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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1811.11658 | Nadja Tschentscher | Nadja Tschentscher, Anja Ruisinger, Helen Blank, Begona Diaz,
Katharina von Kriegstein | Reduced structural connectivity between left auditory thalamus and the
motion-sensitive planum temporale in developmental dyslexia | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Developmental dyslexia is characterized by the inability to acquire typical
reading and writing skills. Dyslexia has been frequently linked to cerebral
cortex alterations; however recent evidence also points towards sensory
thalamus dysfunctions: dyslexics showed reduced responses in the left auditory
thalamus (media... | [
{
"created": "Wed, 28 Nov 2018 16:31:43 GMT",
"version": "v1"
}
] | 2018-11-29 | [
[
"Tschentscher",
"Nadja",
""
],
[
"Ruisinger",
"Anja",
""
],
[
"Blank",
"Helen",
""
],
[
"Diaz",
"Begona",
""
],
[
"von Kriegstein",
"Katharina",
""
]
] | Developmental dyslexia is characterized by the inability to acquire typical reading and writing skills. Dyslexia has been frequently linked to cerebral cortex alterations; however recent evidence also points towards sensory thalamus dysfunctions: dyslexics showed reduced responses in the left auditory thalamus (medial ... |
2401.17478 | Joaquin Torres | Gustavo Menesse and Akke Mats Houben and Jordi Soriano and Joaquin J.
Torres | Integrated Information Decomposition Unveils Major Structural Traits of
$In$ $Silico$ and $In$ $Vitro$ Neuronal Networks | 13 pages, 5 figures | Chaos: An Interdisciplinary Journal of Nonlinear Science 34(5),
053139 (2024) | 10.1063/5.0201454 | null | q-bio.NC cond-mat.dis-nn | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The properties of complex networked systems arise from the interplay between
the dynamics of their elements and the underlying topology. Thus, to understand
their behaviour, it is crucial to convene as much information as possible about
their topological organization. However, in a large systems such as neuronal
netw... | [
{
"created": "Tue, 30 Jan 2024 22:23:05 GMT",
"version": "v1"
},
{
"created": "Mon, 17 Jun 2024 10:53:14 GMT",
"version": "v2"
}
] | 2024-06-18 | [
[
"Menesse",
"Gustavo",
""
],
[
"Houben",
"Akke Mats",
""
],
[
"Soriano",
"Jordi",
""
],
[
"Torres",
"Joaquin J.",
""
]
] | The properties of complex networked systems arise from the interplay between the dynamics of their elements and the underlying topology. Thus, to understand their behaviour, it is crucial to convene as much information as possible about their topological organization. However, in a large systems such as neuronal networ... |
2112.02027 | Grace Lindsay | Grace W. Lindsay, Josh Merel, Tom Mrsic-Flogel, Maneesh Sahani | Divergent representations of ethological visual inputs emerge from
supervised, unsupervised, and reinforcement learning | 23 total pages, 9 main figures, 8 Supplementary figures | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Artificial neural systems trained using reinforcement, supervised, and
unsupervised learning all acquire internal representations of high dimensional
input. To what extent these representations depend on the different learning
objectives is largely unknown. Here we compare the representations learned by
eight differe... | [
{
"created": "Fri, 3 Dec 2021 17:18:09 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Feb 2022 15:53:36 GMT",
"version": "v2"
}
] | 2022-02-09 | [
[
"Lindsay",
"Grace W.",
""
],
[
"Merel",
"Josh",
""
],
[
"Mrsic-Flogel",
"Tom",
""
],
[
"Sahani",
"Maneesh",
""
]
] | Artificial neural systems trained using reinforcement, supervised, and unsupervised learning all acquire internal representations of high dimensional input. To what extent these representations depend on the different learning objectives is largely unknown. Here we compare the representations learned by eight different... |
0903.1557 | Douady Stephane | Etienne Couturier, Sylvain Courrech du Pont, Stephane Douady | Steric Constraints as a Global Regulation of Growing Leaf Shape | 6 pages 4 figures, Supplementary materials (8 pages, 7 figures) | PLoS ONE 4(11): e7968 | 10.1371/journal.pone.0007968 (2009) | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Shape is one of the important characteristics for the structures observed in
living organisms. Whereas biologists have proposed models where the shape is
controlled on a molecular level [1], physicists, following Turing [2] and
d'Arcy Thomson [3], have developed theories where patterns arise spontaneously
[4]. Here, ... | [
{
"created": "Mon, 9 Mar 2009 13:42:34 GMT",
"version": "v1"
}
] | 2010-10-11 | [
[
"Couturier",
"Etienne",
""
],
[
"Pont",
"Sylvain Courrech du",
""
],
[
"Douady",
"Stephane",
""
]
] | Shape is one of the important characteristics for the structures observed in living organisms. Whereas biologists have proposed models where the shape is controlled on a molecular level [1], physicists, following Turing [2] and d'Arcy Thomson [3], have developed theories where patterns arise spontaneously [4]. Here, we... |
0704.3808 | Jakob Enemark | Jakob Enemark and Kim Sneppen | On Gene Duplication Models for Evolving Regulatory Networks | 14 pages, 7 figures | null | 10.1088/1742-5468/2007/11/P11007 | null | q-bio.PE q-bio.OT | null | Background: Duplication of genes is important for evolution of molecular
networks. Many authors have therefore considered gene duplication as a driving
force in shaping the topology of molecular networks. In particular it has been
noted that growth via duplication would act as an implicit way of preferential
attachme... | [
{
"created": "Sat, 28 Apr 2007 16:16:09 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Jul 2007 10:06:28 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Enemark",
"Jakob",
""
],
[
"Sneppen",
"Kim",
""
]
] | Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted that growth via duplication would act as an implicit way of preferential attachment... |
2405.10432 | Michael Baker Ph.D. | Yoshinao Katsu, Jiawen Zhang, Michael E. Baker | Lysine-Cysteine-Serine-Tryptophan Inserted into the DNA-Binding Domain
of Human Mineralocorticoid Receptor Increases Transcriptional Activation by
Aldosterone | 21 pages, 5 figures | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Due to alternative splicing in an ancestral DNA-binding domain (DBD) of the
mineralocorticoid receptor (MR), humans contain two almost identical MR
transcripts with either 984 amino acids (MR-984) or 988 amino acids (MR-988),
in which their DBDs differ by only four amino acids, Lys,Cys,Ser,Trp (KCSW).
Human MRs also ... | [
{
"created": "Thu, 16 May 2024 20:30:18 GMT",
"version": "v1"
}
] | 2024-05-20 | [
[
"Katsu",
"Yoshinao",
""
],
[
"Zhang",
"Jiawen",
""
],
[
"Baker",
"Michael E.",
""
]
] | Due to alternative splicing in an ancestral DNA-binding domain (DBD) of the mineralocorticoid receptor (MR), humans contain two almost identical MR transcripts with either 984 amino acids (MR-984) or 988 amino acids (MR-988), in which their DBDs differ by only four amino acids, Lys,Cys,Ser,Trp (KCSW). Human MRs also co... |
1710.03071 | R. Ozgur Doruk | Ozgur Doruk, Kechen Zhang | Building a Dynamical Network Model from Neural Spiking Data: Application
of Poisson Likelihood | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Research showed that, the information transmitted in biological neurons is
encoded in the instants of successive action potentials or their firing rate.
In addition to that, in-vivo operation of the neuron makes measurement
difficult and thus continuous data collection is restricted. Due to those
reasons, classical m... | [
{
"created": "Mon, 9 Oct 2017 13:05:20 GMT",
"version": "v1"
},
{
"created": "Mon, 8 Jan 2018 19:14:34 GMT",
"version": "v2"
}
] | 2018-01-10 | [
[
"Doruk",
"Ozgur",
""
],
[
"Zhang",
"Kechen",
""
]
] | Research showed that, the information transmitted in biological neurons is encoded in the instants of successive action potentials or their firing rate. In addition to that, in-vivo operation of the neuron makes measurement difficult and thus continuous data collection is restricted. Due to those reasons, classical mea... |
q-bio/0701053 | Giuseppe Vitiello | Walter J. Freeman and Giuseppe Vitiello | Dissipation and spontaneous symmetry breaking in brain dynamics | Restyled, slight changes in title and abstract, updated bibliography,
J. Phys. A: Math. Theor. Vol. 41 (2008) in print | null | 10.1088/1751-8113/41/30/304042 | null | q-bio.NC quant-ph | null | We compare the predictions of the dissipative quantum model of brain with
neurophysiological data collected from electroencephalograms resulting from
high-density arrays fixed on the surfaces of primary sensory and limbic areas
of trained rabbits and cats. Functional brain imaging in relation to behavior
reveals the ... | [
{
"created": "Wed, 31 Jan 2007 05:50:47 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Feb 2008 09:48:44 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Freeman",
"Walter J.",
""
],
[
"Vitiello",
"Giuseppe",
""
]
] | We compare the predictions of the dissipative quantum model of brain with neurophysiological data collected from electroencephalograms resulting from high-density arrays fixed on the surfaces of primary sensory and limbic areas of trained rabbits and cats. Functional brain imaging in relation to behavior reveals the fo... |
1206.3148 | Emilio N.M. Cirillo | D. Andreucci, D. Bellaveglia, E. N. M. Cirillo, S. Marconi | Effect of intracellular diffusion on current-voltage curves in potassium
channels | 13 pages, 5 figure | Discrete and Continuous Dynamical System Series B, 19, 1837-1853,
2014 | null | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the effect of intracellular ion diffusion on ionic currents
permeating through the cell membrane. Ion flux across the cell membrane is
mediated by special proteins forming specific channels. The structure of
potassium channels have been widely studied in recent years with remarkable
results: very precise mea... | [
{
"created": "Thu, 14 Jun 2012 15:43:23 GMT",
"version": "v1"
}
] | 2015-02-20 | [
[
"Andreucci",
"D.",
""
],
[
"Bellaveglia",
"D.",
""
],
[
"Cirillo",
"E. N. M.",
""
],
[
"Marconi",
"S.",
""
]
] | We study the effect of intracellular ion diffusion on ionic currents permeating through the cell membrane. Ion flux across the cell membrane is mediated by special proteins forming specific channels. The structure of potassium channels have been widely studied in recent years with remarkable results: very precise measu... |
1505.03560 | Sebastiano Stramaglia | Ibai Diez, Asier Erramuzpe, Inaki Escudero, Beatriz Mateos, Alberto
Cabrera, Daniele Marinazzo, Ernesto J. Sanz-Arigita, Sebastiano Stramaglia
and Jesus M. Cortes | Information flow between resting state networks | 47 pages, 5 figures, 4 tables, 3 supplementary figures. Accepted for
publication in Brain Connectivity in its current form | null | null | null | q-bio.NC physics.data-an q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The resting brain dynamics self-organizes into a finite number of correlated
patterns known as resting state networks (RSNs). It is well known that
techniques like independent component analysis can separate the brain activity
at rest to provide such RSNs, but the specific pattern of interaction between
RSNs is not y... | [
{
"created": "Wed, 13 May 2015 21:45:44 GMT",
"version": "v1"
}
] | 2015-05-15 | [
[
"Diez",
"Ibai",
""
],
[
"Erramuzpe",
"Asier",
""
],
[
"Escudero",
"Inaki",
""
],
[
"Mateos",
"Beatriz",
""
],
[
"Cabrera",
"Alberto",
""
],
[
"Marinazzo",
"Daniele",
""
],
[
"Sanz-Arigita",
"Ernesto J.",
""... | The resting brain dynamics self-organizes into a finite number of correlated patterns known as resting state networks (RSNs). It is well known that techniques like independent component analysis can separate the brain activity at rest to provide such RSNs, but the specific pattern of interaction between RSNs is not yet... |
1205.5433 | Peter Jarvis | P. D. Jarvis and J. G. Sumner | Adventures in Invariant Theory | 12 pp, includes supplementary discussion of examples | ANZIAM J. 56 (2014) 105-115 | 10.1017/S1446181114000327 | null | q-bio.QM math.GR math.ST q-bio.PE quant-ph stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We provide an introduction to enumerating and constructing invariants of
group representations via character methods. The problem is contextualised via
two case studies arising from our recent work: entanglement measures, for
characterising the structure of state spaces for composite quantum systems; and
Markov invar... | [
{
"created": "Wed, 23 May 2012 05:04:58 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Jul 2013 03:32:05 GMT",
"version": "v2"
}
] | 2019-02-20 | [
[
"Jarvis",
"P. D.",
""
],
[
"Sumner",
"J. G.",
""
]
] | We provide an introduction to enumerating and constructing invariants of group representations via character methods. The problem is contextualised via two case studies arising from our recent work: entanglement measures, for characterising the structure of state spaces for composite quantum systems; and Markov invaria... |
2106.15365 | Catharina Elisabeth Graafland | Catharina Elisabeth Graafland and Jos\'e Manuel Guti\'errez | Learning complex dependency structure of gene regulatory networks from
high dimensional micro-array data with Gaussian Bayesian networks | 20 pages, 5 figures | Sci Rep 12, 18704 (2022) | 10.1038/s41598-022-21957-z | null | q-bio.MN cs.LG q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Gene expression datasets consist of thousand of genes with relatively small
samplesizes (i.e. are large-$p$-small-$n$). Moreover, dependencies of various
orders co-exist in the datasets. In the Undirected probabilistic Graphical
Model (UGM) framework the Glasso algorithm has been proposed to deal with high
dimensiona... | [
{
"created": "Mon, 28 Jun 2021 15:04:35 GMT",
"version": "v1"
},
{
"created": "Mon, 14 Feb 2022 17:34:12 GMT",
"version": "v2"
}
] | 2022-12-21 | [
[
"Graafland",
"Catharina Elisabeth",
""
],
[
"Gutiérrez",
"José Manuel",
""
]
] | Gene expression datasets consist of thousand of genes with relatively small samplesizes (i.e. are large-$p$-small-$n$). Moreover, dependencies of various orders co-exist in the datasets. In the Undirected probabilistic Graphical Model (UGM) framework the Glasso algorithm has been proposed to deal with high dimensional ... |
2109.01176 | Artem Novozhilov | Alexander S. Bratus, Anastasiia V. Korushkina, Artem S. Novozhilov | Food webs and the principle of evolutionary adaptation | 14 pages, 7 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | A principle of evolutionary adaptation is applied to the Lotka--Volterra
