id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1405.0929 | Thomas Hopf | Thomas A. Hopf, Charlotta P.I. Sch\"arfe, Jo\~ao P.G.L.M. Rodrigues,
Anna G. Green, Chris Sander, Alexandre M.J.J. Bonvin, Debora S. Marks | Sequence co-evolution gives 3D contacts and structures of protein
complexes | null | null | 10.7554/eLife.03430 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein-protein interactions are fundamental to many biological processes.
Experimental screens have identified tens of thousands of interactions and
structural biology has provided detailed functional insight for select 3D
protein complexes. An alternative rich source of information about protein
interactions is the... | [
{
"created": "Mon, 5 May 2014 15:30:27 GMT",
"version": "v1"
},
{
"created": "Fri, 23 May 2014 20:49:25 GMT",
"version": "v2"
},
{
"created": "Tue, 16 Sep 2014 15:10:32 GMT",
"version": "v3"
}
] | 2016-08-11 | [
[
"Hopf",
"Thomas A.",
""
],
[
"Schärfe",
"Charlotta P. I.",
""
],
[
"Rodrigues",
"João P. G. L. M.",
""
],
[
"Green",
"Anna G.",
""
],
[
"Sander",
"Chris",
""
],
[
"Bonvin",
"Alexandre M. J. J.",
""
],
[
"Marks",
... | Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the e... |
1501.04874 | Alexander K. Vidybida | A. K. Vidybida | Output stream of leaky integrate and fire neuron | 11 pages, 1 Figure. Language is still Ukrainian. This is an extended
version of the previous version. The proofs of statements are added as well
as 1 Figure | Reports of the National Academy of Science of Ukraine, 2014, 12,
pp. 18-23 | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Probability density function of output interspike intervals is found in exact
form for leaky integrate and fire neuron stimulated with Poisson stream. The
diffusion approximation is not exploited.
| [
{
"created": "Tue, 20 Jan 2015 16:42:08 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Apr 2015 13:29:10 GMT",
"version": "v2"
},
{
"created": "Tue, 29 Dec 2015 12:04:03 GMT",
"version": "v3"
}
] | 2015-12-31 | [
[
"Vidybida",
"A. K.",
""
]
] | Probability density function of output interspike intervals is found in exact form for leaky integrate and fire neuron stimulated with Poisson stream. The diffusion approximation is not exploited. |
1412.2447 | David Krakauer | David Krakauer, Nils Bertschinger, Eckehard Olbrich, Nihat Ay, Jessica
C. Flack | The Information Theory of Individuality | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider biological individuality in terms of information theoretic and
graphical principles. Our purpose is to extract through an algorithmic
decomposition system-environment boundaries supporting individuality. We infer
or detect evolved individuals rather than assume that they exist. Given a set
of consistent m... | [
{
"created": "Mon, 8 Dec 2014 04:53:00 GMT",
"version": "v1"
}
] | 2014-12-09 | [
[
"Krakauer",
"David",
""
],
[
"Bertschinger",
"Nils",
""
],
[
"Olbrich",
"Eckehard",
""
],
[
"Ay",
"Nihat",
""
],
[
"Flack",
"Jessica C.",
""
]
] | We consider biological individuality in terms of information theoretic and graphical principles. Our purpose is to extract through an algorithmic decomposition system-environment boundaries supporting individuality. We infer or detect evolved individuals rather than assume that they exist. Given a set of consistent mea... |
1202.4378 | Joachim Krug | Ivan G. Szendro, Martijn F. Schenk, Jasper Franke, Joachim Krug and J.
Arjan G. M. de Visser | Quantitative analyses of empirical fitness landscapes | 24 pages, 5 figures; to appear in Journal of Statistical Mechanics:
Theory and Experiment | J. Stat. Mech. P01005 (2013) | 10.1088/1742-5468/2013/01/P01005 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The concept of a fitness landscape is a powerful metaphor that offers insight
into various aspects of evolutionary processes and guidance for the study of
evolution. Until recently, empirical evidence on the ruggedness of these
landscapes was lacking, but since it became feasible to construct all possible
genotypes c... | [
{
"created": "Mon, 20 Feb 2012 16:55:32 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Oct 2012 17:04:21 GMT",
"version": "v2"
}
] | 2013-01-18 | [
[
"Szendro",
"Ivan G.",
""
],
[
"Schenk",
"Martijn F.",
""
],
[
"Franke",
"Jasper",
""
],
[
"Krug",
"Joachim",
""
],
[
"de Visser",
"J. Arjan G. M.",
""
]
] | The concept of a fitness landscape is a powerful metaphor that offers insight into various aspects of evolutionary processes and guidance for the study of evolution. Until recently, empirical evidence on the ruggedness of these landscapes was lacking, but since it became feasible to construct all possible genotypes con... |
2002.03821 | Thomas G\"otz | Thomas G\"otz | First attempts to model the dynamics of the Coronavirus outbreak 2020 | 8 pages, 7 gigures | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Since the end of 2019 an outbreak of a new strain of coronavirus, called
2019--nCoV, is reported from China and later other parts of the world. Since
January 21, WHO reports daily data on confirmed cases and deaths from both
China and other countries. In this work we present some discrete and continuous
models to dis... | [
{
"created": "Mon, 10 Feb 2020 14:48:04 GMT",
"version": "v1"
}
] | 2020-02-11 | [
[
"Götz",
"Thomas",
""
]
] | Since the end of 2019 an outbreak of a new strain of coronavirus, called 2019--nCoV, is reported from China and later other parts of the world. Since January 21, WHO reports daily data on confirmed cases and deaths from both China and other countries. In this work we present some discrete and continuous models to discr... |
1903.09542 | Manuel Baltieri Mr | Manuel Baltieri and Christopher L. Buckley | Nonmodular architectures of cognitive systems based on active inference | Accepted at IJCNN 2019 | null | 10.1109/IJCNN.2019.8852048 | null | q-bio.NC cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In psychology and neuroscience it is common to describe cognitive systems as
input/output devices where perceptual and motor functions are implemented in a
purely feedforward, open-loop fashion. On this view, perception and action are
often seen as encapsulated modules with limited interaction between them. While
emb... | [
{
"created": "Fri, 22 Mar 2019 15:00:25 GMT",
"version": "v1"
}
] | 2022-03-10 | [
[
"Baltieri",
"Manuel",
""
],
[
"Buckley",
"Christopher L.",
""
]
] | In psychology and neuroscience it is common to describe cognitive systems as input/output devices where perceptual and motor functions are implemented in a purely feedforward, open-loop fashion. On this view, perception and action are often seen as encapsulated modules with limited interaction between them. While embod... |
1802.00023 | Siby Abraham | Jyotshna Dongardivev, Siby Abraham | Reaching Optimized Parameter Set, Protein Secondary Structure Prediction
Using Neural Network | 22 pages, 9 figures, 28 tables | Neural Computing and Applications (2017)28,1947 to 1974 | 10.1007/s00521-015-2150-2 10.1007/s00521-015-2150-2
10.1007/s00521-015-2150-2 | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose an optimized parameter set for protein secondary structure
prediction using three layer feed forward back propagation neural network. The
methodology uses four parameters viz. encoding scheme, window size, number of
neurons in the hidden layer and type of learning algorithm. The input layer of
the network ... | [
{
"created": "Wed, 31 Jan 2018 19:14:38 GMT",
"version": "v1"
}
] | 2018-02-02 | [
[
"Dongardivev",
"Jyotshna",
""
],
[
"Abraham",
"Siby",
""
]
] | We propose an optimized parameter set for protein secondary structure prediction using three layer feed forward back propagation neural network. The methodology uses four parameters viz. encoding scheme, window size, number of neurons in the hidden layer and type of learning algorithm. The input layer of the network co... |
2002.03173 | Chengxin Zhang | Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen
Zhou, Yang Zhang | Protein structure and sequence re-analysis of 2019-nCoV genome does not
indicate snakes as its intermediate host or the unique similarity between its
spike protein insertions and HIV-1 | Structure models for 2019-nCoV proteins are available at
https://zhanglab.ccmb.med.umich.edu/C-I-TASSER/2019-nCov/ | J. Proteome Res. 2020, 19, 4, 1351-1360 | 10.1021/acs.jproteome.0c00129 | null | q-bio.GN q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | As the infection of 2019-nCoV coronavirus is quickly developing into a global
pneumonia epidemic, careful analysis of its transmission and cellular
mechanisms is sorely needed. In this report, we re-analyzed the computational
approaches and findings presented in two recent manuscripts by Ji et al.
(https://doi.org/10... | [
{
"created": "Sat, 8 Feb 2020 14:24:59 GMT",
"version": "v1"
}
] | 2020-04-28 | [
[
"Zhang",
"Chengxin",
""
],
[
"Zheng",
"Wei",
""
],
[
"Huang",
"Xiaoqiang",
""
],
[
"Bell",
"Eric W.",
""
],
[
"Zhou",
"Xiaogen",
""
],
[
"Zhang",
"Yang",
""
]
] | As the infection of 2019-nCoV coronavirus is quickly developing into a global pneumonia epidemic, careful analysis of its transmission and cellular mechanisms is sorely needed. In this report, we re-analyzed the computational approaches and findings presented in two recent manuscripts by Ji et al. (https://doi.org/10.1... |
2310.11247 | Francoise Lecaignard | Francoise Lecaignard and Jeremie Mattout | Mismatch Negativity: time for deconstruction | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Error signals are the cornerstone of predictive coding and are widely
considered essential to sensory perception and beyond. The mismatch negativity
(MMN) is arguably the most emblematic and most studied brain error signal. It
is affected in many brain disorders. However, its precise algorithmic function
and the unde... | [
{
"created": "Tue, 17 Oct 2023 13:15:42 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Jan 2024 10:38:19 GMT",
"version": "v2"
},
{
"created": "Tue, 6 Feb 2024 20:57:51 GMT",
"version": "v3"
}
] | 2024-02-08 | [
[
"Lecaignard",
"Francoise",
""
],
[
"Mattout",
"Jeremie",
""
]
] | Error signals are the cornerstone of predictive coding and are widely considered essential to sensory perception and beyond. The mismatch negativity (MMN) is arguably the most emblematic and most studied brain error signal. It is affected in many brain disorders. However, its precise algorithmic function and the underl... |
2303.11099 | Thomas Wahl | Thomas Wahl, Michel Duprez, Axel Hutt | Closed-loop neurostimulation in real-time for the treatment of
pathological brain rhythms | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Mental disorders may exhibit pathological brain rhythms and neurostimulation
promises to alleviate of patients' symptoms by modifying these rhythms. Today,
most neurostimulation schemes are open-loop, i.e. administer experimental
stimulation protocols independent of the patients brain activity which may
yield a sub-o... | [
{
"created": "Mon, 20 Mar 2023 13:34:22 GMT",
"version": "v1"
}
] | 2023-03-21 | [
[
"Wahl",
"Thomas",
""
],
[
"Duprez",
"Michel",
""
],
[
"Hutt",
"Axel",
""
]
] | Mental disorders may exhibit pathological brain rhythms and neurostimulation promises to alleviate of patients' symptoms by modifying these rhythms. Today, most neurostimulation schemes are open-loop, i.e. administer experimental stimulation protocols independent of the patients brain activity which may yield a sub-opt... |
2002.07716 | Bartosz Jura | Bartosz Jura | Synaptic clock as a neural substrate of consciousness | 16 pages, 4 figures; added references, extended discussion of the
time consciousness literature | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this theoretical work the temporal aspect of consciousness is analyzed. We
start from the notion that while conscious experience seems to change
constantly, yet for any of its contents to be consciously perceived they must
last for some non-zero duration of time, which appears to constitute certain
conflict. We po... | [
{
"created": "Tue, 18 Feb 2020 16:43:58 GMT",
"version": "v1"
},
{
"created": "Sat, 5 Mar 2022 21:16:46 GMT",
"version": "v2"
}
] | 2022-03-08 | [
[
"Jura",
"Bartosz",
""
]
] | In this theoretical work the temporal aspect of consciousness is analyzed. We start from the notion that while conscious experience seems to change constantly, yet for any of its contents to be consciously perceived they must last for some non-zero duration of time, which appears to constitute certain conflict. We posi... |
1904.01637 | Safoora Yousefi | Safoora Yousefi, Amirreza Shaban, Mohamed Amgad, Ramraj Chandradevan,
Lee A. D. Cooper | Learning Clinical Outcomes from Heterogeneous Genomic Data Sources | null | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Translating the vast data generated by genomic platforms into reliable
predictions of clinical outcomes remains a critical challenge in realizing the
promise of genomic medicine largely due to small number of independent samples.
