc, (2)
NACORS, LLC - National Accountable Care Organization Research Services) | Using routinely collected patient data to support clinical trials
research in accountable care organizations | 11 pages including cover, 4 figures, 2 tables | null | null | null | q-bio.QM cs.CY cs.IR | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Background: More than half (57%) of pharma clinical research spend is in
support of clinical trials. One reason is that Electronic Health Record (EHR)
systems and HIPAA privacy rules often limit how broadly patient information can
be shared, resulting in laborious human efforts to manually collect,
de-identify, and s... | [
{
"created": "Mon, 25 Jun 2018 22:13:30 GMT",
"version": "v1"
}
] | 2018-07-03 | [
[
"McMurry",
"Andrew J",
""
],
[
"Zhang",
"Richen",
""
],
[
"Foxman",
"Alex",
""
],
[
"Reiter",
"Lawrence",
""
],
[
"Schnel",
"Ronny",
""
],
[
"Brandman",
"DeLeys",
""
]
] | Background: More than half (57%) of pharma clinical research spend is in support of clinical trials. One reason is that Electronic Health Record (EHR) systems and HIPAA privacy rules often limit how broadly patient information can be shared, resulting in laborious human efforts to manually collect, de-identify, and sum... |
1310.8139 | Ido Kanter | Roni Vardi, Amir Goldental, Shoshana Guberman, Alexander Kalmanovich,
Hagar Marmari and Ido Kanter | Sudden synchrony leaps accompanied by frequency multiplications in
neuronal activity | 23 pages, 3 figures | Front. Neural Circuits, 30 October 2013 | 10.3389/fncir.2013.00176 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A classical view of neural coding relies on temporal firing synchrony among
functional groups of neurons; however the underlying mechanism remains an
enigma. Here we experimentally demonstrate a mechanism where time-lags among
neuronal spiking leap from several tens of milliseconds to nearly zero-lag
synchrony. It al... | [
{
"created": "Wed, 30 Oct 2013 13:14:09 GMT",
"version": "v1"
}
] | 2013-10-31 | [
[
"Vardi",
"Roni",
""
],
[
"Goldental",
"Amir",
""
],
[
"Guberman",
"Shoshana",
""
],
[
"Kalmanovich",
"Alexander",
""
],
[
"Marmari",
"Hagar",
""
],
[
"Kanter",
"Ido",
""
]
] | A classical view of neural coding relies on temporal firing synchrony among functional groups of neurons; however the underlying mechanism remains an enigma. Here we experimentally demonstrate a mechanism where time-lags among neuronal spiking leap from several tens of milliseconds to nearly zero-lag synchrony. It also... |
2210.03231 | Qiang Li | Qiang Li, Greg Ver Steeg, Shujian Yu, Jesus Malo | Functional Connectome of the Human Brain with Total Correlation | 22 pages, 13 figures | Entropy 2022, 24(12), 1725; | 10.3390/e24121725 | null | q-bio.NC math.ST stat.TH | http://creativecommons.org/licenses/by/4.0/ | Recent studies proposed the use of Total Correlation to describe functional
connectivity among brain regions as a multivariate alternative to conventional
pair-wise measures such as correlation or mutual information. In this work we
build on this idea to infer a large scale (whole brain) connectivity network
based on... | [
{
"created": "Thu, 6 Oct 2022 21:56:30 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Oct 2022 16:09:16 GMT",
"version": "v2"
},
{
"created": "Wed, 12 Oct 2022 14:37:35 GMT",
"version": "v3"
},
{
"created": "Mon, 14 Nov 2022 10:57:22 GMT",
"version": "v4"
}
] | 2022-11-28 | [
[
"Li",
"Qiang",
""
],
[
"Steeg",
"Greg Ver",
""
],
[
"Yu",
"Shujian",
""
],
[
"Malo",
"Jesus",
""
]
] | Recent studies proposed the use of Total Correlation to describe functional connectivity among brain regions as a multivariate alternative to conventional pair-wise measures such as correlation or mutual information. In this work we build on this idea to infer a large scale (whole brain) connectivity network based on T... |
q-bio/0611040 | Gerhard Schmid | G. Schmid, I. Goychuk and P. Hanggi | Capacitance fluctuations causing channel noise reduction in stochastic
Hodgkin-Huxley systems | 18 pages | Physical Biology 3, 248254 (2006) | 10.1088/1478-3975/3/4/002 | null | q-bio.NC q-bio.SC | null | Voltage-dependent ion channels determine the electric properties of axonal
cell membranes. They not only allow the passage of ions through the cell
membrane but also contribute to an additional charging of the cell membrane
resulting in the so-called capacitance loading. The switching of the channel
gates between an ... | [
{
"created": "Fri, 10 Nov 2006 13:19:55 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Schmid",
"G.",
""
],
[
"Goychuk",
"I.",
""
],
[
"Hanggi",
"P.",
""
]
] | Voltage-dependent ion channels determine the electric properties of axonal cell membranes. They not only allow the passage of ions through the cell membrane but also contribute to an additional charging of the cell membrane resulting in the so-called capacitance loading. The switching of the channel gates between an op... |
2104.02174 | Saumya Yashmohini Sahai | Saumya Yashmohini Sahai, Saket Gurukar, Wasiur R. KhudaBukhsh,
Srinivasan Parthasarathy, Grzegorz A. Rempala | A Machine Learning Model for Nowcasting Epidemic Incidence | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Due to delay in reporting, the daily national and statewide COVID-19
incidence counts are often unreliable and need to be estimated from recent
data. This process is known in economics as nowcasting. We describe in this
paper a simple random forest statistical model for nowcasting the COVID - 19
daily new infection c... | [
{
"created": "Mon, 5 Apr 2021 22:28:38 GMT",
"version": "v1"
}
] | 2021-04-07 | [
[
"Sahai",
"Saumya Yashmohini",
""
],
[
"Gurukar",
"Saket",
""
],
[
"KhudaBukhsh",
"Wasiur R.",
""
],
[
"Parthasarathy",
"Srinivasan",
""
],
[
"Rempala",
"Grzegorz A.",
""
]
] | Due to delay in reporting, the daily national and statewide COVID-19 incidence counts are often unreliable and need to be estimated from recent data. This process is known in economics as nowcasting. We describe in this paper a simple random forest statistical model for nowcasting the COVID - 19 daily new infection cou... |
1805.00570 | Ruth Collins | Cecil Barnett-Neefs and Ruth N. Collins | Identification of a complete YPT1 Rab GTPase sequence from the fungal
pathogen Colletotrichum incanum | 4 figures, 1 Appendix | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Colletotrichum represent a genus of fungal species primarily known as plant
pathogens with severe economic impacts in temperate, subtropical and tropical
climates Consensus taxonomy and classification systems for Colletotrichum
species have been undergoing revision as high resolution genomic data becomes
available. H... | [
{
"created": "Tue, 1 May 2018 22:21:54 GMT",
"version": "v1"
}
] | 2018-05-03 | [
[
"Barnett-Neefs",
"Cecil",
""
],
[
"Collins",
"Ruth N.",
""
]
] | Colletotrichum represent a genus of fungal species primarily known as plant pathogens with severe economic impacts in temperate, subtropical and tropical climates Consensus taxonomy and classification systems for Colletotrichum species have been undergoing revision as high resolution genomic data becomes available. Her... |
2205.13493 | Valentin Schmutz | Shuqi Wang, Valentin Schmutz, Guillaume Bellec, Wulfram Gerstner | Mesoscopic modeling of hidden spiking neurons | 23 pages, 7 figures | null | null | null | q-bio.NC cs.LG stat.ML | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Can we use spiking neural networks (SNN) as generative models of
multi-neuronal recordings, while taking into account that most neurons are
unobserved? Modeling the unobserved neurons with large pools of hidden spiking
neurons leads to severely underconstrained problems that are hard to tackle
with maximum likelihood... | [
{
"created": "Thu, 26 May 2022 17:04:39 GMT",
"version": "v1"
},
{
"created": "Sat, 7 Jan 2023 16:25:16 GMT",
"version": "v2"
}
] | 2023-01-10 | [
[
"Wang",
"Shuqi",
""
],
[
"Schmutz",
"Valentin",
""
],
[
"Bellec",
"Guillaume",
""
],
[
"Gerstner",
"Wulfram",
""
]
] | Can we use spiking neural networks (SNN) as generative models of multi-neuronal recordings, while taking into account that most neurons are unobserved? Modeling the unobserved neurons with large pools of hidden spiking neurons leads to severely underconstrained problems that are hard to tackle with maximum likelihood e... |
q-bio/0609019 | Bruce Ayati | Bruce P. Ayati and Isaac Klapper | A Multiscale Model of Biofilm as a Senescence-Structured Fluid | null | Multiscale Modeling & Simulation, Vol. 6, No. 2, pp. 347-365, 2007 | 10.1137/060669796 | null | q-bio.CB | null | We derive a physiologically structured multiscale model for biofilm
development. The model has components on two spatial scales, which induce
different time scales into the problem. The macroscopic behavior of the system
is modeled using growth-induced flow in a domain with a moving boundary.
