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
values | categories stringlengths 8 87 | license stringclasses 9
values | orig_abstract stringlengths 27 3.76k | versions listlengths 1 15 | update_date stringlengths 10 10 | authors_parsed listlengths 1 147 | abstract stringlengths 24 3.75k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2010.01758 | Claudia Solis-Lemus | Claudia Solis-Lemus, Arrigo Coen, Cecile Ane | On the Identifiability of Phylogenetic Networks under a Pseudolikelihood
model | null | null | null | null | q-bio.PE math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Tree of Life is the graphical structure that represents the evolutionary
process from single-cell organisms at the origin of life to the vast
biodiversity we see today. Reconstructing this tree from genomic sequences is
challenging due to the variety of biological forces that shape the signal in
the data, and man... | [
{
"created": "Mon, 5 Oct 2020 03:28:25 GMT",
"version": "v1"
}
] | 2020-10-06 | [
[
"Solis-Lemus",
"Claudia",
""
],
[
"Coen",
"Arrigo",
""
],
[
"Ane",
"Cecile",
""
]
] | The Tree of Life is the graphical structure that represents the evolutionary process from single-cell organisms at the origin of life to the vast biodiversity we see today. Reconstructing this tree from genomic sequences is challenging due to the variety of biological forces that shape the signal in the data, and many ... |
1804.04538 | Priya Ranjan | Anju Mishra, Shanu Sharma, Sanjay Kumar, Priya Ranjan, and Amit
Ujlayan | Automated Classification of Hand-grip action on Objects using Machine
Learning | This is a report on an ongoing project | null | null | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain computer interface is the current area of research to provide
assistance to disabled persons. To cope up with the growing needs of BCI
applications, this paper presents an automated classification scheme for
handgrip actions on objects by using Electroencephalography (EEG) data. The
presented approach focuses o... | [
{
"created": "Fri, 9 Mar 2018 11:51:43 GMT",
"version": "v1"
}
] | 2018-04-13 | [
[
"Mishra",
"Anju",
""
],
[
"Sharma",
"Shanu",
""
],
[
"Kumar",
"Sanjay",
""
],
[
"Ranjan",
"Priya",
""
],
[
"Ujlayan",
"Amit",
""
]
] | Brain computer interface is the current area of research to provide assistance to disabled persons. To cope up with the growing needs of BCI applications, this paper presents an automated classification scheme for handgrip actions on objects by using Electroencephalography (EEG) data. The presented approach focuses on ... |
1003.5839 | Arne Traulsen | Chaitanya S. Gokhale and Arne Traulsen | Evolutionary games in the multiverse | null | PNAS 107, 5500-5504 (2010) | 10.1073/pnas.0912214107 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolutionary game dynamics of two players with two strategies has been
studied in great detail. These games have been used to model many biologically
relevant scenarios, ranging from social dilemmas in mammals to microbial
diversity. Some of these games may in fact take place between a number of
individuals and not j... | [
{
"created": "Tue, 30 Mar 2010 15:05:56 GMT",
"version": "v1"
}
] | 2010-03-31 | [
[
"Gokhale",
"Chaitanya S.",
""
],
[
"Traulsen",
"Arne",
""
]
] | Evolutionary game dynamics of two players with two strategies has been studied in great detail. These games have been used to model many biologically relevant scenarios, ranging from social dilemmas in mammals to microbial diversity. Some of these games may in fact take place between a number of individuals and not jus... |
1212.0662 | Nicolas Perony | Nicolas Perony, Barbara K\"onig, and Frank Schweitzer | A stochastic model of social interaction in wild house mice | 12 pages, 5 figures, 2 tables. Originally published in the
Proceedings of the European Conference on Complex Systems 2010 (ECCS'10),
Lisbon, September 13-17, 2010 | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate to what extent the interaction dynamics of a population of
wild house mouse (Mus musculus domesticus) in their environment can be
explained by a simple stochastic model. We use a Markov chain model to describe
the transitions of mice in a discrete space of nestboxes, and implement a
multi-agent simulat... | [
{
"created": "Tue, 4 Dec 2012 10:07:56 GMT",
"version": "v1"
}
] | 2012-12-05 | [
[
"Perony",
"Nicolas",
""
],
[
"König",
"Barbara",
""
],
[
"Schweitzer",
"Frank",
""
]
] | We investigate to what extent the interaction dynamics of a population of wild house mouse (Mus musculus domesticus) in their environment can be explained by a simple stochastic model. We use a Markov chain model to describe the transitions of mice in a discrete space of nestboxes, and implement a multi-agent simulatio... |
q-bio/0701009 | Johannes Wollbold | Johannes Wollbold | Attribute Exploration of Discrete Temporal Transitions | Only the email address and reference have been replaced | In: Gely, A. et al.. Contributions to ICFCA 2007 - 5th
International Conference on Formal Concept Analysis. Clermont-Ferrand 2007,
121-130 | null | null | q-bio.QM cs.AI q-bio.MN | null | Discrete temporal transitions occur in a variety of domains, but this work is
mainly motivated by applications in molecular biology: explaining and analyzing
observed transcriptome and proteome time series by literature and database
knowledge. The starting point of a formal concept analysis model is presented.
The ob... | [
{
"created": "Thu, 4 Jan 2007 14:10:51 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Sep 2007 08:46:00 GMT",
"version": "v2"
}
] | 2007-09-18 | [
[
"Wollbold",
"Johannes",
""
]
] | Discrete temporal transitions occur in a variety of domains, but this work is mainly motivated by applications in molecular biology: explaining and analyzing observed transcriptome and proteome time series by literature and database knowledge. The starting point of a formal concept analysis model is presented. The obje... |
1810.06831 | Andrew Francis | Michael Hendriksen and Andrew Francis | Lattice consensus: A partial order on phylogenetic trees that induces an
associatively stable consensus method | The paper has an error in the proof of Theorem 5.3, and this affects
5.4, which is incorrect (there is a counterexample to the Theorem statement).
As a consequence the results in Section 6 about a consensus method are
vacuous. Some results in the paper stand, for instance the results in
Sections 2, 3, 4, and 7 | null | null | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There is a long tradition of the axiomatic study of consensus methods in
phylogenetics that satisfy certain desirable properties. One
recently-introduced property is associative stability, which is desirable
because it confers a computational advantage, in that the consensus method only
needs to be computed "pairwise... | [
{
"created": "Tue, 16 Oct 2018 06:26:40 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Oct 2018 07:14:08 GMT",
"version": "v2"
}
] | 2018-10-22 | [
[
"Hendriksen",
"Michael",
""
],
[
"Francis",
"Andrew",
""
]
] | There is a long tradition of the axiomatic study of consensus methods in phylogenetics that satisfy certain desirable properties. One recently-introduced property is associative stability, which is desirable because it confers a computational advantage, in that the consensus method only needs to be computed "pairwise".... |
2012.02246 | Gabriel Schamberg | Gabriel Schamberg, Sourish Chakravarty, Taylor E. Baum, Emery N. Brown | Inferring neural dynamics during burst suppression using a
neurophysiology-inspired switching state-space model | To appear in the proceedings of the 2020 IEEE Asilomar Conference on
Signals, Systems, and Computers | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Burst suppression is an electroencephalography (EEG) pattern associated with
profoundly inactivated brain states characterized by cerebral metabolic
depression. Its distinctive feature is alternation between short temporal
segments of near-isoelectric inactivity (suppressions) and relatively
high-voltage activity (bu... | [
{
"created": "Thu, 3 Dec 2020 20:30:46 GMT",
"version": "v1"
}
] | 2020-12-07 | [
[
"Schamberg",
"Gabriel",
""
],
[
"Chakravarty",
"Sourish",
""
],
[
"Baum",
"Taylor E.",
""
],
[
"Brown",
"Emery N.",
""
]
] | Burst suppression is an electroencephalography (EEG) pattern associated with profoundly inactivated brain states characterized by cerebral metabolic depression. Its distinctive feature is alternation between short temporal segments of near-isoelectric inactivity (suppressions) and relatively high-voltage activity (burs... |
2007.03157 | Shiladitya Banerjee | Jake Cornwall Scoones, Deb Sankar Banerjee, Shiladitya Banerjee | Size-regulated symmetry breaking in reaction-diffusion models of
developmental transitions | 11 pages, 5 figures, Perspective Article | null | null | null | q-bio.TO nlin.PS physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | The development of multicellular organisms proceeds through a series of
morphogenetic and cell-state transitions, transforming homogeneous zygotes into
complex adults by a process of self-organization. Many of these transitions are
achieved by spontaneous symmetry breaking mechanisms, allowing cells and
tissues to ac... | [
{
"created": "Tue, 7 Jul 2020 01:29:09 GMT",
"version": "v1"
}
] | 2020-07-08 | [
[
"Scoones",
"Jake Cornwall",
""
],
[
"Banerjee",
"Deb Sankar",
""
],
[
"Banerjee",
"Shiladitya",
""
]
] | The development of multicellular organisms proceeds through a series of morphogenetic and cell-state transitions, transforming homogeneous zygotes into complex adults by a process of self-organization. Many of these transitions are achieved by spontaneous symmetry breaking mechanisms, allowing cells and tissues to acqu... |
2308.05685 | Netta Haroush | Netta Haroush, Michal Levo, Eric Wieschaus and Thomas Gregor | Functional analysis of a gene locus in response to non-canonical
combinations of transcription factors | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcription factor combinations determine gene locus activity and thereby
cell identity. However, the precise link between concentrations of such
activating transcription factors and target-gene activity is ambiguous. Here we
investigate this link for the gap gene dependent activation of the even-skipped
(eve) locu... | [
{
"created": "Thu, 10 Aug 2023 16:38:59 GMT",
"version": "v1"
}
] | 2023-08-11 | [
[
"Haroush",
"Netta",
""
],
[
"Levo",
"Michal",
""
],
[
"Wieschaus",
"Eric",
""
],
[
"Gregor",
"Thomas",
""
]
] | Transcription factor combinations determine gene locus activity and thereby cell identity. However, the precise link between concentrations of such activating transcription factors and target-gene activity is ambiguous. Here we investigate this link for the gap gene dependent activation of the even-skipped (eve) locus ... |
1602.05177 | Olivier Sperandio | G Moroy (UMR S973, UP7), O Sperandio (UMR S973, UP7), S Rielland (UMR
S973, UP7), S Khemka (LBPA), K Druart (UMR S973, UP7), D. Goyal (LBPA), D.
Perahia (LBPA), M. A. Miteva (UMR S973, UP7) | Sampling of conformational ensemble for virtual screening using
molecular dynamics simulations and normal mode analysis | null | Future Medicinal Chemistry, 2015, 7 (17), pp.2317-2331 | 10.4155/fmc.15.150 | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Aim: Molecular dynamics simulations and normal mode analysis are
well-established approaches to generate receptor conformational ensembles
(RCEs) for ligand docking and virtual screening. Here, we report new fast
molecular dynamics-based and normal mode analysis-based protocols combined with
conformational pocket cla... | [
{
"created": "Tue, 16 Feb 2016 20:42:10 GMT",
"version": "v1"
}
] | 2016-02-17 | [
[
"Moroy",
"G",
"",
"UMR S973, UP7"
],
[
"Sperandio",
"O",
"",
"UMR S973, UP7"
],
[
"Rielland",
"S",
"",
"UMR\n S973, UP7"
],
[
"Khemka",
"S",
"",
"LBPA"
],
[
"Druart",
"K",
"",
"UMR S973, UP7"
],
[
"Goyal",
... | Aim: Molecular dynamics simulations and normal mode analysis are well-established approaches to generate receptor conformational ensembles (RCEs) for ligand docking and virtual screening. Here, we report new fast molecular dynamics-based and normal mode analysis-based protocols combined with conformational pocket class... |
2310.13598 | Laurent Gatto | Samuel Gr\'egoire and Christophe Vanderaa and S\'ebastien Pyr dit Ruys
and Gabriel Mazzucchelli and Christopher Kune and Didier Vertommen and
Laurent Gatto | Standardised workflow for mass spectrometry-based single-cell proteomics
data processing and analysis using the scp package | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | Mass spectrometry (MS) based single-cell proteomics (SCP) explores cellular
heterogeneity by focusing on the functional effectors of the cells - proteins.
