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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1908.07075 | Andrey Morgulis | Andrey Morgulis, Konstantin Ilin | Drift, stabilizing and destabilizing for a Patlak-Keller-Segel system
with the short-wavelength external signal | null | null | null | null | q-bio.PE nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This article aims at exploring the short-wavelength stabilization and
destabilization of the advection-diffusion systems formulated using the
Patlak-Keller-Segel cross-diffusion. We study a model of the taxis partly
driven by an external signal. We address the general short-wavelength signal
using the homogenization ... | [
{
"created": "Mon, 19 Aug 2019 21:26:50 GMT",
"version": "v1"
},
{
"created": "Mon, 2 Sep 2019 17:15:55 GMT",
"version": "v2"
},
{
"created": "Fri, 21 Aug 2020 10:58:56 GMT",
"version": "v3"
}
] | 2020-08-24 | [
[
"Morgulis",
"Andrey",
""
],
[
"Ilin",
"Konstantin",
""
]
] | This article aims at exploring the short-wavelength stabilization and destabilization of the advection-diffusion systems formulated using the Patlak-Keller-Segel cross-diffusion. We study a model of the taxis partly driven by an external signal. We address the general short-wavelength signal using the homogenization te... |
2012.07608 | Frederic Barraquand | Alix M.C. Sauve, Rachel A. Taylor, Fr\'ed\'eric Barraquand | The effect of seasonal strength and abruptness on predator-prey dynamics | null | null | 10.1016/j.jtbi.2020.110175 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Coupled dynamical systems in ecology are known to respond to the seasonal
forcing of their parameters with multiple dynamical behaviours, ranging from
seasonal cycles to chaos. Seasonal forcing is predominantly modelled as a sine
wave but the transition between seasons is often more sudden. Some studies
mentioned the... | [
{
"created": "Mon, 14 Dec 2020 14:58:48 GMT",
"version": "v1"
}
] | 2020-12-15 | [
[
"Sauve",
"Alix M. C.",
""
],
[
"Taylor",
"Rachel A.",
""
],
[
"Barraquand",
"Frédéric",
""
]
] | Coupled dynamical systems in ecology are known to respond to the seasonal forcing of their parameters with multiple dynamical behaviours, ranging from seasonal cycles to chaos. Seasonal forcing is predominantly modelled as a sine wave but the transition between seasons is often more sudden. Some studies mentioned the r... |
2104.10678 | Christopher Thron | Christopher Thron, Vianney Mbazumutima, Luis Vargas Tamayo, Leonard
Todjihounde | Cost Effective Reproduction Number Based Strategies for Reducing Deaths
from COVID-19 | 36 pages, 20 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | In epidemiology, the effective reproduction number $R_e$ is used to
characterize the growth rate of an epidemic outbreak. In this paper, we
investigate properties of $R_e$ for a modified SEIR model of COVID-19 in the
city of Houston, TX USA, in which the population is divided into low-risk and
high-risk subpopulation... | [
{
"created": "Mon, 19 Apr 2021 18:56:16 GMT",
"version": "v1"
}
] | 2021-04-22 | [
[
"Thron",
"Christopher",
""
],
[
"Mbazumutima",
"Vianney",
""
],
[
"Tamayo",
"Luis Vargas",
""
],
[
"Todjihounde",
"Leonard",
""
]
] | In epidemiology, the effective reproduction number $R_e$ is used to characterize the growth rate of an epidemic outbreak. In this paper, we investigate properties of $R_e$ for a modified SEIR model of COVID-19 in the city of Houston, TX USA, in which the population is divided into low-risk and high-risk subpopulations.... |
2401.06155 | Xiuyuan Hu | Xiuyuan Hu, Guoqing Liu, Yang Zhao, Hao Zhang | De novo Drug Design using Reinforcement Learning with Multiple GPT
Agents | Accepted by NeurIPS 2023 | null | null | null | q-bio.BM cs.CE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | De novo drug design is a pivotal issue in pharmacology and a new area of
focus in AI for science research. A central challenge in this field is to
generate molecules with specific properties while also producing a wide range
of diverse candidates. Although advanced technologies such as transformer
models and reinforc... | [
{
"created": "Thu, 21 Dec 2023 13:24:03 GMT",
"version": "v1"
}
] | 2024-01-15 | [
[
"Hu",
"Xiuyuan",
""
],
[
"Liu",
"Guoqing",
""
],
[
"Zhao",
"Yang",
""
],
[
"Zhang",
"Hao",
""
]
] | De novo drug design is a pivotal issue in pharmacology and a new area of focus in AI for science research. A central challenge in this field is to generate molecules with specific properties while also producing a wide range of diverse candidates. Although advanced technologies such as transformer models and reinforcem... |
0809.4080 | Sahand Jamal Rahi | Sahand Jamal Rahi, Peter Virnau, Leonid A. Mirny, Mehran Kardar | Predicting Transcription Factor Specificity with All-Atom Models | 26 pages, 3 figures | Nucleic Acids Res. 36, 6209-6217 (2008) | 10.1093/nar/gkn589 | null | q-bio.BM physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The binding of a transcription factor (TF) to a DNA operator site can
initiate or repress the expression of a gene. Computational prediction of sites
recognized by a TF has traditionally relied upon knowledge of several cognate
sites, rather than an ab initio approach. Here, we examine the possibility of
using struct... | [
{
"created": "Wed, 24 Sep 2008 04:16:58 GMT",
"version": "v1"
}
] | 2008-11-10 | [
[
"Rahi",
"Sahand Jamal",
""
],
[
"Virnau",
"Peter",
""
],
[
"Mirny",
"Leonid A.",
""
],
[
"Kardar",
"Mehran",
""
]
] | The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites, rather than an ab initio approach. Here, we examine the possibility of using structur... |
1904.06973 | Ali Jalilvand | Ali Jalilvand, Behzad Akbari, Fatemeh Zare Mirakabad, Foad Ghaderi | Disease gene prioritization using network topological analysis from a
sequence based human functional linkage network | null | null | null | null | q-bio.MN q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sequencing large number of candidate disease genes which cause diseases in
order to identify the relationship between them is an expensive and
time-consuming task. To handle these challenges, different computational
approaches have been developed. Based on the observation that genes associated
with similar diseases h... | [
{
"created": "Mon, 15 Apr 2019 11:39:11 GMT",
"version": "v1"
}
] | 2019-04-16 | [
[
"Jalilvand",
"Ali",
""
],
[
"Akbari",
"Behzad",
""
],
[
"Mirakabad",
"Fatemeh Zare",
""
],
[
"Ghaderi",
"Foad",
""
]
] | Sequencing large number of candidate disease genes which cause diseases in order to identify the relationship between them is an expensive and time-consuming task. To handle these challenges, different computational approaches have been developed. Based on the observation that genes associated with similar diseases hav... |
2006.15548 | Gang Yi | Qiuyue Duan, Qi Yan, Yuqi Huang, Wenxiu Zhang, Shuhui Zhao, Gang Yi | Polymerase/nicking enzyme powered dual-template multi-cycled G-triplex
machine for HIV-1 determination | 16 pages, 7 Postscript figures, 3 tables | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We proposed a dual-template multi-cycled DNA nanomachine driven by polymerase
nicking enzyme with high efficiency. The reaction system simply consists of two
templates (T1, T2) and two enzymes (KF polymerase, Nb.BbvCI). The two templates
are similar in structure (X-X-Y, Y-Y-C): primer recognition region, primer
analo... | [
{
"created": "Sun, 28 Jun 2020 09:14:10 GMT",
"version": "v1"
}
] | 2020-06-30 | [
[
"Duan",
"Qiuyue",
""
],
[
"Yan",
"Qi",
""
],
[
"Huang",
"Yuqi",