models, in particular to the food webs. We present a relatively simple
computational algorithm of optimization with respect to a given criterion. This
algorithm boils down to a sequence of easy to solve linear programming
problems. As a criterio... | [
{
"created": "Thu, 2 Sep 2021 19:07:50 GMT",
"version": "v1"
}
] | 2021-09-06 | [
[
"Bratus",
"Alexander S.",
""
],
[
"Korushkina",
"Anastasiia V.",
""
],
[
"Novozhilov",
"Artem S.",
""
]
] | A principle of evolutionary adaptation is applied to the Lotka--Volterra models, in particular to the food webs. We present a relatively simple computational algorithm of optimization with respect to a given criterion. This algorithm boils down to a sequence of easy to solve linear programming problems. As a criterion ... |
1411.2761 | Oleg Usatenko | S.S. Melnik and O.V. Usatenko | Entropy and long-range correlations in DNA sequences | 8 pages, 5 figures | Comput.Biol.Chem.53, 26 (2014) | 10.1016/j.compbiolchem.2014.08.006 | null | q-bio.OT cond-mat.soft cond-mat.stat-mech physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze the structure of DNA molecules of different organisms by using the
additive Markov chain approach. Transforming nucleotide sequences into binary
strings, we perform statistical analysis of the corresponding "texts". We
develop the theory of N-step additive binary stationary ergodic Markov chains
and analyz... | [
{
"created": "Tue, 11 Nov 2014 10:53:55 GMT",
"version": "v1"
}
] | 2014-11-14 | [
[
"Melnik",
"S. S.",
""
],
[
"Usatenko",
"O. V.",
""
]
] | We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop the theory of N-step additive binary stationary ergodic Markov chains and analyze ... |
1606.03813 | Adam Marblestone | Adam Marblestone, Greg Wayne, Konrad Kording | Towards an integration of deep learning and neuroscience | null | null | 10.3389/fncom.2016.00094 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuroscience has focused on the detailed implementation of computation,
studying neural codes, dynamics and circuits. In machine learning, however,
artificial neural networks tend to eschew precisely designed codes, dynamics or
circuits in favor of brute force optimization of a cost function, often using
simple and r... | [
{
"created": "Mon, 13 Jun 2016 05:08:39 GMT",
"version": "v1"
}
] | 2020-02-04 | [
[
"Marblestone",
"Adam",
""
],
[
"Wayne",
"Greg",
""
],
[
"Kording",
"Konrad",
""
]
] | Neuroscience has focused on the detailed implementation of computation, studying neural codes, dynamics and circuits. In machine learning, however, artificial neural networks tend to eschew precisely designed codes, dynamics or circuits in favor of brute force optimization of a cost function, often using simple and rel... |
1208.5954 | Adel Dayarian | Adel Dayarian and Boris I Shraiman | How to infer relative fitness from a sample of genomic sequences | null | null | null | NSF-KITP-12-148 | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mounting evidence suggests that natural populations can harbor extensive
fitness diversity with numerous genomic loci under selection. It is also known
that genealogical trees for populations under selection are quantifiably
different from those expected under neutral evolution and described
statistically by Kingman'... | [
{
"created": "Wed, 29 Aug 2012 16:07:26 GMT",
"version": "v1"
},
{
"created": "Thu, 3 Jan 2013 00:14:40 GMT",
"version": "v2"
}
] | 2013-01-04 | [
[
"Dayarian",
"Adel",
""
],
[
"Shraiman",
"Boris I",
""
]
] | Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from those expected under neutral evolution and described statistically by Kingman's ... |
1907.05184 | Robert West Mr | Robert West and Mauro Mobilia | Fixation properties of rock-paper-scissors games in fluctuating
populations | 31 pages, 15 figures: Main text (18 pages, 9 figures) followed by
Supplementary Material (13 pages, 6 figures). Supplementary Information and
resources available at https://doi.org/10.6084/m9.figshare.8858273.v1 | J. Theor. Biol. 491, 110135 (2020) | 10.1016/j.jtbi.2019.110135 | null | q-bio.PE cond-mat.stat-mech nlin.AO physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rock-paper-scissors games metaphorically model cyclic dominance in ecology
and microbiology. In a static environment, these models are characterized by
fixation probabilities obeying two different "laws" in large and small
well-mixed populations. Here, we investigate the evolution of these
three-species models subjec... | [
{
"created": "Thu, 11 Jul 2019 13:29:15 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Jul 2019 10:59:05 GMT",
"version": "v2"
},
{
"created": "Mon, 24 Feb 2020 20:39:54 GMT",
"version": "v3"
}
] | 2020-02-26 | [
[
"West",
"Robert",
""
],
[
"Mobilia",
"Mauro",
""
]
] | Rock-paper-scissors games metaphorically model cyclic dominance in ecology and microbiology. In a static environment, these models are characterized by fixation probabilities obeying two different "laws" in large and small well-mixed populations. Here, we investigate the evolution of these three-species models subject ... |
1707.05019 | Pietro Faccioli | Fang Wang, Simone Orioli, Alan Ianeselli, Giovanni Spagnolli, Silvio a
Beccara, Anne Gershenson, Pietro Faccioli and Patrick L. Wintrode | All-atom simulations reveal how single point mutations promote serpin
misfolding | Final version. Supplementary Information included | Biophys. J. 114, 2083 (2018) | 10.1016/j.bpj.2018.03.027 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein misfolding is implicated in many diseases, including the
serpinopathies. For the canonical inhibitory serpin {\alpha}1-antitrypsin
(A1AT), mutations can result in protein deficiencies leading to lung disease,
and misfolded mutants can accumulate in hepatocytes leading to liver disease.
Using all-atom simulati... | [
{
"created": "Mon, 17 Jul 2017 07:07:36 GMT",
"version": "v1"
},
{
"created": "Mon, 18 Jun 2018 10:03:02 GMT",
"version": "v2"
}
] | 2018-06-19 | [
[
"Wang",
"Fang",
""
],
[
"Orioli",
"Simone",
""
],
[
"Ianeselli",
"Alan",
""
],
[
"Spagnolli",
"Giovanni",
""
],
[
"Beccara",
"Silvio a",
""
],
[
"Gershenson",
"Anne",
""
],
[
"Faccioli",
"Pietro",
""
],
... | Protein misfolding is implicated in many diseases, including the serpinopathies. For the canonical inhibitory serpin {\alpha}1-antitrypsin (A1AT), mutations can result in protein deficiencies leading to lung disease, and misfolded mutants can accumulate in hepatocytes leading to liver disease. Using all-atom simulation... |
2202.10919 | Nam Nguyen | Nam Nguyen and Kwang-Cheng Chen | Translational Quantum Machine Intelligence for Modeling Tumor Dynamics
in Oncology | Withdraw because of error. The error is RY rotation fomular | null | null | null | q-bio.OT quant-ph | http://creativecommons.org/licenses/by/4.0/ | Quantifying the dynamics of tumor burden reveals useful information about
cancer evolution concerning treatment effects and drug resistance, which play a
crucial role in advancing model-informed drug developments (MIDD) towards
personalized medicine and precision oncology. The emergence of Quantum Machine
Intelligenc... | [
{
"created": "Mon, 21 Feb 2022 08:46:58 GMT",
"version": "v1"
},
{
"created": "Fri, 1 Jul 2022 13:20:26 GMT",
"version": "v2"
},
{
"created": "Sat, 7 Jan 2023 13:43:12 GMT",
"version": "v3"
}
] | 2023-01-10 | [
[
"Nguyen",
"Nam",
""
],
[
"Chen",
"Kwang-Cheng",
""
]
] | Quantifying the dynamics of tumor burden reveals useful information about cancer evolution concerning treatment effects and drug resistance, which play a crucial role in advancing model-informed drug developments (MIDD) towards personalized medicine and precision oncology. The emergence of Quantum Machine Intelligence ... |
q-bio/0601001 | William Bialek | William Bialek and Sima Setayeshgar | Cooperativity, sensitivity and noise in biochemical signaling | null | null | null | null | q-bio.MN q-bio.SC | null | Cooperative interactions among the binding of multiple signaling molecules is
a common mechanism for enhancing the sensitivity of biological signaling
systems. It is widely assumed that this increase in sensitivity of the mean
response implies the ability to detect smaller signals. We show that, quite
generally, ther... | [
{
"created": "Sat, 31 Dec 2005 20:38:39 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bialek",
"William",
""
],
[
"Setayeshgar",
"Sima",
""
]
] | Cooperative interactions among the binding of multiple signaling molecules is a common mechanism for enhancing the sensitivity of biological signaling systems. It is widely assumed that this increase in sensitivity of the mean response implies the ability to detect smaller signals. We show that, quite generally, there ... |
0906.3391 | David Hochberg | David Hochberg (Centro de Astrobiologia (CSIC-INTA), Madrid, Spain) | Mirror symmetry breaking and restoration: the role of noise and chiral
bias | 4 pages, 3 figures, to appear in the Physical Review Letters | Physical Review Letters 102, 248101 (2009) | 10.1103/PhysRevLett.102.248101 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The nonequilibrium effective potential is computed for the Frank model of
spontaneous mirror symmetry breaking (SMSB) in chemistry in which external
noise is introduced to account for random environmental effects. When these
fluctuations exceed a critical magnitude, mirror symmetry is restored. The
competition betwee... | [
{
"created": "Thu, 18 Jun 2009 09:42:08 GMT",
"version": "v1"
}
] | 2009-06-29 | [
[
"Hochberg",
"David",
"",
"Centro de Astrobiologia"
]
] | The nonequilibrium effective potential is computed for the Frank model of spontaneous mirror symmetry breaking (SMSB) in chemistry in which external noise is introduced to account for random environmental effects. When these fluctuations exceed a critical magnitude, mirror symmetry is restored. The competition between ... |
1705.04739 | Eilidh Noyes | Eilidh Noyes and Alice J. O'Toole | Face recognition assessments used in the study of super-recognisers | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The purpose of this paper is to provide a brief overview of nine assessments
of face processing skills. These tests have been used commonly in recent years
to gauge the skills of perspective 'super-recognisers' with respect to the
general population. In the literature, a person has been considered to be a
'super-reco... | [
{
"created": "Fri, 12 May 2017 20:02:11 GMT",
"version": "v1"
}
] | 2017-05-16 | [
[
"Noyes",
"Eilidh",
""
],
[
"O'Toole",
"Alice J.",
""
]
] | The purpose of this paper is to provide a brief overview of nine assessments of face processing skills. These tests have been used commonly in recent years to gauge the skills of perspective 'super-recognisers' with respect to the general population. In the literature, a person has been considered to be a 'super-recogn... |
2103.00335 | Alan Rogers | Alan R. Rogers and Stephen P. Wooding | Expectation of the Site Frequency Spectrum | 3 pages; 1 figure; no plans to publish elsewhere | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The site frequency spectrum describes variation among a set of n DNA
sequences. Its i'th entry (i=1,2,...,n-1) is the number of nucleotide sites at
which the mutant allele is present in i copies. Under selective neutrality,
random mating, and constant population size, the expected value of the spectrum
is well known ... | [
{
"created": "Sat, 27 Feb 2021 21:44:31 GMT",
"version": "v1"
}
] | 2021-03-02 | [
[
"Rogers",
"Alan R.",
""
],
[
"Wooding",
"Stephen P.",
""
]
] | The site frequency spectrum describes variation among a set of n DNA sequences. Its i'th entry (i=1,2,...,n-1) is the number of nucleotide sites at which the mutant allele is present in i copies. Under selective neutrality, random mating, and constant population size, the expected value of the spectrum is well known bu... |
1709.02008 | Zachary Kilpatrick PhD | Zachary P Kilpatrick and Daniel B Poll | Neural field model of memory-guided search | 17 pages, 10 figures | Phys. Rev. E 96, 062411 (2017) | 10.1103/PhysRevE.96.062411 | null | q-bio.NC nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many organisms can remember locations they have previously visited during a
search. Visual search experiments have shown exploration is guided away from
these locations, reducing the overlap of the search path before finding a
hidden target. We develop and analyze a two-layer neural field model that
encodes positiona... | [
{
"created": "Wed, 6 Sep 2017 21:34:57 GMT",
"version": "v1"
}
] | 2017-12-27 | [
[
"Kilpatrick",
"Zachary P",
""
],
[
"Poll",
"Daniel B",
""
]
] | Many organisms can remember locations they have previously visited during a search. Visual search experiments have shown exploration is guided away from these locations, reducing the overlap of the search path before finding a hidden target. We develop and analyze a two-layer neural field model that encodes positional ... |
1511.05589 | Majid Zerafat Angiz | Mohammad Gholizadeh, Majid Zerafat Angiz L., Seyed Mahmoud Davoodi,
Rajab Khalilpour, Anita Talib, Khairun Yahya, Sahubar Ali Nadhar Khan | An alternative aggregate preference ranking algorithm to assess
environmental effects on macrobenthic abundance in coastal water | null | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Coastal marine waters are ranked among the most important aquatic ecosystems
on earth in terms of ecological and economic significance. Since the Industrial
Revolution, human activities have drastically changed coastal marine
ecosystems. The development of rules and regulations to protect these
ecosystems against hum... | [
{
"created": "Tue, 25 Aug 2015 01:23:43 GMT",
"version": "v1"
}
] | 2015-11-19 | [
[
"Gholizadeh",
"Mohammad",
""
],
[
"L.",
"Majid Zerafat Angiz",
""
],
[
"Davoodi",
"Seyed Mahmoud",
""
],
[
"Khalilpour",
"Rajab",
""
],
[
"Talib",
"Anita",
""
],
[
"Yahya",
"Khairun",
""
],
[
"Khan",
"Sahubar A... | Coastal marine waters are ranked among the most important aquatic ecosystems on earth in terms of ecological and economic significance. Since the Industrial Revolution, human activities have drastically changed coastal marine ecosystems. The development of rules and regulations to protect these ecosystems against human... |
2310.00062 | Brian Camley | Aparajita Kashyap, Wei Wang, and Brian A. Camley | Tradeoffs in concentration sensing in dynamic environments | null | null | null | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When cells measure concentrations of chemical signals, they may average
multiple measurements over time in order to reduce noise in their measurements.