However, extracting meaningful biological information from MS data is far from
trivial, especially with single cells. Currently, data analysis workflows are
substa... | [
{
"created": "Fri, 20 Oct 2023 15:46:51 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Dec 2023 16:47:50 GMT",
"version": "v2"
}
] | 2023-12-14 | [
[
"Grégoire",
"Samuel",
""
],
[
"Vanderaa",
"Christophe",
""
],
[
"Ruys",
"Sébastien Pyr dit",
""
],
[
"Mazzucchelli",
"Gabriel",
""
],
[
"Kune",
"Christopher",
""
],
[
"Vertommen",
"Didier",
""
],
[
"Gatto",
"La... | Mass spectrometry (MS) based single-cell proteomics (SCP) explores cellular heterogeneity by focusing on the functional effectors of the cells - proteins. However, extracting meaningful biological information from MS data is far from trivial, especially with single cells. Currently, data analysis workflows are substant... |
2012.03720 | Leon Avery | Leon Avery, Brian Ingalls, Catherine Dumur, Alexander Artyukhin | A Keller-Segel model for C elegans L1 aggregation | null | null | 10.1371/journal.pcbi.1009231 | null | q-bio.MN q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | We describe a mathematical model for the aggregation of starved first-stage C
elegans larvae (L1s). We propose that starved L1s produce and respond
chemotactically to two labile diffusible chemical signals, a short-range
attractant and a longer range repellent. This model takes the mathematical form
of three coupled ... | [
{
"created": "Fri, 4 Dec 2020 17:27:23 GMT",
"version": "v1"
},
{
"created": "Fri, 7 May 2021 16:03:43 GMT",
"version": "v2"
}
] | 2021-09-15 | [
[
"Avery",
"Leon",
""
],
[
"Ingalls",
"Brian",
""
],
[
"Dumur",
"Catherine",
""
],
[
"Artyukhin",
"Alexander",
""
]
] | We describe a mathematical model for the aggregation of starved first-stage C elegans larvae (L1s). We propose that starved L1s produce and respond chemotactically to two labile diffusible chemical signals, a short-range attractant and a longer range repellent. This model takes the mathematical form of three coupled pa... |
1111.2019 | Santiago Ra\'ul Doyle | Santiago R. Doyle, Florencia Carusela, Sebasti\'an Guala and Fernando
Momo | A null model for testing thermodynamic optimization in ecological
systems | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Several authors have hypothesized that ecological systems are subject to
thermodynamic optimization, which, if proven correct, could represent a long
sought general principle of organization in ecology. Although there have been
recent advances, this still remains as an unresolved topic, and ecologists lack
a general ... | [
{
"created": "Tue, 8 Nov 2011 19:14:37 GMT",
"version": "v1"
}
] | 2011-11-09 | [
[
"Doyle",
"Santiago R.",
""
],
[
"Carusela",
"Florencia",
""
],
[
"Guala",
"Sebastián",
""
],
[
"Momo",
"Fernando",
""
]
] | Several authors have hypothesized that ecological systems are subject to thermodynamic optimization, which, if proven correct, could represent a long sought general principle of organization in ecology. Although there have been recent advances, this still remains as an unresolved topic, and ecologists lack a general me... |
2102.00002 | Elvira Di Nardo Prof. | A. Buonocore, A. Di Crescenzo, E. Di Nardo | Input-output behaviour of a model neuron with alternating drift | null | BioSystems (2002) 67, 27-34 | 10.1016/S0303-2647(02)00060-6 | null | q-bio.NC math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The input-output behaviour of the Wiener neuronal model subject to
alternating input is studied under the assumption that the effect of such an
input is to make the drift itself of an alternating type. Firing densities and
related statistics are obtained via simulations of the sample-paths of the
process in the follo... | [
{
"created": "Sun, 31 Jan 2021 16:30:22 GMT",
"version": "v1"
}
] | 2021-02-02 | [
[
"Buonocore",
"A.",
""
],
[
"Di Crescenzo",
"A.",
""
],
[
"Di Nardo",
"E.",
""
]
] | The input-output behaviour of the Wiener neuronal model subject to alternating input is studied under the assumption that the effect of such an input is to make the drift itself of an alternating type. Firing densities and related statistics are obtained via simulations of the sample-paths of the process in the followi... |
0801.3675 | Paolo Ribeca | Paolo Ribeca and Emanuele Raineri | Faster exact Markovian probability functions for motif occurrences: a
DFA-only approach | 18 pages, 7 figures and 2 tables | null | 10.1093/bioinformatics/btn525 | null | q-bio.GN q-bio.QM | null | Background: The computation of the statistical properties of motif
occurrences has an obviously relevant practical application: for example,
patterns that are significantly over- or under-represented in the genome are
interesting candidates for biological roles. However, the problem is
computationally hard; as a resu... | [
{
"created": "Thu, 24 Jan 2008 15:39:48 GMT",
"version": "v1"
}
] | 2021-11-01 | [
[
"Ribeca",
"Paolo",
""
],
[
"Raineri",
"Emanuele",
""
]
] | Background: The computation of the statistical properties of motif occurrences has an obviously relevant practical application: for example, patterns that are significantly over- or under-represented in the genome are interesting candidates for biological roles. However, the problem is computationally hard; as a result... |
1112.3640 | Christopher L. Henley | Hanrong Chen, C. L. Henley, and B. Xu | Propagating left/right asymmetry in the zebrafish embryo:
one-dimensional model | 13 pages, 5 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During embryonic development in vertebrates, left-right (L/R) asymmetry is
reliably generated by a conserved mechanism: a L/R asymmetric signal is
transmitted from the embryonic node to other parts of the embryo by the L/R
asymmetric expression and diffusion of the TGF-$\beta$ related proteins Nodal
and Lefty via pro... | [
{
"created": "Thu, 15 Dec 2011 20:29:10 GMT",
"version": "v1"
}
] | 2011-12-16 | [
[
"Chen",
"Hanrong",
""
],
[
"Henley",
"C. L.",
""
],
[
"Xu",
"B.",
""
]
] | During embryonic development in vertebrates, left-right (L/R) asymmetry is reliably generated by a conserved mechanism: a L/R asymmetric signal is transmitted from the embryonic node to other parts of the embryo by the L/R asymmetric expression and diffusion of the TGF-$\beta$ related proteins Nodal and Lefty via propa... |
1311.5517 | Helene Hill | Joel H Pitt and Helene Z Hill | Statistical Detection of Potentially Fabricated Data | 31 pages of text including 2 figures, 3 tables and an Appendix
containing the mathematical derivation of a model for detecting and
quantifying the probability for the occurrence of the average of 3 counts as
one of those counts. 166 pages of raw data that were used in the analyses | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Scientific fraud is an increasingly vexing problem. Many current programs for
fraud detection focus on image manipulation, while techniques for detection
based on anomalous patterns that may be discoverable in the underlying
numerical data get much less attention, even though these techniques are often
easy to apply.... | [
{
"created": "Thu, 21 Nov 2013 19:03:55 GMT",
"version": "v1"
}
] | 2013-11-22 | [
[
"Pitt",
"Joel H",
""
],
[
"Hill",
"Helene Z",
""
]
] | Scientific fraud is an increasingly vexing problem. Many current programs for fraud detection focus on image manipulation, while techniques for detection based on anomalous patterns that may be discoverable in the underlying numerical data get much less attention, even though these techniques are often easy to apply. W... |
2302.12455 | Eitan Lerner | Evelyn Ploetz, Benjamin Ambrose, Anders Barth, Richard B\"orner, Felix
Erichson, Achillefs N. Kapanidis, Harold D. Kim, Marcia Levitus, Timothy M.
Lohman, Abhishek Mazumder, David S. Rueda, Fabio D. Steffen, Thorben Cordes,
Steven W. Magennis and Eitan Lerner | A new twist on PIFE: photoisomerisation-related fluorescence enhancement | No Comments | null | 10.1088/2050-6120/acfb58 | null | q-bio.BM q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | PIFE was first used as an acronym for protein-induced fluorescence
enhancement, which refers to the increase in fluorescence observed upon the
interaction of a fluorophore, such as a cyanine, with a protein. This
fluorescence enhancement is due to changes in the rate of cis/trans
photoisomerisation. It is clear now t... | [
{
"created": "Fri, 24 Feb 2023 05:11:25 GMT",
"version": "v1"
},
{
"created": "Mon, 10 Jul 2023 10:01:48 GMT",
"version": "v2"
}
] | 2023-10-24 | [
[
"Ploetz",
"Evelyn",
""
],
[
"Ambrose",
"Benjamin",
""
],
[
"Barth",
"Anders",
""
],
[
"Börner",
"Richard",
""
],
[
"Erichson",
"Felix",
""
],
[
"Kapanidis",
"Achillefs N.",
""
],
[
"Kim",
"Harold D.",
""
... | PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate of cis/trans photoisomerisation. It is clear now tha... |
1305.4354 | Steven Frank | Steven A. Frank | Natural selection. VII. History and interpretation of kin selection
theory | null | null | 10.1111/jeb.12131 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Kin selection theory is a kind of causal analysis. The initial form of kin
selection ascribed cause to costs, benefits, and genetic relatedness. The
theory then slowly developed a deeper and more sophisticated approach to
partitioning the causes of social evolution. Controversy followed because
causal analysis inevit... | [
{
"created": "Sun, 19 May 2013 12:18:53 GMT",
"version": "v1"
}
] | 2014-06-18 | [
[
"Frank",
"Steven A.",
""
]
] | Kin selection theory is a kind of causal analysis. The initial form of kin selection ascribed cause to costs, benefits, and genetic relatedness. The theory then slowly developed a deeper and more sophisticated approach to partitioning the causes of social evolution. Controversy followed because causal analysis inevitab... |
1409.4404 | Almaz Mustafin | Almaz Mustafin | Awakened oscillations in coupled consumer-resource pairs | 31 pages, 8 figures 2 tables, 48 references | Journal of Applied Mathematics 2014 (2014), Article ID 561958,
pages 1-20 | 10.1155/2014/561958 | null | q-bio.PE nlin.AO physics.optics | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The paper concerns two interacting consumer-resource pairs based on
chemostat-like equations under the assumption that the dynamics of the resource
is considerably slower than that of the consumer. The presence of two different
time scales enables to carry out a fairly complete analysis of the problem.
This is done b... | [
{
"created": "Sun, 14 Sep 2014 07:32:22 GMT",
"version": "v1"
}
] | 2014-09-17 | [
[
"Mustafin",
"Almaz",
""
]
] | The paper concerns two interacting consumer-resource pairs based on chemostat-like equations under the assumption that the dynamics of the resource is considerably slower than that of the consumer. The presence of two different time scales enables to carry out a fairly complete analysis of the problem. This is done by ... |
2012.00281 | Muriel Gros-Balthazard | Muriel Gros-Balthazard and Jonathan M. Flowers | A brief history of the origin of domesticated date palms | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The study of the origins of crops is of interest from both a fundamental
evolutionary understanding viewpoint, and from an applied agricultural
technology perspective. The date palm (Phoenix dactylifera L.) is the iconic
fruit crop of hot and arid regions of North Africa and the Middle East,
producing sugar-rich frui... | [
{
"created": "Tue, 1 Dec 2020 05:40:54 GMT",
"version": "v1"
}
] | 2020-12-02 | [
[
"Gros-Balthazard",
"Muriel",
""
],
[
"Flowers",
"Jonathan M.",
""
]
] | The study of the origins of crops is of interest from both a fundamental evolutionary understanding viewpoint, and from an applied agricultural technology perspective. The date palm (Phoenix dactylifera L.) is the iconic fruit crop of hot and arid regions of North Africa and the Middle East, producing sugar-rich fruits... |
0903.4168 | Satoru Hayasaka | Satoru Hayasaka, Paul J. Laurienti | Degree distributions in mesoscopic and macroscopic functional brain
networks | null | null | null | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigated the degree distribution of brain networks extracted from
functional magnetic resonance imaging of the human brain. In particular, the
distributions are compared between macroscopic brain networks using
region-based nodes and mesoscopic brain networks using voxel-based nodes. We
found that the distribu... | [
{
"created": "Tue, 24 Mar 2009 19:42:36 GMT",
"version": "v1"
}
] | 2009-03-25 | [
[
"Hayasaka",
"Satoru",
""
],
[
"Laurienti",
"Paul J.",
""
]
] | We investigated the degree distribution of brain networks extracted from functional magnetic resonance imaging of the human brain. In particular, the distributions are compared between macroscopic brain networks using region-based nodes and mesoscopic brain networks using voxel-based nodes. We found that the distributi... |
2101.08211 | Xinwei Yu | Xinwei Yu, Matthew S. Creamer, Francesco Randi, Anuj K. Sharma, Scott
W. Linderman, Andrew M. Leifer | Fast deep learning correspondence for neuron tracking and identification
in C.elegans using synthetic training | 5 figures | eLife 2021;10:e66410 | 10.7554/eLife.66410 | null | q-bio.QM cs.CV q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We present an automated method to track and identify neurons in C. elegans,
called "fast Deep Learning Correspondence" or fDLC, based on the transformer
network architecture. The model is trained once on empirically derived
synthetic data and then predicts neural correspondence across held-out real
animals via transf... | [
{
"created": "Wed, 20 Jan 2021 16:46:37 GMT",
"version": "v1"
}
] | 2021-07-16 | [
[
"Yu",
"Xinwei",
""
],
[
"Creamer",
"Matthew S.",
""
],
[
"Randi",
"Francesco",
""
],
[
"Sharma",
"Anuj K.",
""
],
[
"Linderman",
"Scott W.",
""
],
[
"Leifer",
"Andrew M.",
""
]
] | We present an automated method to track and identify neurons in C. elegans, called "fast Deep Learning Correspondence" or fDLC, based on the transformer network architecture. The model is trained once on empirically derived synthetic data and then predicts neural correspondence across held-out real animals via transfer... |
q-bio/0508040 | Chih-Yuan Tseng | Hung-I Pai, Chih-Yuan Tseng and HC Lee | Identifying Biomagnetic Sources in the Brain by the Maximum Entropy
Approach | 8 pages, 8 figures. Presented at 25th International Workshop on
Bayesian Inference and Maximum Entropy Methods in Science and Engineering,
San Jose, CA, USA Aug 7-12, 2005 | p. 527 in "Bayesian Inference and Maximum Entropy Methods in
Science and Engineering" ed. by K. H. Knuth, A. E. Abbda, R. D. Moriss, and
J. P. Castle (A.I.P. Vol. 803, 2005) | 10.1063/1.2149834 | null | q-bio.NC q-bio.QM | null | Magnetoencephalographic (MEG) measurements record magnetic fields generated
from neurons while information is being processed in the brain. The inverse
problem of identifying sources of biomagnetic fields and deducing their
intensities from MEG measurements is ill-posed when the number of field
detectors is far less ... | [
{
"created": "Mon, 29 Aug 2005 03:21:25 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Pai",
"Hung-I",
""
],
[
"Tseng",
"Chih-Yuan",
""
],
[
"Lee",
"HC",
""
]
] | Magnetoencephalographic (MEG) measurements record magnetic fields generated from neurons while information is being processed in the brain. The inverse problem of identifying sources of biomagnetic fields and deducing their intensities from MEG measurements is ill-posed when the number of field detectors is far less th... |
1612.05463 | Thomas Gueudr\'e PhD | Thomas Gueudr\'e | Growth over time-correlated disorder: a spectral approach to Mean-field | 10 pages + Appendix | Phys. Rev. E 95, 042134 (2017) | 10.1103/PhysRevE.95.042134 | null | q-bio.PE cond-mat.dis-nn cond-mat.stat-mech physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We generalize a model of growth over a disordered environment, to a large
class of It\=o processes. In particular, we study how the microscopic
properties of the noise influence the macroscopic growth rate. The present
model can account for growth processes in large dimensions, and provides a bed
to understand better... | [
{
"created": "Fri, 16 Dec 2016 13:38:24 GMT",
"version": "v1"
}
] | 2017-04-26 | [
[
"Gueudré",
"Thomas",
""
]
] | We generalize a model of growth over a disordered environment, to a large class of It\=o processes. In particular, we study how the microscopic properties of the noise influence the macroscopic growth rate. The present model can account for growth processes in large dimensions, and provides a bed to understand better t... |
2402.18583 | Ling Yang | Zhilin Huang, Ling Yang, Zaixi Zhang, Xiangxin Zhou, Yu Bao, Xiawu
Zheng, Yuwei Yang, Yu Wang, Wenming Yang | Binding-Adaptive Diffusion Models for Structure-Based Drug Design | Accepted by AAAI 2024. Project:
https://github.com/YangLing0818/BindDM | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Structure-based drug design (SBDD) aims to generate 3D ligand molecules that
bind to specific protein targets. Existing 3D deep generative models including
diffusion models have shown great promise for SBDD. However, it is complex to
capture the essential protein-ligand interactions exactly in 3D space for
molecular ... | [
{
"created": "Mon, 15 Jan 2024 00:34:00 GMT",
"version": "v1"
}
] | 2024-03-01 | [
[
"Huang",
"Zhilin",
""
],
[
"Yang",
"Ling",
""
],
[
"Zhang",
"Zaixi",
""
],
[
"Zhou",
"Xiangxin",
""
],
[
"Bao",
"Yu",
""
],
[
"Zheng",
"Xiawu",
""
],
[
"Yang",
"Yuwei",
""
],
[
"Wang",
"Yu",
... | Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to capture the essential protein-ligand interactions exactly in 3D space for molecular ge... |
2110.14602 | Vitaly Vanchurin | Vitaly Vanchurin, Yuri I. Wolf, Mikhail I. Katsnelson, Eugene V.