""
],
[
"Zhang",
"Wenxiu",
""
],
[
"Zhao",
"Shuhui",
""
],
[
"Yi",
"Gang",
""
]
] | We proposed a dual-template multi-cycled DNA nanomachine driven by polymerase nicking enzyme with high efficiency. The reaction system simply consists of two templates (T1, T2) and two enzymes (KF polymerase, Nb.BbvCI). The two templates are similar in structure (X-X-Y, Y-Y-C): primer recognition region, primer analogu... |
0910.4067 | Steven Kelk | Katharina T. Huber, Leo van Iersel, Steven Kelk and Radoslaw Suchecki | A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently much attention has been devoted to the construction of phylogenetic
networks which generalize phylogenetic trees in order to accommodate complex
evolutionary processes. Here we present an efficient, practical algorithm for
reconstructing level-1 phylogenetic networks - a type of network slightly more
general... | [
{
"created": "Wed, 21 Oct 2009 12:17:05 GMT",
"version": "v1"
}
] | 2009-10-22 | [
[
"Huber",
"Katharina T.",
""
],
[
"van Iersel",
"Leo",
""
],
[
"Kelk",
"Steven",
""
],
[
"Suchecki",
"Radoslaw",
""
]
] | Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for reconstructing level-1 phylogenetic networks - a type of network slightly more general t... |
2211.01867 | Ishraq Ahmed | Ishraq U. Ahmed, Helen M. Byrne, Mary R. Myerscough | Macrophage anti-inflammatory behaviour in a multiphase model of
atherosclerotic plaque development | null | Bull Math Biol 85, 37 (2023) | 10.1007/s11538-023-01142-7 | null | q-bio.CB q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Atherosclerosis is an inflammatory disease characterised by the formation of
plaques, which are deposits of lipids and cholesterol-laden macrophages that
form in the artery wall. The inflammation is often non-resolving, due in large
part to changes in normal macrophage anti-inflammatory behaviour that are
induced by ... | [
{
"created": "Thu, 3 Nov 2022 14:56:41 GMT",
"version": "v1"
}
] | 2024-01-19 | [
[
"Ahmed",
"Ishraq U.",
""
],
[
"Byrne",
"Helen M.",
""
],
[
"Myerscough",
"Mary R.",
""
]
] | Atherosclerosis is an inflammatory disease characterised by the formation of plaques, which are deposits of lipids and cholesterol-laden macrophages that form in the artery wall. The inflammation is often non-resolving, due in large part to changes in normal macrophage anti-inflammatory behaviour that are induced by th... |
2007.12073 | Shujaat Khan Engr | Seongyong Park, Shujaat Khan, Abdul Wahab | E3-targetPred: Prediction of E3-Target Proteins Using Deep Latent Space
Encoding | Submitted to IEEE/ACM transactions on computational biology and
bioinformatics | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding E3 ligase and target substrate interactions are important for
cell biology and therapeutic development. However, experimental identification
of E3 target relationships is not an easy task due to the labor-intensive
nature of the experiments. In this article, a sequence-based E3-target
prediction model i... | [
{
"created": "Fri, 26 Jun 2020 17:21:30 GMT",
"version": "v1"
}
] | 2020-07-24 | [
[
"Park",
"Seongyong",
""
],
[
"Khan",
"Shujaat",
""
],
[
"Wahab",
"Abdul",
""
]
] | Understanding E3 ligase and target substrate interactions are important for cell biology and therapeutic development. However, experimental identification of E3 target relationships is not an easy task due to the labor-intensive nature of the experiments. In this article, a sequence-based E3-target prediction model is ... |
1602.08526 | Hyun Youk | Eduardo P. Olimpio, Diego R. Gomez-Alvarez, Hyun Youk | Progress towards quantitative design principles of multicellular systems | Invited review - Submitted version - 36 pages (including 6 figures at
the end) | null | null | null | q-bio.MN physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Living systems, particularly multicellular systems, often seem hopelessly
complex. But recent studies have suggested that beneath this complexity, there
may be unifying quantitative principles that we are only now starting to
unravel. All cells interact with their environments and with other cells.
Communication amon... | [
{
"created": "Fri, 26 Feb 2016 22:42:21 GMT",
"version": "v1"
}
] | 2016-03-01 | [
[
"Olimpio",
"Eduardo P.",
""
],
[
"Gomez-Alvarez",
"Diego R.",
""
],
[
"Youk",
"Hyun",
""
]
] | Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All cells interact with their environments and with other cells. Communication among ... |
1406.1675 | Michael Bowler Ph D | Michael G Bowler, Colleen K Kelly | On the statistical machinery of alien species | 14 pages, 3 figures. Follows and strengthens arXiv:1004.2271 .
Version 2 has 16 pages and 3 figures. It differs from the original version in
a revised and extended discussion of the biological aspects and a small
change in a parameter to improve agreement with data | Entropy (2017) 19 674 | 10.3390/e19120674 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many species of plants are found in regions to which they are alien and their
global distribution has been found to exhibit several remarkable
patterns,characterised by exponential functions of the kind that could arise
through versions of MacArthur's broken stick. We show here that these various
patterns are all qua... | [
{
"created": "Fri, 6 Jun 2014 13:09:58 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Jul 2016 11:57:41 GMT",
"version": "v2"
}
] | 2017-12-12 | [
[
"Bowler",
"Michael G",
""
],
[
"Kelly",
"Colleen K",
""
]
] | Many species of plants are found in regions to which they are alien and their global distribution has been found to exhibit several remarkable patterns,characterised by exponential functions of the kind that could arise through versions of MacArthur's broken stick. We show here that these various patterns are all quant... |
1310.2063 | J.H. van Hateren | J.H. van Hateren | Active causation and the origin of meaning | revised and extended | Biological Cybernetics 109, 33-46 (2015) | 10.1007/s00422-014-0622-6 | null | q-bio.PE cs.NE nlin.AO q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Purpose and meaning are necessary concepts for understanding mind and
culture, but appear to be absent from the physical world and are not part of
the explanatory framework of the natural sciences. Understanding how meaning
(in the broad sense of the term) could arise from a physical world has proven
to be a tough pr... | [
{
"created": "Tue, 8 Oct 2013 09:49:39 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Oct 2013 11:37:41 GMT",
"version": "v2"
},
{
"created": "Tue, 18 Feb 2014 15:10:27 GMT",
"version": "v3"
},
{
"created": "Sun, 25 May 2014 08:39:42 GMT",
"version": "v4"
}
] | 2015-02-04 | [
[
"van Hateren",
"J. H.",
""
]
] | Purpose and meaning are necessary concepts for understanding mind and culture, but appear to be absent from the physical world and are not part of the explanatory framework of the natural sciences. Understanding how meaning (in the broad sense of the term) could arise from a physical world has proven to be a tough prob... |
1305.2086 | Bob Eisenberg | Bob Eisenberg | Interacting Ions in Biophysics: Real is not Ideal | null | Biophysical Journal (2013) 104:1849-1866 | 10.1016/j.bpj.2013.03.049 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ions in water are important in biology, from molecules to organs.
Classically, ions in water are treated as ideal noninteracting particles in a
perfect gas. Excess free energy of ion was zero. Mathematics was not available
to deal consistently with flows, or interactions with ions or boundaries.
