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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1110.4070 | Gilberto Gonzalez | Jose L. Herrera and Gilberto Gonzalez-Parra | Dynamical graphs for the SI epidemiological model | 9 pages, 2 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we study the susceptible-infectious (SI) epidemiological model
using dynamical graphs. Dynamical structures have been recently applied in many
areas including complex systems. Dynamical structures include the mutual
interaction between the structure topology and the characteristics of its
members. Dynam... | [
{
"created": "Tue, 18 Oct 2011 17:50:08 GMT",
"version": "v1"
}
] | 2011-10-19 | [
[
"Herrera",
"Jose L.",
""
],
[
"Gonzalez-Parra",
"Gilberto",
""
]
] | In this paper we study the susceptible-infectious (SI) epidemiological model using dynamical graphs. Dynamical structures have been recently applied in many areas including complex systems. Dynamical structures include the mutual interaction between the structure topology and the characteristics of its members. Dynamic... |
1905.02053 | Christoph Zechner | David T. Gonzales and T-Y Dora Tang and Christoph Zechner | Moment-based analysis of biochemical networks in a heterogeneous
population of communicating cells | 6 pages, 5 Figures | null | null | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cells can utilize chemical communication to exchange information and
coordinate their behavior in the presence of noise. Communication can reduce
noise to shape a collective response, or amplify noise to generate distinct
phenotypic subpopulations. Here we discuss a moment-based approach to study how
cell-cell commun... | [
{
"created": "Mon, 6 May 2019 14:08:16 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Jul 2019 12:19:28 GMT",
"version": "v2"
},
{
"created": "Mon, 23 Sep 2019 11:45:05 GMT",
"version": "v3"
}
] | 2019-09-24 | [
[
"Gonzales",
"David T.",
""
],
[
"Tang",
"T-Y Dora",
""
],
[
"Zechner",
"Christoph",
""
]
] | Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic subpopulations. Here we discuss a moment-based approach to study how cell-cell communic... |
2404.08101 | Samuel Lippl | Samuel Lippl, Raphael Gerraty, John Morrison, Nikolaus Kriegeskorte | Source Invariance and Probabilistic Transfer: A Testable Theory of
Probabilistic Neural Representations | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | As animals interact with their environments, they must infer properties of
their surroundings. Some animals, including humans, can represent uncertainty
about those properties. But when, if ever, do they use probability
distributions to represent their uncertainty? It depends on which definition we
choose. In this pa... | [
{
"created": "Thu, 11 Apr 2024 19:38:07 GMT",
"version": "v1"
}
] | 2024-04-15 | [
[
"Lippl",
"Samuel",
""
],
[
"Gerraty",
"Raphael",
""
],
[
"Morrison",
"John",
""
],
[
"Kriegeskorte",
"Nikolaus",
""
]
] | As animals interact with their environments, they must infer properties of their surroundings. Some animals, including humans, can represent uncertainty about those properties. But when, if ever, do they use probability distributions to represent their uncertainty? It depends on which definition we choose. In this pape... |
1202.0501 | Leo Lahti | Leo Lahti, Juha E. A. Knuuttila, Samuel Kaski | Global modeling of transcriptional responses in interaction networks | 19 pages, 13 figures | Global modeling of transcriptional responses in interaction
networks. Leo Lahti, Juha E.A. Knuuttila, and Samuel Kaski. Bioinformatics
26(21):2713-2720, 2010 | 10.1093/bioinformatics/btq500 | null | q-bio.MN cs.CE q-bio.QM stat.AP stat.ML | http://creativecommons.org/licenses/by/3.0/ | Motivation: Cell-biological processes are regulated through a complex network
of interactions between genes and their products. The processes, their
activating conditions, and the associated transcriptional responses are often
unknown. Organism-wide modeling of network activation can reveal unique and
shared mechanis... | [
{
"created": "Thu, 2 Feb 2012 17:40:14 GMT",
"version": "v1"
}
] | 2012-02-03 | [
[
"Lahti",
"Leo",
""
],
[
"Knuuttila",
"Juha E. A.",
""
],
[
"Kaski",
"Samuel",
""
]
] | Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms... |
1805.03233 | Juan Lorenzo Rodriguez-Flores Ph.D. | Khalid A. Fakhro, Michelle R. Staudt, Monica Denise Ramstetter, Amal
Robay, Joel A. Malek, Ramin Badii, Ajayeb Al-Nabet Al-Marri, Charbel Abi
Khalil, Alya Al-Shakaki, Omar Chidiac, Dora Stadler, Mahmoud Zirie, Amin
Jayyousi, Jacqueline Salit, Jason G. Mezey, Ronald G. Crystal, and Juan L.
Rodriguez-Flores | The Qatar Genome: A Population-Specific Tool for Precision Medicine in
the Middle East | Includes supplementary figures missing from publisher website | Hum Genome Var. 2016 Jun 30;3:16016 | 10.1038/hgv.2016.16 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reaching the full potential of precision medicine depends on the quality of
personalized genome interpretation. In order to facilitate precision medicine
in regions of the Middle East and North Africa (MENA), a population-specific
reference genome for the indigenous Arab popula-tion of Qatar (QTRG) was
constructed by... | [
{
"created": "Tue, 8 May 2018 19:04:37 GMT",
"version": "v1"
},
{
"created": "Sun, 13 May 2018 12:25:23 GMT",
"version": "v2"
}
] | 2018-05-15 | [
[
"Fakhro",
"Khalid A.",
""
],
[
"Staudt",
"Michelle R.",
""
],
[
"Ramstetter",
"Monica Denise",
""
],
[
"Robay",
"Amal",
""
],
[
"Malek",
"Joel A.",
""
],
[
"Badii",
"Ramin",
""
],
[
"Al-Marri",
"Ajayeb Al-Nabet... | Reaching the full potential of precision medicine depends on the quality of personalized genome interpretation. In order to facilitate precision medicine in regions of the Middle East and North Africa (MENA), a population-specific reference genome for the indigenous Arab popula-tion of Qatar (QTRG) was constructed by i... |
2107.07938 | Gilberto Nakamura | F. Meloni, G. Nakamura, B. Grammaticos, A. S. Martinez, M. Badoual | Modeling cooperation and competition in biological communities | 24 pages, 16 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The far-reaching consequences of ecological interactions in the dynamics of
biological communities remain an intriguing subject. For decades, competition
has been a cornerstone in ecological processes, but mounting evidence shows
that cooperation does also contribute to the structure of biological
communities. Here, ... | [
{
"created": "Fri, 16 Jul 2021 14:54:09 GMT",
"version": "v1"
}
] | 2021-07-19 | [
[
"Meloni",
"F.",
""
],
[
"Nakamura",
"G.",
""
],
[
"Grammaticos",
"B.",
""
],
[
"Martinez",
"A. S.",
""
],
[
"Badoual",
"M.",
""
]
] | The far-reaching consequences of ecological interactions in the dynamics of biological communities remain an intriguing subject. For decades, competition has been a cornerstone in ecological processes, but mounting evidence shows that cooperation does also contribute to the structure of biological communities. Here, we... |
1108.1150 | Steffen Schaper | Steffen Schaper, Iain G. Johnston and Ard A. Louis | Epistasis can lead to fragmented neutral spaces and contingency in
evolution | 21 pages, 21 figures | Proc. R. Soc. B 7 May 2012 vol. 279 no. 1734 1777-1783 | 10.1098/rspb.2011.2183 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In evolution, the effects of a single deleterious mutation can sometimes be
compensated for by a second mutation which recovers the original phenotype.
Such epistatic interactions have implications for the structure of genome space
- namely, that networks of genomes encoding the same phenotype may not be
connected by... | [
{
"created": "Thu, 4 Aug 2011 17:50:50 GMT",
"version": "v1"
},
{
"created": "Tue, 6 Dec 2011 19:08:02 GMT",
"version": "v2"
}
] | 2015-03-19 | [
[
"Schaper",
"Steffen",
""
],
[
"Johnston",
"Iain G.",
""
],
[
"Louis",
"Ard A.",
""
]
] | In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space - namely, that networks of genomes encoding the same phenotype may not be connected by s... |
2112.09079 | Suraj Shankar | Roberto Benzi, David R. Nelson, Suraj Shankar, Federico Toschi,
Xiaojue Zhu | Spatial population genetics with fluid flow | 29 pages, 22 figures | Rep. Prog. Phys. 85 096601, 2022 | 10.1088/1361-6633/ac8231 | null | q-bio.PE cond-mat.soft cond-mat.stat-mech physics.flu-dyn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The growth and evolution of microbial populations is often subjected to
advection by fluid flows in spatially extended environments, with immediate
consequences for questions of spatial population genetics in marine ecology,
planktonic diversity and origin of life scenarios. Here, we review recent
progress made in un... | [
{
"created": "Thu, 16 Dec 2021 18:03:56 GMT",
"version": "v1"
},
{
"created": "Thu, 30 Jun 2022 15:47:39 GMT",
"version": "v2"
}
] | 2022-08-26 | [
[
"Benzi",
"Roberto",
""
],
[
"Nelson",
"David R.",
""
],
[
"Shankar",
"Suraj",
""
],
[
"Toschi",
"Federico",
""
],
[
"Zhu",
"Xiaojue",
""
]
] | The growth and evolution of microbial populations is often subjected to advection by fluid flows in spatially extended environments, with immediate consequences for questions of spatial population genetics in marine ecology, planktonic diversity and origin of life scenarios. Here, we review recent progress made in unde... |
1304.6034 | Louis Scheffer | Louis K. Scheffer, Bill Karsh, Shiv Vitaladevun | Automated Alignment of Imperfect EM Images for Neural Reconstruction | 23 pages, 10 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The most established method of reconstructing neural circuits from animals
involves slicing tissue very thin, then taking mosaics of electron microscope
(EM) images. To trace neurons across different images and through different
sections, these images must be accurately aligned, both with the others in the
same secti... | [
{
"created": "Mon, 22 Apr 2013 18:00:14 GMT",
"version": "v1"
}
] | 2013-04-23 | [
[
"Scheffer",
"Louis K.",
""
],
[
"Karsh",
"Bill",
""
],
[
"Vitaladevun",
"Shiv",
""
]
] | The most established method of reconstructing neural circuits from animals involves slicing tissue very thin, then taking mosaics of electron microscope (EM) images. To trace neurons across different images and through different sections, these images must be accurately aligned, both with the others in the same section... |
1703.07943 | Haiping Huang | Haiping Huang | Role of zero synapses in unsupervised feature learning | 6 pages, 4 figures, to appear in J. Phys A as a LETTER | null | 10.1088/1751-8121/aaa631 | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Synapses in real neural circuits can take discrete values, including zero
(silent or potential) synapses. The computational role of zero synapses in
unsupervised feature learning of unlabeled noisy data is still unclear, thus it
is important to understand how the sparseness of synaptic activity is shaped
during learn... | [
{
"created": "Thu, 23 Mar 2017 06:19:47 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Jun 2017 08:07:52 GMT",
"version": "v2"
},
{
"created": "Wed, 12 Jul 2017 05:13:42 GMT",
"version": "v3"
},
{
"created": "Wed, 10 Jan 2018 06:57:00 GMT",
"version": "v4"
}
] | 2018-01-11 | [
[
"Huang",
"Haiping",
""
]
] | Synapses in real neural circuits can take discrete values, including zero (silent or potential) synapses. The computational role of zero synapses in unsupervised feature learning of unlabeled noisy data is still unclear, thus it is important to understand how the sparseness of synaptic activity is shaped during learnin... |
2212.14754 | J. C. Phillips | J. C. Phillips | Biophysical Sequence Analysis of Functional Differences of Piezo1 and
Piezo2 | 10 page, two figures | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Because of their large size and widespread mechanosensitive interactions the
only recently discovered titled transmembrane proteins have attracted much
attention. Here we present and discuss their hydropathic profiles using a new
method of sequence analysis. We find large-scale similarities and differences
not obtain... | [
{
"created": "Tue, 27 Dec 2022 17:48:55 GMT",
"version": "v1"
}
] | 2023-01-02 | [
[
"Phillips",
"J. C.",
""
]
] | Because of their large size and widespread mechanosensitive interactions the only recently discovered titled transmembrane proteins have attracted much attention. Here we present and discuss their hydropathic profiles using a new method of sequence analysis. We find large-scale similarities and differences not obtainab... |
1407.1627 | Kavita Jain | Brian Charlesworth and Kavita Jain | Purifying selection, drift and reversible mutation with arbitrarily high
mutation rates | Supplementary Information available on request | Genetics 198, 1587-1602 (2014) | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Some species exhibit very high levels of DNA sequence variability; there is
also evidence for the existence of heritable epigenetic variants that
experience state changes at a much higher rate than sequence variants. In both
cases, the resulting high diversity levels within a population (hyperdiversity)
mean that sta... | [
{
"created": "Mon, 7 Jul 2014 08:54:47 GMT",
"version": "v1"
}
] | 2016-01-13 | [
[
"Charlesworth",
"Brian",
""
],
[
"Jain",
"Kavita",
""
]
] | Some species exhibit very high levels of DNA sequence variability; there is also evidence for the existence of heritable epigenetic variants that experience state changes at a much higher rate than sequence variants. In both cases, the resulting high diversity levels within a population (hyperdiversity) mean that stand... |
1509.00801 | Samuel Scarpino | Samuel V. Scarpino, Antoine Allard, Laurent Hebert-Dufresne | Prudent behaviour accelerates disease transmission | null | Nature Physics 12, 1042-1046 (2016) | 10.1038/nphys3832 | null | q-bio.QM nlin.AO physics.soc-ph q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Infectious diseases often spread faster near their peak than would be
predicted given early data on transmission. Despite the commonality of this
phenomena, there are no known general mechanisms able to cause an exponentially
spreading dis- ease to begin spreading faster. Indeed most features of real
world social net... | [
{
"created": "Wed, 2 Sep 2015 17:57:24 GMT",
"version": "v1"
}
] | 2017-07-06 | [
[
"Scarpino",
"Samuel V.",
""
],
[
"Allard",
"Antoine",
""
],
[
"Hebert-Dufresne",
"Laurent",
""
]
] | Infectious diseases often spread faster near their peak than would be predicted given early data on transmission. Despite the commonality of this phenomena, there are no known general mechanisms able to cause an exponentially spreading dis- ease to begin spreading faster. Indeed most features of real world social netwo... |
2012.02628 | Jonathan Cohen | Jonathan D. Cohen | A Mitigation Score for COVID-19 | 15 pages, 12 figures | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | This note describes a simple score to indicate the effectiveness of
mitigation against infections of COVID-19 as observed by new case counts. The
score includes normalization, making comparisons across jurisdictions possible.