Koonin | Towards a Theory of Evolution as Multilevel Learning | 29 pages, 3 figures | null | 10.1073/pnas.2120037119 | null | q-bio.PE cond-mat.dis-nn cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We apply the theory of learning to physically renormalizable systems in an
attempt to develop a theory of biological evolution, including the origin of
life, as multilevel learning. We formulate seven fundamental principles of
evolution that appear to be necessary and sufficient to render a universe
observable and sh... | [
{
"created": "Wed, 27 Oct 2021 17:21:16 GMT",
"version": "v1"
}
] | 2022-10-12 | [
[
"Vanchurin",
"Vitaly",
""
],
[
"Wolf",
"Yuri I.",
""
],
[
"Katsnelson",
"Mikhail I.",
""
],
[
"Koonin",
"Eugene V.",
""
]
] | We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution that appear to be necessary and sufficient to render a universe observable and show... |
1308.6240 | Wentian Li | Wentian Li, Jan Freudenberg, Pedro Miramontes | Diminishing Return for Increased Mappability with Longer Sequencing
Reads: Implications of the k-mer Distributions in the Human Genome | 5 figures | BMC Bioinformatics, 15:2 (2014) | 10.1186/1471-2105-15-2 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The amount of non-unique sequence (non-singletons) in a genome directly
affects the difficulty of read alignment to a reference assembly for high
throughput-sequencing data. Although a greater length increases the chance for
reads being uniquely mapped to the reference genome, a quantitative analysis of
the influence... | [
{
"created": "Wed, 28 Aug 2013 18:14:47 GMT",
"version": "v1"
}
] | 2017-03-03 | [
[
"Li",
"Wentian",
""
],
[
"Freudenberg",
"Jan",
""
],
[
"Miramontes",
"Pedro",
""
]
] | The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a greater length increases the chance for reads being uniquely mapped to the reference genome, a quantitative analysis of the influence o... |
2302.04338 | Viren Shah | Viren Shah, Justin Womack, Anthony E. Zamora, Scott S. Terhune, and
Ranjan K. Dash | Simulating the Evolution of Signaling Signatures during CART-Cell --
Tumor Cell Interactions | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Immunotherapies have been proven to have significant therapeutic efficacy in
the treatment of cancer. The last decade has seen adoptive cell therapies, such
as chimeric antigen receptor T-cell (CART-cell) therapy, gain FDA approval
against specific cancers. Additionally, there are numerous clinical trials
ongoing inv... | [
{
"created": "Wed, 8 Feb 2023 21:10:58 GMT",
"version": "v1"
}
] | 2023-02-10 | [
[
"Shah",
"Viren",
""
],
[
"Womack",
"Justin",
""
],
[
"Zamora",
"Anthony E.",
""
],
[
"Terhune",
"Scott S.",
""
],
[
"Dash",
"Ranjan K.",
""
]
] | Immunotherapies have been proven to have significant therapeutic efficacy in the treatment of cancer. The last decade has seen adoptive cell therapies, such as chimeric antigen receptor T-cell (CART-cell) therapy, gain FDA approval against specific cancers. Additionally, there are numerous clinical trials ongoing inves... |
0801.0253 | William Bialek | Greg J. Stephens and William Bialek | Toward a statistical mechanics of four letter words | null | null | 10.1103/PhysRevE.81.066119 | null | q-bio.NC cs.CL physics.data-an physics.soc-ph | null | We consider words as a network of interacting letters, and approximate the
probability distribution of states taken on by this network. Despite the
intuition that the rules of English spelling are highly combinatorial (and
arbitrary), we find that maximum entropy models consistent with pairwise
correlations among let... | [
{
"created": "Mon, 31 Dec 2007 23:51:51 GMT",
"version": "v1"
}
] | 2013-05-29 | [
[
"Stephens",
"Greg J.",
""
],
[
"Bialek",
"William",
""
]
] | We consider words as a network of interacting letters, and approximate the probability distribution of states taken on by this network. Despite the intuition that the rules of English spelling are highly combinatorial (and arbitrary), we find that maximum entropy models consistent with pairwise correlations among lette... |
1011.2939 | Bob Eisenberg | Bob Eisenberg | From Structure to Function in Open Ionic Channels | Nearly final version of publication | Journal of Membrane Biol. 171, 1-24 (1999) | 10.1007/s002329900554 | null | q-bio.BM cond-mat.soft math-ph math.MP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a simple working hypothesis that all permeation properties of
open ionic channels can be predicted by understanding electrodiffusion in fixed
structures, without invoking conformation changes, or changes in chemical
bonds. We know, of course, that ions can bind to specific protein structures,
and that thi... | [
{
"created": "Fri, 12 Nov 2010 15:10:07 GMT",
"version": "v1"
}
] | 2015-03-17 | [
[
"Eisenberg",
"Bob",
""
]
] | We consider a simple working hypothesis that all permeation properties of open ionic channels can be predicted by understanding electrodiffusion in fixed structures, without invoking conformation changes, or changes in chemical bonds. We know, of course, that ions can bind to specific protein structures, and that this ... |
2312.15055 | Kexuan Li | Kexuan Li | Deep Learning for Efficient GWAS Feature Selection | null | null | null | null | q-bio.GN cs.LG stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genome-Wide Association Studies (GWAS) face unique challenges in the era of
big genomics data, particularly when dealing with ultra-high-dimensional
datasets where the number of genetic features significantly exceeds the
available samples. This paper introduces an extension to the feature selection
methodology propos... | [
{
"created": "Fri, 22 Dec 2023 20:35:47 GMT",
"version": "v1"
}
] | 2023-12-27 | [
[
"Li",
"Kexuan",
""
]
] | Genome-Wide Association Studies (GWAS) face unique challenges in the era of big genomics data, particularly when dealing with ultra-high-dimensional datasets where the number of genetic features significantly exceeds the available samples. This paper introduces an extension to the feature selection methodology proposed... |
1612.02116 | Tarunendu Mapder | Tarunendu Mapder | Signal Manifestation Trade-offs in Incoherent Feed-Forward Loops | 10 pages, 4 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Signal processing in biological systems is delicately executed by specialised
networks, which are modular assemblies of network motifs. The motifs are
independently functional circuits found in enormous numbers in any living cell.
A very common network motif is the feed-forward loop (FFL), which regulates a
downstrea... | [
{
"created": "Wed, 7 Dec 2016 05:18:04 GMT",
"version": "v1"
}
] | 2016-12-08 | [
[
"Mapder",
"Tarunendu",
""
]
] | Signal processing in biological systems is delicately executed by specialised networks, which are modular assemblies of network motifs. The motifs are independently functional circuits found in enormous numbers in any living cell. A very common network motif is the feed-forward loop (FFL), which regulates a downstream ... |
1011.2699 | Sang Hoon Lee | Sang Hoon Lee, Pan-Jun Kim, Hawoong Jeong | Global organization of protein complexome in the yeast Saccharomyces
cerevisiae | 48 pages, 6 figures, 3 tables, 8 additional files (3 supporting
tables and 5 supporting figures) on the Web | BMC Syst. Biol. 5, 126 (2011) | 10.1186/1752-0509-5-126 | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Proteins in organisms, rather than act alone, usually form protein complexes
to perform cellular functions. We analyze the topological network structure of
protein complexes and their component proteins in the budding yeast in terms of
the bipartite network and its projections, where the complexes and proteins are
it... | [
{
"created": "Thu, 11 Nov 2010 16:18:03 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Apr 2011 18:32:49 GMT",
"version": "v2"
},
{
"created": "Thu, 11 Aug 2011 17:14:49 GMT",
"version": "v3"
},
{
"created": "Mon, 15 Aug 2011 10:35:04 GMT",
"version": "v4"
}
] | 2011-08-16 | [
[
"Lee",
"Sang Hoon",
""
],
[
"Kim",
"Pan-Jun",
""
],
[
"Jeong",
"Hawoong",
""
]
] | Proteins in organisms, rather than act alone, usually form protein complexes to perform cellular functions. We analyze the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the bipartite network and its projections, where the complexes and proteins are its ... |
1010.2829 | Andrew Noble | Andrew E. Noble, Nico M. Temme, William F. Fagan, Timothy H. Keitt | A sampling theory for asymmetric communities | 46 pages, 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce the first analytical model of asymmetric community dynamics to
yield Hubbell's neutral theory in the limit of functional equivalence among all
species. Our focus centers on an asymmetric extension of Hubbell's local
community dynamics, while an analogous extension of Hubbell's metacommunity
dynamics is d... | [
{
"created": "Thu, 14 Oct 2010 05:17:57 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Dec 2010 02:31:07 GMT",
"version": "v2"
}
] | 2010-12-06 | [
[
"Noble",
"Andrew E.",
""
],
[
"Temme",
"Nico M.",
""
],
[
"Fagan",
"William F.",
""
],
[
"Keitt",
"Timothy H.",
""
]
] | We introduce the first analytical model of asymmetric community dynamics to yield Hubbell's neutral theory in the limit of functional equivalence among all species. Our focus centers on an asymmetric extension of Hubbell's local community dynamics, while an analogous extension of Hubbell's metacommunity dynamics is def... |
q-bio/0402018 | Peng-Ye Wang | Ping Xie, Shuo-Xing Dou, Peng-Ye Wang | Dynamics of heterodimeric kinesins and cooperation of kinesins | 18 pages, 5 figures | null | null | null | q-bio.BM | null | Using the model for the processive movement of a dimeric kinesin we proposed
before, we study the dynamics of a number of mutant homodimeric and
heterodimeric kinesins that were constructed by Kaseda et al. (Kaseda, K.,
Higuchi, H. and Hirose, K. PNAS 99, 16058 (2002)). The theoretical results of
ATPase rate per head... | [
{
"created": "Mon, 9 Feb 2004 05:32:00 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Xie",
"Ping",
""
],
[
"Dou",
"Shuo-Xing",
""
],
[
"Wang",
"Peng-Ye",
""
]
] | Using the model for the processive movement of a dimeric kinesin we proposed before, we study the dynamics of a number of mutant homodimeric and heterodimeric kinesins that were constructed by Kaseda et al. (Kaseda, K., Higuchi, H. and Hirose, K. PNAS 99, 16058 (2002)). The theoretical results of ATPase rate per head, ... |
1404.4005 | Premal Shah | Premal Shah, David M. McCandlish and Joshua B. Plotkin | Historical contingency and entrenchment in protein evolution under
purifying selection | 42 pages, 13 figures | null | 10.1073/pnas.1412933112 | null | q-bio.PE q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The fitness contribution of an allele at one genetic site may depend on
alleles at other sites, a phenomenon known as epistasis. Epistasis can
profoundly influence the process of evolution in populations under selection,
and can shape the course of protein evolution across divergent species. Whereas
epistasis between... | [
{
"created": "Tue, 15 Apr 2014 18:18:39 GMT",
"version": "v1"
},
{
"created": "Tue, 29 Apr 2014 17:03:56 GMT",
"version": "v2"
},
{
"created": "Tue, 15 Jul 2014 19:36:56 GMT",
"version": "v3"
}
] | 2015-06-11 | [
[
"Shah",
"Premal",
""
],
[
"McCandlish",
"David M.",
""
],
[
"Plotkin",
"Joshua B.",
""
]
] | The fitness contribution of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations under selection, and can shape the course of protein evolution across divergent species. Whereas epistasis between a... |
q-bio/0701028 | Francesco Pederiva | M. Sega, P. Faccioli, F. Pederiva, G. Garberoglio, H. Orland | Quantitative Protein Dynamics from Dominant Folding Pathways | 4 pages, 1 figure | null | 10.1103/PhysRevLett.99.118102 | null | q-bio.QM cond-mat.soft q-bio.BM | null | We develop a theoretical approach to the protein folding problem based on
out-of-equilibrium stochastic dynamics. Within this framework, the
computational difficulties related to the existence of large time scale gaps in
the protein folding problem are removed and simulating the entire reaction in
atomistic details u... | [
{
"created": "Thu, 18 Jan 2007 10:18:25 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Sega",
"M.",
""
],
[
"Faccioli",
"P.",
""
],
[
"Pederiva",
"F.",
""
],
[
"Garberoglio",
"G.",
""
],
[
"Orland",
"H.",
""
]
] | We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding problem are removed and simulating the entire reaction in atomistic details usi... |
0807.1059 | Michel Aoun | Michel Aoun, Jean-Yves Cabon, Annick Hourmant | Potential Phytoextraction with in-vitro regenerated plantlets of
Brassica juncea (L.) Czern. in presence of CdCl$_2$: Cadmium accumulation and
physiological parameter measurement | 12 pages, 2 figures and 2 tables | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Heavy metal contamination of agricultural land is partly responsible for
limiting crop productivity. Cd$^{2+}$ is known as a non-essentiel HM that can
be harmful to plants even at low concentrations. Brassica juncea (L.) is able
to accumulate more than 400 $\mu$g.g$^{-1}$ D.W. in the shoot, a physiological
trait whic... | [
{
"created": "Mon, 7 Jul 2008 16:13:56 GMT",
"version": "v1"
}
] | 2008-07-08 | [
[
"Aoun",
"Michel",
""
],
[
"Cabon",
"Jean-Yves",
""
],
[
"Hourmant",
"Annick",
""
]
] | Heavy metal contamination of agricultural land is partly responsible for limiting crop productivity. Cd$^{2+}$ is known as a non-essentiel HM that can be harmful to plants even at low concentrations. Brassica juncea (L.) is able to accumulate more than 400 $\mu$g.g$^{-1}$ D.W. in the shoot, a physiological trait which ... |
1903.10131 | Zachary Kilpatrick PhD | Nicholas W. Barendregt, Kre\v{s}imir Josi\'c, and Zachary P.