In this paper, we show that neural networks can be trained to predict clinical
outcomes ... | [
{
"created": "Tue, 2 Apr 2019 19:36:51 GMT",
"version": "v1"
}
] | 2019-04-04 | [
[
"Yousefi",
"Safoora",
""
],
[
"Shaban",
"Amirreza",
""
],
[
"Amgad",
"Mohamed",
""
],
[
"Chandradevan",
"Ramraj",
""
],
[
"Cooper",
"Lee A. D.",
""
]
] | Translating the vast data generated by genomic platforms into reliable predictions of clinical outcomes remains a critical challenge in realizing the promise of genomic medicine largely due to small number of independent samples. In this paper, we show that neural networks can be trained to predict clinical outcomes us... |
0801.1012 | George Tsibidis | George D. Tsibidis and Nektarios Tavernarakis | Nemo: a computational tool for analyzing nematode locomotion | 12 pages, 2 figures. accepted by BMC Neuroscience 2007, 8:86 | BMC Neuroscience 2007, 8:86 | null | null | q-bio.OT q-bio.GN q-bio.QM | null | The nematode Caenorhabditis elegans responds to an impressive range of
chemical, mechanical and thermal stimuli and is extensively used to investigate
the molecular mechanisms that mediate chemosensation, mechanotransduction and
thermosensation. The main behavioral output of these responses is manifested as
alteratio... | [
{
"created": "Mon, 7 Jan 2008 15:00:52 GMT",
"version": "v1"
}
] | 2008-02-21 | [
[
"Tsibidis",
"George D.",
""
],
[
"Tavernarakis",
"Nektarios",
""
]
] | The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and thermosensation. The main behavioral output of these responses is manifested as alterations... |
2102.11013 | Juntang Zhuang | Juntang Zhuang, Nicha Dvornek, Sekhar Tatikonda, Xenophon
Papademetris, Pamela Ventola, James Duncan | Multiple-shooting adjoint method for whole-brain dynamic causal modeling | 27th International Conference on Information Processing in Medical
Imaging | null | null | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dynamic causal modeling (DCM) is a Bayesian framework to infer directed
connections between compartments, and has been used to describe the
interactions between underlying neural populations based on functional
neuroimaging data. DCM is typically analyzed with the expectation-maximization
(EM) algorithm. However, bec... | [
{
"created": "Sun, 14 Feb 2021 05:00:12 GMT",
"version": "v1"
}
] | 2021-02-23 | [
[
"Zhuang",
"Juntang",
""
],
[
"Dvornek",
"Nicha",
""
],
[
"Tatikonda",
"Sekhar",
""
],
[
"Papademetris",
"Xenophon",
""
],
[
"Ventola",
"Pamela",
""
],
[
"Duncan",
"James",
""
]
] | Dynamic causal modeling (DCM) is a Bayesian framework to infer directed connections between compartments, and has been used to describe the interactions between underlying neural populations based on functional neuroimaging data. DCM is typically analyzed with the expectation-maximization (EM) algorithm. However, becau... |
1609.06424 | {\O}rnulf Borgan | {\O}rnulf Borgan (Department of Mathematics, University of Oslo) | Do Japanese and Italian women live longer than women in Scandinavia? | 7 pages, 3 figures | null | null | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Life expectancies at birth are routinely computed from period life tables.
Such period life expectancies may be distorted by selection when comparing
countries where the living conditions improved earlier (like Norway and Sweden)
with countries where they improved later (like Italy and Japan). One way to get
a fair c... | [
{
"created": "Wed, 21 Sep 2016 06:13:03 GMT",
"version": "v1"
}
] | 2016-09-22 | [
[
"Borgan",
"Ørnulf",
"",
"Department of Mathematics, University of Oslo"
]
] | Life expectancies at birth are routinely computed from period life tables. Such period life expectancies may be distorted by selection when comparing countries where the living conditions improved earlier (like Norway and Sweden) with countries where they improved later (like Italy and Japan). One way to get a fair com... |
1809.01281 | Nadine Chang | Nadine Chang, John A. Pyles, Abhinav Gupta, Michael J. Tarr, Elissa M.
Aminoff | BOLD5000: A public fMRI dataset of 5000 images | Currently in submission to Scientific Data | null | 10.1038/s41597-019-0052-3 | null | q-bio.NC cs.CV | http://creativecommons.org/licenses/by/4.0/ | Vision science, particularly machine vision, has been revolutionized by
introducing large-scale image datasets and statistical learning approaches.
Yet, human neuroimaging studies of visual perception still rely on small
numbers of images (around 100) due to time-constrained experimental procedures.
To apply statisti... | [
{
"created": "Wed, 5 Sep 2018 00:50:34 GMT",
"version": "v1"
}
] | 2020-01-23 | [
[
"Chang",
"Nadine",
""
],
[
"Pyles",
"John A.",
""
],
[
"Gupta",
"Abhinav",
""
],
[
"Tarr",
"Michael J.",
""
],
[
"Aminoff",
"Elissa M.",
""
]
] | Vision science, particularly machine vision, has been revolutionized by introducing large-scale image datasets and statistical learning approaches. Yet, human neuroimaging studies of visual perception still rely on small numbers of images (around 100) due to time-constrained experimental procedures. To apply statistica... |
1510.07992 | Ben Nolting | Christopher M. Moore, Christopher R. Stieha, Ben C. Nolting, Maria K.
Cameron, and Karen C. Abbott | QPot: An R Package for Stochastic Differential Equation Quasi-Potential
Analysis | null | null | null | null | q-bio.QM math.DS math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | QPot is an R package for analyzing two-dimensional systems of stochastic
differential equations. It provides users with a wide range of tools to
simulate, analyze, and visualize the dynamics of these systems. One of QPot's
key features is the computation of the quasi-potential, an important tool for
studying stochast... | [
{
"created": "Tue, 27 Oct 2015 17:10:57 GMT",
"version": "v1"
}
] | 2015-10-28 | [
[
"Moore",
"Christopher M.",
""
],
[
"Stieha",
"Christopher R.",
""
],
[
"Nolting",
"Ben C.",
""
],
[
"Cameron",
"Maria K.",
""
],
[
"Abbott",
"Karen C.",
""
]
] | QPot is an R package for analyzing two-dimensional systems of stochastic differential equations. It provides users with a wide range of tools to simulate, analyze, and visualize the dynamics of these systems. One of QPot's key features is the computation of the quasi-potential, an important tool for studying stochastic... |
1005.1142 | Atsushi Kamimura | Atsushi Kamimura and Kunihiko Kaneko | Reproduction of a Protocell by Replication of Minority Molecule in
Catalytic Reaction Network | 13 pages, 7 figures, submitted for publication | null | 10.1103/PhysRevLett.105.268103 | null | q-bio.CB cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For understanding the origin of life, it is essential to explain the
development of a compartmentalized structure, which undergoes growth and
division, from a set of chemical reactions. In this study, a hypercycle with
two chemicals that mutually catalyze each other is considered in order to show
that the reproductio... | [
{
"created": "Fri, 7 May 2010 07:20:29 GMT",
"version": "v1"
}
] | 2015-05-18 | [
[
"Kamimura",
"Atsushi",
""
],
[
"Kaneko",
"Kunihiko",
""
]
] | For understanding the origin of life, it is essential to explain the development of a compartmentalized structure, which undergoes growth and division, from a set of chemical reactions. In this study, a hypercycle with two chemicals that mutually catalyze each other is considered in order to show that the reproduction ... |
1807.03091 | Aleksandr Aravkin | Chris Vogl, Peng Zheng, Stephen P. Seslar, and Aleksandr Y. Aravkin | Computer Assisted Localization of a Heart Arrhythmia | 4 pages, 5 figures | null | null | null | q-bio.TO math.OC stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the problem of locating a point-source heart arrhythmia using
data from a standard diagnostic procedure, where a reference catheter is placed
in the heart, and arrival times from a second diagnostic catheter are recorded
as the diagnostic catheter moves around within the heart. We model this
situation as ... | [
{
"created": "Mon, 9 Jul 2018 13:06:38 GMT",
"version": "v1"
}
] | 2018-07-10 | [
[
"Vogl",
"Chris",
""
],
[
"Zheng",
"Peng",
""
],
[
"Seslar",
"Stephen P.",
""
],
[
"Aravkin",
"Aleksandr Y.",
""
]
] | We consider the problem of locating a point-source heart arrhythmia using data from a standard diagnostic procedure, where a reference catheter is placed in the heart, and arrival times from a second diagnostic catheter are recorded as the diagnostic catheter moves around within the heart. We model this situation as a ... |
2012.15681 | William Bialek | Vasyl Alba, Gordon J. Berman, William Bialek, and Joshua W. Shaevitz | Exploring a strongly non-Markovian animal behavior | null | null | null | null | q-bio.NC cond-mat.stat-mech | http://creativecommons.org/licenses/by/4.0/ | A freely walking fly visits roughly 100 stereotyped states in a strongly
non-Markovian sequence. To explore these dynamics, we develop a generalization
of the information bottleneck method, compressing the large number of
behavioral states into a more compact description that maximally preserves the
correlations betw... | [
{
"created": "Thu, 31 Dec 2020 16:02:44 GMT",
"version": "v1"
}
] | 2021-01-01 | [
[
"Alba",
"Vasyl",
""
],
[
"Berman",
"Gordon J.",
""
],
[
"Bialek",
"William",
""
],
[
"Shaevitz",
"Joshua W.",
""
]
] | A freely walking fly visits roughly 100 stereotyped states in a strongly non-Markovian sequence. To explore these dynamics, we develop a generalization of the information bottleneck method, compressing the large number of behavioral states into a more compact description that maximally preserves the correlations betwee... |
1710.02362 | Cyril Karamaoun | Cyril Karamaoun, Beno\^it Haut and Alain Van Muylem | A new role for exhaled nitric oxide as a functional marker of peripheral
airway caliber changes: a theoretical study | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Though considered as an inflammation marker, exhaled nitric oxide (FENO) was
shown to be sensitive to airway caliber changes to such an extent that it might
be considered as a marker of them. It is thus important to understand how these
changes and their localization mechanically affect the total NO flux
penetrating ... | [
{
"created": "Fri, 6 Oct 2017 12:07:33 GMT",
"version": "v1"
}
] | 2017-10-09 | [
[
"Karamaoun",
"Cyril",
""
],
[
"Haut",
"Benoît",
""
],
[
"Van Muylem",
"Alain",
""
]
] | Though considered as an inflammation marker, exhaled nitric oxide (FENO) was shown to be sensitive to airway caliber changes to such an extent that it might be considered as a marker of them. It is thus important to understand how these changes and their localization mechanically affect the total NO flux penetrating th... |
1104.5008 | William Bruno Ph.D. | William J. Bruno | What does photon energy tell us about cellphone safety? | 6 pages. Revision includes appended response to published critique by
B. Leikind | null | null | null | q-bio.OT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has been argued that cellphones are safe because a single microwave photon
does not have enough energy to break a chemical bond. We show that cellphone
technology operates in the classical wave limit, not the single photon limit.
Based on energy densities relative to thermal energy, we estimate thresholds at
which... | [
{
"created": "Tue, 26 Apr 2011 19:58:26 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Apr 2017 03:00:34 GMT",
"version": "v2"
}
] | 2017-04-26 | [
[
"Bruno",
"William J.",
""
]
] | It has been argued that cellphones are safe because a single microwave photon does not have enough energy to break a chemical bond. We show that cellphone technology operates in the classical wave limit, not the single photon limit. Based on energy densities relative to thermal energy, we estimate thresholds at which e... |
1911.06921 | Joseph Natale | Joseph L. Natale, H. George E. Hentschel, Ilya Nemenman | Precise Spatial Memory in Local Random Networks | 9 pages, 5 figures; presented at APS March Meeting 2019 conference
(http://meetings.aps.org/Meeting/MAR19/Session/R67.10) | Phys. Rev. E 102, 022405 (2020) | 10.1103/PhysRevE.102.022405 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Self-sustained, elevated neuronal activity persisting on time scales of ten
seconds or longer is thought to be vital for aspects of working memory,
including brain representations of real space. Continuous-attractor neural
networks, one of the most well-known modeling frameworks for persistent
activity, have been abl... | [
{
"created": "Sat, 16 Nov 2019 00:24:04 GMT",
"version": "v1"
}
] | 2020-08-19 | [
[
"Natale",
"Joseph L.",
""
],
[
"Hentschel",
"H. George E.",
""
],
[
"Nemenman",
"Ilya",
""
]
] | Self-sustained, elevated neuronal activity persisting on time scales of ten seconds or longer is thought to be vital for aspects of working memory, including brain representations of real space. Continuous-attractor neural networks, one of the most well-known modeling frameworks for persistent activity, have been able ... |
1510.04180 | Andrew Hart PhD | Andrew Hart and Servet Mart\'inez | An Entropy-Based Technique for Classifying Bacterial Chromosomes
According to Synonymous Codon Usage | 22 pages, 3 figures | null | null | null | q-bio.GN math.PR stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a framework based on conditional entropy and the Dirichlet
distribution for classifying chromosomes based on the degree to which they use
synonymous codons uniformly or preferentially, that is, whether or not codons
that code for an amino acid appear with the same relative frequency. Applying
the approach ... | [
{
"created": "Wed, 14 Oct 2015 16:03:09 GMT",
"version": "v1"
}
] | 2015-10-15 | [
[
"Hart",
"Andrew",
""
],
[
"Martínez",
"Servet",
""
]
] | We present a framework based on conditional entropy and the Dirichlet distribution for classifying chromosomes based on the degree to which they use synonymous codons uniformly or preferentially, that is, whether or not codons that code for an amino acid appear with the same relative frequency. Applying the approach to... |
1712.00919 | Erin Gorsich | Erin E. Gorsich, Rampal S. Etienne, Jan Medlock, Brianna R. Beechler,
Johannie M. Spaan, Robert S. Spaan, Vanessa O. Ezenwa, Anna E. Jolles | Interactions between chronic diseases: asymmetric outcomes of
co-infection at individual and population scales | 13 pages, 4 figures, 3 documents in the supporting information | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Co-infecting parasites and pathogens remain a leading challenge for global
public health due to their consequences for individual-level infection risk and
disease progression. However, a clear understanding of the population-level
consequences of co-infection is lacking. Here, we constructed a model that
includes thr... | [
{
"created": "Mon, 4 Dec 2017 06:15:22 GMT",
"version": "v1"
}
] | 2017-12-05 | [
[
"Gorsich",
"Erin E.",
""
],
[
"Etienne",
"Rampal S.",
""
],
[
"Medlock",
"Jan",
""
],
[
"Beechler",
"Brianna R.",
""
],
[
"Spaan",
"Johannie M.",
""
],
[
"Spaan",
"Robert S.",
""
],
[
"Ezenwa",
"Vanessa O.",
... | Co-infecting parasites and pathogens remain a leading challenge for global public health due to their consequences for individual-level infection risk and disease progression. However, a clear understanding of the population-level consequences of co-infection is lacking. Here, we constructed a model that includes three... |
1001.4914 | David Morrison | Meaghan E. Jenkins, David A. Morrison, Tony D. Auld | Estimating seed bank accumulation and dynamics in three obligate-seeder
Proteaceae species | 15 pages, including 4 Figures and 4 Tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The seed bank dynamics of the three co-occurring obligate-seeder (i.e.