The smoothing employed provides robustness in the face of reporting vagaries
while retaining... | [
{
"created": "Wed, 2 Dec 2020 21:25:50 GMT",
"version": "v1"
}
] | 2020-12-07 | [
[
"Cohen",
"Jonathan D.",
""
]
] | This note describes a simple score to indicate the effectiveness of mitigation against infections of COVID-19 as observed by new case counts. The score includes normalization, making comparisons across jurisdictions possible. The smoothing employed provides robustness in the face of reporting vagaries while retaining s... |
1004.2035 | Maxim Paliy Dr. | Maxim Paliy, Roderick Melnik, Bruce A. Shapiro | Coarse Graining RNA Nanostructures for Molecular Dynamics Simulations | null | null | 10.1088/1478-3975/7/3/036001 | null | q-bio.QM physics.bio-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A series of coarse-grained models have been developed for the study of the
molecular dynamics of RNA nanostructures. The models in the series have one to
three beads per nucleotide and include different amounts of detailed structural
information. Such a treatment allows us to reach, for the systems of thousands
of nu... | [
{
"created": "Mon, 12 Apr 2010 19:50:08 GMT",
"version": "v1"
}
] | 2015-05-18 | [
[
"Paliy",
"Maxim",
""
],
[
"Melnik",
"Roderick",
""
],
[
"Shapiro",
"Bruce A.",
""
]
] | A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for the systems of thousands of nucl... |
1712.06451 | Roland Kr\"amer | Ulrich Warttinger, Christina Giese, Roland Kr\"amer | Quantification of sulfated polysaccharides in mouse and rat plasma by
the Heparin Red mix-and-read fluorescence assay | 19 pages, 8 figures, 3 schemes, 4 tables. arXiv admin note: text
overlap with arXiv:1712.03377 | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sulfated polysaccharides constitute a large and complex group of
macromolecules which possess a wide range of important biological properties.
Many of them hold promise as new therapeutics, but determination of their blood
levels during pharmacokinetic studies can be challenging. Heparin Red, a
commercial mix-and-rea... | [
{
"created": "Fri, 15 Dec 2017 14:28:26 GMT",
"version": "v1"
}
] | 2017-12-19 | [
[
"Warttinger",
"Ulrich",
""
],
[
"Giese",
"Christina",
""
],
[
"Krämer",
"Roland",
""
]
] | Sulfated polysaccharides constitute a large and complex group of macromolecules which possess a wide range of important biological properties. Many of them hold promise as new therapeutics, but determination of their blood levels during pharmacokinetic studies can be challenging. Heparin Red, a commercial mix-and-read ... |
1704.01841 | Greg Gloor Dr | Jia R. Wu, Jean M. Macklaim, Briana L. Genge, and Gregory B. Gloor | Finding the centre: corrections for asymmetry in high-throughput
sequencing datasets | Preliminary conference paper for CoDaWork 2017. Outlines asymmetry
correction incorporated into the Bioconductor package ALDEx2 | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | High throughput sequencing is a technology that allows for the generation of
millions of reads of genomic data regarding a study of interest, and data from
high throughput sequencing platforms are usually count compositions. Subsequent
analysis of such data can yield information on tran- scription profiles,
microbial... | [
{
"created": "Thu, 6 Apr 2017 13:41:48 GMT",
"version": "v1"
}
] | 2017-04-07 | [
[
"Wu",
"Jia R.",
""
],
[
"Macklaim",
"Jean M.",
""
],
[
"Genge",
"Briana L.",
""
],
[
"Gloor",
"Gregory B.",
""
]
] | High throughput sequencing is a technology that allows for the generation of millions of reads of genomic data regarding a study of interest, and data from high throughput sequencing platforms are usually count compositions. Subsequent analysis of such data can yield information on tran- scription profiles, microbial d... |
1609.03925 | Yue Wu | Dongmei Li, Yue Wu, Panpan Wen, Weihua Liu | The qualitative analysis of the impact of media delay on the control of
infectious disease | 19 pages, 7 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we consider the impact of time delay by media on the control
of the disease. We set up a class of SISM epidemic model with the time delay
and the cumulative density of awareness caused by media. The sufficient
condition of global asymptotic stability of disease-free equilibrium is
approved. We get the ... | [
{
"created": "Mon, 12 Sep 2016 01:28:11 GMT",
"version": "v1"
}
] | 2016-09-14 | [
[
"Li",
"Dongmei",
""
],
[
"Wu",
"Yue",
""
],
[
"Wen",
"Panpan",
""
],
[
"Liu",
"Weihua",
""
]
] | In this paper, we consider the impact of time delay by media on the control of the disease. We set up a class of SISM epidemic model with the time delay and the cumulative density of awareness caused by media. The sufficient condition of global asymptotic stability of disease-free equilibrium is approved. We get the gl... |
q-bio/0509028 | Martin Huber | Martin Tobias Huber And Hans Albert Braun | Stimulus - response curves of a neuronal model for noisy subthreshold
oscillations and related spike generation | 19 pages, 7 figures | null | 10.1103/PhysRevE.73.041929 | null | q-bio.NC | null | We investigate the stimulus-dependent tuning properties of a noisy ionic
conductance model for intrinsic subthreshold oscillations in membrane potential
and associated spike generation. On depolarization by an applied current, the
model exhibits subthreshold oscillatory activity with occasional spike
generation when ... | [
{
"created": "Thu, 22 Sep 2005 15:40:24 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Braun",
"Martin Tobias Huber And Hans Albert",
""
]
] | We investigate the stimulus-dependent tuning properties of a noisy ionic conductance model for intrinsic subthreshold oscillations in membrane potential and associated spike generation. On depolarization by an applied current, the model exhibits subthreshold oscillatory activity with occasional spike generation when os... |
2111.05855 | Takuma Usuzaki Dr | Takuma Usuzaki, Kengo Takahash, Kazuma Umemiya | A new radiomics feature: image frequency analysis | 4 pages, 5 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Radiomics is a promising technology that focuses on improvements of image
analysis, using an automated high-throughput extraction of quantitative
features. However, the character of lesion is affected by the surrounding
tissue. A lesion on medical image should be characterized from the
inter-relation between lesion a... | [
{
"created": "Wed, 10 Nov 2021 09:44:45 GMT",
"version": "v1"
}
] | 2021-11-12 | [
[
"Usuzaki",
"Takuma",
""
],
[
"Takahash",
"Kengo",
""
],
[
"Umemiya",
"Kazuma",
""
]
] | Radiomics is a promising technology that focuses on improvements of image analysis, using an automated high-throughput extraction of quantitative features. However, the character of lesion is affected by the surrounding tissue. A lesion on medical image should be characterized from the inter-relation between lesion and... |
1502.04591 | Yintao Wang | Yintao Wang, Hao He, Shaoyang Wang, Yaohui Liu, Minglie Hu, Youjia
Cao, Chingyue Wang | Photostimulation activates restorable fragmentation of single
mitochondrion by initiating oxide flashes | null | null | null | null | q-bio.SC physics.optics q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mitochondrial research is important to ageing, apoptosis, and mitochondrial
diseases. In previous works, mitochondria are usually stimulated indirectly by
proapoptotic drugs to study mitochondrial development, which is in lack of
controllability, or spatial and temporal resolution. These chemicals or even
gene techni... | [
{
"created": "Mon, 16 Feb 2015 16:06:21 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Feb 2015 13:54:30 GMT",
"version": "v2"
}
] | 2015-02-18 | [
[
"Wang",
"Yintao",
""
],
[
"He",
"Hao",
""
],
[
"Wang",
"Shaoyang",
""
],
[
"Liu",
"Yaohui",
""
],
[
"Hu",
"Minglie",
""
],
[
"Cao",
"Youjia",
""
],
[
"Wang",
"Chingyue",
""
]
] | Mitochondrial research is important to ageing, apoptosis, and mitochondrial diseases. In previous works, mitochondria are usually stimulated indirectly by proapoptotic drugs to study mitochondrial development, which is in lack of controllability, or spatial and temporal resolution. These chemicals or even gene techniqu... |
2312.10519 | Vishal Rana | Vishal Rana, Jianhao Peng, Chao Pan, Hanbaek Lyu, Albert Cheng, Minji
Kim, Olgica Milenkovic | Interpretable Online Network Dictionary Learning for Inferring
Long-Range Chromatin Interactions | null | null | null | null | q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Dictionary learning (DL) is commonly used in computational biology to tackle
ubiquitous clustering problems due to its conceptual simplicity and relatively
low computational complexity. However, DL algorithms produce results that lack
interpretability and are not optimized for large-scale graph-structured data.
We pr... | [
{
"created": "Sat, 16 Dec 2023 18:47:09 GMT",
"version": "v1"
}
] | 2023-12-19 | [
[
"Rana",
"Vishal",
""
],
[
"Peng",
"Jianhao",
""
],
[
"Pan",
"Chao",
""
],
[
"Lyu",
"Hanbaek",
""
],
[
"Cheng",
"Albert",
""
],
[
"Kim",
"Minji",
""
],
[
"Milenkovic",
"Olgica",
""
]
] | Dictionary learning (DL) is commonly used in computational biology to tackle ubiquitous clustering problems due to its conceptual simplicity and relatively low computational complexity. However, DL algorithms produce results that lack interpretability and are not optimized for large-scale graph-structured data. We prop... |
2201.02869 | Wesley Cota | Arthur Schulenburg, Wesley Cota, Guilherme S. Costa, Silvio C.
Ferreira | Effects of infection fatality ratio and social contact matrices on
vaccine prioritization strategies | 13 pages, 10 figures, 2 tables. Accepted in Chaos: An
Interdisciplinary Journal of Nonlinear Science | Chaos 32, 093102 (2022) | 10.1063/5.0096532 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Effective strategies of vaccine prioritization are essential to mitigate the
impacts of severe infectious diseases. We investigate the role of infection
fatality ratio (IFR) and social contact matrices on vaccination prioritization
using a compartmental epidemic model fueled by real-world data of different
diseases a... | [
{
"created": "Sat, 8 Jan 2022 17:57:44 GMT",
"version": "v1"
},
{
"created": "Sun, 7 Aug 2022 13:21:54 GMT",
"version": "v2"
}
] | 2023-10-04 | [
[
"Schulenburg",
"Arthur",
""
],
[
"Cota",
"Wesley",
""
],
[
"Costa",
"Guilherme S.",
""
],
[
"Ferreira",
"Silvio C.",
""
]
] | Effective strategies of vaccine prioritization are essential to mitigate the impacts of severe infectious diseases. We investigate the role of infection fatality ratio (IFR) and social contact matrices on vaccination prioritization using a compartmental epidemic model fueled by real-world data of different diseases and... |
2012.08667 | Luca Faes | Gorana Mijatovic, Yuri Antonacci, Tatjana Loncar-Turukalo, Ludovico
Minati and Luca Faes | An information-theoretic framework to measure the dynamic interaction
between neural spike trains | 12 pages, 7 figures; supplementary material at
www.lucafaes.net/TEMI.html | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Understanding the interaction patterns among simultaneous recordings of spike
trains from multiple neuronal units is a key topic in neuroscience. However, an
optimal approach of assessing these interactions has not been established, as
existing methods either do not consider the inherent point process nature of
spike... | [
{
"created": "Tue, 15 Dec 2020 23:27:24 GMT",
"version": "v1"
}
] | 2020-12-17 | [
[
"Mijatovic",
"Gorana",
""
],
[
"Antonacci",
"Yuri",
""
],
[
"Loncar-Turukalo",
"Tatjana",
""
],
[
"Minati",
"Ludovico",
""
],
[
"Faes",
"Luca",
""
]
] | Understanding the interaction patterns among simultaneous recordings of spike trains from multiple neuronal units is a key topic in neuroscience. However, an optimal approach of assessing these interactions has not been established, as existing methods either do not consider the inherent point process nature of spike t... |
2203.12290 | Renata Rychtarikova | Ali Ghaznavi, Renata Rychtarikova, Mohammadmehdi Saberioon, Dalibor
Stys | Cell segmentation from telecentric bright-field transmitted light
microscopy images using a Residual Attention U-Net: a case study on HeLa line | 32 pages, 7 figures | Computers in Biology and Medicine, 105805 (2022) | 10.1016/j.compbiomed.2022.105805 | null | q-bio.QM cs.CV eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Living cell segmentation from bright-field light microscopy images is
challenging due to the image complexity and temporal changes in the living
cells. Recently developed deep learning (DL)-based methods became popular in
medical and microscopy image segmentation tasks due to their success and
promising outcomes. The... | [
{
"created": "Wed, 23 Mar 2022 09:20:30 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Jun 2022 08:33:37 GMT",
"version": "v2"
},
{
"created": "Wed, 6 Jul 2022 14:08:18 GMT",
"version": "v3"
}
] | 2022-07-07 | [
[
"Ghaznavi",
"Ali",
""
],
[
"Rychtarikova",
"Renata",
""
],
[
"Saberioon",
"Mohammadmehdi",
""
],
[
"Stys",
"Dalibor",
""
]
] | Living cell segmentation from bright-field light microscopy images is challenging due to the image complexity and temporal changes in the living cells. Recently developed deep learning (DL)-based methods became popular in medical and microscopy image segmentation tasks due to their success and promising outcomes. The m... |
0902.4692 | Michael McGuigan | Michael McGuigan | The Tiger and the Sun: Solar Power Plants and Wildlife Sanctuaries | 19 pages, 4 tables, 9 figures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We discuss separate and integrated approaches to building scalable solar
power plants and wildlife sanctuaries. Both solar power plants and wildlife
sanctuaries need a lot of land. We quantify some of the requirements using
various estimates of the rate of solar power production as well as the rate of
adding wildlife... | [
{
"created": "Thu, 26 Feb 2009 20:33:23 GMT",
"version": "v1"
}
] | 2009-02-27 | [
[
"McGuigan",
"Michael",
""
]
] | We discuss separate and integrated approaches to building scalable solar power plants and wildlife sanctuaries. Both solar power plants and wildlife sanctuaries need a lot of land. We quantify some of the requirements using various estimates of the rate of solar power production as well as the rate of adding wildlife t... |
0712.0846 | Kai Miller | Kai J. Miller, Larry B. Sorensen, Jeffrey G. Ojemann, Marcel den Nijs | ECoG observations of power-law scaling in the human cortex | 4 pages, 4 figures | null | null | null | q-bio.NC cond-mat.other | null | We report the results of our search for power-law electrical signals in the
human brain, using subdural electrocorticographic recordings from the surface
of the cortex. The power spectral density (PSD) of these signals has the
power-law form $ P(f)\sim f^{-\chi} $ from 80 to 500 Hz. This scaling index
$\chi = 4.0\pm ... | [
{
"created": "Wed, 5 Dec 2007 23:04:04 GMT",
"version": "v1"
}
] | 2007-12-11 | [
[
"Miller",
"Kai J.",
""
],
[
"Sorensen",
"Larry B.",
""
],
[
"Ojemann",
"Jeffrey G.",
""
],
[
"Nijs",
"Marcel den",
""
]
] | We report the results of our search for power-law electrical signals in the human brain, using subdural electrocorticographic recordings from the surface of the cortex. The power spectral density (PSD) of these signals has the power-law form $ P(f)\sim f^{-\chi} $ from 80 to 500 Hz. This scaling index $\chi = 4.0\pm 0.... |
2010.01260 | Hong-Li Zeng | Hong-Li Zeng, Vito Dichio, Edwin Rodr\'iguez Horta, Kaisa Thorell, and
Erik Aurell | Global analysis of more than 50,000 SARS-Cov-2 genomes reveals epistasis
between 8 viral genes | 22 pages, 11 pages | null | 10.1073/pnas.2012331117 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genome-wide epistasis analysis is a powerful tool to infer gene interactions,
which can guide drug and vaccine development and lead to a deeper understanding
of microbial pathogenesis. We have considered all complete SARS-CoV-2 genomes
deposited in the GISAID repository until \textbf{four} different cut-off dates,
an... | [
{
"created": "Sat, 3 Oct 2020 02:19:29 GMT",
"version": "v1"
}
] | 2022-05-18 | [
[
"Zeng",
"Hong-Li",
""
],
[
"Dichio",
"Vito",
""
],
[
"Horta",
"Edwin Rodríguez",
""
],
[
"Thorell",
"Kaisa",
""
],
[
"Aurell",
"Erik",
""
]
] | Genome-wide epistasis analysis is a powerful tool to infer gene interactions, which can guide drug and vaccine development and lead to a deeper understanding of microbial pathogenesis. We have considered all complete SARS-CoV-2 genomes deposited in the GISAID repository until \textbf{four} different cut-off dates, and ... |
2209.06948 | Thor Andreassen | Thor E. Andreassen, Donald R. Hume, Landon D. Hamilton, Sean E.
