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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
q-bio/0411050 | Suan Li Mai | Mai Suan Li, D.K. Klimov, D. Thirumalai | Finite size effects on thermal denaturation of globular proteins | 3 figures. Physical Review Letters (in press) | null | 10.1103/PhysRevLett.93.268107 | null | q-bio.BM q-bio.QM | null | Finite size effects on the cooperative thermal denaturation of proteins are
considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta,
where N is the number of amino acids. Surprisingly, we find that zeta is
universal with zeta = 1 + gamma, where the exponent gamma characterizes the
divergence of ... | [
{
"created": "Sun, 28 Nov 2004 15:44:42 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Li",
"Mai Suan",
""
],
[
"Klimov",
"D. K.",
""
],
[
"Thirumalai",
"D.",
""
]
] | Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta, where N is the number of amino acids. Surprisingly, we find that zeta is universal with zeta = 1 + gamma, where the exponent gamma characterizes the divergence of th... |
1805.04616 | Maxwell Zimmerman | Maxwell I. Zimmerman, Justin R. Porter, Xianqiang Sun, Roseane R.
Silva, and Gregory R. Bowman | Choice of adaptive sampling strategy impacts state discovery, transition
probabilities, and the apparent mechanism of conformational changes | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Interest in equilibrium-based sampling methods has grown with recent advances
in computational hardware and Markov state modeling (MSM) methods, yet
outstanding questions remain that hinder widespread adoption. Namely, how do
sampling strategies explore conformational space and how might this influence
predictions? H... | [
{
"created": "Fri, 11 May 2018 23:12:11 GMT",
"version": "v1"
}
] | 2018-05-15 | [
[
"Zimmerman",
"Maxwell I.",
""
],
[
"Porter",
"Justin R.",
""
],
[
"Sun",
"Xianqiang",
""
],
[
"Silva",
"Roseane R.",
""
],
[
"Bowman",
"Gregory R.",
""
]
] | Interest in equilibrium-based sampling methods has grown with recent advances in computational hardware and Markov state modeling (MSM) methods, yet outstanding questions remain that hinder widespread adoption. Namely, how do sampling strategies explore conformational space and how might this influence predictions? Her... |
1711.07473 | Kye-Ryong Sin | Hyon-Hui Ri, Yong-A Choe, Jong-Ho Yun, Kye-Ryong Sin | Determination of carbohydrates in infant milk powders by
ultra-performance liquid chromatography with evaporative light scattering
detector and BEH HILIC column | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The possibility of carbohydrate separation in BEH HILIC (Ethylene Bridged
Hybride, Hydrophilic Interaction Liquid Chromatography) column was studied by
ultra-performance liquid chromatography (UPLC) with evaporative light
scattering detector (ELSD) and mobile phase containing amine compounds as
modifiers. The chromat... | [
{
"created": "Mon, 20 Nov 2017 08:23:41 GMT",
"version": "v1"
}
] | 2017-11-22 | [
[
"Ri",
"Hyon-Hui",
""
],
[
"Choe",
"Yong-A",
""
],
[
"Yun",
"Jong-Ho",
""
],
[
"Sin",
"Kye-Ryong",
""
]
] | The possibility of carbohydrate separation in BEH HILIC (Ethylene Bridged Hybride, Hydrophilic Interaction Liquid Chromatography) column was studied by ultra-performance liquid chromatography (UPLC) with evaporative light scattering detector (ELSD) and mobile phase containing amine compounds as modifiers. The chromatog... |
1701.07379 | Jose Vanterler Da Costa Sousa | Jos\'e Vanterler da Costa Sousa, Edmundo Capelas de Oliveira and Luiz
Alberto Magna | Fractional Calculus and the ESR test | 19 pages and 2 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a partial differential equation associated with a mathematical
model describing the concentration of nutrients in blood which interferes
directly on the erythrocyte sedimentation rate in the case of an average fluid
velocity equal to zero. Introducing the fractional derivative in the Caputo
sense, we prop... | [
{
"created": "Thu, 29 Dec 2016 13:52:46 GMT",
"version": "v1"
}
] | 2017-01-27 | [
[
"Sousa",
"José Vanterler da Costa",
""
],
[
"de Oliveira",
"Edmundo Capelas",
""
],
[
"Magna",
"Luiz Alberto",
""
]
] | We consider a partial differential equation associated with a mathematical model describing the concentration of nutrients in blood which interferes directly on the erythrocyte sedimentation rate in the case of an average fluid velocity equal to zero. Introducing the fractional derivative in the Caputo sense, we propos... |
1810.11818 | Konstantin Blyuss | F. Fatehi, Y.N. Kyrychko, R. Molchanov, K.B. Blyuss | Bifurcations and multi-stability in a model of cytokine-mediated
autoimmunity | 26 pages, 10 figures, accepted for publication in Int. J. Bif. Chaos | null | 10.1142/S0218127419500342 | null | q-bio.QM nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper investigates the dynamics of immune response and autoimmunity with
particular emphasis on the role of regulatory T cells (Tregs), T cells with
different activation thresholds, and cytokines in mediating T cell activity.
Analysis of the steady states yields parameter regions corresponding to regimes
of norm... | [
{
"created": "Sun, 28 Oct 2018 14:28:22 GMT",
"version": "v1"
}
] | 2019-05-01 | [
[
"Fatehi",
"F.",
""
],
[
"Kyrychko",
"Y. N.",
""
],
[
"Molchanov",
"R.",
""
],
[
"Blyuss",
"K. B.",
""
]
] | This paper investigates the dynamics of immune response and autoimmunity with particular emphasis on the role of regulatory T cells (Tregs), T cells with different activation thresholds, and cytokines in mediating T cell activity. Analysis of the steady states yields parameter regions corresponding to regimes of normal... |
1302.5484 | Marisa Eisenberg | Marisa Eisenberg | Input-output equivalence and identifiability: some simple
generalizations of the differential algebra approach | Notes on the relationship between input-output equivalence and
structural identifiability | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we give an overview of the differential algebra approach to
identifiability, and then note a very simple observation about input-output
equivalence and identifiability, that describes the identifiability equivalence
between input-output equivalent models. We then give several simple
consequences of thi... | [
{
"created": "Fri, 22 Feb 2013 05:01:53 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Aug 2019 05:43:42 GMT",
"version": "v2"
}
] | 2019-08-20 | [
[
"Eisenberg",
"Marisa",
""
]
] | In this paper, we give an overview of the differential algebra approach to identifiability, and then note a very simple observation about input-output equivalence and identifiability, that describes the identifiability equivalence between input-output equivalent models. We then give several simple consequences of this ... |
1410.8564 | John Drake | John M. Drake, RajReni B. Kaul, Laura Alexander, Suzanne M. O'Regan,
Andrew M. Kramer, J. Tomlin Pulliam, Matthew J. Ferrari, and Andrew W. Park | Ebola cases and health system demand in Liberia | Includes supplement | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In 2014, a major epidemic of human Ebola virus disease emerged in West
Africa, where human-to-human transmission has now been been sustained for
greater than 10 months. In the summer of 2014, there was great uncertainty
about the answers to several key policy questions concerning the path to
containment. In recent ye... | [
{
"created": "Thu, 30 Oct 2014 21:29:17 GMT",
"version": "v1"
}
] | 2014-11-03 | [
[
"Drake",
"John M.",
""
],
[
"Kaul",
"RajReni B.",
""
],
[
"Alexander",
"Laura",
""
],
[
"O'Regan",
"Suzanne M.",
""
],
[
"Kramer",
"Andrew M.",
""
],
[
"Pulliam",
"J. Tomlin",
""
],
[
"Ferrari",
"Matthew J.",
... | In 2014, a major epidemic of human Ebola virus disease emerged in West Africa, where human-to-human transmission has now been been sustained for greater than 10 months. In the summer of 2014, there was great uncertainty about the answers to several key policy questions concerning the path to containment. In recent year... |
2105.08944 | Jacob Russin | Jacob Russin, Maryam Zolfaghar, Seongmin A. Park, Erie Boorman,
Randall C. O'Reilly | Complementary Structure-Learning Neural Networks for Relational
Reasoning | 7 pages, 4 figures, Accepted to CogSci 2021 for poster presentation | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by/4.0/ | The neural mechanisms supporting flexible relational inferences, especially
in novel situations, are a major focus of current research. In the
complementary learning systems framework, pattern separation in the hippocampus
allows rapid learning in novel environments, while slower learning in neocortex
accumulates sma... | [
{
"created": "Wed, 19 May 2021 06:25:21 GMT",
"version": "v1"
}
] | 2021-05-20 | [
[
"Russin",
"Jacob",
""
],
[
"Zolfaghar",
"Maryam",
""
],
[
"Park",
"Seongmin A.",
""
],
[
"Boorman",
"Erie",
""
],
[
"O'Reilly",
"Randall C.",
""
]
] | The neural mechanisms supporting flexible relational inferences, especially in novel situations, are a major focus of current research. In the complementary learning systems framework, pattern separation in the hippocampus allows rapid learning in novel environments, while slower learning in neocortex accumulates small... |
1501.03463 | Andrew Leifer | Jeffrey P. Nguyen and Frederick B. Shipley and Ashley N. Linder and
George S. Plummer and Joshua W. Shaevitz and Andrew M. Leifer | Whole-brain calcium imaging with cellular resolution in freely behaving
C. elegans | 33 pages, 6 main figures, 7 supplementary figures | null | 10.1073/pnas.1507110112 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ability to acquire large-scale recordings of neuronal activity in awake
and unrestrained animals poses a major challenge for studying neural coding of
animal behavior. We present a new instrument capable of recording intracellular
calcium transients from every neuron in the head of a freely behaving C.