Kilpatrick | Analyzing dynamic decision-making models using Chapman-Kolmogorov
equations | 24 pages, 9 figures | null | null | null | q-bio.NC math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Decision-making in dynamic environments typically requires adaptive evidence
accumulation that weights new evidence more heavily than old observations.
Recent experimental studies of dynamic decision tasks require subjects to make
decisions for which the correct choice switches stochastically throughout a
single tria... | [
{
"created": "Mon, 25 Mar 2019 04:29:34 GMT",
"version": "v1"
}
] | 2019-03-26 | [
[
"Barendregt",
"Nicholas W.",
""
],
[
"Josić",
"Krešimir",
""
],
[
"Kilpatrick",
"Zachary P.",
""
]
] | Decision-making in dynamic environments typically requires adaptive evidence accumulation that weights new evidence more heavily than old observations. Recent experimental studies of dynamic decision tasks require subjects to make decisions for which the correct choice switches stochastically throughout a single trial.... |
2212.12542 | Antoine Villie | Antoine Villi\'e, Philippe Veber, Yohann de Castro, Laurent Jacob | Neural Networks beyond explainability: Selective inference for sequence
motifs | null | null | null | null | q-bio.GN cs.LG stat.ML | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Over the past decade, neural networks have been successful at making
predictions from biological sequences, especially in the context of regulatory
genomics. As in other fields of deep learning, tools have been devised to
extract features such as sequence motifs that can explain the predictions made
by a trained netw... | [
{
"created": "Fri, 23 Dec 2022 10:49:07 GMT",
"version": "v1"
}
] | 2022-12-27 | [
[
"Villié",
"Antoine",
""
],
[
"Veber",
"Philippe",
""
],
[
"de Castro",
"Yohann",
""
],
[
"Jacob",
"Laurent",
""
]
] | Over the past decade, neural networks have been successful at making predictions from biological sequences, especially in the context of regulatory genomics. As in other fields of deep learning, tools have been devised to extract features such as sequence motifs that can explain the predictions made by a trained networ... |
2303.04902 | Yamin Li | Yamin Li, Saishuang Wu, Jiayang Xu, Haiwa Wang, Qi Zhu, Wen Shi, Yue
Fang, Fan Jiang, Shanbao Tong, Yunting Zhang, Xiaoli Guo | Inter-brain substrates of role switching during mother-child interaction | null | null | 10.1002/hbm.26672 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mother-child interaction is highly dynamic and reciprocal. Switching roles in
these back-and-forth interactions serves as a crucial feature of reciprocal
behaviors while the underlying neural entrainment is still not well-studied.
Here, we designed a role-controlled cooperative task with dual EEG recording to
study h... | [
{
"created": "Wed, 8 Mar 2023 21:43:26 GMT",
"version": "v1"
}
] | 2024-04-04 | [
[
"Li",
"Yamin",
""
],
[
"Wu",
"Saishuang",
""
],
[
"Xu",
"Jiayang",
""
],
[
"Wang",
"Haiwa",
""
],
[
"Zhu",
"Qi",
""
],
[
"Shi",
"Wen",
""
],
[
"Fang",
"Yue",
""
],
[
"Jiang",
"Fan",
""
],
... | Mother-child interaction is highly dynamic and reciprocal. Switching roles in these back-and-forth interactions serves as a crucial feature of reciprocal behaviors while the underlying neural entrainment is still not well-studied. Here, we designed a role-controlled cooperative task with dual EEG recording to study how... |
1402.4824 | Sergio G\'omez | Sara Teller, Clara Granell, Manlio De Domenico, Jordi Soriano, Sergio
Gomez, Alex Arenas | Emergence of assortative mixing between clusters of cultured neurons | 33 pages, 10 figures | PLOS Comput. Biol. 10(9) (2014) e1003796 | 10.1371/journal.pcbi.1003796 | null | q-bio.NC cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The analysis of the activity of neuronal cultures is considered to be a good
proxy of the functional connectivity of in vivo neuronal tissues. Thus, the
functional complex network inferred from activity patterns is a promising way
to unravel the interplay between structure and functionality of neuronal
systems. Here,... | [
{
"created": "Wed, 19 Feb 2014 21:05:25 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Jul 2014 19:13:46 GMT",
"version": "v2"
}
] | 2014-09-09 | [
[
"Teller",
"Sara",
""
],
[
"Granell",
"Clara",
""
],
[
"De Domenico",
"Manlio",
""
],
[
"Soriano",
"Jordi",
""
],
[
"Gomez",
"Sergio",
""
],
[
"Arenas",
"Alex",
""
]
] | The analysis of the activity of neuronal cultures is considered to be a good proxy of the functional connectivity of in vivo neuronal tissues. Thus, the functional complex network inferred from activity patterns is a promising way to unravel the interplay between structure and functionality of neuronal systems. Here, w... |
0910.2660 | John Hopfield | J. J. Hopfield and Carlos D. Brody | Sequence reproduction, single trial learning, and mimicry based on a
mammalian-like distributed code for time | 18 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Animals learn tasks requiring a sequence of actions over time. Waiting a
given time before taking an action is a simple example. Mimicry is a complex
example, e.g. in humans, humming a brief tune you have just heard.
Re-experiencing a sensory pattern mentally must involve reproducing a sequence
of neural activities o... | [
{
"created": "Wed, 14 Oct 2009 16:12:16 GMT",
"version": "v1"
}
] | 2009-10-15 | [
[
"Hopfield",
"J. J.",
""
],
[
"Brody",
"Carlos D.",
""
]
] | Animals learn tasks requiring a sequence of actions over time. Waiting a given time before taking an action is a simple example. Mimicry is a complex example, e.g. in humans, humming a brief tune you have just heard. Re-experiencing a sensory pattern mentally must involve reproducing a sequence of neural activities ove... |
2104.08334 | Cem \"Ozel | Cem \"Ozel, Muharrem Erdem Bo\u{g}o\c{c}lu, Ceren Ke\c{c}eciler, Ecem
Kaplan and Sevil Y\"ucel | Utilization of the simulated flue gas on the cultivation of Chlorella
protothecoides | 6 pages, 6 figures | Journal of the Indian Chemical Society (2019), 96, 1137-1142 | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years, fossil-based fuels have been used to supply the energy needs
of the world. Fossil-based fuels induce accumulation of the atmospheric CO2
which causes global warming. One of CO2 source is flue gas emission from the
power plant. The microalgae have been considered excellent biological materials
for red... | [
{
"created": "Fri, 16 Apr 2021 19:31:43 GMT",
"version": "v1"
}
] | 2021-04-20 | [
[
"Özel",
"Cem",
""
],
[
"Boğoçlu",
"Muharrem Erdem",
""
],
[
"Keçeciler",
"Ceren",
""
],
[
"Kaplan",
"Ecem",
""
],
[
"Yücel",
"Sevil",
""
]
] | In recent years, fossil-based fuels have been used to supply the energy needs of the world. Fossil-based fuels induce accumulation of the atmospheric CO2 which causes global warming. One of CO2 source is flue gas emission from the power plant. The microalgae have been considered excellent biological materials for reduc... |
0905.1458 | Michael Krumin | Michael Krumin, Avner Shimron and Shy Shoham | Correlation-distortion based identification of Linear-Nonlinear-Poisson
models | null | null | 10.1007/s10827-009-0184-0 | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Linear-Nonlinear-Poisson (LNP) models are a popular and powerful tool for
describing encoding (stimulus-response) transformations by single sensory as
well as motor neurons. Recently, there has been rising interest in the second-
and higher-order correlation structure of neural spike trains, and how it may
be related... | [
{
"created": "Sun, 10 May 2009 09:01:18 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Oct 2009 01:00:23 GMT",
"version": "v2"
}
] | 2016-09-08 | [
[
"Krumin",
"Michael",
""
],
[
"Shimron",
"Avner",
""
],
[
"Shoham",
"Shy",
""
]
] | Linear-Nonlinear-Poisson (LNP) models are a popular and powerful tool for describing encoding (stimulus-response) transformations by single sensory as well as motor neurons. Recently, there has been rising interest in the second- and higher-order correlation structure of neural spike trains, and how it may be related t... |
2112.03151 | Refath Bari | Refath Bari | A Neuronal Noise Critique of Integrated Information Theory | Submitted to PLoS ONE | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Integrated Information Theory (IIT) is an audacious attempt to pin down the
abstract, phenomenological experiences of consciousness into a rigorous,
mathematical framework. We show that IIT's stance in regards to neuronal noise
is inconsistent with experimental data demonstrating that neuronal noise in the
brain play... | [
{
"created": "Mon, 6 Dec 2021 16:37:39 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Dec 2021 15:38:19 GMT",
"version": "v2"
}
] | 2021-12-10 | [
[
"Bari",
"Refath",
""
]
] | Integrated Information Theory (IIT) is an audacious attempt to pin down the abstract, phenomenological experiences of consciousness into a rigorous, mathematical framework. We show that IIT's stance in regards to neuronal noise is inconsistent with experimental data demonstrating that neuronal noise in the brain plays ... |
2007.03678 | Ada Sedova | Scott LeGrand, Aaron Scheinberg, Andreas F. Tillack, Mathialakan
Thavappiragasam, Josh V. Vermaas, Rupesh Agarwal, Jeff Larkin, Duncan Poole,
Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli,
Oscar Hernandez, Jeremy C. Smith and Ada Sedova | GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer:
Porting, Optimization, and Application to COVID-19 Research | null | null | 10.1145/3388440.3412472 | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein-ligand docking is an in silico tool used to screen potential drug
compounds for their ability to bind to a given protein receptor within a
drug-discovery campaign. Experimental drug screening is expensive and time
consuming, and it is desirable to carry out large scale docking calculations in
a high-throughpu... | [
{
"created": "Mon, 6 Jul 2020 20:31:12 GMT",
"version": "v1"
}
] | 2020-11-16 | [
[
"LeGrand",
"Scott",
""
],
[
"Scheinberg",
"Aaron",
""
],
[
"Tillack",
"Andreas F.",
""
],
[
"Thavappiragasam",
"Mathialakan",
""
],
[
"Vermaas",
"Josh V.",
""
],
[
"Agarwal",
"Rupesh",
""
],
[
"Larkin",
"Jeff",... | Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it is desirable to carry out large scale docking calculations in a high-throughput ... |
1511.04470 | Richard Barnes | Richard Barnes, Clarence Lehman | Modeling of Bovine Spongiform Encephalopathy in a Two-Species Feedback
Loop | 12 pages, 4 figures | Epidemics. Vol. 5, Issue 2, June 2013, pp 85--91 | 10.1016/j.epidem.2013.04.001 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bovine spongiform encephalopathy, otherwise known as mad cow disease, can
spread when an individual cow consumes feed containing the infected tissues of
another individual, forming a one-species feedback loop. Such feedback is the
primary means of transmission for BSE during epidemic conditions. Following
outbreaks i... | [
{
"created": "Fri, 13 Nov 2015 22:01:12 GMT",
"version": "v1"
}
] | 2015-11-17 | [
[
"Barnes",
"Richard",
""
],
[
"Lehman",
"Clarence",
""
]
] | Bovine spongiform encephalopathy, otherwise known as mad cow disease, can spread when an individual cow consumes feed containing the infected tissues of another individual, forming a one-species feedback loop. Such feedback is the primary means of transmission for BSE during epidemic conditions. Following outbreaks in ... |
2001.06773 | Wei Zhao | Qing Nie, Lingxia Qiao, Yuchi Qiu, Lei Zhang and Wei Zhao | Noise control and utility: from regulatory network to spatial patterning | null | null | null | null | q-bio.MN q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stochasticity (or noise) at cellular and molecular levels has been observed
extensively as a universal feature for living systems. However, how living
systems deal with noise while performing desirable biological functions remains
a major mystery. Regulatory network configurations, such as their topology and
timescal... | [
{
"created": "Sun, 19 Jan 2020 04:39:38 GMT",
"version": "v1"
}
] | 2020-01-22 | [
[
"Nie",
"Qing",
""
],
[
"Qiao",
"Lingxia",
""
],
[
"Qiu",
"Yuchi",
""
],
[
"Zhang",
"Lei",
""
],
[
"Zhao",
"Wei",
""
]
] | Stochasticity (or noise) at cellular and molecular levels has been observed extensively as a universal feature for living systems. However, how living systems deal with noise while performing desirable biological functions remains a major mystery. Regulatory network configurations, such as their topology and timescale,... |
1710.08149 | Mo Zhang | Mo Zhang, Xiang Li, Mengjia Xu, Quanzheng Li | Image Segmentation and Classification for Sickle Cell Disease using
Deformable U-Net | null | null | null | null | q-bio.CB cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reliable cell segmentation and classification from biomedical images is a
crucial step for both scientific research and clinical practice. A major
challenge for more robust segmentation and classification methods is the large
variations in the size, shape and viewpoint of the cells, combining with the
low image quali... | [
{
"created": "Mon, 23 Oct 2017 08:53:07 GMT",
"version": "v1"
},
{
"created": "Tue, 24 Oct 2017 02:26:00 GMT",
"version": "v2"
},
{
"created": "Sun, 29 Oct 2017 04:02:32 GMT",
"version": "v3"
}
] | 2017-10-31 | [
[
"Zhang",
"Mo",
""
],
[
"Li",
"Xiang",
""
],
[
"Xu",
"Mengjia",
""
],
[
"Li",
"Quanzheng",
""
]
] | Reliable cell segmentation and classification from biomedical images is a crucial step for both scientific research and clinical practice. A major challenge for more robust segmentation and classification methods is the large variations in the size, shape and viewpoint of the cells, combining with the low image quality... |
