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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0808.3511 | K. P. Unnikrishnan | P.S. Sastry (Indian Institute of Science), and K.P. Unnikrishnan
(General Motors Research) | Conditional probability based significance tests for sequential patterns
in multi-neuronal spike trains | 35 pages, 7 figures | null | null | null | q-bio.NC cond-mat.dis-nn cs.DB q-bio.QM stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we consider the problem of detecting statistically significant
sequential patterns in multi-neuronal spike trains. These patterns are
characterized by ordered sequences of spikes from different neurons with
specific delays between spikes. We have previously proposed a data mining
scheme to efficiently d... | [
{
"created": "Tue, 26 Aug 2008 13:28:43 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Aug 2008 02:15:45 GMT",
"version": "v2"
}
] | 2008-08-28 | [
[
"Sastry",
"P. S.",
"",
"Indian Institute of Science"
],
[
"Unnikrishnan",
"K. P.",
"",
"General Motors Research"
]
] | In this paper we consider the problem of detecting statistically significant sequential patterns in multi-neuronal spike trains. These patterns are characterized by ordered sequences of spikes from different neurons with specific delays between spikes. We have previously proposed a data mining scheme to efficiently dis... |
1710.04173 | Sabine Ploux Dr. | Sabine Ploux, Rui Wang, ZhengFeng Zhong, Hai Zhao, Yang Xin and
Bao-Liang Lu | Structural Stability of Lexical Semantic Spaces: Nouns in Chinese and
French | 17 pages, 4 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many studies in the neurosciences have dealt with the semantic processing of
words or categories, but few have looked into the semantic organization of the
lexicon thought as a system. The present study was designed to try to move
towards this goal, using both electrophysiological and corpus-based data, and
to compar... | [
{
"created": "Wed, 11 Oct 2017 16:59:12 GMT",
"version": "v1"
}
] | 2017-10-12 | [
[
"Ploux",
"Sabine",
""
],
[
"Wang",
"Rui",
""
],
[
"Zhong",
"ZhengFeng",
""
],
[
"Zhao",
"Hai",
""
],
[
"Xin",
"Yang",
""
],
[
"Lu",
"Bao-Liang",
""
]
] | Many studies in the neurosciences have dealt with the semantic processing of words or categories, but few have looked into the semantic organization of the lexicon thought as a system. The present study was designed to try to move towards this goal, using both electrophysiological and corpus-based data, and to compare ... |
1303.4229 | Nicolas Innocenti | Nicolas Innocenti and Erik Aurell | Lognormality and oscillations in the coverage of high-throughput
transcriptomic data towards gene ends | null | J. Stat. Mech. (2013) P10013 | 10.1088/1742-5468/2013/10/P10013 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | High-throughput transcriptomics experiments have reached the stage where the
count of the number of reads alignable to a given position can be treated as an
almost-continuous signal. This allows to ask questions of
biophysical/biotechnical nature, but which may still have biological
implications. Here we show that wh... | [
{
"created": "Mon, 18 Mar 2013 12:36:53 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Jul 2013 20:34:33 GMT",
"version": "v2"
},
{
"created": "Wed, 28 Aug 2013 15:03:56 GMT",
"version": "v3"
}
] | 2014-10-02 | [
[
"Innocenti",
"Nicolas",
""
],
[
"Aurell",
"Erik",
""
]
] | High-throughput transcriptomics experiments have reached the stage where the count of the number of reads alignable to a given position can be treated as an almost-continuous signal. This allows to ask questions of biophysical/biotechnical nature, but which may still have biological implications. Here we show that when... |
1904.08182 | Carolin Loos | Carolin Loos, Jan Hasenauer | Mathematical modeling of variability in intracellular signaling | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Cellular signaling is essential in information processing and decision
making. Therefore, a variety of experimental approaches have been developed to
study signaling on bulk and single-cell level. Single-cell measurements of
signaling molecules demonstrated a substantial cell-to-cell variability,
raising questions ab... | [
{
"created": "Wed, 17 Apr 2019 11:08:06 GMT",
"version": "v1"
}
] | 2019-04-18 | [
[
"Loos",
"Carolin",
""
],
[
"Hasenauer",
"Jan",
""
]
] | Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling molecules demonstrated a substantial cell-to-cell variability, raising questions abou... |
1501.06530 | David Bardos | David C. Bardos, Gurutzeta Guillera-Arroita and Brendan A. Wintle | Covariate influence in spatially autocorrelated occupancy and abundance
data | References updated | null | null | null | q-bio.QM stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The autologistic model and related auto-models, commonly applied as
autocovariate regression, offer distinct advantages for analysing spatially
autocorrelated ecological data. However, comparative studies by Carl and K\"uhn
(Ecol. Model., 2007, 207, 159), Dormann (Ecol. Model., 2007, 207, 234), Dormann
et al. (Ecogra... | [
{
"created": "Mon, 26 Jan 2015 19:21:43 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Jan 2015 17:00:12 GMT",
"version": "v2"
}
] | 2015-01-28 | [
[
"Bardos",
"David C.",
""
],
[
"Guillera-Arroita",
"Gurutzeta",
""
],
[
"Wintle",
"Brendan A.",
""
]
] | The autologistic model and related auto-models, commonly applied as autocovariate regression, offer distinct advantages for analysing spatially autocorrelated ecological data. However, comparative studies by Carl and K\"uhn (Ecol. Model., 2007, 207, 159), Dormann (Ecol. Model., 2007, 207, 234), Dormann et al. (Ecograph... |
1907.01588 | Elahe Arani | Elahe Arani, Sofia Triantafillou and Konrad P. Kording | Reverse engineering neural networks from many partial recordings | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Much of neuroscience aims at reverse engineering the brain, but we only
record a small number of neurons at a time. We do not currently know if reverse
engineering the brain requires us to simultaneously record most neurons or if
multiple recordings from smaller subsets suffice. This is made even more
important by th... | [
{
"created": "Tue, 2 Jul 2019 19:15:30 GMT",
"version": "v1"
}
] | 2019-07-04 | [
[
"Arani",
"Elahe",
""
],
[
"Triantafillou",
"Sofia",
""
],
[
"Kording",
"Konrad P.",
""
]
] | Much of neuroscience aims at reverse engineering the brain, but we only record a small number of neurons at a time. We do not currently know if reverse engineering the brain requires us to simultaneously record most neurons or if multiple recordings from smaller subsets suffice. This is made even more important by the ... |
1105.1117 | Alfonso P\'erez-Escudero | Alfonso P\'erez-Escudero, Gonzalo G. de Polavieja | Collective Animal Behavior from Bayesian Estimation and Probability
Matching | 19 pages, including Supplemental Figures and Supplemental Text. In
press in PLoS Computational Biology | PLoS Comput Biol 7(11): e1002282 (2011) | 10.1371/journal.pcbi.1002282 | null | q-bio.QM cs.SI nlin.AO physics.data-an physics.soc-ph q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Animals living in groups make movement decisions that depend, among other
factors, on social interactions with other group members. Our present
understanding of social rules in animal collectives is mainly based on
empirical fits to observations, with less emphasis in obtaining
first-principles approaches that allow ... | [
{
"created": "Thu, 5 May 2011 16:32:59 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Nov 2011 13:59:44 GMT",
"version": "v2"
}
] | 2011-11-22 | [
[
"Pérez-Escudero",
"Alfonso",
""
],
[
"de Polavieja",
"Gonzalo G.",
""
]
] | Animals living in groups make movement decisions that depend, among other factors, on social interactions with other group members. Our present understanding of social rules in animal collectives is mainly based on empirical fits to observations, with less emphasis in obtaining first-principles approaches that allow th... |
2110.11501 | Rui Ponte Costa | Joseph Pemberton and Ellen Boven and Richard Apps and Rui Ponte Costa | Cortico-cerebellar networks as decoupling neural interfaces | To appear in Advances in Neural Information Processing Systems 35
(NeurIPS 2021); 15 pages and 5 figures in the main manuscript; 8 pages and 8
figures in the supplementary material | null | null | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The brain solves the credit assignment problem remarkably well. For credit to
be assigned across neural networks they must, in principle, wait for specific
neural computations to finish. How the brain deals with this inherent locking
problem has remained unclear. Deep learning methods suffer from similar locking
cons... | [
{
"created": "Thu, 21 Oct 2021 22:02:38 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Oct 2021 12:57:34 GMT",
"version": "v2"
}
] | 2021-10-29 | [
[
"Pemberton",
"Joseph",
""
],
[
"Boven",
"Ellen",
""
],
[
"Apps",
"Richard",
""
],
[
"Costa",
"Rui Ponte",
""
]
] | The brain solves the credit assignment problem remarkably well. For credit to be assigned across neural networks they must, in principle, wait for specific neural computations to finish. How the brain deals with this inherent locking problem has remained unclear. Deep learning methods suffer from similar locking constr... |
1812.02121 | Cinzia Soresina | Sara Pasquali and Cinzia Soresina and Gianni Gilioli | The effects of fecundity, mortality and distribution of the initial
condition in phenological models | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pest phenological models describe the cumulative flux of the individuals into
each stage of the life cycle of a stage-structured population. Phenological
models are widely used tools in pest control decision making. Despite the fact
that these models do not provide information on population abundance, they
share some... | [
{
"created": "Wed, 5 Dec 2018 17:20:46 GMT",
"version": "v1"
}
] | 2018-12-06 | [
[
"Pasquali",
"Sara",
""
],
[
"Soresina",
"Cinzia",
""
],
[
"Gilioli",
"Gianni",
""
]
] | Pest phenological models describe the cumulative flux of the individuals into each stage of the life cycle of a stage-structured population. Phenological models are widely used tools in pest control decision making. Despite the fact that these models do not provide information on population abundance, they share some a... |
1811.12314 | Zhiqin Xu | Zhi-Qin John Xu, Douglas Zhou, David Cai | Swift Two-sample Test on High-dimensional Neural Spiking Data | 10 pages, 6 figures | null | null | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To understand how neural networks process information, it is important to
investigate how neural network dynamics varies with respect to different
stimuli. One challenging task is to design efficient statistical approaches to
analyze multiple spike train data obtained from a short recording time. Based
on the develop... | [
{
"created": "Sun, 11 Nov 2018 20:40:41 GMT",
"version": "v1"
}
] | 2018-11-30 | [
[
"Xu",
"Zhi-Qin John",
""
],
[
"Zhou",
"Douglas",
""
],
[
"Cai",
"David",
""
]
] | To understand how neural networks process information, it is important to investigate how neural network dynamics varies with respect to different stimuli. One challenging task is to design efficient statistical approaches to analyze multiple spike train data obtained from a short recording time. Based on the developme... |
2109.02228 | Christopher Nottingham | Christopher D. Nottingham and Russell B. Millar | spatialSim: multi-species spatiotemporal size-structured operating model
for management strategy evaluation | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spatiotemporal processes have the potential to be one of the most influential
factors governing how fisheries targeting sedentary species respond to
harvesting. Despite this, management strategy evaluation often fails to account
for space or does so at low resolutions due to compute constraints. In this
paper, a mult... | [
{
"created": "Mon, 6 Sep 2021 03:44:17 GMT",
"version": "v1"
}
] | 2021-09-07 | [
[
"Nottingham",
"Christopher D.",
""
],
[
"Millar",
"Russell B.",
""
]
] | Spatiotemporal processes have the potential to be one of the most influential factors governing how fisheries targeting sedentary species respond to harvesting. Despite this, management strategy evaluation often fails to account for space or does so at low resolutions due to compute constraints. In this paper, a multi-... |
1407.3543 | Peter Gawthrop | Peter Gawthrop, Henrik Gollee and Ian Loram | Intermittent Control in Man and Machine | null | null | null | null | q-bio.QM cs.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Intermittent control has a long history in the physiological literature and
there is strong experimental evidence that some human control systems are
intermittent. Intermittent control has also appeared in various forms in the
engineering literature. This article discusses a particular mathematical model
of Event-dri... | [
{
"created": "Mon, 14 Jul 2014 06:07:37 GMT",
"version": "v1"
}
] | 2014-07-23 | [
[
"Gawthrop",
"Peter",
""
],
[
"Gollee",
"Henrik",
""
],
[
"Loram",
"Ian",
""
]
] | Intermittent control has a long history in the physiological literature and there is strong experimental evidence that some human control systems are intermittent. Intermittent control has also appeared in various forms in the engineering literature. This article discusses a particular mathematical model of Event-drive... |
0709.0225 | Jonas Cremer | Jonas Cremer, Tobias Reichenbach, Erwin Frey | Anomalous finite-size effects in the Battle of the Sexes | 8 pages, 5 figures. To appear in the ECCS '07 issue, Eur. Phys. J. B
(2008) | Eur. Phys. J. B 63, 373-380 (2008) | 10.1140/epjb/e2008-00036-x | LMU-ASC 67/07 | q-bio.PE cond-mat.stat-mech physics.bio-ph | null | The Battle of the Sexes describes asymmetric conflicts in mating behavior of
males and females. Males can be philanderer or faithful, while females are
either fast or coy, leading to a cyclic dynamics. The adjusted replicator
equation predicts stable coexistence of all four strategies. In this situation,
we consider ... | [
{
"created": "Mon, 3 Sep 2007 13:21:44 GMT",
"version": "v1"
}
] | 2008-08-31 | [
[
"Cremer",
"Jonas",
""
],
[
"Reichenbach",
"Tobias",
""
],
[
"Frey",
"Erwin",
""
]
] | The Battle of the Sexes describes asymmetric conflicts in mating behavior of males and females. Males can be philanderer or faithful, while females are either fast or coy, leading to a cyclic dynamics. The adjusted replicator equation predicts stable coexistence of all four strategies. In this situation, we consider th... |
2407.21087 | Efrat Monsonego Ornan | Gal Becker, Jerome Nicolas Janssen, Rotem Kalev-Altman, Dana Meilich,
Astar Shitrit, Svetlana Penn, Ram Reifen and Efrat Monsonego Ornan | Plant and insect proteins support optimal bone growth and development;
Evidences from a pre-clinical model | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | By 2050, the global population will exceed 9 billion, demanding a 70%
increase in food production. Animal proteins alone may not suffice and
contribute to global warming. Alternative proteins such as legumes, algae, and
insects are being explored, but their health impacts are largely unknown. For
this, three-week-old... | [
{
"created": "Tue, 30 Jul 2024 15:03:54 GMT",
"version": "v1"
}
] | 2024-08-01 | [
[
"Becker",
"Gal",
""
],
[
"Janssen",
"Jerome Nicolas",
""
],
[
"Kalev-Altman",
"Rotem",
""
],
[
"Meilich",
"Dana",
""
],
[
"Shitrit",
"Astar",
""
],
[
"Penn",
"Svetlana",
""
],
[
"Reifen",
"Ram",
""
],
[... | By 2050, the global population will exceed 9 billion, demanding a 70% increase in food production. Animal proteins alone may not suffice and contribute to global warming. Alternative proteins such as legumes, algae, and insects are being explored, but their health impacts are largely unknown. For this, three-week-old r... |
q-bio/0311001 | Rajesh Karmakar | Indrani Bose and Rajesh Karmakar | Mathematical models of haploinsufficiency | 13 pages, 5 figures | null | null | null | q-bio.OT cond-mat.stat-mech q-bio.QM | null | We study simple mathematical models of gene expression to explore the
possible origins of haploinsufficiency (HI). In a diploid organism, each gene
exists in two copies and when one of these is mutated, the amount of proteins
synthesized is reduced and may fall below a threshold level for the onset of
some desired ac... | [
{
"created": "Mon, 3 Nov 2003 11:06:52 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bose",
"Indrani",
""
],
[
"Karmakar",
"Rajesh",
""
]
] | We study simple mathematical models of gene expression to explore the possible origins of haploinsufficiency (HI). In a diploid organism, each gene exists in two copies and when one of these is mutated, the amount of proteins synthesized is reduced and may fall below a threshold level for the onset of some desired acti... |
2307.14550 | Kristina Crona | Kristina Crona | Irreversible evolution, obstacles in fitness landscapes and persistent
drug resistance | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | We use fitness graphs, or directed cube graphs, for analyzing evolutionary
reversibility. The main application is antimicrobial drug resistance.