Cell-level processes are... | [
{
"created": "Wed, 13 Sep 2006 18:47:29 GMT",
"version": "v1"
}
] | 2023-02-14 | [
[
"Ayati",
"Bruce P.",
""
],
[
"Klapper",
"Isaac",
""
]
] | We derive a physiologically structured multiscale model for biofilm development. The model has components on two spatial scales, which induce different time scales into the problem. The macroscopic behavior of the system is modeled using growth-induced flow in a domain with a moving boundary. Cell-level processes are i... |
q-bio/0508016 | Veit Schw\"ammle | V. Schw\"ammle, K. Luz-Burgoa, J. S. S\'a Martins and S. Moss de
Oliveira | Phase transition in a mean-field model for sympatric speciation | accepted for Physica A | null | 10.1016/j.physa.2006.01.076 | null | q-bio.PE | null | We introduce an analytical model for population dynamics with intra-specific
competition, mutation and assortative mating as basic ingredients. The set of
equations that describes the time evolution of population size in a mean-field
approximation may be decoupled. We find a phase transition leading to sympatric
spec... | [
{
"created": "Mon, 15 Aug 2005 20:15:14 GMT",
"version": "v1"
}
] | 2015-06-26 | [
[
"Schwämmle",
"V.",
""
],
[
"Luz-Burgoa",
"K.",
""
],
[
"Martins",
"J. S. Sá",
""
],
[
"de Oliveira",
"S. Moss",
""
]
] | We introduce an analytical model for population dynamics with intra-specific competition, mutation and assortative mating as basic ingredients. The set of equations that describes the time evolution of population size in a mean-field approximation may be decoupled. We find a phase transition leading to sympatric specia... |
2309.07356 | Jinzhi Lei | Rongsheng Huang, Qiaojun Situ, Jinzhi Lei | Dynamics of cell-type transition mediated by epigenetic modifications | 34 pages, 12 figures | null | null | null | q-bio.QM math-ph math.MP q-bio.CB | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Maintaining tissue homeostasis requires appropriate regulation of stem cell
differentiation. The Waddington landscape posits that gene circuits in a cell
form a potential landscape of different cell types, wherein cells follow
attractors of the probability landscape to develop into distinct cell types.
However, how a... | [
{
"created": "Wed, 13 Sep 2023 23:54:56 GMT",
"version": "v1"
}
] | 2023-09-15 | [
[
"Huang",
"Rongsheng",
""
],
[
"Situ",
"Qiaojun",
""
],
[
"Lei",
"Jinzhi",
""
]
] | Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of the probability landscape to develop into distinct cell types. However, how adu... |
2402.12405 | Meng Xiao | Cong Li, Meng Xiao, Pengfei Wang, Guihai Feng, Xin Li, Yuanchun Zhou | scInterpreter: Training Large Language Models to Interpret scRNA-seq
Data for Cell Type Annotation | 4 pages, submitted to FCS | null | null | null | q-bio.GN cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite the inherent limitations of existing Large Language Models in
directly reading and interpreting single-cell omics data, they demonstrate
significant potential and flexibility as the Foundation Model. This research
focuses on how to train and adapt the Large Language Model with the capability
to interpret and ... | [
{
"created": "Sun, 18 Feb 2024 05:39:00 GMT",
"version": "v1"
}
] | 2024-02-21 | [
[
"Li",
"Cong",
""
],
[
"Xiao",
"Meng",
""
],
[
"Wang",
"Pengfei",
""
],
[
"Feng",
"Guihai",
""
],
[
"Li",
"Xin",
""
],
[
"Zhou",
"Yuanchun",
""
]
] | Despite the inherent limitations of existing Large Language Models in directly reading and interpreting single-cell omics data, they demonstrate significant potential and flexibility as the Foundation Model. This research focuses on how to train and adapt the Large Language Model with the capability to interpret and di... |
1606.03592 | Robert Leech | Peter J. Hellyer, Claudia Clopath, Angie A. Kehagia, Federico E.
Turkheimer, Robert Leech | Balanced activation in a simple embodied neural simulation | 26 pages, 7 figures, associated github repository:
https://github.com/c3nl-neuraldynamics/Avatar | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years, there have been many computational simulations of
spontaneous neural dynamics. Here, we explore a model of spontaneous neural
dynamics and allow it to control a virtual agent moving in a simple
environment. This setup generates interesting brain-environment feedback
interactions that rapidly destabil... | [
{
"created": "Sat, 11 Jun 2016 13:39:43 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Aug 2016 09:52:31 GMT",
"version": "v2"
}
] | 2016-08-19 | [
[
"Hellyer",
"Peter J.",
""
],
[
"Clopath",
"Claudia",
""
],
[
"Kehagia",
"Angie A.",
""
],
[
"Turkheimer",
"Federico E.",
""
],
[
"Leech",
"Robert",
""
]
] | In recent years, there have been many computational simulations of spontaneous neural dynamics. Here, we explore a model of spontaneous neural dynamics and allow it to control a virtual agent moving in a simple environment. This setup generates interesting brain-environment feedback interactions that rapidly destabiliz... |
1703.10481 | Kumar Sankar Ray | Mandrita Mondal and Kumar S. Ray | DNA Tweezers Based on Semantics of DNA Strand Graph | 22 pages, 11 figures. arXiv admin note: substantial text overlap with
arXiv:1702.05383 | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Because of the limitations of classical silicon based computational
technology, several alternatives to traditional method in form of
unconventional computing have been proposed. In this paper we will focus on DNA
computing which is showing the possibility of excellence for its massive
parallelism, potential for info... | [
{
"created": "Wed, 29 Mar 2017 09:03:27 GMT",
"version": "v1"
}
] | 2017-03-31 | [
[
"Mondal",
"Mandrita",
""
],
[
"Ray",
"Kumar S.",
""
]
] | Because of the limitations of classical silicon based computational technology, several alternatives to traditional method in form of unconventional computing have been proposed. In this paper we will focus on DNA computing which is showing the possibility of excellence for its massive parallelism, potential for inform... |
2004.14290 | Maria McGee | Maria P McGee, Michael Morykwas, Mary Kerns, Anirudh Vashisht, Ashok N
Hegde and Louis Argenta | Interstitial cells and neurons respond to variations in hydration | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dehydration and brain interstitial fluid alterations associate to cognitive
dysfunction. We now explore whether changes in matrix hydration are a possible
common signal for modulation of water-transfer rates and neuron function.