fire-sensitive) Proteaceae species, Banksia ericifolia, Banksia marginata and
Petrophile pulchella, were examined at sites of varying time since the most
recent fire (i.e. plant age) in the Sydney region. Significant variation among
species was fo... | [
{
"created": "Wed, 27 Jan 2010 11:35:02 GMT",
"version": "v1"
}
] | 2010-01-28 | [
[
"Jenkins",
"Meaghan E.",
""
],
[
"Morrison",
"David A.",
""
],
[
"Auld",
"Tony D.",
""
]
] | The seed bank dynamics of the three co-occurring obligate-seeder (i.e. fire-sensitive) Proteaceae species, Banksia ericifolia, Banksia marginata and Petrophile pulchella, were examined at sites of varying time since the most recent fire (i.e. plant age) in the Sydney region. Significant variation among species was foun... |
1602.06937 | Luis Bonilla L. | F. Terragni, M. Carretero, V. Capasso and L. L. Bonilla | Stochastic Model of Tumor-induced Angiogenesis: Ensemble Averages and
Deterministic Equations | 26 pages, 8 figures | Phys. Rev. E 93, 022413 (2016) | 10.1103/PhysRevE.93.022413 | null | q-bio.TO cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A recent conceptual model of tumor-driven angiogenesis including branching,
elongation, and anastomosis of blood vessels captures some of the intrinsic
multiscale structures of this complex system, yet allowing to extract a
deterministic integro-partial differential description of the vessel tip
density [Phys. Rev. E... | [
{
"created": "Mon, 22 Feb 2016 20:54:16 GMT",
"version": "v1"
}
] | 2016-02-24 | [
[
"Terragni",
"F.",
""
],
[
"Carretero",
"M.",
""
],
[
"Capasso",
"V.",
""
],
[
"Bonilla",
"L. L.",
""
]
] | A recent conceptual model of tumor-driven angiogenesis including branching, elongation, and anastomosis of blood vessels captures some of the intrinsic multiscale structures of this complex system, yet allowing to extract a deterministic integro-partial differential description of the vessel tip density [Phys. Rev. E 9... |
2102.04746 | Mats Brun PhD | Mats K. Brun, Elyes Ahmed, Jan Martin Nordbotten, Nils Christian
Stenseth | Modeling the process of speciation using a multi-scale framework
including error estimates | 27 pages, 27 figures | null | null | null | q-bio.PE math.AP | http://creativecommons.org/licenses/by/4.0/ | This paper concerns the modeling and numerical simulation of the process of
speciation. In particular, given conditions for which one or more speciation
events within an ecosystem occur, our aim is to develop the necessary modeling
and simulation tools. Care is also taken to establish a solid mathematical
foundation ... | [
{
"created": "Tue, 9 Feb 2021 10:26:16 GMT",
"version": "v1"
},
{
"created": "Thu, 7 Oct 2021 16:17:05 GMT",
"version": "v2"
}
] | 2021-10-08 | [
[
"Brun",
"Mats K.",
""
],
[
"Ahmed",
"Elyes",
""
],
[
"Nordbotten",
"Jan Martin",
""
],
[
"Stenseth",
"Nils Christian",
""
]
] | This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and simulation tools. Care is also taken to establish a solid mathematical foundation on... |
1106.1723 | Mike Steel Prof. | David Bryant and Mike Steel | 'Bureaucratic' set systems, and their role in phylogenetics | 6 pages, 1 figure | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We say that a collection $\Cc$ of subsets of $X$ is {\em bureaucratic} if
every maximal hierarchy on $X$ contained in $\Cc$ is also maximum. We
characterise bureaucratic set systems and show how they arise in phylogenetics.
This framework has several useful algorithmic consequences: we generalize some
earlier results... | [
{
"created": "Thu, 9 Jun 2011 07:37:27 GMT",
"version": "v1"
}
] | 2011-06-10 | [
[
"Bryant",
"David",
""
],
[
"Steel",
"Mike",
""
]
] | We say that a collection $\Cc$ of subsets of $X$ is {\em bureaucratic} if every maximal hierarchy on $X$ contained in $\Cc$ is also maximum. We characterise bureaucratic set systems and show how they arise in phylogenetics. This framework has several useful algorithmic consequences: we generalize some earlier results a... |
2204.07904 | Madhur Mangalam | Damian G. Kelty-Stephen, Madhur Mangalam | Turing's cascade instability supports the coordination of the mind,
brain, and behavior | 53 pages, 13 figures | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Turing inspired a computer metaphor of the mind and brain that has been handy
and has spawned decades of empirical investigation, but he did much more and
offered behavioral and cognitive sciences another metaphor--that of the
cascade. The time has come to confront Turing's cascading instability, which
suggests a geo... | [
{
"created": "Sun, 17 Apr 2022 02:22:30 GMT",
"version": "v1"
}
] | 2022-04-19 | [
[
"Kelty-Stephen",
"Damian G.",
""
],
[
"Mangalam",
"Madhur",
""
]
] | Turing inspired a computer metaphor of the mind and brain that has been handy and has spawned decades of empirical investigation, but he did much more and offered behavioral and cognitive sciences another metaphor--that of the cascade. The time has come to confront Turing's cascading instability, which suggests a geome... |
q-bio/0511043 | Gasper Tkacik | Noam Slonim, Gurinder Singh Atwal, Gasper Tkacik, William Bialek | Information based clustering | To appear in Proceedings of the National Academy of Sciences USA, 11
pages, 9 figures | null | 10.1073/pnas.0507432102 | null | q-bio.QM | null | In an age of increasingly large data sets, investigators in many different
disciplines have turned to clustering as a tool for data analysis and
exploration. Existing clustering methods, however, typically depend on several
nontrivial assumptions about the structure of data. Here we reformulate the
clustering problem... | [
{
"created": "Sat, 26 Nov 2005 04:53:47 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Slonim",
"Noam",
""
],
[
"Atwal",
"Gurinder Singh",
""
],
[
"Tkacik",
"Gasper",
""
],
[
"Bialek",
"William",
""
]
] | In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here we reformulate the clustering problem f... |
1210.7414 | Asaf Gal | Asaf Gal and Shimon Marom | Self-organized criticality in single neuron excitability | 5 pages, 2 figures | Phys. Rev. E 88, 062717 (2013) | 10.1103/PhysRevE.88.062717 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present experimental and theoretical arguments, at the single neuron
level, suggesting that neuronal response fluctuations reflect a process that
positions the neuron near a transition point that separates excitable and
unexcitable phases. This view is supported by the dynamical properties of the
system as observe... | [
{
"created": "Sun, 28 Oct 2012 07:30:49 GMT",
"version": "v1"
},
{
"created": "Tue, 30 Oct 2012 19:34:24 GMT",
"version": "v2"
},
{
"created": "Wed, 31 Oct 2012 15:21:20 GMT",
"version": "v3"
},
{
"created": "Wed, 27 Feb 2013 11:46:34 GMT",
"version": "v4"
},
{
"c... | 2013-12-25 | [
[
"Gal",
"Asaf",
""
],
[
"Marom",
"Shimon",
""
]
] | We present experimental and theoretical arguments, at the single neuron level, suggesting that neuronal response fluctuations reflect a process that positions the neuron near a transition point that separates excitable and unexcitable phases. This view is supported by the dynamical properties of the system as observed ... |
2008.10992 | Tim Friede | Tobias M\"utze and Tim Friede | Data monitoring committees for clinical trials evaluating treatments of
COVID-19 | null | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The first cases of coronavirus disease 2019 (COVID-19) were reported in
December 2019 and the outbreak of SARS-CoV-2 was declared a pandemic in March
2020 by the World Health Organization. This sparked a plethora of
investigations into diagnostics and vaccination for SARS-CoV-2, as well as
treatments for COVID-19. Si... | [
{
"created": "Thu, 20 Aug 2020 08:59:34 GMT",
"version": "v1"
}
] | 2020-08-26 | [
[
"Mütze",
"Tobias",
""
],
[
"Friede",
"Tim",
""
]
] | The first cases of coronavirus disease 2019 (COVID-19) were reported in December 2019 and the outbreak of SARS-CoV-2 was declared a pandemic in March 2020 by the World Health Organization. This sparked a plethora of investigations into diagnostics and vaccination for SARS-CoV-2, as well as treatments for COVID-19. Sinc... |
0903.0731 | David Lusseau | David Lusseau and Larissa Conradt | The emergence of unshared consensus decisions in bottlenose dolphins | 17 pages, 3 figures. in press as part of the special issue "Social
Networks: new perspectives" of Behavioral Ecology and Sociobiology | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Unshared consensus decision-making processes, in which one or a small number
of individuals make the decision for the rest of a group, are rarely
documented. However, this mechanism can be beneficial for all group members
when one individual has greater knowledge about the benefits of the decision
than other group me... | [
{
"created": "Wed, 4 Mar 2009 11:11:31 GMT",
"version": "v1"
}
] | 2009-03-05 | [
[
"Lusseau",
"David",
""
],
[
"Conradt",
"Larissa",
""
]
] | Unshared consensus decision-making processes, in which one or a small number of individuals make the decision for the rest of a group, are rarely documented. However, this mechanism can be beneficial for all group members when one individual has greater knowledge about the benefits of the decision than other group memb... |
1206.4812 | Gilles Wainrib | Mathieu Galtier, Gilles Wainrib | A biological gradient descent for prediction through a combination of
STDP and homeostatic plasticity | 36 pages, 3 figures | null | null | null | q-bio.NC cs.NE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Identifying, formalizing and combining biological mechanisms which implement
known brain functions, such as prediction, is a main aspect of current research
in theoretical neuroscience. In this letter, the mechanisms of Spike Timing
Dependent Plasticity (STDP) and homeostatic plasticity, combined in an original
mathe... | [
{
"created": "Thu, 21 Jun 2012 09:13:39 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Jun 2013 16:11:01 GMT",
"version": "v2"
}
] | 2013-06-12 | [
[
"Galtier",
"Mathieu",
""
],
[
"Wainrib",
"Gilles",
""
]
] | Identifying, formalizing and combining biological mechanisms which implement known brain functions, such as prediction, is a main aspect of current research in theoretical neuroscience. In this letter, the mechanisms of Spike Timing Dependent Plasticity (STDP) and homeostatic plasticity, combined in an original mathema... |
1005.5292 | Luciano Teresi | Paola Nardinocchi, Luciano Teresi, Valerio Varano | Myocardial Contractions and the Ventricular Pressure--Volume
Relationship | 16 pages, 18 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a reduced-order heart model with the aim of introducing a novel
point of view in the interpretation of the pressure-volume loops. The novelty
of the approach is based on the definition of active contraction as opposed to
that of active stress. The consequences of the assumption are discussed with
reference... | [
{
"created": "Fri, 28 May 2010 13:48:52 GMT",
"version": "v1"
}
] | 2010-05-31 | [
[
"Nardinocchi",
"Paola",
""
],
[
"Teresi",
"Luciano",
""
],
[
"Varano",
"Valerio",
""
]
] | We present a reduced-order heart model with the aim of introducing a novel point of view in the interpretation of the pressure-volume loops. The novelty of the approach is based on the definition of active contraction as opposed to that of active stress. The consequences of the assumption are discussed with reference t... |
0706.3681 | Marcin Molski | Marcin Molski | On the Classification Scheme for Phenomenological Universalities in
Growth Problems in Physics and Other Sciences | null | null | null | null | q-bio.OT q-bio.QM | null | Comment on "Classification Scheme for Phenomenological Universalities in
Growth Problems in Physics and Other Sciences" by P. Castorina, P. P. Delsanto
and C. Guiot, Phys. Rev. Lett. {\bf 96}, 188701 (2006) is presented. It has
been proved that the West-like function of growth derived by the authors is
incorrect and ... | [
{
"created": "Mon, 25 Jun 2007 17:40:10 GMT",
"version": "v1"
}
] | 2007-06-26 | [
[
"Molski",
"Marcin",
""
]
] | Comment on "Classification Scheme for Phenomenological Universalities in Growth Problems in Physics and Other Sciences" by P. Castorina, P. P. Delsanto and C. Guiot, Phys. Rev. Lett. {\bf 96}, 188701 (2006) is presented. It has been proved that the West-like function of growth derived by the authors is incorrect and th... |
2111.11753 | Flavia Feliciangeli | Hanan Dreiwi, Flavia Feliciangeli, Mario Castro, Grant Lythe, Carmen
Molina-Par\'is, Mart\'in L\'opez-Garc\'ia | A stochastic model of cell proliferation and death across a sequence of
compartments | 22 pages, 8 figures | null | null | null | q-bio.CB math.DS | http://creativecommons.org/licenses/by/4.0/ | Cells of the human body have nearly identical genome but exhibit very
different phenotypes that allow them to carry out specific functions and react
to changes in their surrounding environment. This division of labour is
achieved by cellular division and cellular differentiation, events which lead
to a population of ... | [
{
"created": "Tue, 23 Nov 2021 10:00:59 GMT",
"version": "v1"
}
] | 2021-11-24 | [
[
"Dreiwi",
"Hanan",
""
],
[
"Feliciangeli",
"Flavia",
""
],
[
"Castro",
"Mario",
""
],
[
"Lythe",
"Grant",
""
],
[
"Molina-París",
"Carmen",
""
],
[
"López-García",
"Martín",
""
]
] | Cells of the human body have nearly identical genome but exhibit very different phenotypes that allow them to carry out specific functions and react to changes in their surrounding environment. This division of labour is achieved by cellular division and cellular differentiation, events which lead to a population of ce... |
q-bio/0702012 | Changbong Hyeon | Changbong Hyeon and Jose N. Onuchic | Internal strain regulates the nucleotide binding site of the kinesin
leading head | 34 pages, 9 Figures | PNAS (2007) vol 104, 2175-2180 | 10.1073/pnas.0610939104 | null | q-bio.BM physics.bio-ph | null | In the presence of ATP, kinesin proceeds along the protofilament of
microtubule by alternated binding of two motor domains on the tubulin binding
sites. Since the processivity of kinesin is much higher than other motor
proteins, it has been speculated that there exists a mechanism for allosteric
regulation between th... | [
{
"created": "Wed, 7 Feb 2007 18:55:00 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Hyeon",
"Changbong",
""
],
[
"Onuchic",
"Jose N.",
""
]
] | In the presence of ATP, kinesin proceeds along the protofilament of microtubule by alternated binding of two motor domains on the tubulin binding sites. Since the processivity of kinesin is much higher than other motor proteins, it has been speculated that there exists a mechanism for allosteric regulation between the ... |
1809.02506 | Mohammad Golbabaee | Arnold Julian Vinoj Benjamin, Pedro A. G\'omez, Mohammad Golbabaee,
Tim Sprenger, Marion I. Menzel, Mike E. Davies, Ian Marshall | Balanced multi-shot EPI for accelerated Cartesian MRF: An alternative to
spiral MRF | Proceedings of the Joint Annual Meeting ISMRM-ESMRMB 2018 - Paris | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The main purpose of this study is to show that a highly accelerated Cartesian
MRF scheme using a multi-shot EPI readout (i.e. multi-shot EPI-MRF) can produce
good quality multi-parametric maps such as T1, T2 and proton density (PD) in a
sufficiently short scan duration that is similar to conventional MRF. This
multi-... | [
{
"created": "Thu, 6 Sep 2018 12:51:58 GMT",
"version": "v1"
}
] | 2018-09-10 | [
[
"Benjamin",
"Arnold Julian Vinoj",
""
],
[
"Gómez",
"Pedro A.",
""
],
[
"Golbabaee",
"Mohammad",
""
],
[
"Sprenger",
"Tim",
""
],
[
"Menzel",
"Marion I.",
""
],
[
"Davies",
"Mike E.",
""
],
[
"Marshall",
"Ian",... | The main purpose of this study is to show that a highly accelerated Cartesian MRF scheme using a multi-shot EPI readout (i.e. multi-shot EPI-MRF) can produce good quality multi-parametric maps such as T1, T2 and proton density (PD) in a sufficiently short scan duration that is similar to conventional MRF. This multi-sh... |
2308.10645 | Gerald Cooray PhD | Gerald K. Cooray, Vernon Cooray and Karl Friston | Canonical Cortical Field Theories | 19 pages, 1 figure | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | We characterise the dynamics of neuronal activity, in terms of field theory,
using neural units placed on a 2D-lattice modelling the cortical surface. The
electrical activity of neuronal units was analysed with the aim of deriving a
neural field model with a simple functional form that still able to predict or
reprod... | [
{
"created": "Mon, 21 Aug 2023 11:34:05 GMT",
"version": "v1"
}
] | 2023-08-22 | [
[
"Cooray",
"Gerald K.",
""
],
[
"Cooray",
"Vernon",
""
],
[
"Friston",
"Karl",
""
]
] | We characterise the dynamics of neuronal activity, in terms of field theory, using neural units placed on a 2D-lattice modelling the cortical surface. The electrical activity of neuronal units was analysed with the aim of deriving a neural field model with a simple functional form that still able to predict or reproduc... |
1305.5103 | Miloje Rakocevic M. | Miloje M. Rakocevic | Harmonic mean as a determinant of the genetic code | 20 pages, 14 tables, 5 boxes, 12 footnotes, 4 appendices with 8
tables and 3 surveys; in Conclusion: the hypothesis about extraterrestrial
life | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is shown that there is a sense in splitting Genetic Code Table (GCT) into
three parts using the harmonic mean, calculated by the formula H (a, b) = 2ab /
(a + b), where a = 63 and b = 31.5. Within these three parts, the amino acids
(AAs) are positioned on the basis of the validity of the evident regularities
of ke... | [
{
"created": "Tue, 21 May 2013 18:04:17 GMT",
"version": "v1"
},
{
"created": "Sat, 1 Jun 2013 18:51:31 GMT",
"version": "v2"
},
{
"created": "Sat, 8 Jun 2013 08:44:04 GMT",
"version": "v3"
},
{
"created": "Wed, 12 Jun 2013 10:36:23 GMT",
"version": "v4"
}
] | 2013-06-13 | [
[
"Rakocevic",
"Miloje M.",
""
]
] | It is shown that there is a sense in splitting Genetic Code Table (GCT) into three parts using the harmonic mean, calculated by the formula H (a, b) = 2ab / (a + b), where a = 63 and b = 31.5. Within these three parts, the amino acids (AAs) are positioned on the basis of the validity of the evident regularities of key ... |
1708.04168 | Karlis Kanders | Karlis Kanders, Tom Lorimer, Yoko Uwate, Willi-Hans Steeb and Ruedi
Stoop | Robust transformations of firing patterns for neural networks | null | null | null | null | q-bio.NC nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As a promising computational paradigm, occurrence of critical states in
artificial and biological neural networks has attracted wide-spread attention.