Reversible drug resistance has been observed both clinically and
experimentally. If drug resistance depends on a single point mutation, then a
possible scenario is that the ... | [
{
"created": "Thu, 27 Jul 2023 00:17:48 GMT",
"version": "v1"
}
] | 2023-07-28 | [
[
"Crona",
"Kristina",
""
]
] | We use fitness graphs, or directed cube graphs, for analyzing evolutionary reversibility. The main application is antimicrobial drug resistance. Reversible drug resistance has been observed both clinically and experimentally. If drug resistance depends on a single point mutation, then a possible scenario is that the mu... |
2301.08785 | Rene Warren | Lauren Coombe, Ren\'e L. Warren, Johnathan Wong, Vladimir Nikolic,
Inanc Birol | ntLink: a toolkit for de novo genome assembly scaffolding and mapping
using long reads | 23 pages, 2 figures | Current Protocols, 3(4), e733 (2023) | 10.1002/cpz1.733 | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | With the increasing affordability and accessibility of genome sequencing
data, de novo genome assembly is an important first step to a wide variety of
downstream studies and analyses. Therefore, bioinformatics tools that enable
the generation of high-quality genome assemblies in a computationally efficient
manner are... | [
{
"created": "Fri, 20 Jan 2023 20:08:00 GMT",
"version": "v1"
}
] | 2023-06-09 | [
[
"Coombe",
"Lauren",
""
],
[
"Warren",
"René L.",
""
],
[
"Wong",
"Johnathan",
""
],
[
"Nikolic",
"Vladimir",
""
],
[
"Birol",
"Inanc",
""
]
] | With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the generation of high-quality genome assemblies in a computationally efficient manner are e... |
2407.12051 | Zhiyuan Peng | Zhiyuan Peng, Yuanbo Tang, Yang Li | Dy-mer: An Explainable DNA Sequence Representation Scheme using Sparse
Recovery | null | null | null | null | q-bio.GN cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | DNA sequences encode vital genetic and biological information, yet these
unfixed-length sequences cannot serve as the input of common data mining
algorithms. Hence, various representation schemes have been developed to
transform DNA sequences into fixed-length numerical representations. However,
these schemes face di... | [
{
"created": "Sat, 6 Jul 2024 15:08:31 GMT",
"version": "v1"
}
] | 2024-07-18 | [
[
"Peng",
"Zhiyuan",
""
],
[
"Tang",
"Yuanbo",
""
],
[
"Li",
"Yang",
""
]
] | DNA sequences encode vital genetic and biological information, yet these unfixed-length sequences cannot serve as the input of common data mining algorithms. Hence, various representation schemes have been developed to transform DNA sequences into fixed-length numerical representations. However, these schemes face diff... |
0806.3048 | Dejan Stokic | Dejan Stokic, Rudolf Hanel, Stefan Thurner | A fast and efficient gene-network reconstruction method from multiple
over-expression experiments | 10 pages, 3 figures | null | null | null | q-bio.MN q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reverse engineering of gene regulatory networks presents one of the big
challenges in systems biology. Gene regulatory networks are usually inferred
from a set of single-gene over-expressions and/or knockout experiments.
Functional relationships between genes are retrieved either from the steady
state gene expression... | [
{
"created": "Wed, 18 Jun 2008 16:57:10 GMT",
"version": "v1"
}
] | 2008-06-19 | [
[
"Stokic",
"Dejan",
""
],
[
"Hanel",
"Rudolf",
""
],
[
"Thurner",
"Stefan",
""
]
] | Reverse engineering of gene regulatory networks presents one of the big challenges in systems biology. Gene regulatory networks are usually inferred from a set of single-gene over-expressions and/or knockout experiments. Functional relationships between genes are retrieved either from the steady state gene expressions ... |
2003.06122 | Waradon Sungnak | Waradon Sungnak, Ni Huang, Christophe B\'ecavin, Marijn Berg, HCA Lung
Biological Network | SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and
Ciliated Cells within Human Airways | null | Nature Medicine, 2020 | 10.1038/s41591-020-0868-6 | null | q-bio.CB | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The SARS-CoV-2 coronavirus, the etiologic agent responsible for COVID-19
coronavirus disease, is a global threat. To better understand viral tropism, we
assessed the RNA expression of the coronavirus receptor, ACE2, as well as the
viral S protein priming protease TMPRSS2 thought to govern viral entry in
single-cell R... | [
{
"created": "Fri, 13 Mar 2020 05:29:24 GMT",
"version": "v1"
}
] | 2020-04-27 | [
[
"Sungnak",
"Waradon",
""
],
[
"Huang",
"Ni",
""
],
[
"Bécavin",
"Christophe",
""
],
[
"Berg",
"Marijn",
""
],
[
"Network",
"HCA Lung Biological",
""
]
] | The SARS-CoV-2 coronavirus, the etiologic agent responsible for COVID-19 coronavirus disease, is a global threat. To better understand viral tropism, we assessed the RNA expression of the coronavirus receptor, ACE2, as well as the viral S protein priming protease TMPRSS2 thought to govern viral entry in single-cell RNA... |
2002.08501 | Mark Byrne | Mark Byrne | Simple post-translational circadian clock models from selective
sequestration | 8 pages, submitted to JBR | null | null | null | q-bio.MN q-bio.BM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is possible that there are post-translational circadian oscillators that
continue functioning in the absence of negative feedback transcriptional
repression in many cell types from diverse organisms. Apart from the KaiABC
system from cyanobacteria, the molecular components and interactions required
to create in-vi... | [
{
"created": "Thu, 20 Feb 2020 00:02:24 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Feb 2020 05:03:42 GMT",
"version": "v2"
}
] | 2020-02-24 | [
[
"Byrne",
"Mark",
""
]
] | It is possible that there are post-translational circadian oscillators that continue functioning in the absence of negative feedback transcriptional repression in many cell types from diverse organisms. Apart from the KaiABC system from cyanobacteria, the molecular components and interactions required to create in-vitr... |
2206.02249 | Adedapo Alabi | Adedapo Alabi, Dieter Vanderelst and Ali Minai | Rapid Learning of Spatial Representations for Goal-Directed Navigation
Based on a Novel Model of Hippocampal Place Fields | null | null | null | null | q-bio.NC cs.NE | http://creativecommons.org/licenses/by/4.0/ | The discovery of place cells and other spatially modulated neurons in the
hippocampal complex of rodents has been crucial to elucidating the neural basis
of spatial cognition. More recently, the replay of neural sequences encoding
previously experienced trajectories has been observed during consummatory
behavior pote... | [
{
"created": "Sun, 5 Jun 2022 19:50:33 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Jun 2022 13:19:40 GMT",
"version": "v2"
},
{
"created": "Sat, 14 Jan 2023 00:25:40 GMT",
"version": "v3"
}
] | 2023-01-18 | [
[
"Alabi",
"Adedapo",
""
],
[
"Vanderelst",
"Dieter",
""
],
[
"Minai",
"Ali",
""
]
] | The discovery of place cells and other spatially modulated neurons in the hippocampal complex of rodents has been crucial to elucidating the neural basis of spatial cognition. More recently, the replay of neural sequences encoding previously experienced trajectories has been observed during consummatory behavior potent... |
q-bio/0505002 | Elchanan Mossel | Elchanan Mossel, Eric Vigoda | Limitations of Markov chain Monte Carlo algorithms for Bayesian
Inference of phylogeny | Published at http://dx.doi.org/10.1214/105051600000000538 in the
Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute
of Mathematical Statistics (http://www.imstat.org) | Annals of Applied Probability 2006, Vol. 16, No. 4, 2215-2234 | 10.1214/105051600000000538 | IMS-AAP-AAP0205 | q-bio.PE q-bio.GN | null | Markov chain Monte Carlo algorithms play a key role in the Bayesian approach
to phylogenetic inference. In this paper, we present the first theoretical work
analyzing the rate of convergence of several Markov chains widely used in
phylogenetic inference. We analyze simple, realistic examples where these
Markov chains... | [
{
"created": "Mon, 2 May 2005 18:41:17 GMT",
"version": "v1"
},
{
"created": "Tue, 24 May 2005 02:43:48 GMT",
"version": "v2"
},
{
"created": "Thu, 22 Dec 2005 19:33:12 GMT",
"version": "v3"
},
{
"created": "Mon, 12 Jun 2006 21:29:57 GMT",
"version": "v4"
},
{
"cr... | 2007-05-23 | [
[
"Mossel",
"Elchanan",
""
],
[
"Vigoda",
"Eric",
""
]
] | Markov chain Monte Carlo algorithms play a key role in the Bayesian approach to phylogenetic inference. In this paper, we present the first theoretical work analyzing the rate of convergence of several Markov chains widely used in phylogenetic inference. We analyze simple, realistic examples where these Markov chains f... |
0807.3350 | Bradly Alicea | Bradly Alicea | Evaluating Intraspecific Variation and Interspecific Diversity:
comparing humans and fish species | Masters thesis | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The analysis of eight molecular datasets involving human and teleost examples
along with morphological samples from several groups of Neotropical electric
fish (Order: Gymnotiformes) were used in this thesis to test the dynamics of
both intraspecific variation and interspecific diversity. In terms of
investigating mo... | [
{
"created": "Tue, 22 Jul 2008 01:29:45 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Nov 2013 07:45:08 GMT",
"version": "v2"
}
] | 2013-12-02 | [
[
"Alicea",
"Bradly",
""
]
] | The analysis of eight molecular datasets involving human and teleost examples along with morphological samples from several groups of Neotropical electric fish (Order: Gymnotiformes) were used in this thesis to test the dynamics of both intraspecific variation and interspecific diversity. In terms of investigating mole... |
2206.06691 | Mrinal Kanti Pal | Mrinal Kanti Pal, Swarup Poria | Effect of Non-local Grazing on Dry-land Vegetation Dynamics | 13 pages, 6 figures | null | null | null | q-bio.PE math.DS nlin.PS | http://creativecommons.org/licenses/by/4.0/ | Dry-land ecosystem has turned into a matter of grave concern, due to growing
threat of land degradation and bioproductivity-loss. Self-organized vegetation
patterns are a remarkable characteristic of these ecosystems; apart from being
visually captivating, patterns modulate the system-response to increasing
environme... | [
{
"created": "Tue, 14 Jun 2022 08:46:45 GMT",
"version": "v1"
},
{
"created": "Sat, 24 Sep 2022 14:00:18 GMT",
"version": "v2"
}
] | 2022-09-27 | [
[
"Pal",
"Mrinal Kanti",
""
],
[
"Poria",
"Swarup",
""
]
] | Dry-land ecosystem has turned into a matter of grave concern, due to growing threat of land degradation and bioproductivity-loss. Self-organized vegetation patterns are a remarkable characteristic of these ecosystems; apart from being visually captivating, patterns modulate the system-response to increasing environment... |
1710.00495 | Diwakar Shukla | Zahra Shamsi, Kevin J. Cheng and Diwakar Shukla | REinforcement learning based Adaptive samPling: REAPing Rewards by
Exploring Protein Conformational Landscapes | null | null | null | null | q-bio.BM physics.bio-ph physics.chem-ph | http://creativecommons.org/licenses/by/4.0/ | One of the key limitations of Molecular Dynamics simulations is the
computational intractability of sampling protein conformational landscapes
associated with either large system size or long timescales. To overcome this
bottleneck, we present the REinforcement learning based Adaptive samPling
(REAP) algorithm that a... | [
{
"created": "Mon, 2 Oct 2017 05:57:07 GMT",
"version": "v1"
},
{
"created": "Thu, 5 Jul 2018 20:16:49 GMT",
"version": "v2"
}
] | 2018-07-09 | [
[
"Shamsi",
"Zahra",
""
],
[
"Cheng",
"Kevin J.",
""
],
[
"Shukla",
"Diwakar",
""
]
] | One of the key limitations of Molecular Dynamics simulations is the computational intractability of sampling protein conformational landscapes associated with either large system size or long timescales. To overcome this bottleneck, we present the REinforcement learning based Adaptive samPling (REAP) algorithm that aim... |
1604.07457 | Panqu Wang | Panqu Wang, Garrison Cottrell | Modeling the Contribution of Central Versus Peripheral Vision in Scene,
Object, and Face Recognition | CogSci 2016 Conference Paper | null | null | null | q-bio.NC cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is commonly believed that the central visual field is important for
recognizing objects and faces, and the peripheral region is useful for scene
recognition. However, the relative importance of central versus peripheral
information for object, scene, and face recognition is unclear. In a behavioral
study, Larson a... | [
{
"created": "Mon, 25 Apr 2016 22:01:50 GMT",
"version": "v1"
}
] | 2016-04-27 | [
[
"Wang",
"Panqu",
""
],
[
"Cottrell",
"Garrison",
""
]
] | It is commonly believed that the central visual field is important for recognizing objects and faces, and the peripheral region is useful for scene recognition. However, the relative importance of central versus peripheral information for object, scene, and face recognition is unclear. In a behavioral study, Larson and... |