2208.10545 | Miguel Ib\'a\~nez Berganza | Miguel Ib\'a\~nez-Berganza, Carlo Lucibello, Luca Mariani, Giovanni
Pezzulo | Information-theoretical analysis of the neural code for decoupled face
representation | 26 pages, 8 figures (+11 pages, 7 figures in the supporting
information section). In v3: new figure 8 in section 3.2.3; further details
added to the supporting information; title changed | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Processing faces accurately and efficiently is a key capability of humans and
other animals that engage in sophisticated social tasks. Recent studies
reported a decoupled coding for faces in the primate inferotemporal cortex,
with two separate neural populations coding for the geometric position of
(texture-free) fac... | [
{
"created": "Mon, 22 Aug 2022 18:50:34 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Aug 2022 06:25:07 GMT",
"version": "v2"
},
{
"created": "Wed, 18 Jan 2023 14:33:21 GMT",
"version": "v3"
}
] | 2023-01-19 | [
[
"Ibáñez-Berganza",
"Miguel",
""
],
[
"Lucibello",
"Carlo",
""
],
[
"Mariani",
"Luca",
""
],
[
"Pezzulo",
"Giovanni",
""
]
] | Processing faces accurately and efficiently is a key capability of humans and other animals that engage in sophisticated social tasks. Recent studies reported a decoupled coding for faces in the primate inferotemporal cortex, with two separate neural populations coding for the geometric position of (texture-free) facia... |
1212.3807 | Irina Kareva | Irina Kareva, Benjamin Morin, Georgy Karev | Preventing the tragedy of the commons through punishment of
over-consumers and encouragement of under-consumers | null | null | null | null | q-bio.PE math.CA | http://creativecommons.org/licenses/publicdomain/ | The conditions that can lead to the exploitative depletion of a shared
resource, i.e, the tragedy of the commons, can be reformulated as a game of
prisoner's dilemma: while preserving the common resource is in the best
interest of the group, over-consumption is in the interest of each particular
individual at any giv... | [
{
"created": "Sun, 16 Dec 2012 17:28:41 GMT",
"version": "v1"
}
] | 2012-12-18 | [
[
"Kareva",
"Irina",
""
],
[
"Morin",
"Benjamin",
""
],
[
"Karev",
"Georgy",
""
]
] | The conditions that can lead to the exploitative depletion of a shared resource, i.e, the tragedy of the commons, can be reformulated as a game of prisoner's dilemma: while preserving the common resource is in the best interest of the group, over-consumption is in the interest of each particular individual at any given... |
2305.02082 | Jacob Thorstensen | Jacob Thorstensen, Tyler Henderson and Justin Kavanagh | Serotonergic and noradrenergic contributions to human motor cortical and
spinal motoneuronal excitability | 38 pages, 3 tables, no figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Animal models indicate that motor behaviour is shaped by monoamine
neurotransmitters released diffusely throughout the brain and spinal cord. We
present strong evidence that human motor pathways are equally affected by
neuromodulation through noradrenergic and serotonergic projections arising from
the brainstem. To d... | [
{
"created": "Thu, 27 Apr 2023 23:10:10 GMT",
"version": "v1"
}
] | 2023-05-04 | [
[
"Thorstensen",
"Jacob",
""
],
[
"Henderson",
"Tyler",
""
],
[
"Kavanagh",
"Justin",
""
]
] | Animal models indicate that motor behaviour is shaped by monoamine neurotransmitters released diffusely throughout the brain and spinal cord. We present strong evidence that human motor pathways are equally affected by neuromodulation through noradrenergic and serotonergic projections arising from the brainstem. To do ... |
2309.15950 | Susan Martonosi | Abraham Holleran and Susan E. Martonosi and Michael Veatch | To Give or Not To Give: Pandemic Vaccine Donation Policy | 21 pages, 4 figures. arXiv admin note: substantial text overlap with
arXiv:2303.05917 | null | null | null | q-bio.PE math.OC physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | The global SARS-CoV-2 (COVID-19) pandemic highlighted the challenge of
equitable vaccine distribution between high- and low-income countries. Many
high-income countries were reluctant or slow to distribute extra doses of the
vaccine to lower-income countries via the COVID-19 Vaccines Global Access
(COVAX) collaborati... | [
{
"created": "Wed, 27 Sep 2023 19:08:35 GMT",
"version": "v1"
}
] | 2023-09-29 | [
[
"Holleran",
"Abraham",
""
],
[
"Martonosi",
"Susan E.",
""
],
[
"Veatch",
"Michael",
""
]
] | The global SARS-CoV-2 (COVID-19) pandemic highlighted the challenge of equitable vaccine distribution between high- and low-income countries. Many high-income countries were reluctant or slow to distribute extra doses of the vaccine to lower-income countries via the COVID-19 Vaccines Global Access (COVAX) collaboration... |
2407.08751 | Auguste Schulz | Jaivardhan Kapoor, Auguste Schulz, Julius Vetter, Felix Pei, Richard
Gao, Jakob H. Macke | Latent Diffusion for Neural Spiking Data | null | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Modern datasets in neuroscience enable unprecedented inquiries into the
relationship between complex behaviors and the activity of many simultaneously
recorded neurons. While latent variable models can successfully extract
low-dimensional embeddings from such recordings, using them to generate
realistic spiking data,... | [
{
"created": "Thu, 27 Jun 2024 13:47:06 GMT",
"version": "v1"
}
] | 2024-07-15 | [
[
"Kapoor",
"Jaivardhan",
""
],
[
"Schulz",
"Auguste",
""
],
[
"Vetter",
"Julius",
""
],
[
"Pei",
"Felix",
""
],
[
"Gao",
"Richard",
""
],
[
"Macke",
"Jakob H.",
""
]
] | Modern datasets in neuroscience enable unprecedented inquiries into the relationship between complex behaviors and the activity of many simultaneously recorded neurons. While latent variable models can successfully extract low-dimensional embeddings from such recordings, using them to generate realistic spiking data, e... |
q-bio/0506012 | Yongyun Ji | Yong-Yun Ji, You-Quan Li, Jun-Wen Mao and Xiao-Wei Tang | The prion-like folding behavior in aggregated proteins | 7 pages, 6 figures | Physical Review E 72, 041912 (2005), Virtual Journal of Biological
Physics Research(October 15, 2005) | 10.1103/PhysRevE.72.041912 | null | q-bio.BM | null | We investigate the folding behavior of protein sequences by numerically
studying all sequences with maximally compact lattice model through exhaustive
enumeration. We get the prion-like behavior of protein folding. Individual
proteins remaining stable in the isolated native state may change their
conformations when t... | [
{
"created": "Thu, 9 Jun 2005 05:11:24 GMT",
"version": "v1"
}
] | 2014-11-18 | [
[
"Ji",
"Yong-Yun",
""
],
[
"Li",
"You-Quan",
""
],
[
"Mao",
"Jun-Wen",
""
],
[
"Tang",
"Xiao-Wei",
""
]
] | We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins remaining stable in the isolated native state may change their conformations when the... |
2109.06011 | Jan Sosulski | Jan Sosulski, David H\"ubner, Aaron Klein, Michael Tangermann | Online Optimization of Stimulation Speed in an Auditory Brain-Computer
Interface under Time Constraints | null | null | null | null | q-bio.NC cs.LG stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The decoding of brain signals recorded via, e.g., an electroencephalogram,
using machine learning is key to brain-computer interfaces (BCIs). Stimulation
parameters or other experimental settings of the BCI protocol typically are
chosen according to the literature. The decoding performance directly depends
on the cho... | [
{
"created": "Thu, 26 Aug 2021 08:18:03 GMT",
"version": "v1"
}
] | 2021-09-14 | [
[
"Sosulski",
"Jan",
""
],
[
"Hübner",
"David",
""
],
[
"Klein",
"Aaron",
""
],
[
"Tangermann",
"Michael",
""
]
] | The decoding of brain signals recorded via, e.g., an electroencephalogram, using machine learning is key to brain-computer interfaces (BCIs). Stimulation parameters or other experimental settings of the BCI protocol typically are chosen according to the literature. The decoding performance directly depends on the choic... |
2209.08402 | Heyrim Cho | Heyrim Cho, Allison L. Lewis, Kathleen M. Storey, Helen M. Byrne | Designing experimental conditions to use the Lotka-Volterra model to
infer tumor cell line interaction types | 25 pages, 18 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The Lotka-Volterra model is widely used to model interactions between two
species. Here, we generate synthetic data mimicking competitive, mutualistic
and antagonistic interactions between two tumor cell lines, and then use the
Lotka-Volterra model to infer the interaction type. Structural identifiability
of the Lotk... | [
{
"created": "Sat, 17 Sep 2022 20:59:42 GMT",
"version": "v1"
}
] | 2022-09-20 | [
[
"Cho",
"Heyrim",
""
],
[
"Lewis",
"Allison L.",
""
],
[
"Storey",
"Kathleen M.",
""
],
[
"Byrne",
"Helen M.",
""
]
] | The Lotka-Volterra model is widely used to model interactions between two species. Here, we generate synthetic data mimicking competitive, mutualistic and antagonistic interactions between two tumor cell lines, and then use the Lotka-Volterra model to infer the interaction type. Structural identifiability of the Lotka-... |
0910.1953 | Yunfeng Shan Dr. | Yunfeng Shan, and Xiu-Qing Li | GeneSupport Maximum Gene-Support Tree Approach to Species Phylogeny
Inference | Application note | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Summary: GeneSupport implements a genome-scale algorithm: Maximum
Gene-Support Tree to estimate species tree from gene trees based on multilocus
sequences. It provides a new option for multiple genes to infer species tree.
It is incorporated into popular phylogentic program: PHYLIP package with the
same usage and use... | [
{
"created": "Sat, 10 Oct 2009 22:31:55 GMT",
"version": "v1"
}
] | 2009-10-13 | [
[
"Shan",
"Yunfeng",
""
],
[
"Li",
"Xiu-Qing",
""
]
] | Summary: GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is incorporated into popular phylogentic program: PHYLIP package with the same usage and user ... |
2012.05538 | Qiyao Peng | Qiyao Peng, Fred Vermolen, Daphne Weihs | A Formalism for Modelling Traction forces and Cell Shape Evolution
during Cell Migration in Various Biomedical Processes | null | null | 10.1007/s10237-021-01456-2 | null | q-bio.CB cs.NA math.NA | http://creativecommons.org/licenses/by/4.0/ | The phenomenological model for cell shape deformation and cell migration
(Chen et.al. 2018; Vermolen and Gefen 2012) is extended with the incorporation
of cell traction forces and the evolution of cell equilibrium shapes as a
result of cell differentiation. Plastic deformations of the extracellular
matrix are modelle... | [
{
"created": "Thu, 10 Dec 2020 09:29:44 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Apr 2021 14:08:25 GMT",
"version": "v2"
}
] | 2021-04-27 | [
[
"Peng",
"Qiyao",
""
],
[
"Vermolen",
"Fred",
""
],
[
"Weihs",
"Daphne",
""
]
] | The phenomenological model for cell shape deformation and cell migration (Chen et.al. 2018; Vermolen and Gefen 2012) is extended with the incorporation of cell traction forces and the evolution of cell equilibrium shapes as a result of cell differentiation. Plastic deformations of the extracellular matrix are modelled ... |
2009.00359 | Eva Smij\'akov\'a | Lubos Brim, Samuel Pastva, David Safranek, Eva Smijakova | Parallel One-Step Control of Parametrised Boolean Networks | null | null | null | null | q-bio.MN cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Boolean network (BN) is a simple model widely used to study complex dynamic
behaviour of biological systems. Nonetheless, it might be difficult to gather
enough data to precisely capture the behavior of a biological system into a set
of Boolean functions. These issues can be dealt with to some extent using
parametris... | [
{
"created": "Tue, 1 Sep 2020 11:29:43 GMT",
"version": "v1"
}
] | 2020-09-02 | [
[
"Brim",
"Lubos",
""
],
[
"Pastva",
"Samuel",
""
],
[
"Safranek",
"David",
""
],
[
"Smijakova",
"Eva",
""
]
] | Boolean network (BN) is a simple model widely used to study complex dynamic behaviour of biological systems. Nonetheless, it might be difficult to gather enough data to precisely capture the behavior of a biological system into a set of Boolean functions. These issues can be dealt with to some extent using parametrised... |
1611.04872 | Emanuela Merelli | Marco Piangerelli, Matteo Rucco and Emanuela Merelli | Topological classifier for detecting the emergence of epileptic seizures | Open data: Physionet data-set | BMC Res Notes 11, 392, 2018 | 10.1186/s13104-018-3482-7 | null | q-bio.NC cs.IT math.IT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we study how to apply topological data analysis to create a
method suitable to classify EEGs of patients affected by epilepsy. The
topological space constructed from the collection of EEGs signals is analyzed
by Persistent Entropy acting as a global topological feature for discriminating
between healthy ... | [
{
"created": "Sat, 12 Nov 2016 10:11:30 GMT",
"version": "v1"
}
] | 2020-09-14 | [
[
"Piangerelli",
"Marco",
""
],
[
"Rucco",
"Matteo",
""
],
[
"Merelli",
"Emanuela",
""
]
] | In this work we study how to apply topological data analysis to create a method suitable to classify EEGs of patients affected by epilepsy. The topological space constructed from the collection of EEGs signals is analyzed by Persistent Entropy acting as a global topological feature for discriminating between healthy an... |
2211.16599 | Dale Zhou | Dale Zhou, Jason Z. Kim, Adam R. Pines, Valerie J. Sydnor, David R.