Higinbotham, Kevin B. Shelburne | Automated 2D and 3D Finite Element Overclosure Adjustment and Mesh
Morphing Using Generalized Regression Neural Networks | Updates were made to the original article to include a new algorithm
capable of rapid morphing of generated meshes, and the validation included.
New Paper total is 40 Pages, 10 Figures, 4 Tables | Automated 2D and 3D finite element overclosure adjustment and mesh
morphing using generalized regression neural networks, Medical Engineering &
Physics, Volume 126, 2024, 104136, ISSN 1350-4533 | 10.1016/j.medengphy.2024.104136 | null | q-bio.QM cs.NA math.NA | http://creativecommons.org/licenses/by-sa/4.0/ | Computer representations of three-dimensional (3D) geometries are crucial for
simulating systems and processes in engineering and science. In medicine, and
more specifically, biomechanics and orthopaedics, obtaining and using 3D
geometries is critical to many workflows. However, while many tools exist to
obtain 3D ge... | [
{
"created": "Wed, 14 Sep 2022 21:48:55 GMT",
"version": "v1"
},
{
"created": "Wed, 19 Apr 2023 17:35:18 GMT",
"version": "v2"
},
{
"created": "Mon, 9 Oct 2023 20:07:38 GMT",
"version": "v3"
}
] | 2024-04-05 | [
[
"Andreassen",
"Thor E.",
""
],
[
"Hume",
"Donald R.",
""
],
[
"Hamilton",
"Landon D.",
""
],
[
"Higinbotham",
"Sean E.",
""
],
[
"Shelburne",
"Kevin B.",
""
]
] | Computer representations of three-dimensional (3D) geometries are crucial for simulating systems and processes in engineering and science. In medicine, and more specifically, biomechanics and orthopaedics, obtaining and using 3D geometries is critical to many workflows. However, while many tools exist to obtain 3D geom... |
2110.11914 | Meghdad Saeedian | Meghdad Saeedian, Emanuele Pigani, Amos Maritan, Samir Suweis, and
Sandro Azaele | Effect of delay on the emergent stability patterns in Generalized
Lotka-Volterra ecological dynamics | null | null | null | null | q-bio.PE physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Understanding the conditions of feasibility and stability in ecological
systems is a major challenge in theoretical ecology. The seminal work of May in
1972 and recent developments based on the theory of random matrices have shown
the existence of emergent universal patterns of both stability and feasibility
in ecolo... | [
{
"created": "Fri, 22 Oct 2021 16:56:53 GMT",
"version": "v1"
}
] | 2021-10-25 | [
[
"Saeedian",
"Meghdad",
""
],
[
"Pigani",
"Emanuele",
""
],
[
"Maritan",
"Amos",
""
],
[
"Suweis",
"Samir",
""
],
[
"Azaele",
"Sandro",
""
]
] | Understanding the conditions of feasibility and stability in ecological systems is a major challenge in theoretical ecology. The seminal work of May in 1972 and recent developments based on the theory of random matrices have shown the existence of emergent universal patterns of both stability and feasibility in ecologi... |
1911.09268 | Michel Pleimling | Ryan Baker and Michel Pleimling | The effect of habitats and fitness on species coexistence in systems
with cyclic dominance | 21 pages, 9 figures, accepted for publication in Journal of
Theoretical Biology | J. Theor. Biol. 486, 110084 (2020) | 10.1016/j.jtbi.2019.110084 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cyclic dominance between species may yield spiral waves that are known to
provide a mechanism enabling persistent species coexistence. This observation
holds true even in presence of spatial heterogeneity in the form of quenched
disorder. In this work we study the effects on spatio-temporal patterns and
species coexi... | [
{
"created": "Thu, 21 Nov 2019 03:28:05 GMT",
"version": "v1"
}
] | 2020-02-05 | [
[
"Baker",
"Ryan",
""
],
[
"Pleimling",
"Michel",
""
]
] | Cyclic dominance between species may yield spiral waves that are known to provide a mechanism enabling persistent species coexistence. This observation holds true even in presence of spatial heterogeneity in the form of quenched disorder. In this work we study the effects on spatio-temporal patterns and species coexist... |
1206.5557 | Sepehr Ehsani | Sepehr Ehsani | Simple variation of the logistic map as a model to invoke questions on
cellular protein trafficking | 11 pages, 6 figures, 1 table | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many open problems in biology, as in the physical sciences, display nonlinear
and 'chaotic' dynamics, which, to the extent possible, cannot be reasonably
understood. Moreover, mathematical models which aim to predict/estimate unknown
aspects of a biological system cannot provide more information about the set of
biol... | [
{
"created": "Mon, 25 Jun 2012 01:35:36 GMT",
"version": "v1"
}
] | 2012-06-26 | [
[
"Ehsani",
"Sepehr",
""
]
] | Many open problems in biology, as in the physical sciences, display nonlinear and 'chaotic' dynamics, which, to the extent possible, cannot be reasonably understood. Moreover, mathematical models which aim to predict/estimate unknown aspects of a biological system cannot provide more information about the set of biolog... |
1802.01375 | Yasser A. Ahmed | Yasser A. Ahmed and Mohammed Abdelsabour-Khalaf | Adipochondrocytes in rabbit auricular cartilage | Adipochondrocytes in rabbit auricular cartilage | null | null | null | q-bio.TO | http://creativecommons.org/publicdomain/zero/1.0/ | Chondrocytes are described as one cell population in different cartilage
types. The auricular cartilage in mouse and rat contains unique chondrocytes
similar in morphology to white adipocytes and known as lipochondrocytes.
Lipochondrocytes were not mentioned in other species. The current study aimed
to explore the ex... | [
{
"created": "Mon, 5 Feb 2018 13:11:02 GMT",
"version": "v1"
}
] | 2018-02-06 | [
[
"Ahmed",
"Yasser A.",
""
],
[
"Abdelsabour-Khalaf",
"Mohammed",
""
]
] | Chondrocytes are described as one cell population in different cartilage types. The auricular cartilage in mouse and rat contains unique chondrocytes similar in morphology to white adipocytes and known as lipochondrocytes. Lipochondrocytes were not mentioned in other species. The current study aimed to explore the exis... |
1710.02600 | Robert Endres | Robert G. Endres | Entropy production selects nonequilibrium states in multistable systems | 15 pages, 4 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Far-from-equilibrium thermodynamics underpins the emergence of life, but how
has been a long-outstanding puzzle. Best candidate theories based on the
maximum entropy production principle could not be unequivocally proven, in part
due to complicated physics, unintuitive stochastic thermodynamics, and the
existence of ... | [
{
"created": "Fri, 6 Oct 2017 22:15:08 GMT",
"version": "v1"
}
] | 2017-10-10 | [
[
"Endres",
"Robert G.",
""
]
] | Far-from-equilibrium thermodynamics underpins the emergence of life, but how has been a long-outstanding puzzle. Best candidate theories based on the maximum entropy production principle could not be unequivocally proven, in part due to complicated physics, unintuitive stochastic thermodynamics, and the existence of al... |
2302.00104 | Xizhe Zhang | Xinru Wei, Shuai Dong, Zhao Su, Lili Tang, Pengfei Zhao, Chunyu Pan,
Fei Wang, Yanqing Tang, Weixiong Zhang, Xizhe Zhang | NetMoST: A network-based machine learning approach for subtyping
schizophrenia using polygenic SNP allele biomarkers | 21 pages,4 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Subtyping neuropsychiatric disorders like schizophrenia is essential for
improving the diagnosis and treatment of complex diseases. Subtyping
schizophrenia is challenging because it is polygenic and genetically
heterogeneous, rendering the standard symptom-based diagnosis often unreliable
and unrepeatable. We develop... | [
{
"created": "Tue, 31 Jan 2023 21:11:27 GMT",
"version": "v1"
},
{
"created": "Fri, 10 Mar 2023 10:08:07 GMT",
"version": "v2"
}
] | 2023-03-13 | [
[
"Wei",
"Xinru",
""
],
[
"Dong",
"Shuai",
""
],
[
"Su",
"Zhao",
""
],
[
"Tang",
"Lili",
""
],
[
"Zhao",
"Pengfei",
""
],
[
"Pan",
"Chunyu",
""
],
[
"Wang",
"Fei",
""
],
[
"Tang",
"Yanqing",
"... | Subtyping neuropsychiatric disorders like schizophrenia is essential for improving the diagnosis and treatment of complex diseases. Subtyping schizophrenia is challenging because it is polygenic and genetically heterogeneous, rendering the standard symptom-based diagnosis often unreliable and unrepeatable. We developed... |
2005.02567 | Friedrich Sommer | Christopher Warner, Friedrich T. Sommer | A Model for Image Segmentation in Retina | 39 pages, 20 figures | null | null | null | q-bio.NC cs.NE eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While traditional feed-forward filter models can reproduce the rate responses
of retinal ganglion neurons to simple stimuli, they cannot explain why
synchrony between spikes is much higher than expected by Poisson firing [6],
and can be sometimes rhythmic [25, 16]. Here we investigate the hypothesis that
synchrony in... | [
{
"created": "Wed, 6 May 2020 02:58:18 GMT",
"version": "v1"
}
] | 2020-05-07 | [
[
"Warner",
"Christopher",
""
],
[
"Sommer",
"Friedrich T.",
""
]
] | While traditional feed-forward filter models can reproduce the rate responses of retinal ganglion neurons to simple stimuli, they cannot explain why synchrony between spikes is much higher than expected by Poisson firing [6], and can be sometimes rhythmic [25, 16]. Here we investigate the hypothesis that synchrony in p... |
0907.4765 | Frederick W. Cummings | F. W. Cummings | Phyllotaxis, a model | 11 pages, two figures, one table | null | null | null | q-bio.TO q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A model of the regular arrangement of leaves on a plant stem (phyllotactic
patterns) is proposed, based on a new plant pattern algorithm. Tripartite
patterning is proposed to occur by the interaction of two signaling pathways.