| [
{
"created": "Mon, 27 Apr 2020 12:40:19 GMT",
"version": "v1"
}
] | 2020-04-30 | [
[
"McGee",
"Maria P",
""
],
[
"Morykwas",
"Michael",
""
],
[
"Kerns",
"Mary",
""
],
[
"Vashisht",
"Anirudh",
""
],
[
"Hegde",
"Ashok N",
""
],
[
"Argenta",
"Louis",
""
]
] | Dehydration and brain interstitial fluid alterations associate to cognitive dysfunction. We now explore whether changes in matrix hydration are a possible common signal for modulation of water-transfer rates and neuron function. |
1908.07960 | Niv DeMalach | DeMalach Niv, Po-Ju Ke, Tadashi Fukami | The effects of ecological selection on species diversity and trait
distribution: predictions and an empirical test | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ecological selection is a major driver of community assembly. Selection is
classified as stabilizing when species with intermediate trait values gain the
highest reproductive success, whereas selection is considered directional when
fitness is highest for species with extreme trait values. Previous studies have
inves... | [
{
"created": "Wed, 21 Aug 2019 16:05:43 GMT",
"version": "v1"
},
{
"created": "Wed, 12 May 2021 10:24:18 GMT",
"version": "v2"
}
] | 2021-05-13 | [
[
"Niv",
"DeMalach",
""
],
[
"Ke",
"Po-Ju",
""
],
[
"Fukami",
"Tadashi",
""
]
] | Ecological selection is a major driver of community assembly. Selection is classified as stabilizing when species with intermediate trait values gain the highest reproductive success, whereas selection is considered directional when fitness is highest for species with extreme trait values. Previous studies have investi... |
2403.10478 | Michael Brocidiacono | Michael Brocidiacono, Konstantin I. Popov, Alexander Tropsha | An Improved Metric and Benchmark for Assessing the Performance of
Virtual Screening Models | 10 pages, 4 figures, and 4 tables. The source code is available at
https://github.com/molecularmodelinglab/bigbind | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Structure-based virtual screening (SBVS) is a key workflow in computational
drug discovery. SBVS models are assessed by measuring the enrichment of known
active molecules over decoys in retrospective screens. However, the standard
formula for enrichment cannot estimate model performance on very large
libraries. Addit... | [
{
"created": "Fri, 15 Mar 2024 17:09:02 GMT",
"version": "v1"
}
] | 2024-03-18 | [
[
"Brocidiacono",
"Michael",
""
],
[
"Popov",
"Konstantin I.",
""
],
[
"Tropsha",
"Alexander",
""
]
] | Structure-based virtual screening (SBVS) is a key workflow in computational drug discovery. SBVS models are assessed by measuring the enrichment of known active molecules over decoys in retrospective screens. However, the standard formula for enrichment cannot estimate model performance on very large libraries. Additio... |
1401.4956 | Nicola Palmieri | Nicola Palmieri, Carolin Kosiol, Christian Schl\"otterer | The life cycle of Drosophila orphan genes | 47 pages, 19 figures | null | 10.7554/elife.01311 | null | q-bio.GN | http://creativecommons.org/licenses/by/3.0/ | Orphans are genes restricted to a single phylogenetic lineage and emerge at
high rates. While this predicts an accumulation of genes, the gene number has
remained remarkably constant through evolution. This paradox has not yet been
resolved. Because orphan genes have been mainly analyzed over long evolutionary
time s... | [
{
"created": "Mon, 20 Jan 2014 16:03:15 GMT",
"version": "v1"
}
] | 2014-01-23 | [
[
"Palmieri",
"Nicola",
""
],
[
"Kosiol",
"Carolin",
""
],
[
"Schlötterer",
"Christian",
""
]
] | Orphans are genes restricted to a single phylogenetic lineage and emerge at high rates. While this predicts an accumulation of genes, the gene number has remained remarkably constant through evolution. This paradox has not yet been resolved. Because orphan genes have been mainly analyzed over long evolutionary time sca... |
q-bio/0406028 | Long Wang | Long Wang | Aggregation of foraging swarms | null | null | null | null | q-bio.CB | null | In this paper we consider a continuous-time anisotropic swarm model with an
attraction/repulsion function and study its aggregation properties. It is shown
that the swarm members will aggregate and eventually form a cohesive cluster of
finite size around the swarm center. We also study the swarm cohesiveness when
the... | [
{
"created": "Mon, 14 Jun 2004 18:56:27 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Wang",
"Long",
""
]
] | In this paper we consider a continuous-time anisotropic swarm model with an attraction/repulsion function and study its aggregation properties. It is shown that the swarm members will aggregate and eventually form a cohesive cluster of finite size around the swarm center. We also study the swarm cohesiveness when the m... |
1601.06943 | Simone Pigolotti | Simone Pigolotti, Roberto Benzi | Competition between fast- and slow-diffusing species in non-homogeneous
environments | 11 pages, 6 figures, accepted for publication in J. Theo. Biol | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study an individual-based model in which two spatially-distributed
species, characterized by different diffusivities, compete for resources. We
consider three different ecological settings. In the first, diffusing faster
has a cost in terms of reproduction rate. In the second case, resources are not
uniformly dist... | [
{
"created": "Tue, 26 Jan 2016 09:30:01 GMT",
"version": "v1"
}
] | 2016-01-27 | [
[
"Pigolotti",
"Simone",
""
],
[
"Benzi",
"Roberto",
""
]
] | We study an individual-based model in which two spatially-distributed species, characterized by different diffusivities, compete for resources. We consider three different ecological settings. In the first, diffusing faster has a cost in terms of reproduction rate. In the second case, resources are not uniformly distri... |
2303.06060 | Liwei Huang | Liwei Huang, Zhengyu Ma, Liutao Yu, Huihui Zhou, Yonghong Tian | Deep Spiking Neural Networks with High Representation Similarity Model
Visual Pathways of Macaque and Mouse | Accepted by Proceedings of the 37th AAAI Conference on Artificial
Intelligence (AAAI-23) | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deep artificial neural networks (ANNs) play a major role in modeling the
visual pathways of primate and rodent. However, they highly simplify the
computational properties of neurons compared to their biological counterparts.