1706.06089 | Alberto Sorrentino | Filippo Rossi, Gianvittorio Luria, Sara Sommariva and Alberto
Sorrentino | Bayesian multi--dipole localization and uncertainty quantification from
simultaneous EEG and MEG recordings | 4 pages, 3 figures -- conference paper from EMBEC 2017, Tampere,
Finland | null | 10.1007/978-981-10-5122-7_211 | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We deal with estimation of multiple dipoles from combined MEG and EEG
time--series. We use a sequential Monte Carlo algorithm to characterize the
posterior distribution of the number of dipoles and their locations. By
considering three test cases, we show that using the combined data the method
can localize sources t... | [
{
"created": "Mon, 19 Jun 2017 17:59:44 GMT",
"version": "v1"
}
] | 2017-06-20 | [
[
"Rossi",
"Filippo",
""
],
[
"Luria",
"Gianvittorio",
""
],
[
"Sommariva",
"Sara",
""
],
[
"Sorrentino",
"Alberto",
""
]
] | We deal with estimation of multiple dipoles from combined MEG and EEG time--series. We use a sequential Monte Carlo algorithm to characterize the posterior distribution of the number of dipoles and their locations. By considering three test cases, we show that using the combined data the method can localize sources tha... |
2206.07015 | Shuke Zhang | Shuke Zhang, Yanzhao Jin, Tianmeng Liu, Qi Wang, Zhaohui Zhang,
Shuliang Zhao, Bo Shan | SS-GNN: A Simple-Structured Graph Neural Network for Affinity Prediction | null | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Efficient and effective drug-target binding affinity (DTBA) prediction is a
challenging task due to the limited computational resources in practical
applications and is a crucial basis for drug screening. Inspired by the good
representation ability of graph neural networks (GNNs), we propose a
simple-structured GNN m... | [
{
"created": "Wed, 25 May 2022 04:47:13 GMT",
"version": "v1"
}
] | 2022-06-15 | [
[
"Zhang",
"Shuke",
""
],
[
"Jin",
"Yanzhao",
""
],
[
"Liu",
"Tianmeng",
""
],
[
"Wang",
"Qi",
""
],
[
"Zhang",
"Zhaohui",
""
],
[
"Zhao",
"Shuliang",
""
],
[
"Shan",
"Bo",
""
]
] | Efficient and effective drug-target binding affinity (DTBA) prediction is a challenging task due to the limited computational resources in practical applications and is a crucial basis for drug screening. Inspired by the good representation ability of graph neural networks (GNNs), we propose a simple-structured GNN mod... |
1605.02992 | David Richards | David M. Richards, Robert G. Endres | Target shape dependence in a simple model of receptor-mediated
endocytosis and phagocytosis | 18 pages, 5 figures | Proc Natl Acad Sci USA 113(22):6113-6118 (2016) | 10.1073/pnas.1521974113 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phagocytosis and receptor-mediated endocytosis are vitally important particle
uptake mechanisms in many cell types, ranging from single-cell organisms to
immune cells. In both processes, engulfment by the cell depends critically on
both particle shape and orientation. However, most previous theoretical work
has focus... | [
{
"created": "Tue, 10 May 2016 13:17:29 GMT",
"version": "v1"
}
] | 2016-06-02 | [
[
"Richards",
"David M.",
""
],
[
"Endres",
"Robert G.",
""
]
] | Phagocytosis and receptor-mediated endocytosis are vitally important particle uptake mechanisms in many cell types, ranging from single-cell organisms to immune cells. In both processes, engulfment by the cell depends critically on both particle shape and orientation. However, most previous theoretical work has focused... |
2008.12020 | Sayantari Ghosh | Sayantari Ghosh and Saumik Bhattacharya | A Data-driven Understanding of COVID-19 Dynamics Using Sequential
Genetic Algorithm Based Probabilistic Cellular Automata | 27 pages, 9 figures | null | null | null | q-bio.QM cs.LG cs.NE nlin.CG physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | COVID-19 pandemic is severely impacting the lives of billions across the
globe. Even after taking massive protective measures like nation-wide
lockdowns, discontinuation of international flight services, rigorous testing
etc., the infection spreading is still growing steadily, causing thousands of
deaths and serious ... | [
{
"created": "Thu, 27 Aug 2020 09:53:21 GMT",
"version": "v1"
}
] | 2020-08-28 | [
[
"Ghosh",
"Sayantari",
""
],
[
"Bhattacharya",
"Saumik",
""
]
] | COVID-19 pandemic is severely impacting the lives of billions across the globe. Even after taking massive protective measures like nation-wide lockdowns, discontinuation of international flight services, rigorous testing etc., the infection spreading is still growing steadily, causing thousands of deaths and serious so... |
2104.11844 | Brian Corneil | Sebastian J Lehmann and Brian D Corneil | Completing the puzzle: why studies in non-human primates are needed to
better understand the effects of non-invasive brain stimulation | 56 pages, 2 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Brain stimulation is a core method in neuroscience. Numerous non-invasive
brain stimulation (NIBS) techniques are currently in use in basic and clinical
research, and recent advances promise the ability to non-invasively access deep
brain structures. While encouraging, there is a surprising gap in our
understanding o... | [
{
"created": "Sat, 24 Apr 2021 00:31:06 GMT",
"version": "v1"
},
{
"created": "Mon, 1 Nov 2021 17:37:52 GMT",
"version": "v2"
}
] | 2021-11-02 | [
[
"Lehmann",
"Sebastian J",
""
],
[
"Corneil",
"Brian D",
""
]
] | Brain stimulation is a core method in neuroscience. Numerous non-invasive brain stimulation (NIBS) techniques are currently in use in basic and clinical research, and recent advances promise the ability to non-invasively access deep brain structures. While encouraging, there is a surprising gap in our understanding of ... |
1603.00200 | Javier Buldu | David Papo, Massimiliano Zanin, Johann H. Mart\'inez, and Javier M.
Buld\'u | Beware of the Small-World neuroscientist! | null | Front. Hum. Neurosci. 10:96 (2016) | 10.3389/fnhum.2016.00096 | null | q-bio.NC physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The SW has undeniably been one of the most popular network descriptors in the
neuroscience literature. Two main reasons for its lasting popularity are its
apparent ease of computation and the intuitions it is thought to provide on how
networked systems operate. Over the last few years, some pitfalls of the SW
constru... | [
{
"created": "Tue, 1 Mar 2016 09:44:36 GMT",
"version": "v1"
}
] | 2016-03-02 | [
[
"Papo",
"David",
""
],
[
"Zanin",
"Massimiliano",
""
],
[
"Martínez",
"Johann H.",
""
],
[
"Buldú",
"Javier M.",
""
]
] | The SW has undeniably been one of the most popular network descriptors in the neuroscience literature. Two main reasons for its lasting popularity are its apparent ease of computation and the intuitions it is thought to provide on how networked systems operate. Over the last few years, some pitfalls of the SW construct... |
1008.1273 | Anyou Wang | Anyou Wang, Hong Li | A Systemic Receptor Network Triggered by Human cytomegalovirus Entry | 26 pages | Advances in Virology Volume 2011 (2011), Article ID 262080, 11
pages | 10.1155/2011/262080 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Virus entry is a multistep process that triggers a variety of cellular
pathways interconnecting into a complex network, yet the molecular complexity
of this network remains largely unsolved. Here, by employing systems biology
approach, we reveal a systemic virus-entry network initiated by human
cytomegalovirus (HCMV)... | [
{
"created": "Fri, 6 Aug 2010 20:16:33 GMT",
"version": "v1"
}
] | 2011-05-17 | [
[
"Wang",
"Anyou",
""
],
[
"Li",
"Hong",
""
]
] | Virus entry is a multistep process that triggers a variety of cellular pathways interconnecting into a complex network, yet the molecular complexity of this network remains largely unsolved. Here, by employing systems biology approach, we reveal a systemic virus-entry network initiated by human cytomegalovirus (HCMV), ... |
1701.06349 | Aparna Rai | Aparna Rai, Priodyuti Pradhan, Jyothi Nagraj, K. Lohitesh, Rajdeep
Chowdhury, Sarika Jalan | Understanding cancer complexome using networks, spectral graph theory
and multilayer framework | 25 pages, 6 figures, accepted in scientific reports (in press) | null | 10.1038/srep41676 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cancer complexome comprises a heterogeneous and multifactorial milieu that
varies in cytology, physiology, signaling mechanisms and response to therapy.
The combined framework of network theory and spectral graph theory along with
the multilayer anal- ysis provides a comprehensive approach to analyze the
proteomic da... | [
{
"created": "Mon, 23 Jan 2017 11:56:06 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Mar 2017 05:46:16 GMT",
"version": "v2"
}
] | 2017-03-03 | [
[
"Rai",
"Aparna",
""
],
[
"Pradhan",
"Priodyuti",
""
],
[
"Nagraj",
"Jyothi",
""
],
[
"Lohitesh",
"K.",
""
],
[
"Chowdhury",
"Rajdeep",
""
],
[
"Jalan",
"Sarika",
""
]
] | Cancer complexome comprises a heterogeneous and multifactorial milieu that varies in cytology, physiology, signaling mechanisms and response to therapy. The combined framework of network theory and spectral graph theory along with the multilayer anal- ysis provides a comprehensive approach to analyze the proteomic data... |
1402.3632 | Benjamin Good | Benjamin M. Good, Salvatore Loguercio, Obi L. Griffith, Max Nanis,
Chunlei Wu, Andrew I. Su | The Cure: Making a game of gene selection for breast cancer survival
prediction | null | Good BM, Loguercio S, Griffith OL, Nanis M, Wu C, Su AI The Cure:
Design and Evaluation of a Crowdsourcing Game for Gene Selection for Breast
Cancer Survival Prediction JMIR Serious Games 2014;2(2):e7 | 10.2196/games.3350 | null | q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by/3.0/ | Motivation: Molecular signatures for predicting breast cancer prognosis could
greatly improve care through personalization of treatment. Computational
analyses of genome-wide expression datasets have identified such signatures,
but these signatures leave much to be desired in terms of accuracy,
reproducibility and bi... | [
{
"created": "Sat, 15 Feb 2014 01:07:23 GMT",
"version": "v1"
}
] | 2014-07-31 | [
[
"Good",
"Benjamin M.",
""
],
[
"Loguercio",
"Salvatore",
""
],
[
"Griffith",
"Obi L.",
""
],
[
"Nanis",
"Max",
""
],
[
"Wu",
"Chunlei",
""
],
[
"Su",
"Andrew I.",
""
]
] | Motivation: Molecular signatures for predicting breast cancer prognosis could greatly improve care through personalization of treatment. Computational analyses of genome-wide expression datasets have identified such signatures, but these signatures leave much to be desired in terms of accuracy, reproducibility and biol... |
2209.10545 | Niloofar Aghaieabiane | Niloofar Aghaieabiane and Ioannis Koutis | SGC: A semi-supervised pipeline for gene clustering using self-training
approach in gene co-expression networks | null | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A widely used approach for extracting information from gene expression data
employ the construction of a gene co-expression network and the subsequent
application of algorithms that discover network structure. In particular, a
common goal is the computational discovery of gene clusters, commonly called
modules. When ... | [
{
"created": "Wed, 21 Sep 2022 14:51:08 GMT",
"version": "v1"
}
] | 2022-09-23 | [
[
"Aghaieabiane",
"Niloofar",
""
],
[
"Koutis",
"Ioannis",
""
]
] | A widely used approach for extracting information from gene expression data employ the construction of a gene co-expression network and the subsequent application of algorithms that discover network structure. In particular, a common goal is the computational discovery of gene clusters, commonly called modules. When ap... |
2305.14404 | Shuqiang Wang | Qiankun Zuo, Baiying Lei, Ning Zhong, Yi Pan, Shuqiang Wang | Brain Structure-Function Fusing Representation Learning using
Adversarial Decomposed-VAE for Analyzing MCI | null | null | null | null | q-bio.NC cs.AI cs.LG eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Integrating the brain structural and functional connectivity features is of
great significance in both exploring brain science and analyzing cognitive
impairment clinically. However, it remains a challenge to effectively fuse
structural and functional features in exploring the brain network. In this
paper, a novel br... | [
{
"created": "Tue, 23 May 2023 11:19:02 GMT",
"version": "v1"
}
] | 2023-05-25 | [
[
"Zuo",
"Qiankun",
""
],
[
"Lei",
"Baiying",
""
],
[
"Zhong",
"Ning",
""
],
[
"Pan",
"Yi",
""
],
[
"Wang",
"Shuqiang",
""
]
] | Integrating the brain structural and functional connectivity features is of great significance in both exploring brain science and analyzing cognitive impairment clinically. However, it remains a challenge to effectively fuse structural and functional features in exploring the brain network. In this paper, a novel brai... |
1907.00249 | Jude Kong | Christina P. Tadiri, Jude D. Kong, Gregor F. Fussmann, Marilyn E.