elegans wi... | [
{
"created": "Wed, 14 Jan 2015 20:07:59 GMT",
"version": "v1"
}
] | 2015-12-31 | [
[
"Nguyen",
"Jeffrey P.",
""
],
[
"Shipley",
"Frederick B.",
""
],
[
"Linder",
"Ashley N.",
""
],
[
"Plummer",
"George S.",
""
],
[
"Shaevitz",
"Joshua W.",
""
],
[
"Leifer",
"Andrew M.",
""
]
] | The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals poses a major challenge for studying neural coding of animal behavior. We present a new instrument capable of recording intracellular calcium transients from every neuron in the head of a freely behaving C. elegans with... |
1906.03660 | Margaret Cheung | Andrei G. Gasic, Mayank M. Boob, Maxim B. Prigozhin, Dirar Homouz,
Caleb M. Daugherty, Martin Gruebele, Margaret S. Cheung | Critical phenomena in the temperature-pressure-crowding phase diagram of
a protein | 5 figures | Phys. Rev. X 9, 041035 (2019) | 10.1103/PhysRevX.9.041035 | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the cell, proteins fold and perform complex functions through global
structural rearrangements. Function requires a protein to be at the brink of
stability to be susceptible to small environmental fluctuations, yet stable
enough to maintain structural integrity. These apparently conflicting behaviors
are exhibited... | [
{
"created": "Sun, 9 Jun 2019 15:37:04 GMT",
"version": "v1"
}
] | 2020-11-17 | [
[
"Gasic",
"Andrei G.",
""
],
[
"Boob",
"Mayank M.",
""
],
[
"Prigozhin",
"Maxim B.",
""
],
[
"Homouz",
"Dirar",
""
],
[
"Daugherty",
"Caleb M.",
""
],
[
"Gruebele",
"Martin",
""
],
[
"Cheung",
"Margaret S.",
... | In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to maintain structural integrity. These apparently conflicting behaviors are exhibited b... |
0904.1959 | Emilio Hernandez-Garcia | E. Tew Kai (1), V. Rossi (2), J. Sudre (2), H. Weimerskirch (3), C.
Lopez (4), E. Hernandez-Garcia (4), F. Marsac (1), and V. Garcon (2) ((1)
THETIS, Sete; (2) LEGOS, Toulouse; (3) C.E.B. Chize; (4) IFISC, Palma de
Mallorca) | Top marine predators track Lagrangian coherent structures | null | Proceedings of the National Academy of Sciences of the USA (PNAS)
106, 8245-8250 (2009) | 10.1073/pnas.0811034106 | null | q-bio.PE nlin.CD physics.ao-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Meso- and submesoscales (fronts, eddies, filaments) in surface ocean flow
have a crucial influence on marine ecosystems. Their dynamics partly control
the foraging behaviour and the displacement of marine top predators (tuna,
birds, turtles, and cetaceans). In this work we focus on the role of
submesoscale structures... | [
{
"created": "Mon, 13 Apr 2009 15:52:30 GMT",
"version": "v1"
}
] | 2009-05-25 | [
[
"Kai",
"E. Tew",
""
],
[
"Rossi",
"V.",
""
],
[
"Sudre",
"J.",
""
],
[
"Weimerskirch",
"H.",
""
],
[
"Lopez",
"C.",
""
],
[
"Hernandez-Garcia",
"E.",
""
],
[
"Marsac",
"F.",
""
],
[
"Garcon",
"V... | Meso- and submesoscales (fronts, eddies, filaments) in surface ocean flow have a crucial influence on marine ecosystems. Their dynamics partly control the foraging behaviour and the displacement of marine top predators (tuna, birds, turtles, and cetaceans). In this work we focus on the role of submesoscale structures i... |
1308.5548 | Pierre Sens | Serge Dmitrieff, and Pierre Sens | Transient domain formation in membrane-bound organelles undergoing
maturation | 7 pages, 6 figures | null | 10.1103/PhysRevE.88.062704 | null | q-bio.SC cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The membrane components of cellular organelles have been shown to segregate
into domains as the result of biochemical maturation. We propose that the
dynamical competition between maturation and lateral segregation of membrane
components regulates domain formation. We study a two- component fluid membrane
in which en... | [
{
"created": "Mon, 26 Aug 2013 11:53:39 GMT",
"version": "v1"
}
] | 2015-06-17 | [
[
"Dmitrieff",
"Serge",
""
],
[
"Sens",
"Pierre",
""
]
] | The membrane components of cellular organelles have been shown to segregate into domains as the result of biochemical maturation. We propose that the dynamical competition between maturation and lateral segregation of membrane components regulates domain formation. We study a two- component fluid membrane in which enzy... |
2011.05304 | Ishan Barman | Santosh Kumar Paidi, Joel Rodriguez Troncoso, Piyush Raj, Paola
Monterroso Diaz, David E. Lee, Narasimhan Rajaram, Ishan Barman | Label-free Raman spectroscopy and machine learning enables sensitive
evaluation of differential response to immunotherapy | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Cancer immunotherapy provides durable clinical benefit in only a small
fraction of patients, particularly due to a lack of reliable biomarkers for
accurate prediction of treatment outcomes and evaluation of response. Here, we
demonstrate the first application of label-free Raman spectroscopy for
elucidating biochemic... | [
{
"created": "Tue, 10 Nov 2020 18:39:14 GMT",
"version": "v1"
}
] | 2020-11-11 | [
[
"Paidi",
"Santosh Kumar",
""
],
[
"Troncoso",
"Joel Rodriguez",
""
],
[
"Raj",
"Piyush",
""
],
[
"Diaz",
"Paola Monterroso",
""
],
[
"Lee",
"David E.",
""
],
[
"Rajaram",
"Narasimhan",
""
],
[
"Barman",
"Ishan"... | Cancer immunotherapy provides durable clinical benefit in only a small fraction of patients, particularly due to a lack of reliable biomarkers for accurate prediction of treatment outcomes and evaluation of response. Here, we demonstrate the first application of label-free Raman spectroscopy for elucidating biochemical... |
1204.5517 | William Holmes | Benjamin Lin and William R. Holmes and ChiaoChun Wang and Tasuku Ueno
and Andrew Harwell and Leah Edelstein-Keshet and Takanari Inoue and Andre
Levchenko and | Synthetic spatially graded Rac activation drives directed cell
polarization and locomotion | null | null | 10.1073/pnas.1210295109 | null | q-bio.MN q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Migrating cells possess intracellular gradients of Rho GTPases, but it is
unknown whether these shallow gradients themselves can induce motility. Here we
describe a new method to present cells with induced linear gradients of active,
endogenous Rac without receptor activation. Gradients as low as 15% were
sufficient ... | [
{
"created": "Wed, 25 Apr 2012 00:17:58 GMT",
"version": "v1"
}
] | 2015-06-04 | [
[
"Lin",
"Benjamin",
""
],
[
"Holmes",
"William R.",
""
],
[
"Wang",
"ChiaoChun",
""
],
[
"Ueno",
"Tasuku",
""
],
[
"Harwell",
"Andrew",
""
],
[
"Edelstein-Keshet",
"Leah",
""
],
[
"Inoue",
"Takanari",
""
]... | Migrating cells possess intracellular gradients of Rho GTPases, but it is unknown whether these shallow gradients themselves can induce motility. Here we describe a new method to present cells with induced linear gradients of active, endogenous Rac without receptor activation. Gradients as low as 15% were sufficient to... |
1610.03986 | Wolfgang Halter | Wolfgang Halter, Jan Maximilian Montenbruck and Frank Allg\"ower | Geometric stability considerations of the ribosome flow model with pool | Published in the Proceedings of the 22nd International Symposium on
the Mathematical Theory of Networks and Systems, 2016,