Instead, Spiking Neural Networks (SNNs) are more biologically plausible models
since spiking ... | [
{
"created": "Thu, 9 Mar 2023 13:07:30 GMT",
"version": "v1"
},
{
"created": "Mon, 27 Mar 2023 10:12:45 GMT",
"version": "v2"
},
{
"created": "Wed, 5 Apr 2023 12:29:38 GMT",
"version": "v3"
},
{
"created": "Fri, 12 May 2023 09:16:39 GMT",
"version": "v4"
},
{
"cre... | 2023-05-23 | [
[
"Huang",
"Liwei",
""
],
[
"Ma",
"Zhengyu",
""
],
[
"Yu",
"Liutao",
""
],
[
"Zhou",
"Huihui",
""
],
[
"Tian",
"Yonghong",
""
]
] | Deep artificial neural networks (ANNs) play a major role in modeling the visual pathways of primate and rodent. However, they highly simplify the computational properties of neurons compared to their biological counterparts. Instead, Spiking Neural Networks (SNNs) are more biologically plausible models since spiking ne... |
1904.01903 | Gerhard Wolber | David Schaller, Szymon Pach and Gerhard Wolber | PyRod -- Tracing Water Molecules in Molecular Dynamics Simulations | null | J.Chem.Inf.Model. (2019) 2818-2829 | 10.1021/acs.jcim.9b00281 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ligands entering a protein binding pocket essentially compete with water
molecules for binding to the protein. Hence, the location and thermodynamic
properties of water molecules in protein structures have gained increased
attention in the drug design community. Including corresponding data into 3D
pharmacophore mode... | [
{
"created": "Wed, 3 Apr 2019 10:36:49 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Aug 2019 12:02:25 GMT",
"version": "v2"
}
] | 2019-08-28 | [
[
"Schaller",
"David",
""
],
[
"Pach",
"Szymon",
""
],
[
"Wolber",
"Gerhard",
""
]
] | Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the drug design community. Including corresponding data into 3D pharmacophore modeli... |
1310.4547 | Mike Steel Prof. | Joshua I Smith, Mike Steel, Wim Hordijk | Autocatalytic sets in a partitioned biochemical network | 28 pages, 8 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In previous work, RAF theory has been developed as a tool for making
theoretical progress on the origin of life question, providing insight into the
structure and occurrence of self-sustaining and collectively autocatalytic sets
within catalytic polymer networks. We present here an extension in which there
are two "i... | [
{
"created": "Wed, 16 Oct 2013 23:36:14 GMT",
"version": "v1"
}
] | 2013-10-18 | [
[
"Smith",
"Joshua I",
""
],
[
"Steel",
"Mike",
""
],
[
"Hordijk",
"Wim",
""
]
] | In previous work, RAF theory has been developed as a tool for making theoretical progress on the origin of life question, providing insight into the structure and occurrence of self-sustaining and collectively autocatalytic sets within catalytic polymer networks. We present here an extension in which there are two "ind... |
2103.12173 | Michael Thorne | Michael Thorne | Tipping Cycles | null | null | null | null | q-bio.PE math.CA | http://creativecommons.org/licenses/by/4.0/ | Ecological systems are studied using many different approaches and
mathematical tools. One approach, based on the Jacobian of Lotka-Volterra type
models, has been a staple of mathematical ecology for years, leading to many
ideas such as on questions of system stability. Instability in such methods is
determined by th... | [
{
"created": "Mon, 22 Mar 2021 20:43:39 GMT",
"version": "v1"
},
{
"created": "Mon, 29 Mar 2021 08:37:03 GMT",
"version": "v2"
},
{
"created": "Thu, 24 Jun 2021 10:18:29 GMT",
"version": "v3"
}
] | 2021-06-25 | [
[
"Thorne",
"Michael",
""
]
] | Ecological systems are studied using many different approaches and mathematical tools. One approach, based on the Jacobian of Lotka-Volterra type models, has been a staple of mathematical ecology for years, leading to many ideas such as on questions of system stability. Instability in such methods is determined by the ... |
2310.01100 | Houwen Xin | Lizhi Xin, Kevin Xin, Houwen Xin | A computational model for synaptic message transmission | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | A computational model incorporating insights from quantum theory is proposed
to describe and explain synaptic message transmission. We propose that
together, neurotransmitters and their corresponding receptors, function as a
physical "quantum decision tree" to "decide" whether to excite or inhibit the
synapse. When a... | [
{
"created": "Mon, 2 Oct 2023 11:19:57 GMT",
"version": "v1"
}
] | 2023-10-03 | [
[
"Xin",
"Lizhi",
""
],
[
"Xin",
"Kevin",
""
],
[
"Xin",
"Houwen",
""
]
] | A computational model incorporating insights from quantum theory is proposed to describe and explain synaptic message transmission. We propose that together, neurotransmitters and their corresponding receptors, function as a physical "quantum decision tree" to "decide" whether to excite or inhibit the synapse. When a n... |
2004.06311 | Weijie Pang | Weijie Pang | Public Health Policy: COVID-19 Epidemic and SEIR Model with Asymptomatic
Viral Carriers | 17 pages, 10 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We measure the effect of different public health regulations to the spread of
COVID-19, based on a SEIRA model -- a SEIR model including asymptomatic
transmissions. The cumulative confirmed cases and death show nonlinear positive
relationship with the value of asymptomatic rate. Based on this model, we
analyze the in... | [
{
"created": "Tue, 14 Apr 2020 05:33:41 GMT",
"version": "v1"
}
] | 2020-04-15 | [
[
"Pang",
"Weijie",
""
]
] | We measure the effect of different public health regulations to the spread of COVID-19, based on a SEIRA model -- a SEIR model including asymptomatic transmissions. The cumulative confirmed cases and death show nonlinear positive relationship with the value of asymptomatic rate. Based on this model, we analyze the inhi... |
2009.10014 | Madhav Marathe | Aniruddha Adiga, Devdatt Dubhashi, Bryan Lewis, Madhav Marathe,
Srinivasan Venkatramanan, Anil Vullikanti | Models for COVID-19 Pandemic: A Comparative Analysis | null | null | null | null | q-bio.PE cs.AI | http://creativecommons.org/licenses/by/4.0/ | COVID-19 pandemic represents an unprecedented global health crisis in the
last 100 years. Its economic, social and health impact continues to grow and is
likely to end up as one of the worst global disasters since the 1918 pandemic
and the World Wars. Mathematical models have played an important role in the
ongoing c... | [
{
"created": "Mon, 21 Sep 2020 16:42:00 GMT",
"version": "v1"
}
] | 2020-09-22 | [
[
"Adiga",
"Aniruddha",
""
],
[
"Dubhashi",
"Devdatt",
""
],
[
"Lewis",
"Bryan",
""
],
[
"Marathe",
"Madhav",
""
],
[
"Venkatramanan",
"Srinivasan",
""
],
[
"Vullikanti",
"Anil",
""
]
] | COVID-19 pandemic represents an unprecedented global health crisis in the last 100 years. Its economic, social and health impact continues to grow and is likely to end up as one of the worst global disasters since the 1918 pandemic and the World Wars. Mathematical models have played an important role in the ongoing cri... |