Roalf, John A. Detre, Ruben C. Gur, Raquel E. Gur, Theodore D. Satterthwaite,
Dani S. Bassett | Compression supports low-dimensional representations of behavior across
neural circuits | arXiv admin note: text overlap with arXiv:2001.05078 | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Dimensionality reduction, a form of compression, can simplify representations
of information to increase efficiency and reveal general patterns. Yet, this
simplification also forfeits information, thereby reducing representational
capacity. Hence, the brain may benefit from generating both compressed and
uncompressed... | [
{
"created": "Tue, 29 Nov 2022 21:26:10 GMT",
"version": "v1"
}
] | 2022-12-01 | [
[
"Zhou",
"Dale",
""
],
[
"Kim",
"Jason Z.",
""
],
[
"Pines",
"Adam R.",
""
],
[
"Sydnor",
"Valerie J.",
""
],
[
"Roalf",
"David R.",
""
],
[
"Detre",
"John A.",
""
],
[
"Gur",
"Ruben C.",
""
],
[
"Gu... | Dimensionality reduction, a form of compression, can simplify representations of information to increase efficiency and reveal general patterns. Yet, this simplification also forfeits information, thereby reducing representational capacity. Hence, the brain may benefit from generating both compressed and uncompressed a... |
1511.01956 | Elizabeth Allman | Elizabeth S. Allman, John A. Rhodes, Seth Sullivant | Statistically-Consistent k-mer Methods for Phylogenetic Tree
Reconstruction | 25 pages, 9 figures figure added, to appear, JCB | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Frequencies of $k$-mers in sequences are sometimes used as a basis for
inferring phylogenetic trees without first obtaining a multiple sequence
alignment. We show that a standard approach of using the squared-Euclidean
distance between $k$-mer vectors to approximate a tree metric can be
statistically inconsistent. To... | [
{
"created": "Thu, 5 Nov 2015 23:46:49 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Jan 2016 18:48:11 GMT",
"version": "v2"
}
] | 2016-01-15 | [
[
"Allman",
"Elizabeth S.",
""
],
[
"Rhodes",
"John A.",
""
],
[
"Sullivant",
"Seth",
""
]
] | Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between $k$-mer vectors to approximate a tree metric can be statistically inconsistent. To r... |
2305.08316 | Ziyuan Zhao | Ziyuan Zhao, Peisheng Qian, Xulei Yang, Zeng Zeng, Cuntai Guan, Wai
Leong Tam, Xiaoli Li | SemiGNN-PPI: Self-Ensembling Multi-Graph Neural Network for Efficient
and Generalizable Protein-Protein Interaction Prediction | Accepted by IJCAI 2023 | null | null | null | q-bio.MN cs.AI cs.CE cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein-protein interactions (PPIs) are crucial in various biological
processes and their study has significant implications for drug development and
disease diagnosis. Existing deep learning methods suffer from significant
performance degradation under complex real-world scenarios due to various
factors, e.g., label... | [
{
"created": "Mon, 15 May 2023 03:06:44 GMT",
"version": "v1"
}
] | 2023-05-16 | [
[
"Zhao",
"Ziyuan",
""
],
[
"Qian",
"Peisheng",
""
],
[
"Yang",
"Xulei",
""
],
[
"Zeng",
"Zeng",
""
],
[
"Guan",
"Cuntai",
""
],
[
"Tam",
"Wai Leong",
""
],
[
"Li",
"Xiaoli",
""
]
] | Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance degradation under complex real-world scenarios due to various factors, e.g., label s... |
2405.09327 | C\'ecile An\'e | Benjamin Teo, Paul Bastide, C\'ecile An\'e | Leveraging graphical model techniques to study evolution on phylogenetic
networks | null | null | null | null | q-bio.PE stat.CO | http://creativecommons.org/licenses/by/4.0/ | The evolution of molecular and phenotypic traits is commonly modelled using
Markov processes along a rooted phylogeny. This phylogeny can be a tree, or a
network if it includes reticulations, representing events such as hybridization
or admixture. Computing the likelihood of data observed at the leaves is costly
as t... | [
{
"created": "Wed, 15 May 2024 13:27:03 GMT",
"version": "v1"
}
] | 2024-05-16 | [
[
"Teo",
"Benjamin",
""
],
[
"Bastide",
"Paul",
""
],
[
"Ané",
"Cécile",
""
]
] | The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a rooted phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture. Computing the likelihood of data observed at the leaves is costly as the... |
2104.01468 | Nathan Ranno | Nathan Ranno, Dong Si | Neural Representations of Cryo-EM Maps and a Graph-Based Interpretation | 15 pages, 8 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Advances in imagery at atomic and near-atomic resolution, such as cryogenic
electron microscopy (cryo-EM), have led to an influx of high resolution images
of proteins and other macromolecular structures to data banks worldwide.
Producing a protein structure from the discrete voxel grid data of cryo-EM maps
involves i... | [
{
"created": "Sat, 3 Apr 2021 19:49:16 GMT",
"version": "v1"
}
] | 2021-04-06 | [
[
"Ranno",
"Nathan",
""
],
[
"Si",
"Dong",
""
]
] | Advances in imagery at atomic and near-atomic resolution, such as cryogenic electron microscopy (cryo-EM), have led to an influx of high resolution images of proteins and other macromolecular structures to data banks worldwide. Producing a protein structure from the discrete voxel grid data of cryo-EM maps involves int... |
2303.14248 | Mattia Sensi | Rossella Della Marca, Alberto d'Onofrio, Mattia Sensi, Sara Sottile | A geometric analysis of the impact of large but finite switching rates
on vaccination evolutionary games | 26 pages, 6 figures | Nonlinear Analysis: Real World Applications, Volume 75, February
2024, 103986 | 10.1016/j.nonrwa.2023.103986 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In contemporary society, social networks accelerate decision dynamics causing
a rapid switch of opinions in a number of fields, including the prevention of
infectious diseases by means of vaccines. This means that opinion dynamics can
nowadays be much faster than the spread of epidemics. Hence, we propose a
Susceptib... | [
{
"created": "Fri, 24 Mar 2023 19:26:51 GMT",
"version": "v1"
}
] | 2023-11-06 | [
[
"Della Marca",
"Rossella",
""
],
[
"d'Onofrio",
"Alberto",
""
],
[
"Sensi",
"Mattia",
""
],
[
"Sottile",
"Sara",
""
]
] | In contemporary society, social networks accelerate decision dynamics causing a rapid switch of opinions in a number of fields, including the prevention of infectious diseases by means of vaccines. This means that opinion dynamics can nowadays be much faster than the spread of epidemics. Hence, we propose a Susceptible... |
2310.20601 | Jacob Tanner | Jacob Tanner, Sina Mansour L., Ludovico Coletta, Alessandro Gozzi,
Richard F. Betzel | Functional connectivity modules in recurrent neural networks: function,
origin and dynamics | null | null | null | null | q-bio.NC cs.AI cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Understanding the ubiquitous phenomenon of neural synchronization across
species and organizational levels is crucial for decoding brain function.
Despite its prevalence, the specific functional role, origin, and dynamical
implication of modular structures in correlation-based networks remains
ambiguous. Using recurr... | [
{
"created": "Tue, 31 Oct 2023 16:37:01 GMT",
"version": "v1"
}
] | 2023-11-01 | [
[
"Tanner",
"Jacob",
""
],
[
"L.",
"Sina Mansour",
""
],
[
"Coletta",
"Ludovico",
""
],
[
"Gozzi",
"Alessandro",
""
],
[
"Betzel",
"Richard F.",
""
]
] | Understanding the ubiquitous phenomenon of neural synchronization across species and organizational levels is crucial for decoding brain function. Despite its prevalence, the specific functional role, origin, and dynamical implication of modular structures in correlation-based networks remains ambiguous. Using recurren... |
2311.13801 | Sikta Das Adhikari | Sikta Das Adhikari, Jiaxin Yang, Jianrong Wang, Yuehua Cui | A selective review of recent developments in spatially variable gene
detection for spatial transcriptomics | null | null | 10.1016/j.csbj.2024.01.016 | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | With the emergence of advanced spatial transcriptomic technologies, there has
been a surge in research papers dedicated to analyzing spatial transcriptomics
data, resulting in significant contributions to our understanding of biology.
The initial stage of downstream analysis of spatial transcriptomic data has
centere... | [
{
"created": "Thu, 23 Nov 2023 04:20:14 GMT",
"version": "v1"
}
] | 2024-04-11 | [
[
"Adhikari",
"Sikta Das",
""
],
[
"Yang",
"Jiaxin",
""
],
[
"Wang",
"Jianrong",
""
],
[
"Cui",
"Yuehua",
""
]
] | With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The initial stage of downstream analysis of spatial transcriptomic data has centered ... |
1812.05668 | Jiansheng Wu | Hang Yu, Ziyi Liu, Jiansheng Wu | Forgetting in order to Remember Better | 4 pages, 2 figures | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In human memory, forgetting occur rapidly after the remembering and the rate
of forgetting slowed down as time went. This is so-called the Ebbinghaus
forgetting curve. There are many explanations of how this curve occur based on
the properties of the brains. In this article, we use a simple mathematical
model to expl... | [
{
"created": "Wed, 12 Dec 2018 18:54:27 GMT",
"version": "v1"
}
] | 2018-12-17 | [
[
"Yu",
"Hang",
""
],
[
"Liu",
"Ziyi",
""
],
[
"Wu",
"Jiansheng",
""
]
] | In human memory, forgetting occur rapidly after the remembering and the rate of forgetting slowed down as time went. This is so-called the Ebbinghaus forgetting curve. There are many explanations of how this curve occur based on the properties of the brains. In this article, we use a simple mathematical model to explai... |
2201.08980 | Thomas Sturm | Christoph L\"uders, Thomas Sturm, Ovidiu Radulescu | ODEbase: A Repository of ODE Systems for Systems Biology | null | null | null | null | q-bio.MN cs.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, symbolic computation and computer algebra systems have been
successfully applied in systems biology, especially in chemical reaction
network theory. One advantage of symbolic computation is its potential for
qualitative answers to biological questions. Qualitative methods analyze
dynamical input systems as ... | [
{
"created": "Sat, 22 Jan 2022 07:22:01 GMT",
"version": "v1"
}
] | 2022-01-25 | [
[
"Lüders",
"Christoph",
""
],
[
"Sturm",
"Thomas",
""
],
[
"Radulescu",
"Ovidiu",
""
]
] | Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to biological questions. Qualitative methods analyze dynamical input systems as fo... |
0710.1333 | Jesus M. Cortes | J.M. Cortes, A. Greve, A.B. Barrett and M.C.W. van Rossum | Dynamics and robustness of familiarity memory | 22 pages, 3 figures | null | null | null | q-bio.NC | null | When one is presented with an item or a face, one can sometimes have a sense
of recognition without being able to recall where or when one has encountered
it before. This sense of recognition is known as familiarity. Following
previous computational models of familiarity memory we investigate the
dynamical properties... | [
{
"created": "Sun, 7 Oct 2007 00:14:07 GMT",
"version": "v1"
}
] | 2007-10-09 | [
[
"Cortes",
"J. M.",
""
],
[
"Greve",
"A.",
""
],
[
"Barrett",
"A. B.",
""
],
[
"van Rossum",
"M. C. W.",
""
]
] | When one is presented with an item or a face, one can sometimes have a sense of recognition without being able to recall where or when one has encountered it before. This sense of recognition is known as familiarity. Following previous computational models of familiarity memory we investigate the dynamical properties o... |
q-bio/0406004 | Manoj Gopalakrishnan | Manoj Gopalakrishnan, Kimberly Forsten-Williams, Theressa R. Cassino,
Luz Padro, Thomas E. Ryan and Uwe C. Tauber | Ligand Rebinding: Self-consistent Mean-field Theory and Numerical
Simulations Applied to SPR Studies | minor errors in notation corrected, added figure, appendix and
glossary, 37 pages, to appear in Eur. Biophys. J | Eur. Biophys. J. 34 (2005) 943 | null | null | q-bio.QM cond-mat.stat-mech q-bio.SC | null | Rebinding of dissociated ligands from cell surface proteins can confound
quantitative measurements of dissociation rates important for characterizing
the affinity of binding interactions. This can be true also for in vitro
techniques such as surface plasmon resonance (SPR). We present experimental
results using SPR f... | [
{
"created": "Wed, 2 Jun 2004 07:05:42 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Oct 2004 08:23:48 GMT",
"version": "v2"
},
{
"created": "Tue, 1 Feb 2005 12:16:39 GMT",
"version": "v3"
}
] | 2007-05-23 | [
[
"Gopalakrishnan",
"Manoj",
""
],
[
"Forsten-Williams",
"Kimberly",
""
],
[
"Cassino",
"Theressa R.",
""
],
[
"Padro",
"Luz",
""
],
[
"Ryan",
"Thomas E.",
""
],
[
"Tauber",
"Uwe C.",
""
]
] | Rebinding of dissociated ligands from cell surface proteins can confound quantitative measurements of dissociation rates important for characterizing the affinity of binding interactions. This can be true also for in vitro techniques such as surface plasmon resonance (SPR). We present experimental results using SPR for... |
2105.02144 | Sandeep Juneja | Sandeep Juneja and Daksh Mittal | Modelling the Second Covid-19 Wave in Mumbai | 34 pages, 33 figures (including 3 tables) | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | India has been hit by a huge second wave of Covid-19 that started in
mid-February 2021. Mumbai was amongst the first cities to see the increase. In
this report, we use our agent based simulator to computationally study the
second wave in Mumbai. We build upon our earlier analysis, where projections
were made from Nov... | [
{
"created": "Wed, 5 May 2021 15:51:56 GMT",
"version": "v1"
}
] | 2021-05-06 | [
[
"Juneja",
"Sandeep",
""
],
[
"Mittal",
"Daksh",
""
]
] | India has been hit by a huge second wave of Covid-19 that started in mid-February 2021. Mumbai was amongst the first cities to see the increase. In this report, we use our agent based simulator to computationally study the second wave in Mumbai. We build upon our earlier analysis, where projections were made from Novem... |
2304.12825 | Fang Sun | Fang Sun, Zhihao Zhan, Hongyu Guo, Ming Zhang, Jian Tang | GraphVF: Controllable Protein-Specific 3D Molecule Generation with
Variational Flow | 15 pages, 8 figures | null | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by-sa/4.0/ | Designing molecules that bind to specific target proteins is a fundamental
task in drug discovery. Recent models leverage geometric constraints to
generate ligand molecules that bind cohesively with specific protein pockets.