However, when cells are in a environment that changes over time, past
measurements may not reflect current conditions - creating a new source of
error that trades off... | [
{
"created": "Fri, 29 Sep 2023 18:09:19 GMT",
"version": "v1"
}
] | 2023-10-03 | [
[
"Kashyap",
"Aparajita",
""
],
[
"Wang",
"Wei",
""
],
[
"Camley",
"Brian A.",
""
]
] | When cells measure concentrations of chemical signals, they may average multiple measurements over time in order to reduce noise in their measurements. However, when cells are in a environment that changes over time, past measurements may not reflect current conditions - creating a new source of error that trades off a... |
2306.14667 | Quang Dang Nguyen | Quang Dang Nguyen, Sheryl L. Chang, Christina M. Jamerlan, Mikhail
Prokopenko | Measuring unequal distribution of pandemic severity across census years,
variants of concern and interventions | 43 pages, 25 figures, source code: https://zenodo.org/record/5778218 | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Diverse and complex intervention policies deployed over the last years have
shown varied effectiveness in controlling the COVID-19 pandemic. However, a
systematic analysis and modelling of the combined effects of different viral
lineages and complex intervention policies remains a challenge. Using
large-scale agent-b... | [
{
"created": "Mon, 26 Jun 2023 13:01:21 GMT",
"version": "v1"
}
] | 2023-06-27 | [
[
"Nguyen",
"Quang Dang",
""
],
[
"Chang",
"Sheryl L.",
""
],
[
"Jamerlan",
"Christina M.",
""
],
[
"Prokopenko",
"Mikhail",
""
]
] | Diverse and complex intervention policies deployed over the last years have shown varied effectiveness in controlling the COVID-19 pandemic. However, a systematic analysis and modelling of the combined effects of different viral lineages and complex intervention policies remains a challenge. Using large-scale agent-bas... |
1602.06466 | Roland Langrock | Vianey Leos-Barajas, Theoni Photopoulou, Roland Langrock, Toby A.
Patterson, Yuuki Watanabe, Megan Murgatroyd, Yannis P. Papastamatiou | Analysis of animal accelerometer data using hidden Markov models | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Use of accelerometers is now widespread within animal biotelemetry as they
provide a means of measuring an animal's activity in a meaningful and
quantitative way where direct observation is not possible. In sequential
acceleration data there is a natural dependence between observations of
movement or behaviour, a fac... | [
{
"created": "Sat, 20 Feb 2016 21:41:27 GMT",
"version": "v1"
}
] | 2016-02-23 | [
[
"Leos-Barajas",
"Vianey",
""
],
[
"Photopoulou",
"Theoni",
""
],
[
"Langrock",
"Roland",
""
],
[
"Patterson",
"Toby A.",
""
],
[
"Watanabe",
"Yuuki",
""
],
[
"Murgatroyd",
"Megan",
""
],
[
"Papastamatiou",
"Yan... | Use of accelerometers is now widespread within animal biotelemetry as they provide a means of measuring an animal's activity in a meaningful and quantitative way where direct observation is not possible. In sequential acceleration data there is a natural dependence between observations of movement or behaviour, a fact ... |
0906.1472 | Kay J\"org Wiese | Francois David and Kay Joerg Wiese | Field Theory of the RNA Freezing Transition | 96 pages, 188 figures. v2: minor corrections | J. Stat. Mech. (2009) P10019 | 10.1088/1742-5468/2009/10/P10019 | LPTENS 09/18, t09/074 | q-bio.BM cond-mat.dis-nn q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Folding of RNA is subject to a competition between entropy, relevant at high
temperatures, and the random, or random looking, sequence, determining the low-
temperature phase. It is known from numerical simulations that for random as
well as biological sequences, high- and low-temperature phases are different,
e.g. t... | [
{
"created": "Mon, 8 Jun 2009 11:45:54 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Jun 2009 17:12:22 GMT",
"version": "v2"
}
] | 2015-05-13 | [
[
"David",
"Francois",
""
],
[
"Wiese",
"Kay Joerg",
""
]
] | Folding of RNA is subject to a competition between entropy, relevant at high temperatures, and the random, or random looking, sequence, determining the low- temperature phase. It is known from numerical simulations that for random as well as biological sequences, high- and low-temperature phases are different, e.g. the... |
1106.4880 | Ying Ding | Qian Zhu, Yuyin Sun, Sashikiran Challa, Ying Ding, Michael S.
Lajiness, David J. Wild | Semantic Inference using Chemogenomics Data for Drug Discovery | 23 pages, 9 figures, 4 tables | null | 10.1186/1471-2105-12-256 | null | q-bio.QM cs.DL cs.IR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background Semantic Web Technology (SWT) makes it possible to integrate and
search the large volume of life science datasets in the public domain, as
demonstrated by well-known linked data projects such as LODD, Bio2RDF, and
Chem2Bio2RDF. Integration of these sets creates large networks of information.
We have previo... | [
{
"created": "Fri, 24 Jun 2011 03:21:56 GMT",
"version": "v1"
}
] | 2011-06-27 | [
[
"Zhu",
"Qian",
""
],
[
"Sun",
"Yuyin",
""
],
[
"Challa",
"Sashikiran",
""
],
[
"Ding",
"Ying",
""
],
[
"Lajiness",
"Michael S.",
""
],
[
"Wild",
"David J.",
""
]
] | Background Semantic Web Technology (SWT) makes it possible to integrate and search the large volume of life science datasets in the public domain, as demonstrated by well-known linked data projects such as LODD, Bio2RDF, and Chem2Bio2RDF. Integration of these sets creates large networks of information. We have previous... |
1810.11594 | Brian Hu | Brian Hu and Stefan Mihalas | Convolutional neural networks with extra-classical receptive fields | null | null | null | null | q-bio.NC cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Convolutional neural networks (CNNs) have had great success in many
real-world applications and have also been used to model visual processing in
the brain. However, these networks are quite brittle - small changes in the
input image can dramatically change a network's output prediction. In contrast
to what is known ... | [
{
"created": "Sat, 27 Oct 2018 04:15:50 GMT",
"version": "v1"
}
] | 2018-10-30 | [
[
"Hu",
"Brian",
""
],
[
"Mihalas",
"Stefan",
""
]
] | Convolutional neural networks (CNNs) have had great success in many real-world applications and have also been used to model visual processing in the brain. However, these networks are quite brittle - small changes in the input image can dramatically change a network's output prediction. In contrast to what is known fr... |
1908.01917 | Louxin Zhang | Gabriel Cardona, Louxin Zhang | Counting Tree-Child Networks and Their Subclasses | 24 pages, 2 tables and 9 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Galled trees are studied as a recombination model in population genetics.
This class of phylogenetic networks is generalized into tree-child, galled and
reticulation-visible network classes by relaxing a structural condition imposed
on galled trees. We count tree-child networks through enumerating their
component gra... | [
{
"created": "Tue, 6 Aug 2019 01:07:43 GMT",
"version": "v1"
},
{
"created": "Wed, 7 Aug 2019 23:25:55 GMT",
"version": "v2"
},
{
"created": "Wed, 26 Feb 2020 21:58:09 GMT",
"version": "v3"
}
] | 2020-02-28 | [
[
"Cardona",
"Gabriel",
""
],
[
"Zhang",
"Louxin",
""
]
] | Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on galled trees. We count tree-child networks through enumerating their component graph... |
1508.03026 | David Murrugarra | David Murrugarra and Elena S. Dimitrova | Molecular Network Control Through Boolean Canalization | null | EURASIP Journal on Bioinformatics and Systems Biology, 2015:9,
2015 | 10.1186/s13637-015-0029-2 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Boolean networks are an important class of computational models for molecular
interaction networks. Boolean canalization, a type of hierarchical clustering
of the inputs of a Boolean function, has been extensively studied in the
context of network modeling where each layer of canalization adds a degree of
stability i... | [
{
"created": "Wed, 12 Aug 2015 18:49:12 GMT",
"version": "v1"
},
{
"created": "Sun, 25 Oct 2015 00:27:17 GMT",
"version": "v2"
}
] | 2024-07-09 | [
[
"Murrugarra",
"David",
""
],
[
"Dimitrova",
"Elena S.",
""
]
] | Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of network modeling where each layer of canalization adds a degree of stability in ... |
2005.10598 | Peter Thomas PhD | Shusen Pu and Peter J. Thomas | Fast and Accurate Langevin Simulations of Stochastic Hodgkin-Huxley
Dynamics | 55 pages, 9 figures | null | 10.1162/neco_a_01312 | null | q-bio.NC cs.NA math.NA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fox and Lu introduced a Langevin framework for discrete-time stochastic
models of randomly gated ion channels such as the Hodgkin-Huxley (HH) system.
They derived a Fokker-Planck equation with state-dependent diffusion tensor $D$
and suggested a Langevin formulation with noise coefficient matrix $S$ such
that $SS^\in... | [
{
"created": "Thu, 21 May 2020 12:19:56 GMT",
"version": "v1"
}
] | 2020-11-18 | [
[
"Pu",
"Shusen",
""
],
[
"Thomas",
"Peter J.",
""
]
] | Fox and Lu introduced a Langevin framework for discrete-time stochastic models of randomly gated ion channels such as the Hodgkin-Huxley (HH) system. They derived a Fokker-Planck equation with state-dependent diffusion tensor $D$ and suggested a Langevin formulation with noise coefficient matrix $S$ such that $SS^\inte... |
2307.01499 | Roozbeh Farhoodi | Roozbeh Farhoodi, Phil Wilkes, Anirudh M. Natarajan, Samantha
Ing-Esteves, Julie L. Lefebvre, Mathias Disney, Konrad P. Kording | Comparing dendritic trees with actual trees | null | null | null | null | q-bio.NC q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Since they became observable, neuron morphologies have been informally
compared with biological trees but they are studied by distinct communities,
neuroscientists, and ecologists. The apparent structural similarity suggests
there may be common quantitative rules and constraints. However, there are also
reasons to be... | [
{
"created": "Tue, 4 Jul 2023 06:12:28 GMT",
"version": "v1"
}
] | 2023-07-06 | [
[
"Farhoodi",
"Roozbeh",
""
],
[
"Wilkes",
"Phil",
""
],
[
"Natarajan",
"Anirudh M.",
""
],
[
"Ing-Esteves",
"Samantha",
""
],
[
"Lefebvre",
"Julie L.",
""
],
[
"Disney",
"Mathias",
""
],
[
"Kording",
"Konrad P."... | Since they became observable, neuron morphologies have been informally compared with biological trees but they are studied by distinct communities, neuroscientists, and ecologists. The apparent structural similarity suggests there may be common quantitative rules and constraints. However, there are also reasons to beli... |
1312.3926 | Nicholas Dulvy | Nicholas K. Dulvy, Sarah L. Fowler, John A. Musick, Rachel D.
Cavanagh, Peter M. Kyne, Lucy R. Harrison, John K. Carlson, Lindsay N. K.
Davidson, Sonja V. Fordham, Malcolm P. Francis, Caroline M. Pollock, Colin A.
Simpfendorfer, George H. Burgess, Kent E. Carpenter, Leonard J. V. Compagno,
David A. Ebert, Claud... | Extinction risk and conservation of the world's sharks and rays | Accepted for publication in eLIFE on 5th December 2013. 83 pages, 9
tables, 10 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/3.0/ | The rapid expansion of human activities threatens ocean-wide biodiversity
loss. Numerous marine animal populations have declined, yet it remains unclear
whether these trends are symptomatic of a chronic accumulation of global marine
extinction risk. We present the first systematic analysis of threat for a
globally-di... | [
{
"created": "Thu, 12 Dec 2013 18:03:52 GMT",
"version": "v1"
}
] | 2013-12-16 | [
[
"Dulvy",
"Nicholas K.",
""
],
[
"Fowler",
"Sarah L.",
""
],
[
"Musick",
"John A.",
""
],
[
"Cavanagh",
"Rachel D.",
""
],
[
"Kyne",
"Peter M.",
""
],
[
"Harrison",
"Lucy R.",
""
],
[
"Carlson",
"John K.",
"... | The rapid expansion of human activities threatens ocean-wide biodiversity loss. Numerous marine animal populations have declined, yet it remains unclear whether these trends are symptomatic of a chronic accumulation of global marine extinction risk. We present the first systematic analysis of threat for a globally-dist... |
1509.09285 | Mallenahalli Naresh Kumar Prof. Dr. | C. S. Murthy, M. V.R. Sesha Sai, M. Naresh Kumar, P. S. Roy | Temporal divergence in cropping pattern and its implications on
geospatial drought assessment | 9 pages, 14 figures | Geocarto International 10/2009, 24(5):377-395 | 10.1080/10106040802601037 | null | q-bio.QM physics.geo-ph q-bio.PE | http://creativecommons.org/licenses/by-sa/4.0/ | Time series data on cropping pattern at disaggregated level were analysed and
its implications on geospatial drought assessment were demonstrated. An index
of Cropping Pattern Dissimilarity (CP-DI) between a pair of years, developed in
this study, proved that the cropping pattern of a year has a higher degree of
simi... | [
{
"created": "Sat, 26 Sep 2015 14:25:35 GMT",
"version": "v1"
}
] | 2016-10-31 | [
[
"Murthy",
"C. S.",
""
],
[
"Sai",
"M. V. R. Sesha",
""
],
[
"Kumar",
"M. Naresh",
""
],
[
"Roy",
"P. S.",
""
]
] | Time series data on cropping pattern at disaggregated level were analysed and its implications on geospatial drought assessment were demonstrated. An index of Cropping Pattern Dissimilarity (CP-DI) between a pair of years, developed in this study, proved that the cropping pattern of a year has a higher degree of simila... |
2202.04501 | Hossein Nemati | Hossein Nemati (1), Mohammad Reza Ejtehadi (1), Kamran Kaveh (2) ((1)
Sharif University of Technology, Physics Department (2) University of
Washington, Department of Applied Mathematics) | Counterintuitive properties of fixation probability and fixation time in
population structures with spatially periodic resource distribution | 28 pages, 14 figures (10 in main text and 4 in appendices).