Each pathway produces stimulated extracellular emission of like ligand upon
activation of i... | [
{
"created": "Mon, 27 Jul 2009 20:40:00 GMT",
"version": "v1"
}
] | 2009-07-29 | [
[
"Cummings",
"F. W.",
""
]
] | A model of the regular arrangement of leaves on a plant stem (phyllotactic patterns) is proposed, based on a new plant pattern algorithm. Tripartite patterning is proposed to occur by the interaction of two signaling pathways. Each pathway produces stimulated extracellular emission of like ligand upon activation of its... |
1101.5495 | Sophio Bakhtadze | Sophio Bakhtadze, Marine Janelidze, Nana Khachapuridze | Impact of EEG biofeedback on event-related potentials (ERPs) in
attention-deficit hyperactivity (ADHD) children | 31 pages, 4 tables, 10 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Impact of EEG biofeedback on event-related potentials (ERPs) in
attention-deficit hyperactivity (ADHD) children. Introduction: ADHD is one of
the most widely spread condition of school aged children affecting 5% of
children of this age.The core clinical signs of ADHD are inattention,
restlessness and impulsivity. Acc... | [
{
"created": "Fri, 28 Jan 2011 10:03:39 GMT",
"version": "v1"
}
] | 2011-01-31 | [
[
"Bakhtadze",
"Sophio",
""
],
[
"Janelidze",
"Marine",
""
],
[
"Khachapuridze",
"Nana",
""
]
] | Impact of EEG biofeedback on event-related potentials (ERPs) in attention-deficit hyperactivity (ADHD) children. Introduction: ADHD is one of the most widely spread condition of school aged children affecting 5% of children of this age.The core clinical signs of ADHD are inattention, restlessness and impulsivity. Accor... |
1607.04158 | Jose A. Cuesta | Jos\'e A. Cuesta, Gustav W. Delius, and Richard Law | Sheldon Spectrum and the Plankton Paradox: Two Sides of the Same Coin. A
trait-based plankton size-spectrum model | 26 pages, 1 figure, needs Springer class file svjour3.cls | J. Math. Biol. (2017) 1--30 | 10.1007/s00285-017-1132-7 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Sheldon spectrum describes a remarkable regularity in aquatic ecosystems:
the biomass density as a function of logarithmic body mass is approximately
constant over many orders of magnitude. While size-spectrum models have
explained this phenomenon for assemblages of multicellular organisms, this
paper introduces ... | [
{
"created": "Thu, 14 Jul 2016 15:00:04 GMT",
"version": "v1"
}
] | 2017-05-26 | [
[
"Cuesta",
"José A.",
""
],
[
"Delius",
"Gustav W.",
""
],
[
"Law",
"Richard",
""
]
] | The Sheldon spectrum describes a remarkable regularity in aquatic ecosystems: the biomass density as a function of logarithmic body mass is approximately constant over many orders of magnitude. While size-spectrum models have explained this phenomenon for assemblages of multicellular organisms, this paper introduces a ... |
1610.09045 | Gajendra Katuwal | Gajendra Jung Katuwal, Robert Chen | Machine Learning Model Interpretability for Precision Medicine | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Interpretability of machine learning models is critical for data-driven
precision medicine efforts. However, highly predictive models are generally
complex and are difficult to interpret. Here using Model-Agnostic Explanations
algorithm, we show that complex models such as random forest can be made
interpretable. Usi... | [
{
"created": "Fri, 28 Oct 2016 01:08:56 GMT",
"version": "v1"
}
] | 2016-10-31 | [
[
"Katuwal",
"Gajendra Jung",
""
],
[
"Chen",
"Robert",
""
]
] | Interpretability of machine learning models is critical for data-driven precision medicine efforts. However, highly predictive models are generally complex and are difficult to interpret. Here using Model-Agnostic Explanations algorithm, we show that complex models such as random forest can be made interpretable. Using... |
1409.2210 | Liane Gabora | Liane Gabora | Why Blind-Variation Selective-Retention is an Inappropriate Explanatory
Framework for Creativity | 6 pages | Physics of Life Reviews, 7(2), 182-183, 2010 | 10.1016/j.plrev.2010.04.008 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Simonton is attempting to salvage the Blind Variation Selective Retention
theory of creativity (often referred to as the Darwinian theory of creativity)
by dissociating it from Darwinism. This is a necessary move for complex reasons
outlined in detail elsewhere. However, whether or not one calls BVSR a
Darwinian theo... | [
{
"created": "Mon, 8 Sep 2014 05:39:08 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Jul 2019 21:41:09 GMT",
"version": "v2"
}
] | 2019-07-17 | [
[
"Gabora",
"Liane",
""
]
] | Simonton is attempting to salvage the Blind Variation Selective Retention theory of creativity (often referred to as the Darwinian theory of creativity) by dissociating it from Darwinism. This is a necessary move for complex reasons outlined in detail elsewhere. However, whether or not one calls BVSR a Darwinian theory... |
2011.09703 | Regis Faure | Olga Gherbovet (TBI), Fernando Ferreira (TBI), Apolline Cl\'ement
(TBI), M\'elanie Ragon (TBI), Julien Durand (TBI), Sophie Bozonnet (TBI),
Michael O'Donohue (TBI), R\'egis Faur\'e (TBI) | Regioselective chemo-enzymatic syntheses of ferulate conjugates as
chromogenic substrates for feruloyl esterases | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Generally, carbohydrate-active enzymes are studied using chromogenic
substrates that provide quick and easy color-based detection of enzyme-mediated
hydrolysis. In the case of feruloyl esterases, commercially available
chromogenic ferulate derivatives are both costly and limited in terms of their
experimental applica... | [
{
"created": "Thu, 19 Nov 2020 08:13:12 GMT",
"version": "v1"
}
] | 2020-11-20 | [
[
"Gherbovet",
"Olga",
"",
"TBI"
],
[
"Ferreira",
"Fernando",
"",
"TBI"
],
[
"Clément",
"Apolline",
"",
"TBI"
],
[
"Ragon",
"Mélanie",
"",
"TBI"
],
[
"Durand",
"Julien",
"",
"TBI"
],
[
"Bozonnet",
"Sophie",
... | Generally, carbohydrate-active enzymes are studied using chromogenic substrates that provide quick and easy color-based detection of enzyme-mediated hydrolysis. In the case of feruloyl esterases, commercially available chromogenic ferulate derivatives are both costly and limited in terms of their experimental applicati... |
1911.11466 | Nimrod Sherf | Nimrod Sherf, Maoz Shamir | Multiplexing rhythmic information by spike timing dependent plasticity | 14 pages, 7 figures | null | 10.1371/journal.pcbi.1008000 | null | q-bio.NC nlin.AO physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Rhythmic activity has been associated with a wide range of cognitive
processes. Previous studies have shown that spike-timing-dependent plasticity
can facilitate the transfer of rhythmic activity downstream the information
processing pathway. However, STDP has also been known to generate strong
winner-take-all like c... | [
{
"created": "Tue, 26 Nov 2019 11:37:52 GMT",
"version": "v1"
}
] | 2020-09-09 | [
[
"Sherf",
"Nimrod",
""
],
[
"Shamir",
"Maoz",
""
]
] | Rhythmic activity has been associated with a wide range of cognitive processes. Previous studies have shown that spike-timing-dependent plasticity can facilitate the transfer of rhythmic activity downstream the information processing pathway. However, STDP has also been known to generate strong winner-take-all like com... |
1808.00864 | Teresa Pegan | Teresa M. Pegan, David W. Winkler, Mark F. Haussmann and Maren N.
Vitousek | Brief increases in corticosterone affect morphology, stress responses,
and telomere length, but not post-fledging movements, in a wild songbird | 35 pages, 4 figures, 1 appendix | null | 10.1086/702827 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Organisms are frequently exposed to challenges during development, such as
poor weather and food shortage. Such challenges can initiate the hormonal
stress response, which involves secretion of glucocorticoids. Although the
hormonal stress response helps organisms deal with challenges, long-term
exposure to high leve... | [
{
"created": "Tue, 31 Jul 2018 22:56:11 GMT",
"version": "v1"
}
] | 2019-03-08 | [
[
"Pegan",
"Teresa M.",
""
],
[
"Winkler",
"David W.",
""
],
[
"Haussmann",
"Mark F.",
""
],
[
"Vitousek",
"Maren N.",
""
]
] | Organisms are frequently exposed to challenges during development, such as poor weather and food shortage. Such challenges can initiate the hormonal stress response, which involves secretion of glucocorticoids. Although the hormonal stress response helps organisms deal with challenges, long-term exposure to high levels... |
2311.10410 | Lisa Roux | Lisa Roux (NYU Langone Medical Center), Eran Stark (NYU Langone
Medical Center), Lucas Sjulson (NYU Langone Medical Center), Gy\"orgy
Buzs\'aki (NYU Langone Medical Center) | In vivo optogenetic identification and manipulation of GABAergic
interneuron subtypes | null | Current Opinion in Neurobiology, 2014, 26, pp.88 - 95 | 10.1016/j.conb.2013.12.013 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Identification and manipulation of different GABAergic interneuron classes in
the behaving animal are important to understand their role in circuit dynamics
and behavior. The combination of optogenetics and large-scale neuronal
recordings allows specific interneuron populations to be identified and
perturbed for circ... | [
{
"created": "Fri, 17 Nov 2023 09:27:19 GMT",
"version": "v1"
}
] | 2023-11-20 | [
[
"Roux",
"Lisa",
"",
"NYU Langone Medical Center"
],
[
"Stark",
"Eran",
"",
"NYU Langone\n Medical Center"
],
[
"Sjulson",
"Lucas",
"",
"NYU Langone Medical Center"
],
[
"Buzsáki",
"György",
"",
"NYU Langone Medical Center"
]
] | Identification and manipulation of different GABAergic interneuron classes in the behaving animal are important to understand their role in circuit dynamics and behavior. The combination of optogenetics and large-scale neuronal recordings allows specific interneuron populations to be identified and perturbed for circui... |
q-bio/0507030 | Luc Frappat | Luc Frappat, Antonino Sciarrino | Conspiracy in bacterial genomes | revised version: introduction and conclusion enhanced, references
added, figures added, some tables removed | null | 10.1016/j.physa.2006.02.008 | LAPTH-1108/05 and DSF-23/05 | q-bio.GN | null | The rank ordered distribution of the codon usage frequencies for 123
bacteriae is best fitted by a three parameters function that is the sum of a
constant, an exponential and a linear term in the rank n. The parameters depend
(two parabolically) from the total GC content. The rank ordered distribution of
the amino ac... | [
{
"created": "Wed, 20 Jul 2005 11:46:08 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Feb 2006 18:09:15 GMT",
"version": "v2"
}
] | 2009-11-11 | [
[
"Frappat",
"Luc",
""
],
[
"Sciarrino",
"Antonino",
""
]
] | The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two parabolically) from the total GC content. The rank ordered distribution of the amino acid... |
1702.08747 | Michael Adamer | Michael F Adamer, Thomas E Woolley, and Heather A Harrington | Graph-Facilitated Resonant Mode Counting in Stochastic Interaction
Networks | 5 pages, 4 figures | null | null | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Oscillations in a stochastic dynamical system, whose deterministic
counterpart has a stable steady state, are a widely reported phenomenon.
Traditional methods of finding parameter regimes for stochastically-driven
resonances are, however, cumbersome for any but the smallest networks. In this
letter we show by exampl... | [
{
"created": "Tue, 28 Feb 2017 11:24:14 GMT",
"version": "v1"
}
] | 2017-03-01 | [
[
"Adamer",
"Michael F",
""
],
[
"Woolley",
"Thomas E",
""
],
[
"Harrington",
"Heather A",
""
]
] | Oscillations in a stochastic dynamical system, whose deterministic counterpart has a stable steady state, are a widely reported phenomenon. Traditional methods of finding parameter regimes for stochastically-driven resonances are, however, cumbersome for any but the smallest networks. In this letter we show by example ... |
0807.4272 | Tijana Ivancevic | Tijana T. Ivancevic, Murk J. Bottema and Lakhmi C. Jain | A Theoretical Model of Chaotic Attractor in Tumor Growth and Metastasis | 17 pages, 7 figures, Latex | null | null | null | q-bio.CB q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper proposes a novel chaotic reaction-diffusion model of cellular
tumor growth and metastasis. The model is based on the multiscale diffusion
cancer-invasion model (MDCM) and formulated by introducing strong nonlinear
coupling into the MDCM. The new model exhibits temporal chaotic behavior (which
resembles the... | [
{
"created": "Sun, 27 Jul 2008 04:54:40 GMT",
"version": "v1"
}
] | 2008-07-29 | [
[
"Ivancevic",
"Tijana T.",
""
],
[
"Bottema",
"Murk J.",
""
],
[
"Jain",
"Lakhmi C.",
""
]
] | This paper proposes a novel chaotic reaction-diffusion model of cellular tumor growth and metastasis. The model is based on the multiscale diffusion cancer-invasion model (MDCM) and formulated by introducing strong nonlinear coupling into the MDCM. The new model exhibits temporal chaotic behavior (which resembles the c... |
2307.09877 | Alain Nogaret | Paul G Morris, Joseph D. Taylor, Julian F. R. Paton and Alain Nogaret | Single shot diagnosis of ion channel dysfunction from assimilation of
cell membrane dynamics | 42 pages, 6 figures, 3 tables | null | null | null | q-bio.QM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Many neurological diseases originate in the dysfunction of cellular ion
channels. Their diagnosis presents a challenge especially when alterations in
the complement of ion channels are a priori unknown. Current approaches based
on voltage clamps lack the throughput necessary to identify the mutations
causing changes ... | [
{
"created": "Wed, 19 Jul 2023 10:15:07 GMT",
"version": "v1"
}
] | 2023-07-20 | [
[
"Morris",
"Paul G",
""
],
[
"Taylor",
"Joseph D.",
""
],
[
"Paton",
"Julian F. R.",
""
],
[
"Nogaret",
"Alain",
""
]
] | Many neurological diseases originate in the dysfunction of cellular ion channels. Their diagnosis presents a challenge especially when alterations in the complement of ion channels are a priori unknown. Current approaches based on voltage clamps lack the throughput necessary to identify the mutations causing changes in... |
q-bio/0403005 | Ping Ao | X.-M. Zhu, L. Yin, L. Hood, and P. Ao | Calculating Biological Behaviors of Epigenetic States in Phage lambda
Life Cycle | 16 pages, 3 figures, 1 table | Functional and Integrative Genomics (2004) | 10.1007/s10142-003-0095-5 | null | q-bio.MN q-bio.QM | null | Gene regulatory network of lambda phage is one the best studied model systems
in molecular biology. More 50 years of experimental study has provided a
tremendous amount of data at all levels: physics, chemistry, DNA, protein, and
function. However, its stability and robustness for both wild type and mutants
has been ... | [
{
"created": "Wed, 3 Mar 2004 17:56:01 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Zhu",
"X. -M.",
""
],
[
"Yin",
"L.",
""
],
[
"Hood",
"L.",
""
],
[
"Ao",
"P.",
""
]
] | Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function. However, its stability and robustness for both wild type and mutants has been a ... |
1302.1909 | Alexandre Ferreira Ramos | Alexandre F. Ramos and Jose Eduardo M. Hornos and John Reinitz | Noise reduction by coupling of stochastic processes and canalization in
biology | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Randomness is an unavoidable feature of the intracellular environment due to
chemical reactants being present in low copy number. That phenomenon, predicted
by Delbr\"uck long ago \cite{delbruck40}, has been detected in both prokaryotic
\cite{elowitz02,cai06} and eukaryotic \cite{blake03} cells after the
development ... | [
{
"created": "Thu, 7 Feb 2013 23:32:19 GMT",
"version": "v1"
}
] | 2013-02-11 | [
[
"Ramos",
"Alexandre F.",
""
],
[
"Hornos",
"Jose Eduardo M.",
""
],
[
"Reinitz",
"John",
""
]
] | Randomness is an unavoidable feature of the intracellular environment due to chemical reactants being present in low copy number. That phenomenon, predicted by Delbr\"uck long ago \cite{delbruck40}, has been detected in both prokaryotic \cite{elowitz02,cai06} and eukaryotic \cite{blake03} cells after the development of... |
2405.18456 | Arash Shaban-Nejad | Fekede Asefa Kumsa, Jay H. Fowke, Soheil Hashtarkhani, Brianna M.