http://hdl.handle.net/11299/181518 | null | null | null | q-bio.SC math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In order to better understand the process of gene translation, the ribosome
flow model (RFM) with pool was introduced recently. This model describes the
movement of several ribosomes along an mRNA template and simultaneously
captures the dynamics of the finite pool of ribosomes. Studying this system
with respect to t... | [
{
"created": "Thu, 13 Oct 2016 09:13:17 GMT",
"version": "v1"
}
] | 2016-10-14 | [
[
"Halter",
"Wolfgang",
""
],
[
"Montenbruck",
"Jan Maximilian",
""
],
[
"Allgöwer",
"Frank",
""
]
] | In order to better understand the process of gene translation, the ribosome flow model (RFM) with pool was introduced recently. This model describes the movement of several ribosomes along an mRNA template and simultaneously captures the dynamics of the finite pool of ribosomes. Studying this system with respect to the... |
q-bio/0502026 | Mazza | Martin Gander, Christian Mazza, Hansklaus Rummler | Stochastic gene expression in switching environments | 14 pages, 5 figures | null | null | null | q-bio.PE q-bio.CB | null | We study a stochastic model proposed recently in the genetic literature to
explain the heterogeneity of cell populations or of gene products. Cells are
located in two colonies, whose sizes fluctuate as birth and migration processes
in switching environments. We prove that there is a range of parameters where
heteroge... | [
{
"created": "Tue, 22 Feb 2005 13:56:05 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Gander",
"Martin",
""
],
[
"Mazza",
"Christian",
""
],
[
"Rummler",
"Hansklaus",
""
]
] | We study a stochastic model proposed recently in the genetic literature to explain the heterogeneity of cell populations or of gene products. Cells are located in two colonies, whose sizes fluctuate as birth and migration processes in switching environments. We prove that there is a range of parameters where heterogene... |
2110.13909 | Ghazal ArabiDarrehDor | Ghazal ArabiDarrehDor, Ali Tivay, Chris Meador, George C. Kramer,
Jin-Oh Hahn, and Jose Salinas | Mathematical Modeling, In-Human Evaluation and Analysis of Volume
Kinetics and Kidney Function after Burn Injury and Resuscitation | 24 pages The final version of this paper has been accepted for
publication in the IEEE Journal of Transactions on Biomedical Engineering
(2021) and is available for early access at
https://ieeexplore.ieee.org/document/9478222 | null | 10.1109/TBME.2021.3094515 | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Existing burn resuscitation protocols exhibit large variability in treatment
efficacy. Hence, they must be further optimized based on comprehensive
knowledge of burn pathophysiology. A physics-based mathematical model that can
replicate physiological responses in diverse burn patients can serve as an
attractive basis... | [
{
"created": "Sun, 24 Oct 2021 21:40:21 GMT",
"version": "v1"
}
] | 2021-10-28 | [
[
"ArabiDarrehDor",
"Ghazal",
""
],
[
"Tivay",
"Ali",
""
],
[
"Meador",
"Chris",
""
],
[
"Kramer",
"George C.",
""
],
[
"Hahn",
"Jin-Oh",
""
],
[
"Salinas",
"Jose",
""
]
] | Existing burn resuscitation protocols exhibit large variability in treatment efficacy. Hence, they must be further optimized based on comprehensive knowledge of burn pathophysiology. A physics-based mathematical model that can replicate physiological responses in diverse burn patients can serve as an attractive basis t... |
1906.01094 | Cecilia Jarne Dr | Cecilia Jarne and Rodrigo Laje | Exploring weight initialization, diversity of solutions, and degradation
in recurrent neural networks trained for temporal and decision-making tasks | null | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recurrent Neural Networks (RNNs) are frequently used to model aspects of
brain function and structure. In this work, we trained small fully-connected
RNNs to perform temporal and flow control tasks with time-varying stimuli. Our
results show that different RNNs can solve the same task by converging to
different under... | [
{
"created": "Mon, 3 Jun 2019 21:56:48 GMT",
"version": "v1"
},
{
"created": "Fri, 13 Sep 2019 16:23:44 GMT",
"version": "v2"
},
{
"created": "Tue, 1 Oct 2019 14:18:27 GMT",
"version": "v3"
},
{
"created": "Mon, 21 Dec 2020 14:04:01 GMT",
"version": "v4"
},
{
"cre... | 2023-06-29 | [
[
"Jarne",
"Cecilia",
""
],
[
"Laje",
"Rodrigo",
""
]
] | Recurrent Neural Networks (RNNs) are frequently used to model aspects of brain function and structure. In this work, we trained small fully-connected RNNs to perform temporal and flow control tasks with time-varying stimuli. Our results show that different RNNs can solve the same task by converging to different underly... |
1607.04064 | Michael Margaliot | Yoram Zarai and Michael Margaliot and Tamir Tuller | On the Ribosomal Density that Maximizes Protein Translation Rate | null | null | 10.1371/journal.pone.0166481 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During mRNA translation, several ribosomes attach to the same mRNA molecule
simultaneously translating it into a protein. This pipelining increases the
protein production rate. A natural and important question is what ribosomal
density maximizes the protein production rate. Using mathematical models of
ribosome flow ... | [
{
"created": "Thu, 14 Jul 2016 10:13:44 GMT",
"version": "v1"
}
] | 2017-02-08 | [
[
"Zarai",
"Yoram",
""
],
[
"Margaliot",
"Michael",
""
],
[
"Tuller",
"Tamir",
""
]
] | During mRNA translation, several ribosomes attach to the same mRNA molecule simultaneously translating it into a protein. This pipelining increases the protein production rate. A natural and important question is what ribosomal density maximizes the protein production rate. Using mathematical models of ribosome flow al... |
2012.09723 | Hsin-Yu Lai | Hsin-Yu Lai, Gladynel Saavedra-Pena, Charles G. Sodini, Thomas Heldt,
Vivienne Sze | App-based saccade latency and error determination across the adult age
spectrum | 11 pages, 16 figures, journal | null | null | null | q-bio.NC eess.IV eess.SP q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | We aid in neurocognitive monitoring outside the hospital environment by
enabling app-based measurements of visual reaction time (saccade latency) and
error rate in a cohort of subjects spanning the adult age spectrum. Methods: We
developed an iOS app to record subjects with the frontal camera during pro- and
anti-sac... | [
{
"created": "Mon, 14 Dec 2020 02:02:02 GMT",
"version": "v1"
}
] | 2020-12-18 | [
[
"Lai",
"Hsin-Yu",
""
],
[
"Saavedra-Pena",
"Gladynel",
""
],
[
"Sodini",
"Charles G.",
""
],
[
"Heldt",
"Thomas",
""
],
[
"Sze",
"Vivienne",
""
]
] | We aid in neurocognitive monitoring outside the hospital environment by enabling app-based measurements of visual reaction time (saccade latency) and error rate in a cohort of subjects spanning the adult age spectrum. Methods: We developed an iOS app to record subjects with the frontal camera during pro- and anti-sacca... |
2310.07442 | Andrea Radici | Andrea Radici, Daniele Bevacqua, Leonardo Miele, Davide Martinetti | Network-thinking to optimize surveillance and control of crop parasites.