Corresponding authors: Kamran Kaveh(kkaveh@uw.edu, kkavehma@gmail.com) and
Mohammad Reza Ejtehadi(ejtehadi@sharif.edu) | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Resource are often not uniformly distributed within a population. Spatial
variations of concentration of a resource, change the fitness of competing
strategies locally. The notion of fitness varying with respect to both genotype
and environment is important in modeling cancer initiation, microbial evolution
and evolu... | [
{
"created": "Wed, 9 Feb 2022 15:03:18 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Apr 2022 18:24:38 GMT",
"version": "v2"
}
] | 2022-04-08 | [
[
"Nemati",
"Hossein",
""
],
[
"Ejtehadi",
"Mohammad Reza",
""
],
[
"Kaveh",
"Kamran",
""
]
] | Resource are often not uniformly distributed within a population. Spatial variations of concentration of a resource, change the fitness of competing strategies locally. The notion of fitness varying with respect to both genotype and environment is important in modeling cancer initiation, microbial evolution and evoluti... |
q-bio/0410008 | Lior Pachter | Roderic Guigo, Ewan Birney, Michael Brent, Emmanouil Dermitzakis, Lior
Pachter, Hugues Roest Crollius, Victor Solovyev, Michael Q. Zhang | Needed for completion of the human genome: hypothesis driven experiments
and biologically realistic mathematical models | Report and discussion resulting from the `Fundacio La Caixa' gene
finding meeting held November 21 and 22 2003 in Barcelona | null | null | null | q-bio.GN | null | With the sponsorship of ``Fundacio La Caixa'' we met in Barcelona, November
21st and 22nd, to analyze the reasons why, after the completion of the human
genome sequence, the identification all protein coding genes and their variants
remains a distant goal. Here we report on our discussions and summarize some of
the m... | [
{
"created": "Wed, 6 Oct 2004 22:08:40 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Guigo",
"Roderic",
""
],
[
"Birney",
"Ewan",
""
],
[
"Brent",
"Michael",
""
],
[
"Dermitzakis",
"Emmanouil",
""
],
[
"Pachter",
"Lior",
""
],
[
"Crollius",
"Hugues Roest",
""
],
[
"Solovyev",
"Victor",
""
... | With the sponsorship of ``Fundacio La Caixa'' we met in Barcelona, November 21st and 22nd, to analyze the reasons why, after the completion of the human genome sequence, the identification all protein coding genes and their variants remains a distant goal. Here we report on our discussions and summarize some of the maj... |
2008.03135 | Babacar Mbaye Ndiaye | Babacar Mbaye Ndiaye, Mouhamadou A.M.T. Balde, Diaraf Seck | Visualization and machine learning for forecasting of COVID-19 in
Senegal | null | null | null | null | q-bio.PE stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this article, we give visualization and different machine learning
technics for two weeks and 40 days ahead forecast based on public data. On July
15, 2020, Senegal reopened its airspace doors, while the number of confirmed
cases is still increasing. The population no longer respects hygiene measures,
social dista... | [
{
"created": "Thu, 6 Aug 2020 15:50:30 GMT",
"version": "v1"
}
] | 2020-08-10 | [
[
"Ndiaye",
"Babacar Mbaye",
""
],
[
"Balde",
"Mouhamadou A. M. T.",
""
],
[
"Seck",
"Diaraf",
""
]
] | In this article, we give visualization and different machine learning technics for two weeks and 40 days ahead forecast based on public data. On July 15, 2020, Senegal reopened its airspace doors, while the number of confirmed cases is still increasing. The population no longer respects hygiene measures, social distanc... |
2006.00280 | Changchuan Yin Dr. | Changchuan Yin | Dinucleotide repeats in coronavirus SARS-CoV-2 genome: evolutionary
implications | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ongoing global pandemic of infection disease COVID-19 caused by the 2019
novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to
public health and the economy since it was identified in China, December 2019.
The genome of SARS-CoV-2 had been sequenced and structurally annotated, yet
little... | [
{
"created": "Sat, 30 May 2020 14:17:50 GMT",
"version": "v1"
}
] | 2020-06-02 | [
[
"Yin",
"Changchuan",
""
]
] | The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy since it was identified in China, December 2019. The genome of SARS-CoV-2 had been sequenced and structurally annotated, yet little i... |
2108.01210 | Joel Ye | Joel Ye, Chethan Pandarinath | Representation learning for neural population activity with Neural Data
Transformers | null | null | 10.51628/001c.27358 | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Neural population activity is theorized to reflect an underlying dynamical
structure. This structure can be accurately captured using state space models
with explicit dynamics, such as those based on recurrent neural networks
(RNNs). However, using recurrence to explicitly model dynamics necessitates
sequential proce... | [
{
"created": "Mon, 2 Aug 2021 23:36:39 GMT",
"version": "v1"
}
] | 2023-07-21 | [
[
"Ye",
"Joel",
""
],
[
"Pandarinath",
"Chethan",
""
]
] | Neural population activity is theorized to reflect an underlying dynamical structure. This structure can be accurately captured using state space models with explicit dynamics, such as those based on recurrent neural networks (RNNs). However, using recurrence to explicitly model dynamics necessitates sequential process... |
1011.1192 | Dante Chialvo | Dante R. Chialvo, Daniel Fraiman | What kind of noise is brain noise: anomalous scaling behavior of the
resting brain activity fluctuations | null | Frontiers in Fractals Physiology, (3) 307 (2012) | 10.3389/fphys.2012.00307 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The continuous interaction between brain regions "at rest" defines the
so-called resting state networks (RSN) which can be reconstructed from the
analysis of functional magnetic resonance imaging (fMRI) data. What dynamical
mechanism allows for a flexible large-scale organization of the RSN still
remains an important... | [
{
"created": "Thu, 4 Nov 2010 15:54:51 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Aug 2012 09:50:50 GMT",
"version": "v2"
}
] | 2012-08-10 | [
[
"Chialvo",
"Dante R.",
""
],
[
"Fraiman",
"Daniel",
""
]
] | The continuous interaction between brain regions "at rest" defines the so-called resting state networks (RSN) which can be reconstructed from the analysis of functional magnetic resonance imaging (fMRI) data. What dynamical mechanism allows for a flexible large-scale organization of the RSN still remains an important c... |
2307.11555 | Laurent Perrinet | Laurent U Perrinet | Accurate Detection of Spiking Motifs by Learning Heterogeneous Delays of
a Spiking Neural Network | ICANN 2023 Special Session on Recent Advances in Spiking Neural
Networks - Conference paper | null | 10.1007/978-3-031-44207-0_31 | null | q-bio.NC | http://creativecommons.org/licenses/by-sa/4.0/ | Recently, interest has grown in exploring the hypothesis that neural activity
conveys information through precise spiking motifs. To investigate this
phenomenon, various algorithms have been proposed to detect such motifs in
Single Unit Activity (SUA) recorded from populations of neurons. In this study,
we present a ... | [
{
"created": "Fri, 21 Jul 2023 13:04:28 GMT",
"version": "v1"
},
{
"created": "Mon, 25 Sep 2023 19:29:15 GMT",
"version": "v2"
}
] | 2023-09-27 | [
[
"Perrinet",
"Laurent U",
""
]
] | Recently, interest has grown in exploring the hypothesis that neural activity conveys information through precise spiking motifs. To investigate this phenomenon, various algorithms have been proposed to detect such motifs in Single Unit Activity (SUA) recorded from populations of neurons. In this study, we present a no... |
1803.02953 | Hang Xie | Hang Xie, Yang Jiao, Qihui Fan, Miaomiao Hai, Jiaen Yang, Zhijian Hu,
Yue Yang, Jianwei Shuai, Guo Chen, Ruchuan Liu, Liyu Liu | Modeling Three-dimensional Invasive Solid Tumor Growth in Heterogeneous
Microenvironment under Chemotherapy | 41 pages, 8 figures | null | 10.1371/journal.pone.0206292 | null | q-bio.TO q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A systematic understanding of the evolution and growth dynamics of invasive
solid tumors in response to different chemotherapy strategies is crucial for
the development of individually optimized oncotherapy. Here, we develop a
hybrid three-dimensional (3D) computational model that integrates
pharmacokinetic model, co... | [
{
"created": "Thu, 8 Mar 2018 03:28:50 GMT",
"version": "v1"
}
] | 2020-07-01 | [
[
"Xie",
"Hang",
""
],
[
"Jiao",
"Yang",
""
],
[
"Fan",
"Qihui",
""
],
[
"Hai",
"Miaomiao",
""
],
[
"Yang",
"Jiaen",
""
],
[
"Hu",
"Zhijian",
""
],
[
"Yang",
"Yue",
""
],
[
"Shuai",
"Jianwei",
... | A systematic understanding of the evolution and growth dynamics of invasive solid tumors in response to different chemotherapy strategies is crucial for the development of individually optimized oncotherapy. Here, we develop a hybrid three-dimensional (3D) computational model that integrates pharmacokinetic model, cont... |
1811.01935 | Sudeepto Bhattacharya Dr | Shashankaditya Upadhyay, Sudeepto Bhattacharya | A comparative study of ecological networks using spectral projections of
normalized graph Laplacian | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ecological networks originating as a result of three different ecological
processes are examined and cross-compared to assess if the underlying
ecological processes in these systems produce considerable difference in the
structure of the networks. Absence of any significant difference in the
structure of the networks... | [
{
"created": "Mon, 5 Nov 2018 05:49:03 GMT",
"version": "v1"
}
] | 2018-11-07 | [
[
"Upadhyay",
"Shashankaditya",
""
],
[
"Bhattacharya",
"Sudeepto",
""
]
] | Ecological networks originating as a result of three different ecological processes are examined and cross-compared to assess if the underlying ecological processes in these systems produce considerable difference in the structure of the networks. Absence of any significant difference in the structure of the networks m... |
2408.05258 | Wenwen Min | Wenwen Min, Zhen Wang, Fangfang Zhu, Taosheng Xu, Shunfang Wang | scASDC: Attention Enhanced Structural Deep Clustering for Single-cell
RNA-seq Data | null | null | null | null | q-bio.GN cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Single-cell RNA sequencing (scRNA-seq) data analysis is pivotal for
understanding cellular heterogeneity. However, the high sparsity and complex
noise patterns inherent in scRNA-seq data present significant challenges for
traditional clustering methods. To address these issues, we propose a deep
clustering method, At... | [
{
"created": "Fri, 9 Aug 2024 09:10:36 GMT",
"version": "v1"
}
] | 2024-08-13 | [
[
"Min",
"Wenwen",
""
],
[
"Wang",
"Zhen",
""
],
[
"Zhu",
"Fangfang",
""
],
[
"Xu",
"Taosheng",
""
],
[
"Wang",
"Shunfang",
""
]
] | Single-cell RNA sequencing (scRNA-seq) data analysis is pivotal for understanding cellular heterogeneity. However, the high sparsity and complex noise patterns inherent in scRNA-seq data present significant challenges for traditional clustering methods. To address these issues, we propose a deep clustering method, Atte... |
1311.2643 | Mark McDonnell | Brett A. Schmerl and Mark D. McDonnell | Channel noise induced stochastic facilitation in an auditory brainstem
neuron model | Published by Physical Review E, November 2013 (this version 17 pages
total - 10 text, 1 refs, 6 figures/tables); Associated matlab code is
available online in the ModelDB repository at
http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=151483 | Physical Review E, 88: 052722, 2013 | 10.1103/PhysRevE.88.052722 | null | q-bio.NC q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuronal membrane potentials fluctuate stochastically due to conductance
changes caused by random transitions between the open and close states of ion
channels. Although it has previously been shown that channel noise can
nontrivially affect neuronal dynamics, it is unknown whether ion-channel noise
is strong enough ... | [
{
"created": "Mon, 11 Nov 2013 23:00:00 GMT",
"version": "v1"
},
{
"created": "Thu, 5 Dec 2013 11:40:54 GMT",
"version": "v2"
}
] | 2013-12-06 | [
[
"Schmerl",
"Brett A.",
""
],
[
"McDonnell",
"Mark D.",
""
]
] | Neuronal membrane potentials fluctuate stochastically due to conductance changes caused by random transitions between the open and close states of ion channels. Although it has previously been shown that channel noise can nontrivially affect neuronal dynamics, it is unknown whether ion-channel noise is strong enough to... |
2007.16151 | Jason Hindes | Jason Hindes, Simone Bianco, and Ira B. Schwartz | Optimal periodic closure for minimizing risk in emerging disease
outbreaks | supplementary material included in ancillary files | PLoS ONE 16(1): e0244706 (2021) | 10.1371/journal.pone.0244706 | null | q-bio.PE physics.bio-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Without vaccines and treatments, societies must rely on non-pharmaceutical
intervention strategies to control the spread of emerging diseases such as
COVID-19. Though complete lockdown is epidemiologically effective, because it
eliminates infectious contacts, it comes with significant costs. Several recent
studies ha... | [
{
"created": "Fri, 31 Jul 2020 16:10:39 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Jan 2021 15:04:53 GMT",
"version": "v2"
}
] | 2021-01-08 | [
[
"Hindes",
"Jason",
""
],
[
"Bianco",
"Simone",
""
],
[
"Schwartz",
"Ira B.",
""
]
] | Without vaccines and treatments, societies must rely on non-pharmaceutical intervention strategies to control the spread of emerging diseases such as COVID-19. Though complete lockdown is epidemiologically effective, because it eliminates infectious contacts, it comes with significant costs. Several recent studies have... |
1905.09104 | S{\o}ren Toxvaerd | S{\o}ren Toxvaerd | A Prerequisite for Life | null | Journal of Theoretical Biology 474, 48-51, (2019) | 10.1016/j.jtbi.2019.05.001 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The complex physicochemical structures and chemical reactions in living
organism have some common features: (1) The life processes take place in the
cytosol in the cells, which, from a physicochemical point of view is an
emulsion of biomolecules in a dilute aqueous suspension. (2) All living systems
are homochiral wi... | [
{
"created": "Wed, 22 May 2019 12:34:29 GMT",
"version": "v1"
}
] | 2019-05-23 | [
[
"Toxvaerd",
"Søren",
""
]
] | The complex physicochemical structures and chemical reactions in living organism have some common features: (1) The life processes take place in the cytosol in the cells, which, from a physicochemical point of view is an emulsion of biomolecules in a dilute aqueous suspension. (2) All living systems are homochiral with... |
1109.3670 | Heather Harrington | Heather A. Harrington, Kenneth L. Ho, Thomas Thorne, and Michael P. H.