An often-made explicit or implicit assumption is that one single critical state
is responsible for two separate notions of criticality (avalanche criticality
and dynam... | [
{
"created": "Mon, 14 Aug 2017 15:11:04 GMT",
"version": "v1"
}
] | 2017-08-15 | [
[
"Kanders",
"Karlis",
""
],
[
"Lorimer",
"Tom",
""
],
[
"Uwate",
"Yoko",
""
],
[
"Steeb",
"Willi-Hans",
""
],
[
"Stoop",
"Ruedi",
""
]
] | As a promising computational paradigm, occurrence of critical states in artificial and biological neural networks has attracted wide-spread attention. An often-made explicit or implicit assumption is that one single critical state is responsible for two separate notions of criticality (avalanche criticality and dynamic... |
2201.09654 | Hal Sorbonne Universite Gestionnaire | F\'abio Carneiro (ICM), Dario Saracino (ARAMIS), Vincent Huin (LilNCog
(ex-JPARC)), Fabienne Clot, C\'ecile Delorme, Aur\'elie M\'eneret (ICM),
St\'ephane Thobois (CNC), Florence Cormier, Jean Christophe Corvol (ICM),
Timoth\'ee Lenglet, Marie Vidailhet (ICM), Marie-Odile Habert (LIB), Audrey
Gabelle (PSNREC), ... | Isolated parkinsonism is an atypical presentation of GRN and C9orf72
gene mutations | null | Parkinsonism and Related Disorders, Elsevier, 2020, 80, pp.73-81 | 10.1016/j.parkreldis.2020.09.019 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Introduction: A phenotype of isolated parkinsonism mimicking Idiopathic
Parkinson's Disease (IPD) is a rare clinical presentation of GRN and C9orf72
mutations, the major genetic causes of frontotemporal dementia (FTD). It still
remains controversial if this association is fortuitous or not, and which
clinical clues c... | [
{
"created": "Mon, 24 Jan 2022 13:18:40 GMT",
"version": "v1"
}
] | 2022-01-25 | [
[
"Carneiro",
"Fábio",
"",
"ICM"
],
[
"Saracino",
"Dario",
"",
"ARAMIS"
],
[
"Huin",
"Vincent",
"",
"LilNCog"
],
[
"Clot",
"Fabienne",
"",
"ICM"
],
[
"Delorme",
"Cécile",
"",
"ICM"
],
[
"Méneret",
"Aurélie",
... | Introduction: A phenotype of isolated parkinsonism mimicking Idiopathic Parkinson's Disease (IPD) is a rare clinical presentation of GRN and C9orf72 mutations, the major genetic causes of frontotemporal dementia (FTD). It still remains controversial if this association is fortuitous or not, and which clinical clues cou... |
1512.00810 | Carsten Allefeld | Carsten Allefeld, Kai G\"orgen, John-Dylan Haynes | Valid population inference for information-based imaging: From the
second-level $t$-test to prevalence inference | manuscript accepted by NeuroImage, plus minor fixes and a note added
after publication | NeuroImage 141: 378-392, 2016 | 10.1016/j.neuroimage.2016.07.040 | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In multivariate pattern analysis of neuroimaging data, 'second-level'
inference is often performed by entering classification accuracies into a
$t$-test vs chance level across subjects. We argue that while the
random-effects analysis implemented by the $t$-test does provide population
inference if applied to activati... | [
{
"created": "Wed, 2 Dec 2015 18:59:46 GMT",
"version": "v1"
},
{
"created": "Wed, 1 Jun 2016 19:46:45 GMT",
"version": "v2"
},
{
"created": "Wed, 10 Aug 2016 17:00:26 GMT",
"version": "v3"
}
] | 2016-08-11 | [
[
"Allefeld",
"Carsten",
""
],
[
"Görgen",
"Kai",
""
],
[
"Haynes",
"John-Dylan",
""
]
] | In multivariate pattern analysis of neuroimaging data, 'second-level' inference is often performed by entering classification accuracies into a $t$-test vs chance level across subjects. We argue that while the random-effects analysis implemented by the $t$-test does provide population inference if applied to activation... |
0711.2058 | Igor M. Suslov | I. M. Suslov (P.L.Kapitza Institute for Physical Problems, Moscow,
Russia) | Computer Model of a "Sense of Humour". I. General Algorithm | 10 pages, 3 figures included; continuation of this series to appear | Biofizika SSSR 37, 318 (1992) [Biophysics 37, 242 (1992)] | null | null | q-bio.NC cs.AI | null | A computer model of a "sense of humour" is proposed. The humorous effect is
interpreted as a specific malfunction in the course of information processing
due to the need for the rapid deletion of the false version transmitted into
consciousness. The biological function of a sense of humour consists in
speeding up the... | [
{
"created": "Tue, 13 Nov 2007 19:00:32 GMT",
"version": "v1"
}
] | 2007-11-27 | [
[
"Suslov",
"I. M.",
"",
"P.L.Kapitza Institute for Physical Problems, Moscow,\n Russia"
]
] | A computer model of a "sense of humour" is proposed. The humorous effect is interpreted as a specific malfunction in the course of information processing due to the need for the rapid deletion of the false version transmitted into consciousness. The biological function of a sense of humour consists in speeding up the b... |
0708.3869 | Guy Katriel | Guy Katriel | Existence of periodic solutions for enzyme-catalysed reactions with
periodic substrate input | null | Discrete & Continuous Dynamical Systems - Supplements, September
2007 | null | null | q-bio.BM nlin.AO | null | Considering a basic enzyme-catalysed reaction, in which the rate of input of
the substrate varies periodically in time, we give a necessary and sufficient
condition for the existence of a periodic solution of the reaction equations.
The proof employs the Leray-Schauder degree, applied to an appropriately
constructed ... | [
{
"created": "Tue, 28 Aug 2007 23:18:05 GMT",
"version": "v1"
}
] | 2011-11-10 | [
[
"Katriel",
"Guy",
""
]
] | Considering a basic enzyme-catalysed reaction, in which the rate of input of the substrate varies periodically in time, we give a necessary and sufficient condition for the existence of a periodic solution of the reaction equations. The proof employs the Leray-Schauder degree, applied to an appropriately constructed ho... |
2008.08073 | Jerome Feldman | Jerome A. Feldman (ICSI and UC Berkeley) | On the Evolution of Subjective Experience | 49 pages 5 figures. This 7/22/2021 version preserves all the content
of the previous version and adds additional discussion (in italics). It also
includes several new references to connect with current literature. A
companion arXiv article has also been updated | null | null | null | q-bio.NC cs.NE q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Subjective Experience (SE) is part of the ancient mind-body problem, which
continues to be one of deepest mysteries of science. Despite major advances in
many fields, there is still no plausible causal link between SE and its
realization in the body. The core issue is the incompatibility of objective
(3rd person) pub... | [
{
"created": "Tue, 18 Aug 2020 17:54:39 GMT",
"version": "v1"
},
{
"created": "Fri, 23 Jul 2021 17:41:53 GMT",
"version": "v2"
},
{
"created": "Fri, 25 Mar 2022 18:16:35 GMT",
"version": "v3"
}
] | 2022-03-29 | [
[
"Feldman",
"Jerome A.",
"",
"ICSI and UC Berkeley"
]
] | Subjective Experience (SE) is part of the ancient mind-body problem, which continues to be one of deepest mysteries of science. Despite major advances in many fields, there is still no plausible causal link between SE and its realization in the body. The core issue is the incompatibility of objective (3rd person) publi... |
1302.4111 | Thomas R. Weikl | Thomas R. Weikl and Bahram Hemmateenejad | How conformational changes can affect catalysis, inhibition and drug
resistance of enzymes with induced-fit binding mechanism such as the HIV-1
protease | 9 pages, 2 figures, 3 tables; to appear in "BBA Proteins and
Proteomics" as part of a special issue with the title "The emerging dynamic
view of proteins: Protein plasticity in allostery, evolution and
self-assembly." | null | 10.1016/j.bbapap.2013.01.027 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A central question is how the conformational changes of proteins affect their
function and the inhibition of this function by drug molecules. Many enzymes
change from an open to a closed conformation upon binding of substrate or
inhibitor molecules. These conformational changes have been suggested to follow
an induce... | [
{
"created": "Sun, 17 Feb 2013 19:41:07 GMT",
"version": "v1"
}
] | 2013-02-19 | [
[
"Weikl",
"Thomas R.",
""
],
[
"Hemmateenejad",
"Bahram",
""
]
] | A central question is how the conformational changes of proteins affect their function and the inhibition of this function by drug molecules. Many enzymes change from an open to a closed conformation upon binding of substrate or inhibitor molecules. These conformational changes have been suggested to follow an induced-... |
0711.4724 | Yannick Brohard | Laurence Gaume (AMAP), Yo\"el Forterre (IUSTI) | A viscoelastic deadly fluid in carnivorous pitcher plants | null | PLoS ONE 2, 11 (2007) on-line | 10.1063/1.2964772 | A-07-32 | q-bio.PE | null | Background : The carnivorous plants of the genus Nepenthes, widely
distributed in the Asian tropics, rely mostly on nutrients derived from
arthropods trapped in their pitcher-shaped leaves and digested by their
enzymatic fluid. The genus exhibits a great diversity of prey and pitcher forms
and its mechanism of trappi... | [
{
"created": "Thu, 29 Nov 2007 14:07:15 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Gaume",
"Laurence",
"",
"AMAP"
],
[
"Forterre",
"Yoël",
"",
"IUSTI"
]
] | Background : The carnivorous plants of the genus Nepenthes, widely distributed in the Asian tropics, rely mostly on nutrients derived from arthropods trapped in their pitcher-shaped leaves and digested by their enzymatic fluid. The genus exhibits a great diversity of prey and pitcher forms and its mechanism of trapping... |
1710.11569 | Adam Noel | Adam Noel, Shayan Monabbati, Dimitrios Makrakis, Andrew W. Eckford | Timing Control of Single Neuron Spikes with Optogenetic Stimulation | 6 pages, 8 figures, 3 tables. To be presented at the 2018 IEEE
International Conference on Communications (IEEE ICC 2018) in May 2018 | null | 10.1109/ICC.2018.8422667 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper predicts the ability to externally control the firing times of a
cortical neuron whose behavior follows the Izhikevich neuron model. The
Izhikevich neuron model provides an efficient and biologically plausible method
to track a cortical neuron's membrane potential and its firing times. The
external control... | [
{
"created": "Tue, 31 Oct 2017 16:33:45 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Feb 2018 08:29:49 GMT",
"version": "v2"
}
] | 2018-09-06 | [
[
"Noel",
"Adam",
""
],
[
"Monabbati",
"Shayan",
""
],
[
"Makrakis",
"Dimitrios",
""
],
[
"Eckford",
"Andrew W.",
""
]
] | This paper predicts the ability to externally control the firing times of a cortical neuron whose behavior follows the Izhikevich neuron model. The Izhikevich neuron model provides an efficient and biologically plausible method to track a cortical neuron's membrane potential and its firing times. The external control i... |
1503.05140 | Ehsaneddin Asgari | Ehsaneddin Asgari and Mohammad R.K. Mofrad | ProtVec: A Continuous Distributed Representation of Biological Sequences | null | PLoS ONE 10(11): e0141287, 2015 | 10.1371/journal.pone.0141287 | null | q-bio.QM cs.AI cs.LG q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a new representation and feature extraction method for
biological sequences. Named bio-vectors (BioVec) to refer to biological
sequences in general with protein-vectors (ProtVec) for proteins (amino-acid
sequences) and gene-vectors (GeneVec) for gene sequences, this representation
can be widely used in a... | [
{
"created": "Tue, 17 Mar 2015 17:55:22 GMT",
"version": "v1"
},
{
"created": "Thu, 26 May 2016 20:17:51 GMT",
"version": "v2"
}
] | 2016-05-30 | [
[
"Asgari",
"Ehsaneddin",
""
],
[
"Mofrad",
"Mohammad R. K.",
""
]
] | We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-vectors (GeneVec) for gene sequences, this representation can be widely used in app... |
2207.12914 | Miguel Aguilera | Miguel Aguilera, \'Angel Poc-L\'opez, Conor Heins, Christopher L.