1409.0590 | Christoph Adami | Christoph Adami | Information-theoretic considerations concerning the origin of life | 10 pages, one figure. Expanded discussion of experiments with
biopolymers | Origins of Life and Evolution of the Bioshperes 45 (2015) 9439 | 10.1007/s11084-015-9439-0 | null | q-bio.PE cs.IT math.IT nlin.AO q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Research investigating the origins of life usually focuses on exploring
possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic
approaches. Little work has been done exploring fundamental issues concerning
the spontaneous emergence of life using only concepts (such as information and
evolution... | [
{
"created": "Tue, 2 Sep 2014 02:02:39 GMT",
"version": "v1"
},
{
"created": "Sat, 22 Nov 2014 18:09:39 GMT",
"version": "v2"
}
] | 2015-06-24 | [
[
"Adami",
"Christoph",
""
]
] | Research investigating the origins of life usually focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Little work has been done exploring fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) ... |
1003.2879 | Nicolas Brodu | Nicolas Brodu, Fabien Lotte, Anatole L\'ecuyer | Exploring Two Novel Features for EEG-based Brain-Computer Interfaces:
Multifractal Cumulants and Predictive Complexity | Updated with more subjects. Separated out the band-power comparisons
in a companion article after reviewer feedback. Source code and companion
article are available at
http://nicolas.brodu.numerimoire.net/en/recherche/publications | null | null | null | q-bio.NC physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we introduce two new features for the design of
electroencephalography (EEG) based Brain-Computer Interfaces (BCI): one feature
based on multifractal cumulants, and one feature based on the predictive
complexity of the EEG time series. The multifractal cumulants feature measures
the signal regularity, ... | [
{
"created": "Mon, 15 Mar 2010 10:20:14 GMT",
"version": "v1"
},
{
"created": "Sat, 18 Sep 2010 15:52:09 GMT",
"version": "v2"
}
] | 2010-09-21 | [
[
"Brodu",
"Nicolas",
""
],
[
"Lotte",
"Fabien",
""
],
[
"Lécuyer",
"Anatole",
""
]
] | In this paper, we introduce two new features for the design of electroencephalography (EEG) based Brain-Computer Interfaces (BCI): one feature based on multifractal cumulants, and one feature based on the predictive complexity of the EEG time series. The multifractal cumulants feature measures the signal regularity, wh... |
1209.0985 | Leonid Belous | Yu. V. Rubin, L. F. Belous | Molecular structure and interactions of nucleic acid components in
nanopaticles: ab initio calculations | 8 pages, 4 figures; http://www.ujp.bitp.kiev.ua | Ukrainian Journal of Physics, 2012, Vol. 57, no. 7, pp. 723-731 | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Self-associates of nucleic acid components (stacking trimers and tetramers of
the base pairs of nucleic acids) and short fragments of nucleic acids are
nanoparticles (linear sizes of these particles are more than 10 A. Modern
quantum-mechanical methods and softwares allow one to perform ab initio
calculations of the ... | [
{
"created": "Wed, 5 Sep 2012 14:02:49 GMT",
"version": "v1"
}
] | 2012-09-06 | [
[
"Rubin",
"Yu. V.",
""
],
[
"Belous",
"L. F.",
""
]
] | Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A. Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the sy... |
1304.6098 | Melissa Wilson Sayres | Melissa A. Wilson Sayres | Timing of ancient human Y lineage depends on the mutation rate: A
comment on Mendez et al | 5 pages, 1 table | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mendez et al. recently report the identification of a Y chromosome lineage
from an African American that is an outgroup to all other known Y haplotypes,
and report a time to most recent common ancestor, TMRCA, for human Y lineages
that is substantially longer than any previous estimate. The identification of
a novel ... | [
{
"created": "Mon, 22 Apr 2013 20:26:19 GMT",
"version": "v1"
}
] | 2013-04-24 | [
[
"Sayres",
"Melissa A. Wilson",
""
]
] | Mendez et al. recently report the identification of a Y chromosome lineage from an African American that is an outgroup to all other known Y haplotypes, and report a time to most recent common ancestor, TMRCA, for human Y lineages that is substantially longer than any previous estimate. The identification of a novel Y ... |
1206.0362 | Philippe Robert S. | Vincent Fromion and Emanuele Leoncini and Philippe Robert | Stochastic Gene Expression in Cells: A Point Process Approach | null | null | null | null | q-bio.QM math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper investigates the stochastic fluctuations of the number of copies
of a given protein in a cell. This problem has already been addressed in the
past and closed-form expressions of the mean and variance have been obtained
for a simplified stochastic model of the gene expression. These results have
been obtain... | [
{
"created": "Sat, 2 Jun 2012 10:47:00 GMT",
"version": "v1"
}
] | 2012-06-05 | [
[
"Fromion",
"Vincent",
""
],
[
"Leoncini",
"Emanuele",
""
],
[
"Robert",
"Philippe",
""
]
] | This paper investigates the stochastic fluctuations of the number of copies of a given protein in a cell. This problem has already been addressed in the past and closed-form expressions of the mean and variance have been obtained for a simplified stochastic model of the gene expression. These results have been obtained... |
2003.03223 | Andrea Gianotti Prof | Mattia Di Nunzio, Gianfranco Picone, Federica Pasini, Elena Chiarello,
Maria Fiorenza Caboni, Francesco Capozzi, Andrea Gianotti, Alessandra Bordoni | Olive oil by-product as functional ingredient in bakery products | null | Food Research International, 131, 108940 (2020) | 10.1016/j.foodres.2019.108940 | null | q-bio.TO q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | By-products represent a major disposal problem for the food industry, but
they are also promising sources of bioactive compounds. Olive pomace, one of
the main by-products of olive oil production, is a potential low-cost,
phenol-rich ingredient for the formulation of functional food. In this study,
bakery products en... | [
{
"created": "Fri, 28 Feb 2020 11:08:34 GMT",
"version": "v1"
}
] | 2020-06-29 | [
[
"Di Nunzio",
"Mattia",
""
],
[
"Picone",
"Gianfranco",
""
],
[
"Pasini",
"Federica",
""
],
[
"Chiarello",
"Elena",
""
],
[
"Caboni",
"Maria Fiorenza",
""
],
[
"Capozzi",
"Francesco",
""
],
[
"Gianotti",
"Andrea... | By-products represent a major disposal problem for the food industry, but they are also promising sources of bioactive compounds. Olive pomace, one of the main by-products of olive oil production, is a potential low-cost, phenol-rich ingredient for the formulation of functional food. In this study, bakery products enri... |