Non-classical approac... | [
{
"created": "Thu, 9 May 2013 13:36:45 GMT",
"version": "v1"
}
] | 2015-06-15 | [
[
"Eisenberg",
"Bob",
""
]
] | Ions in water are important in biology, from molecules to organs. Classically, ions in water are treated as ideal noninteracting particles in a perfect gas. Excess free energy of ion was zero. Mathematics was not available to deal consistently with flows, or interactions with ions or boundaries. Non-classical approache... |
1702.05739 | Julian Garcia | Rui Chen, Garcia Julian and Meyer Bernd | Social learning in a simple task allocation game | null | null | null | null | q-bio.PE cs.MA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the effects of social interactions in task al- location using
Evolutionary Game Theory (EGT). We propose a simple task-allocation game and
study how different learning mechanisms can give rise to specialised and non-
specialised colonies under different ecological conditions. By combining
agent-based s... | [
{
"created": "Sun, 19 Feb 2017 11:06:28 GMT",
"version": "v1"
}
] | 2017-02-21 | [
[
"Chen",
"Rui",
""
],
[
"Julian",
"Garcia",
""
],
[
"Bernd",
"Meyer",
""
]
] | We investigate the effects of social interactions in task al- location using Evolutionary Game Theory (EGT). We propose a simple task-allocation game and study how different learning mechanisms can give rise to specialised and non- specialised colonies under different ecological conditions. By combining agent-based sim... |
1808.06307 | Johan Nygren | Johan Nygren | The speciation of Australopithecus and Paranthropus was caused by
introgression from the Gorilla lineage | 6 pages, 7 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The discovery of Paranthropus deyiremeda in 3.3-3.5 million year old fossil
sites in Afar (Haile-Selassie, 2015), together with 30% of the gorilla genome
showing lineage sorting between humans and chimpanzees (Scally, 2012), and a
NUMT ("nuclear mitochondrial DNA segment") that is shared by both gorillas,
humans and ... | [
{
"created": "Mon, 20 Aug 2018 05:25:52 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Aug 2018 00:45:06 GMT",
"version": "v2"
}
] | 2018-08-22 | [
[
"Nygren",
"Johan",
""
]
] | The discovery of Paranthropus deyiremeda in 3.3-3.5 million year old fossil sites in Afar (Haile-Selassie, 2015), together with 30% of the gorilla genome showing lineage sorting between humans and chimpanzees (Scally, 2012), and a NUMT ("nuclear mitochondrial DNA segment") that is shared by both gorillas, humans and ch... |
1812.03455 | Gr\'egory Dumont | Gregory Dumont and Boris Gutkin | Macroscopic phase resetting-curves determine oscillatory coherence and
signal transfer in inter-coupled neural circuits | 35 pages, 9 figures | null | 10.1371/journal.pcbi.1007019 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Macroscopic oscillations of different brain regions show multiple phase
relationships that are persistent across time and have been implicated routing
information. Various cellular level mechanisms influence the network dynamics
and structure the macroscopic firing patterns. Key question is to identify the
biophysica... | [
{
"created": "Sun, 9 Dec 2018 10:26:18 GMT",
"version": "v1"
}
] | 2019-06-19 | [
[
"Dumont",
"Gregory",
""
],
[
"Gutkin",
"Boris",
""
]
] | Macroscopic oscillations of different brain regions show multiple phase relationships that are persistent across time and have been implicated routing information. Various cellular level mechanisms influence the network dynamics and structure the macroscopic firing patterns. Key question is to identify the biophysical ... |
1011.0669 | Robert Rosenbaum | Robert Rosenbaum, Jianfu Ma, Fabien Marpeau, Aditya Barua, Kresimir
Josic | Finite volume and asymptotic methods for stochastic neuron models with
correlated inputs | null | null | null | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a pair of stochastic integrate and fire neurons receiving
correlated stochastic inputs. The evolution of this system can be described by
the corresponding Fokker-Planck equation with non-trivial boundary conditions
resulting from the refractory period and firing threshold. We propose a finite
volume metho... | [
{
"created": "Tue, 2 Nov 2010 16:41:12 GMT",
"version": "v1"
},
{
"created": "Mon, 13 Dec 2010 16:37:43 GMT",
"version": "v2"
}
] | 2010-12-14 | [
[
"Rosenbaum",
"Robert",
""
],
[
"Ma",
"Jianfu",
""
],
[
"Marpeau",
"Fabien",
""
],
[
"Barua",
"Aditya",
""
],
[
"Josic",
"Kresimir",
""
]
] | We consider a pair of stochastic integrate and fire neurons receiving correlated stochastic inputs. The evolution of this system can be described by the corresponding Fokker-Planck equation with non-trivial boundary conditions resulting from the refractory period and firing threshold. We propose a finite volume method ... |
2005.00394 | Sophie Abby | Sophie Saphia Abby, Katayoun Kazemzadeh, Charles Vragniau, Ludovic
Pelosi and Fabien Pierrel | Bacterial pathways for the biosynthesis of ubiquinone | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ubiquinone is an important component of the electron transfer chains in
proteobacteria and eukaryotes. The biosynthesis of ubiquinone requires multiple
steps, most of which are common to bacteria and eukaryotes. Whereas the enzymes
of the mitochondrial pathway that produces ubiquinone are highly similar across
eukary... | [
{
"created": "Fri, 1 May 2020 14:19:58 GMT",
"version": "v1"
}
] | 2020-05-04 | [
[
"Abby",
"Sophie Saphia",
""
],
[
"Kazemzadeh",
"Katayoun",
""
],
[
"Vragniau",
"Charles",
""
],
[
"Pelosi",
"Ludovic",
""
],
[
"Pierrel",
"Fabien",
""
]
] | Ubiquinone is an important component of the electron transfer chains in proteobacteria and eukaryotes. The biosynthesis of ubiquinone requires multiple steps, most of which are common to bacteria and eukaryotes. Whereas the enzymes of the mitochondrial pathway that produces ubiquinone are highly similar across eukaryot... |
1904.05467 | Mohammad Nami | Ali-Mohammad Kamali, Mohammad Javad Gholamzadeh, Seyedeh Zahra
Mousavi, Maryam Vasaghi Gharamaleki, Mohammad Nami | Improved visual function in a case of ultra-low vision following
ischemic encephalopathy following transcranial electrical stimulation; A case
study | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cortical visual impairment is amongst the key pathological causes of
pediatric visual abnormalities predominantly resulting from hypoxic-ischemic
brain injury. Such an injury results in profound visual impairments which
severely impairs the patient's quality of life. Given the nature of the
pathology, treatments are ... | [
{
"created": "Wed, 10 Apr 2019 22:34:17 GMT",
"version": "v1"
}
] | 2019-04-12 | [
[
"Kamali",
"Ali-Mohammad",
""
],
[
"Gholamzadeh",
"Mohammad Javad",
""
],
[
"Mousavi",
"Seyedeh Zahra",
""
],
[
"Gharamaleki",
"Maryam Vasaghi",
""
],
[
"Nami",
"Mohammad",
""
]
] | Cortical visual impairment is amongst the key pathological causes of pediatric visual abnormalities predominantly resulting from hypoxic-ischemic brain injury. Such an injury results in profound visual impairments which severely impairs the patient's quality of life. Given the nature of the pathology, treatments are mo... |
1512.07033 | Ezio Di Costanzo | Ezio Di Costanzo, Alessandro Giacomello, Elisa Messina, Roberto
Natalini, Giuseppe Pontrelli, Fabrizio Rossi, Robert Smits, Monika
Twarogowska | A discrete in continuous mathematical model of cardiac progenitor cells
formation and growth as spheroid clusters (Cardiospheres) | null | Mathematical Medicine and Biology, 35-1, 121-144, 2018 | 10.1093/imammb/dqw022 | null | q-bio.CB q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a discrete in continuous mathematical model describing the in
vitro growth process of biophsy-derived mammalian cardiac progenitor cells
growing as clusters in the form of spheres (Cardiospheres). The approach is
hybrid: discrete at cellular scale and continuous at molecular level. In the
present model cel... | [
{
"created": "Tue, 22 Dec 2015 11:17:19 GMT",
"version": "v1"
}
] | 2018-08-15 | [
[
"Di Costanzo",
"Ezio",
""
],
[
"Giacomello",
"Alessandro",
""
],
[
"Messina",
"Elisa",
""
],
[
"Natalini",
"Roberto",
""
],
[
"Pontrelli",
"Giuseppe",
""
],
[
"Rossi",
"Fabrizio",
""
],
[
"Smits",
"Robert",
... | We propose a discrete in continuous mathematical model describing the in vitro growth process of biophsy-derived mammalian cardiac progenitor cells growing as clusters in the form of spheres (Cardiospheres). The approach is hybrid: discrete at cellular scale and continuous at molecular level. In the present model cells... |
2205.03382 | Gabriel Palma | Gabriel R. Palma, Renato M. Coutinho, Wesley A. C. Godoy, Fernando L.