Buckley | Knitting a Markov blanket is hard when you are out-of-equilibrium: two
examples in canonical nonequilibrium models | null | null | null | null | q-bio.NC cond-mat.dis-nn nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bayesian theories of biological and brain function speculate that Markov
blankets (a conditional independence separating a system from external states)
play a key role for facilitating inference-like behaviour in living systems.
Although it has been suggested that Markov blankets are commonplace in sparsely
connected... | [
{
"created": "Tue, 26 Jul 2022 14:06:37 GMT",
"version": "v1"
}
] | 2022-07-27 | [
[
"Aguilera",
"Miguel",
""
],
[
"Poc-López",
"Ángel",
""
],
[
"Heins",
"Conor",
""
],
[
"Buckley",
"Christopher L.",
""
]
] | Bayesian theories of biological and brain function speculate that Markov blankets (a conditional independence separating a system from external states) play a key role for facilitating inference-like behaviour in living systems. Although it has been suggested that Markov blankets are commonplace in sparsely connected, ... |
q-bio/0605007 | Enrico Carlon | T. Heim, J. Klein Wolterink, E. Carlon, G. T. Barkema | Effective affinities in microarray data | 8 pages, 6 figures | J. Phys.: Condens. Matter 18, S525(2006) | 10.1088/0953-8984/18/18/S03 | null | q-bio.BM cond-mat.soft physics.chem-ph | null | In the past couple of years several studies have shown that hybridization in
Affymetrix DNA microarrays can be rather well understood on the basis of simple
models of physical chemistry. In the majority of the cases a Langmuir isotherm
was used to fit experimental data. Although there is a general consensus about
thi... | [
{
"created": "Thu, 4 May 2006 09:18:07 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Heim",
"T.",
""
],
[
"Wolterink",
"J. Klein",
""
],
[
"Carlon",
"E.",
""
],
[
"Barkema",
"G. T.",
""
]
] | In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this ... |
2009.02707 | Bryan M. Li | Bryan M. Li, Theoklitos Amvrosiadis, Nathalie Rochefort, Arno Onken | Synthesising Realistic Calcium Traces of Neuronal Populations Using GAN | null | null | null | null | q-bio.NC cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Calcium imaging has become a powerful and popular technique to monitor the
activity of large populations of neurons in vivo. However, for ethical
considerations and despite recent technical developments, recordings are still
constrained to a limited number of trials and animals. This limits the amount
of data availab... | [
{
"created": "Sun, 6 Sep 2020 10:58:11 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Sep 2020 03:58:43 GMT",
"version": "v2"
},
{
"created": "Sat, 4 Feb 2023 11:40:48 GMT",
"version": "v3"
}
] | 2023-02-07 | [
[
"Li",
"Bryan M.",
""
],
[
"Amvrosiadis",
"Theoklitos",
""
],
[
"Rochefort",
"Nathalie",
""
],
[
"Onken",
"Arno",
""
]
] | Calcium imaging has become a powerful and popular technique to monitor the activity of large populations of neurons in vivo. However, for ethical considerations and despite recent technical developments, recordings are still constrained to a limited number of trials and animals. This limits the amount of data available... |
0905.3297 | Armen Allahverdyan | Armen E. Allahverdyan and Chin-Kun Hu | Replicators in Fine-grained Environment: Adaptation and Polymorphism | 4 pages, 2 figures | Phys. Rev. Lett., 102, 058102 (2009) | 10.1103/PhysRevLett.102.058102 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Selection in a time-periodic environment is modeled via the two-player
replicator dynamics. For sufficiently fast environmental changes, this is
reduced to a multi-player replicator dynamics in a constant environment. The
two-player terms correspond to the time-averaged payoffs, while the three and
four-player terms ... | [
{
"created": "Wed, 20 May 2009 12:46:56 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Allahverdyan",
"Armen E.",
""
],
[
"Hu",
"Chin-Kun",
""
]
] | Selection in a time-periodic environment is modeled via the two-player replicator dynamics. For sufficiently fast environmental changes, this is reduced to a multi-player replicator dynamics in a constant environment. The two-player terms correspond to the time-averaged payoffs, while the three and four-player terms ar... |
q-bio/0405021 | Christel Kamp | Christel Kamp, Kim Christensen | Spectral Analysis of Protein-Protein Interactions in Drosophila
melanogaster | 9 pages RevTeX including 8 figures | null | 10.1103/PhysRevE.71.041911 | null | q-bio.MN cond-mat.stat-mech | null | Within a case study on the protein-protein interaction network (PIN) of
Drosophila melanogaster we investigate the relation between the network's
spectral properties and its structural features such as the prevalence of
specific subgraphs or duplicate nodes as a result of its evolutionary history.
The discrete part o... | [
{
"created": "Wed, 26 May 2004 20:21:53 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Kamp",
"Christel",
""
],
[
"Christensen",
"Kim",
""
]
] | Within a case study on the protein-protein interaction network (PIN) of Drosophila melanogaster we investigate the relation between the network's spectral properties and its structural features such as the prevalence of specific subgraphs or duplicate nodes as a result of its evolutionary history. The discrete part of ... |
1107.3112 | Michael Courtney | Joshua Daviscourt, Joshua Huertas, and Michael Courtney | An Assessment of Weight-Length Relationships for Muskellunge,Northern
Pike, and Chain Pickerel In Carlander's Handbook of Freshwater Fishery
Biology | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Carlander's Handbook of Freshwater Fishery Biology (1969) contains life
history data from many species of freshwater fish found in North America. It
has been cited over 1200 times and used to produce standard-weight curves for
some species. Recent work (Cole-Fletcher et al. 2011) suggests Carlander (1969)
contains nu... | [
{
"created": "Fri, 15 Jul 2011 17:26:24 GMT",
"version": "v1"
}
] | 2011-07-18 | [
[
"Daviscourt",
"Joshua",
""
],
[
"Huertas",
"Joshua",
""
],
[
"Courtney",
"Michael",
""
]
] | Carlander's Handbook of Freshwater Fishery Biology (1969) contains life history data from many species of freshwater fish found in North America. It has been cited over 1200 times and used to produce standard-weight curves for some species. Recent work (Cole-Fletcher et al. 2011) suggests Carlander (1969) contains nume... |
1609.00779 | Hongyu Miao | Shupeng Gui, Rui Chen, Liang Wu, Ji Liu, Hongyu Miao | A Scalable Algorithm for Structure Identification of Complex Gene
Regulatory Network from Temporal Expression Data | 14 pages, 2 figures, 2 tables | BMC Bioinformatics 2017 18:74 | 10.1186/s12859-017-1489-z | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Gene regulatory interactions are of fundamental importance to
various biological functions and processes. However, only a few previous
computational studies have claimed success in revealing genome-wide regulatory
landscapes from temporal gene expression data, especially for complex
eukaryotes like human.... | [
{
"created": "Sat, 3 Sep 2016 01:52:19 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Feb 2017 15:22:24 GMT",
"version": "v2"
}
] | 2017-02-09 | [
[
"Gui",
"Shupeng",
""
],
[
"Chen",
"Rui",
""
],
[
"Wu",
"Liang",
""
],
[
"Liu",
"Ji",
""
],
[
"Miao",
"Hongyu",
""
]
] | Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes from temporal gene expression data, especially for complex eukaryotes like human. M... |
2201.07233 | Michelle Adams | Berk C. Ugurdag, Serena Akt\"urk, Michelle Adams | Meta-analysis for Discovering Which Genes are Differentially Expressed
in Neuroinflammation | 6 pages, 2 tables | null | null | null | q-bio.OT | http://creativecommons.org/publicdomain/zero/1.0/ | Neuroinflammation is a significant aspect of many neurological diseases of
Homo sapiens, and the genes that are differentially expressed in this process
should be well understood to gather the nature of such diseases. We have
conducted a meta-analysis (based on a combined adjusted P value and logFC
scheme) of 6 multi... | [
{
"created": "Tue, 18 Jan 2022 18:14:02 GMT",
"version": "v1"
}
] | 2022-01-20 | [
[
"Ugurdag",
"Berk C.",
""
],
[
"Aktürk",
"Serena",
""
],
[
"Adams",
"Michelle",
""
]
] | Neuroinflammation is a significant aspect of many neurological diseases of Homo sapiens, and the genes that are differentially expressed in this process should be well understood to gather the nature of such diseases. We have conducted a meta-analysis (based on a combined adjusted P value and logFC scheme) of 6 multi-s... |
2007.03902 | Paul Hurtado | Paul J. Hurtado and Cameron Richards | Building Mean Field State Transition Models Using The Generalized Linear
Chain Trick and Continuous Time Markov Chain Theory | 27 pages, 4 figures, 2 ancillary files (R code for two figures).
Journal of Biological Dynamics (2021) | null | 10.1080/17513758.2021.1912418 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The well-known Linear Chain Trick (LCT) allows modelers to derive mean field
ODEs that assume gamma (Erlang) distributed passage times, by transitioning
individuals sequentially through a chain of sub-states. The time spent in these
states is the sum of $k$ exponentially distributed random variables, and is
thus gamm... | [
{
"created": "Wed, 8 Jul 2020 05:02:42 GMT",
"version": "v1"
}
] | 2021-05-25 | [
[
"Hurtado",
"Paul J.",
""
],
[
"Richards",
"Cameron",
""
]
] | The well-known Linear Chain Trick (LCT) allows modelers to derive mean field ODEs that assume gamma (Erlang) distributed passage times, by transitioning individuals sequentially through a chain of sub-states. The time spent in these states is the sum of $k$ exponentially distributed random variables, and is thus gamma ... |
2010.01914 | Patrick Krauss | Patrick Krauss and Achim Schilling | Towards a Cognitive Computational Neuroscience of Auditory Phantom
Perceptions | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In order to gain a mechanistic understanding of how tinnitus emerges in the
brain, we must build biologically plausible computational models that mimic
both tinnitus development and perception, and test the tentative models with
brain and behavioral experiments. With a special focus on tinnitus research, we
review re... | [
{
"created": "Mon, 5 Oct 2020 10:55:03 GMT",
"version": "v1"
}
] | 2020-10-06 | [
[
"Krauss",
"Patrick",
""
],
[
"Schilling",
"Achim",
""
]
] | In order to gain a mechanistic understanding of how tinnitus emerges in the brain, we must build biologically plausible computational models that mimic both tinnitus development and perception, and test the tentative models with brain and behavioral experiments. With a special focus on tinnitus research, we review rece... |
1607.07970 | Krzysztof Bartoszek | Krzysztof Bartoszek, Sylvain Gl\'emin, Ingemar Kaj, Martin Lascoux | The Ornstein-Uhlenbeck process with migration: evolution with
interactions | null | Journal of Theoretical Biology 429:35-45, 2017 | 10.1016/j.jtbi.2017.06.011 | null | q-bio.PE math.PR stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the
evolution of phenotypic traits along phylogenies. The standard OU process
includes drift and stabilizing selection and assumes that species evolve
independently. However, especially in plants, there is ample evidence of
hybridization and in... | [
{
"created": "Wed, 27 Jul 2016 06:10:03 GMT",
"version": "v1"
}
] | 2020-11-23 | [
[
"Bartoszek",
"Krzysztof",
""
],
[
"Glémin",
"Sylvain",
""
],
[
"Kaj",
"Ingemar",
""
],
[
"Lascoux",
"Martin",
""
]
] | The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the evolution of phenotypic traits along phylogenies. The standard OU process includes drift and stabilizing selection and assumes that species evolve independently. However, especially in plants, there is ample evidence of hybridization and intr... |
1006.0018 | Teruhiko Yoneyama | Teruhiko Yoneyama and Mukkai S. Krishnamoorthy | Simulating the Spread of Influenza Pandemic of 2009 Considering
International Traffic | null | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by/3.0/ | Pandemics have the potential to cause immense disruption and damage to
communities and societies. In this paper, we model the Influenza Pandemic of
2009. We propose a hybrid model to determine how the pandemic spreads through
the world. The model considers both the SEIR-based model for local areas and
the network mod... | [
{
"created": "Tue, 11 May 2010 22:10:23 GMT",
"version": "v1"
}
] | 2010-06-02 | [
[
"Yoneyama",
"Teruhiko",
""
],
[
"Krishnamoorthy",
"Mukkai S.",
""
]
] | Pandemics have the potential to cause immense disruption and damage to communities and societies. In this paper, we model the Influenza Pandemic of 2009. We propose a hybrid model to determine how the pandemic spreads through the world. The model considers both the SEIR-based model for local areas and the network model... |
1111.4779 | David Lukatsky | Ariel Afek, Itamar Sela, Noa Musa-Lempel, and David B. Lukatsky | Nonspecific transcription factor-DNA binding influences nucleosome
occupancy in yeast | null | Biophysical Journal, Volume 101, Issue 10, 2465-2475 (2011) | 10.1016/j.bpj.2011.10.012 | null | q-bio.BM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quantitative understanding of the principles regulating nucleosome occupancy
on a genome-wide level is a central issue in eukaryotic genomics. Here, we
address this question using budding yeast, Saccharomyces cerevisiae, as a model
organism. We perform a genome-wide computational analysis of nonspecific
transcription... | [
{
"created": "Mon, 21 Nov 2011 07:57:40 GMT",
"version": "v1"
}
] | 2011-11-22 | [
[
"Afek",
"Ariel",
""
],
[
"Sela",
"Itamar",
""
],
[
"Musa-Lempel",
"Noa",
""
],
[
"Lukatsky",
"David B.",
""
]
] | Quantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model organism. We perform a genome-wide computational analysis of nonspecific transcription f... |
1603.00459 | Renaud Bastien | Renaud Bastien, Yasmine Meroz | The Kinematics of Plant Nutation Reveals a Simple Relation Between
Curvature and the Orientation of Differential Growth | null | null | 10.1371/journal.pcbi.1005238 | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Nutation is an oscillatory movement that plants display during their
development. Despite its ubiquity among plants movements, the relation between
the observed movement and the underlying biological mechanisms remains unclear.