Scott, and Hao Wang | A Data-Validated Host-Parasite Model for Infectious Disease Outbreaks | * Equally contributing first authors | null | 10.3389/fevo.2019.00307 | null | q-bio.PE math.DS stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The use of model experimental systems and mathematical models is important to
further understanding of infectious disease dynamics and strategize disease
mitigation. Gyrodactylids are helminth ectoparasites of teleost fish which have
many dynamical characteristics of microparasites but offer the advantage that
they c... | [
{
"created": "Sat, 29 Jun 2019 18:21:46 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Aug 2019 17:12:46 GMT",
"version": "v2"
}
] | 2019-08-30 | [
[
"Tadiri",
"Christina P.",
""
],
[
"Kong",
"Jude D.",
""
],
[
"Fussmann",
"Gregor F.",
""
],
[
"Scott",
"Marilyn E.",
""
],
[
"Wang",
"Hao",
""
]
] | The use of model experimental systems and mathematical models is important to further understanding of infectious disease dynamics and strategize disease mitigation. Gyrodactylids are helminth ectoparasites of teleost fish which have many dynamical characteristics of microparasites but offer the advantage that they can... |
1903.07308 | Toni Giorgino | Toni Giorgino, Davide Mattioni, Amal Hassan, Mario Milani, Eloise
Mastrangelo, Alberto Barbiroli, Adriaan Verhelle, Jan Gettemans, Maria Monica
Barzago, Luisa Diomede, Matteo de Rosa | Nanobody interaction unveils structure, dynamics and proteotoxicity of
the Finnish-type amyloidogenic gelsolin variant | null | Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease.
Volume 1865, Issue 3, 1 March 2019, Pages 648-660 | 10.1016/j.bbadis.2019.01.010 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | AGel amyloidosis, formerly known as familial amyloidosis of the Finnish-type,
is caused by pathological aggregation of proteolytic fragments of plasma
gelsolin. So far, four mutations in the gelsolin gene have been reported as
responsible for the disease. Although D187N is the first identified variant and
the best ch... | [
{
"created": "Mon, 18 Mar 2019 08:50:30 GMT",
"version": "v1"
}
] | 2019-03-19 | [
[
"Giorgino",
"Toni",
""
],
[
"Mattioni",
"Davide",
""
],
[
"Hassan",
"Amal",
""
],
[
"Milani",
"Mario",
""
],
[
"Mastrangelo",
"Eloise",
""
],
[
"Barbiroli",
"Alberto",
""
],
[
"Verhelle",
"Adriaan",
""
],... | AGel amyloidosis, formerly known as familial amyloidosis of the Finnish-type, is caused by pathological aggregation of proteolytic fragments of plasma gelsolin. So far, four mutations in the gelsolin gene have been reported as responsible for the disease. Although D187N is the first identified variant and the best char... |
1404.7791 | Alexander Iomin | A. Iomin | Maximum therapeutic effect of glioma treatment by radio-frequency
electric field | Published in Chaos, Solitons & Fractals (2014) | null | 10.1016/j.chaos.2014.11.020 | null | q-bio.CB cond-mat.stat-mech physics.bio-ph physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An influence of a radio-frequency electric field on glioma - brain cancer
development is considered. A specific task emerging here is whether this new
medical technology is effective against invasive cells with a high motility,
when switching between migrating and proliferating phenotypes takes place. This
therapeuti... | [
{
"created": "Wed, 30 Apr 2014 16:41:56 GMT",
"version": "v1"
},
{
"created": "Sat, 13 Dec 2014 10:22:00 GMT",
"version": "v2"
}
] | 2015-06-19 | [
[
"Iomin",
"A.",
""
]
] | An influence of a radio-frequency electric field on glioma - brain cancer development is considered. A specific task emerging here is whether this new medical technology is effective against invasive cells with a high motility, when switching between migrating and proliferating phenotypes takes place. This therapeutic ... |
2403.14741 | Alexei Vazquez | Alexei Vazquez | Selective advantage of aerobic glycolysis over oxidative phosphorylation | 4 pages, 1 table | null | null | null | q-bio.BM physics.bio-ph q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | The utilization of glycolysis in aerobic conditions have been a subject of
debate for more than a century. A hypothesis supported by previous data is that
glycolysis has a higher rate of ATP production per protein mass and per
occupied volume than oxidative phosphorylation (OxPhos). However, a recent work
by Shen et ... | [
{
"created": "Thu, 21 Mar 2024 17:53:31 GMT",
"version": "v1"
}
] | 2024-03-25 | [
[
"Vazquez",
"Alexei",
""
]
] | The utilization of glycolysis in aerobic conditions have been a subject of debate for more than a century. A hypothesis supported by previous data is that glycolysis has a higher rate of ATP production per protein mass and per occupied volume than oxidative phosphorylation (OxPhos). However, a recent work by Shen et al... |
2202.12711 | Mansoor Haider | Mansoor A. Haider, Katherine J. Pearce, Naomi C. Chesler, Nicholas A.
Hill and Mette S. Olufsen | Application and reduction of a nonlinear hyperelastic wall model
capturing ex vivo relationships between fluid pressure, area and wall
thickness in normal and hypertensive murine left pulmonary arteries | null | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Pulmonary hypertension is a cardiovascular disorder manifested by elevated
arterial blood pressure together with vessel wall stiffening and thickening due
to alterations in collagen, elastin and smooth muscle cells. Hypoxia-induced
(type 3) pulmonary hypertension can be studied in animals exposed to a low
oxygen envi... | [
{
"created": "Fri, 11 Feb 2022 17:35:28 GMT",
"version": "v1"
}
] | 2022-02-28 | [
[
"Haider",
"Mansoor A.",
""
],
[
"Pearce",
"Katherine J.",
""
],
[
"Chesler",
"Naomi C.",
""
],
[
"Hill",
"Nicholas A.",
""
],
[
"Olufsen",
"Mette S.",
""
]
] | Pulmonary hypertension is a cardiovascular disorder manifested by elevated arterial blood pressure together with vessel wall stiffening and thickening due to alterations in collagen, elastin and smooth muscle cells. Hypoxia-induced (type 3) pulmonary hypertension can be studied in animals exposed to a low oxygen enviro... |
1402.0042 | Dennis Kostka | Dennis Kostka, Tara Friedrich, Alisha K. Holloway, Katherine S.
Pollard | motifDiverge: a model for assessing the statistical significance of gene
regulatory motif divergence between two DNA sequences | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Next-generation sequencing technology enables the identification of thousands
of gene regulatory sequences in many cell types and organisms. We consider the
problem of testing if two such sequences differ in their number of binding site
motifs for a given transcription factor (TF) protein. Binding site motifs
impart ... | [
{
"created": "Sat, 1 Feb 2014 02:00:16 GMT",
"version": "v1"
}
] | 2014-02-04 | [
[
"Kostka",
"Dennis",
""
],
[
"Friedrich",
"Tara",
""
],
[
"Holloway",
"Alisha K.",
""
],
[
"Pollard",
"Katherine S.",
""
]
] | Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site motifs for a given transcription factor (TF) protein. Binding site motifs impart re... |
2101.08860 | Jingyi Jessica Li | Nan Miles Xi and Jingyi Jessica Li | Protocol for Executing and Benchmarking Eight Computational
Doublet-Detection Methods in Single-Cell RNA Sequencing Data Analysis | null | STAR Protocols 2(3) (2021) 100699 | 10.1016/j.xpro.2021.100699 | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The existence of doublets is a key confounder in single-cell RNA sequencing
(scRNA-seq) data analysis. Computational methods have been developed for
detecting doublets from scRNA-seq data. We developed an R package
DoubletCollection to integrate the installation and execution of eight
doublet-detection methods. Doubl... | [
{
"created": "Thu, 21 Jan 2021 21:38:36 GMT",
"version": "v1"
},
{
"created": "Thu, 3 Jun 2021 01:21:49 GMT",
"version": "v2"
},
{
"created": "Fri, 25 Jun 2021 22:30:51 GMT",
"version": "v3"
}
] | 2021-12-01 | [
[
"Xi",
"Nan Miles",
""
],
[
"Li",
"Jingyi Jessica",
""
]
] | The existence of doublets is a key confounder in single-cell RNA sequencing (scRNA-seq) data analysis. Computational methods have been developed for detecting doublets from scRNA-seq data. We developed an R package DoubletCollection to integrate the installation and execution of eight doublet-detection methods. Doublet... |
1703.03441 | Indika Rajapakse | Scott Ronquist, Geoff Patterson, Markus Brown, Haiming Chen, Anthony
Bloch, Lindsey Muir, Roger Brockett, Indika Rajapakse | An Algorithm for Cellular Reprogramming | null | null | 10.1073/pnas.1712350114 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The day we understand the time evolution of subcellular elements at a level
of detail comparable to physical systems governed by Newton's laws of motion
seems far away. Even so, quantitative approaches to cellular dynamics add to
our understanding of cell biology, providing data-guided frameworks that allow
us to dev... | [
{
"created": "Thu, 9 Mar 2017 19:49:58 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Jul 2017 01:24:38 GMT",
"version": "v2"
}
] | 2022-06-08 | [
[
"Ronquist",
"Scott",
""
],
[
"Patterson",
"Geoff",
""
],
[
"Brown",
"Markus",
""
],
[
"Chen",
"Haiming",
""
],
[
"Bloch",
"Anthony",
""
],
[
"Muir",
"Lindsey",
""
],
[
"Brockett",
"Roger",
""
],
[
"... | The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology, providing data-guided frameworks that allow us to devel... |
1301.0209 | Fabio Lorenzo Traversa Ph.D. | Fabio Lorenzo Traversa, Yuriy V. Pershin, Massimiliano Di Ventra | Memory models of adaptive behaviour | null | IEEE Transactions on Neural Networks and Learning Systems, vol.
24, is. 9, pg. 1437 - 1448, year 2013 | 10.1109/TNNLS.2013.2261545 | null | q-bio.CB cond-mat.other nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Adaptive response to a varying environment is a common feature of biological
organisms. Reproducing such features in electronic systems and circuits is of
great importance for a variety of applications. Here, we consider memory models
inspired by an intriguing ability of slime molds to both memorize the period of
tem... | [
{
"created": "Wed, 2 Jan 2013 11:06:36 GMT",
"version": "v1"
},
{
"created": "Thu, 2 May 2013 00:18:00 GMT",
"version": "v2"
}
] | 2013-10-29 | [
[
"Traversa",
"Fabio Lorenzo",
""
],
[
"Pershin",
"Yuriy V.",
""
],
[
"Di Ventra",
"Massimiliano",
""
]
] | Adaptive response to a varying environment is a common feature of biological organisms. Reproducing such features in electronic systems and circuits is of great importance for a variety of applications. Here, we consider memory models inspired by an intriguing ability of slime molds to both memorize the period of tempe... |
2312.17513 | Jessica Dubois | Jessica Dubois (CEA, INSERM) | Multi-modal MRI sensitive to age: Focus on early brain development in
infants | null | Handbook of Pediatric Brain Imaging: Methods and Applications,
2021, 978-0128166338 | null | null | q-bio.NC eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Exploring the developing brain is a major issue in understanding what enables
children to acquire amazing abilities, and how early disruptions can lead to a
wide range of neurodevelopmental disorders. MRI plays a key role here by
providing a non-invasive way to link brain and behavioral changes. Several
modalities ar... | [
{
"created": "Fri, 29 Dec 2023 08:20:48 GMT",
"version": "v1"
}
] | 2024-01-01 | [
[
"Dubois",
"Jessica",
"",
"CEA, INSERM"
]
] | Exploring the developing brain is a major issue in understanding what enables children to acquire amazing abilities, and how early disruptions can lead to a wide range of neurodevelopmental disorders. MRI plays a key role here by providing a non-invasive way to link brain and behavioral changes. Several modalities are ... |
2212.08638 | Saskia De Vries | Saskia E. J. de Vries, Joshua H. Siegle, Christof Koch | Sharing Neurophysiology Data from the Allen Brain Observatory: Lessons
Learned | 20 pages, 4 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Making all data for any observation or experiment openly available is a
defining feature of empirical science (e.g., nullius in verba, the motto of the
Royal Society). It enhances transparency, reproducibility, and societal trust.
While embraced in spirit by many, in practice open data sharing remains the
exception i... | [
{
"created": "Fri, 16 Dec 2022 18:30:47 GMT",
"version": "v1"
}
] | 2022-12-19 | [
[
"de Vries",
"Saskia E. J.",
""
],
[
"Siegle",
"Joshua H.",
""
],
[
"Koch",
"Christof",
""
]
] | Making all data for any observation or experiment openly available is a defining feature of empirical science (e.g., nullius in verba, the motto of the Royal Society). It enhances transparency, reproducibility, and societal trust. While embraced in spirit by many, in practice open data sharing remains the exception in ... |
2104.01457 | Mar\'ia Vallet-Regi | R.Diez-Orejas, L.Casarrubios, M.J. Feito, J.M.Rojo, M.Vallet-Regi,
D.Arcos, M.T.Portoles | Effects of mesoporous SiO2-CaO nanospheres on the murine peritoneal
macrophages -- Candida albicans interface | 35 pages, 6 figures | Int Immunopharmacol International Immunopharmacology. 2021 Mar
20;94:107457 | 10.1016/j.intimp.2021.107457 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The use of nanoparticles for intracellular drug delivery could reduce the
toxicity and side effects of the drug but, the uptake of these nanocarriers
could induce adverse effects on cells and tissues after their incorporation.