C\^onsoli and Roberto A. Kraenkel | Bacteriophage effect on parasitism resistance | 19 pages | null | null | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Many studies have shown that the protection of the host
$\it{Acyrthosiphon~pisum}$ (Hemiptera, Aphididae) against the parasitoid
$\it{Aphidius~ervi}$ (Hymenoptera, Braconidae) is conferred by the interaction
between the secondary endosymbiont $\it{Hamiltonella~defensa}$ and the
bacteriophage $\it{APSE}$ ($\it{Acyrtho... | [
{
"created": "Fri, 6 May 2022 17:30:10 GMT",
"version": "v1"
}
] | 2022-05-09 | [
[
"Palma",
"Gabriel R.",
""
],
[
"Coutinho",
"Renato M.",
""
],
[
"Godoy",
"Wesley A. C.",
""
],
[
"Cônsoli",
"Fernando L.",
""
],
[
"Kraenkel",
"Roberto A.",
""
]
] | Many studies have shown that the protection of the host $\it{Acyrthosiphon~pisum}$ (Hemiptera, Aphididae) against the parasitoid $\it{Aphidius~ervi}$ (Hymenoptera, Braconidae) is conferred by the interaction between the secondary endosymbiont $\it{Hamiltonella~defensa}$ and the bacteriophage $\it{APSE}$ ($\it{Acyrthosi... |
2003.01214 | Ana Pastore Y Piontti | Dina Mistry (1), Maria Litvinova (2 and 3), Ana Pastore y Piontti (2),
Matteo Chinazzi (2), Laura Fumanelli (4), Marcelo F. C. Gomes (5), Syed A.
Haque (2), Quan-Hui Liu (6), Kunpeng Mu (2), Xinyue Xiong (2), M. Elizabeth
Halloran (7 and 8), Ira M. Longini Jr. (9), Stefano Merler (4), Marco Ajelli
(4), Alessand... | Inferring high-resolution human mixing patterns for disease modeling | 18 pages, 7 figures | null | null | null | q-bio.PE physics.soc-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mathematical and computational modeling approaches are increasingly used as
quantitative tools in the analysis and forecasting of infectious disease
epidemics. The growing need for realism in addressing complex public health
questions is however calling for accurate models of the human contact patterns
that govern th... | [
{
"created": "Tue, 25 Feb 2020 22:33:39 GMT",
"version": "v1"
}
] | 2020-03-04 | [
[
"Mistry",
"Dina",
"",
"2 and 3"
],
[
"Litvinova",
"Maria",
"",
"2 and 3"
],
[
"Piontti",
"Ana Pastore y",
"",
"7 and 8"
],
[
"Chinazzi",
"Matteo",
"",
"7 and 8"
],
[
"Fumanelli",
"Laura",
"",
"7 and 8"
],
[
"Go... | Mathematical and computational modeling approaches are increasingly used as quantitative tools in the analysis and forecasting of infectious disease epidemics. The growing need for realism in addressing complex public health questions is however calling for accurate models of the human contact patterns that govern the ... |
2007.06602 | Peter Ashcroft | Peter Ashcroft, Jana S. Huisman, Sonja Lehtinen, Judith A. Bouman,
Christian L. Althaus, Roland R. Regoes, Sebastian Bonhoeffer | COVID-19 infectivity profile correction | 5 pages, 2 figures | null | null | null | q-bio.PE stat.ME | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The infectivity profile of an individual with COVID-19 is attributed to the
paper Temporal dynamics in viral shedding and transmissibility of COVID-19 by
He et al., published in Nature Medicine in April 2020. However, the analysis
within this paper contains a mistake such that the published infectivity
profile is inc... | [
{
"created": "Mon, 13 Jul 2020 18:08:03 GMT",
"version": "v1"
}
] | 2020-07-15 | [
[
"Ashcroft",
"Peter",
""
],
[
"Huisman",
"Jana S.",
""
],
[
"Lehtinen",
"Sonja",
""
],
[
"Bouman",
"Judith A.",
""
],
[
"Althaus",
"Christian L.",
""
],
[
"Regoes",
"Roland R.",
""
],
[
"Bonhoeffer",
"Sebastian"... | The infectivity profile of an individual with COVID-19 is attributed to the paper Temporal dynamics in viral shedding and transmissibility of COVID-19 by He et al., published in Nature Medicine in April 2020. However, the analysis within this paper contains a mistake such that the published infectivity profile is incor... |
1902.08902 | Michael Assaf | Carmel Sagi and Michael Assaf | Time Distribution for Persistent Viral Infection | 19 pages, 12 figures | J. Stat. Mech. (2019), P063403 | 10.1088/1742-5468/ab1dd7 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the early stages of viral infection, and the distribution of times
to obtain a persistent infection. The virus population proliferates by entering
and reproducing inside a target cell until a sufficient number of new virus
particles are released via a burst, with a given burst size distribution, which
result... | [
{
"created": "Sun, 24 Feb 2019 07:02:35 GMT",
"version": "v1"
},
{
"created": "Wed, 10 Jul 2019 10:35:01 GMT",
"version": "v2"
}
] | 2019-07-11 | [
[
"Sagi",
"Carmel",
""
],
[
"Assaf",
"Michael",
""
]
] | We study the early stages of viral infection, and the distribution of times to obtain a persistent infection. The virus population proliferates by entering and reproducing inside a target cell until a sufficient number of new virus particles are released via a burst, with a given burst size distribution, which results ... |
2112.10730 | Nils Winter | Nils R. Winter, Ramona Leenings, Jan Ernsting, Kelvin Sarink, Lukas
Fisch, Daniel Emden, Julian Blanke, Janik Goltermann, Nils Opel, Carlotta
Barkhau, Susanne Meinert, Katharina Dohm, Jonathan Repple, Marco Mauritz,
Marius Gruber, Elisabeth J. Leehr, Dominik Grotegerd, Ronny Redlich, Andreas
Jansen, Igor Nenadi... | More Alike than Different: Quantifying Deviations of Brain Structure and
Function in Major Depressive Disorder across Neuroimaging Modalities | 12 pages, 3 figures | null | null | null | q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Introduction: Identifying neurobiological differences between patients
suffering from Major Depressive Disorder (MDD) and healthy individuals has been
a mainstay of clinical neuroscience for decades. However, recent meta- and
mega-analyses have raised concerns regarding the replicability and clinical
relevance of bra... | [
{
"created": "Mon, 20 Dec 2021 18:27:07 GMT",
"version": "v1"
}
] | 2021-12-21 | [
[
"Winter",
"Nils R.",
""
],
[
"Leenings",
"Ramona",
""
],
[
"Ernsting",
"Jan",
""
],
[
"Sarink",
"Kelvin",
""
],
[
"Fisch",
"Lukas",
""
],
[
"Emden",
"Daniel",
""
],
[
"Blanke",
"Julian",
""
],
[
"Go... | Introduction: Identifying neurobiological differences between patients suffering from Major Depressive Disorder (MDD) and healthy individuals has been a mainstay of clinical neuroscience for decades. However, recent meta- and mega-analyses have raised concerns regarding the replicability and clinical relevance of brain... |
2112.12839 | Srikanth Namuduri | Srikanth Namuduri, Prateek Mehta, Lise Barbe, Stephanie Lam, Zohreh
Faghihmonzavi, Steve Finkbeiner, Shekhar Bhansali | Faster Deep Ensemble Averaging for Quantification of DNA Damage from
Comet Assay Images With Uncertainty Estimates | null | null | null | null | q-bio.QM cs.CV cs.LG eess.IV | http://creativecommons.org/licenses/by/4.0/ | Several neurodegenerative diseases involve the accumulation of cellular DNA
damage. Comet assays are a popular way of estimating the extent of DNA damage.