Stumpf | A parameter-free model discrimination criterion based on steady-state
coplanarity | 13 pages, 3 figures. In press, PNAS | null | 10.1073/pnas.1117073109 | null | q-bio.QM math.AG math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We describe a novel procedure for deciding when a mass-action model is
incompatible with observed steady-state data that does not require any
parameter estimation. Thus, we avoid the difficulties of nonlinear optimization
typically associated with methods based on parameter fitting. The key idea is
to use the model e... | [
{
"created": "Fri, 16 Sep 2011 17:27:57 GMT",
"version": "v1"
},
{
"created": "Wed, 12 Oct 2011 13:34:01 GMT",
"version": "v2"
},
{
"created": "Thu, 16 Aug 2012 14:40:24 GMT",
"version": "v3"
}
] | 2015-05-30 | [
[
"Harrington",
"Heather A.",
""
],
[
"Ho",
"Kenneth L.",
""
],
[
"Thorne",
"Thomas",
""
],
[
"Stumpf",
"Michael P. H.",
""
]
] | We describe a novel procedure for deciding when a mass-action model is incompatible with observed steady-state data that does not require any parameter estimation. Thus, we avoid the difficulties of nonlinear optimization typically associated with methods based on parameter fitting. The key idea is to use the model equ... |
1904.06514 | Fabrizio Pucci Dr. | Fabrizio Pucci, Alexander Schug | Shedding light on the dark matter of the biomolecular structural
universe: Progress in RNA 3D structure prediction | 14 pages, 4 figures | null | null | null | q-bio.MN physics.bio-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Structured RNA plays many functionally relevant roles in molecular life.
Structural information, while required to understand the functional cycles in
detail, is challenging to gather. Computational methods promise to complement
experimental efforts by predicting three-dimensional RNA models. Here, we
provide a conci... | [
{
"created": "Sat, 13 Apr 2019 09:58:49 GMT",
"version": "v1"
}
] | 2019-04-16 | [
[
"Pucci",
"Fabrizio",
""
],
[
"Schug",
"Alexander",
""
]
] | Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement experimental efforts by predicting three-dimensional RNA models. Here, we provide a concise... |
1803.10996 | Hyeongki Kim | Hyeongki Kim | Dihedral angle prediction using generative adversarial networks | 72 pages, MSc thesis under the supervision of Assoc. Prof. Thomas
Hamelryck and Asst. Prof. Wouter Boomsma | null | null | null | q-bio.BM cs.LG stat.ML | http://creativecommons.org/licenses/by/4.0/ | Several dihedral angles prediction methods were developed for protein
structure prediction and their other applications. However, distribution of
predicted angles would not be similar to that of real angles. To address this
we employed generative adversarial networks (GAN). Generative adversarial
networks are compose... | [
{
"created": "Thu, 29 Mar 2018 10:02:14 GMT",
"version": "v1"
}
] | 2018-03-30 | [
[
"Kim",
"Hyeongki",
""
]
] | Several dihedral angles prediction methods were developed for protein structure prediction and their other applications. However, distribution of predicted angles would not be similar to that of real angles. To address this we employed generative adversarial networks (GAN). Generative adversarial networks are composed ... |
q-bio/0603017 | Eugene Shakhnovich | D.B. Lyjatsky and E.I.Shakhnovich | Enhanced self-attraction of proteins and its evolutionary implications | null | null | null | null | q-bio.BM q-bio.MN | null | Statistical analysis of protein-protein interactions shows anomalously high
frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33,
3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438,
878-81] demonstrate that maintaining low sequence identity is a key
evolutionary mecha... | [
{
"created": "Thu, 16 Mar 2006 18:42:27 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Lyjatsky",
"D. B.",
""
],
[
"Shakhnovich",
"E. I.",
""
]
] | Statistical analysis of protein-protein interactions shows anomalously high frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33, 3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438, 878-81] demonstrate that maintaining low sequence identity is a key evolutionary mechani... |
1312.5582 | Andrew Dhawan | A. Dhawan, M. Kohandel, R. P. Hill, S. Sivaloganathan | Tumour Control Probability in Cancer Stem Cells Hypothesis | 18 pages, 5 figures | null | 10.1371/journal.pone.0096093 | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The tumour control probability (TCP) is a formalism derived to compare
various treatment regimens of radiation therapy, defined as the probability
that given a prescribed dose of radiation, a tumour has been eradicated or
controlled. In the traditional view of cancer, all cells share the ability to
divide without lim... | [
{
"created": "Thu, 19 Dec 2013 15:24:21 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Jan 2014 19:54:20 GMT",
"version": "v2"
}
] | 2015-06-18 | [
[
"Dhawan",
"A.",
""
],
[
"Kohandel",
"M.",
""
],
[
"Hill",
"R. P.",
""
],
[
"Sivaloganathan",
"S.",
""
]
] | The tumour control probability (TCP) is a formalism derived to compare various treatment regimens of radiation therapy, defined as the probability that given a prescribed dose of radiation, a tumour has been eradicated or controlled. In the traditional view of cancer, all cells share the ability to divide without limit... |
2010.11641 | Dmitry Ignatov | Dmitry I. Ignatov and Gennady V. Khvorykh and Andrey V. Khrunin and
Stefan Nikoli\'c and Makhmud Shaban and Elizaveta A. Petrova and Evgeniya A.
Koltsova and Fouzi Takelait and Dmitrii Egurnov | Object-Attribute Biclustering for Elimination of Missing Genotypes in
Ischemic Stroke Genome-Wide Data | Accepted to AIST 2020 | AIST 2020 (CCIS series) | null | null | q-bio.GN cs.LG stat.AP | http://creativecommons.org/licenses/by/4.0/ | Missing genotypes can affect the efficacy of machine learning approaches to
identify the risk genetic variants of common diseases and traits. The problem
occurs when genotypic data are collected from different experiments with
different DNA microarrays, each being characterised by its pattern of uncalled
(missing) ge... | [
{
"created": "Thu, 22 Oct 2020 12:27:43 GMT",
"version": "v1"
},
{
"created": "Sun, 25 Oct 2020 10:29:44 GMT",
"version": "v2"
}
] | 2020-10-27 | [
[
"Ignatov",
"Dmitry I.",
""
],
[
"Khvorykh",
"Gennady V.",
""
],
[
"Khrunin",
"Andrey V.",
""
],
[
"Nikolić",
"Stefan",
""
],
[
"Shaban",
"Makhmud",
""
],
[
"Petrova",
"Elizaveta A.",
""
],
[
"Koltsova",
"Evgeni... | Missing genotypes can affect the efficacy of machine learning approaches to identify the risk genetic variants of common diseases and traits. The problem occurs when genotypic data are collected from different experiments with different DNA microarrays, each being characterised by its pattern of uncalled (missing) geno... |
2005.01356 | Didier Pinault | Didier Pinault (FMTS) | A single psychotomimetic dose of ketamine decreases thalamocortical
spindles and delta oscillations in the sedated rat | Schizophrenia Research, Elsevier, In press | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: In patients with psychotic disorders, sleep spindles are reduced,
supporting the hypothesis that the thalamus and glutamate receptors play a
crucial etio-pathophysiological role, whose underlying mechanisms remain
unknown. We hypothesized that a reduced function of NMDA receptors is involved
in the spindl... | [
{
"created": "Mon, 4 May 2020 09:57:47 GMT",
"version": "v1"
}
] | 2020-05-05 | [
[
"Pinault",
"Didier",
"",
"FMTS"
]
] | Background: In patients with psychotic disorders, sleep spindles are reduced, supporting the hypothesis that the thalamus and glutamate receptors play a crucial etio-pathophysiological role, whose underlying mechanisms remain unknown. We hypothesized that a reduced function of NMDA receptors is involved in the spindle ... |
0704.2132 | Roberto Chignola | C. Tomelleri, E. Milotti, C. Dalla Pellegrina, O. Perbellini, A. Del
Fabbro, M. T. Scupoli and R. Chignola | A quantitative study on the growth variability of tumour cell clones in
vitro | 31 pages, 5 figures | null | null | null | q-bio.CB q-bio.QM | null | Objectives: In this study, we quantify the growth variability of tumour cell
clones from a human leukemia cell line. Materials and methods: We have used
microplate spectrophotometry to measure the growth kinetics of hundreds of
individual cell clones from the Molt3 cell line. The growth rate of each clonal
population... | [
{
"created": "Tue, 17 Apr 2007 10:30:56 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Tomelleri",
"C.",
""
],
[
"Milotti",
"E.",
""
],
[
"Pellegrina",
"C. Dalla",
""
],
[
"Perbellini",
"O.",
""
],
[
"Del Fabbro",
"A.",
""
],
[
"Scupoli",
"M. T.",
""
],
[
"Chignola",
"R.",
""
]
] | Objectives: In this study, we quantify the growth variability of tumour cell clones from a human leukemia cell line. Materials and methods: We have used microplate spectrophotometry to measure the growth kinetics of hundreds of individual cell clones from the Molt3 cell line. The growth rate of each clonal population h... |
2309.16498 | Yi Jiang | Xiuxiu He, Kuangcai Chen, Ning Fang, Yi Jiang | Coordinates in low-dimensional cell shape-space discriminate migration
dynamics from single static cell images | 29 pages, 9 figures | null | null | null | q-bio.CB physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Cell shape has long been used to discern cell phenotypes and states, but the
underlying premise has not been quantitatively tested. Here, we show that a
single cell image can be used to discriminate its migration behavior by
analyzing a large number of cell migration data in vitro. We analyzed a large
number of two-d... | [
{
"created": "Thu, 28 Sep 2023 15:06:36 GMT",
"version": "v1"
}
] | 2023-09-29 | [
[
"He",
"Xiuxiu",
""
],
[
"Chen",
"Kuangcai",
""
],
[
"Fang",
"Ning",
""
],
[
"Jiang",
"Yi",
""
]
] | Cell shape has long been used to discern cell phenotypes and states, but the underlying premise has not been quantitatively tested. Here, we show that a single cell image can be used to discriminate its migration behavior by analyzing a large number of cell migration data in vitro. We analyzed a large number of two-dim... |
2009.01083 | Alvaro Pastor | Alvaro Pastor | Memory systems of the brain | 36 pages, 4 figures, draft | null | 10.31219/OSF.IO/W6KN9 | null | q-bio.NC | http://creativecommons.org/licenses/by-sa/4.0/ | Humans have long been fascinated by how memories are formed, how they can be
damaged or lost, or still seem vibrant after many years. Thus the search for
the locus and organization of memory has had a long history, in which the
notion that is is composed of distinct systems developed during the second half
of the 20t... | [
{
"created": "Tue, 1 Sep 2020 11:59:17 GMT",
"version": "v1"
}
] | 2020-09-03 | [
[
"Pastor",
"Alvaro",
""
]
] | Humans have long been fascinated by how memories are formed, how they can be damaged or lost, or still seem vibrant after many years. Thus the search for the locus and organization of memory has had a long history, in which the notion that is is composed of distinct systems developed during the second half of the 20th ... |
1603.02007 | Christian Scheppach | Christian Scheppach, Hugh P.C. Robinson | Fluctuation analysis in nonstationary conditions: single Ca channel
current in cortical pyramidal neurons | null | Biophys. J., 5th Dec. 2017, 113(11):2383-2395 | 10.1016/j.bpj.2017.09.025 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fluctuation analysis is a method which allows measurement of the single
channel current of ion channels even when it is too small to be resolved
directly with the patch clamp technique. This is the case for voltage-gated
Ca2+ channels (VGCCs). They are present in all mammalian central neurons,
controlling presynaptic... | [
{
"created": "Mon, 7 Mar 2016 11:14:19 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Jun 2016 09:49:36 GMT",
"version": "v2"
},
{
"created": "Tue, 29 Aug 2017 12:55:07 GMT",
"version": "v3"
}
] | 2017-12-13 | [
[
"Scheppach",
"Christian",
""
],
[
"Robinson",
"Hugh P. C.",
""
]
] | Fluctuation analysis is a method which allows measurement of the single channel current of ion channels even when it is too small to be resolved directly with the patch clamp technique. This is the case for voltage-gated Ca2+ channels (VGCCs). They are present in all mammalian central neurons, controlling presynaptic r... |
1407.4116 | Min-Sheng Peng MSP | Ni-Ni Shi, Long Fan, Yong-Gang Yao, Min-Sheng Peng, Ya-Ping Zhang | Mitochondrial Genomes of Domestic Animals Need Scrutiny | 129 Pages, 1 figure, 3 tables, and 5 supplementary materials | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences
have been deposited in GenBank for eight common domestic animals (i.e. cattle,
dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors
or relatives. Nevertheless, few efforts have been performed to evaluate the
sequence... | [
{
"created": "Wed, 16 Jul 2014 01:18:22 GMT",
"version": "v1"
}
] | 2014-07-17 | [
[
"Shi",
"Ni-Ni",
""
],
[
"Fan",
"Long",
""
],
[
"Yao",
"Yong-Gang",
""
],
[
"Peng",
"Min-Sheng",
""
],
[
"Zhang",
"Ya-Ping",
""
]
] | More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (i.e. cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives. Nevertheless, few efforts have been performed to evaluate the sequence d... |
2105.13722 | Archishman Raju | David A. Rand, Archishman Raju, Meritxell Saez, Francis Corson, and
Eric D. Siggia | Geometry of Gene Regulatory Dynamics | null | null | 10.1073/pnas.2109729118 | null | q-bio.QM math.DS physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Embryonic development leads to the reproducible and ordered appearance of
complexity from egg to adult. The successive differentiation of different cell
types, that elaborates this complexity, result from the activity of gene
networks and was likened by Waddington to a flow through a landscape in which
valleys repres... | [
{
"created": "Fri, 28 May 2021 10:40:39 GMT",
"version": "v1"
}
] | 2022-05-11 | [
[
"Rand",
"David A.",
""
],
[
"Raju",
"Archishman",
""
],
[
"Saez",
"Meritxell",
""
],
[
"Corson",
"Francis",
""
],
[
"Siggia",
"Eric D.",
""
]
] | Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types, that elaborates this complexity, result from the activity of gene networks and was likened by Waddington to a flow through a landscape in which valleys represen... |
1907.03755 | Ahmed BaniMustafa | Ahmed BaniMustafa and Nigel Hardy | Applications of a Novel Knowledge Discovery and Data Mining Process