Macrophages play a central role in host defense and are responsible for in vivo
nanoparticl... | [
{
"created": "Sat, 3 Apr 2021 18:08:28 GMT",
"version": "v1"
}
] | 2021-04-06 | [
[
"Diez-Orejas",
"R.",
""
],
[
"Casarrubios",
"L.",
""
],
[
"Feito",
"M. J.",
""
],
[
"Rojo",
"J. M.",
""
],
[
"Vallet-Regi",
"M.",
""
],
[
"Arcos",
"D.",
""
],
[
"Portoles",
"M. T.",
""
]
] | The use of nanoparticles for intracellular drug delivery could reduce the toxicity and side effects of the drug but, the uptake of these nanocarriers could induce adverse effects on cells and tissues after their incorporation. Macrophages play a central role in host defense and are responsible for in vivo nanoparticle ... |
q-bio/0507034 | Leonard M. Sander | Evgeniy Khain and Leonard M. Sander | Dynamics and pattern formation in invasive tumor growth | 4 pages, 4 figures | null | 10.1103/PhysRevLett.96.188103 | null | q-bio.CB | null | In this work, we study the in-vitro dynamics of the most malignant form of
the primary brain tumor: Glioblastoma Multiforme. Typically, the growing tumor
consists of the inner dense proliferating zone and the outer less dense
invasive region. Experiments with different types of cells show qualitatively
different beha... | [
{
"created": "Fri, 22 Jul 2005 16:36:33 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Khain",
"Evgeniy",
""
],
[
"Sander",
"Leonard M.",
""
]
] | In this work, we study the in-vitro dynamics of the most malignant form of the primary brain tumor: Glioblastoma Multiforme. Typically, the growing tumor consists of the inner dense proliferating zone and the outer less dense invasive region. Experiments with different types of cells show qualitatively different behavi... |
1505.06440 | Kimberly Glass | Marieke Lydia Kuijjer, Matthew Tung, GuoCheng Yuan, John Quackenbush,
Kimberly Glass | Estimating sample-specific regulatory networks | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Biological systems are driven by intricate interactions among the complex
array of molecules that comprise the cell. Many methods have been developed to
reconstruct network models of those interactions. These methods often draw on
large numbers of samples with measured gene expression profiles to infer
connections be... | [
{
"created": "Sun, 24 May 2015 13:45:51 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Jun 2018 15:24:31 GMT",
"version": "v2"
}
] | 2018-06-29 | [
[
"Kuijjer",
"Marieke Lydia",
""
],
[
"Tung",
"Matthew",
""
],
[
"Yuan",
"GuoCheng",
""
],
[
"Quackenbush",
"John",
""
],
[
"Glass",
"Kimberly",
""
]
] | Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large numbers of samples with measured gene expression profiles to infer connections betw... |
1610.02395 | Salvador Malo | Salvador Malo | Causal-order superposition as an enabler of free will | 6 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is often argued that bottom-up causation under a physicalist, reductionist
worldview precludes free will in the libertarian sense. On the one hand, the
paradigm of classical mechanics makes determinism inescapable, while on the
other, the leading models that allow a role for quantum effects are
noncommittal regard... | [
{
"created": "Sat, 8 Oct 2016 00:39:25 GMT",
"version": "v1"
}
] | 2016-10-11 | [
[
"Malo",
"Salvador",
""
]
] | It is often argued that bottom-up causation under a physicalist, reductionist worldview precludes free will in the libertarian sense. On the one hand, the paradigm of classical mechanics makes determinism inescapable, while on the other, the leading models that allow a role for quantum effects are noncommittal regardin... |
2002.00200 | Bob Eisenberg | Robert S. Eisenberg | Energetic Controls are Essential: New and Notable Note for Biophysical
Journal | Biophysical Journal (2020) | null | 101.1016/j.bpj.2020.01.029 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mikhail Shapiro's lab investigated a promising new method for non-invasive
control of calcium currents in individual cells in the nervous system by the
selective heating of nanoparticles and show that simple physical laws, properly
applied, explain what is happening, and so can be a foundation for constructing
improv... | [
{
"created": "Sat, 1 Feb 2020 12:41:31 GMT",
"version": "v1"
}
] | 2020-06-16 | [
[
"Eisenberg",
"Robert S.",
""
]
] | Mikhail Shapiro's lab investigated a promising new method for non-invasive control of calcium currents in individual cells in the nervous system by the selective heating of nanoparticles and show that simple physical laws, properly applied, explain what is happening, and so can be a foundation for constructing improved... |
2407.09100 | Polina Turishcheva | Polina Turishcheva, Paul G. Fahey, Michaela Vystr\v{c}ilov\'a, Laura
Hansel, Rachel Froebe, Kayla Ponder, Yongrong Qiu, Konstantin F. Willeke,
Mohammad Bashiri, Ruslan Baikulov, Yu Zhu, Lei Ma, Shan Yu, Tiejun Huang,
Bryan M. Li, Wolf De Wulf, Nina Kudryashova, Matthias H. Hennig, Nathalie L.
Rochefort, Arno On... | Retrospective for the Dynamic Sensorium Competition for predicting
large-scale mouse primary visual cortex activity from videos | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Understanding how biological visual systems process information is
challenging because of the nonlinear relationship between visual input and
neuronal responses. Artificial neural networks allow computational
neuroscientists to create predictive models that connect biological and machine
vision. Machine learning has ... | [
{
"created": "Fri, 12 Jul 2024 09:02:10 GMT",
"version": "v1"
}
] | 2024-07-15 | [
[
"Turishcheva",
"Polina",
""
],
[
"Fahey",
"Paul G.",
""
],
[
"Vystrčilová",
"Michaela",
""
],
[
"Hansel",
"Laura",
""
],
[
"Froebe",
"Rachel",
""
],
[
"Ponder",
"Kayla",
""
],
[
"Qiu",
"Yongrong",
""
],
... | Understanding how biological visual systems process information is challenging because of the nonlinear relationship between visual input and neuronal responses. Artificial neural networks allow computational neuroscientists to create predictive models that connect biological and machine vision. Machine learning has be... |
2007.05228 | Vo Hong Thanh | Vo Hong Thanh, Dani Korpela and Pekka Orponen | Cotranscriptional kinetic folding of RNA secondary structures including
pseudoknots | 20 pages, 15 figures | Journal of Computational Biology, 2021 | 10.1089/cmb.2020.0606 | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Computational prediction of RNA structures is an important problem in
computational structural biology. Studies of RNA structure formation often
assume that the process starts from a fully synthesized sequence. Experimental
evidence, however, has shown that RNA folds concurrently with its elongation.
We investigate R... | [
{
"created": "Fri, 10 Jul 2020 08:06:15 GMT",
"version": "v1"
},
{
"created": "Tue, 1 Dec 2020 10:28:31 GMT",
"version": "v2"
},
{
"created": "Tue, 8 Dec 2020 15:17:37 GMT",
"version": "v3"
},
{
"created": "Sun, 21 Feb 2021 12:53:10 GMT",
"version": "v4"
},
{
"cre... | 2021-04-28 | [
[
"Thanh",
"Vo Hong",
""
],
[
"Korpela",
"Dani",
""
],
[
"Orponen",
"Pekka",
""
]
] | Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence, however, has shown that RNA folds concurrently with its elongation. We investigate RNA... |
2208.04186 | Maciej Roso{\l} | Maciej Roso{\l}, Jakub S. G\k{a}sior, Iwona Walecka, Bo\.zena Werner,
Gerard Cybulski, Marcel M{\l}y\'nczak | Causality in cardiorespiratory signals in pediatric cardiac patients | Accepted for the 44th International Engineering in Medicine and
Biology Conference, EMBC 2022, organized by IEEE Engineering in Medicine and
Biology Society | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Four different Granger causality-based methods - one linear and three
nonlinear (Granger Causality, Kernel Granger Causality, large-scale Nonlinear
Granger Causality, and Neural Network Granger Causality) were used for
assessment and causal-based quantification of the respiratory sinus arrythmia
(RSA) in the group of... | [
{
"created": "Fri, 5 Aug 2022 09:24:46 GMT",
"version": "v1"
}
] | 2022-08-09 | [
[
"Rosoł",
"Maciej",
""
],
[
"Gąsior",
"Jakub S.",
""
],
[
"Walecka",
"Iwona",
""
],
[
"Werner",
"Bożena",
""
],
[
"Cybulski",
"Gerard",
""
],
[
"Młyńczak",
"Marcel",
""
]
] | Four different Granger causality-based methods - one linear and three nonlinear (Granger Causality, Kernel Granger Causality, large-scale Nonlinear Granger Causality, and Neural Network Granger Causality) were used for assessment and causal-based quantification of the respiratory sinus arrythmia (RSA) in the group of p... |
2004.13017 | Karl Friston | Karl J. Friston, Thomas Parr, Peter Zeidman, Adeel Razi, Guillaume
Flandin, Jean Daunizeau, Oliver J. Hulme, Alexander J. Billig, Vladimir
Litvak, Cathy J. Price, Rosalyn J. Moran and Christian Lambert | Second waves, social distancing, and the spread of COVID-19 across
America | Technical report: 35 pages, 14 figures, 1 table | null | null | null | q-bio.PE q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | We recently described a dynamic causal model of a COVID-19 outbreak within a
single region. Here, we combine several of these (epidemic) models to create a
(pandemic) model of viral spread among regions. Our focus is on a second wave
of new cases that may result from loss of immunity--and the exchange of people
betwe... | [
{
"created": "Sun, 26 Apr 2020 14:38:29 GMT",
"version": "v1"
}
] | 2020-04-29 | [
[
"Friston",
"Karl J.",
""
],
[
"Parr",
"Thomas",
""
],
[
"Zeidman",
"Peter",
""
],
[
"Razi",
"Adeel",
""
],
[
"Flandin",
"Guillaume",
""
],
[
"Daunizeau",
"Jean",
""
],
[
"Hulme",
"Oliver J.",
""
],
[
... | We recently described a dynamic causal model of a COVID-19 outbreak within a single region. Here, we combine several of these (epidemic) models to create a (pandemic) model of viral spread among regions. Our focus is on a second wave of new cases that may result from loss of immunity--and the exchange of people between... |
2401.15727 | Francisco Torres-Ruiz | Antonio Di Crescenzo, Paola Paraggio, Patricia Rom\'an-Rom\'an,
Francisco Torres-Ruiz | Applications of the multi-sigmoidal deterministic and stochastic
logistic models for plant dynamics | 28 pages, 30 figures | Applied Mathematical Modelling, 92, 2021,884-904 | 10.1016/j.apm.2020.11.046 | null | q-bio.PE math.PR | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We consider a generalization of the classical logistic growth model
introducing more than one inflection point. The growth, called multi-sigmoidal,
is firstly analyzed from a deterministic point of view in order to obtain the
main properties of the curve, such as the limit behavior, the inflection points
and the thre... | [
{
"created": "Sun, 28 Jan 2024 18:43:50 GMT",
"version": "v1"
}
] | 2024-01-31 | [
[
"Di Crescenzo",
"Antonio",
""
],
[
"Paraggio",
"Paola",
""
],
[
"Román-Román",
"Patricia",
""
],
[
"Torres-Ruiz",
"Francisco",
""
]
] | We consider a generalization of the classical logistic growth model introducing more than one inflection point. The growth, called multi-sigmoidal, is firstly analyzed from a deterministic point of view in order to obtain the main properties of the curve, such as the limit behavior, the inflection points and the thresh... |
2206.04915 | \'Eric Herbert | Clara Ledoux, Florence Chapeland-Leclerc, Gwena\"el Ruprich-Robert,
C\'ecilia Bob\'ee, Christophe Lalanne, \'Eric Herbert, Pascal David | Prediction and experimental evidence of the optimisation of the angular
branching process in the thallus growth of Podospora anserina | Submitted to Scientific Report | null | 10.1038/s41598-022-16245-9 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Based upon apical growth and hyphal branching, the two main processes that
drive the growth pattern of a fungal network, we propose here a two-dimensions
simulation based on a binary-tree modelling allowing us to extract the main
characteristics of a generic thallus growth. In particular, we showed that, in
a homogen... | [
{
"created": "Fri, 10 Jun 2022 07:29:20 GMT",
"version": "v1"
}
] | 2022-07-21 | [
[
"Ledoux",
"Clara",
""
],
[
"Chapeland-Leclerc",
"Florence",
""
],
[
"Ruprich-Robert",
"Gwenaël",
""
],
[
"Bobée",
"Cécilia",
""
],
[
"Lalanne",
"Christophe",
""
],
[
"Herbert",
"Éric",
""
],
[
"David",
"Pascal"... | Based upon apical growth and hyphal branching, the two main processes that drive the growth pattern of a fungal network, we propose here a two-dimensions simulation based on a binary-tree modelling allowing us to extract the main characteristics of a generic thallus growth. In particular, we showed that, in a homogeneo... |
1701.02988 | Dmitri Parkhomchuk | Alexey A. Shadrin and Dmitri V. Parkhomchuk | Darwinian Genetic Drift | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genetic drift is stochastic fluctuations of alleles frequencies in a
population due to sampling effects. We consider a model of drift in an
equilibrium population, with high mutation rates: few functional mutations per
generation. Such mutation rates are common in multicellular organisms including
humans, however the... | [
{
"created": "Wed, 11 Jan 2017 14:36:41 GMT",
"version": "v1"
}
] | 2017-01-12 | [
[
"Shadrin",
"Alexey A.",
""
],
[
"Parkhomchuk",
"Dmitri V.",
""
]
] | Genetic drift is stochastic fluctuations of alleles frequencies in a population due to sampling effects. We consider a model of drift in an equilibrium population, with high mutation rates: few functional mutations per generation. Such mutation rates are common in multicellular organisms including humans, however they ... |
1304.5947 | Carsten Baldauf | Carsten Baldauf, Kevin Pagel, Stephan Warnke, Gert von Helden, Beate
Koksch, Volker Blum, Matthias Scheffler | How Cations Change Peptide Structure | 30 pages, 7 figures | Chem. Eur. J. 2013 (19) 11224-11234 | 10.1002/chem.201204554 | null | q-bio.BM physics.bio-ph physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Specific interactions between cations and proteins have a strong impact on
peptide and protein structure. We here shed light on the nature of the
underlying interactions, especially regarding the effects on the polyamide
backbone structure. To do so, we compare the conformational ensembles of model
peptides in isolat... | [
{
"created": "Mon, 22 Apr 2013 13:35:15 GMT",
"version": "v1"
},
{
"created": "Mon, 29 Apr 2013 11:21:38 GMT",
"version": "v2"
}
] | 2013-08-27 | [
[
"Baldauf",
"Carsten",
""
],
[
"Pagel",
"Kevin",
""
],
[
"Warnke",
"Stephan",
""
],
[
"von Helden",
"Gert",
""
],
[
"Koksch",
"Beate",
""
],
[
"Blum",
"Volker",
""
],
[
"Scheffler",
"Matthias",
""
]
] | Specific interactions between cations and proteins have a strong impact on peptide and protein structure. We here shed light on the nature of the underlying interactions, especially regarding the effects on the polyamide backbone structure. To do so, we compare the conformational ensembles of model peptides in isolatio... |
1501.06947 | Vahid Salari | Vahid Salari, Felix Scholkmann, Farhad Shahbazi, Istvan Bokkon, Jack
Tuszynski | Comment on Activation of Visual Pigments by Light and Heat (Science 332,
1307-312, 2011) | 7 pages, 3 figures | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is known that the Arrhenius equation, based on the Boltzmann distribution,
can model only a part (e.g. half of the activation energy) for retinal discrete
dark noise observed for vertebrate rod and cone pigments. Luo et al (Science,
332, 1307-312, 2011) presented a new approach to explain this discrepancy by
showi... | [
{
"created": "Tue, 27 Jan 2015 22:12:19 GMT",
"version": "v1"
},
{
"created": "Thu, 14 May 2015 21:57:52 GMT",
"version": "v2"
}
] | 2015-05-18 | [
[
"Salari",
"Vahid",
""
],
[
"Scholkmann",
"Felix",
""
],
[
"Shahbazi",
"Farhad",
""
],
[
"Bokkon",
"Istvan",
""
],
[
"Tuszynski",
"Jack",
""
]
] | It is known that the Arrhenius equation, based on the Boltzmann distribution, can model only a part (e.g. half of the activation energy) for retinal discrete dark noise observed for vertebrate rod and cone pigments. Luo et al (Science, 332, 1307-312, 2011) presented a new approach to explain this discrepancy by showing... |
2110.15066 | Vitaly Vanchurin | Vitaly Vanchurin, Yuri I. Wolf, Eugene V. Koonin, Mikhail I.