Current literature on the use of deep learning to quantify DNA damage presents
an empirical approach to hyper-parameter optimization and does not include
uncertain... | [
{
"created": "Thu, 23 Dec 2021 20:48:28 GMT",
"version": "v1"
}
] | 2021-12-28 | [
[
"Namuduri",
"Srikanth",
""
],
[
"Mehta",
"Prateek",
""
],
[
"Barbe",
"Lise",
""
],
[
"Lam",
"Stephanie",
""
],
[
"Faghihmonzavi",
"Zohreh",
""
],
[
"Finkbeiner",
"Steve",
""
],
[
"Bhansali",
"Shekhar",
""
... | Several neurodegenerative diseases involve the accumulation of cellular DNA damage. Comet assays are a popular way of estimating the extent of DNA damage. Current literature on the use of deep learning to quantify DNA damage presents an empirical approach to hyper-parameter optimization and does not include uncertainty... |
1402.1728 | Chris Cotsapas | Boel Brynedal, Towfique Raj, Barbara E Stranger, Robert Bjornson,
Benjamin M Neale, Benjamin F Voight, Chris Cotsapas | Cross-phenotype meta-analysis reveals large-scale trans-eQTLs mediating
patterns of transcriptional co-regulation | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Genetic variation affecting gene regulation is a central driver of phenotypic
differences between individuals and can be used to uncover how biological
processes are organized in a cell. Although detecting cis-eQTLs is now routine,
trans-eQTLs have proven more challenging to find due to the modest variance
explained ... | [
{
"created": "Fri, 7 Feb 2014 18:38:11 GMT",
"version": "v1"
}
] | 2014-02-10 | [
[
"Brynedal",
"Boel",
""
],
[
"Raj",
"Towfique",
""
],
[
"Stranger",
"Barbara E",
""
],
[
"Bjornson",
"Robert",
""
],
[
"Neale",
"Benjamin M",
""
],
[
"Voight",
"Benjamin F",
""
],
[
"Cotsapas",
"Chris",
""
... | Genetic variation affecting gene regulation is a central driver of phenotypic differences between individuals and can be used to uncover how biological processes are organized in a cell. Although detecting cis-eQTLs is now routine, trans-eQTLs have proven more challenging to find due to the modest variance explained an... |
1912.07782 | Jinyue Cui | Jinyue Cui | Process simulation and optimization of agro-systems by DNDC model | arXiv admin note: This submission has been removed by arXiv
administrators because the submitter did not have the right to agree to the
license at the time of submission | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many people are still facing hunger and the global food shortages is still an
urgent problem. Meanwhile, global warming is still severe. Therefore, we
propose a simulation-based optimization approach for improving crop yield and
reducing the greenhouse gas emissions (GHG) of agriculture system. We simulated
and verif... | [
{
"created": "Fri, 13 Dec 2019 04:02:54 GMT",
"version": "v1"
},
{
"created": "Fri, 27 Mar 2020 19:07:54 GMT",
"version": "v2"
}
] | 2020-08-13 | [
[
"Cui",
"Jinyue",
""
]
] | Many people are still facing hunger and the global food shortages is still an urgent problem. Meanwhile, global warming is still severe. Therefore, we propose a simulation-based optimization approach for improving crop yield and reducing the greenhouse gas emissions (GHG) of agriculture system. We simulated and verifie... |
0709.2243 | Alessandro Pelizzola | Pierpaolo Bruscolini, Alessandro Pelizzola and Marco Zamparo | Rate Determining Factors in Protein Model Structures | 4 pages, 2 figures | Phys. Rev. Lett. 99, 038103 (2007) | 10.1103/PhysRevLett.99.038103 | null | q-bio.BM cond-mat.stat-mech | null | Previous research has shown a strong correlation of protein folding rates to
the native state geometry, yet a complete explanation for this dependence is
still lacking. Here we study the rate-geometry relationship with a simple
statistical physics model, and focus on two classes of model geometries,
representing idea... | [
{
"created": "Fri, 14 Sep 2007 09:48:22 GMT",
"version": "v1"
}
] | 2007-09-17 | [
[
"Bruscolini",
"Pierpaolo",
""
],
[
"Pelizzola",
"Alessandro",
""
],
[
"Zamparo",
"Marco",
""
]
] | Previous research has shown a strong correlation of protein folding rates to the native state geometry, yet a complete explanation for this dependence is still lacking. Here we study the rate-geometry relationship with a simple statistical physics model, and focus on two classes of model geometries, representing ideal ... |
1508.03774 | Mike Steel Prof. | Jamie V. de Jong, Jeanette C McLeod and Mike Steel | Neighbourhoods of phylogenetic trees: exact and asymptotic counts | 41 pages | null | null | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A central theme in phylogenetics is the reconstruction and analysis of
evolutionary trees from a given set of data. To determine the optimal search
methods for reconstructing trees, it is crucial to understand the size and
structure of the neighbourhoods of trees under tree rearrangement operations.
The diameter and ... | [
{
"created": "Sat, 15 Aug 2015 22:24:33 GMT",
"version": "v1"
}
] | 2016-08-15 | [
[
"de Jong",
"Jamie V.",
""
],
[
"McLeod",
"Jeanette C",
""
],
[
"Steel",
"Mike",
""
]
] | A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the neighbourhoods of trees under tree rearrangement operations. The diameter and si... |
2211.13712 | Ulisse Ferrari | Gabriel Mahuas, Olivier Marre, Thierry Mora, Ulisse Ferrari | A small-correlation expansion to quantify information in noisy sensory
systems | null | null | null | null | q-bio.NC cond-mat.dis-nn | http://creativecommons.org/licenses/by/4.0/ | Neural networks encode information through their collective spiking activity
in response to external stimuli. This population response is noisy and strongly
correlated, with complex interplay between correlations induced by the
stimulus, and correlations caused by shared noise. Understanding how these
correlations af... | [
{
"created": "Thu, 24 Nov 2022 17:00:32 GMT",
"version": "v1"
}
] | 2022-11-28 | [
[
"Mahuas",
"Gabriel",
""
],
[
"Marre",
"Olivier",
""
],
[
"Mora",
"Thierry",
""
],
[
"Ferrari",
"Ulisse",
""
]
] | Neural networks encode information through their collective spiking activity in response to external stimuli. This population response is noisy and strongly correlated, with complex interplay between correlations induced by the stimulus, and correlations caused by shared noise. Understanding how these correlations affe... |
2108.02066 | Alejandro Tabas | Alejandro Tabas, Stefan Kiebel, Michael Marxen, and Katharina von
Kriegstein | Fast frequency modulation is encoded according to the listener
expectations in the human subcortical auditory pathway | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-sa/4.0/ | Expectations aid and bias our perception. In speech, expected words are
easier to recognise than unexpected words, particularly in noisy environments,
and incorrect expectations can make us misunderstand our conversational
partner. Expectations are combined with the output from the sensory pathways to
form representa... | [
{
"created": "Wed, 4 Aug 2021 13:48:51 GMT",
"version": "v1"
}
] | 2021-08-05 | [
[
"Tabas",
"Alejandro",
""
],
[
"Kiebel",
"Stefan",
""
],
[
"Marxen",
"Michael",
""
],
[
"von Kriegstein",
"Katharina",
""
]
] | Expectations aid and bias our perception. In speech, expected words are easier to recognise than unexpected words, particularly in noisy environments, and incorrect expectations can make us misunderstand our conversational partner. Expectations are combined with the output from the sensory pathways to form representati... |
1304.2266 | Mark Rowan | Mark Rowan and Samuel Neymotin | Synaptic Scaling Balances Learning in a Spiking Model of Neocortex | 10 pages | M. Rowan and S. Neymotin. Synaptic scaling balances learning in a
spiking model of neocortex. In M. Tomassini et al., eds, 11th Int. Conf.