1709.10483 | Alexandra Badea | Robert J Anderson, James J Cook, Natalie A Delpratt, John C Nouls, Bin
Gu, James O McNamara, Brian B Avants, G Allan Johnson, Alexandra Badea | Small Animal Multivariate Brain Analysis (SAMBA): A High Throughput
Pipeline with a Validation Framework | 48 pages, 9 Figures, 3 Tables, 1 Suppl Table, 7 SupplementaryTables | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While many neuroscience questions aim to understand the human brain, much
current knowledge has been gained using animal models, which replicate genetic,
structural, and connectivity aspects of the human brain. While voxel-based
analysis (VBA) of preclinical magnetic resonance images is widely-used, a
thorough examin... | [
{
"created": "Fri, 29 Sep 2017 16:28:46 GMT",
"version": "v1"
},
{
"created": "Mon, 21 May 2018 13:50:16 GMT",
"version": "v2"
}
] | 2018-05-22 | [
[
"Anderson",
"Robert J",
""
],
[
"Cook",
"James J",
""
],
[
"Delpratt",
"Natalie A",
""
],
[
"Nouls",
"John C",
""
],
[
"Gu",
"Bin",
""
],
[
"McNamara",
"James O",
""
],
[
"Avants",
"Brian B",
""
],
[
... | While many neuroscience questions aim to understand the human brain, much current knowledge has been gained using animal models, which replicate genetic, structural, and connectivity aspects of the human brain. While voxel-based analysis (VBA) of preclinical magnetic resonance images is widely-used, a thorough examinat... |
1912.11356 | Muhammad Nabeel Asim | Muhammad Nabeel Asima, Muhammad Imran Malik, Andreas Dengela, Sheraz
Ahmed | A Robust and Precise ConvNet for small non-coding RNA classification
(RPC-snRC) | 34 pages | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by/4.0/ | Functional or non-coding RNAs are attracting more attention as they are now
potentially considered valuable resources in the development of new drugs
intended to cure several human diseases. The identification of drugs targeting
the regulatory circuits of functional RNAs depends on knowing its family, a
task which is... | [
{
"created": "Mon, 23 Dec 2019 08:33:42 GMT",
"version": "v1"
}
] | 2019-12-25 | [
[
"Asima",
"Muhammad Nabeel",
""
],
[
"Malik",
"Muhammad Imran",
""
],
[
"Dengela",
"Andreas",
""
],
[
"Ahmed",
"Sheraz",
""
]
] | Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the regulatory circuits of functional RNAs depends on knowing its family, a task which is k... |
1705.10516 | Daniel Hoffmann | Farnoush Farahpour, Mohammadkarim Saeedghalati, Verena Brauer, Daniel
Hoffmann | Trade-off shapes diversity in eco-evolutionary dynamics | null | null | 10.7554/eLife.36273 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce an Interaction and Trade-off based Eco-Evolutionary Model
(ITEEM), in which species are competing for common resources in a well-mixed
system, and their evolution in interaction trait space is subject to a
life-history trade-off between replication rate and competitive ability. We
demonstrate that the st... | [
{
"created": "Tue, 30 May 2017 09:23:00 GMT",
"version": "v1"
}
] | 2018-09-07 | [
[
"Farahpour",
"Farnoush",
""
],
[
"Saeedghalati",
"Mohammadkarim",
""
],
[
"Brauer",
"Verena",
""
],
[
"Hoffmann",
"Daniel",
""
]
] | We introduce an Interaction and Trade-off based Eco-Evolutionary Model (ITEEM), in which species are competing for common resources in a well-mixed system, and their evolution in interaction trait space is subject to a life-history trade-off between replication rate and competitive ability. We demonstrate that the stre... |
1702.00031 | Lee Worden | Lee Worden, Travis C. Porco | Products of Compartmental Models in Epidemiology | null | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we show that many structured epidemic models may be described
using a straightforward product structure. Such products, derived from products
of directed graphs, may represent useful refinements including geographic and
demographic structure, age structure, gender, risk groups, or immunity status.
Exte... | [
{
"created": "Tue, 31 Jan 2017 19:33:20 GMT",
"version": "v1"
},
{
"created": "Wed, 28 Jun 2017 23:40:49 GMT",
"version": "v2"
}
] | 2017-06-30 | [
[
"Worden",
"Lee",
""
],
[
"Porco",
"Travis C.",
""
]
] | In this paper, we show that many structured epidemic models may be described using a straightforward product structure. Such products, derived from products of directed graphs, may represent useful refinements including geographic and demographic structure, age structure, gender, risk groups, or immunity status. Extens... |
0902.3147 | Claude Pasquier | Claude Pasquier (IBDC) | Biological data integration using Semantic Web technologies | null | Biochimie 90, 4 (2008) 584-94 | 10.1016/j.biochi.2008.02.007 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Current research in biology heavily depends on the availability and efficient
use of information. In order to build new knowledge, various sources of
biological data must often be combined. Semantic Web technologies, which
provide a common framework allowing data to be shared and reused between
applications, can be a... | [
{
"created": "Wed, 18 Feb 2009 14:05:06 GMT",
"version": "v1"
}
] | 2009-02-19 | [
[
"Pasquier",
"Claude",
"",
"IBDC"
]
] | Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common framework allowing data to be shared and reused between applications, can be app... |
0704.1811 | Samarth Swarup | Samarth Swarup and Les Gasser | Unifying Evolutionary and Network Dynamics | 11 pages, 12 figures, Accepted for publication in Physical Review E | null | 10.1103/PhysRevE.75.066114 | null | q-bio.QM q-bio.PE | null | Many important real-world networks manifest "small-world" properties such as
scale-free degree distributions, small diameters, and clustering. The most
common model of growth for these networks is "preferential attachment", where
nodes acquire new links with probability proportional to the number of links
they alread... | [
{
"created": "Fri, 13 Apr 2007 19:56:37 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Swarup",
"Samarth",
""
],
[
"Gasser",
"Les",
""
]
] | Many important real-world networks manifest "small-world" properties such as scale-free degree distributions, small diameters, and clustering. The most common model of growth for these networks is "preferential attachment", where nodes acquire new links with probability proportional to the number of links they already ... |
0908.4508 | Peter Csermely | Gabor I. Simko, David Gyurko, Daniel V. Veres, Tibor Nanasi, Peter
Csermely | Network strategies to understand the aging process and help age-related
drug design | an invited paper to Genome Medicine with 8 pages, 2 figures, 1 table
and 46 references | Genome Medicine (2009) 1, 90 | 10.1186/gm90 | null | q-bio.MN physics.bio-ph q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent studies have demonstrated that network approaches are highly
appropriate tools to understand the extreme complexity of the aging process.