White, Martha J. Shrubsole, Arash Shaban-Nejad | The association between neighborhood obesogenic factors and prostate
cancer risk and mortality: the Southern Community Cohort Study | 18 Pages, 1 Figure, 8 Tables | Front Oncol Frontiers in Oncology, 2024 Apr 9:14:1343070 | 10.3389/fonc.2024.1343070 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Prostate cancer is one of the leading causes of cancer-related mortality
among men in the U.S. We examined the role of neighborhood obesogenic
attributes on prostate cancer risk and mortality in the Southern Community
Cohort Study (SCCS). From 34,166 SCCS male participants, 28,356 were included
in the analysis. We as... | [
{
"created": "Tue, 28 May 2024 15:53:19 GMT",
"version": "v1"
}
] | 2024-05-30 | [
[
"Kumsa",
"Fekede Asefa",
""
],
[
"Fowke",
"Jay H.",
""
],
[
"Hashtarkhani",
"Soheil",
""
],
[
"White",
"Brianna M.",
""
],
[
"Shrubsole",
"Martha J.",
""
],
[
"Shaban-Nejad",
"Arash",
""
]
] | Prostate cancer is one of the leading causes of cancer-related mortality among men in the U.S. We examined the role of neighborhood obesogenic attributes on prostate cancer risk and mortality in the Southern Community Cohort Study (SCCS). From 34,166 SCCS male participants, 28,356 were included in the analysis. We asse... |
1910.03491 | Adriano Siqueira Francisco | Adriano Francisco Siqueira, Morun Bernardino Neto, Ana Lucia Gabas
Ferreira, Luciana Alves de Medeiros, Mario da Silva Garrote-Filho, Ubirajara
Coutinho Filho, Nilson Penha-Silva | Stochastic modeling of hyposmotic lysis and characterization of
different osmotic stability subgroups of human erythrocytes | null | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This study proposes a novel stochastic model for the study of hyposmotic
hemolysis. This model is capable of reproducing both the kinetics in the
transient phase and the lysis equilibrium in the stationary phase, as well as
the variability of the experimental measurements. The stationary distribution
of this model ca... | [
{
"created": "Tue, 8 Oct 2019 15:57:40 GMT",
"version": "v1"
}
] | 2019-10-09 | [
[
"Siqueira",
"Adriano Francisco",
""
],
[
"Neto",
"Morun Bernardino",
""
],
[
"Ferreira",
"Ana Lucia Gabas",
""
],
[
"de Medeiros",
"Luciana Alves",
""
],
[
"Garrote-Filho",
"Mario da Silva",
""
],
[
"Filho",
"Ubirajara Coutinh... | This study proposes a novel stochastic model for the study of hyposmotic hemolysis. This model is capable of reproducing both the kinetics in the transient phase and the lysis equilibrium in the stationary phase, as well as the variability of the experimental measurements. The stationary distribution of this model can ... |
1406.3075 | Istvan Kiss Z | David Juher, Istvan Z. Kiss, Joan Saldana | Analysis of an epidemic model with awareness decay on regular random
networks | null | Journal of Theoretical Biology, 365 (2015): 457-468 | 10.1016/j.jtbi.2014.10.013 | null | q-bio.QM math.DS nlin.AO q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The existence of a die-out threshold (different from the classic
disease-invasion one) defining a region of slow extinction of an epidemic has
been proved elsewhere for susceptible-aware-infectious-susceptible models
without awareness decay, through bifurcation analysis. By means of an
equivalent mean-field model def... | [
{
"created": "Wed, 11 Jun 2014 22:01:20 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Dec 2014 13:47:20 GMT",
"version": "v2"
}
] | 2016-10-19 | [
[
"Juher",
"David",
""
],
[
"Kiss",
"Istvan Z.",
""
],
[
"Saldana",
"Joan",
""
]
] | The existence of a die-out threshold (different from the classic disease-invasion one) defining a region of slow extinction of an epidemic has been proved elsewhere for susceptible-aware-infectious-susceptible models without awareness decay, through bifurcation analysis. By means of an equivalent mean-field model defin... |
1311.5544 | Salvatore De Martino | G. Buccheri, E. De Lauro, S. De Martino, M. Falanga | Experimental investigation of the trachea oscillation and its role in
the pitch production | null | null | null | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Several experiments have been performed to investigate the mechanical
vibrations associated with trachea and larynx when Italian vowels are emitted.
The mechanical measurements have been made by using two laser Doppler
vibrometers (based on the well-known not-invasive optical measurement
technique) coupled with the a... | [
{
"created": "Thu, 31 Oct 2013 13:47:15 GMT",
"version": "v1"
}
] | 2013-11-22 | [
[
"Buccheri",
"G.",
""
],
[
"De Lauro",
"E.",
""
],
[
"De Martino",
"S.",
""
],
[
"Falanga",
"M.",
""
]
] | Several experiments have been performed to investigate the mechanical vibrations associated with trachea and larynx when Italian vowels are emitted. The mechanical measurements have been made by using two laser Doppler vibrometers (based on the well-known not-invasive optical measurement technique) coupled with the aco... |
2005.09805 | Cintia Menendez | Cintia A. Menendez, Fabian Bylehn, Gustavo R. Perez-Lemus, Walter
Alvarado and Juan J. de Pablo | Molecular Characterization of Ebselen Binding Activity to SARS-CoV-2
Main Protease | 10 pages, 5 figures | null | null | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Coronavirus Disease (COVID-19) pandemic caused by the SARS-coronavirus 2
(SARS-CoV-2) urgently calls for the design of drugs directed against this new
virus. Given its essential role in proteolytic processing, the main protease
Mpro has been identified as an attractive candidate for drugs against
SARS-CoV-2 and s... | [
{
"created": "Wed, 20 May 2020 00:52:57 GMT",
"version": "v1"
}
] | 2020-05-21 | [
[
"Menendez",
"Cintia A.",
""
],
[
"Bylehn",
"Fabian",
""
],
[
"Perez-Lemus",
"Gustavo R.",
""
],
[
"Alvarado",
"Walter",
""
],
[
"de Pablo",
"Juan J.",
""
]
] | The Coronavirus Disease (COVID-19) pandemic caused by the SARS-coronavirus 2 (SARS-CoV-2) urgently calls for the design of drugs directed against this new virus. Given its essential role in proteolytic processing, the main protease Mpro has been identified as an attractive candidate for drugs against SARS-CoV-2 and sim... |
1503.07794 | Bhavin Khatri | Bhavin S. Khatri and Richard A. Goldstein | A simple biophysical model predicts more rapid accumulation of hybrid
incompatibilities in small populations | 13 pages, 6 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/3.0/ | Speciation is fundamental to the huge diversity of life on Earth. Evidence
suggests reproductive isolation arises most commonly in allopatry with a higher
speciation rate in small populations. Current theory does not address this
dependence in the important weak mutation regime. Here, we examine a
biophysical model o... | [
{
"created": "Thu, 26 Mar 2015 17:16:54 GMT",
"version": "v1"
}
] | 2015-03-27 | [
[
"Khatri",
"Bhavin S.",
""
],
[
"Goldstein",
"Richard A.",
""
]
] | Speciation is fundamental to the huge diversity of life on Earth. Evidence suggests reproductive isolation arises most commonly in allopatry with a higher speciation rate in small populations. Current theory does not address this dependence in the important weak mutation regime. Here, we examine a biophysical model of ... |
1805.10248 | Wentian Li | Wentian Li, Dimitrios Thanos, Astero Provata | Quantifying Local Randomness in Human DNA and RNA Sequences Using Erdos
Motifs | 4 figures | Journal of Theoretical Biology, 461:41-50 (2019) | 10.1016/j.jtbi.2018.09.031 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In 1932, Paul Erdos asked whether a random walk constructed from a binary
sequence can achieve the lowest possible deviation (lowest discrepancy), for
the sequence itself and for all its subsequences formed by homogeneous
arithmetic progressions. Although avoiding low discrepancy is impossible for
infinite sequences,... | [
{
"created": "Fri, 25 May 2018 16:59:50 GMT",
"version": "v1"
},
{
"created": "Sat, 29 Sep 2018 18:40:47 GMT",
"version": "v2"
}
] | 2018-10-31 | [
[
"Li",
"Wentian",
""
],
[
"Thanos",
"Dimitrios",
""
],
[
"Provata",
"Astero",
""
]
] | In 1932, Paul Erdos asked whether a random walk constructed from a binary sequence can achieve the lowest possible deviation (lowest discrepancy), for the sequence itself and for all its subsequences formed by homogeneous arithmetic progressions. Although avoiding low discrepancy is impossible for infinite sequences, a... |
1711.09536 | Shatrunjai Singh | Shatrunjai P. Singh and Swagata Karkare | Stress, Depression and Neuroplasticity | 6 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modifications of signaling pathways and synapses owing to changing behaviors,
environments, numerous neural modulation as well as brain-tissue injuries is
defined as neuroplasticity in developmental neurology. The central purpose of
the review is to gain a better understanding of the relation between stress,
depressi... | [
{
"created": "Mon, 27 Nov 2017 04:57:02 GMT",
"version": "v1"
}
] | 2017-11-28 | [
[
"Singh",
"Shatrunjai P.",
""
],
[
"Karkare",
"Swagata",
""
]
] | Modifications of signaling pathways and synapses owing to changing behaviors, environments, numerous neural modulation as well as brain-tissue injuries is defined as neuroplasticity in developmental neurology. The central purpose of the review is to gain a better understanding of the relation between stress, depression... |
1408.4221 | Deok-Sun Lee | Deok-Sun Lee | Evolution of regulatory networks towards adaptability and stability in a
changing environment | 11 pages, 6 Figures | Physical Review E 90, 052822 (2014) | 10.1103/PhysRevE.90.052822 | null | q-bio.MN physics.bio-ph q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Diverse biological networks exhibit universal features distinguished from
those of random networks, calling much attention to their origins and
implications. Here we propose a minimal evolution model of Boolean regulatory
networks, which evolve by selectively rewiring links towards enhancing
adaptability to a changin... | [
{
"created": "Tue, 19 Aug 2014 06:39:36 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Nov 2014 01:38:03 GMT",
"version": "v2"
}
] | 2014-11-26 | [
[
"Lee",
"Deok-Sun",
""
]
] | Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which evolve by selectively rewiring links towards enhancing adaptability to a changing ... |
2007.09025 | Alexandru Hening | Alexandru Hening and Dang H. Nguyen and Peter Chesson | A general theory of coexistence and extinction for stochastic ecological
communities | 65 pages, 3 figures | J. Math. Biol. 82, 56 (2021) | null | null | q-bio.PE math.DS math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze a general theory for coexistence and extinction of ecological
communities that are influenced by stochastic temporal environmental
fluctuations. The results apply to discrete time (stochastic difference
equations), continuous time (stochastic differential equations), compact and
non-compact state spaces an... | [
{
"created": "Fri, 17 Jul 2020 14:41:20 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Feb 2021 17:53:19 GMT",
"version": "v2"
}
] | 2021-05-19 | [
[
"Hening",
"Alexandru",
""
],
[
"Nguyen",
"Dang H.",
""
],
[
"Chesson",
"Peter",
""
]
] | We analyze a general theory for coexistence and extinction of ecological communities that are influenced by stochastic temporal environmental fluctuations. The results apply to discrete time (stochastic difference equations), continuous time (stochastic differential equations), compact and non-compact state spaces and ... |
1306.4021 | Simon Gravel | Simon Gravel, Fouad Zakharia, Andres Moreno-Estrada, Jake K Byrnes,
Marina Muzzio, Juan L. Rodriguez-Flores, Eimear E. Kenny, Christopher R.