A review | 21 pages, 3 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Increasing cultivated lands, crop homogenization and global food trade have
fostered the spread of crop pests and diseases. Optimizing crop protection is
urgently needed to ensure food safety. One aspect of crop protection is
surveillance, which focuses on the early detection of a parasite, and control,
aiming to fig... | [
{
"created": "Wed, 11 Oct 2023 12:47:29 GMT",
"version": "v1"
}
] | 2023-10-12 | [
[
"Radici",
"Andrea",
""
],
[
"Bevacqua",
"Daniele",
""
],
[
"Miele",
"Leonardo",
""
],
[
"Martinetti",
"Davide",
""
]
] | Increasing cultivated lands, crop homogenization and global food trade have fostered the spread of crop pests and diseases. Optimizing crop protection is urgently needed to ensure food safety. One aspect of crop protection is surveillance, which focuses on the early detection of a parasite, and control, aiming to fight... |
1403.4479 | Claus Bornemann PhD | Claus Bornemann | Virus-Encoded Ribonucleotide Reductases | 3 pages, 39 references | null | null | null | q-bio.BM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ribonucleotide reductases are encoded by many viruses, but without other
enzymes of nucleotide metabolism of no obvious use. A look at the enzymes'
molecular properties and their possible mutator action may give clues.
| [
{
"created": "Tue, 18 Mar 2014 14:41:26 GMT",
"version": "v1"
}
] | 2014-03-19 | [
[
"Bornemann",
"Claus",
""
]
] | Ribonucleotide reductases are encoded by many viruses, but without other enzymes of nucleotide metabolism of no obvious use. A look at the enzymes' molecular properties and their possible mutator action may give clues. |
2408.05420 | J Gregory Caporaso | Isaiah Raspet, Elizabeth Gehret, Chloe Herman, Jeff Meilander, Andrew
Manley, Anthony Simard, Evan Bolyen, J. Gregory Caporaso | Facilitating bootstrapped and rarefaction-based microbiome diversity
analysis with q2-boots | 5 pages, 1 figure, 1 supplementary table | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Background: We present q2-boots, a QIIME 2 plugin that facilitates
bootstrapped and rarefaction-based microbiome diversity analysis. This plugin
provides eight new actions that allow users to apply any of thirty different
alpha diversity metrics and twenty-two beta diversity metrics to bootstrapped
or rarefied featur... | [
{
"created": "Sat, 10 Aug 2024 03:12:15 GMT",
"version": "v1"
}
] | 2024-08-13 | [
[
"Raspet",
"Isaiah",
""
],
[
"Gehret",
"Elizabeth",
""
],
[
"Herman",
"Chloe",
""
],
[
"Meilander",
"Jeff",
""
],
[
"Manley",
"Andrew",
""
],
[
"Simard",
"Anthony",
""
],
[
"Bolyen",
"Evan",
""
],
[
... | Background: We present q2-boots, a QIIME 2 plugin that facilitates bootstrapped and rarefaction-based microbiome diversity analysis. This plugin provides eight new actions that allow users to apply any of thirty different alpha diversity metrics and twenty-two beta diversity metrics to bootstrapped or rarefied feature ... |
1502.03201 | Yann Ponty | Jozef Hale\v{s}, J\'an Ma\v{n}uch (UBC-Computer Science), Yann Ponty
(LIX, AMIB), Ladislav Stacho | Combinatorial RNA Design: Designability and Structure-Approximating
Algorithm | CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun
2015, Ischia Island, Italy. LNCS, 2015 | null | null | null | q-bio.QM cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, we consider the Combinatorial RNA Design problem, a minimal
instance of the RNA design problem which aims at finding a sequence that admits
a given target as its unique base pair maximizing structure. We provide
complete characterizations for the structures that can be designed using
restricted alphabet... | [
{
"created": "Wed, 11 Feb 2015 06:47:23 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Jun 2015 08:34:03 GMT",
"version": "v2"
}
] | 2015-06-22 | [
[
"Haleš",
"Jozef",
"",
"UBC-Computer Science"
],
[
"Maňuch",
"Ján",
"",
"UBC-Computer Science"
],
[
"Ponty",
"Yann",
"",
"LIX, AMIB"
],
[
"Stacho",
"Ladislav",
""
]
] | In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete characterizations for the structures that can be designed using restricted alphabets.... |
2303.10724 | Josinaldo Menezes | J. Menezes | Mobility restrictions in response to local epidemic outbreaks in
rock-paper-scissors models | 11 pages, 12 figures | Journal of Physics: Complex. 5, 015018 (2024) | 10.1088/2632-072X/ad2d5b | null | q-bio.PE nlin.AO nlin.PS physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study a three-species cyclic model whose organisms are vulnerable to
contamination with an infectious disease which propagates person-to-person. We
consider that individuals of one species perform an evolutionary
self-preservation strategy by reducing the mobility rate to minimise infection
risk whenever an epidem... | [
{
"created": "Sun, 19 Mar 2023 17:43:28 GMT",
"version": "v1"
}
] | 2024-06-05 | [
[
"Menezes",
"J.",
""
]
] | We study a three-species cyclic model whose organisms are vulnerable to contamination with an infectious disease which propagates person-to-person. We consider that individuals of one species perform an evolutionary self-preservation strategy by reducing the mobility rate to minimise infection risk whenever an epidemic... |
2401.14665 | Yipin Lei | Yipin Lei, Xu Wang, Meng Fang, Han Li, Xiang Li, Jianyang Zeng | PepGB: Facilitating peptide drug discovery via graph neural networks | null | null | null | null | q-bio.BM cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Peptides offer great biomedical potential and serve as promising drug
candidates. Currently, the majority of approved peptide drugs are directly
derived from well-explored natural human peptides. It is quite necessary to
utilize advanced deep learning techniques to identify novel peptide drugs in
the vast, unexplored... | [
{
"created": "Fri, 26 Jan 2024 06:13:09 GMT",
"version": "v1"
}
] | 2024-01-29 | [
[
"Lei",
"Yipin",
""
],
[
"Wang",
"Xu",
""
],
[
"Fang",
"Meng",
""
],
[
"Li",
"Han",
""
],
[
"Li",
"Xiang",
""
],
[
"Zeng",
"Jianyang",
""
]
] | Peptides offer great biomedical potential and serve as promising drug candidates. Currently, the majority of approved peptide drugs are directly derived from well-explored natural human peptides. It is quite necessary to utilize advanced deep learning techniques to identify novel peptide drugs in the vast, unexplored b... |
2101.08731 | Tomas Barta | Tomas Barta and Lubomir Kostal | Regular spiking in high conductance states: the essential role of
inhibition | null | Phys. Rev. E 103, 022408 (2021) | 10.1103/PhysRevE.103.022408 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Strong inhibitory input to neurons, which occurs in balanced states of neural
networks, increases synaptic current fluctuations. This has led to the
assumption that inhibition contributes to the high spike-firing irregularity
observed in vivo. We used single compartment neuronal models with
time-correlated (due to sy... | [
{
"created": "Thu, 21 Jan 2021 17:14:25 GMT",
"version": "v1"
},
{
"created": "Thu, 4 Feb 2021 14:50:11 GMT",
"version": "v2"
},
{
"created": "Thu, 18 Feb 2021 16:30:18 GMT",
"version": "v3"
}
] | 2021-02-19 | [
[
"Barta",
"Tomas",
""
],
[
"Kostal",
"Lubomir",
""
]
] | Strong inhibitory input to neurons, which occurs in balanced states of neural networks, increases synaptic current fluctuations. This has led to the assumption that inhibition contributes to the high spike-firing irregularity observed in vivo. We used single compartment neuronal models with time-correlated (due to syna... |
2106.09444 | Birgitta Dresp-Langley | Birgitta Dresp-Langley, JM Wandeto | Unsupervised classification of cell imaging data using the quantization
error in a Self Organizing Map | arXiv admin note: substantial text overlap with arXiv:2011.05209,
arXiv:2011.03970 | In HR Arabnia, K Ferens, D de la Fuente, EB Kozerenko, JA Olivas
Varela, FG Tinetti (Eds.), Transactions on Computational Science and
Computational Intelligence. Springer-Nature, 2021, pp. 201-210 | 10.1007/978-3-030-70296-0_16 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This study exploits previously demonstrated properties such as sensitivity to
the spatial extent and the intensity of local image contrast of the
quantization error in the output of a Self Organizing Map (SOM QE). Here, the
SOM QE is applied to double color staining based cell viability data in 96
image simulations. ... | [
{
"created": "Thu, 17 Jun 2021 12:53:55 GMT",
"version": "v1"
}
] | 2021-10-18 | [
[
"Dresp-Langley",
"Birgitta",
""
],
[
"Wandeto",
"JM",
""
]
] | This study exploits previously demonstrated properties such as sensitivity to the spatial extent and the intensity of local image contrast of the quantization error in the output of a Self Organizing Map (SOM QE). Here, the SOM QE is applied to double color staining based cell viability data in 96 image simulations. Th... |
1702.00094 | Masaki Ogura Dr. | Masaki Ogura, Masashi Wakaiki, Harvey Rubin, Victor M. Preciado | Delayed Bet-Hedging Resilience Strategies Under Environmental
Fluctuations | null | null | 10.1103/PhysRevE.95.052404 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many biological populations, such as bacterial colonies, have developed
through evolution a protection mechanism, called bet-hedging, to increase their
probability of survival under stressful environmental fluctutation. In this
context, the concept of preadaptation refers to a common type of bet-hedging
protection st... | [
{
"created": "Wed, 1 Feb 2017 00:41:23 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Apr 2017 01:57:52 GMT",
"version": "v2"
}
] | 2017-05-24 | [
[
"Ogura",
"Masaki",
""
],
[
"Wakaiki",
"Masashi",
""
],
[
"Rubin",
"Harvey",
""
],
[
"Preciado",
"Victor M.",
""
]
] | Many biological populations, such as bacterial colonies, have developed through evolution a protection mechanism, called bet-hedging, to increase their probability of survival under stressful environmental fluctutation. In this context, the concept of preadaptation refers to a common type of bet-hedging protection stra... |
1607.02581 | Raul Isea | Raul Isea | A Potential Correlation Between the Temperature of the Pacific Ocean and
Data from Google Trends May Yield a Warning Sign for the Outbreak of Zika | 3 pages, 2 figures, Open Access | American Journal of Social Sciences (2016), Vol. 4, No. 2, pp.