Model for Metabolomics | references information updated | null | null | null | q-bio.QM cs.DB cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work demonstrates the execution of a novel process model for knowledge
discovery and data mining for metabolomics (MeKDDaM). It aims to illustrate
MeKDDaM process model applicability using four different real-world
applications and to highlight its strengths and unique features. The
demonstrated applications pro... | [
{
"created": "Tue, 9 Jul 2019 01:14:55 GMT",
"version": "v1"
},
{
"created": "Tue, 30 Jul 2019 07:57:31 GMT",
"version": "v2"
}
] | 2019-07-31 | [
[
"BaniMustafa",
"Ahmed",
""
],
[
"Hardy",
"Nigel",
""
]
] | This work demonstrates the execution of a novel process model for knowledge discovery and data mining for metabolomics (MeKDDaM). It aims to illustrate MeKDDaM process model applicability using four different real-world applications and to highlight its strengths and unique features. The demonstrated applications provi... |
0705.0666 | Tom Michoel | Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, Tim
Van den Bulcke, Koenraad Van Leemput, Piet van Remortel, Martin Kuiper,
Kathleen Marchal, Yves Van de Peer | Validating module network learning algorithms using simulated data | 13 pages, 6 figures + 2 pages, 2 figures supplementary information | BMC Bioinformatics 2007, 8(Suppl 2):S5 | 10.1186/1471-2105-8-S2-S5 | null | q-bio.QM q-bio.MN | null | In recent years, several authors have used probabilistic graphical models to
learn expression modules and their regulatory programs from gene expression
data. Here, we demonstrate the use of the synthetic data generator SynTReN for
the purpose of testing and comparing module network learning algorithms. We
introduce ... | [
{
"created": "Fri, 4 May 2007 16:18:59 GMT",
"version": "v1"
}
] | 2007-11-15 | [
[
"Michoel",
"Tom",
""
],
[
"Maere",
"Steven",
""
],
[
"Bonnet",
"Eric",
""
],
[
"Joshi",
"Anagha",
""
],
[
"Saeys",
"Yvan",
""
],
[
"Bulcke",
"Tim Van den",
""
],
[
"Van Leemput",
"Koenraad",
""
],
[
... | In recent years, several authors have used probabilistic graphical models to learn expression modules and their regulatory programs from gene expression data. Here, we demonstrate the use of the synthetic data generator SynTReN for the purpose of testing and comparing module network learning algorithms. We introduce a ... |
1605.05291 | Jing Wu | Jing Wu, Benjamin R. Shuman, Bingni W. Brunton, Katherine M. Steele,
Jared D. Olson, Rajesh P.N. Rao, Jeffrey G. Ojemann | Multistep Model for Predicting Upper-Limb 3D Isometric Force Application
from Pre-Movement Electrocorticographic Features | 4 pages, 3 figures, accepted to EMBC 2016 (38th Annual International
Conference of the IEEE Engineering in Medicine and Biology Society) | null | 10.1109/EMBC.2016.7591010 | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural correlates of movement planning onset and direction may be present in
human electrocorticography in the signal dynamics of both motor and non-motor
cortical regions. We use a three-stage model of jPCA reduced-rank hidden Markov
model (jPCA-RR-HMM), regularized shrunken-centroid discriminant analysis (RDA),
and... | [
{
"created": "Tue, 17 May 2016 19:14:03 GMT",
"version": "v1"
}
] | 2016-10-26 | [
[
"Wu",
"Jing",
""
],
[
"Shuman",
"Benjamin R.",
""
],
[
"Brunton",
"Bingni W.",
""
],
[
"Steele",
"Katherine M.",
""
],
[
"Olson",
"Jared D.",
""
],
[
"Rao",
"Rajesh P. N.",
""
],
[
"Ojemann",
"Jeffrey G.",
... | Neural correlates of movement planning onset and direction may be present in human electrocorticography in the signal dynamics of both motor and non-motor cortical regions. We use a three-stage model of jPCA reduced-rank hidden Markov model (jPCA-RR-HMM), regularized shrunken-centroid discriminant analysis (RDA), and L... |
1801.01651 | Leonardo L. Gollo | Penelope Kale, Andrew Zalesky, Leonardo L. Gollo | Estimating the impact of structural directionality: How reliable are
undirected connectomes? | 29 pages, 6 figures, 9 supplementary figures, 4 supplementary tables | Network Neuroscience (2018) | 10.1162/NETN_a_00040 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Directionality is a fundamental feature of network connections. Most
structural brain networks are intrinsically directed because of the nature of
chemical synapses, which comprise most neuronal connections. Due to limitations
of non-invasive imaging techniques, the directionality of connections between
structurally ... | [
{
"created": "Fri, 5 Jan 2018 07:27:47 GMT",
"version": "v1"
}
] | 2018-01-19 | [
[
"Kale",
"Penelope",
""
],
[
"Zalesky",
"Andrew",
""
],
[
"Gollo",
"Leonardo L.",
""
]
] | Directionality is a fundamental feature of network connections. Most structural brain networks are intrinsically directed because of the nature of chemical synapses, which comprise most neuronal connections. Due to limitations of non-invasive imaging techniques, the directionality of connections between structurally co... |
1402.0632 | Binay Panda | Saurabh Gupta, Sanjoy Chaudhury 'and' Binay Panda | MUSIC: A Hybrid Computing Environment for Burrows-Wheeler Alignment for
Massive Amount of Short Read Sequence Data | 4 Pages, 1 Table, 4 Figures, Accepted in MECBME, 2014 for
presentation, To be indexed in IEEExPlore | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | High-throughput DNA sequencers are becoming indispensable in our
understanding of diseases at molecular level, in marker-assisted selection in
agriculture and in microbial genetics research. These sequencing instruments
produce enormous amount of data (often terabytes of raw data in a month) that
requires efficient a... | [
{
"created": "Tue, 4 Feb 2014 06:32:42 GMT",
"version": "v1"
}
] | 2014-02-05 | [
[
"Gupta",
"Saurabh",
""
],
[
"Panda",
"Sanjoy Chaudhury 'and' Binay",
""
]
] | High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous amount of data (often terabytes of raw data in a month) that requires efficient ana... |
1809.00895 | Marta Diaz Ms | Marta Diaz-delCastillo, Soren H. Christiansen, Camilla K. Appel, Sarah
Falka, David P. D. Woldbye and Anne-Marie Heegaarda | Neuropeptide Y is up-regulated and induces antinociception in
cancer-induced bone pain | 23 pages, 4 figures | Neuroscience. 2018 Aug 1;384:111-119. Epub 2018 May 29. PMID:
29852245 | 10.1016/j.neuroscience.2018.05.025 | null | q-bio.NC q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pain remains a major concern in patients suffering from metastatic cancer to
the bone and more knowledge of the condition, as well as novel treatment
avenues, are called for. Neuropeptide Y (NPY) is a highly conserved peptide
that appears to play a central role in nociceptive signaling in inflammatory
and neuropathic... | [
{
"created": "Tue, 4 Sep 2018 11:28:34 GMT",
"version": "v1"
}
] | 2018-09-10 | [
[
"Diaz-delCastillo",
"Marta",
""
],
[
"Christiansen",
"Soren H.",
""
],
[
"Appel",
"Camilla K.",
""
],
[
"Falka",
"Sarah",
""
],
[
"Woldbye",
"David P. D.",
""
],
[
"Heegaarda",
"Anne-Marie",
""
]
] | Pain remains a major concern in patients suffering from metastatic cancer to the bone and more knowledge of the condition, as well as novel treatment avenues, are called for. Neuropeptide Y (NPY) is a highly conserved peptide that appears to play a central role in nociceptive signaling in inflammatory and neuropathic p... |
1210.8415 | Markus Dahlem | Markus A. Dahlem and Jan Tusch | Predicted selective increase of cortical magnification due to cortical
folding | 22 pages, 6 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The cortical magnification matrix M is introduced founded on a notion similar
to that of the scalar cortical magnification factor M. Unlike M, this matrix is
suitable to describe anisotropy in cortical magnification, which is of
particular interest in the highly gyrified human cerebral cortex. The advantage
of our te... | [
{
"created": "Wed, 31 Oct 2012 17:47:21 GMT",
"version": "v1"
}
] | 2012-11-01 | [
[
"Dahlem",
"Markus A.",
""
],
[
"Tusch",
"Jan",
""
]
] | The cortical magnification matrix M is introduced founded on a notion similar to that of the scalar cortical magnification factor M. Unlike M, this matrix is suitable to describe anisotropy in cortical magnification, which is of particular interest in the highly gyrified human cerebral cortex. The advantage of our tens... |
1605.01592 | Alberto Ferrari | Alberto Ferrari and Mario Comelli | A comparison of methods for the analysis of binomial proportion data in
behavioral research | 26 pages, 4 figures, 3 tables | null | null | null | q-bio.QM q-bio.NC stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In behavioral and psychiatric research, data consisting of a per-subject
proportion of "successes" and "failures" over a finite number of trials often
arise. This kind of clustered binary data are usually non-normally distributed,
which can cause issues with parameter estimation and predictions if the usual
general l... | [
{
"created": "Thu, 5 May 2016 13:50:49 GMT",
"version": "v1"
},
{
"created": "Fri, 6 May 2016 15:47:12 GMT",
"version": "v2"
}
] | 2016-05-09 | [
[
"Ferrari",
"Alberto",
""
],
[
"Comelli",
"Mario",
""
]
] | In behavioral and psychiatric research, data consisting of a per-subject proportion of "successes" and "failures" over a finite number of trials often arise. This kind of clustered binary data are usually non-normally distributed, which can cause issues with parameter estimation and predictions if the usual general lin... |
1907.11280 | Breno de Oliveira Ferraz | P.P. Avelino, B.F. de Oliveira, and R.S. Trintin | Predominance of the weakest species in Lotka-Volterra and May-Leonard
implementations of the rock-paper-scissors model | 7 pages and 6 figures | Phys. Rev. E 100, 042209 (2019) | 10.1103/PhysRevE.100.042209 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We revisit the problem of the predominance of the 'weakest' species in the
context of Lotka-Volterra and May-Leonard implementations of a spatial
stochastic rock-paper-scissors model in which one of the species has its
predation probability reduced by $0 < \mathcal{P}_w < 1$. We show that,despite
the different popula... | [
{
"created": "Thu, 25 Jul 2019 19:14:46 GMT",
"version": "v1"
}
] | 2019-10-16 | [
[
"Avelino",
"P. P.",
""
],
[
"de Oliveira",
"B. F.",
""
],
[
"Trintin",
"R. S.",
""
]
] | We revisit the problem of the predominance of the 'weakest' species in the context of Lotka-Volterra and May-Leonard implementations of a spatial stochastic rock-paper-scissors model in which one of the species has its predation probability reduced by $0 < \mathcal{P}_w < 1$. We show that,despite the different populati... |
1609.06335 | Anthony Gitter | Anthony Gitter, Furong Huang, Ragupathyraj Valluvan, Ernest Fraenkel,
Animashree Anandkumar | Unsupervised learning of transcriptional regulatory networks via latent
tree graphical models | 37 pages, 9 figures | null | null | null | q-bio.MN cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene expression is a readily-observed quantification of transcriptional
activity and cellular state that enables the recovery of the relationships
between regulators and their target genes. Reconstructing transcriptional
regulatory networks from gene expression data is a problem that has attracted
much attention, but... | [
{
"created": "Tue, 20 Sep 2016 20:14:15 GMT",
"version": "v1"
}
] | 2016-09-22 | [
[
"Gitter",
"Anthony",
""
],
[
"Huang",
"Furong",
""
],
[
"Valluvan",
"Ragupathyraj",
""
],
[
"Fraenkel",
"Ernest",
""
],
[
"Anandkumar",
"Animashree",
""
]
] | Gene expression is a readily-observed quantification of transcriptional activity and cellular state that enables the recovery of the relationships between regulators and their target genes. Reconstructing transcriptional regulatory networks from gene expression data is a problem that has attracted much attention, but p... |
2106.11698 | Zheng Zhao | Zheng Zhao and Philip E. Bourne | Advance in Reversible Covalent Kinase Inhibitors | 55 pages; 12 figures | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Reversible covalent kinase inhibitors (RCKIs) are a class of novel kinase
inhibitors attracting increasing attention because they simultaneously show the
selectivity of covalent kinase inhibitors, yet avoid permanent
protein-modification-induced adverse effects. Over the last decade, RCKIs have
been reported to targe... | [
{
"created": "Tue, 22 Jun 2021 12:02:30 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Feb 2023 12:51:03 GMT",
"version": "v2"
}
] | 2023-02-23 | [
[
"Zhao",
"Zheng",
""
],
[
"Bourne",
"Philip E.",
""
]
] | Reversible covalent kinase inhibitors (RCKIs) are a class of novel kinase inhibitors attracting increasing attention because they simultaneously show the selectivity of covalent kinase inhibitors, yet avoid permanent protein-modification-induced adverse effects. Over the last decade, RCKIs have been reported to target ... |
0709.0679 | Joshua Shaevitz | Joshua W. Shaevitz, Daniel A. Fletcher | Curvature and torsion in growing actin networks | null | null | 10.1088/1478-3975/5/2/026006 | null | q-bio.BM physics.bio-ph q-bio.CB | null | Intracellular pathogens such as Listeria monocytogenes and Rickettsia
rickettsii move within a host cell by polymerizing a comet-tail of actin fibers
that ultimately pushes the cell forward. This dense network of cross-linked
actin polymers typically exhibits a striking curvature that causes bacteria to
move in gentl... | [
{
"created": "Wed, 5 Sep 2007 15:48:38 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Shaevitz",
"Joshua W.",
""
],
[
"Fletcher",
"Daniel A.",
""
]
] | Intracellular pathogens such as Listeria monocytogenes and Rickettsia rickettsii move within a host cell by polymerizing a comet-tail of actin fibers that ultimately pushes the cell forward. This dense network of cross-linked actin polymers typically exhibits a striking curvature that causes bacteria to move in gently ... |
1012.2730 | Christian Brouder | Vahid Salari and Christian Brouder | Comment on "Delayed luminescence of biological systems in terms of
coherent states" [Phys. Lett. A 293 (2002) 93] | 2 pages, no figure | Phys. Lett. A 375 (2011) 2531-2 | 10.1016/j.physleta.2011.05.017 | null | q-bio.QM quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Popp and Yan [F. A. Popp, Y. Yan, Phys. Lett. A 293 (2002) 93] proposed a
model for delayed luminescence based on a single time-dependent coherent state.