Adaptive and Natural Comp. Algorithms (ICANNGA), LNCS vol. 7824, pp. 20-29,
Lausanne, 2013. Springer | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Learning in the brain requires complementary mechanisms: potentiation and
activity-dependent homeostatic scaling. We introduce synaptic scaling to a
biologically-realistic spiking model of neocortex which can learn changes in
oscillatory rhythms using STDP, and show that scaling is necessary to balance
both positive ... | [
{
"created": "Mon, 8 Apr 2013 16:54:24 GMT",
"version": "v1"
}
] | 2013-04-09 | [
[
"Rowan",
"Mark",
""
],
[
"Neymotin",
"Samuel",
""
]
] | Learning in the brain requires complementary mechanisms: potentiation and activity-dependent homeostatic scaling. We introduce synaptic scaling to a biologically-realistic spiking model of neocortex which can learn changes in oscillatory rhythms using STDP, and show that scaling is necessary to balance both positive an... |
1504.00374 | Alan Rogers | Alan R. Rogers | Rate of Adaptive Evolution under Blending Inheritance | 4 pages, no figures; relevant to the history of biology | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | In a population of size N, adaptive evolution is 2N times faster under
Mendelian inheritance than the rate implied by Victorian theories of heredity
and evolution.
| [
{
"created": "Wed, 1 Apr 2015 20:15:35 GMT",
"version": "v1"
},
{
"created": "Fri, 18 Dec 2015 16:23:10 GMT",
"version": "v2"
},
{
"created": "Thu, 28 Jan 2016 20:42:22 GMT",
"version": "v3"
},
{
"created": "Sun, 28 Feb 2021 17:42:25 GMT",
"version": "v4"
},
{
"cr... | 2021-08-03 | [
[
"Rogers",
"Alan R.",
""
]
] | In a population of size N, adaptive evolution is 2N times faster under Mendelian inheritance than the rate implied by Victorian theories of heredity and evolution. |
1210.1095 | Francesco Vezzi | Francesco Vezzi, Giuseppe Narzisi and Bud Mishra | Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and
Assemblathons | Submitted to PLoS One. Supplementary material available at
http://www.nada.kth.se/~vezzi/publications/supplementary.pdf and
http://cs.nyu.edu/mishra/PUBLICATIONS/12.supplementaryFRC.pdf | null | 10.1371/journal.pone.0052210 | null | q-bio.GN cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In just the last decade, a multitude of bio-technologies and software
pipelines have emerged to revolutionize genomics. To further their central
goal, they aim to accelerate and improve the quality of de novo whole-genome
assembly starting from short DNA reads. However, the performance of each of
these tools is conti... | [
{
"created": "Wed, 3 Oct 2012 13:02:30 GMT",
"version": "v1"
}
] | 2015-06-11 | [
[
"Vezzi",
"Francesco",
""
],
[
"Narzisi",
"Giuseppe",
""
],
[
"Mishra",
"Bud",
""
]
] | In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting from short DNA reads. However, the performance of each of these tools is conting... |
1911.07322 | Issaka Haruna Mr | Issaka Haruna, Oluwole Daniel Makinde and David Mwangi Theuri | Modelling of Bad Biomass Invasion of a Food Chain Ecosystem with Optimal
Control | 20 pages, 12 figures | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we provide a model to describe the dynamics of the species of
the ecosystem after it has been raided by a bad competing specie. The competing
specie invades the native plants for nutrition, carbon dioxide and space. This
affects the population of the native species of the ecosystem. The effect of
the ba... | [
{
"created": "Sun, 17 Nov 2019 19:39:55 GMT",
"version": "v1"
}
] | 2019-11-19 | [
[
"Haruna",
"Issaka",
""
],
[
"Makinde",
"Oluwole Daniel",
""
],
[
"Theuri",
"David Mwangi",
""
]
] | In this paper we provide a model to describe the dynamics of the species of the ecosystem after it has been raided by a bad competing specie. The competing specie invades the native plants for nutrition, carbon dioxide and space. This affects the population of the native species of the ecosystem. The effect of the bad ... |
1203.5885 | Korbinian Strimmer | Sebastian Gibb and Korbinian Strimmer | MALDIquant: a versatile R package for the analysis of mass spectrometry
data | 5 pages, 1 figure | Bioinformatics 2012, Vol. 28, Issue 17, 2270-2271 | 10.1093/bioinformatics/bts447 | null | q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Summary: MALDIquant is an R package providing a complete and modular analysis
pipeline for quantitative analysis of mass spectrometry data. MALDIquant is
specifically designed with application in clinical diagnostics in mind and
implements sophisticated routines for importing raw data, preprocessing,
non-linear peak ... | [
{
"created": "Tue, 27 Mar 2012 07:45:50 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Jun 2012 08:23:05 GMT",
"version": "v2"
},
{
"created": "Wed, 4 Jul 2012 13:14:00 GMT",
"version": "v3"
}
] | 2012-08-30 | [
[
"Gibb",
"Sebastian",
""
],
[
"Strimmer",
"Korbinian",
""
]
] | Summary: MALDIquant is an R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in mind and implements sophisticated routines for importing raw data, preprocessing, non-linear peak al... |
2112.10093 | Martin Weigt | Juan Rodriguez-Rivas, Giancarlo Croce, Maureen Muscat, Martin Weigt | Epistatic models predict mutable sites in SARS-CoV-2 proteins and
epitopes | 21 pages + supplementary information | null | 10.1073/pnas.2113118119 | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The emergence of new variants of SARS-CoV-2 is a major concern given their
potential impact on the transmissibility and pathogenicity of the virus as well
as the efficacy of therapeutic interventions. Here, we predict the mutability
of all positions in SARS-CoV-2 protein domains to forecast the appearance of
unseen v... | [
{
"created": "Sun, 19 Dec 2021 09:20:16 GMT",
"version": "v1"
}
] | 2022-05-11 | [
[
"Rodriguez-Rivas",
"Juan",
""
],
[
"Croce",
"Giancarlo",
""
],
[
"Muscat",
"Maureen",
""
],
[
"Weigt",
"Martin",
""
]
] | The emergence of new variants of SARS-CoV-2 is a major concern given their potential impact on the transmissibility and pathogenicity of the virus as well as the efficacy of therapeutic interventions. Here, we predict the mutability of all positions in SARS-CoV-2 protein domains to forecast the appearance of unseen var... |
0803.0888 | Sergey Petoukhov | Sergey V. Petoukhov (Department of Biomechanics, Mechanical
Engineering Research Institute of the Russian Academy of Sciences) | Matrix genetics, part 1: permutations of positions in triplets and
symmetries of genetic matrices | 34 pages; 25 figures; added materials and corrections in section 11 | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Kronecker family of the genetic matrices is investigated, which is based
on the genetic matrix [C T; A G], where C, T, A, G are the letters of the
genetic alphabet. The matrix [C T; A G] in the second Kronecker power is the
(4*4)-matrix of 16 duplets. The matrix [C T; A G] in the third Kronecker power
is the (8*8... | [
{
"created": "Thu, 6 Mar 2008 15:15:44 GMT",
"version": "v1"
},
{
"created": "Mon, 29 Mar 2010 14:51:07 GMT",
"version": "v2"
},
{
"created": "Thu, 15 Apr 2010 08:55:52 GMT",
"version": "v3"
},
{
"created": "Wed, 9 May 2012 14:28:09 GMT",
"version": "v4"
},
{
"cre... | 2013-01-17 | [
[
"Petoukhov",
"Sergey V.",
"",
"Department of Biomechanics, Mechanical\n Engineering Research Institute of the Russian Academy of Sciences"
]
] | The Kronecker family of the genetic matrices is investigated, which is based on the genetic matrix [C T; A G], where C, T, A, G are the letters of the genetic alphabet. The matrix [C T; A G] in the second Kronecker power is the (4*4)-matrix of 16 duplets. The matrix [C T; A G] in the third Kronecker power is the (8*8)-... |
1312.6439 | Michael Harvey | Michael G. Harvey, Brian Tilston Smith, Travis C. Glenn, Brant C.