The generality of the network concept helps to define and study the aging of
technological, social networks and ecosystems, which may give novel concepts to
cure age-related... | [
{
"created": "Mon, 31 Aug 2009 11:51:36 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Sep 2009 20:30:40 GMT",
"version": "v2"
}
] | 2009-09-28 | [
[
"Simko",
"Gabor I.",
""
],
[
"Gyurko",
"David",
""
],
[
"Veres",
"Daniel V.",
""
],
[
"Nanasi",
"Tibor",
""
],
[
"Csermely",
"Peter",
""
]
] | Recent studies have demonstrated that network approaches are highly appropriate tools to understand the extreme complexity of the aging process. The generality of the network concept helps to define and study the aging of technological, social networks and ecosystems, which may give novel concepts to cure age-related d... |
2005.07856 | Kai Guo | Zhihan Wang, Kai Guo, Pan Gao, Qinqin Pu, Min Wu, Changlong Li and
Junguk Hur | Identification of Repurposable Drugs and Adverse Drug Reactions for
Various Courses of COVID-19 Based on Single-Cell RNA Sequencing Data | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Coronavirus disease 2019 (COVID-19) has impacted almost every part of human
life worldwide, posing a massive threat to human health. There is no specific
drug for COVID-19, highlighting the urgent need for the development of
effective therapeutics. To identify potentially repurposable drugs, we employed
a systematic ... | [
{
"created": "Sat, 16 May 2020 03:30:17 GMT",
"version": "v1"
},
{
"created": "Fri, 4 Dec 2020 16:25:20 GMT",
"version": "v2"
}
] | 2020-12-07 | [
[
"Wang",
"Zhihan",
""
],
[
"Guo",
"Kai",
""
],
[
"Gao",
"Pan",
""
],
[
"Pu",
"Qinqin",
""
],
[
"Wu",
"Min",
""
],
[
"Li",
"Changlong",
""
],
[
"Hur",
"Junguk",
""
]
] | Coronavirus disease 2019 (COVID-19) has impacted almost every part of human life worldwide, posing a massive threat to human health. There is no specific drug for COVID-19, highlighting the urgent need for the development of effective therapeutics. To identify potentially repurposable drugs, we employed a systematic ap... |
2105.07390 | Saurav Mandal PhD | Saurav Mandal, Akshansh Gupta and Waribam Pratibha Chanu | Survival prediction of head and neck squamous cell carcinoma using
machine learning models | 3 figures | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Head and Neck Squamous Cell Carcinoma (HNSCC) is one of cancer type that is
most distressing leading to acute pain, effecting speech and primary survival
functions such as swallowing and breathing. The morbidity and mortality of
HNSCC patients have not significantly improved even tough there has been
advancement in s... | [
{
"created": "Sun, 16 May 2021 09:34:29 GMT",
"version": "v1"
}
] | 2021-05-18 | [
[
"Mandal",
"Saurav",
""
],
[
"Gupta",
"Akshansh",
""
],
[
"Chanu",
"Waribam Pratibha",
""
]
] | Head and Neck Squamous Cell Carcinoma (HNSCC) is one of cancer type that is most distressing leading to acute pain, effecting speech and primary survival functions such as swallowing and breathing. The morbidity and mortality of HNSCC patients have not significantly improved even tough there has been advancement in sur... |
1711.09015 | Dayun Yan | Dayun Yan, Jonathan H. Sherman, Jerome Canady, Barry Trink, Michael
Keidar | The cellular ROS-scavenging function, a key factor determining the
specific vulnerability of cancer cells to cold atmospheric plasma in vitro | null | null | null | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cold atmospheric plasma (CAP) has shown its promising application in cancer
treatment both in vitro and in vivo. However, the anti-cancer mechanism is
still largely unknown. CAP may kill cancer cells via triggering the rise of
intracellular ROS, DNA damage, mitochondrial damage, or cellular membrane
damage. While, th... | [
{
"created": "Fri, 24 Nov 2017 15:18:52 GMT",
"version": "v1"
}
] | 2017-11-27 | [
[
"Yan",
"Dayun",
""
],
[
"Sherman",
"Jonathan H.",
""
],
[
"Canady",
"Jerome",
""
],
[
"Trink",
"Barry",
""
],
[
"Keidar",
"Michael",
""
]
] | Cold atmospheric plasma (CAP) has shown its promising application in cancer treatment both in vitro and in vivo. However, the anti-cancer mechanism is still largely unknown. CAP may kill cancer cells via triggering the rise of intracellular ROS, DNA damage, mitochondrial damage, or cellular membrane damage. While, the ... |
1111.6353 | Kevin Lin | Kevin K. Lin, Kyle C. A. Wedgwood, Stephen Coombes, Lai-Sang Young | Limitations of perturbative techniques in the analysis of rhythms and
oscillations | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Perturbation theory is an important tool in the analysis of oscillators and
their response to external stimuli. It is predicated on the assumption that the
perturbations in question are "sufficiently weak", an assumption that is not
always valid when perturbative methods are applied. In this paper, we identify
a numb... | [
{
"created": "Mon, 28 Nov 2011 06:28:53 GMT",
"version": "v1"
},
{
"created": "Wed, 18 Jan 2012 04:02:23 GMT",
"version": "v2"
}
] | 2012-01-19 | [
[
"Lin",
"Kevin K.",
""
],
[
"Wedgwood",
"Kyle C. A.",
""
],
[
"Coombes",
"Stephen",
""
],
[
"Young",
"Lai-Sang",
""
]
] | Perturbation theory is an important tool in the analysis of oscillators and their response to external stimuli. It is predicated on the assumption that the perturbations in question are "sufficiently weak", an assumption that is not always valid when perturbative methods are applied. In this paper, we identify a number... |
1610.02864 | Roshan Prizak | Tamar Friedlander, Roshan Prizak, Nicholas H. Barton, and Ga\v{s}per
Tka\v{c}ik | Evolution of new regulatory functions on biophysically realistic fitness
landscapes | null | null | 10.1038/s41467-017-00238-8 | null | q-bio.PE q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Regulatory networks consist of interacting molecules with a high degree of
mutual chemical specificity. How can these molecules evolve when their function
depends on maintenance of interactions with cognate partners and simultaneous
avoidance of deleterious "crosstalk" with non-cognate molecules? Although
physical mo... | [
{
"created": "Mon, 10 Oct 2016 11:47:01 GMT",
"version": "v1"
},
{
"created": "Mon, 27 Feb 2017 10:31:33 GMT",
"version": "v2"
}
] | 2017-11-01 | [
[
"Friedlander",
"Tamar",
""
],
[
"Prizak",
"Roshan",
""
],
[
"Barton",
"Nicholas H.",
""
],
[
"Tkačik",
"Gašper",
""
]
] | Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous avoidance of deleterious "crosstalk" with non-cognate molecules? Although physical mode... |
q-bio/0404036 | Lutz Brusch | Lutz Brusch, Gianaurelio Cuniberti, Martin Bertau | Model evaluation for glycolytic oscillations in yeast biotransformations
of xenobiotics | null | Biophysical Chemistry 109, 413-426 (2004) | 10.1016/j.bpc.2003.12.004 | null | q-bio.MN q-bio.QM | null | Anaerobic glycolysis in yeast perturbed by the reduction of xenobiotic
ketones is studied numerically in two models which possess the same topology
but different levels of complexity. By comparing both models' predictions for
concentrations and fluxes as well as steady or oscillatory temporal behavior we
answer the q... | [
{
"created": "Mon, 26 Apr 2004 15:36:01 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Brusch",
"Lutz",
""
],
[
"Cuniberti",
"Gianaurelio",
""
],
[
"Bertau",
"Martin",
""
]
] | Anaerobic glycolysis in yeast perturbed by the reduction of xenobiotic ketones is studied numerically in two models which possess the same topology but different levels of complexity. By comparing both models' predictions for concentrations and fluxes as well as steady or oscillatory temporal behavior we answer the que... |
2005.08012 | Ian Craig | L.E. Olivier, I.K. Craig | An epidemiological model for the spread of COVID-19: A South African