We show that the general solution of their model corresponds to a luminescence
that is a linear function of time. Therefore, their model is not compatible
with any ... | [
{
"created": "Mon, 13 Dec 2010 13:55:34 GMT",
"version": "v1"
}
] | 2011-06-22 | [
[
"Salari",
"Vahid",
""
],
[
"Brouder",
"Christian",
""
]
] | Popp and Yan [F. A. Popp, Y. Yan, Phys. Lett. A 293 (2002) 93] proposed a model for delayed luminescence based on a single time-dependent coherent state. We show that the general solution of their model corresponds to a luminescence that is a linear function of time. Therefore, their model is not compatible with any me... |
2301.04542 | Maria Virginia Bolelli | Maria Virginia Bolelli, Giovanna Citti, Alessandro Sarti, Steven W.
Zucker | Good continuation in 3D: the neurogeometry of stereo vision | null | null | null | null | q-bio.NC math.DG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Classical good continuation for image curves is based on $2D$ position and
orientation. It is supported by the columnar organization of cortex, by
psychophysical experiments, and by rich models of (differential) geometry. Here
we extend good continuation to stereo. We introduce a neurogeometric model, in
which the pa... | [
{
"created": "Wed, 11 Jan 2023 16:12:49 GMT",
"version": "v1"
}
] | 2023-01-12 | [
[
"Bolelli",
"Maria Virginia",
""
],
[
"Citti",
"Giovanna",
""
],
[
"Sarti",
"Alessandro",
""
],
[
"Zucker",
"Steven W.",
""
]
] | Classical good continuation for image curves is based on $2D$ position and orientation. It is supported by the columnar organization of cortex, by psychophysical experiments, and by rich models of (differential) geometry. Here we extend good continuation to stereo. We introduce a neurogeometric model, in which the para... |
1404.5827 | Ulrich S. Schwarz | Heinrich C. R. Klein and Ulrich S. Schwarz (Heidelberg University) | Studying protein assembly with reversible Brownian dynamics of patchy
particles | Revtex, 41 pages, 9 figures, includes some small corrections compared
to first version | J. Chem. Phys. 140, 184112 (2014) | 10.1063/1.4873708 | null | q-bio.SC cond-mat.soft cond-mat.stat-mech q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Assembly of protein complexes like virus shells, the centriole, the nuclear
pore complex or the actin cytoskeleton is strongly determined by their spatial
structure. Moreover it is becoming increasingly clear that the reversible
nature of protein assembly is also an essential element for their biological
function. He... | [
{
"created": "Wed, 23 Apr 2014 14:10:32 GMT",
"version": "v1"
},
{
"created": "Mon, 12 May 2014 15:51:22 GMT",
"version": "v2"
}
] | 2014-05-13 | [
[
"Klein",
"Heinrich C. R.",
"",
"Heidelberg University"
],
[
"Schwarz",
"Ulrich S.",
"",
"Heidelberg University"
]
] | Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here... |
1502.05331 | Nicholas Putnam | Nicholas H. Putnam, Brendan O'Connell, Jonathan C. Stites, Brandon J.
Rice, Andrew Fields, Paul D. Hartley, Charles W. Sugnet, David Haussler,
Daniel S. Rokhsar, Richard E. Green | Chromosome-scale shotgun assembly using an in vitro method for
long-range linkage | null | null | 10.1101/gr.193474.115 | null | q-bio.GN q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Long-range and highly accurate de novo assembly from short-read data is one
of the most pressing challenges in genomics. Recently, it has been shown that
read pairs generated by proximity ligation of DNA in chromatin of living tissue
can address this problem. These data dramatically increase the scaffold
contiguity o... | [
{
"created": "Wed, 18 Feb 2015 18:29:50 GMT",
"version": "v1"
}
] | 2016-02-11 | [
[
"Putnam",
"Nicholas H.",
""
],
[
"O'Connell",
"Brendan",
""
],
[
"Stites",
"Jonathan C.",
""
],
[
"Rice",
"Brandon J.",
""
],
[
"Fields",
"Andrew",
""
],
[
"Hartley",
"Paul D.",
""
],
[
"Sugnet",
"Charles W.",
... | Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem. These data dramatically increase the scaffold contiguity of ... |
1410.5930 | Marco Brigham | Marco Brigham and Alain Destexhe | Non-stationary filtered shot noise processes and applications to
neuronal membranes | 18 pages, 13 figures | Physical Review E 91: 062102, 2015 | 10.1103/PhysRevE.91.062102 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Filtered shot noise processes have proven to be very effective in modelling
the evolution of systems exposed to stochastic shot noise sources, and have
been applied to a wide variety of fields ranging from electronics through
biology. In particular, they can model the membrane potential Vm of neurons
driven by stocha... | [
{
"created": "Wed, 22 Oct 2014 07:45:17 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Feb 2015 09:56:46 GMT",
"version": "v2"
},
{
"created": "Sun, 13 Sep 2015 13:48:58 GMT",
"version": "v3"
}
] | 2015-09-15 | [
[
"Brigham",
"Marco",
""
],
[
"Destexhe",
"Alain",
""
]
] | Filtered shot noise processes have proven to be very effective in modelling the evolution of systems exposed to stochastic shot noise sources, and have been applied to a wide variety of fields ranging from electronics through biology. In particular, they can model the membrane potential Vm of neurons driven by stochast... |
2311.01320 | Yuehua Liu | Menghan Zhang and Yuehua Liu | The molecular pathology of genioglossus in obstructive sleep apnea | null | null | null | null | q-bio.MN q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Obstructive sleep apnea (OSA) is a sleep respiratory disease characterized by
sleep snoring accompanied by apnea and daytime sleeplessness. It is a complex
disease, with the multifactorial etiology, and the pathology is incompletely
understood. Genioglossus (GG), the largest dilator of upper airway, whose
fatigue is ... | [
{
"created": "Thu, 2 Nov 2023 15:33:26 GMT",
"version": "v1"
}
] | 2023-11-03 | [
[
"Zhang",
"Menghan",
""
],
[
"Liu",
"Yuehua",
""
]
] | Obstructive sleep apnea (OSA) is a sleep respiratory disease characterized by sleep snoring accompanied by apnea and daytime sleeplessness. It is a complex disease, with the multifactorial etiology, and the pathology is incompletely understood. Genioglossus (GG), the largest dilator of upper airway, whose fatigue is st... |
q-bio/0503032 | Akira Kinjo | Akira R. Kinjo, Ken Nishikawa | Predicting Secondary Structures, Contact Numbers, and Residue-wise
Contact Orders of Native Protein Structure from Amino Acid Sequence by
Critical Random Networks | 20 pages, 1 figure, 5 tables; minor revision; accepted for
publication in BIOPHYSICS | BIOPHYSICS Vol. 1, pp. 67-74 (2005) | 10.2142/biophysics.1.67 | null | q-bio.BM | null | Prediction of one-dimensional protein structures such as secondary structures
and contact numbers is useful for the three-dimensional structure prediction
and important for the understanding of sequence-structure relationship. Here we
present a new machine-learning method, critical random networks (CRNs), for
predict... | [
{
"created": "Tue, 22 Mar 2005 05:48:19 GMT",
"version": "v1"
},
{
"created": "Sat, 23 Jul 2005 05:20:02 GMT",
"version": "v2"
},
{
"created": "Thu, 20 Oct 2005 08:02:43 GMT",
"version": "v3"
}
] | 2007-05-23 | [
[
"Kinjo",
"Akira R.",
""
],
[
"Nishikawa",
"Ken",
""
]
] | Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we present a new machine-learning method, critical random networks (CRNs), for predictin... |
2408.03436 | Laleh Alisaraie | Luckman Qasim, Laleh Alisaraie | ProS2Vi: a Python Tool for Visualizing Proteins Secondary Structure | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-sa/4.0/ | The Protein Secondary Structure Visualizer ProS2Vi is a novel Python-based
visualization tool designed to enhance the analysis and accessibility of
protein secondary structures calculated and identified by the Dictionary of
Secondary Structure of Proteins algorithm. Leveraging robust Python libraries
such as Biopytho... | [
{
"created": "Tue, 6 Aug 2024 20:22:34 GMT",
"version": "v1"
}
] | 2024-08-08 | [
[
"Qasim",
"Luckman",
""
],
[
"Alisaraie",
"Laleh",
""
]
] | The Protein Secondary Structure Visualizer ProS2Vi is a novel Python-based visualization tool designed to enhance the analysis and accessibility of protein secondary structures calculated and identified by the Dictionary of Secondary Structure of Proteins algorithm. Leveraging robust Python libraries such as Biopython ... |
2202.07854 | Hiro-Sato Niwa | Hiro-Sato Niwa | Broken symmetry of recruitment fluctuations in marine fishes:
L\'evy-stable laws and beyond | 15 pages, 3 figures. arXiv admin note: text overlap with
arXiv:2202.06206 | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recruitment is calculated by summing random offspring-numbers entering the
population, where the number of summands (i.e. spawning population size) is
also a random process. A priori, it is not clear that individual reproductive
variability would have a significant impact on aggregate measures for
monitoring populati... | [
{
"created": "Wed, 16 Feb 2022 04:26:10 GMT",
"version": "v1"
}
] | 2022-02-17 | [
[
"Niwa",
"Hiro-Sato",
""
]
] | Recruitment is calculated by summing random offspring-numbers entering the population, where the number of summands (i.e. spawning population size) is also a random process. A priori, it is not clear that individual reproductive variability would have a significant impact on aggregate measures for monitoring population... |
1205.2059 | Richard A Neher | Richard A. Neher, Marija Vucelja, Marc M\'ezard, Boris I. Shraiman | Emergence of clones in sexual populations | revised version | null | 10.1088/1742-5468/2013/01/P01008 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In sexual population, recombination reshuffles genetic variation and produces
novel combinations of existing alleles, while selection amplifies the fittest
genotypes in the population. If recombination is more rapid than selection,
populations consist of a diverse mixture of many genotypes, as is observed in
many pop... | [
{
"created": "Wed, 9 May 2012 18:25:55 GMT",
"version": "v1"
},
{
"created": "Sat, 21 Jul 2012 14:26:48 GMT",
"version": "v2"
}
] | 2015-06-05 | [
[
"Neher",
"Richard A.",
""
],
[
"Vucelja",
"Marija",
""
],
[
"Mézard",
"Marc",
""
],
[
"Shraiman",
"Boris I.",
""
]
] | In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection, populations consist of a diverse mixture of many genotypes, as is observed in many popul... |
0903.4027 | Dustin Cartwright | Dustin A. Cartwright, Siobhan M. Brady, David A. Orlando, Bernd
Sturmfels, Philip N. Benfey | Reconstructing Spatiotemporal Gene Expression Data from Partial
Observations | 19 pages, 4 figures | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Developmental transcriptional networks in plants and animals operate in both
space and time. To understand these transcriptional networks it is essential to
obtain whole-genome expression data at high spatiotemporal resolution.
Substantial amounts of spatial and temporal microarray expression data
previously have bee... | [
{
"created": "Tue, 24 Mar 2009 07:28:41 GMT",
"version": "v1"
}
] | 2009-03-25 | [
[
"Cartwright",
"Dustin A.",
""
],
[
"Brady",
"Siobhan M.",
""
],
[
"Orlando",
"David A.",
""
],
[
"Sturmfels",
"Bernd",
""
],
[
"Benfey",
"Philip N.",
""
]
] | Developmental transcriptional networks in plants and animals operate in both space and time. To understand these transcriptional networks it is essential to obtain whole-genome expression data at high spatiotemporal resolution. Substantial amounts of spatial and temporal microarray expression data previously have been ... |
2406.07715 | Max Dabagia | Max Dabagia, Daniel Mitropolsky, Christos H. Papadimitriou, Santosh S.