Gignoux, Brian K. Maples, Wilfried Guiblet, Julie Dutil, Marc Via, Karla
Sandoval, Gabriel Bedoya, Taras K Oleksyk, Andres Ruiz-Linares, Esteban G
Burchard, Juan Carlos Ma... | Reconstructing Native American Migrations from Whole-genome and
Whole-exome Data | 30 pages, inludes supplement. v2 contains clarifications, extra
analyses, and a change in the language classification scheme used | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There is great scientific and popular interest in understanding the genetic
history of populations in the Americas. We wish to understand when different
regions of the continent were inhabited, where settlers came from, and how
current inhabitants relate genetically to earlier populations. Recent studies
unraveled pa... | [
{
"created": "Mon, 17 Jun 2013 21:15:39 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Nov 2013 23:00:19 GMT",
"version": "v2"
}
] | 2013-11-19 | [
[
"Gravel",
"Simon",
""
],
[
"Zakharia",
"Fouad",
""
],
[
"Moreno-Estrada",
"Andres",
""
],
[
"Byrnes",
"Jake K",
""
],
[
"Muzzio",
"Marina",
""
],
[
"Rodriguez-Flores",
"Juan L.",
""
],
[
"Kenny",
"Eimear E.",
... | There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled part... |
2209.13530 | Islem Rekik | Imen Jegham and Islem Rekik | Meta-RegGNN: Predicting Verbal and Full-Scale Intelligence Scores using
Graph Neural Networks and Meta-Learning | null | null | null | null | q-bio.NC cs.AI cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Decrypting intelligence from the human brain construct is vital in the
detection of particular neurological disorders. Recently, functional brain
connectomes have been used successfully to predict behavioral scores. However,
state-of-the-art methods, on one hand, neglect the topological properties of
the connectomes ... | [
{
"created": "Wed, 14 Sep 2022 07:19:03 GMT",
"version": "v1"
}
] | 2022-09-28 | [
[
"Jegham",
"Imen",
""
],
[
"Rekik",
"Islem",
""
]
] | Decrypting intelligence from the human brain construct is vital in the detection of particular neurological disorders. Recently, functional brain connectomes have been used successfully to predict behavioral scores. However, state-of-the-art methods, on one hand, neglect the topological properties of the connectomes an... |
1809.08214 | Anatoly Sorokin | Anatoly Sorokin, Oksana Sorokina and J. Douglas Armstrong | RKappa: Software for Analyzing Rule-Based Models | 33 pages, 13 figures, this manuscript was prepared for the Methods in
Molecular Biology series | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | RKappa is a framework for the development, simulation and analysis of
rule-base models within the mature statistically empowered R environment. It is
designed for model editing, parameter identification, simulation, sensitivity
analysis and visualisation. The framework is optimised for high-performance
computing plat... | [
{
"created": "Fri, 21 Sep 2018 17:15:53 GMT",
"version": "v1"
}
] | 2018-09-24 | [
[
"Sorokin",
"Anatoly",
""
],
[
"Sorokina",
"Oksana",
""
],
[
"Armstrong",
"J. Douglas",
""
]
] | RKappa is a framework for the development, simulation and analysis of rule-base models within the mature statistically empowered R environment. It is designed for model editing, parameter identification, simulation, sensitivity analysis and visualisation. The framework is optimised for high-performance computing platfo... |
2407.10019 | Trevor Reckell | Trevor Reckell, Beckett Sterner, Petar Jevti\'c, Reggie Davidrajuh | A Numerical Comparison of Petri Net and Ordinary Differential Equation
SIR Component Models | 27 pages, 11 figures, six equations, and associated code can be found
in GitHub repository
https://github.com/trevorreckell/Numerical-Comparison-of-PN-vs-ODE-for-SIR | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Petri nets are a promising modeling framework for epidemiology, including the
spread of disease across populations or within an individual. In particular,
the Susceptible-Infectious-Recovered (SIR) compartment model is foundational
for population epidemiological modeling and has been implemented in several
prior Petr... | [
{
"created": "Sat, 13 Jul 2024 22:31:15 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Jul 2024 15:16:26 GMT",
"version": "v2"
}
] | 2024-07-18 | [
[
"Reckell",
"Trevor",
""
],
[
"Sterner",
"Beckett",
""
],
[
"Jevtić",
"Petar",
""
],
[
"Davidrajuh",
"Reggie",
""
]
] | Petri nets are a promising modeling framework for epidemiology, including the spread of disease across populations or within an individual. In particular, the Susceptible-Infectious-Recovered (SIR) compartment model is foundational for population epidemiological modeling and has been implemented in several prior Petri ... |
q-bio/0611042 | Stefan Carstea | A.S.Carstea | Proteomic nonlinear waves in networks of transcriptional regulators | 4 pages, 5 figures | null | null | null | q-bio.GN | null | A chain of connected genes with activation-repression links is analysed. It
is shown that for various promoter activity functions (parametrised by Hill
coefficient) the equations describing the concentrations of transcription
factors, are differential-difference KdV-type with perturbations. In the case
of large Hill ... | [
{
"created": "Tue, 14 Nov 2006 10:03:39 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Carstea",
"A. S.",
""
]
] | A chain of connected genes with activation-repression links is analysed. It is shown that for various promoter activity functions (parametrised by Hill coefficient) the equations describing the concentrations of transcription factors, are differential-difference KdV-type with perturbations. In the case of large Hill co... |
2212.04953 | Meryem Banu Cavlak | Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina,
Jo\"el Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, Onur
Mutlu | TargetCall: Eliminating the Wasted Computation in Basecalling via
Pre-Basecalling Filtering | null | null | null | null | q-bio.GN cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Basecalling is an essential step in nanopore sequencing analysis where the
raw signals of nanopore sequencers are converted into nucleotide sequences,
i.e., reads. State-of-the-art basecallers employ complex deep learning models
to achieve high basecalling accuracy. This makes basecalling
computationally-inefficient ... | [
{
"created": "Fri, 9 Dec 2022 16:03:34 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Sep 2023 15:42:54 GMT",
"version": "v2"
}
] | 2023-09-15 | [
[
"Cavlak",
"Meryem Banu",
""
],
[
"Singh",
"Gagandeep",
""
],
[
"Alser",
"Mohammed",
""
],
[
"Firtina",
"Can",
""
],
[
"Lindegger",
"Joël",
""
],
[
"Sadrosadati",
"Mohammad",
""
],
[
"Ghiasi",
"Nika Mansouri",
... | Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art basecallers employ complex deep learning models to achieve high basecalling accuracy. This makes basecalling computationally-inefficient an... |
1311.6222 | Da Zhou Dr. | Da Zhou and Yue Wang and Bin Wu | A multi-phenotypic cancer model with cell plasticity | 29 pages,6 figures | null | 10.1016/j.jtbi.2014.04.039 | null | q-bio.CB q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The conventional cancer stem cell (CSC) theory indicates a hierarchy of CSCs
and non-stem cancer cells (NSCCs), that is, CSCs can differentiate into NSCCs
but not vice versa. However, an alternative paradigm of CSC theory with
reversible cell plasticity among cancer cells has received much attention very
recently. He... | [
{
"created": "Mon, 25 Nov 2013 07:57:36 GMT",
"version": "v1"
},
{
"created": "Fri, 9 May 2014 07:41:51 GMT",
"version": "v2"
}
] | 2014-05-29 | [
[
"Zhou",
"Da",
""
],
[
"Wang",
"Yue",
""
],
[
"Wu",
"Bin",
""
]
] | The conventional cancer stem cell (CSC) theory indicates a hierarchy of CSCs and non-stem cancer cells (NSCCs), that is, CSCs can differentiate into NSCCs but not vice versa. However, an alternative paradigm of CSC theory with reversible cell plasticity among cancer cells has received much attention very recently. Here... |
1003.4044 | Denis Tolkunov | George Locke, Denis Tolkunov, Zarmik Moqtaderi, Kevin Struhl, and
Alexandre V. Morozov | High-throughput sequencing reveals a simple model of nucleosome
energetics | 36 pages, 13 figures | PNAS vol. 107 no. 49 (2010), 20998-21003 | 10.1073/pnas.1003838107 | null | q-bio.GN q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We use nucleosome maps obtained by high-throughput sequencing to study
sequence specificity of intrinsic histone-DNA interactions. In contrast with
previous approaches, we employ an analogy between a classical one-dimensional
fluid of finite-size particles in an arbitrary external potential and arrays of
DNA-bound hi... | [
{
"created": "Mon, 22 Mar 2010 02:15:58 GMT",
"version": "v1"
}
] | 2015-05-18 | [
[
"Locke",
"George",
""
],
[
"Tolkunov",
"Denis",
""
],
[
"Moqtaderi",
"Zarmik",
""
],
[
"Struhl",
"Kevin",
""
],
[
"Morozov",
"Alexandre V.",
""
]
] | We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size particles in an arbitrary external potential and arrays of DNA-bound hist... |
0707.3465 | Claus O. Wilke | Eric Brunet, Igor M. Rouzine, Claus O. Wilke | The stochastic edge in adaptive evolution | 36 pages, 4 figures | null | null | null | q-bio.PE | null | In a recent article, Desai and Fisher (2007) proposed that the speed of
adaptation in an asexual population is determined by the dynamics of the
stochastic edge of the population, that is, by the emergence and subsequent
establishment of rare mutants that exceed the fitness of all sequences
currently present in the p... | [
{
"created": "Mon, 23 Jul 2007 23:31:29 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Dec 2007 23:22:06 GMT",
"version": "v2"
}
] | 2007-12-19 | [
[
"Brunet",
"Eric",
""
],
[
"Rouzine",
"Igor M.",
""
],
[
"Wilke",
"Claus O.",
""
]
] | In a recent article, Desai and Fisher (2007) proposed that the speed of adaptation in an asexual population is determined by the dynamics of the stochastic edge of the population, that is, by the emergence and subsequent establishment of rare mutants that exceed the fitness of all sequences currently present in the pop... |
q-bio/0311031 | Dmitri Volchenkov | D. Volchenkov, R. Lima | Homogeneous and Scalable Gene Expression Regulatory Networks with Random
Layouts of Switching Parameters | LaTeX, 30 pages, 20 pictures | null | null | null | q-bio.MN | null | We consider a model of large regulatory gene expression networks where the
thresholds activating the sigmoidal interactions between genes and the signs of
these interactions are shuffled randomly. Such an approach allows for a
qualitative understanding of network dynamics in a lack of empirical data
concerning the la... | [
{
"created": "Fri, 21 Nov 2003 18:08:07 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Volchenkov",
"D.",
""
],
[
"Lima",
"R.",
""
]
] | We consider a model of large regulatory gene expression networks where the thresholds activating the sigmoidal interactions between genes and the signs of these interactions are shuffled randomly. Such an approach allows for a qualitative understanding of network dynamics in a lack of empirical data concerning the larg... |
2004.01966 | Kei Tokita | Atsuki Nakai, Yoko Inui, Kei Tokita | Facultative predation can alter the ant-aphid population | 28 pages, 6 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although ant--aphid interactions are the most typical example of mutualism
between insect species, some studies suggest that ant attendance is not always
advantageous for the aphids because they may pay a physiological cost. In this
study, we propose a new mathematical model of an ant--aphid system considering
the co... | [
{
"created": "Sat, 4 Apr 2020 16:11:06 GMT",
"version": "v1"
}
] | 2020-04-07 | [
[
"Nakai",
"Atsuki",
""
],
[
"Inui",
"Yoko",
""
],
[
"Tokita",
"Kei",
""
]
] | Although ant--aphid interactions are the most typical example of mutualism between insect species, some studies suggest that ant attendance is not always advantageous for the aphids because they may pay a physiological cost. In this study, we propose a new mathematical model of an ant--aphid system considering the cost... |
2005.12376 | Sebasti\'an Contreras | Sebasti\'an Contreras, Juan Pablo Biron-Lattes, H. Andr\'es
Villavicencio, David Medina-Ortiz, Nyna Llanovarced-Kawles, \'Alvaro
Olivera-Nappa | Statistically-based methodology for revealing real contagion trends and
correcting delay-induced errors in the assessment of COVID-19 pandemic | null | Chaos Solitons Fractals 139 (2020) 110087 | 10.1016/j.chaos.2020.110087 | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | COVID-19 pandemic has reshaped our world in a timescale much shorter than
what we can understand. Particularities of SARS-CoV-2, such as its persistence
in surfaces and the lack of a curative treatment or vaccine against COVID-19,
have pushed authorities to apply restrictive policies to control its spreading.