However, these models cannot effectively generate 3D molecules with 2D skeletal
curtailments ... | [
{
"created": "Thu, 23 Feb 2023 17:32:49 GMT",
"version": "v1"
}
] | 2023-04-26 | [
[
"Sun",
"Fang",
""
],
[
"Zhan",
"Zhihao",
""
],
[
"Guo",
"Hongyu",
""
],
[
"Zhang",
"Ming",
""
],
[
"Tang",
"Jian",
""
]
] | Designing molecules that bind to specific target proteins is a fundamental task in drug discovery. Recent models leverage geometric constraints to generate ligand molecules that bind cohesively with specific protein pockets. However, these models cannot effectively generate 3D molecules with 2D skeletal curtailments an... |
2209.00380 | Nathalie Buonviso | Maxime Juventin, Mickael Zbili, Nicolas Fourcaud-Trocm\'e, Samuel
Garcia, Nathalie Buonviso (CRNL), Corine Amat | Respiratory rhythm entrains membrane potential and spiking of
non-olfactory neurons | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years, several studies have tended to show a respiratory drive in
numerous brain areas so that the respiratory rhythm could be considered as a
master clock promoting communication between distant brain areas. However,
outside of the olfactory system it is not known if respiration-related
oscillation (RRo) c... | [
{
"created": "Thu, 1 Sep 2022 11:49:58 GMT",
"version": "v1"
}
] | 2022-09-02 | [
[
"Juventin",
"Maxime",
"",
"CRNL"
],
[
"Zbili",
"Mickael",
"",
"CRNL"
],
[
"Fourcaud-Trocmé",
"Nicolas",
"",
"CRNL"
],
[
"Garcia",
"Samuel",
"",
"CRNL"
],
[
"Buonviso",
"Nathalie",
"",
"CRNL"
],
[
"Amat",
"C... | In recent years, several studies have tended to show a respiratory drive in numerous brain areas so that the respiratory rhythm could be considered as a master clock promoting communication between distant brain areas. However, outside of the olfactory system it is not known if respiration-related oscillation (RRo) cou... |
1105.0515 | Yunkyu Sohn | Yunkyu Sohn, Jung-Kyoo Choi and T.K. Ahn | Core-Periphery Segregation in Evolving Prisoner's Dilemma Networks | null | null | null | null | q-bio.PE cs.SI physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dense cooperative networks are an essential element of social capital for a
prosperous society. These networks enable individuals to overcome collective
action dilemmas by enhancing trust. In many biological and social settings,
network structures evolve endogenously as agents exit relationships and build
new ones. H... | [
{
"created": "Tue, 3 May 2011 08:40:31 GMT",
"version": "v1"
},
{
"created": "Sun, 9 Dec 2012 14:38:34 GMT",
"version": "v2"
}
] | 2012-12-11 | [
[
"Sohn",
"Yunkyu",
""
],
[
"Choi",
"Jung-Kyoo",
""
],
[
"Ahn",
"T. K.",
""
]
] | Dense cooperative networks are an essential element of social capital for a prosperous society. These networks enable individuals to overcome collective action dilemmas by enhancing trust. In many biological and social settings, network structures evolve endogenously as agents exit relationships and build new ones. How... |
2004.01011 | Ellen Baake | Ellen Baake and Anton Wakolbinger | Microbial populations under selection | to appear in: Probabilistic Structures in Evolution, E.~Baake and
A.~Wakolbinger (eds.), EMS Publishing House, Zurich | in: Probabilistic Structures in Evolution (E. Baake, A.
Wakolbinger, eds.), EMS Press, Berlin, 2021, pp. 43-68 | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This chapter gives a synopsis of recent approaches to model and analyse the
evolution of microbial populations under selection. The first part reviews two
population genetic models of Lenski's long-term evolution experiment with
Escherichia coli, where models aim at explaining the observed curve of the
evolution of t... | [
{
"created": "Thu, 2 Apr 2020 14:04:27 GMT",
"version": "v1"
}
] | 2021-06-30 | [
[
"Baake",
"Ellen",
""
],
[
"Wakolbinger",
"Anton",
""
]
] | This chapter gives a synopsis of recent approaches to model and analyse the evolution of microbial populations under selection. The first part reviews two population genetic models of Lenski's long-term evolution experiment with Escherichia coli, where models aim at explaining the observed curve of the evolution of the... |
1304.2960 | Kieran Smallbone | Kieran Smallbone | Standardized network reconstruction of E. coli metabolism | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/publicdomain/ | We have created a genome-scale network reconstruction of Escherichia coli
metabolism. Existing reconstructions were improved in terms of annotation
standards, to facilitate their subsequent use in dynamic modelling. The
resultant network is available from EcoliNet (http://ecoli.sf.net/).
| [
{
"created": "Tue, 9 Apr 2013 09:07:13 GMT",
"version": "v1"
}
] | 2013-04-11 | [
[
"Smallbone",
"Kieran",
""
]
] | We have created a genome-scale network reconstruction of Escherichia coli metabolism. Existing reconstructions were improved in terms of annotation standards, to facilitate their subsequent use in dynamic modelling. The resultant network is available from EcoliNet (http://ecoli.sf.net/). |
2108.12386 | Kapila Gunasekera PhD | Daniel Nilsson, Kapila Gunasekera, Jan Mani, Magne Osteras, Laurent
Farinelli, Loic Baerlocher, Isabel Roditi, Torsten Ochsenreiter | Spliced Leader Trapping Reveals Widespread Alternative Splicing Patterns
in the Highly Dynamic Transcriptome of Trypanosoma brucei | 13 pages, 8 figures | null | 10.1371/journal.ppat.1001037 | null | q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Trans-splicing of leader sequences onto the 59ends of mRNAs is a widespread
phenomenon in protozoa, nematodes and some chordates. Using parallel sequencing
we have developed a method to simultaneously map 59splice sites and analyze the
corresponding gene expression profile, that we term spliced leader trapping
(SLT).... | [
{
"created": "Fri, 27 Aug 2021 16:48:46 GMT",
"version": "v1"
}
] | 2021-08-30 | [
[
"Nilsson",
"Daniel",
""
],
[
"Gunasekera",
"Kapila",
""
],
[
"Mani",
"Jan",
""
],
[
"Osteras",
"Magne",
""
],
[
"Farinelli",
"Laurent",
""
],
[
"Baerlocher",
"Loic",
""
],
[
"Roditi",
"Isabel",
""
],
[
... | Trans-splicing of leader sequences onto the 59ends of mRNAs is a widespread phenomenon in protozoa, nematodes and some chordates. Using parallel sequencing we have developed a method to simultaneously map 59splice sites and analyze the corresponding gene expression profile, that we term spliced leader trapping (SLT). T... |
1008.4938 | Randen Patterson | Yoojin Hong, Kyung Dae Ko, Gaurav Bhardwaj, Zhenhai Zhang, Damian B.
van Rossum, and Randen L. Patterson | Towards Solving the Inverse Protein Folding Problem | 22 pages, 11 figures | null | null | null | q-bio.QM cs.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurately assigning folds for divergent protein sequences is a major
obstacle to structural studies and underlies the inverse protein folding
problem. Herein, we outline our theories for fold-recognition in the
"twilight-zone" of sequence similarity (<25% identity). Our analyses
demonstrate that structural sequence ... | [
{
"created": "Sun, 29 Aug 2010 15:34:02 GMT",
"version": "v1"
}
] | 2010-08-31 | [
[
"Hong",
"Yoojin",
""
],
[
"Ko",
"Kyung Dae",
""
],
[
"Bhardwaj",
"Gaurav",
""
],
[
"Zhang",
"Zhenhai",
""
],
[
"van Rossum",
"Damian B.",
""
],
[
"Patterson",
"Randen L.",
""
]
] | Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies and underlies the inverse protein folding problem. Herein, we outline our theories for fold-recognition in the "twilight-zone" of sequence similarity (<25% identity). Our analyses demonstrate that structural sequence pr... |
1307.4789 | Wes Maciejewski | Wes Maciejewski | Reproductive Value in Graph-structured Populations | null | Journal of Theoretical Biology, (2014), vol.340, pp.285-293 | 10.1016/j.jtbi.2013.09.032 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolutionary graph theory has grown to be an area of intense study. Despite
the amount of interest in the field, it seems to have grown separate from other
subfields of population genetics and evolution. In the current work I introduce
the concept of Fisher's (1930) reproductive value into the study of evolution
on g... | [
{
"created": "Wed, 17 Jul 2013 20:56:44 GMT",
"version": "v1"
}
] | 2014-07-30 | [
[
"Maciejewski",
"Wes",
""
]
] | Evolutionary graph theory has grown to be an area of intense study. Despite the amount of interest in the field, it seems to have grown separate from other subfields of population genetics and evolution. In the current work I introduce the concept of Fisher's (1930) reproductive value into the study of evolution on gra... |
2107.12799 | Mohammad Reza Dayer | Mohammad Reza Dayer | New Candidates for Furin Inhibition as Probable Treat for COVID-19:
Docking Output | null | null | null | null | q-bio.BM q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Furin is a serine protease that takes part in the processing and activation
of the host cell pre-proteins. The enzyme also plays an important role in the
activation of several viruses like the newly emerging SARS-CoV-2 virus that
causes COVID-19 disease with a high rate of virulence and mortality. Unlike
viral enzyme... | [
{
"created": "Tue, 27 Jul 2021 13:12:57 GMT",
"version": "v1"
}
] | 2021-07-28 | [
[
"Dayer",
"Mohammad Reza",
""
]
] | Furin is a serine protease that takes part in the processing and activation of the host cell pre-proteins. The enzyme also plays an important role in the activation of several viruses like the newly emerging SARS-CoV-2 virus that causes COVID-19 disease with a high rate of virulence and mortality. Unlike viral enzymes,... |
2008.01810 | Neta Maimon | Assaf Suberry, Neta B. Maimon and Zohar Eitan | Sad syntax? Tonal closure Affects Children's Perception of Emotional
Valence | 44 pages, 7 figures, 1 table, 1 appendix | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Western music is largely governed by tonality, a quasi syntactic system
regulating musical continuity and closure. Converging measures have established
the psychological reality of tonality as a cognitive schema raising distinct
expectancy for both adults and children. However, while tonal expectations were
associate... | [
{
"created": "Tue, 4 Aug 2020 20:13:53 GMT",
"version": "v1"
}
] | 2020-08-06 | [
[
"Suberry",
"Assaf",
""
],
[
"Maimon",
"Neta B.",
""
],
[
"Eitan",
"Zohar",
""
]
] | Western music is largely governed by tonality, a quasi syntactic system regulating musical continuity and closure. Converging measures have established the psychological reality of tonality as a cognitive schema raising distinct expectancy for both adults and children. However, while tonal expectations were associated ... |
2405.09953 | Jessica Thompson | Jessica A.F. Thompson, Hannah Sheahan, Tsvetomira Dumbalska, Julian
Sandbrink, Manuela Piazza, Christopher Summerfield | Zero-shot counting with a dual-stream neural network model | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Deep neural networks have provided a computational framework for
understanding object recognition, grounded in the neurophysiology of the
primate ventral stream, but fail to account for how we process relational
aspects of a scene. For example, deep neural networks fail at problems that
involve enumerating the number... | [
{
"created": "Thu, 16 May 2024 09:56:37 GMT",
"version": "v1"
}
] | 2024-05-17 | [
[
"Thompson",
"Jessica A. F.",
""
],
[
"Sheahan",
"Hannah",
""
],
[
"Dumbalska",
"Tsvetomira",
""
],
[
"Sandbrink",
"Julian",
""
],
[
"Piazza",
"Manuela",
""
],
[
"Summerfield",
"Christopher",
""
]
] | Deep neural networks have provided a computational framework for understanding object recognition, grounded in the neurophysiology of the primate ventral stream, but fail to account for how we process relational aspects of a scene. For example, deep neural networks fail at problems that involve enumerating the number o... |
2003.05694 | Maryam Al Shehhi Dr | Maryam R. Al Shehhi, David Nelson, Rashid R Alkhori, Rashid Alshihi,
and Kourosh Salehi-Ashtiani | Characterizing Algal blooms in a shallow and a deep channel over a
decade (2008-2018) | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The outbreaks of algal blooms occur in both shallow and deep-water bodies. To
compare the characteristics of algal blooms in the shallow and deep water, we
consider the Arabian Gulf and Sea of Oman as a case study. While the Arabian
Gulf is a shallow region dominated by advective features, the Sea of Oman is a
deep c... | [
{
"created": "Thu, 12 Mar 2020 10:30:41 GMT",
"version": "v1"
},
{
"created": "Mon, 16 Mar 2020 14:12:33 GMT",
"version": "v2"
}
] | 2020-03-17 | [
[
"Shehhi",
"Maryam R. Al",
""
],
[
"Nelson",
"David",
""
],
[
"Alkhori",
"Rashid R",
""
],
[
"Alshihi",
"Rashid",
""
],
[
"Salehi-Ashtiani",
"Kourosh",
""
]
] | The outbreaks of algal blooms occur in both shallow and deep-water bodies. To compare the characteristics of algal blooms in the shallow and deep water, we consider the Arabian Gulf and Sea of Oman as a case study. While the Arabian Gulf is a shallow region dominated by advective features, the Sea of Oman is a deep cha... |
1402.0451 | Adriano Barra Dr. | Elena Agliari and Elena Biselli and Adele De Ninno and Giovanna
Schiavoni and Lucia Gabriele and Anna Gerardino and Fabrizio Mattei and
Adriano Barra and Luca Businaro | Cancer-driven dynamics of immune cells in a microfluidic environment | null | Nature Scientific Reports 4, 6639 (2014) | 10.1038/srep06639 | Roma01.Math | q-bio.CB cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Scope of the present work is to frame into a rigorous, quantitative scaffold