Katsnelson | Thermodynamics of Evolution and the Origin of Life | 23 pages | null | 10.1073/pnas.2120042119 | null | q-bio.PE cond-mat.dis-nn cond-mat.stat-mech cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We outline a phenomenological theory of evolution and origin of life by
combining the formalism of classical thermodynamics with a statistical
description of learning. The maximum entropy principle constrained by the
requirement for minimization of the loss function is employed to derive a
canonical ensemble of organ... | [
{
"created": "Thu, 28 Oct 2021 12:27:33 GMT",
"version": "v1"
}
] | 2022-10-12 | [
[
"Vanchurin",
"Vitaly",
""
],
[
"Wolf",
"Yuri I.",
""
],
[
"Koonin",
"Eugene V.",
""
],
[
"Katsnelson",
"Mikhail I.",
""
]
] | We outline a phenomenological theory of evolution and origin of life by combining the formalism of classical thermodynamics with a statistical description of learning. The maximum entropy principle constrained by the requirement for minimization of the loss function is employed to derive a canonical ensemble of organis... |
1712.05182 | Giuditta Franco | Giuditta Franco, Francesco Bellamoli, and Silvia Lampis | Experimental Analysis of XPCR-based protocols | 14 pages, 10 figures, experimental results, not yet published | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper reports some experimental results validating in a broader context
a variant of PCR, called XPCR, previously introduced and tested on relatively
short synthetic DNA sequences. Basic XPCR technique confirmed to work as
expected, to concatenate two genes of different lengths, while a library of all
permutatio... | [
{
"created": "Thu, 14 Dec 2017 11:40:19 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Dec 2017 14:58:32 GMT",
"version": "v2"
}
] | 2017-12-18 | [
[
"Franco",
"Giuditta",
""
],
[
"Bellamoli",
"Francesco",
""
],
[
"Lampis",
"Silvia",
""
]
] | This paper reports some experimental results validating in a broader context a variant of PCR, called XPCR, previously introduced and tested on relatively short synthetic DNA sequences. Basic XPCR technique confirmed to work as expected, to concatenate two genes of different lengths, while a library of all permutations... |
1605.01421 | Stefan Widgren | Stefan Widgren, Pavol Bauer, Robin Eriksson, Stefan Engblom | SimInf: An R package for Data-driven Stochastic Disease Spread
Simulations | The manual has been updated to the latest version of SimInf (v6.0.0).
41 pages, 16 figures | J. Stat. Softw., 91(12):1--42 (2019) | 10.18637/jss.v091.i12 | null | q-bio.PE stat.AP stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present the R package SimInf which provides an efficient and very flexible
framework to conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates infection dynamics
in subpopulations as continuous-time Markov chains using the Gillespie
stochastic sim... | [
{
"created": "Wed, 4 May 2016 20:16:20 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Jun 2017 19:04:00 GMT",
"version": "v2"
},
{
"created": "Thu, 3 May 2018 16:56:46 GMT",
"version": "v3"
}
] | 2021-08-10 | [
[
"Widgren",
"Stefan",
""
],
[
"Bauer",
"Pavol",
""
],
[
"Eriksson",
"Robin",
""
],
[
"Engblom",
"Stefan",
""
]
] | We present the R package SimInf which provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simul... |
1711.02448 | Rui Ponte Costa | Rui Ponte Costa, Yannis M. Assael, Brendan Shillingford, Nando de
Freitas and Tim P. Vogels | Cortical microcircuits as gated-recurrent neural networks | To appear in Advances in Neural Information Processing Systems 30
(NIPS 2017). 13 pages, 2 figures (and 1 supp. figure) | null | null | null | q-bio.NC cs.NE stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cortical circuits exhibit intricate recurrent architectures that are
remarkably similar across different brain areas. Such stereotyped structure
suggests the existence of common computational principles. However, such
principles have remained largely elusive. Inspired by gated-memory networks,
namely long short-term ... | [
{
"created": "Tue, 7 Nov 2017 13:03:35 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Jan 2018 17:29:28 GMT",
"version": "v2"
}
] | 2018-01-04 | [
[
"Costa",
"Rui Ponte",
""
],
[
"Assael",
"Yannis M.",
""
],
[
"Shillingford",
"Brendan",
""
],
[
"de Freitas",
"Nando",
""
],
[
"Vogels",
"Tim P.",
""
]
] | Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term me... |
2108.12261 | Xilin Liu | Xilin Liu, Andrew G. Richardson | A System-on-Chip for Closed-loop Optogenetic Sleep Modulation | 8 pages, 9 figures, 2 tables | null | null | null | q-bio.NC cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stimulation of target neuronal populations using optogenetic techniques
during specific sleep stages has begun to elucidate the mechanisms and effects
of sleep. To conduct closed-loop optogenetic sleep studies in untethered
animals, we designed a fully integrated, low-power system-on-chip (SoC) for
real-time sleep st... | [
{
"created": "Sat, 17 Jul 2021 01:03:48 GMT",
"version": "v1"
}
] | 2021-08-30 | [
[
"Liu",
"Xilin",
""
],
[
"Richardson",
"Andrew G.",
""
]
] | Stimulation of target neuronal populations using optogenetic techniques during specific sleep stages has begun to elucidate the mechanisms and effects of sleep. To conduct closed-loop optogenetic sleep studies in untethered animals, we designed a fully integrated, low-power system-on-chip (SoC) for real-time sleep stag... |
1301.5512 | Amaury Lambert | Amaury Lambert and H\'el\`ene Morlon and Rampal S. Etienne | The reconstructed tree in the lineage-based model of protracted
speciation | 27 pages, 5 figures | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A popular line of research in evolutionary biology is the use of
time-calibrated phylogenies for the inference of diversification processes.
This requires computing the likelihood of a given ultrametric tree as the
reconstructed tree produced by a given model of diversification. Etienne &
Rosindell (2012) proposed a ... | [
{
"created": "Wed, 23 Jan 2013 14:29:24 GMT",
"version": "v1"
}
] | 2013-01-24 | [
[
"Lambert",
"Amaury",
""
],
[
"Morlon",
"Hélène",
""
],
[
"Etienne",
"Rampal S.",
""
]
] | A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree produced by a given model of diversification. Etienne & Rosindell (2012) proposed a li... |
q-bio/0404028 | Frank Schweitzer | Robert Mach, Frank Schweitzer | Modeling Vortex Swarming In Daphnia | 24 pages including 11 multi-part figs. Major revisions compared to
version 1, new results on transition from uncorrelated rotation to vortex
swarming. Extended discussion. For related publications see
http://www.sg.ethz.ch/people/scfrank/Publications | Bulletin of Mathematical Biology, vol. 69 (2007) pp. 539-562 | 10.1007/s11538-006-9135-3 | null | q-bio.PE cond-mat.stat-mech physics.bio-ph | null | Based on experimental observations in \textit{Daphnia}, we introduce an
agent-based model for the motion of single and swarms of animals. Each agent is
described by a stochastic equation that also considers the conditions for
active biological motion. An environmental potential further reflects local
conditions for \... | [
{
"created": "Thu, 22 Apr 2004 23:06:38 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Nov 2004 07:19:59 GMT",
"version": "v2"
},
{
"created": "Fri, 16 Mar 2007 10:17:46 GMT",
"version": "v3"
}
] | 2007-05-23 | [
[
"Mach",
"Robert",
""
],
[
"Schweitzer",
"Frank",
""
]
] | Based on experimental observations in \textit{Daphnia}, we introduce an agent-based model for the motion of single and swarms of animals. Each agent is described by a stochastic equation that also considers the conditions for active biological motion. An environmental potential further reflects local conditions for \te... |
0909.0189 | Zhanghan Wu | Zhanghan Wu, Vlad Elgart, Hong Qian, Jianhua Xing | Amplification and detection of single molecule conformational
fluctuation through a protein interaction network with bimodal distributions | 9 pages, 5 figures | J. Phys. Chem. B, 2009, 113 (36), pp 12375-12381 | 10.1021/jp903548d | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A protein undergoes conformational dynamics with multiple time scales, which
results in fluctuating enzyme activities. Recent studies in single molecule
enzymology have observe this "age-old" dynamic disorder phenomenon directly.
However, the single molecule technique has its limitation. To be able to
observe this mo... | [
{
"created": "Tue, 1 Sep 2009 14:13:09 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Wu",
"Zhanghan",
""
],
[
"Elgart",
"Vlad",
""
],
[
"Qian",
"Hong",
""
],
[
"Xing",
"Jianhua",
""
]
] | A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However, the single molecule technique has its limitation. To be able to observe this mole... |
1909.10405 | John-Antonio Argyriadis | John-Antonio Argyriadis, Yang-Hui He, Vishnu Jejjala, Djordje Minic | Dynamics of genetic code evolution: The emergence of universality | 38 pages | Phys. Rev. E 103, 052409 (2021) | 10.1103/PhysRevE.103.052409 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the dynamics of genetic code evolution. The model of Vetsigian et
al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to
demonstrate convergence of the genetic code to a near universal solution. We
reproduce and analyze the algorithm as a dynamical system. All the parameters
used in the ... | [
{
"created": "Mon, 23 Sep 2019 14:59:09 GMT",
"version": "v1"
},
{
"created": "Fri, 27 Nov 2020 17:59:57 GMT",
"version": "v2"
}
] | 2021-05-26 | [
[
"Argyriadis",
"John-Antonio",
""
],
[
"He",
"Yang-Hui",
""
],
[
"Jejjala",
"Vishnu",
""
],
[
"Minic",
"Djordje",
""
]
] | We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce and analyze the algorithm as a dynamical system. All the parameters used in the mo... |
2202.07325 | Christopher Overton | Christopher E. Overton, Luke Webb, Uma Datta, Mike Fursman, Jo
Hardstaff, Iina Hiironen, Karthik Paranthaman, Heather Riley, James Sedgwick,
Julia Verne, Steve Willner, Lorenzo Pellis, Ian Hall | Novel methods for estimating the instantaneous and overall COVID-19 case
fatality risk among care home residents in England | null | null | 10.1371/journal.pcbi.1010554 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The COVID-19 pandemic has had high mortality rates in the elderly and frail
worldwide, particularly in care homes. This is driven by the difficulty of
isolating care homes from the wider community, the large population sizes
within care facilities (relative to typical households), and the age/frailty of
the residents... | [
{
"created": "Tue, 15 Feb 2022 11:28:28 GMT",
"version": "v1"
}
] | 2023-01-11 | [
[
"Overton",
"Christopher E.",
""
],
[
"Webb",
"Luke",
""
],
[
"Datta",
"Uma",
""
],
[
"Fursman",
"Mike",
""
],
[
"Hardstaff",
"Jo",
""
],
[
"Hiironen",
"Iina",
""
],
[
"Paranthaman",
"Karthik",
""
],
[
... | The COVID-19 pandemic has had high mortality rates in the elderly and frail worldwide, particularly in care homes. This is driven by the difficulty of isolating care homes from the wider community, the large population sizes within care facilities (relative to typical households), and the age/frailty of the residents. ... |
2211.08522 | Michael Levin | Leo Pio-Lopez, Johanna Bischof, Jennifer V. LaPalme, and Michael Levin | The scaling of goals via homeostasis: an evolutionary simulation,
experiment and analysis | 27 pages, 11 Figures, 2 Algorithms | null | null | null | q-bio.PE cs.MA cs.NE q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | All cognitive agents are composite beings. Specifically, complex living
agents consist of cells, which are themselves competent sub-agents navigating
physiological and metabolic spaces. Behavior science, evolutionary
developmental biology, and the field of machine intelligence all seek an answer
to the scaling of bio... | [
{
"created": "Tue, 15 Nov 2022 21:48:44 GMT",
"version": "v1"
}
] | 2022-11-17 | [
[
"Pio-Lopez",
"Leo",
""
],
[
"Bischof",
"Johanna",
""
],
[
"LaPalme",
"Jennifer V.",
""
],
[
"Levin",
"Michael",
""
]
] | All cognitive agents are composite beings. Specifically, complex living agents consist of cells, which are themselves competent sub-agents navigating physiological and metabolic spaces. Behavior science, evolutionary developmental biology, and the field of machine intelligence all seek an answer to the scaling of biolo... |
2208.14445 | Zahra Riahi Samani | Zahra Riahi Samani, Drew Parker, Hamed Akbari, Spyridon Bakas, Ronald
L. Wolf, Steven Brem, Ragini Verma | Artificial intelligence-based locoregional markers of brain peritumoral
microenvironment | null | null | null | null | q-bio.QM cs.CV eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In malignant primary brain tumors, cancer cells infiltrate into the
peritumoral brain structures which results in inevitable recurrence.