12-14 | null | null | q-bio.PE | http://creativecommons.org/publicdomain/zero/1.0/ | There has been a large number of reported cases of the occurrence of Zika in
different countries in 2016 and it is necessary to develop an early warning
system to initiate preventive campaigns against the disease. A potential early
warning system based on the rise in ocean temperature of the Pacific Ni\~no
Index is p... | [
{
"created": "Sat, 9 Jul 2016 07:58:46 GMT",
"version": "v1"
}
] | 2016-07-12 | [
[
"Isea",
"Raul",
""
]
] | There has been a large number of reported cases of the occurrence of Zika in different countries in 2016 and it is necessary to develop an early warning system to initiate preventive campaigns against the disease. A potential early warning system based on the rise in ocean temperature of the Pacific Ni\~no Index is pro... |
2004.06021 | Ivan Cherednik | Ivan Cherednik | Momentum managing epidemic spread and Bessel functions | 54 pages, 29 figures, v5: the two-phase formula for the spread was
added covering practically the whole periods of Covid-19 in many countries;
v6: the second waves were considered, editing; v7: some data refreshed,
Journal reference added | Chaos, Solitons & Fractals, Volume 139, October 2020, 110234 | 10.1016/j.chaos.2020.110234 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Starting with the power law for the total number of detected infections, we
propose differential equations describing the effect of momentum epidemic
management. Our 2-phase formula matches very well the curves of the total
numbers of the Covid-19 infections in many countries; the first phase is
described by Bessel f... | [
{
"created": "Mon, 13 Apr 2020 15:54:31 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Apr 2020 16:19:53 GMT",
"version": "v2"
},
{
"created": "Mon, 20 Apr 2020 15:36:56 GMT",
"version": "v3"
},
{
"created": "Thu, 7 May 2020 10:18:50 GMT",
"version": "v4"
},
{
"cr... | 2020-10-12 | [
[
"Cherednik",
"Ivan",
""
]
] | Starting with the power law for the total number of detected infections, we propose differential equations describing the effect of momentum epidemic management. Our 2-phase formula matches very well the curves of the total numbers of the Covid-19 infections in many countries; the first phase is described by Bessel fun... |
2311.16784 | Giuseppe Tronci | Charles Brooker, Giuseppe Tronci | Infection-responsivity of Commercial Dressings Through Halochromic
Drop-casting | 6 pages, 3 figures, 2 tables. Accepted in AIP conference proceedings | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Infection control remains one of the most challenging tasks in wound care,
due to growing antimicrobial resistance and ineffective infection diagnostic
tools at the point-of-care. To integrate therapeutic wound dressings with wound
monitoring capability at the point-of-care to enable informed clinical
decision-making... | [
{
"created": "Tue, 28 Nov 2023 13:47:22 GMT",
"version": "v1"
}
] | 2023-11-29 | [
[
"Brooker",
"Charles",
""
],
[
"Tronci",
"Giuseppe",
""
]
] | Infection control remains one of the most challenging tasks in wound care, due to growing antimicrobial resistance and ineffective infection diagnostic tools at the point-of-care. To integrate therapeutic wound dressings with wound monitoring capability at the point-of-care to enable informed clinical decision-making, ... |
q-bio/0502006 | Ophir Flomenbom | Ophir Flomenbom, Joseph Klafter, and Attila Szabo | What can one learn from two-state single molecule trajectories? | Biophys. J., in press (2005) | Biophys. J. 88, 3780-3783 (2005) | 10.1529/biophysj.104.055905 | null | q-bio.SC q-bio.QM | null | A time trajectory of an observable that fluctuates between two values (say,
on and off), stemming from some unknown multi-substate kinetic scheme, is the
output of many single molecule experiments. Here we show that when all
successive waiting times along the trajectory are uncorrelated the on and the
off waiting tim... | [
{
"created": "Tue, 8 Feb 2005 00:56:08 GMT",
"version": "v1"
}
] | 2010-08-16 | [
[
"Flomenbom",
"Ophir",
""
],
[
"Klafter",
"Joseph",
""
],
[
"Szabo",
"Attila",
""
]
] | A time trajectory of an observable that fluctuates between two values (say, on and off), stemming from some unknown multi-substate kinetic scheme, is the output of many single molecule experiments. Here we show that when all successive waiting times along the trajectory are uncorrelated the on and the off waiting time ... |
2108.02810 | Sujit Datta | Daniel B. Amchin, Jenna A. Ott, Tapomoy Bhattacharjee, Sujit S. Datta | Influence of confinement on the spreading of bacterial populations | null | PLoS Computational Biology, 18, e1010063 (2022) | 10.1371/journal.pcbi.1010063 | null | q-bio.PE cond-mat.soft nlin.PS physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The spreading of bacterial populations is central to processes in
agriculture, the environment, and medicine. However, existing models of
spreading typically focus on cells in unconfined settings--despite the fact
that many bacteria inhabit complex and crowded environments, such as soils,
sediments, and biological ti... | [
{
"created": "Thu, 5 Aug 2021 18:53:51 GMT",
"version": "v1"
}
] | 2022-06-07 | [
[
"Amchin",
"Daniel B.",
""
],
[
"Ott",
"Jenna A.",
""
],
[
"Bhattacharjee",
"Tapomoy",
""
],
[
"Datta",
"Sujit S.",
""
]
] | The spreading of bacterial populations is central to processes in agriculture, the environment, and medicine. However, existing models of spreading typically focus on cells in unconfined settings--despite the fact that many bacteria inhabit complex and crowded environments, such as soils, sediments, and biological tiss... |
2401.08585 | Stephen Clark | Sean Tull, Razin A. Shaikh, Sara Sabrina Zemljic and Stephen Clark | From Conceptual Spaces to Quantum Concepts: Formalising and Learning
Structured Conceptual Models | This article consolidates our previous reports on concept
formalisation and learning: arXiv:2302.14822 and arXiv:2203.11216 | null | null | null | q-bio.NC cs.AI quant-ph | http://creativecommons.org/licenses/by/4.0/ | In this article we present a new modelling framework for structured concepts
using a category-theoretic generalisation of conceptual spaces, and show how
the conceptual representations can be learned automatically from data, using
two very different instantiations: one classical and one quantum. A
contribution of the... | [
{
"created": "Mon, 6 Nov 2023 15:08:22 GMT",
"version": "v1"
}
] | 2024-01-18 | [
[
"Tull",
"Sean",
""
],
[
"Shaikh",
"Razin A.",
""
],
[
"Zemljic",
"Sara Sabrina",
""
],
[
"Clark",
"Stephen",
""
]
] | In this article we present a new modelling framework for structured concepts using a category-theoretic generalisation of conceptual spaces, and show how the conceptual representations can be learned automatically from data, using two very different instantiations: one classical and one quantum. A contribution of the w... |
1310.1453 | Yoshinori Takano | Yoshinori Takano, Yoshito Chikaraishi, Naohiko Ohkouchi | Enantiomer-specific isotope analysis of D- and L-alanine: Nitrogen
isotopic hetero- and homogeneity in microbial and chemical processes | ISBN: 9784876989607 | Earth, Life, and Isotopes (Kyoto University Press), pp. 387-402
(2010) | null | null | q-bio.BM astro-ph.EP | http://creativecommons.org/licenses/publicdomain/ | Nitrogen isotopic hetero- and homogeneity of D-{\alpha}-alanine and
L-{\alpha}-alanine were investigated in microbial processes in the domain