Here we show that the kinematics of the full organ in 3D gives a simple picture
of plant n... | [
{
"created": "Tue, 1 Mar 2016 11:41:46 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Oct 2016 15:10:41 GMT",
"version": "v2"
}
] | 2017-02-08 | [
[
"Bastien",
"Renaud",
""
],
[
"Meroz",
"Yasmine",
""
]
] | Nutation is an oscillatory movement that plants display during their development. Despite its ubiquity among plants movements, the relation between the observed movement and the underlying biological mechanisms remains unclear. Here we show that the kinematics of the full organ in 3D gives a simple picture of plant nut... |
2010.12065 | Nabit Bajwa | Nabit Bajwa, Kedar Bajwa, Atif Rana, M. Faique Shakeel, Kashif Haqqi
and Suleiman Ali Khan | A generalized deep learning model for multi-disease Chest X-Ray
diagnostics | null | null | null | null | q-bio.QM cs.CV cs.LG eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the generalizability of deep convolutional neural network
(CNN) on the task of disease classification from chest x-rays collected over
multiple sites. We systematically train the model using datasets from three
independent sites with different patient populations: National Institute of
Health (NIH), St... | [
{
"created": "Sat, 17 Oct 2020 18:57:40 GMT",
"version": "v1"
}
] | 2020-10-26 | [
[
"Bajwa",
"Nabit",
""
],
[
"Bajwa",
"Kedar",
""
],
[
"Rana",
"Atif",
""
],
[
"Shakeel",
"M. Faique",
""
],
[
"Haqqi",
"Kashif",
""
],
[
"Khan",
"Suleiman Ali",
""
]
] | We investigate the generalizability of deep convolutional neural network (CNN) on the task of disease classification from chest x-rays collected over multiple sites. We systematically train the model using datasets from three independent sites with different patient populations: National Institute of Health (NIH), Stan... |
1407.5105 | Ankit Khambhati | Ankit Khambhati, Brian Litt, Danielle S. Bassett | Dynamic network drivers of seizure generation, propagation and
termination in human epilepsy | 7 pages, 5 figures; Supplementary Materials: 5 pages, 3 figures, 1
table | null | 10.1371/journal.pcbi.1004608 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Drug-resistant epilepsy is traditionally characterized by pathologic cortical
tissue comprised of seizure-initiating `foci'. These `foci' are thought to be
embedded within an epileptic network whose functional architecture dynamically
reorganizes during seizures through synchronous and asynchronous
neurophysiologic p... | [
{
"created": "Fri, 18 Jul 2014 20:12:16 GMT",
"version": "v1"
}
] | 2016-02-17 | [
[
"Khambhati",
"Ankit",
""
],
[
"Litt",
"Brian",
""
],
[
"Bassett",
"Danielle S.",
""
]
] | Drug-resistant epilepsy is traditionally characterized by pathologic cortical tissue comprised of seizure-initiating `foci'. These `foci' are thought to be embedded within an epileptic network whose functional architecture dynamically reorganizes during seizures through synchronous and asynchronous neurophysiologic pro... |
q-bio/0703006 | Thierry Rabilloud | Mireille Chevallet (BBSI), H\'el\`ene Diemer (IPHC), Alain van
Dorsselaer (IPHC), Christian Villiers, Thierry Rabilloud (BBSI) | Toward a better analysis of secreted proteins: the example of the
myeloid cells secretome | sous presse sans Proteomics | null | null | null | q-bio.GN | null | The analysis of secreted proteins represents a challenge for current
proteomics techniques. Proteins are usually secreted at low concentrations in
the culture media, which makes their recovery difficult. In addition, culture
media are rich in salts and other compounds interfering with most proteomics
techniques, whic... | [
{
"created": "Fri, 2 Mar 2007 10:35:11 GMT",
"version": "v1"
}
] | 2016-08-14 | [
[
"Chevallet",
"Mireille",
"",
"BBSI"
],
[
"Diemer",
"Hélène",
"",
"IPHC"
],
[
"van Dorsselaer",
"Alain",
"",
"IPHC"
],
[
"Villiers",
"Christian",
"",
"BBSI"
],
[
"Rabilloud",
"Thierry",
"",
"BBSI"
]
] | The analysis of secreted proteins represents a challenge for current proteomics techniques. Proteins are usually secreted at low concentrations in the culture media, which makes their recovery difficult. In addition, culture media are rich in salts and other compounds interfering with most proteomics techniques, which ... |
2403.18666 | Kieren Sharma | Kieren Sharma, Lucia Marucci, Zahraa S. Abdallah | FluxGAT: Integrating Flux Sampling with Graph Neural Networks for
Unbiased Gene Essentiality Classification | null | null | null | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene essentiality, the necessity of a specific gene for the survival of an
organism, is crucial to our understanding of cellular processes and identifying
drug targets. Experimental determination of gene essentiality requires large
growth screens that are time-consuming and expensive, motivating the
development of in... | [
{
"created": "Wed, 27 Mar 2024 15:09:46 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Mar 2024 14:52:36 GMT",
"version": "v2"
}
] | 2024-03-29 | [
[
"Sharma",
"Kieren",
""
],
[
"Marucci",
"Lucia",
""
],
[
"Abdallah",
"Zahraa S.",
""
]
] | Gene essentiality, the necessity of a specific gene for the survival of an organism, is crucial to our understanding of cellular processes and identifying drug targets. Experimental determination of gene essentiality requires large growth screens that are time-consuming and expensive, motivating the development of in-s... |
2407.13514 | Anass B. El-Yaagoubi | Anass B. El-Yaagoubi and Moo K. Chung and Hernando Ombao | Topological Analysis of Seizure-Induced Changes in Brain Hierarchy
Through Effective Connectivity | null | null | null | null | q-bio.NC stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Traditional Topological Data Analysis (TDA) methods, such as Persistent
Homology (PH), rely on distance measures (e.g., cross-correlation, partial
correlation, coherence, and partial coherence) that are symmetric by
definition. While useful for studying topological patterns in functional brain
connectivity, the main ... | [
{
"created": "Thu, 18 Jul 2024 13:45:08 GMT",
"version": "v1"
}
] | 2024-07-19 | [
[
"El-Yaagoubi",
"Anass B.",
""
],
[
"Chung",
"Moo K.",
""
],
[
"Ombao",
"Hernando",
""
]
] | Traditional Topological Data Analysis (TDA) methods, such as Persistent Homology (PH), rely on distance measures (e.g., cross-correlation, partial correlation, coherence, and partial coherence) that are symmetric by definition. While useful for studying topological patterns in functional brain connectivity, the main li... |
2008.12104 | Mai He | Mai He (1), Priya Skaria (1), Kasey Kreutz (1), Ling Chen (2), Ian
Hagemann (1), Ebony B. Carter (3), Indira U. Mysorekar (1,3), D Michael
Nelson (3), John Pfeifer (1), Louis P. Dehner (1) ((1) Department of
Pathology & Immunology, Washington University in St. Louis School of
Medicine, St. Louis, MO, USA (2) Di... | Histopathology of Third Trimester Placenta from SARS-CoV-2-Positive
Women | Two tables | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: This study aims to investigate whether maternal SARS-CoV-2 status
affect placental pathology. Methods: A retrospective case-control study was
conducted by reviewing charts and slides of placentas between April 1 to July
24, 2020. Clinical history of COVID-19 were searched in Pathology Database
(CoPath). C... | [
{
"created": "Wed, 5 Aug 2020 20:35:52 GMT",
"version": "v1"
}
] | 2020-08-28 | [
[
"He",
"Mai",
""
],
[
"Skaria",
"Priya",
""
],
[
"Kreutz",
"Kasey",
""
],
[
"Chen",
"Ling",
""
],
[
"Hagemann",
"Ian",
""
],
[
"Carter",
"Ebony B.",
""
],
[
"Mysorekar",
"Indira U.",
""
],
[
"Nelson"... | Background: This study aims to investigate whether maternal SARS-CoV-2 status affect placental pathology. Methods: A retrospective case-control study was conducted by reviewing charts and slides of placentas between April 1 to July 24, 2020. Clinical history of COVID-19 were searched in Pathology Database (CoPath). Con... |
0912.5409 | William Bialek | Gasper Tkacik, Elad Schneidman, Michael J. Berry II and William Bialek | Spin glass models for a network of real neurons | This is an extended version of arXiv:q-bio.NC/0611072 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ising models with pairwise interactions are the least structured, or
maximum-entropy, probability distributions that exactly reproduce measured
pairwise correlations between spins. Here we use this equivalence to construct
Ising models that describe the correlated spiking activity of populations of 40
neurons in the ... | [
{
"created": "Wed, 30 Dec 2009 02:59:05 GMT",
"version": "v1"
}
] | 2009-12-31 | [
[
"Tkacik",
"Gasper",
""
],
[
"Schneidman",
"Elad",
""
],
[
"Berry",
"Michael J.",
"II"
],
[
"Bialek",
"William",
""
]
] | Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the sa... |
q-bio/0310014 | Balint Szabo | B. Szabo, Zs. Kornyei, J. Zach, D. Selmeczi, G. Csucs, A. Czirok, T.
Vicsek | Auto-reverse nuclear migration in bipolar mammalian cells on
micropatterned surfaces | Figures and supplemental videos: http://esr.elte.hu/nuclearmotility | Cell Motility and the Cytoskeleton 59(1), 38-49 (2004) | null | null | q-bio.CB | null | A novel assay based on micropatterning and time-lapse microscopy has been
developed for the study of nuclear migration dynamics in cultured mammalian
cells. When cultured on 10-20 um wide adhesive stripes, the motility of C6
glioma and primary mouse fibroblast cells is diminished. Nevertheless, nuclei
perform an unex... | [
{
"created": "Tue, 14 Oct 2003 09:18:27 GMT",
"version": "v1"
},
{
"created": "Sun, 9 May 2004 13:12:21 GMT",
"version": "v2"
},
{
"created": "Tue, 17 Aug 2004 11:32:07 GMT",
"version": "v3"
}
] | 2009-09-29 | [
[
"Szabo",
"B.",
""
],
[
"Kornyei",
"Zs.",
""
],
[
"Zach",
"J.",
""
],
[
"Selmeczi",
"D.",
""
],
[
"Csucs",
"G.",
""
],
[
"Czirok",
"A.",
""
],
[
"Vicsek",
"T.",
""
]
] | A novel assay based on micropatterning and time-lapse microscopy has been developed for the study of nuclear migration dynamics in cultured mammalian cells. When cultured on 10-20 um wide adhesive stripes, the motility of C6 glioma and primary mouse fibroblast cells is diminished. Nevertheless, nuclei perform an unexpe... |
1602.01730 | Robert Wilkinson mr | Robert R. Wilkinson, Frank G. Ball, Kieran J. Sharkey | The deterministic Kermack-McKendrick model bounds the general stochastic
epidemic | null | J. Appl. Probab. Vol. 53, No. 4 (2016) | null | null | q-bio.PE cond-mat.stat-mech math.PR physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We prove that, for Poisson transmission and recovery processes, the classic
Susceptible $\to$ Infected $\to$ Recovered (SIR) epidemic model of Kermack and
McKendrick provides, for any given time $t>0$, a strict lower bound on the
expected number of suscpetibles and a strict upper bound on the expected number
of recov... | [
{
"created": "Thu, 4 Feb 2016 16:26:19 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Mar 2016 11:54:41 GMT",
"version": "v2"
},
{
"created": "Fri, 10 Feb 2017 14:10:25 GMT",
"version": "v3"
}
] | 2017-02-13 | [
[
"Wilkinson",
"Robert R.",
""
],
[
"Ball",
"Frank G.",
""
],
[
"Sharkey",
"Kieran J.",
""
]
] | We prove that, for Poisson transmission and recovery processes, the classic Susceptible $\to$ Infected $\to$ Recovered (SIR) epidemic model of Kermack and McKendrick provides, for any given time $t>0$, a strict lower bound on the expected number of suscpetibles and a strict upper bound on the expected number of recover... |
2205.03635 | Laurent Perrinet | Jean-Nicolas J\'er\'emie, Laurent U Perrinet | Ultrafast Image Categorization in Biology and Neural Models | null | null | 10.3390/vision7020029 | null | q-bio.NC cs.CV | http://creativecommons.org/licenses/by/4.0/ | Humans are able to categorize images very efficiently, in particular to
detect the presence of an animal very quickly. Recently, deep learning
algorithms based on convolutional neural networks (CNNs) have achieved higher
than human accuracy for a wide range of visual categorization tasks. However,
the tasks on which ... | [
{
"created": "Sat, 7 May 2022 11:19:40 GMT",
"version": "v1"
},
{
"created": "Thu, 12 May 2022 14:40:25 GMT",
"version": "v2"
},
{
"created": "Tue, 11 Oct 2022 12:01:17 GMT",
"version": "v3"
},
{
"created": "Wed, 31 May 2023 05:30:51 GMT",
"version": "v4"
}
] | 2023-06-01 | [
[
"Jérémie",
"Jean-Nicolas",
""
],
[
"Perrinet",
"Laurent U",
""
]
] | Humans are able to categorize images very efficiently, in particular to detect the presence of an animal very quickly. Recently, deep learning algorithms based on convolutional neural networks (CNNs) have achieved higher than human accuracy for a wide range of visual categorization tasks. However, the tasks on which th... |
2311.04880 | Christopher Miles | Christopher E. Miles, Scott A. McKinley, Fangyuan Ding, Richard B.