case study | 14 pages, 13 Figures, 1 Table | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An epidemiological model is developed for the spread of COVID-19 in South
Africa. A variant of the classical compartmental SEIR model, called the SEIQRDP
model, is used. As South Africa is still in the early phases of the global
COVID-19 pandemic with the confirmed infectious cases not having peaked, the
SEIQRDP mode... | [
{
"created": "Sat, 16 May 2020 15:11:27 GMT",
"version": "v1"
},
{
"created": "Fri, 22 May 2020 14:47:27 GMT",
"version": "v2"
}
] | 2020-05-25 | [
[
"Olivier",
"L. E.",
""
],
[
"Craig",
"I. K.",
""
]
] | An epidemiological model is developed for the spread of COVID-19 in South Africa. A variant of the classical compartmental SEIR model, called the SEIQRDP model, is used. As South Africa is still in the early phases of the global COVID-19 pandemic with the confirmed infectious cases not having peaked, the SEIQRDP model ... |
1710.09030 | Kevin Supakkul | Kevin Supakkul | Using Positional Heel-marker Data to More Accurately Calculate Stride
Length for Treadmill Walking: A Step Length Approach | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Treadmill walking is a convenient tool for studying the human gait; however,
a common gait parameter, stride length, can be difficult to calculate directly
because relevant reference points continually move backwards. Although there is
no direct calculation of stride length itself, we can use positional
heel-marker d... | [
{
"created": "Wed, 25 Oct 2017 00:42:20 GMT",
"version": "v1"
}
] | 2017-10-26 | [
[
"Supakkul",
"Kevin",
""
]
] | Treadmill walking is a convenient tool for studying the human gait; however, a common gait parameter, stride length, can be difficult to calculate directly because relevant reference points continually move backwards. Although there is no direct calculation of stride length itself, we can use positional heel-marker dat... |
2108.08306 | Muhammad Dawood | Muhammad Dawood, Kim Branson, Nasir M. Rajpoot, Fayyaz ul Amir Afsar
Minhas | ALBRT: Cellular Composition Prediction in Routine Histology Images | 11 pages, 5 figures | null | null | null | q-bio.QM eess.IV | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Cellular composition prediction, i.e., predicting the presence and counts of
different types of cells in the tumor microenvironment from a digitized image
of a Hematoxylin and Eosin (H&E) stained tissue section can be used for various
tasks in computational pathology such as the analysis of cellular topology and
inte... | [
{
"created": "Wed, 18 Aug 2021 15:41:06 GMT",
"version": "v1"
},
{
"created": "Thu, 26 Aug 2021 11:01:02 GMT",
"version": "v2"
}
] | 2021-08-27 | [
[
"Dawood",
"Muhammad",
""
],
[
"Branson",
"Kim",
""
],
[
"Rajpoot",
"Nasir M.",
""
],
[
"Minhas",
"Fayyaz ul Amir Afsar",
""
]
] | Cellular composition prediction, i.e., predicting the presence and counts of different types of cells in the tumor microenvironment from a digitized image of a Hematoxylin and Eosin (H&E) stained tissue section can be used for various tasks in computational pathology such as the analysis of cellular topology and intera... |
1810.01243 | Melpomeni Kalofonou | Mohammed Khwaja, Melpomeni Kalofonou and Chris Toumazou | A Deep Autoencoder System for Differentiation of Cancer Types Based on
DNA Methylation State | null | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A Deep Autoencoder based content retrieval algorithm is proposed for
prediction and differentiation of cancer types based on the presence of
epigenetic patterns of DNA methylation identified in genetic regions known as
CpG islands. The developed deep learning system uses a CpG island state
classification sub-system t... | [
{
"created": "Tue, 2 Oct 2018 13:44:37 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Oct 2018 14:17:49 GMT",
"version": "v2"
}
] | 2018-10-08 | [
[
"Khwaja",
"Mohammed",
""
],
[
"Kalofonou",
"Melpomeni",
""
],
[
"Toumazou",
"Chris",
""
]
] | A Deep Autoencoder based content retrieval algorithm is proposed for prediction and differentiation of cancer types based on the presence of epigenetic patterns of DNA methylation identified in genetic regions known as CpG islands. The developed deep learning system uses a CpG island state classification sub-system to ... |
1908.07837 | Md Abdul Kuddus Mr | Md Abdul Kuddus, Michael T. Meehan, Adeshina I. Adekunle, Lisa J.
White, Emma S. McBryde | Mathematical analysis of a two-strain disease model with amplification | 22 pages, 11 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate a two-strain disease model with amplification to simulate the
prevalence of drug-susceptible (s) and drug-resistant (m) disease strains. We
model the emergence of drug resistance as a consequence of inadequate
treatment, i.e. amplification. We perform a dynamical analysis of the resulting
system and fi... | [
{
"created": "Mon, 19 Aug 2019 23:02:47 GMT",
"version": "v1"
}
] | 2019-08-22 | [
[
"Kuddus",
"Md Abdul",
""
],
[
"Meehan",
"Michael T.",
""
],
[
"Adekunle",
"Adeshina I.",
""
],
[
"White",
"Lisa J.",
""
],
[
"McBryde",
"Emma S.",
""
]
] | We investigate a two-strain disease model with amplification to simulate the prevalence of drug-susceptible (s) and drug-resistant (m) disease strains. We model the emergence of drug resistance as a consequence of inadequate treatment, i.e. amplification. We perform a dynamical analysis of the resulting system and find... |
2208.12032 | Corey Maley | Corey J. Maley | How (and Why) to Think that the Brain is Literally a Computer | null | Frontiers in Computer Science, Section: Theoretical Computer
Science, 2022 | 10.3389/fcomp.2022.970396 | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | The relationship between brains and computers is often taken to be merely
metaphorical. However, genuine computational systems can be implemented in
virtually any media; thus, one can take seriously the view that brains
literally compute. But without empirical criteria for what makes a physical
system genuinely a com... | [
{
"created": "Wed, 24 Aug 2022 15:38:10 GMT",
"version": "v1"
}
] | 2022-08-26 | [
[
"Maley",
"Corey J.",
""
]
] | The relationship between brains and computers is often taken to be merely metaphorical. However, genuine computational systems can be implemented in virtually any media; thus, one can take seriously the view that brains literally compute. But without empirical criteria for what makes a physical system genuinely a compu... |
1609.04973 | Tae-Rin Lee | Tae-Rin Lee, Sung Sic Yoo, Jiho Yang | Generalized Plasma Skimming Model for Cells and Drug Carriers in the
Microvasculature | null | null | 10.1007/s10237-016-0832-z | null | q-bio.TO physics.flu-dyn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In microvascular transport, where both blood and drug carriers are involved,
plasma skimming has a key role on changing hematocrit level and drug carrier
concentration in capillary beds after continuous vessel bifurcation in the
microvasculature. While there have been numerous studies on modeling the plasma
skimming ... | [
{
"created": "Fri, 16 Sep 2016 09:46:20 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Sep 2016 05:38:14 GMT",
"version": "v2"
},
{
"created": "Tue, 20 Sep 2016 07:37:01 GMT",
"version": "v3"
}
] | 2016-09-23 | [
[
"Lee",
"Tae-Rin",
""
],
[
"Yoo",
"Sung Sic",
""
],
[
"Yang",
"Jiho",
""
]
] | In microvascular transport, where both blood and drug carriers are involved, plasma skimming has a key role on changing hematocrit level and drug carrier concentration in capillary beds after continuous vessel bifurcation in the microvasculature. While there have been numerous studies on modeling the plasma skimming of... |
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