Quantitative assessment of infiltrative heterogeneity in the peritumoral
region, the area where biopsy or resection can be hazardous, is important for
clinical decision making. Prev... | [
{
"created": "Mon, 29 Aug 2022 22:04:06 GMT",
"version": "v1"
}
] | 2022-09-01 | [
[
"Samani",
"Zahra Riahi",
""
],
[
"Parker",
"Drew",
""
],
[
"Akbari",
"Hamed",
""
],
[
"Bakas",
"Spyridon",
""
],
[
"Wolf",
"Ronald L.",
""
],
[
"Brem",
"Steven",
""
],
[
"Verma",
"Ragini",
""
]
] | In malignant primary brain tumors, cancer cells infiltrate into the peritumoral brain structures which results in inevitable recurrence. Quantitative assessment of infiltrative heterogeneity in the peritumoral region, the area where biopsy or resection can be hazardous, is important for clinical decision making. Previo... |
2201.13378 | Cooper Mellema | Cooper J. Mellema, Albert Montillo | Novel Machine Learning Approaches for Improving the Reproducibility and
Reliability of Functional and Effective Connectivity from Functional MRI | 23 pages, 5 figures, 3 algorithms, 2 equations, 3 tables, 5 pages
supplemental | null | null | null | q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Objective: New measures of human brain connectivity are needed to address
gaps in the existing measures and facilitate the study of brain function,
cognitive capacity, and identify early markers of human disease. Traditional
approaches to measure functional connectivity between pairs of brain regions in
functional MR... | [
{
"created": "Mon, 31 Jan 2022 17:43:04 GMT",
"version": "v1"
},
{
"created": "Fri, 25 Aug 2023 15:56:04 GMT",
"version": "v2"
}
] | 2023-08-28 | [
[
"Mellema",
"Cooper J.",
""
],
[
"Montillo",
"Albert",
""
]
] | Objective: New measures of human brain connectivity are needed to address gaps in the existing measures and facilitate the study of brain function, cognitive capacity, and identify early markers of human disease. Traditional approaches to measure functional connectivity between pairs of brain regions in functional MRI,... |
1009.3656 | Efstratios Manousakis | Efstratios Manousakis | When perceptual time stands still: Long stable memory in binocular
rivalry | 7 two-column latex pages and 9 eps figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have carried out binocular rivalry experiments with a large number of
subjects to obtain high quality statistics on probability distribution of
dominance duration (PDDD) for two cases where (a) the rival stimulus is
continuously presented and (b) the rival stimulus is periodically removed, with
stimulus-on and sti... | [
{
"created": "Sun, 19 Sep 2010 18:36:31 GMT",
"version": "v1"
}
] | 2010-09-21 | [
[
"Manousakis",
"Efstratios",
""
]
] | We have carried out binocular rivalry experiments with a large number of subjects to obtain high quality statistics on probability distribution of dominance duration (PDDD) for two cases where (a) the rival stimulus is continuously presented and (b) the rival stimulus is periodically removed, with stimulus-on and stimu... |
1703.06532 | Chen Jia | Chen Jia, Peng Xie, Min Chen, Michael Q. Zhang | Stochastic fluctuations can reveal the feedback signs of gene regulatory
networks at the single-molecule level | 13 pages, 5 figures | null | null | null | q-bio.MN cond-mat.stat-mech physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the relationship between spontaneous stochastic fluctuations
and the topology of the underlying gene regulatory network is of fundamental
importance for the study of single-cell stochastic gene expression. Here by
solving the analytical steady-state distribution of the protein copy number in
a general k... | [
{
"created": "Sun, 19 Mar 2017 22:46:36 GMT",
"version": "v1"
},
{
"created": "Tue, 30 May 2017 10:14:25 GMT",
"version": "v2"
},
{
"created": "Mon, 24 Jul 2017 06:53:32 GMT",
"version": "v3"
},
{
"created": "Tue, 24 Oct 2017 17:55:45 GMT",
"version": "v4"
}
] | 2017-10-25 | [
[
"Jia",
"Chen",
""
],
[
"Xie",
"Peng",
""
],
[
"Chen",
"Min",
""
],
[
"Zhang",
"Michael Q.",
""
]
] | Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the analytical steady-state distribution of the protein copy number in a general kin... |
q-bio/0508024 | Sachin Talathi | Henry D.I. Abarbanel, Sachin Talathi | Reading Sequences of Interspike Intervals in Biological Neural Circuits | null | null | null | null | q-bio.OT | null | Sensory systems pass information about an animal's environment to higher
nervous system units through sequences of action potentials. When these action
potentials have essentially equivalent waveforms, all information is contained
in the interspike intervals (ISIs) of the spike sequence. We address the
question: How ... | [
{
"created": "Fri, 19 Aug 2005 17:04:25 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Aug 2005 22:12:32 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Abarbanel",
"Henry D. I.",
""
],
[
"Talathi",
"Sachin",
""
]
] | Sensory systems pass information about an animal's environment to higher nervous system units through sequences of action potentials. When these action potentials have essentially equivalent waveforms, all information is contained in the interspike intervals (ISIs) of the spike sequence. We address the question: How do... |
0903.0184 | Michael B\"orsch | Monika G. Dueser, Nawid Zarrabi, Daniel J. Cipriano, Stefan Ernst,
Gary D. Glick, Stanley D. Dunn, Michael Boersch | 36 degree step size of proton-driven c-ring rotation in FoF1-ATP
synthase | 8 pages, 1 figure | null | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Synthesis of the biological "energy currency molecule" adenosine triphosphate
ATP is accomplished by FoF1-ATP synthase. In the plasma membrane of Escherichia
coli, proton-driven rotation of a ring of 10 c subunits in the Fo motor powers
catalysis in the F1 motor. While F1 uses 120 degree stepping, Fo models predict
a... | [
{
"created": "Sun, 1 Mar 2009 22:11:20 GMT",
"version": "v1"
}
] | 2009-03-03 | [
[
"Dueser",
"Monika G.",
""
],
[
"Zarrabi",
"Nawid",
""
],
[
"Cipriano",
"Daniel J.",
""
],
[
"Ernst",
"Stefan",
""
],
[
"Glick",
"Gary D.",
""
],
[
"Dunn",
"Stanley D.",
""
],
[
"Boersch",
"Michael",
""
]
... | Synthesis of the biological "energy currency molecule" adenosine triphosphate ATP is accomplished by FoF1-ATP synthase. In the plasma membrane of Escherichia coli, proton-driven rotation of a ring of 10 c subunits in the Fo motor powers catalysis in the F1 motor. While F1 uses 120 degree stepping, Fo models predict a s... |
1607.06358 | Ian Vernon Dr | Ian Vernon and Junli Liu and Michael Goldstein and James Rowe and Jen
Topping and Keith Lindsey | Bayesian uncertainty analysis for complex systems biology models:
emulation, global parameter searches and evaluation of gene functions | 26 pages, 13 figures. Version accepted by BMC systems biology | BMC Systems Biology (2018), 12(1) | 10.1186/s12918-017-0484-3 | null | q-bio.MN q-bio.CB q-bio.QM stat.AP stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Many mathematical models have now been employed across every area
of systems biology. These models increasingly involve large numbers of unknown
parameters, have complex structure which can result in substantial evaluation
time relative to the needs of the analysis, and need to be compared to observed
dat... | [
{
"created": "Thu, 21 Jul 2016 15:10:57 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Jan 2018 11:36:41 GMT",
"version": "v2"
}
] | 2018-01-15 | [
[
"Vernon",
"Ian",
""
],
[
"Liu",
"Junli",
""
],
[
"Goldstein",
"Michael",
""
],
[
"Rowe",
"James",
""
],
[
"Topping",
"Jen",
""
],
[
"Lindsey",
"Keith",
""
]
] | Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time relative to the needs of the analysis, and need to be compared to observed data.... |
1203.1471 | Marc Robinson-Rechavi | J. Roux, M. Robinson-Rechavi | Developmental constraints on vertebrate genome evolution | null | PLoS Genetics 4 (2008) e1000311 | 10.1371/journal.pgen.1000311 | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by/3.0/ | Constraints in embryonic development are thought to bias the direction of
evolution by making some changes less likely, and others more likely, depending
on their consequences on ontogeny. Here, we characterize the constraints acting
on genome evolution in vertebrates. We used gene expression data from two
vertebrate... | [
{
"created": "Tue, 6 Mar 2012 12:47:06 GMT",
"version": "v1"
}
] | 2012-03-08 | [
[
"Roux",
"J.",
""
],
[
"Robinson-Rechavi",
"M.",
""
]
] | Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on genome evolution in vertebrates. We used gene expression data from two vertebrates:... |
0812.4341 | Vincent Breton | V. Vincent Breton (LPC-Clermont), A. L. Da Costa (LPC-Clermont), P. De
Vlieger (LPC-Clermont), L. Maigne (LPC-Clermont), D. Sarramia (LPC-Clermont),
Y.-M. Kim, D. Kim, H.Q. Nguyen, T. Solomonides, Y.-T. Wu, T. N. Hai | Innovative in silico approaches to address avian flu using grid
technology | 7 pages, submitted to Infectious Disorders - Drug Targets | Infectious Disorders - Drug Targets (2008) 7 p | null | PCCF RI 0803 | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The recent years have seen the emergence of diseases which have spread very
quickly all around the world either through human travels like SARS or animal
migration like avian flu. Among the biggest challenges raised by infectious
emerging diseases, one is related to the constant mutation of the viruses which
turns th... | [
{
"created": "Tue, 23 Dec 2008 07:06:36 GMT",
"version": "v1"
}
] | 2008-12-24 | [
[
"Breton",
"V. Vincent",
"",
"LPC-Clermont"
],
[
"Da Costa",
"A. L.",
"",
"LPC-Clermont"
],
[
"De Vlieger",
"P.",
"",
"LPC-Clermont"
],
[
"Maigne",
"L.",
"",
"LPC-Clermont"
],
[
"Sarramia",
"D.",
"",
"LPC-Clermont"
],... | The recent years have seen the emergence of diseases which have spread very quickly all around the world either through human travels like SARS or animal migration like avian flu. Among the biggest challenges raised by infectious emerging diseases, one is related to the constant mutation of the viruses which turns them... |
1306.0701 | Daniel Lawson | Daniel John Lawson | Populations in statistical genetic modelling and inference | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | What is a population? This review considers how a population may be defined
in terms of understanding the structure of the underlying genetics of the
individuals involved. The main approach is to consider statistically
identifiable groups of randomly mating individuals, which is well defined in
theory for any type of... | [
{
"created": "Tue, 4 Jun 2013 08:40:06 GMT",
"version": "v1"
}
] | 2013-06-05 | [
[
"Lawson",
"Daniel John",
""
]
] | What is a population? This review considers how a population may be defined in terms of understanding the structure of the underlying genetics of the individuals involved. The main approach is to consider statistically identifiable groups of randomly mating individuals, which is well defined in theory for any type of (... |
1209.5439 | Mike Taylor | Michael P. Taylor and Mathew J. Wedel | Why sauropods had long necks; and why giraffes have short necks | 39 pages, 11 figures, 3 tables | PeerJ 1:e36 (2013) | 10.7717/peerj.36 | null | q-bio.TO q-bio.PE | http://creativecommons.org/licenses/by/3.0/ | The necks of the sauropod dinosaurs reached 15 m in length: six times longer
than that of the world record giraffe and five times longer than those of all
other terrestrial animals. Several anatomical features enabled this extreme
elongation, including: absolutely large body size and quadrupedal stance
providing a st... | [
{
"created": "Mon, 24 Sep 2012 21:51:58 GMT",
"version": "v1"
}
] | 2013-02-13 | [
[
"Taylor",
"Michael P.",
""
],
[
"Wedel",
"Mathew J.",
""
]
] | The necks of the sauropod dinosaurs reached 15 m in length: six times longer than that of the world record giraffe and five times longer than those of all other terrestrial animals. Several anatomical features enabled this extreme elongation, including: absolutely large body size and quadrupedal stance providing a stab... |
0906.0381 | Thilo Gross | Thilo Gross and Ulrike Feudel | Local dynamical equivalence of certain food webs | 20 pages, 5 figures | Ocean Dynamics 59 (2), 417-427, 2009 | 10.1007/s10236-008-0165-2 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An important challenge in theoretical ecology is to find good, coarse-grained
representations of complex food webs. Here we use the approach of generalized
modeling to show that it may be possible to formulate a coarse-graining
algorithm that conserves the local dynamics of the model exactly. We show
examples of food... | [
{
"created": "Tue, 2 Jun 2009 14:57:57 GMT",
"version": "v1"
}
] | 2009-06-03 | [
[
"Gross",
"Thilo",
""
],
[
"Feudel",
"Ulrike",
""
]
] | An important challenge in theoretical ecology is to find good, coarse-grained representations of complex food webs. Here we use the approach of generalized modeling to show that it may be possible to formulate a coarse-graining algorithm that conserves the local dynamics of the model exactly. We show examples of food w... |
0802.1223 | Michael E. Wall | David W. Dreisigmeyer, Jelena Stajic, Ilya Nemenman, William S.