Bacteria and in chemical processes in symmetric organic synthesis. D-alanine is
an enantiomer that is physiologically essential for microbial growth and
metabolic maintenance. ... | [
{
"created": "Sat, 5 Oct 2013 07:52:01 GMT",
"version": "v1"
}
] | 2013-10-08 | [
[
"Takano",
"Yoshinori",
""
],
[
"Chikaraishi",
"Yoshito",
""
],
[
"Ohkouchi",
"Naohiko",
""
]
] | Nitrogen isotopic hetero- and homogeneity of D-{\alpha}-alanine and L-{\alpha}-alanine were investigated in microbial processes in the domain Bacteria and in chemical processes in symmetric organic synthesis. D-alanine is an enantiomer that is physiologically essential for microbial growth and metabolic maintenance. Th... |
1511.07959 | Christoph Adami | Thomas LaBar, Arend Hintze, and Christoph Adami | Evolvability tradeoffs in emergent digital replicators | 26 pages, 5 figures. Revised version, title changed | Artificial Life 22 (2016) 483-498 | 10.1162/ARTL_a_00214 | null | q-bio.PE nlin.AO q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The role of historical contingency in the origin of life is one of the great
unknowns in modern science. Only one example of life exists--one that proceeded
from a single self-replicating organism (or a set of replicating hyper-cycles)
to the vast complexity we see today in Earth's biosphere. We know that emergent
li... | [
{
"created": "Wed, 25 Nov 2015 06:04:05 GMT",
"version": "v1"
},
{
"created": "Thu, 7 Apr 2016 14:05:46 GMT",
"version": "v2"
}
] | 2016-12-07 | [
[
"LaBar",
"Thomas",
""
],
[
"Hintze",
"Arend",
""
],
[
"Adami",
"Christoph",
""
]
] | The role of historical contingency in the origin of life is one of the great unknowns in modern science. Only one example of life exists--one that proceeded from a single self-replicating organism (or a set of replicating hyper-cycles) to the vast complexity we see today in Earth's biosphere. We know that emergent life... |
2103.02417 | Bharath Ambale Venkatesh | Vivek P. Jani, Nadjia Kachenoura, Alban Redheuil, Gisela Teixido-Tura,
Kevin Bouaou, Emilie Bollache, Elie Mousseaux, Alain De Cesare, Shelby Kutty,
Colin O. Wu, David A. Bluemke, Joao A. C. Lima, Bharath Ambale-Venkatesh | Deep Learning-based Automated Aortic Area and Distensibility Assessment:
The Multi-Ethnic Study of Atherosclerosis (MESA) | 25 pages, 5 figures | null | null | null | q-bio.QM eess.IV | http://creativecommons.org/licenses/by-nc-sa/4.0/ | This study applies convolutional neural network (CNN)-based automatic
segmentation and distensibility measurement of the ascending and descending
aorta from 2D phase-contrast cine magnetic resonance imaging (PC-cine MRI)
within the large MESA cohort with subsequent assessment on an external cohort
of thoracic aortic ... | [
{
"created": "Wed, 3 Mar 2021 14:11:24 GMT",
"version": "v1"
}
] | 2021-03-04 | [
[
"Jani",
"Vivek P.",
""
],
[
"Kachenoura",
"Nadjia",
""
],
[
"Redheuil",
"Alban",
""
],
[
"Teixido-Tura",
"Gisela",
""
],
[
"Bouaou",
"Kevin",
""
],
[
"Bollache",
"Emilie",
""
],
[
"Mousseaux",
"Elie",
""
... | This study applies convolutional neural network (CNN)-based automatic segmentation and distensibility measurement of the ascending and descending aorta from 2D phase-contrast cine magnetic resonance imaging (PC-cine MRI) within the large MESA cohort with subsequent assessment on an external cohort of thoracic aortic an... |
q-bio/0508044 | William Bialek | William Bialek | Should you believe that this coin is fair? | null | null | null | null | q-bio.NC q-bio.QM | null | Faced with a sequence of N binary events, such as coin flips (or Ising
spins), it is natural to ask whether these events reflect some underlying
dynamic signals or are just random. Plausible models for the dynamics of hidden
biases lead to surprisingly high probabilities of misidentifying random
sequences as biased. ... | [
{
"created": "Tue, 30 Aug 2005 03:28:36 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bialek",
"William",
""
]
] | Faced with a sequence of N binary events, such as coin flips (or Ising spins), it is natural to ask whether these events reflect some underlying dynamic signals or are just random. Plausible models for the dynamics of hidden biases lead to surprisingly high probabilities of misidentifying random sequences as biased. In... |
2002.02425 | Marco Alberto Javarone | Marco Alberto Javarone, Olivia Gosseries, Daniele Marinazzo, Quentin
Noirhomme, Vincent Bonhomme, Steven Laureys, Srivas Chennu | A mean field approach to model levels of consciousness from EEG
recordings | 23 pages, 6 figures. Accepted for publication in Journal of
Statistical Mechanics: Theory and Experiment | null | null | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a mean-field model for analysing the dynamics of human
consciousness. In particular, inspired by the Giulio Tononi's Integrated
Information Theory and by the Max Tegmark's representation of consciousness, we
study order-disorder phase transitions on Curie-Weiss models generated by
processing EEG signals.... | [
{
"created": "Thu, 6 Feb 2020 18:09:37 GMT",
"version": "v1"
},
{
"created": "Tue, 4 Aug 2020 16:03:08 GMT",
"version": "v2"
}
] | 2020-08-05 | [
[
"Javarone",
"Marco Alberto",
""
],
[
"Gosseries",
"Olivia",
""
],
[
"Marinazzo",
"Daniele",
""
],
[
"Noirhomme",
"Quentin",
""
],
[
"Bonhomme",
"Vincent",
""
],
[
"Laureys",
"Steven",
""
],
[
"Chennu",
"Srivas"... | We introduce a mean-field model for analysing the dynamics of human consciousness. In particular, inspired by the Giulio Tononi's Integrated Information Theory and by the Max Tegmark's representation of consciousness, we study order-disorder phase transitions on Curie-Weiss models generated by processing EEG signals. T... |
2210.01537 | Andreas Christ S{\o}lvsten J{\o}rgensen | Andreas Christ S{\o}lvsten J{\o}rgensen, Ciaran Scott Hill, Marc
Sturrock, Wenhao Tang, Saketh R. Karamched, Dunja Gorup, Mark F. Lythgoe,
Simona Parrinello, Samuel Marguerat, Vahid Shahrezaei | Data-driven spatio-temporal modelling of glioblastoma | 30 pages, 3 figures, 3 tables | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Mathematical oncology provides unique and invaluable insights into tumour
growth on both the microscopic and macroscopic levels. This review presents
state-of-the-art modelling techniques and focuses on their role in
understanding glioblastoma, a malignant form of brain cancer. For each
approach, we summarise the sco... | [
{
"created": "Tue, 4 Oct 2022 11:43:34 GMT",
"version": "v1"
}
] | 2022-10-05 | [
[
"Jørgensen",
"Andreas Christ Sølvsten",
""
],
[
"Hill",
"Ciaran Scott",
""
],
[
"Sturrock",
"Marc",
""
],
[
"Tang",
"Wenhao",
""
],
[
"Karamched",
"Saketh R.",
""
],
[
"Gorup",
"Dunja",
""
],
[
"Lythgoe",
"Mark... | Mathematical oncology provides unique and invaluable insights into tumour growth on both the microscopic and macroscopic levels. This review presents state-of-the-art modelling techniques and focuses on their role in understanding glioblastoma, a malignant form of brain cancer. For each approach, we summarise the scope... |
1312.4590 | John Bechhoefer | A. Baker and J. Bechhoefer | Inferring the spatiotemporal DNA replication program from noisy data | 14 pages, 7 figures | Phys. Rev. E 89, 032703 (2014) | 10.1103/PhysRevE.89.032703 | null | q-bio.QM cond-mat.stat-mech physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We generalize a stochastic model of DNA replication to the case where
replication-origin-initiation rates vary locally along the genome and with
time. Using this generalized model, we address the inverse problem of inferring