Vempala | Coin-Flipping In The Brain: Statistical Learning with Neuronal
Assemblies | 22 pages, 8 figures | null | null | null | q-bio.NC cs.NE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | How intelligence arises from the brain is a central problem in science. A
crucial aspect of intelligence is dealing with uncertainty -- developing good
predictions about one's environment, and converting these predictions into
decisions. The brain itself seems to be noisy at many levels, from chemical
processes which... | [
{
"created": "Tue, 11 Jun 2024 20:51:50 GMT",
"version": "v1"
}
] | 2024-06-13 | [
[
"Dabagia",
"Max",
""
],
[
"Mitropolsky",
"Daniel",
""
],
[
"Papadimitriou",
"Christos H.",
""
],
[
"Vempala",
"Santosh S.",
""
]
] | How intelligence arises from the brain is a central problem in science. A crucial aspect of intelligence is dealing with uncertainty -- developing good predictions about one's environment, and converting these predictions into decisions. The brain itself seems to be noisy at many levels, from chemical processes which d... |
q-bio/0604001 | Alan McKane | A. J. McKane, J. D. Nagy, T. J. Newman, M. O. Stefanini | Amplified biochemical oscillations in cellular systems | 35 pages, 6 figures | null | 10.1007/s10955-006-9221-9 | null | q-bio.CB cond-mat.stat-mech q-bio.BM | null | We describe a mechanism for pronounced biochemical oscillations, relevant to
microscopic systems, such as the intracellular environment. This mechanism
operates for reaction schemes which, when modeled using deterministic rate
equations, fail to exhibit oscillations for any values of rate constants. The
mechanism rel... | [
{
"created": "Sun, 2 Apr 2006 13:58:16 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"McKane",
"A. J.",
""
],
[
"Nagy",
"J. D.",
""
],
[
"Newman",
"T. J.",
""
],
[
"Stefanini",
"M. O.",
""
]
] | We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations, fail to exhibit oscillations for any values of rate constants. The mechanism relie... |
2007.02185 | John Rhodes | Samaneh Yourdkhani, Elizabeth S. Allman, John A. Rhodes | Parameter identifiability for a profile mixture model of protein
evolution | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A Profile Mixture Model is a model of protein evolution, describing sequence
data in which sites are assumed to follow many related substitution processes
on a single evolutionary tree. The processes depend in part on different amino
acid distributions, or profiles, varying over sites in aligned sequences. A
fundamen... | [
{
"created": "Sat, 4 Jul 2020 21:09:41 GMT",
"version": "v1"
}
] | 2020-07-07 | [
[
"Yourdkhani",
"Samaneh",
""
],
[
"Allman",
"Elizabeth S.",
""
],
[
"Rhodes",
"John A.",
""
]
] | A Profile Mixture Model is a model of protein evolution, describing sequence data in which sites are assumed to follow many related substitution processes on a single evolutionary tree. The processes depend in part on different amino acid distributions, or profiles, varying over sites in aligned sequences. A fundamenta... |
2104.01512 | Seyednami Niyakan | Seyednami Niyakan, Ehsan Hajiramezanali, Shahin Boluki, Siamak Zamani
Dadaneh, Xiaoning Qian | SimCD: Simultaneous Clustering and Differential expression analysis for
single-cell transcriptomic data | null | null | null | null | q-bio.GN stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated
genome-scale transcriptomic profiling of individual cells, with the hope of
deconvolving cellular dynamic changes in corresponding cell sub-populations to
better understand molecular mechanisms of different development processes.
Several scRNA-seq a... | [
{
"created": "Sun, 4 Apr 2021 01:06:18 GMT",
"version": "v1"
}
] | 2021-04-06 | [
[
"Niyakan",
"Seyednami",
""
],
[
"Hajiramezanali",
"Ehsan",
""
],
[
"Boluki",
"Shahin",
""
],
[
"Dadaneh",
"Siamak Zamani",
""
],
[
"Qian",
"Xiaoning",
""
]
] | Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated genome-scale transcriptomic profiling of individual cells, with the hope of deconvolving cellular dynamic changes in corresponding cell sub-populations to better understand molecular mechanisms of different development processes. Several scRNA-seq ana... |
0803.0962 | Adilson Enio Motter | Adilson E. Motter, Natali Gulbahce, Eivind Almaas, Albert-Laszlo
Barabasi | Predicting synthetic rescues in metabolic networks | Supplementary Information is available at the Molecular Systems
Biology website: http://www.nature.com/msb/journal/v4/n1/full/msb20081.html | Molecular Systems Biology 4, 168 (2008) | 10.1038/msb.2008.1 | null | q-bio.MN cond-mat.dis-nn q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An important goal of medical research is to develop methods to recover the
loss of cellular function due to mutations and other defects. Many approaches
based on gene therapy aim to repair the defective gene or to insert genes with
compensatory function. Here, we propose an alternative, network-based strategy
that ai... | [
{
"created": "Thu, 6 Mar 2008 20:12:06 GMT",
"version": "v1"
}
] | 2008-03-15 | [
[
"Motter",
"Adilson E.",
""
],
[
"Gulbahce",
"Natali",
""
],
[
"Almaas",
"Eivind",
""
],
[
"Barabasi",
"Albert-Laszlo",
""
]
] | An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with compensatory function. Here, we propose an alternative, network-based strategy that aims... |
0802.2271 | Vasily Ogryzko V | Vasily Ogryzko | Quantum approach to adaptive mutations. Didactic introduction | 29 pages, 16 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A didactic introduction, dated by 1999, to the ideas of the papers
arXiv:q-bio/0701050 and arXiv:0704.0034
| [
{
"created": "Fri, 15 Feb 2008 19:25:34 GMT",
"version": "v1"
}
] | 2008-02-18 | [
[
"Ogryzko",
"Vasily",
""
]
] | A didactic introduction, dated by 1999, to the ideas of the papers arXiv:q-bio/0701050 and arXiv:0704.0034 |
1105.3106 | Ueli Rutishauser | Ueli Rutishauser, Rodney J. Douglas and Jean-Jacques Slotine | Collective stability of networks of winner-take-all circuits | 7 Figures | Neural computation 23(3):735-773, 2011 | 10.1162/NECO_a_00091 | null | q-bio.NC cond-mat.dis-nn cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The neocortex has a remarkably uniform neuronal organization, suggesting that
common principles of processing are employed throughout its extent. In
particular, the patterns of connectivity observed in the superficial layers of
the visual cortex are consistent with the recurrent excitation and inhibitory
feedback req... | [
{
"created": "Mon, 16 May 2011 14:37:15 GMT",
"version": "v1"
}
] | 2011-05-17 | [
[
"Rutishauser",
"Ueli",
""
],
[
"Douglas",
"Rodney J.",
""
],
[
"Slotine",
"Jean-Jacques",
""
]
] | The neocortex has a remarkably uniform neuronal organization, suggesting that common principles of processing are employed throughout its extent. In particular, the patterns of connectivity observed in the superficial layers of the visual cortex are consistent with the recurrent excitation and inhibitory feedback requi... |
q-bio/0702001 | Manikandan Narayanan | Manikandan Narayanan, Richard M. Karp | Comparing Protein Interaction Networks via a Graph Match-and-Split
Algorithm | 15 pages, 4 figures, 6 tables. Supplemental text available at
http://www.cs.berkeley.edu/~nmani/mas-supplement.pdf | null | null | null | q-bio.MN | null | We present a method that compares the protein interaction networks of two
species to detect functionally similar (conserved) protein modules between
them. The method is based on an algorithm we developed to identify matching
subgraphs between two graphs. Unlike previous network comparison methods, our
algorithm has p... | [
{
"created": "Thu, 1 Feb 2007 09:38:57 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Narayanan",
"Manikandan",
""
],
[
"Karp",
"Richard M.",
""
]
] | We present a method that compares the protein interaction networks of two species to detect functionally similar (conserved) protein modules between them. The method is based on an algorithm we developed to identify matching subgraphs between two graphs. Unlike previous network comparison methods, our algorithm has pro... |
2403.14046 | Stephan Pohl | Stephan Pohl, Edgar Y. Walker, David L. Barack, Jennifer Lee, Rachel
N. Denison, Ned Block, Florent Meyniel, Wei Ji Ma | Desiderata of evidence for representation in neuroscience | 50 pages, 11 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | This paper develops a systematic framework for the evidence neuroscientists
use to establish whether a neural response represents a feature. Researchers
try to establish that the neural response is (1) sensitive and (2) specific to
the feature, (3) invariant to other features, and (4) functional, which means
that it ... | [
{
"created": "Thu, 21 Mar 2024 00:07:02 GMT",
"version": "v1"
}
] | 2024-03-22 | [
[
"Pohl",
"Stephan",
""
],
[
"Walker",
"Edgar Y.",
""
],
[
"Barack",
"David L.",
""
],
[
"Lee",
"Jennifer",
""
],
[
"Denison",
"Rachel N.",
""
],
[
"Block",
"Ned",
""
],
[
"Meyniel",
"Florent",
""
],
[
... | This paper develops a systematic framework for the evidence neuroscientists use to establish whether a neural response represents a feature. Researchers try to establish that the neural response is (1) sensitive and (2) specific to the feature, (3) invariant to other features, and (4) functional, which means that it is... |
1802.03800 | Mehmet Tan | Mehmet Tan, Ozan F{\i}rat \"Ozg\"ul, Batuhan Bardak, I\c{s}{\i}ksu
Ek\c{s}io\u{g}lu, Suna Sabuncuo\u{g}lu | Drug response prediction by ensemble learning and drug-induced gene
expression signatures | Will appear in Genomics Journal | null | 10.1016/j.ygeno.2018.07.002 | null | q-bio.GN cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chemotherapeutic response of cancer cells to a given compound is one of the
most fundamental information one requires to design anti-cancer drugs. Recent
advances in producing large drug screens against cancer cell lines provided an
opportunity to apply machine learning methods for this purpose. In addition to
cytoto... | [
{
"created": "Sun, 11 Feb 2018 19:34:10 GMT",
"version": "v1"
},
{
"created": "Fri, 6 Apr 2018 13:25:44 GMT",
"version": "v2"
},
{
"created": "Mon, 16 Jul 2018 08:36:58 GMT",
"version": "v3"
}
] | 2018-07-17 | [
[
"Tan",
"Mehmet",
""
],
[
"Özgül",
"Ozan Fırat",
""
],
[
"Bardak",
"Batuhan",
""
],
[
"Ekşioğlu",
"Işıksu",
""
],
[
"Sabuncuoğlu",
"Suna",
""
]
] | Chemotherapeutic response of cancer cells to a given compound is one of the most fundamental information one requires to design anti-cancer drugs. Recent advances in producing large drug screens against cancer cell lines provided an opportunity to apply machine learning methods for this purpose. In addition to cytotoxi... |
0908.2022 | David Saakian | David B. Saakian, Christof K. Biebricher, Chin-Kun Hu | The intermediate evolution phase in case of truncated selection | 8 pages | Physical Review E 79, 041905 (2009) | 10.1103/PhysRevE.79.041905 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Using methods of statistical physics, we present rigorous theoretical
calculations of Eigen's quasispecies theory with the truncated fitness
landscape which dramatically limits the available sequence space of a
reproducing quasispecies. Depending on the mutation rates, we observe three
phases, a selective one, an int... | [
{
"created": "Fri, 14 Aug 2009 08:02:46 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Saakian",
"David B.",
""
],
[
"Biebricher",
"Christof K.",
""
],
[
"Hu",
"Chin-Kun",
""
]
] | Using methods of statistical physics, we present rigorous theoretical calculations of Eigen's quasispecies theory with the truncated fitness landscape which dramatically limits the available sequence space of a reproducing quasispecies. Depending on the mutation rates, we observe three phases, a selective one, an inter... |
0804.2055 | Francisco J. Cao | M. Bier, F. J. Cao | How occasional backstepping can speed up a processive motor protein | LaTeX, 5 pages, 3 figures | null | 10.1016/j.bpj.2008.12.620 | null | q-bio.SC cond-mat.stat-mech physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on
two legs along the biopolymer microtubule. The number of accidental backsteps
that kinesin takes appears to be much larger than what one would expect given
the amount of free energy that ATP hydrolysis makes available. This is puzzling
as m... | [
{
"created": "Sun, 13 Apr 2008 10:46:12 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Bier",
"M.",
""
],
[
"Cao",
"F. J.",
""
]
] | Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the amount of free energy that ATP hydrolysis makes available. This is puzzling as mor... |
1402.1845 | Michael B\"orsch | Samuel D. Bockenhauer, Thomas M. Duncan, W. E. Moerner, Michael
Boersch | The regulatory switch of F1-ATPase studied by single-molecule FRET in
the ABEL Trap | 14 pages, 5 figures | null | 10.1117/12.2042688 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | F1-ATPase is the soluble portion of the membrane-embedded enzyme FoF1-ATP
synthase that catalyzes the production of adenosine triphosphate in eukaryotic
and eubacterial cells. In reverse, the F1 part can also hydrolyze ATP quickly
at three catalytic binding sites. Therefore, catalysis of 'non-productive' ATP
hydrolys... | [
{
"created": "Sat, 8 Feb 2014 12:17:08 GMT",
"version": "v1"
}
] | 2015-06-18 | [
[
"Bockenhauer",
"Samuel D.",
""
],
[
"Duncan",
"Thomas M.",
""
],
[
"Moerner",
"W. E.",
""
],
[
"Boersch",
"Michael",
""
]
] | F1-ATPase is the soluble portion of the membrane-embedded enzyme FoF1-ATP synthase that catalyzes the production of adenosine triphosphate in eukaryotic and eubacterial cells. In reverse, the F1 part can also hydrolyze ATP quickly at three catalytic binding sites. Therefore, catalysis of 'non-productive' ATP hydrolysis... |
1404.6790 | Mikhail Ivanchenko Dr. | O.V. Bolkhovskaya, D.Yu. Zorin, M.V. Ivanchenko | Assessing T cell clonal size distribution: a non-parametric approach | 13 pages, 3 figures, 2 tables | PLoS ONE 9(10): e108658 | 10.1371/journal.pone.0108658 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Clonal structure of the human peripheral T-cell repertoire is shaped by a
number of homeostatic mechanisms, including antigen presentation, cytokine and
cell regulation. Its accurate tuning leads to a remarkable ability to combat
pathogens in all their variety, while systemic failures may lead to severe
consequences ... | [
{
"created": "Sun, 27 Apr 2014 17:07:17 GMT",
"version": "v1"
},
{
"created": "Thu, 21 Aug 2014 18:05:15 GMT",
"version": "v2"
}
] | 2014-10-07 | [
[
"Bolkhovskaya",
"O. V.",
""
],
[
"Zorin",
"D. Yu.",
""
],
[
"Ivanchenko",
"M. V.",
""
]
] | Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens in all their variety, while systemic failures may lead to severe consequences li... |
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