Lehoucq | Inferring stochastic rates from heterogeneous snapshots of particle
positions | 33 pages, 6 figures | Bulletin of Mathematical Biology 86, 74 (2024) | 10.1007/s11538-024-01301-4 | null | q-bio.SC math.ST physics.bio-ph stat.AP stat.TH | http://creativecommons.org/licenses/by/4.0/ | Many imaging techniques for biological systems -- like fixation of cells
coupled with fluorescence microscopy -- provide sharp spatial resolution in
reporting locations of individuals at a single moment in time but also destroy
the dynamics they intend to capture. These snapshot observations contain no
information ab... | [
{
"created": "Wed, 8 Nov 2023 18:36:41 GMT",
"version": "v1"
}
] | 2024-05-15 | [
[
"Miles",
"Christopher E.",
""
],
[
"McKinley",
"Scott A.",
""
],
[
"Ding",
"Fangyuan",
""
],
[
"Lehoucq",
"Richard B.",
""
]
] | Many imaging techniques for biological systems -- like fixation of cells coupled with fluorescence microscopy -- provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. These snapshot observations contain no information abou... |
1707.00039 | Dan Willard | Dan E. Willard | Implications of the Trivers-Willard Sex Ratio Hypothesis for Avian
Species and Poultry Production, And a Summary of the Historic Context of this
Research | A 30-minute invited talk summarizing the contents of this article was
presented on June 18, 2017 at the Binghamton NEEPS-2017 Conference. The
Version-1 June 27 (2017) draft of this paper was similar to the 30-minute
talk I gave at Binghamton University, and it was disseminated nine days after
this talk. This se... | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | At a theoretical level, the Trivers-Willard Sex Ratio Hypothesis applies to
both avian species and mammals. This article, however, conjectures that at the
statistical level, sex ratio effects are likely to produce sharper numerical
variations among birds than among mammals. We explain this greater statistical
variati... | [
{
"created": "Tue, 27 Jun 2017 21:50:22 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Aug 2017 16:23:57 GMT",
"version": "v2"
}
] | 2017-08-31 | [
[
"Willard",
"Dan E.",
""
]
] | At a theoretical level, the Trivers-Willard Sex Ratio Hypothesis applies to both avian species and mammals. This article, however, conjectures that at the statistical level, sex ratio effects are likely to produce sharper numerical variations among birds than among mammals. We explain this greater statistical variation... |
1705.02380 | Dwayne John | Dwayne John | A Nonconventional Analysis of CD$4^{+}$ and CD$8^{+}$ T Cell Responses
During and After Acute Lymphocytic Choriomeningitis Virus Infection | 3 Figures, 1 table | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A mathematical model from a previous work was re-fitted and analyzed for
experimental data regarding the cellular immune response to the lymphocytic
choriomeningitis virus. Specifically, the $CD8^{+}$ T cell response to six MHC
class I-restricted epitopes (GP* and NP*) and $CD4^{+}$ T cell responses to two
MHC class ... | [
{
"created": "Fri, 5 May 2017 19:53:34 GMT",
"version": "v1"
}
] | 2017-05-09 | [
[
"John",
"Dwayne",
""
]
] | A mathematical model from a previous work was re-fitted and analyzed for experimental data regarding the cellular immune response to the lymphocytic choriomeningitis virus. Specifically, the $CD8^{+}$ T cell response to six MHC class I-restricted epitopes (GP* and NP*) and $CD4^{+}$ T cell responses to two MHC class II... |
1805.03602 | Surya Saha | Prashant S. Hosmani, Teresa Shippy, Sherry Miller, Joshua B. Benoit,
Monica Munoz-Torres, Mirella Flores, Lukas A. Mueller, Helen Wiersma-Koch,
Tom D'elia, Susan J. Brown and Surya Saha | A quick guide for student-driven community genome annotation | null | null | 10.1371/journal.pcbi.1006682 | null | q-bio.GN | http://creativecommons.org/publicdomain/zero/1.0/ | High quality gene models are necessary to expand the molecular and genetic
tools available for a target organism, but these are available for only a
handful of model organisms that have undergone extensive curation and
experimental validation over the course of many years. The majority of gene
models present in biolo... | [
{
"created": "Wed, 9 May 2018 16:01:11 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Oct 2018 10:04:57 GMT",
"version": "v2"
}
] | 2019-06-19 | [
[
"Hosmani",
"Prashant S.",
""
],
[
"Shippy",
"Teresa",
""
],
[
"Miller",
"Sherry",
""
],
[
"Benoit",
"Joshua B.",
""
],
[
"Munoz-Torres",
"Monica",
""
],
[
"Flores",
"Mirella",
""
],
[
"Mueller",
"Lukas A.",
... | High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biologi... |
2011.05321 | Jean-Fran\c{c}ois Cornet | B\'erang\`ere Farges, C\'eline Laroche, Jean-Fran\c{c}ois Cornet and
Claude-Gilles Dussap | Spectral Kinetic Modeling and Long-term Behavior Assessment of
Arthrospira platensis Growth in Photobioreactor under Red (620 nm) Light
Illumination | null | Biotechnology Progress, 2009, 25, 151-162 | 10.1021/bp.95 | null | q-bio.OT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ability to cultivate the cyanobacterium Arhtrospira platensis in
artificially lightened photobioreactors using high energetic efficiency
(quasi-monochromatic) red LED was investigated. In order to reach the same
maximal productivities as with the polychromatic lightening control conditions
(red + blue, P/2e- = 1.... | [
{
"created": "Sat, 7 Nov 2020 14:47:21 GMT",
"version": "v1"
}
] | 2020-11-11 | [
[
"Farges",
"Bérangère",
""
],
[
"Laroche",
"Céline",
""
],
[
"Cornet",
"Jean-François",
""
],
[
"Dussap",
"Claude-Gilles",
""
]
] | The ability to cultivate the cyanobacterium Arhtrospira platensis in artificially lightened photobioreactors using high energetic efficiency (quasi-monochromatic) red LED was investigated. In order to reach the same maximal productivities as with the polychromatic lightening control conditions (red + blue, P/2e- = 1.27... |
q-bio/0604014 | Mariano Cadoni | M. Cadoni, R. De Leo, G. Gaeta | A composite model for DNA torsion dynamics | 29 pages | Phys. Rev. E75 (2007), 021919 | 10.1103/PhysRevE.75.021919 | null | q-bio.BM physics.bio-ph | null | DNA torsion dynamics is essential in the transcription process; a simple
model for it, in reasonable agreement with experimental observations, has been
proposed by Yakushevich (Y) and developed by several authors; in this, the DNA
subunits made of a nucleoside and the attached nitrogen bases are described by
a single... | [
{
"created": "Wed, 12 Apr 2006 13:42:47 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Apr 2006 17:33:18 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Cadoni",
"M.",
""
],
[
"De Leo",
"R.",
""
],
[
"Gaeta",
"G.",
""
]
] | DNA torsion dynamics is essential in the transcription process; a simple model for it, in reasonable agreement with experimental observations, has been proposed by Yakushevich (Y) and developed by several authors; in this, the DNA subunits made of a nucleoside and the attached nitrogen bases are described by a single d... |
2403.03231 | Mikhail Dozmorov | Brydon P. G. Wall, My Nguyen, J. Chuck Harrell, Mikhail G. Dozmorov | Machine and deep learning methods for predicting 3D genome organization | Systematic review, one figure, three tables, 29 pages | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by/4.0/ | Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter
interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B
compartments play critical roles in a wide range of cellular processes by
regulating gene expression. Recent development of chromatin conformation
capture technologies... | [
{
"created": "Mon, 4 Mar 2024 19:04:41 GMT",
"version": "v1"
}
] | 2024-03-07 | [
[
"Wall",
"Brydon P. G.",
""
],
[
"Nguyen",
"My",
""
],
[
"Harrell",
"J. Chuck",
""
],
[
"Dozmorov",
"Mikhail G.",
""
]
] | Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies h... |
1111.4785 | Ivo Sbalzarini | Christian L. Muller, Rajesh Ramaswamy, Ivo F. Sbalzarini | Global parameter identification of stochastic reaction networks from
single trajectories | Article in print as a book chapter in Springer's "Advances in Systems
Biology" | null | null | null | q-bio.MN cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the problem of inferring the unknown parameters of a stochastic
biochemical network model from a single measured time-course of the
concentration of some of the involved species. Such measurements are available,
e.g., from live-cell fluorescence microscopy in image-based systems biology. In
addition, fluc... | [
{
"created": "Mon, 21 Nov 2011 08:30:29 GMT",
"version": "v1"
}
] | 2011-11-22 | [
[
"Muller",
"Christian L.",
""
],
[
"Ramaswamy",
"Rajesh",
""
],
[
"Sbalzarini",
"Ivo F.",
""
]
] | We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctu... |
2407.02440 | Jose Fontanari | Jos\'e F. Fontanari and Mauro Santos | Solving the prisoner's dilemma trap in Hamilton's model of temporarily
formed random groups | null | null | null | null | q-bio.PE nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Explaining the evolution of cooperation in the strong altruism scenario,
where a cooperator does not benefit from her contribution to the public goods,
is a challenging problem that requires positive assortment among cooperators
(i.e., cooperators must tend to associate with other cooperators) or punishment
of defect... | [
{
"created": "Tue, 2 Jul 2024 17:15:34 GMT",
"version": "v1"
}
] | 2024-07-03 | [
[
"Fontanari",
"José F.",
""
],
[
"Santos",
"Mauro",
""
]
] | Explaining the evolution of cooperation in the strong altruism scenario, where a cooperator does not benefit from her contribution to the public goods, is a challenging problem that requires positive assortment among cooperators (i.e., cooperators must tend to associate with other cooperators) or punishment of defector... |
2101.05563 | Giulia Laura Celora | Giulia L. Celora, Helen M. Byrne, Christos Zois, Panos G. Kevrekidis | Phenotypic variation modulates the growth dynamics and response to
radiotherapy of solid tumours under normoxia and hypoxia | null | null | null | null | q-bio.CB nlin.PS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In cancer, treatment failure and disease recurrence have been associated with
small subpopulations of cancer cells with a stem-like phenotype. In this paper,
we develop and investigate a phenotype-structured model of solid tumour growth
in which cells are structured by a stemness level, which varies continuously
betw... | [
{
"created": "Thu, 14 Jan 2021 12:10:53 GMT",
"version": "v1"
}
] | 2021-01-15 | [
[
"Celora",
"Giulia L.",
""
],
[
"Byrne",
"Helen M.",
""
],
[
"Zois",
"Christos",
""
],
[
"Kevrekidis",
"Panos G.",
""
]
] | In cancer, treatment failure and disease recurrence have been associated with small subpopulations of cancer cells with a stem-like phenotype. In this paper, we develop and investigate a phenotype-structured model of solid tumour growth in which cells are structured by a stemness level, which varies continuously betwee... |
0707.2300 | Hiroshi Fujisaki | Hiroshi Fujisaki, John E. Straub | Vibrational energy relaxation (VER) of isotopically labeled amide I
modes in cytochrome c: Theoretical investigation of VER rates and pathways | 10 pages, 5 figures, to be published in J. Phys. Chem. B | null | null | null | q-bio.BM | null | Using a time-dependent perturbation theory, vibrational energy relaxation
(VER) of isotopically labeled amide I modes in cytochrome c solvated with water
is investigated. Contributions to the VER are decomposed into two contributions
from the protein and water. The VER pathways are visualized using radial and
angular... | [
{
"created": "Mon, 16 Jul 2007 11:04:29 GMT",
"version": "v1"
}
] | 2007-07-17 | [
[
"Fujisaki",
"Hiroshi",
""
],
[
"Straub",
"John E.",
""
]
] | Using a time-dependent perturbation theory, vibrational energy relaxation (VER) of isotopically labeled amide I modes in cytochrome c solvated with water is investigated. Contributions to the VER are decomposed into two contributions from the protein and water. The VER pathways are visualized using radial and angular e... |
0803.0465 | Giulia Menconi | Giulia Menconi, Vieri Benci, Marcello Buiatti | Data compression and genomes: a two dimensional life domain map | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We define the complexity of DNA sequences as the information content per
nucleotide, calculated by means of some Lempel-Ziv data compression algorithm.