initiation rates from experimental data concerning replication in cell
populations. Previous ... | [
{
"created": "Mon, 16 Dec 2013 23:12:51 GMT",
"version": "v1"
}
] | 2015-04-02 | [
[
"Baker",
"A.",
""
],
[
"Bechhoefer",
"J.",
""
]
] | We generalize a stochastic model of DNA replication to the case where replication-origin-initiation rates vary locally along the genome and with time. Using this generalized model, we address the inverse problem of inferring initiation rates from experimental data concerning replication in cell populations. Previous wo... |
1010.1743 | Jaewook Joo | Jaewook Joo | Linear noise approximation of noise-induced oscillation in NF-{\kappa}B
signaling network | 19 pages, 5 figures | null | null | null | q-bio.MN q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | NF-{\kappa}B, one of key regulators of inflammation, apoptosis, and
differentiation, was found to have noisy oscillatory shuttling between the
nucleus and the cytoplasm in single cells when cells are stimulated by cytokine
TNF{\alpha}. We present the analytical analysis which uncovers the underlying
physical mechanis... | [
{
"created": "Fri, 8 Oct 2010 17:26:42 GMT",
"version": "v1"
}
] | 2010-10-11 | [
[
"Joo",
"Jaewook",
""
]
] | NF-{\kappa}B, one of key regulators of inflammation, apoptosis, and differentiation, was found to have noisy oscillatory shuttling between the nucleus and the cytoplasm in single cells when cells are stimulated by cytokine TNF{\alpha}. We present the analytical analysis which uncovers the underlying physical mechanisms... |
1304.2018 | Romann Weber | Romann M. Weber | Beyond Spikes: Neural Codes and the Chemical Vocabulary of Cognition | 19 pages, 2 figures; revised version | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, I examine what I refer to as the spike doctrine, which is the
generally held belief in neuroscience that information in the brain is encoded
by sequences of neural action potentials. I present the argument that specific
neurochemicals, and not spikes, are the elementary units of information in the
brai... | [
{
"created": "Sun, 7 Apr 2013 16:23:50 GMT",
"version": "v1"
},
{
"created": "Sun, 2 Jun 2013 13:08:56 GMT",
"version": "v2"
}
] | 2013-06-04 | [
[
"Weber",
"Romann M.",
""
]
] | In this paper, I examine what I refer to as the spike doctrine, which is the generally held belief in neuroscience that information in the brain is encoded by sequences of neural action potentials. I present the argument that specific neurochemicals, and not spikes, are the elementary units of information in the brain.... |
2003.12233 | Tom Chou | Mingtao Xia, Chris D. Greenman, and Tom Chou | PDE models of adder mechanisms in cellular proliferation | 23 pages, 8 figures | null | null | null | q-bio.CB math.AP | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Cell division is a process that involves many biochemical steps and complex
biophysical mechanisms. To simplify the understanding of what triggers cell
division, three basic models that subsume more microscopic cellular processes
associated with cell division have been proposed. Cells can divide based on the
time ela... | [
{
"created": "Fri, 27 Mar 2020 04:50:45 GMT",
"version": "v1"
}
] | 2020-03-30 | [
[
"Xia",
"Mingtao",
""
],
[
"Greenman",
"Chris D.",
""
],
[
"Chou",
"Tom",
""
]
] | Cell division is a process that involves many biochemical steps and complex biophysical mechanisms. To simplify the understanding of what triggers cell division, three basic models that subsume more microscopic cellular processes associated with cell division have been proposed. Cells can divide based on the time elaps... |
1112.3663 | Lorenzo Pareschi | A. Boccabella, R. Natalini, L. Pareschi | On a continuous mixed strategies model for evolutionary game theory | null | Kinetic and Related Models 4, 187-213 (2011) | null | null | q-bio.PE cond-mat.stat-mech math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider an integro-differential model for evolutionary game theory which
describes the evolution of a population adopting mixed strategies. Using a
reformulation based on the first moments of the solution, we prove some
analytical properties of the model and global estimates. The asymptotic
behavior and the stabi... | [
{
"created": "Wed, 14 Dec 2011 17:45:16 GMT",
"version": "v1"
}
] | 2011-12-19 | [
[
"Boccabella",
"A.",
""
],
[
"Natalini",
"R.",
""
],
[
"Pareschi",
"L.",
""
]
] | We consider an integro-differential model for evolutionary game theory which describes the evolution of a population adopting mixed strategies. Using a reformulation based on the first moments of the solution, we prove some analytical properties of the model and global estimates. The asymptotic behavior and the stabili... |
1407.5856 | Alejandro F Villaverde | Alejandro F Villaverde, David Henriques, Kieran Smallbone, Sophia
Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio
Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger,
and Julio R Banga | BioPreDyn-bench: benchmark problems for kinetic modelling in systems
biology | null | BMC Systems Biology 2015 9:8 | 10.1186/s12918-015-0144- | null | q-bio.QM cs.CE q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dynamic modelling is one of the cornerstones of systems biology. Many
research efforts are currently being invested in the development and
exploitation of large-scale kinetic models. The associated problems of
parameter estimation (model calibration) and optimal experimental design are
particularly challenging. The c... | [
{
"created": "Tue, 22 Jul 2014 13:31:05 GMT",
"version": "v1"
}
] | 2017-03-22 | [
[
"Villaverde",
"Alejandro F",
""
],
[
"Henriques",
"David",
""
],
[
"Smallbone",
"Kieran",
""
],
[
"Bongard",
"Sophia",
""
],
[
"Schmid",
"Joachim",
""
],
[
"Cicin-Sain",
"Damjan",
""
],
[
"Crombach",
"Anton",
... | Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of parameter estimation (model calibration) and optimal experimental design are particularly challenging. The com... |
1701.02908 | Ricardo Martinez-Garcia | Ricardo Martinez-Garcia | Nonequilibrium Statistical Physics in Ecology: Vegetation Patterns,
Animal Mobility and Temporal Fluctuations | PhD Thesis | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This thesis focuses on the applications of mathematical tools and concepts
brought from nonequilibrium statistical physics to the modeling of ecological
problems.
The first part provides a short introduction where the theoretical concepts
and mathematical tools that are going to be used in subsequent chapters are
p... | [
{
"created": "Wed, 11 Jan 2017 09:56:45 GMT",
"version": "v1"
}
] | 2017-01-12 | [
[
"Martinez-Garcia",
"Ricardo",
""
]
] | This thesis focuses on the applications of mathematical tools and concepts brought from nonequilibrium statistical physics to the modeling of ecological problems. The first part provides a short introduction where the theoretical concepts and mathematical tools that are going to be used in subsequent chapters are prese... |
1411.4121 | Zuo-Bing Wu | Zuo-Bing Wu | Analysis of correlation structures in the Synechocystis PCC6803 genome | 29 pages, 6 figures | Computational Biology and Chemistry, Vol. 53, pp. 49-58 (2014) | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transfer of nucleotide strings in the Synechocystis sp. PCC6803 genome is
investigated to exhibit periodic and non-periodic correlation structures by
using the recurrence plot method and the phase space reconstruction technique.