As data... | [
{
"created": "Mon, 25 May 2020 20:15:37 GMT",
"version": "v1"
},
{
"created": "Wed, 27 May 2020 08:52:12 GMT",
"version": "v2"
},
{
"created": "Wed, 24 Jun 2020 19:13:17 GMT",
"version": "v3"
}
] | 2020-07-14 | [
[
"Contreras",
"Sebastián",
""
],
[
"Biron-Lattes",
"Juan Pablo",
""
],
[
"Villavicencio",
"H. Andrés",
""
],
[
"Medina-Ortiz",
"David",
""
],
[
"Llanovarced-Kawles",
"Nyna",
""
],
[
"Olivera-Nappa",
"Álvaro",
""
]
] | COVID-19 pandemic has reshaped our world in a timescale much shorter than what we can understand. Particularities of SARS-CoV-2, such as its persistence in surfaces and the lack of a curative treatment or vaccine against COVID-19, have pushed authorities to apply restrictive policies to control its spreading. As data d... |
2307.10308 | Benjamin Bolker | Darren Flynn-Primrose and Steven C. Walker and Michael Li and Benjamin
M. Bolker and David J. D. Earn and Jonathan Dushoff | Toward a comprehensive system for constructing compartmental epidemic
models | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-sa/4.0/ | Compartmental models are valuable tools for investigating infectious
diseases. Researchers building such models typically begin with a simple
structure where compartments correspond to individuals with different
epidemiological statuses, e.g., the classic SIR model which splits the
population into susceptible, infect... | [
{
"created": "Wed, 19 Jul 2023 00:18:51 GMT",
"version": "v1"
}
] | 2023-07-21 | [
[
"Flynn-Primrose",
"Darren",
""
],
[
"Walker",
"Steven C.",
""
],
[
"Li",
"Michael",
""
],
[
"Bolker",
"Benjamin M.",
""
],
[
"Earn",
"David J. D.",
""
],
[
"Dushoff",
"Jonathan",
""
]
] | Compartmental models are valuable tools for investigating infectious diseases. Researchers building such models typically begin with a simple structure where compartments correspond to individuals with different epidemiological statuses, e.g., the classic SIR model which splits the population into susceptible, infected... |
0709.2071 | Monika Schoenerklee | Monika Schoenerklee, Momtchil Peev | Parameter Estimation in Biokinetic Degradation Models in Wastewater
Treatment - A Novel Approach Relevant for Micro-pollutant Removal | 20 pages, 4 figures | null | null | null | q-bio.QM | null | In this paper we address a general parameter estimation methodology for an
extended biokinetic degradation model [1] for poorly degradable
micropollutants. In particular we concentrate on parameter estimation of the
micropollutant degradation sub-model by specialised microorganisms. In this
case we focus on the case ... | [
{
"created": "Thu, 13 Sep 2007 13:32:32 GMT",
"version": "v1"
}
] | 2007-09-14 | [
[
"Schoenerklee",
"Monika",
""
],
[
"Peev",
"Momtchil",
""
]
] | In this paper we address a general parameter estimation methodology for an extended biokinetic degradation model [1] for poorly degradable micropollutants. In particular we concentrate on parameter estimation of the micropollutant degradation sub-model by specialised microorganisms. In this case we focus on the case wh... |
q-bio/0412021 | Valmir Barbosa | A. H. L. Porto, V. C. Barbosa | Multiple sequence alignment based on set covers | null | Lecture Notes in Computer Science 3907 (2006), 127-137 | 10.1007/11732242_12 | ES-666/04 | q-bio.QM | null | We introduce a new heuristic for the multiple alignment of a set of
sequences. The heuristic is based on a set cover of the residue alphabet of the
sequences, and also on the determination of a significant set of blocks
comprising subsequences of the sequences to be aligned. These blocks are
obtained with the aid of ... | [
{
"created": "Fri, 10 Dec 2004 17:10:53 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Porto",
"A. H. L.",
""
],
[
"Barbosa",
"V. C.",
""
]
] | We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtained with the aid of a ... |
2208.09648 | Tong Wang | Tong Wang | Research on Creative Thinking Mode Based on Category Theory | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The research on the brain mechanism of creativity mainly has two aspects, one
is the creative thinking process, and the other is the brain structure and
functional connection characteristics of highly creative people. The billions
of nerve cells in the brain connect and interact with each other. The hundreds
of milli... | [
{
"created": "Sat, 20 Aug 2022 09:28:42 GMT",
"version": "v1"
}
] | 2022-08-23 | [
[
"Wang",
"Tong",
""
]
] | The research on the brain mechanism of creativity mainly has two aspects, one is the creative thinking process, and the other is the brain structure and functional connection characteristics of highly creative people. The billions of nerve cells in the brain connect and interact with each other. The hundreds of million... |
1606.06842 | Zhou Xu | Sarah Eug\`ene, Thibault Bourgeron and Zhou Xu | Effects of initial telomere length distribution on senescence onset and
heterogeneity | null | null | null | null | q-bio.GN q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Replicative senescence, induced by telomere shortening, exhibits considerable
asynchrony and heterogeneity, the origins of which remain unclear. Here, we
formally study how telomere shortening mechanisms impact on senescence kinetics
and define two regimes of senescence, depending on the initial telomere length
varia... | [
{
"created": "Wed, 22 Jun 2016 08:04:52 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Nov 2016 10:10:14 GMT",
"version": "v2"
}
] | 2016-11-08 | [
[
"Eugène",
"Sarah",
""
],
[
"Bourgeron",
"Thibault",
""
],
[
"Xu",
"Zhou",
""
]
] | Replicative senescence, induced by telomere shortening, exhibits considerable asynchrony and heterogeneity, the origins of which remain unclear. Here, we formally study how telomere shortening mechanisms impact on senescence kinetics and define two regimes of senescence, depending on the initial telomere length varianc... |
1902.09365 | Solenn Stoeckel | Solenn Stoeckel, Barbara Porro and Sophie Arnaud-Haond | The discernible and hidden effects of clonality on the genotypic and
genetic states of populations: improving our estimation of clonal rates | 45 pages, 4 figures, 1 box and no table; 8 supplementary figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Partial clonality is widespread across the tree of life, but most population
genetics models are designed for exclusively clonal or sexual organisms. This
gap hampers our understanding of the influence of clonality on evolutionary
trajectories and the interpretation of population genetics data. We performed
forward s... | [
{
"created": "Mon, 25 Feb 2019 15:29:57 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Mar 2019 22:26:36 GMT",
"version": "v2"
},
{
"created": "Mon, 1 Jul 2019 19:13:31 GMT",
"version": "v3"
},
{
"created": "Sat, 3 Aug 2019 09:43:26 GMT",
"version": "v4"
}
] | 2019-08-06 | [
[
"Stoeckel",
"Solenn",
""
],
[
"Porro",
"Barbara",
""
],
[
"Arnaud-Haond",
"Sophie",
""
]
] | Partial clonality is widespread across the tree of life, but most population genetics models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetics data. We performed forward sim... |
1904.02979 | Fiona Macfarlane | Fiona R Macfarlane, Mark AJ Chaplain, Tommaso Lorenzi | A stochastic individual-based model to explore the role of spatial
interactions and antigen recognition in the immune response against solid
tumours | null | null | 10.1016/j.jtbi.2019.07.019 | null | q-bio.CB math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spatial interactions between cancer and immune cells, as well as the
recognition of tumour antigens by cells of the immune system, play a key role
in the immune response against solid tumours. The existing mathematical models
generally focus only on one of these key aspects. We present here a spatial
stochastic indiv... | [
{
"created": "Fri, 5 Apr 2019 10:14:37 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Jul 2019 12:00:23 GMT",
"version": "v2"
}
] | 2019-08-05 | [
[
"Macfarlane",
"Fiona R",
""
],
[
"Chaplain",
"Mark AJ",
""
],
[
"Lorenzi",
"Tommaso",
""
]
] | Spatial interactions between cancer and immune cells, as well as the recognition of tumour antigens by cells of the immune system, play a key role in the immune response against solid tumours. The existing mathematical models generally focus only on one of these key aspects. We present here a spatial stochastic individ... |
1811.06809 | Hendrik Richter | Hendrik Richter | Fixation properties of multiple cooperator configurations on regular
graphs | null | Theory in Biosciences (2019) | 10.1007/s12064-019-00293-3 | null | q-bio.PE cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Whether or not cooperation is favored in evolutionary games on graphs depends
on the population structure and spatial properties of the interaction network.
Population structures can be expressed as configurations. Such configurations
extend scenarios with a single cooperator among defectors to any number of
cooperat... | [
{
"created": "Fri, 16 Nov 2018 14:13:51 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Mar 2019 14:13:37 GMT",
"version": "v2"
}
] | 2019-03-21 | [
[
"Richter",
"Hendrik",
""
]
] | Whether or not cooperation is favored in evolutionary games on graphs depends on the population structure and spatial properties of the interaction network. Population structures can be expressed as configurations. Such configurations extend scenarios with a single cooperator among defectors to any number of cooperator... |
1706.03283 | Sachin Talathi | Sachin S. Talathi | Deep Recurrent Neural Networks for seizure detection and early seizure
detection systems | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epilepsy is common neurological diseases, affecting about 0.6-0.8 % of world
population. Epileptic patients suffer from chronic unprovoked seizures, which
can result in broad spectrum of debilitating medical and social consequences.
Since seizures, in general, occur infrequently and are unpredictable, automated
seizu... | [
{
"created": "Sat, 10 Jun 2017 21:29:09 GMT",
"version": "v1"
}
] | 2017-06-13 | [
[
"Talathi",
"Sachin S.",
""
]
] | Epilepsy is common neurological diseases, affecting about 0.6-0.8 % of world population. Epileptic patients suffer from chronic unprovoked seizures, which can result in broad spectrum of debilitating medical and social consequences. Since seizures, in general, occur infrequently and are unpredictable, automated seizure... |
2301.07194 | Jocelyn Faubert PhD | Jean-Marie Hanssens, Bernard Bourdoncle, Jacques Gresset, Jocelyn
Faubert, Pierre Simonet | Distortion in ophthalmic optics: A review of the principal concepts and
models | 38 pages, 11 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Although all members of the ophthalmic community agree that distortion is an
aberration affecting the geometry of an image produced by the periphery of an
ophthalmic lens, there are several approaches for analyzing and quantifying
this aberration. Various concepts have been introduced: ordinary distortion,
stationary... | [
{
"created": "Tue, 17 Jan 2023 21:15:51 GMT",
"version": "v1"
}
] | 2023-01-19 | [
[
"Hanssens",
"Jean-Marie",
""
],
[
"Bourdoncle",
"Bernard",
""
],
[
"Gresset",
"Jacques",
""
],
[
"Faubert",
"Jocelyn",
""
],
[
"Simonet",
"Pierre",
""
]
] | Although all members of the ophthalmic community agree that distortion is an aberration affecting the geometry of an image produced by the periphery of an ophthalmic lens, there are several approaches for analyzing and quantifying this aberration. Various concepts have been introduced: ordinary distortion, stationary d... |
2204.05103 | Juan Vazquez-Rodriguez | Juan Vazquez-Rodriguez (M-PSI), Gr\'egoire Lefebvre, Julien Cumin,
James L. Crowley (M-PSI) | Transformer-Based Self-Supervised Learning for Emotion Recognition | null | 26th International Conference on Pattern Recognition (ICPR 2022),
Aug 2022, Montreal, Canada | null | null | q-bio.NC cs.AI cs.LG eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In order to exploit representations of time-series signals, such as
physiological signals, it is essential that these representations capture
relevant information from the whole signal. In this work, we propose to use a
Transformer-based model to process electrocardiograms (ECG) for emotion
recognition. Attention mec... | [
{
"created": "Fri, 8 Apr 2022 07:14:55 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Jun 2022 09:13:10 GMT",
"version": "v2"
}
] | 2022-06-06 | [
[
"Vazquez-Rodriguez",
"Juan",
"",
"M-PSI"
],
[
"Lefebvre",
"Grégoire",
"",
"M-PSI"
],
[
"Cumin",
"Julien",
"",
"M-PSI"
],
[
"Crowley",
"James L.",
"",
"M-PSI"
]
] | In order to exploit representations of time-series signals, such as physiological signals, it is essential that these representations capture relevant information from the whole signal. In this work, we propose to use a Transformer-based model to process electrocardiograms (ECG) for emotion recognition. Attention mecha... |
1104.4568 | Raul Rabadan | Carlos Xavier Hernandez, Joseph Chan, Hossein Khiabanian, Raul Rabadan | Understanding the Origins of a Pandemic Virus | 13 pages, 2 figures | null | null | ac:129992 | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the origin of infectious diseases provides scientifically based
rationales for implementing public health measures that may help to avoid or
mitigate future epidemics. The recent ancestors of a pandemic virus provide
invaluable information about the set of minimal genomic alterations that
transformed a ... | [
{
"created": "Sat, 23 Apr 2011 15:58:43 GMT",
"version": "v1"
}
] | 2011-04-26 | [
[
"Hernandez",
"Carlos Xavier",
""
],
[
"Chan",
"Joseph",
""
],
[
"Khiabanian",
"Hossein",
""
],
[
"Rabadan",
"Raul",
""
]
] | Understanding the origin of infectious diseases provides scientifically based rationales for implementing public health measures that may help to avoid or mitigate future epidemics. The recent ancestors of a pandemic virus provide invaluable information about the set of minimal genomic alterations that transformed a zo... |
2312.15795 | Assaf Marron | Assaf Marron, Smadar Szekely, Irun R. Cohen, and David Harel | Biparental Reproduction may Enhance Species Sustainability by Conserving
Shared Parental Traits more Faithfully than Monoparental Reproduction | This version has an analytical angle. See V1 for simulations of a
slightly different model | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recognized effects of sexual reproduction and other forms of biparental
reproduction in species sustainment and evolution include the increasing of
diversity, accelerating adaptation, constraining the accumulation of
deleterious mutations, and the homogenization of species genotype.