It is possible to use the statistics of the complexity values of the functional
regions of different complete genomes to distinguish among genomes of different
domain... | [
{
"created": "Tue, 4 Mar 2008 14:47:36 GMT",
"version": "v1"
}
] | 2008-03-05 | [
[
"Menconi",
"Giulia",
""
],
[
"Benci",
"Vieri",
""
],
[
"Buiatti",
"Marcello",
""
]
] | We define the complexity of DNA sequences as the information content per nucleotide, calculated by means of some Lempel-Ziv data compression algorithm. It is possible to use the statistics of the complexity values of the functional regions of different complete genomes to distinguish among genomes of different domains ... |
1810.05823 | Delfim F. M. Torres | Ana P. Lemos-Paiao, Cristiana J. Silva, Delfim F. M. Torres | A cholera mathematical model with vaccination and the biggest outbreak
of world's history | This is a preprint of a paper whose final and definite form is with
'AIMS Mathematics', available in open access from
[http://www.aimspress.com/journal/Math]. Submitted 7-July-2018; Revised
14-Sept-2018; Accepted 12-Oct-2018. arXiv admin note: substantial text
overlap with arXiv:1611.02195 | AIMS Mathematics 3 (2018), no. 4, 448--463 | 10.3934/Math.2018.4.448 | null | q-bio.PE math.CA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose and analyse a mathematical model for cholera considering
vaccination. We show that the model is epidemiologically and mathematically
well posed and prove the existence and uniqueness of disease-free and endemic
equilibrium points. The basic reproduction number is determined and the local
asymptotic stabili... | [
{
"created": "Sat, 13 Oct 2018 08:48:27 GMT",
"version": "v1"
}
] | 2018-10-22 | [
[
"Lemos-Paiao",
"Ana P.",
""
],
[
"Silva",
"Cristiana J.",
""
],
[
"Torres",
"Delfim F. M.",
""
]
] | We propose and analyse a mathematical model for cholera considering vaccination. We show that the model is epidemiologically and mathematically well posed and prove the existence and uniqueness of disease-free and endemic equilibrium points. The basic reproduction number is determined and the local asymptotic stability... |
1401.1129 | Brent Pedersen | Brent S. Pedersen, Kenneth Eyring, Subhajyoti De, Ivana V. Yang and
David A. Schwartz | Fast and accurate alignment of long bisulfite-seq reads | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Summary: Longer sequencing reads, with at least 200 bases per template are
now common. While traditional aligners have adopted new strategies to improve
the mapping of longer reads, aligners specific to bisulfite-sequencing were
optimized when much shorter reads were the norm. We sought to perform the first
compariso... | [
{
"created": "Mon, 6 Jan 2014 16:08:04 GMT",
"version": "v1"
},
{
"created": "Tue, 13 May 2014 15:02:10 GMT",
"version": "v2"
}
] | 2014-05-14 | [
[
"Pedersen",
"Brent S.",
""
],
[
"Eyring",
"Kenneth",
""
],
[
"De",
"Subhajyoti",
""
],
[
"Yang",
"Ivana V.",
""
],
[
"Schwartz",
"David A.",
""
]
] | Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized when much shorter reads were the norm. We sought to perform the first comparison ... |
2302.11438 | Georgiy Karev | Georgiy Karev | On the scope of applicability of the models of Darwinian dynamics | 39 pages, 11 figures | null | null | null | q-bio.PE | http://creativecommons.org/publicdomain/zero/1.0/ | In their well-known textbook (Vincent & Brown, 2005), Vincent and Brown
suggested an attractive approach for studying evolutionary dynamics of
populations that are heterogeneous with respect to some strategy that affects
the fitness of individuals in the population. The authors developed a theory,
whose goal was to e... | [
{
"created": "Wed, 22 Feb 2023 15:22:38 GMT",
"version": "v1"
}
] | 2023-02-23 | [
[
"Karev",
"Georgiy",
""
]
] | In their well-known textbook (Vincent & Brown, 2005), Vincent and Brown suggested an attractive approach for studying evolutionary dynamics of populations that are heterogeneous with respect to some strategy that affects the fitness of individuals in the population. The authors developed a theory, whose goal was to exp... |
0808.1283 | Razvan Radulescu M.D. | Razvan Tudor Radulescu | Peptide strings clues to the genesis and treatment of rheumatoid
arthritis: rebuilding self-protective immunity amid fungal ruins | 15 pages, 3 figures, 3 tables | null | null | null | q-bio.SC q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A recent application of the peptide strings concept has yielded novel
perceptions on cell growth regulation, for instance that of oncoprotein
metastasis. Here, this interdisciplinary approach at the boundary between
physics and biology has been applied to gain a more profound insight into
rheumatoid arthritis. As a r... | [
{
"created": "Sun, 10 Aug 2008 23:03:29 GMT",
"version": "v1"
}
] | 2008-08-12 | [
[
"Radulescu",
"Razvan Tudor",
""
]
] | A recent application of the peptide strings concept has yielded novel perceptions on cell growth regulation, for instance that of oncoprotein metastasis. Here, this interdisciplinary approach at the boundary between physics and biology has been applied to gain a more profound insight into rheumatoid arthritis. As a res... |
1709.03630 | Alex McAvoy | Alex McAvoy, Nicolas Fraiman, Christoph Hauert, John Wakeley, Martin
A. Nowak | Public goods games in populations with fluctuating size | 21 pages; final version | null | 10.1016/j.tpb.2018.01.004 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many mathematical frameworks of evolutionary game dynamics assume that the
total population size is constant and that selection affects only the relative
frequency of strategies. Here, we consider evolutionary game dynamics in an
extended Wright-Fisher process with variable population size. In such a
scenario, it is ... | [
{
"created": "Tue, 12 Sep 2017 00:10:01 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Feb 2018 04:37:42 GMT",
"version": "v2"
}
] | 2018-02-16 | [
[
"McAvoy",
"Alex",
""
],
[
"Fraiman",
"Nicolas",
""
],
[
"Hauert",
"Christoph",
""
],
[
"Wakeley",
"John",
""
],
[
"Nowak",
"Martin A.",
""
]
] | Many mathematical frameworks of evolutionary game dynamics assume that the total population size is constant and that selection affects only the relative frequency of strategies. Here, we consider evolutionary game dynamics in an extended Wright-Fisher process with variable population size. In such a scenario, it is po... |
1306.5355 | Davit Potoyan | D. A. Potoyan and P. G. Wolynes | On the dephasing of genetic oscillations | null | null | 10.1073/pnas.1323433111 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The digital nature of genes combined with the associated low copy numbers of
proteins regulating them is a significant source of stochasticity, which
affects the phase of biochemical oscillations. We provide a theoretical
framework for understanding the dephasing evolution of genetic oscillations by
combining the phe... | [
{
"created": "Sat, 22 Jun 2013 21:26:38 GMT",
"version": "v1"
}
] | 2014-06-03 | [
[
"Potoyan",
"D. A.",
""
],
[
"Wolynes",
"P. G.",
""
]
] | The digital nature of genes combined with the associated low copy numbers of proteins regulating them is a significant source of stochasticity, which affects the phase of biochemical oscillations. We provide a theoretical framework for understanding the dephasing evolution of genetic oscillations by combining the pheno... |
2206.06035 | Ulderico Fugacci | Luca Gagliardi, Andrea Raffo, Ulderico Fugacci, Silvia Biasotti,
Walter Rocchia, Hao Huang, Boulbaba Ben Amor, Yi Fang, Yuanyuan Zhang, Xiao
Wang, Charles Christoffer, Daisuke Kihara, Apostolos Axenopoulos, Stelios
Mylonas, Petros Daras | SHREC 2022: Protein-ligand binding site recognition | null | Computers & Graphics 107 (2022) 20-31 | 10.1016/j.cag.2022.07.005 | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This paper presents the methods that have participated in the SHREC 2022
contest on protein-ligand binding site recognition. The prediction of
protein-ligand binding regions is an active research domain in computational
biophysics and structural biology and plays a relevant role for molecular
docking and drug design.... | [
{
"created": "Mon, 13 Jun 2022 10:43:32 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Jun 2022 14:48:35 GMT",
"version": "v2"
},
{
"created": "Sat, 2 Jul 2022 08:06:13 GMT",
"version": "v3"
},
{
"created": "Wed, 24 Aug 2022 13:06:46 GMT",
"version": "v4"
}
] | 2023-08-10 | [
[
"Gagliardi",
"Luca",
""
],
[
"Raffo",
"Andrea",
""
],
[
"Fugacci",
"Ulderico",
""
],
[
"Biasotti",
"Silvia",
""
],
[
"Rocchia",
"Walter",
""
],
[
"Huang",
"Hao",
""
],
[
"Amor",
"Boulbaba Ben",
""
],
[
... | This paper presents the methods that have participated in the SHREC 2022 contest on protein-ligand binding site recognition. The prediction of protein-ligand binding regions is an active research domain in computational biophysics and structural biology and plays a relevant role for molecular docking and drug design. T... |
1608.00535 | David Murrugarra | David Murrugarra, Jacob Miller, and Alex Mueller | Estimating Propensity Parameters using Google PageRank and Genetic
Algorithms | 20 pages, 4 figures, 2 tables | Frontiers in Neuroscience, 10:513, 2016 | 10.3389/fnins.2016.00513 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stochastic Boolean networks, or more generally, stochastic discrete networks,
are an important class of computational models for molecular interaction
networks. The stochasticity stems from the updating schedule. Standard updating
schedules include the synchronous update, where all the nodes are updated at
the same t... | [
{
"created": "Mon, 1 Aug 2016 19:26:13 GMT",
"version": "v1"
},
{
"created": "Mon, 3 Oct 2016 15:36:52 GMT",
"version": "v2"
},
{
"created": "Mon, 17 Oct 2016 17:22:35 GMT",
"version": "v3"
}
] | 2024-07-09 | [
[
"Murrugarra",
"David",
""
],
[
"Miller",
"Jacob",
""
],
[
"Mueller",
"Alex",
""
]
] | Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same tim... |
2009.01574 | Attila Szolnoki | Marcell Blahota, Istvan Blahota, and Attila Szolnoki | Equal partners do better in defensive alliances | 7 two-column pages, 6 figures, accepted for publication in EPL | EPL 131 (2020) 58002 | 10.1209/0295-5075/131/58002 | null | q-bio.PE cond-mat.stat-mech cs.GT nlin.PS physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cyclic dominance offers not just a way to maintain biodiversity, but also
serves as a sort of defensive alliance against an external invader.
Interestingly, a new level of competition can be observed when two cyclic loops
are present. Here the inner invasion speed plays a decisive role on the
evolutionary outcome, be... | [
{
"created": "Thu, 3 Sep 2020 10:41:06 GMT",
"version": "v1"
}
] | 2020-09-21 | [
[
"Blahota",
"Marcell",
""
],
[
"Blahota",
"Istvan",
""
],
[
"Szolnoki",
"Attila",
""
]
] | Cyclic dominance offers not just a way to maintain biodiversity, but also serves as a sort of defensive alliance against an external invader. Interestingly, a new level of competition can be observed when two cyclic loops are present. Here the inner invasion speed plays a decisive role on the evolutionary outcome, beca... |
2301.04471 | Umberto Michelucci | Francesca Venturini, Michela Sperti, Umberto Michelucci, Arnaud
Gucciardi, Vanessa M. Martos, Marco A. Deriu | Dataset of Fluorescence Spectra and Chemical Parameters of Olive Oils | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This dataset encompasses fluorescence spectra and chemical parameters of 24
olive oil samples from the 2019-2020 harvest provided by the producer Conde de
Benalua, Granada, Spain. The oils are characterized by different qualities: 10
extra virgin olive oil (EVOO), 8 virgin olive oil (VOO), and 6 lampante olive
oil (L... | [
{
"created": "Tue, 10 Jan 2023 10:17:03 GMT",
"version": "v1"
}
] | 2023-01-12 | [
[
"Venturini",
"Francesca",
""
],
[
"Sperti",
"Michela",
""
],
[
"Michelucci",
"Umberto",
""
],
[
"Gucciardi",
"Arnaud",
""
],
[
"Martos",
"Vanessa M.",
""
],
[
"Deriu",
"Marco A.",
""
]
] | This dataset encompasses fluorescence spectra and chemical parameters of 24 olive oil samples from the 2019-2020 harvest provided by the producer Conde de Benalua, Granada, Spain. The oils are characterized by different qualities: 10 extra virgin olive oil (EVOO), 8 virgin olive oil (VOO), and 6 lampante olive oil (LOO... |
2208.11626 | Martin Weigt | Carlos A. Gandarilla-Perez, Sergio Pinilla, Anne-Florence Bitbol,
Martin Weigt | Combining phylogeny and coevolution improves the inference of
interaction partners among paralogous proteins | 19 pages | null | 10.1371/journal.pcbi.1011010 | null | q-bio.BM cond-mat.stat-mech q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Predicting protein-protein interactions from sequences is an important goal
of computational biology. Various sources of information can be used to this
end. Starting from the sequences of two interacting protein families, one can
use phylogeny or residue coevolution to infer which paralogs are specific
interaction p... | [
{
"created": "Wed, 24 Aug 2022 15:51:28 GMT",
"version": "v1"
}
] | 2023-04-26 | [
[
"Gandarilla-Perez",
"Carlos A.",
""
],
[
"Pinilla",
"Sergio",
""
],
[
"Bitbol",
"Anne-Florence",
""
],
[
"Weigt",
"Martin",
""
]
] | Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use phylogeny or residue coevolution to infer which paralogs are specific interaction par... |
1512.00037 | Weiyu Huang | Weiyu Huang, Leah Goldsberry, Nicholas F. Wymbs, Scott T. Grafton,
Danielle S. Bassett and Alejandro Ribeiro | Graph Frequency Analysis of Brain Signals | null | null | 10.1109/JSTSP.2016.2600859 | null | q-bio.NC cs.CE cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper presents methods to analyze functional brain networks and signals
from graph spectral perspectives. The notion of frequency and filters
traditionally defined for signals supported on regular domains such as discrete
time and image grids has been recently generalized to irregular graph domains,
and defines ... | [
{
"created": "Mon, 2 Nov 2015 19:25:39 GMT",
"version": "v1"
},
{
"created": "Tue, 3 May 2016 16:00:32 GMT",
"version": "v2"
}
] | 2016-11-03 | [
[
"Huang",
"Weiyu",
""
],
[
"Goldsberry",
"Leah",
""
],
[
"Wymbs",
"Nicholas F.",
""
],
[
"Grafton",
"Scott T.",
""
],
[
"Bassett",
"Danielle S.",
""
],
[
"Ribeiro",
"Alejandro",
""
]
] | This paper presents methods to analyze functional brain networks and signals from graph spectral perspectives. The notion of frequency and filters traditionally defined for signals supported on regular domains such as discrete time and image grids has been recently generalized to irregular graph domains, and defines br... |
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