Faircloth, and Robb T. Brumfield | Sequence Capture Versus Restriction Site Associated DNA Sequencing for
Phylogeography | 4 Tables, 5 Supplemental Tables, 4 Figures | Systematic Biology 65: 910-924 (2016) | 10.1093/sysbio/syw036 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genomic datasets generated with massively parallel sequencing methods have
the potential to propel systematics in new and exciting directions, but
selecting appropriate markers and methods is not straightforward. We applied
two approaches with particular promise for systematics, restriction site
associated DNA sequen... | [
{
"created": "Sun, 22 Dec 2013 23:02:34 GMT",
"version": "v1"
}
] | 2017-03-28 | [
[
"Harvey",
"Michael G.",
""
],
[
"Smith",
"Brian Tilston",
""
],
[
"Glenn",
"Travis C.",
""
],
[
"Faircloth",
"Brant C.",
""
],
[
"Brumfield",
"Robb T.",
""
]
] | Genomic datasets generated with massively parallel sequencing methods have the potential to propel systematics in new and exciting directions, but selecting appropriate markers and methods is not straightforward. We applied two approaches with particular promise for systematics, restriction site associated DNA sequenci... |
1112.5506 | Joshua Vogelstein | Joshua T. Vogelstein and Carey E. Priebe | Shuffled Graph Classification: Theory and Connectome Applications | 12 pages, 1 figure | null | null | null | q-bio.QM math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop a formalism to address statistical pattern recognition of graph
valued data. Of particular interest is the case of all graphs having the same
number of uniquely labeled vertices. When the vertex labels are latent, such
graphs are called shuffled graphs. Our formalism provides insight to trivially
answer a ... | [
{
"created": "Fri, 23 Dec 2011 02:47:31 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Oct 2012 09:57:12 GMT",
"version": "v2"
}
] | 2012-10-17 | [
[
"Vogelstein",
"Joshua T.",
""
],
[
"Priebe",
"Carey E.",
""
]
] | We develop a formalism to address statistical pattern recognition of graph valued data. Of particular interest is the case of all graphs having the same number of uniquely labeled vertices. When the vertex labels are latent, such graphs are called shuffled graphs. Our formalism provides insight to trivially answer a nu... |
2007.01378 | Enzo Tagliazucchi | Yonatan Sanz Perl, Hern\'an Boccacio, Ignacio P\'erez-Ipi\~na,
Federico Zamberl\'an, Helmut Laufs, Morten Kringelbach, Gustavo Deco, Enzo
Tagliazucchi | Generative embeddings of brain collective dynamics using variational
autoencoders | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the problem of encoding pairwise correlations between coupled
dynamical systems in a low-dimensional latent space based on few distinct
observations. We used variational autoencoders (VAE) to embed temporal
correlations between coupled nonlinear oscillators that model brain states in
the wake-sleep cycle ... | [
{
"created": "Thu, 2 Jul 2020 20:43:52 GMT",
"version": "v1"
}
] | 2020-07-06 | [
[
"Perl",
"Yonatan Sanz",
""
],
[
"Boccacio",
"Hernán",
""
],
[
"Pérez-Ipiña",
"Ignacio",
""
],
[
"Zamberlán",
"Federico",
""
],
[
"Laufs",
"Helmut",
""
],
[
"Kringelbach",
"Morten",
""
],
[
"Deco",
"Gustavo",
... | We consider the problem of encoding pairwise correlations between coupled dynamical systems in a low-dimensional latent space based on few distinct observations. We used variational autoencoders (VAE) to embed temporal correlations between coupled nonlinear oscillators that model brain states in the wake-sleep cycle in... |
2402.05543 | Aida Calvi\~no | Aida Calvi\~no and Almudena Moreno-Ribera and Silvia Pineda | Machine learning applied to omics data | Part of the book "Statistical Methods at the Forefront of Biomedical
Advances" published by Springer Cham | null | 10.1007/978-3-031-32729-2_2 | null | q-bio.GN cs.LG stat.AP | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In this chapter we illustrate the use of some Machine Learning techniques in
the context of omics data. More precisely, we review and evaluate the use of
Random Forest and Penalized Multinomial Logistic Regression for integrative
analysis of genomics and immunomics in pancreatic cancer. Furthermore, we
propose the us... | [
{
"created": "Thu, 8 Feb 2024 10:22:45 GMT",
"version": "v1"
}
] | 2024-02-09 | [
[
"Calviño",
"Aida",
""
],
[
"Moreno-Ribera",
"Almudena",
""
],
[
"Pineda",
"Silvia",
""
]
] | In this chapter we illustrate the use of some Machine Learning techniques in the context of omics data. More precisely, we review and evaluate the use of Random Forest and Penalized Multinomial Logistic Regression for integrative analysis of genomics and immunomics in pancreatic cancer. Furthermore, we propose the use ... |
2204.09291 | Milena Pavlovi\'c | Milena Pavlovi\'c, Ghadi S. Al Hajj, Chakravarthi Kanduri, Johan
Pensar, Mollie Wood, Ludvig M. Sollid, Victor Greiff, Geir Kjetil Sandve | Improving generalization of machine learning-identified biomarkers with
causal modeling: an investigation into immune receptor diagnostics | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Machine learning is increasingly used to discover diagnostic and prognostic
biomarkers from high-dimensional molecular data. However, a variety of factors
related to experimental design may affect the ability to learn generalizable
and clinically applicable diagnostics. Here, we argue that a causal perspective
improv... | [
{
"created": "Wed, 20 Apr 2022 08:15:54 GMT",
"version": "v1"
},
{
"created": "Mon, 3 Apr 2023 09:03:07 GMT",
"version": "v2"
}
] | 2023-04-04 | [
[
"Pavlović",
"Milena",
""
],
[
"Hajj",
"Ghadi S. Al",
""
],
[
"Kanduri",
"Chakravarthi",
""
],
[
"Pensar",
"Johan",
""
],
[
"Wood",
"Mollie",
""
],
[
"Sollid",
"Ludvig M.",
""
],
[
"Greiff",
"Victor",
""
]... | Machine learning is increasingly used to discover diagnostic and prognostic biomarkers from high-dimensional molecular data. However, a variety of factors related to experimental design may affect the ability to learn generalizable and clinically applicable diagnostics. Here, we argue that a causal perspective improves... |
0711.2061 | Igor M. Suslov | I. M. Suslov (P.L.Kapitza Institute for Physical Problems, Moscow,
Russia) | Computer Model of a "Sense of Humour". II. Realization in Neural
Networks | 13 pages, 5 figures included; continuation of this series to appear | Biofizika SSSR 37, 325 (1992) [Biophysics 37, 249 (1992)] | null | null | q-bio.NC cs.AI | null | The computer realization of a "sense of humour" requires the creation of an
algorithm for solving the "linguistic problem", i.e. the problem of recognizing
a continuous sequence of polysemantic images. Such algorithm may be realized in
the Hopfield model of a neural network after its proper modification.