Hlavacek, Michael E. Wall | Determinants of bistability in induction of the Escherichia coli lac
operon | 19 pages, 10 figures, First q-bio Conference on Cellular Information
Processing | null | null | LA-UR-08-0753 | q-bio.CB q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have developed a mathematical model of regulation of expression of the
Escherichia coli lac operon, and have investigated bistability in its
steady-state induction behavior in the absence of external glucose. Numerical
analysis of equations describing regulation by artificial inducers revealed two
natural bistabil... | [
{
"created": "Fri, 8 Feb 2008 22:21:49 GMT",
"version": "v1"
}
] | 2008-02-12 | [
[
"Dreisigmeyer",
"David W.",
""
],
[
"Stajic",
"Jelena",
""
],
[
"Nemenman",
"Ilya",
""
],
[
"Hlavacek",
"William S.",
""
],
[
"Wall",
"Michael E.",
""
]
] | We have developed a mathematical model of regulation of expression of the Escherichia coli lac operon, and have investigated bistability in its steady-state induction behavior in the absence of external glucose. Numerical analysis of equations describing regulation by artificial inducers revealed two natural bistabilit... |
1911.07233 | Sara Clifton | Sara M. Clifton, Rachel J. Whitaker, Zoi Rapti | Temperate and chronic virus competition leads to low lysogen frequency | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The canonical bacteriophage is obligately lytic: the virus infects a
bacterium and hijacks cell functions to produce large numbers of new viruses
which burst from the cell. These viruses are well-studied, but there exist a
wide range of coexisting virus lifestyles that are less understood. Temperate
viruses exhibit b... | [
{
"created": "Sun, 17 Nov 2019 13:32:23 GMT",
"version": "v1"
}
] | 2019-11-19 | [
[
"Clifton",
"Sara M.",
""
],
[
"Whitaker",
"Rachel J.",
""
],
[
"Rapti",
"Zoi",
""
]
] | The canonical bacteriophage is obligately lytic: the virus infects a bacterium and hijacks cell functions to produce large numbers of new viruses which burst from the cell. These viruses are well-studied, but there exist a wide range of coexisting virus lifestyles that are less understood. Temperate viruses exhibit bot... |
1604.02270 | Mikhail Kolmogorov | Mikhail Kolmogorov, Eamonn Kennedy, Zhuxin Dong, Gregory Timp and
Pavel Pevzner | Single-Molecule Protein Identification by Sub-Nanopore Sensors | null | null | 10.1371/journal.pcbi.1005356 | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent advances in top-down mass spectrometry enabled identification of
intact proteins, but this technology still faces challenges. For example,
top-down mass spectrometry suffers from a lack of sensitivity since the ion
counts for a single fragmentation event are often low. In contrast, nanopore
technology is exqui... | [
{
"created": "Fri, 8 Apr 2016 08:16:41 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Jan 2017 23:24:59 GMT",
"version": "v2"
}
] | 2017-07-05 | [
[
"Kolmogorov",
"Mikhail",
""
],
[
"Kennedy",
"Eamonn",
""
],
[
"Dong",
"Zhuxin",
""
],
[
"Timp",
"Gregory",
""
],
[
"Pevzner",
"Pavel",
""
]
] | Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low. In contrast, nanopore technology is exquisi... |
1503.06159 | Roman Bauer | Roman Bauer, Marcus Kaiser and Elizabeth Stoll | A Computational Model Incorporating Neural Stem Cell Dynamics Reproduces
Glioma Incidence across the Lifespan in the Human Population | null | Bauer, Roman, Marcus Kaiser, and Elizabeth Stoll. "A Computational
Model Incorporating Neural Stem Cell Dynamics Reproduces Glioma Incidence
across the Lifespan in the Human Population." PloS one 9.11 (2014): e111219 | 10.1371/journal.pone.0111219 | null | q-bio.CB physics.bio-ph q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Glioma is the most common form of primary brain tumor. Demographically, the
risk of occurrence increases until old age. Here we present a novel
computational model to reproduce the probability of glioma incidence across the
lifespan. Previous mathematical models explaining glioma incidence are framed
in a rather abst... | [
{
"created": "Fri, 20 Mar 2015 17:04:07 GMT",
"version": "v1"
}
] | 2015-03-23 | [
[
"Bauer",
"Roman",
""
],
[
"Kaiser",
"Marcus",
""
],
[
"Stoll",
"Elizabeth",
""
]
] | Glioma is the most common form of primary brain tumor. Demographically, the risk of occurrence increases until old age. Here we present a novel computational model to reproduce the probability of glioma incidence across the lifespan. Previous mathematical models explaining glioma incidence are framed in a rather abstra... |
1304.5487 | Mark Flegg | Mark B. Flegg, S. Jonathan Chapman, Likun Zheng, Radek Erban | Analysis of the two-regime method on square meshes | null | null | null | null | q-bio.QM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The two-regime method (TRM) has been recently developed for optimizing
stochastic reaction-diffusion simulations. It is a multiscale (hybrid)
algorithm which uses stochastic reaction-diffusion models with different levels
of detail in different parts of the computational domain. The coupling
condition on the interfac... | [
{
"created": "Wed, 17 Apr 2013 22:28:32 GMT",
"version": "v1"
}
] | 2013-04-22 | [
[
"Flegg",
"Mark B.",
""
],
[
"Chapman",
"S. Jonathan",
""
],
[
"Zheng",
"Likun",
""
],
[
"Erban",
"Radek",
""
]
] | The two-regime method (TRM) has been recently developed for optimizing stochastic reaction-diffusion simulations. It is a multiscale (hybrid) algorithm which uses stochastic reaction-diffusion models with different levels of detail in different parts of the computational domain. The coupling condition on the interface ... |
2201.11600 | Yujiang Wang | Gabrielle M. Schroeder, Philippa J. Karoly, Matias Maturana, Mariella
Panagiotopoulou, Peter N. Taylor, Mark J. Cook, Yujiang Wang | Chronic iEEG recordings and interictal spike rate reveal multiscale
temporal modulations in seizure states | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background and Objectives: Many biological processes are modulated by rhythms
on circadian and multidien timescales. In focal epilepsy, various seizure
features, such as spread and duration, can change from one seizure to the next
within the same patient. However, the specific timescales of this variability,
as well ... | [
{
"created": "Thu, 27 Jan 2022 15:59:15 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Jun 2023 16:09:09 GMT",
"version": "v2"
}
] | 2023-06-14 | [
[
"Schroeder",
"Gabrielle M.",
""
],
[
"Karoly",
"Philippa J.",
""
],
[
"Maturana",
"Matias",
""
],
[
"Panagiotopoulou",
"Mariella",
""
],
[
"Taylor",
"Peter N.",
""
],
[
"Cook",
"Mark J.",
""
],
[
"Wang",
"Yujia... | Background and Objectives: Many biological processes are modulated by rhythms on circadian and multidien timescales. In focal epilepsy, various seizure features, such as spread and duration, can change from one seizure to the next within the same patient. However, the specific timescales of this variability, as well as... |
1312.5566 | Clemence Martin | Denis Michel (Irset) | Kinetic approaches to lactose operon induction and bimodality | null | Journal of Theoretical Biology 2013;325:62-75 | 10.1016/j.jtbi.2013.02.005 | null | q-bio.MN physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The quasi-equilibrium approximation is acceptable when molecular interactions
are fast enough compared to circuit dynamics, but is no longer allowed when
cellular activities are governed by rare events. A typical example is the
lactose operon (lac), one of the most famous paradigms of transcription
regulation, for wh... | [
{
"created": "Thu, 19 Dec 2013 14:39:32 GMT",
"version": "v1"
}
] | 2013-12-20 | [
[
"Michel",
"Denis",
"",
"Irset"
]
] | The quasi-equilibrium approximation is acceptable when molecular interactions are fast enough compared to circuit dynamics, but is no longer allowed when cellular activities are governed by rare events. A typical example is the lactose operon (lac), one of the most famous paradigms of transcription regulation, for whic... |
2312.12094 | Sheng Xu | Linglin Jing, Sheng Xu, Yifan Wang, Yuzhe Zhou, Tao Shen, Zhigang Ji,
Hui Fang, Zhen Li, Siqi Sun | CrossBind: Collaborative Cross-Modal Identification of Protein
Nucleic-Acid-Binding Residues | Accepted to AAAI-24 | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurate identification of protein nucleic-acid-binding residues poses a
significant challenge with important implications for various biological
processes and drug design. Many typical computational methods for protein
analysis rely on a single model that could ignore either the semantic context
of the protein or th... | [
{
"created": "Tue, 19 Dec 2023 12:17:13 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Dec 2023 07:21:54 GMT",
"version": "v2"
}
] | 2023-12-21 | [
[
"Jing",
"Linglin",
""
],
[
"Xu",
"Sheng",
""
],
[
"Wang",
"Yifan",
""
],
[
"Zhou",
"Yuzhe",
""
],
[
"Shen",
"Tao",
""
],
[
"Ji",
"Zhigang",
""
],
[
"Fang",
"Hui",
""
],
[
"Li",
"Zhen",
""
... | Accurate identification of protein nucleic-acid-binding residues poses a significant challenge with important implications for various biological processes and drug design. Many typical computational methods for protein analysis rely on a single model that could ignore either the semantic context of the protein or the ... |
0706.3101 | Dietrich Stauffer | D. Stauffer | The Penna Model of Biological Aging | 16-page invited review submitted to Bioinformatics and Biology
Insights | null | null | null | q-bio.PE | null | This review deals with computer simulation of biological ageing, particularly
with the Penna model of 1995.
| [
{
"created": "Thu, 21 Jun 2007 08:22:44 GMT",
"version": "v1"
}
] | 2007-06-22 | [
[
"Stauffer",
"D.",
""
]
] | This review deals with computer simulation of biological ageing, particularly with the Penna model of 1995. |
1807.06901 | Pablo Rodr\'iguez-S\'anchez | Pablo Rodr\'iguez-S\'anchez, Egbert H. van Nes, Marten Scheffer | Neutral competition boosts chaos in food webs | Added biodiversity measures, lacking in our previous analysis | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Similarity of competitors has been proposed to facilitate coexistence of
species because it slows down competitive exclusion, thus making it easier for
equalizing mechanisms to maintain diverse communities. On the other hand, chaos
can promote coexistence of species. Here we link these two previously unrelated
findin... | [
{
"created": "Wed, 18 Jul 2018 12:59:01 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Feb 2019 13:17:36 GMT",
"version": "v2"
}
] | 2019-02-27 | [
[
"Rodríguez-Sánchez",
"Pablo",
""
],
[
"van Nes",
"Egbert H.",
""
],
[
"Scheffer",
"Marten",
""
]
] | Similarity of competitors has been proposed to facilitate coexistence of species because it slows down competitive exclusion, thus making it easier for equalizing mechanisms to maintain diverse communities. On the other hand, chaos can promote coexistence of species. Here we link these two previously unrelated findings... |
2003.02251 | Kathryn Link | Kathryn G. Link, Matthew G. Sorrells, Nicholas A. Danes, Keith B.
Neeves, Karin Leiderman, and Aaron L. Fogelson | A Mathematical Model of Platelet Aggregation in an Extravascular Injury
Under Flow | 35 pages, 14 figures | null | null | null | q-bio.CB math.DS q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present the first mathematical model of flow-mediated primary hemostasis
in an extravascular injury, which can track the process from initial deposition
to occlusion. The model consists of a system of ordinary differential equations
(ODE) that describe platelet aggregation (adhesion and cohesion),
soluble-agonist-... | [
{
"created": "Wed, 4 Mar 2020 18:47:01 GMT",
"version": "v1"
}
] | 2020-03-05 | [
[
"Link",
"Kathryn G.",
""
],
[
"Sorrells",
"Matthew G.",
""
],
[
"Danes",
"Nicholas A.",
""
],
[
"Neeves",
"Keith B.",
""
],
[
"Leiderman",
"Karin",
""
],
[
"Fogelson",
"Aaron L.",
""
]
] | We present the first mathematical model of flow-mediated primary hemostasis in an extravascular injury, which can track the process from initial deposition to occlusion. The model consists of a system of ordinary differential equations (ODE) that describe platelet aggregation (adhesion and cohesion), soluble-agonist-de... |
1907.10808 | Ricardo Ugarte | Ricardo Ugarte | Approximate calculation of the binding energy between
17$\beta$-estradiol and human estrogen receptor alpha | 11 pages, 5 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Estrogen receptors (ERs) are a group of proteins activated by
17$\beta$-estradiol. The endocrine-disrupting chemicals (EDCs) mimic estrogen
action by bind directly to the ligand binding domain of ER. From this
perspective, ER represent a good model for identifying and assessing the health
risk of potential EDCs. This... | [
{
"created": "Thu, 25 Jul 2019 02:52:34 GMT",
"version": "v1"
}
] | 2019-07-26 | [
[
"Ugarte",
"Ricardo",
""
]
] | Estrogen receptors (ERs) are a group of proteins activated by 17$\beta$-estradiol. The endocrine-disrupting chemicals (EDCs) mimic estrogen action by bind directly to the ligand binding domain of ER. From this perspective, ER represent a good model for identifying and assessing the health risk of potential EDCs. This a... |
2107.12221 | Umberto Lucia Prof. | Umberto Lucia, Giulia Grisolia | Thermal resonance in cancer | null | null | null | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | In the end of the second decade of 20th century, Warburg showed how cancer
cells present a fermentative respiration process, related to a metabolic
injury. Here, we develop an analysis of the cell process based on its heat
outflow, in order to control cancer progression. Engineering thermodynamics
represent a powerfu... | [
{
"created": "Mon, 26 Jul 2021 13:59:40 GMT",
"version": "v1"
}
] | 2021-07-27 | [
[
"Lucia",
"Umberto",
""
],
[
"Grisolia",
"Giulia",
""
]
] | In the end of the second decade of 20th century, Warburg showed how cancer cells present a fermentative respiration process, related to a metabolic injury. Here, we develop an analysis of the cell process based on its heat outflow, in order to control cancer progression. Engineering thermodynamics represent a powerful ... |
2305.14356 | Rohan Agarwal | Rohan Agarwal | Creativity as Variations on a Theme: Formalizations, Evidence, and
Engineered Applications | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | There are many philosophies and theories on what creativity is and how it
works, but one popular idea is that of variations on a theme and intersection
of concepts. This literature review explores philosophical proposals of how
creativity emerges from variations on a theme, and how formalizations of these
proposals i... | [
{
"created": "Sun, 7 May 2023 22:42:02 GMT",
"version": "v1"
}
] | 2023-05-25 | [
[
"Agarwal",
"Rohan",
""
]
] | There are many philosophies and theories on what creativity is and how it works, but one popular idea is that of variations on a theme and intersection of concepts. This literature review explores philosophical proposals of how creativity emerges from variations on a theme, and how formalizations of these proposals in ... |
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