Nevertheless, many questions remai... | [
{
"created": "Mon, 25 Dec 2023 19:11:43 GMT",
"version": "v1"
},
{
"created": "Fri, 3 May 2024 17:44:20 GMT",
"version": "v2"
}
] | 2024-05-06 | [
[
"Marron",
"Assaf",
""
],
[
"Szekely",
"Smadar",
""
],
[
"Cohen",
"Irun R.",
""
],
[
"Harel",
"David",
""
]
] | Recognized effects of sexual reproduction and other forms of biparental reproduction in species sustainment and evolution include the increasing of diversity, accelerating adaptation, constraining the accumulation of deleterious mutations, and the homogenization of species genotype. Nevertheless, many questions remain ... |
2307.06314 | Matthew Asker | Matthew Asker, Llu\'is Hern\'andez-Navarro, Alastair M. Rucklidge,
Mauro Mobilia | Coexistence of Competing Microbial Strains under Twofold Environmental
Variability and Demographic Fluctuations | 15 pages + appendix of 10 pages (Supplementary Material); Figshare
resources: https://doi.org/10.6084/m9.figshare.23553066 | New J. Phys 25, 123010 (2023) | 10.1088/1367-2630/ad0d36 | null | q-bio.PE cond-mat.stat-mech nlin.AO physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Microbial populations generally evolve in volatile environments, under
conditions fluctuating between harsh and mild, e.g. as the result of sudden
changes in toxin concentration or nutrient abundance. Environmental variability
thus shapes the long-time population dynamics, notably by influencing the
ability of differ... | [
{
"created": "Wed, 12 Jul 2023 17:22:55 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Jul 2023 16:44:46 GMT",
"version": "v2"
},
{
"created": "Thu, 30 Nov 2023 09:46:05 GMT",
"version": "v3"
}
] | 2023-12-07 | [
[
"Asker",
"Matthew",
""
],
[
"Hernández-Navarro",
"Lluís",
""
],
[
"Rucklidge",
"Alastair M.",
""
],
[
"Mobilia",
"Mauro",
""
]
] | Microbial populations generally evolve in volatile environments, under conditions fluctuating between harsh and mild, e.g. as the result of sudden changes in toxin concentration or nutrient abundance. Environmental variability thus shapes the long-time population dynamics, notably by influencing the ability of differen... |
2007.07029 | Alexander Becker | Vladimir Golkov, Alexander Becker, Daniel T. Plop, Daniel
\v{C}uturilo, Neda Davoudi, Jeffrey Mendenhall, Rocco Moretti, Jens Meiler,
Daniel Cremers | Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost
Functions | 10 pages | null | null | null | q-bio.BM cs.LG q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Computer-aided drug discovery is an essential component of modern drug
development. Therein, deep learning has become an important tool for rapid
screening of billions of molecules in silico for potential hits containing
desired chemical features. Despite its importance, substantial challenges
persist in training the... | [
{
"created": "Thu, 25 Jun 2020 08:46:37 GMT",
"version": "v1"
}
] | 2020-07-15 | [
[
"Golkov",
"Vladimir",
""
],
[
"Becker",
"Alexander",
""
],
[
"Plop",
"Daniel T.",
""
],
[
"Čuturilo",
"Daniel",
""
],
[
"Davoudi",
"Neda",
""
],
[
"Mendenhall",
"Jeffrey",
""
],
[
"Moretti",
"Rocco",
""
]... | Computer-aided drug discovery is an essential component of modern drug development. Therein, deep learning has become an important tool for rapid screening of billions of molecules in silico for potential hits containing desired chemical features. Despite its importance, substantial challenges persist in training these... |
2006.14178 | Jonathan Kadmon | Jonathan Kadmon, Jonathan Timcheck, and Surya Ganguli | Predictive coding in balanced neural networks with noise, chaos and
delays | null | null | null | null | q-bio.NC cond-mat.dis-nn stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biological neural networks face a formidable task: performing reliable
computations in the face of intrinsic stochasticity in individual neurons,
imprecisely specified synaptic connectivity, and nonnegligible delays in
synaptic transmission. A common approach to combatting such biological
heterogeneity involves avera... | [
{
"created": "Thu, 25 Jun 2020 05:03:27 GMT",
"version": "v1"
}
] | 2020-06-26 | [
[
"Kadmon",
"Jonathan",
""
],
[
"Timcheck",
"Jonathan",
""
],
[
"Ganguli",
"Surya",
""
]
] | Biological neural networks face a formidable task: performing reliable computations in the face of intrinsic stochasticity in individual neurons, imprecisely specified synaptic connectivity, and nonnegligible delays in synaptic transmission. A common approach to combatting such biological heterogeneity involves averagi... |
2207.09903 | Elena Losero | Elena Losero, Somanath Jagannath, Maurizio Pezzoli, Valentin Goblot,
Hossein Babashah, Hilal A. Lashuel, Christophe Galland, and Niels Quack | Neuronal growth on high-aspect-ratio diamond nanopillar arrays for
biosensing applications | 26 pages. 10 figures | Scientific Reports 13: 5909 (2023) | 10.1038/s41598-023-32235-x | null | q-bio.NC physics.app-ph quant-ph | http://creativecommons.org/licenses/by/4.0/ | Monitoring neuronal activity with simultaneously high spatial and temporal
resolution in living cell cultures is crucial to advance understanding of the
development and functioning of our brain, and to gain further insights in the
origin of brain disorders. While it has been demonstrated that the quantum
sensing capa... | [
{
"created": "Mon, 11 Jul 2022 07:20:28 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Nov 2022 08:26:55 GMT",
"version": "v2"
}
] | 2023-07-18 | [
[
"Losero",
"Elena",
""
],
[
"Jagannath",
"Somanath",
""
],
[
"Pezzoli",
"Maurizio",
""
],
[
"Goblot",
"Valentin",
""
],
[
"Babashah",
"Hossein",
""
],
[
"Lashuel",
"Hilal A.",
""
],
[
"Galland",
"Christophe",
... | Monitoring neuronal activity with simultaneously high spatial and temporal resolution in living cell cultures is crucial to advance understanding of the development and functioning of our brain, and to gain further insights in the origin of brain disorders. While it has been demonstrated that the quantum sensing capabi... |
1309.7798 | Guy-Bart Stan PhD | Rhys Algar and Tom Ellis and Guy-Bart Stan | Modelling the burden caused by gene expression: an in silico
investigation into the interactions between synthetic gene circuits and their
chassis cell | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we motivate and develop a model of gene expression for the
purpose of studying the interaction between synthetic gene circuits and the
chassis cell within which they are in- serted. This model focuses on the
translational aspect of gene expression as this is where the literature
suggests the crucial int... | [
{
"created": "Mon, 30 Sep 2013 11:22:42 GMT",
"version": "v1"
}
] | 2013-10-01 | [
[
"Algar",
"Rhys",
""
],
[
"Ellis",
"Tom",
""
],
[
"Stan",
"Guy-Bart",
""
]
] | In this paper we motivate and develop a model of gene expression for the purpose of studying the interaction between synthetic gene circuits and the chassis cell within which they are in- serted. This model focuses on the translational aspect of gene expression as this is where the literature suggests the crucial inter... |
1405.4327 | Christopher Lee | Christopher Lee, Marc Harper, Dashiell Fryer | The Art of War: Beyond Memory-one Strategies in Population Games | 16 pages, 4 figures | PLoS One. 2015; 10(3): e012062 | 10.1371/journal.pone.0120625 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We define a new strategy for population games based on techniques from
machine learning and statistical inference that is essentially uninvadable and
can successfully invade (significantly more likely than a neutral mutant)
essentially all known memory-one strategies for the prisoner's dilemma and
other population ga... | [
{
"created": "Fri, 16 May 2014 23:25:13 GMT",
"version": "v1"
}
] | 2015-05-11 | [
[
"Lee",
"Christopher",
""
],
[
"Harper",
"Marc",
""
],
[
"Fryer",
"Dashiell",
""
]
] | We define a new strategy for population games based on techniques from machine learning and statistical inference that is essentially uninvadable and can successfully invade (significantly more likely than a neutral mutant) essentially all known memory-one strategies for the prisoner's dilemma and other population game... |
1806.10889 | Adrien Coulier | Adrien Coulier, Andreas Hellander | Orchestral: a lightweight framework for parallel simulations of
cell-cell communication | preprint, 9 pages, 9 figures, submitted to IEEE eScience 2018 | null | null | null | q-bio.CB q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop a modeling and simulation framework capable of massively parallel
simulation of multicellular systems with spatially resolved stochastic kinetics
in individual cells. By the use of operator-splitting we decouple the
simulation of reaction-diffusion kinetics inside the cells from the simulation
of molecular... | [
{
"created": "Thu, 28 Jun 2018 11:30:52 GMT",
"version": "v1"
}
] | 2018-06-29 | [
[
"Coulier",
"Adrien",
""
],
[
"Hellander",
"Andreas",
""
]
] | We develop a modeling and simulation framework capable of massively parallel simulation of multicellular systems with spatially resolved stochastic kinetics in individual cells. By the use of operator-splitting we decouple the simulation of reaction-diffusion kinetics inside the cells from the simulation of molecular c... |
2004.01819 | Rifat Zahan | Rifat Zahan, Ian McQuillan and Nathaniel D. Osgood | DNA Methylation Data to Predict Suicidal and Non-Suicidal Deaths: A
Machine Learning Approach | null | In 2018 IEEE International Conference on Healthcare Informatics
(ICHI) (pp. 363-365). IEEE (2018, June) | 10.1109/ICHI.2018.00057 | null | q-bio.GN cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The objective of this study is to predict suicidal and non-suicidal deaths
from DNA methylation data using a modern machine learning algorithm. We used
support vector machines to classify existing secondary data consisting of
normalized values of methylated DNA probe intensities from tissues of two
cortical brain reg... | [
{
"created": "Sat, 4 Apr 2020 00:34:22 GMT",
"version": "v1"
}
] | 2020-04-07 | [
[
"Zahan",
"Rifat",
""
],
[
"McQuillan",
"Ian",
""
],
[
"Osgood",
"Nathaniel D.",
""
]
] | The objective of this study is to predict suicidal and non-suicidal deaths from DNA methylation data using a modern machine learning algorithm. We used support vector machines to classify existing secondary data consisting of normalized values of methylated DNA probe intensities from tissues of two cortical brain regio... |
1910.04059 | Kezhi Li | Taiyu Zhu, Kezhi Li, Pantelis Georgiou | A Dual-Hormone Closed-Loop Delivery System for Type 1 Diabetes Using
Deep Reinforcement Learning | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a dual-hormone delivery strategy by exploiting deep reinforcement
learning (RL) for people with Type 1 Diabetes (T1D). Specifically, double
dilated recurrent neural networks (RNN) are used to learn the hormone delivery
strategy, trained by a variant of Q-learning, whose inputs are raw data of
glucose \& me... | [
{
"created": "Wed, 9 Oct 2019 15:14:55 GMT",
"version": "v1"
}
] | 2019-10-10 | [
[
"Zhu",
"Taiyu",
""
],
[
"Li",
"Kezhi",
""
],
[
"Georgiou",
"Pantelis",
""
]
] | We propose a dual-hormone delivery strategy by exploiting deep reinforcement learning (RL) for people with Type 1 Diabetes (T1D). Specifically, double dilated recurrent neural networks (RNN) are used to learn the hormone delivery strategy, trained by a variant of Q-learning, whose inputs are raw data of glucose \& meal... |
1202.2518 | Liang Wang | Wang Liang | Segmenting DNA sequence into `words' | 12 pages,2 figures | null | null | null | q-bio.GN cs.CL | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper presents a novel method to segment/decode DNA sequences based on
n-grams statistical language model. Firstly, we find the length of most DNA
'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we
design an unsupervised probability based approach to segment the DNA sequences.
The benc... | [
{
"created": "Sun, 12 Feb 2012 11:23:38 GMT",
"version": "v1"
},
{
"created": "Thu, 23 Feb 2012 02:39:32 GMT",
"version": "v2"
},
{
"created": "Tue, 2 Oct 2012 12:49:43 GMT",
"version": "v3"
},
{
"created": "Sat, 22 Jun 2013 10:14:11 GMT",
"version": "v4"
}
] | 2015-03-13 | [
[
"Liang",
"Wang",
""
]
] | This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an unsupervised probability based approach to segment the DNA sequences. The benchm... |
q-bio/0412037 | HC Paul Lee | Hong-Da Chen, Chang-Heng Chang, Li-Ching Hsieh and Hoong-Chien Lee | Divergence and Shannon information in genomes | 4 pages, 3 tables, 2 figures | null | 10.1103/PhysRevLett.94.178103 | null | q-bio.GN | null | Shannon information (SI) and its special case, divergence, are defined for a
DNA sequence in terms of probabilities of chemical words in the sequence and
are computed for a set of complete genomes highly diverse in length and
composition. We find the following: SI (but not divergence) is inversely
proportional to seq... | [
{
"created": "Sat, 18 Dec 2004 03:15:03 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Chen",
"Hong-Da",
""
],
[
"Chang",
"Chang-Heng",
""
],
[
"Hsieh",
"Li-Ching",
""
],
[
"Lee",
"Hoong-Chien",
""
]
] | Shannon information (SI) and its special case, divergence, are defined for a DNA sequence in terms of probabilities of chemical words in the sequence and are computed for a set of complete genomes highly diverse in length and composition. We find the following: SI (but not divergence) is inversely proportional to seque... |
2311.02226 | Nina Fefferman | Nina H. Fefferman, Michael J. Blum, Lydia Bourouiba, Nathaniel L.
Gibson, Qiang He, Debra L. Miller, Monica Papes, Dana K. Pasquale, Connor
Verheyen, Sadie J. Ryan | The Case for Controls: Identifying outbreak risk factors through
case-control comparisons | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Investigations of infectious disease outbreaks often focus on identifying
place- and context-dependent factors responsible for emergence and spread,
resulting in phenomenological narratives ill-suited to developing generalizable
predictive and preventive measures. We contend that case-control hypothesis
testing is a ... | [
{
"created": "Fri, 3 Nov 2023 20:32:01 GMT",
"version": "v1"
}
] | 2023-11-07 | [
[
"Fefferman",
"Nina H.",
""
],
[
"Blum",
"Michael J.",
""
],
[
"Bourouiba",
"Lydia",
""
],
[
"Gibson",
"Nathaniel L.",
""
],
[
"He",
"Qiang",
""
],
[
"Miller",
"Debra L.",
""
],
[
"Papes",
"Monica",
""
],
... | Investigations of infectious disease outbreaks often focus on identifying place- and context-dependent factors responsible for emergence and spread, resulting in phenomenological narratives ill-suited to developing generalizable predictive and preventive measures. We contend that case-control hypothesis testing is a mo... |
1709.01998 | Olivier Simon | Olivier Simon, Rabi Yacoub, Sanjay Jain, and Pinaki Sarder | Multi-radial LBP Features as a Tool for Rapid Glomerular Detection and
Assessment in Whole Slide Histopathology Images | 14 pages, 6 figures. Added scalebars, and for Fig. 3b a clearer
example of medulla removal | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We demonstrate a simple and effective automated method for the segmentation
of glomeruli from large (~1 gigapixel) histopathological whole-slide images
(WSIs) of thin renal tissue sections and biopsies, using an adaptation of the
well-known local binary patterns (LBP) image feature vector to train a support
vector ma... | [
{
"created": "Wed, 6 Sep 2017 20:54:10 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Sep 2017 15:06:48 GMT",
"version": "v2"
}
] | 2017-09-21 | [
[
"Simon",
"Olivier",
""
],
[
"Yacoub",
"Rabi",
""
],
[
"Jain",
"Sanjay",
""
],
[
"Sarder",
"Pinaki",
""
]
] | We demonstrate a simple and effective automated method for the segmentation of glomeruli from large (~1 gigapixel) histopathological whole-slide images (WSIs) of thin renal tissue sections and biopsies, using an adaptation of the well-known local binary patterns (LBP) image feature vector to train a support vector mach... |
0801.0254 | Reinhard Laubenbacher | Reinhard Laubenbacher and Brandilyn Stigler | Design of experiments and biochemical network inference | To appear in "Algebraic and geometric methods in statistics," P.
Gibilisco, E. Riccomagno, M.-P. Rogantin, H. P. Wynn, eds., Cambridge
University Press, 2008 | Algebraic and Geometric Methods in Statistics. Eds: Gibilisco,
Riccomagno, Rogantin, Wynn, Cambridge University Press (2008) | null | null | q-bio.MN stat.AP | null | Design of experiments is a branch of statistics that aims to identify
efficient procedures for planning experiments in order to optimize knowledge
discovery. Network inference is a subfield of systems biology devoted to the
identification of biochemical networks from experimental data. Common to both
areas of researc... | [
{
"created": "Mon, 31 Dec 2007 23:52:47 GMT",
"version": "v1"
}
] | 2019-07-12 | [
[
"Laubenbacher",
"Reinhard",
""
],
[
"Stigler",
"Brandilyn",
""
]
] | Design of experiments is a branch of statistics that aims to identify efficient procedures for planning experiments in order to optimize knowledge discovery. Network inference is a subfield of systems biology devoted to the identification of biochemical networks from experimental data. Common to both areas of research ... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.