| [
{
"created": "Tue, 13 Nov 2007 20:15:10 GMT",
"version": "v1"
}
] | 2007-11-27 | [
[
"Suslov",
"I. M.",
"",
"P.L.Kapitza Institute for Physical Problems, Moscow,\n Russia"
]
] | The computer realization of a "sense of humour" requires the creation of an algorithm for solving the "linguistic problem", i.e. the problem of recognizing a continuous sequence of polysemantic images. Such algorithm may be realized in the Hopfield model of a neural network after its proper modification. |
0712.1219 | Francois Meyer | Francois G. Meyer and Greg J. Stephens | Locality and low-dimensions in the prediction of natural experience from
fMRI | To appear in: Advances in Neural Information Processing Systems 20,
Scholkopf B., Platt J. and Hofmann T. (Editors), MIT Press, 2008 | null | null | null | q-bio.NC stat.ML | null | Functional Magnetic Resonance Imaging (fMRI) provides dynamical access into
the complex functioning of the human brain, detailing the hemodynamic activity
of thousands of voxels during hundreds of sequential time points. One approach
towards illuminating the connection between fMRI and cognitive function is
through d... | [
{
"created": "Fri, 7 Dec 2007 20:21:18 GMT",
"version": "v1"
},
{
"created": "Sat, 12 Jan 2008 01:00:50 GMT",
"version": "v2"
}
] | 2008-01-16 | [
[
"Meyer",
"Francois G.",
""
],
[
"Stephens",
"Greg J.",
""
]
] | Functional Magnetic Resonance Imaging (fMRI) provides dynamical access into the complex functioning of the human brain, detailing the hemodynamic activity of thousands of voxels during hundreds of sequential time points. One approach towards illuminating the connection between fMRI and cognitive function is through dec... |
1811.02335 | Richard Gerum | Achim Schilling, Richard Gerum, Patrick Krauss, Claus Metzner,
Konstantin Tziridis, Holger Schulze | Objective estimation of sensory thresholds based on neurophysiological
parameters | null | null | 10.3389/fnins.2019.00481 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reliable determination of sensory thresholds is the holy grail of signal
detection theory. However, there exists no gold standard for the estimation of
thresholds based on neurophysiological parameters, although a reliable
estimation method is crucial for both scientific investigations and clinical
diagnosis. Wheneve... | [
{
"created": "Tue, 6 Nov 2018 13:07:32 GMT",
"version": "v1"
}
] | 2019-10-01 | [
[
"Schilling",
"Achim",
""
],
[
"Gerum",
"Richard",
""
],
[
"Krauss",
"Patrick",
""
],
[
"Metzner",
"Claus",
""
],
[
"Tziridis",
"Konstantin",
""
],
[
"Schulze",
"Holger",
""
]
] | Reliable determination of sensory thresholds is the holy grail of signal detection theory. However, there exists no gold standard for the estimation of thresholds based on neurophysiological parameters, although a reliable estimation method is crucial for both scientific investigations and clinical diagnosis. Whenever ... |
1005.3887 | Fabio Pichierri | Fabio Pichierri | The electronic structure and dipole moment of charybdotoxin, a scorpion
venom peptide with K+ channel blocking activity | 16 pages, 6 figures | Computational and Theoretical Chemistry 963 (2011) 384-393 | 10.1016/j.comptc.2010.11.003 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The electronic structure of charybdotoxin (ChTX), a scorpion venom peptide
that is known to act as a potassium channel blocker, is investigated with the
aid of quantum mechanical calculations. The dipole moment vector (145 D) of
ChTX can be stirred by the full length KcsA potassium channel's macrodipole
(403 D) there... | [
{
"created": "Fri, 21 May 2010 05:19:10 GMT",
"version": "v1"
}
] | 2015-03-17 | [
[
"Pichierri",
"Fabio",
""
]
] | The electronic structure of charybdotoxin (ChTX), a scorpion venom peptide that is known to act as a potassium channel blocker, is investigated with the aid of quantum mechanical calculations. The dipole moment vector (145 D) of ChTX can be stirred by the full length KcsA potassium channel's macrodipole (403 D) thereby... |
1304.3546 | Anandarup Bhadra | Anandarup Bhadra, Debottam Bhattacharjee, Manabi Paul and Anindita
Bhadra | The Meat of the Matter: A thumb rule for scavenging dogs? | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Animals that scavenge in and around human localities need to utilize a broad
range of resources. Preference for any one kind of food, under such
circumstances, might be inefficient. Indian free-ranging dogs, Canis lupus
familiaris are scavengers that are heavily dependent on humans for sustaining
their omnivorous die... | [
{
"created": "Fri, 12 Apr 2013 06:30:33 GMT",
"version": "v1"
}
] | 2013-04-15 | [
[
"Bhadra",
"Anandarup",
""
],
[
"Bhattacharjee",
"Debottam",
""
],
[
"Paul",
"Manabi",
""
],
[
"Bhadra",
"Anindita",
""
]
] | Animals that scavenge in and around human localities need to utilize a broad range of resources. Preference for any one kind of food, under such circumstances, might be inefficient. Indian free-ranging dogs, Canis lupus familiaris are scavengers that are heavily dependent on humans for sustaining their omnivorous diet.... |
1310.4258 | Ron Nielsen | Ron W Nielsen (aka Jan Nurzynski) | Scientifically unacceptable concept of the Epoch of Malthusian
Stagnation | 43 pages | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In order to control the growth of human population it is helpful to
understand correctly the mechanism of growth, and the first essential step is
to investigate current interpretations and reject any unscientific
explanations. One of such popular but questionable interpretations is the
concept of the Epoch of Malthus... | [
{
"created": "Wed, 16 Oct 2013 03:49:59 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Oct 2013 00:37:55 GMT",
"version": "v2"
},
{
"created": "Fri, 1 Nov 2013 03:36:02 GMT",
"version": "v3"
}
] | 2017-10-04 | [
[
"Nielsen",
"Ron W",
"",
"aka Jan Nurzynski"
]
] | In order to control the growth of human population it is helpful to understand correctly the mechanism of growth, and the first essential step is to investigate current interpretations and reject any unscientific explanations. One of such popular but questionable interpretations is the concept of the Epoch of Malthusia... |
2209.04923 | Samuel Gershman | Samuel J. Gershman | The molecular memory code and synaptic plasticity: a synthesis | null | null | null | null | q-bio.NC q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | The most widely accepted view of memory in the brain holds that synapses are
the storage sites of memory, and that memories are formed through associative
modification of synapses. This view has been challenged on conceptual and
empirical grounds. As an alternative, it has been proposed that molecules
within the cell... | [
{
"created": "Sun, 11 Sep 2022 19:38:23 GMT",
"version": "v1"
}
] | 2022-09-13 | [
[
"Gershman",
"Samuel J.",
""
]
] | The most widely accepted view of memory in the brain holds that synapses are the storage sites of memory, and that memories are formed through associative modification of synapses. This view has been challenged on conceptual and empirical grounds. As an alternative, it has been proposed that molecules within the cell b... |
1607.04122 | Antoni Aguilar-Mogas | Antoni Aguilar-Mogas (1), Marta Sales-Pardo (1), Miriam Navarro (2 and
3), Ralf Tautenhahn (4), Roger Guimer\`a (1 and 5) and Oscar Yanes (2 and 3)
((1) Departament d'Enginyeria Qu\'imica, Universitat Rovira i Virgili,
Tarragona, Spain, (2) Centre for Omic Sciences, Universitat Rovira i Virgili,
Reus, Spain, (3... | iMet: A computational tool for structural annotation of unknown
metabolites from tandem mass spectra | 21 pages, 6 figures | null | 10.1021/acs.analchem.6b04512 | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Untargeted metabolomic studies are revealing large numbers of naturally
occurring metabolites that cannot be characterized because their chemical
structures and MS/MS spectra are not available in databases. Here we present
iMet, a computational tool based on experimental tandem mass spectrometry that
could potentiall... | [
{
"created": "Thu, 14 Jul 2016 13:25:22 GMT",
"version": "v1"
}
] | 2017-03-17 | [
[
"Aguilar-Mogas",
"Antoni",
"",
"2 and\n 3"
],
[
"Sales-Pardo",
"Marta",
"",
"2 and\n 3"
],
[
"Navarro",
"Miriam",
"",
"2 and\n 3"
],
[
"Tautenhahn",
"Ralf",
"",
"1 and 5"
],
[
"Guimerà",
"Roger",
"",
"1 and 5"
],
... | Untargeted metabolomic studies are revealing large numbers of naturally occurring metabolites that cannot be characterized because their chemical structures and MS/MS spectra are not available in databases. Here we present iMet, a computational tool based on experimental tandem mass spectrometry that could potentially ... |
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