- stemmed from stochastic process theory - two sets of experiments designed to
infer the spontaneous organization of leukocytes against cancer cells, namely
mice splenocytes vs. B16 mouse tumor cells, and embedded in an "ad hoc"
microfluidic... | [
{
"created": "Mon, 3 Feb 2014 18:11:20 GMT",
"version": "v1"
}
] | 2016-02-02 | [
[
"Agliari",
"Elena",
""
],
[
"Biselli",
"Elena",
""
],
[
"De Ninno",
"Adele",
""
],
[
"Schiavoni",
"Giovanna",
""
],
[
"Gabriele",
"Lucia",
""
],
[
"Gerardino",
"Anna",
""
],
[
"Mattei",
"Fabrizio",
""
],
... | Scope of the present work is to frame into a rigorous, quantitative scaffold - stemmed from stochastic process theory - two sets of experiments designed to infer the spontaneous organization of leukocytes against cancer cells, namely mice splenocytes vs. B16 mouse tumor cells, and embedded in an "ad hoc" microfluidic e... |
0910.1830 | Navodit Misra | Navodit Misra, Guy Blelloch, R. Ravi and Russell Schwartz | Generalized Buneman pruning for inferring the most parsimonious
multi-state phylogeny | 15 pages | null | 10.1007/978-3-642-12683-3_24 | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurate reconstruction of phylogenies remains a key challenge in
evolutionary biology. Most biologically plausible formulations of the problem
are formally NP-hard, with no known efficient solution. The standard in
practice are fast heuristic methods that are empirically known to work very
well in general, but can y... | [
{
"created": "Fri, 9 Oct 2009 19:59:00 GMT",
"version": "v1"
},
{
"created": "Fri, 9 Oct 2009 20:11:16 GMT",
"version": "v2"
},
{
"created": "Thu, 15 Apr 2010 01:46:04 GMT",
"version": "v3"
}
] | 2015-05-14 | [
[
"Misra",
"Navodit",
""
],
[
"Blelloch",
"Guy",
""
],
[
"Ravi",
"R.",
""
],
[
"Schwartz",
"Russell",
""
]
] | Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast heuristic methods that are empirically known to work very well in general, but can yie... |
q-bio/0601038 | Michele Bezzi | Michele Bezzi | Quantifying the information transmitted in a single stimulus | 13 pages, 4 figures | null | null | null | q-bio.NC q-bio.QM | null | Shannon mutual information provides a measure of how much information is, on
average, contained in a set of neural activities about a set of stimuli. It has
been extensively used to study neural coding in different brain areas. To apply
a similar approach to investigate single stimulus encoding, we need to
introduce ... | [
{
"created": "Mon, 23 Jan 2006 13:51:28 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bezzi",
"Michele",
""
]
] | Shannon mutual information provides a measure of how much information is, on average, contained in a set of neural activities about a set of stimuli. It has been extensively used to study neural coding in different brain areas. To apply a similar approach to investigate single stimulus encoding, we need to introduce a ... |
2402.10387 | Peter Eckmann | Peter Eckmann, Dongxia Wu, Germano Heinzelmann, Michael K Gilson, Rose
Yu | MFBind: a Multi-Fidelity Approach for Evaluating Drug Compounds in
Practical Generative Modeling | 9 pages, 4 figures | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Current generative models for drug discovery primarily use molecular docking
to evaluate the quality of generated compounds. However, such models are often
not useful in practice because even compounds with high docking scores do not
consistently show experimental activity. More accurate methods for activity
predicti... | [
{
"created": "Fri, 16 Feb 2024 00:48:20 GMT",
"version": "v1"
}
] | 2024-02-19 | [
[
"Eckmann",
"Peter",
""
],
[
"Wu",
"Dongxia",
""
],
[
"Heinzelmann",
"Germano",
""
],
[
"Gilson",
"Michael K",
""
],
[
"Yu",
"Rose",
""
]
] | Current generative models for drug discovery primarily use molecular docking to evaluate the quality of generated compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show experimental activity. More accurate methods for activity prediction... |
1906.01224 | Tomokazu Konishi | Tomokazu Konishi, Haruna Ohrui | A distribution-dependent analysis of open-field test movies | 30 pages, 3 Figures, including supplementary data | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although the open-field test has been widely used, its reliability and
compatibility are frequently questioned. Although many indicating parameters
were introduced for this test, they did not take data distributions into
consideration. This oversight may have caused the problems mentioned above.
Here, an exploratory ... | [
{
"created": "Tue, 4 Jun 2019 06:49:49 GMT",
"version": "v1"
}
] | 2019-06-05 | [
[
"Konishi",
"Tomokazu",
""
],
[
"Ohrui",
"Haruna",
""
]
] | Although the open-field test has been widely used, its reliability and compatibility are frequently questioned. Although many indicating parameters were introduced for this test, they did not take data distributions into consideration. This oversight may have caused the problems mentioned above. Here, an exploratory ap... |
0704.2454 | Vahid Rezania | Vahid Rezania, Jack Tuszynski, Michael Hendzel | Modeling transcription factor binding events to DNA using a random
walker/jumper representation on a 1D/2D lattice with different affinity sites | 24 pages, 9 figures | Physical Biology, 4, 256-267 (2007) | 10.1088/1478-3975/4/4/003 | null | q-bio.QM q-bio.BM | null | Surviving in a diverse environment requires corresponding organism responses.
At the cellular level, such adjustment relies on the transcription factors
(TFs) which must rapidly find their target sequences amidst a vast amount of
non-relevant sequences on DNA molecules. Whether these transcription factors
locate thei... | [
{
"created": "Thu, 19 Apr 2007 03:20:02 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Aug 2007 17:44:57 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Rezania",
"Vahid",
""
],
[
"Tuszynski",
"Jack",
""
],
[
"Hendzel",
"Michael",
""
]
] | Surviving in a diverse environment requires corresponding organism responses. At the cellular level, such adjustment relies on the transcription factors (TFs) which must rapidly find their target sequences amidst a vast amount of non-relevant sequences on DNA molecules. Whether these transcription factors locate their ... |
2406.09094 | Luis Aniello La Rocca | Luis A. La Rocca, Konrad Gerischer, Anton Bovier and Peter M. Krawitz | Refining the drift barrier hypothesis: a role of recessive gene count
and an inhomogeneous Muller`s ratchet | 21 pages, 4 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The drift-barrier hypothesis states that random genetic drift constrains the
refinement of a phenotype under natural selection. The influence of effective
population size and the genome-wide deleterious mutation rate were studied
theoretically, and an inverse relationship between mutation rate and genome
size has bee... | [
{
"created": "Thu, 13 Jun 2024 13:22:41 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Jun 2024 08:58:03 GMT",
"version": "v2"
},
{
"created": "Tue, 23 Jul 2024 09:37:34 GMT",
"version": "v3"
},
{
"created": "Wed, 24 Jul 2024 10:23:03 GMT",
"version": "v4"
}
] | 2024-07-25 | [
[
"La Rocca",
"Luis A.",
""
],
[
"Gerischer",
"Konrad",
""
],
[
"Bovier",
"Anton",
""
],
[
"Krawitz",
"Peter M.",
""
]
] | The drift-barrier hypothesis states that random genetic drift constrains the refinement of a phenotype under natural selection. The influence of effective population size and the genome-wide deleterious mutation rate were studied theoretically, and an inverse relationship between mutation rate and genome size has been ... |
2012.06848 | Arnaud Liehrmann | Arnaud Liehrmann, Guillem Rigaill and Toby Dylan Hocking | Increased peak detection accuracy in over-dispersed ChIP-seq data with
supervised segmentation models | 20 pages, 8 figures; updated broken citations and references | null | null | null | q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Histone modification constitutes a basic mechanism for the
genetic regulation of gene expression. In early 2000s, a powerful technique has
emerged that couples chromatin immunoprecipitation with high-throughput
sequencing (ChIP-seq). This technique provides a direct survey of the DNA
regions associated to... | [
{
"created": "Sat, 12 Dec 2020 16:03:27 GMT",
"version": "v1"
},
{
"created": "Tue, 15 Dec 2020 12:34:48 GMT",
"version": "v2"
}
] | 2020-12-16 | [
[
"Liehrmann",
"Arnaud",
""
],
[
"Rigaill",
"Guillem",
""
],
[
"Hocking",
"Toby Dylan",
""
]
] | Motivation: Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq). This technique provides a direct survey of the DNA regions associated to t... |
2005.12446 | Massimo Marchiori | Massimo Marchiori | COVID-19 and the Social Distancing Paradox: dangers and solutions | 8 pages with 4 figures | null | null | null | q-bio.PE eess.SP physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Without proven effect treatments and vaccines, Social Distancing
is the key protection factor against COVID-19. Social distancing alone should
have been enough to protect again the virus, yet things have gone very
differently, with a big mismatch between theory and practice. What are the
reasons? A big pr... | [
{
"created": "Tue, 26 May 2020 00:01:53 GMT",
"version": "v1"
}
] | 2020-05-27 | [
[
"Marchiori",
"Massimo",
""
]
] | Background: Without proven effect treatments and vaccines, Social Distancing is the key protection factor against COVID-19. Social distancing alone should have been enough to protect again the virus, yet things have gone very differently, with a big mismatch between theory and practice. What are the reasons? A big prob... |
0811.2837 | Tom Chou | Pak-Wing Fok, Chin-Lin Guo, Tom Chou | Charge transport-mediated recruitment of DNA repair enzymes | 9 Figures, Accepted to J. Chem. Phys | Journal of Chemical Physics, 129, 235101, (2008) | 10.1063/1.3026735 | null | q-bio.BM q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Damaged or mismatched bases in DNA can be repaired by Base Excision Repair
(BER) enzymes that replace the defective base. Although the detailed molecular
structures of many BER enzymes are known, how they colocalize to lesions
remains unclear. One hypothesis involves charge transport (CT) along DNA
[Yavin, {\it et al... | [
{
"created": "Tue, 18 Nov 2008 04:38:18 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Fok",
"Pak-Wing",
""
],
[
"Guo",
"Chin-Lin",
""
],
[
"Chou",
"Tom",
""
]
] | Damaged or mismatched bases in DNA can be repaired by Base Excision Repair (BER) enzymes that replace the defective base. Although the detailed molecular structures of many BER enzymes are known, how they colocalize to lesions remains unclear. One hypothesis involves charge transport (CT) along DNA [Yavin, {\it et al.}... |
1304.5836 | Bin Ao | Bin Ao, Sheng Zhang, Caiyong Ye, Lei Chang, Guangming Zhou, Lei Yang | Oscillation in microRNA Feedback Loop | There were some mistakes in the analysis in this paper's first
version submitted on 22 Apr 2013. We corrected them in the second version
submitted on 23 Sep 2013. So please delete the "v1" version of this paper,
Thank you! | null | null | null | q-bio.MN nlin.PS | http://creativecommons.org/licenses/by-nc-sa/3.0/ | The dynamic behaviors of microRNA and mRNA under external stress are studied
with biological experiments and mathematics models. In this study, we developed
a mathematic model to describe the biological phenomenon and for the first time
reported that, as responses to external stress, the expression levels of
microRNA... | [
{
"created": "Mon, 22 Apr 2013 05:39:26 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Sep 2013 09:36:46 GMT",
"version": "v2"
},
{
"created": "Mon, 16 Dec 2013 07:52:20 GMT",
"version": "v3"
}
] | 2013-12-17 | [
[
"Ao",
"Bin",
""
],
[
"Zhang",
"Sheng",
""
],
[
"Ye",
"Caiyong",
""
],
[
"Chang",
"Lei",
""
],
[
"Zhou",
"Guangming",
""
],
[
"Yang",
"Lei",
""
]
] | The dynamic behaviors of microRNA and mRNA under external stress are studied with biological experiments and mathematics models. In this study, we developed a mathematic model to describe the biological phenomenon and for the first time reported that, as responses to external stress, the expression levels of microRNA a... |
2108.01982 | Farzad Fatehi | Farzad Fatehi, Richard J. Bingham, Eric C. Dykeman, Peter G. Stockley,
and Reidun Twarock | An age-structured model of hepatitis B viral infection highlights the
potential of different therapeutic strategies | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Hepatitis B virus is a global health threat, and its elimination by 2030 has
been prioritised by the World Health Organisation. Here we present an
age-structured model for the immune response to an HBV infection, which takes
into account contributions from both cell-mediated and humoral immunity. The
model has been v... | [
{
"created": "Wed, 4 Aug 2021 11:45:12 GMT",
"version": "v1"
}
] | 2021-08-05 | [
[
"Fatehi",
"Farzad",
""
],
[
"Bingham",
"Richard J.",
""
],
[
"Dykeman",
"Eric C.",
""
],
[
"Stockley",
"Peter G.",
""
],
[
"Twarock",
"Reidun",
""
]
] | Hepatitis B virus is a global health threat, and its elimination by 2030 has been prioritised by the World Health Organisation. Here we present an age-structured model for the immune response to an HBV infection, which takes into account contributions from both cell-mediated and humoral immunity. The model has been val... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.