The periodic correlation structures are generated by periodic transfer of
several substri... | [
{
"created": "Sat, 15 Nov 2014 07:40:04 GMT",
"version": "v1"
}
] | 2014-11-18 | [
[
"Wu",
"Zuo-Bing",
""
]
] | Transfer of nucleotide strings in the Synechocystis sp. PCC6803 genome is investigated to exhibit periodic and non-periodic correlation structures by using the recurrence plot method and the phase space reconstruction technique. The periodic correlation structures are generated by periodic transfer of several substring... |
1909.11597 | Abbas Saberi Abbas Ali Saberi | Youness Azimzade, and Abbas Ali Saberi | Short-Range Migration Can Alter Evolutionary Dynamics in Solid Tumors | 8 pages, 6 figures (to appear in JSTAT) | J. Stat. Mech.(JSTAT) (2019) 103502 | 10.1088/1742-5468/ab4983 | null | q-bio.PE cond-mat.soft physics.bio-ph q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here, we investigate how competition in the Eden model is affected by short
range dispersal and the requirement that site updates occur only after several
updates of the same site have been attempted previously. The latter models the
effect of tissue or media resistance to invasion. We found that the existence
of tis... | [
{
"created": "Wed, 25 Sep 2019 16:34:07 GMT",
"version": "v1"
}
] | 2019-12-05 | [
[
"Azimzade",
"Youness",
""
],
[
"Saberi",
"Abbas Ali",
""
]
] | Here, we investigate how competition in the Eden model is affected by short range dispersal and the requirement that site updates occur only after several updates of the same site have been attempted previously. The latter models the effect of tissue or media resistance to invasion. We found that the existence of tissu... |
1101.5865 | Peter Csermely | Peter Csermely, Kuljeet Singh Sandhu, Eszter Hazai, Zsolt Hoksza, Huba
J.M. Kiss, Federico Miozzo, Daniel V. Veres, Francesco Piazza and Ruth
Nussinov | Disordered proteins and network disorder in network descriptions of
protein structure, dynamics and function. Hypotheses and a comprehensive
review | 27 pages, 2 Tables, 5 Figures and 161 references | Current Protein and Peptide Science 13, 19-33 (2012) | null | null | q-bio.MN cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During the last decade, network approaches became a powerful tool to describe
protein structure and dynamics. Here we review the links between disordered
proteins and the associated networks, and describe the consequences of local,
mesoscopic and global network disorder on changes in protein structure and
dynamics. W... | [
{
"created": "Mon, 31 Jan 2011 07:55:53 GMT",
"version": "v1"
},
{
"created": "Sun, 6 Feb 2011 08:27:53 GMT",
"version": "v2"
},
{
"created": "Fri, 2 Mar 2012 15:09:49 GMT",
"version": "v3"
}
] | 2012-03-05 | [
[
"Csermely",
"Peter",
""
],
[
"Sandhu",
"Kuljeet Singh",
""
],
[
"Hazai",
"Eszter",
""
],
[
"Hoksza",
"Zsolt",
""
],
[
"Kiss",
"Huba J. M.",
""
],
[
"Miozzo",
"Federico",
""
],
[
"Veres",
"Daniel V.",
""
]... | During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We ... |
1910.05332 | Wolfram M\"obius | Wolfram M\"obius, Francesca Tesser, Kim M. J. Alards, Roberto Benzi,
David R. Nelson, Federico Toschi | The collective effect of finite-sized inhomogeneities on the spatial
spread of populations in two dimensions | Authors Wolfram M\"obius and Francesca Tesser contributed equally | null | null | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The dynamics of a population expanding into unoccupied habitat has been
primarily studied for situations in which growth and dispersal parameters are
uniform in space or vary in one dimension. Here we study the influence of
finite-sized individual inhomogeneities and their collective effect on front
speed if randomly... | [
{
"created": "Fri, 11 Oct 2019 17:54:18 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Sep 2021 07:52:01 GMT",
"version": "v2"
}
] | 2021-09-21 | [
[
"Möbius",
"Wolfram",
""
],
[
"Tesser",
"Francesca",
""
],
[
"Alards",
"Kim M. J.",
""
],
[
"Benzi",
"Roberto",
""
],
[
"Nelson",
"David R.",
""
],
[
"Toschi",
"Federico",
""
]
] | The dynamics of a population expanding into unoccupied habitat has been primarily studied for situations in which growth and dispersal parameters are uniform in space or vary in one dimension. Here we study the influence of finite-sized individual inhomogeneities and their collective effect on front speed if randomly p... |
2301.03878 | Gabriel Cia | Gabriel Cia, Fabrizio Pucci, Marianne Rooman | Critical review of conformational B-cell epitope prediction methods | 19 pages, 2 figures, 3 tables | Briefings in Bioinformatics, bbac567, 1-9, 2023 | 10.1093/bib/bbac567 | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Accurate in-silico prediction of conformational B-cell epitopes would lead to
major improvements in disease diagnostics, drug design and vaccine development.
A variety of computational methods, mainly based on machine learning
approaches, have been developed in the last decades to tackle this challenging
problem. Her... | [
{
"created": "Tue, 10 Jan 2023 10:01:16 GMT",
"version": "v1"
}
] | 2023-01-11 | [
[
"Cia",
"Gabriel",
""
],
[
"Pucci",
"Fabrizio",
""
],
[
"Rooman",
"Marianne",
""
]
] | Accurate in-silico prediction of conformational B-cell epitopes would lead to major improvements in disease diagnostics, drug design and vaccine development. A variety of computational methods, mainly based on machine learning approaches, have been developed in the last decades to tackle this challenging problem. Here,... |
2205.07656 | Hilla De-Leon | Hilla De-Leon and Francesco Pederiva | Using a physical model and aggregate data to estimate the spreading of
Covid-19 in Israel in the presence of waning immunity and competing variants | 9 pages 8 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In more than two years since the COVID-19 virus was first detected in China,
hundreds of millions of individuals have been infected, and millions have died.
Aside from the immediate need for medical solutions (such as vaccines and
medications) to treat the epidemic, the Corona pandemic has strengthened the
demand for... | [
{
"created": "Mon, 16 May 2022 13:19:52 GMT",
"version": "v1"
}
] | 2022-05-17 | [
[
"De-Leon",
"Hilla",
""
],
[
"Pederiva",
"Francesco",
""
]
] | In more than two years since the COVID-19 virus was first detected in China, hundreds of millions of individuals have been infected, and millions have died. Aside from the immediate need for medical solutions (such as vaccines and medications) to treat the epidemic, the Corona pandemic has strengthened the demand for m... |
1111.7183 | Arry Yanuar | Arry Yanuar, Abdul Mun'im, Akma Bertha Aprima Lagho, Rezi Riadhi
Syahdi, Marjuqi Rahmat, Heru Suhartanto | Medicinal Plants Database and Three Dimensional Structure of the
Chemical Compounds from Medicinal Plants in Indonesia | 4 pages, 3 figures | Int. J. Comp. Sci. Issue (2011), Vol. 8, Issue 5, No. 1, p180 -
183 | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During this era of new drug designing, medicinal plants had become a very
interesting object of further research. Pharmacology screening of active
compound of medicinal plants would be time consuming and costly. Molecular
docking is one of the in silico method which is more efficient compare to in
vitro or in vivo me... | [
{
"created": "Tue, 29 Nov 2011 01:30:06 GMT",
"version": "v1"
}
] | 2012-10-17 | [
[
"Yanuar",
"Arry",
""
],
[
"Mun'im",
"Abdul",
""
],
[
"Lagho",
"Akma Bertha Aprima",
""
],
[
"Syahdi",
"Rezi Riadhi",
""
],
[
"Rahmat",
"Marjuqi",
""
],
[
"Suhartanto",
"Heru",
""
]
] | During this era of new drug designing, medicinal plants had become a very interesting object of further research. Pharmacology screening of active compound of medicinal plants would be time consuming and costly. Molecular docking is one of the in silico method which is more efficient compare to in vitro or in vivo meth... |
2306.03987 | Mary Lisa Manning | Elizabeth Lawson-Keister, Tao Zhang, M. Lisa Manning | Differences in boundary behavior in the 3D vertex and Voronoi models | 10 pages, 5 figures | null | null | null | q-bio.TO cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An important open question in the modeling of biological tissues is how to
identify the right scale for coarse-graining, or equivalently, the right number
of degrees of freedom. For confluent biological tissues, both vertex and
Voronoi models, which differ only in their representation of the degrees of
freedom, have ... | [
{
"created": "Tue, 6 Jun 2023 19:48:41 GMT",
"version": "v1"
}
] | 2023-06-08 | [
[
"Lawson-Keister",
"Elizabeth",
""
],
[
"Zhang",
"Tao",
""
],
[
"Manning",
"M. Lisa",
""
]
] | An important open question in the modeling of biological tissues is how to identify the right scale for coarse-graining, or equivalently, the right number of degrees of freedom. For confluent biological tissues, both vertex and Voronoi models, which differ only in their representation of the degrees of freedom, have ef... |
2009.08309 | Charis Mesaritakis | Menelaos Skontranis, George Sarantoglou, Stavros Deligiannidis, Adonis
Bogris, Charis Mesaritakis | Unsupervised Image Classification Through Time-Multiplexed Photonic
Multi-Layer Spiking Convolutional Neural Network | 4 pages, 3 figures | null | 10.1109/ECOC48923.2020.9333320 | null | q-bio.NC eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present results of a deep photonic spiking convolutional neural network,
based on two-section VCSELs, targeting image classification. Training is based
on unsupervised spike-timing dependent plasticity, whereas neuron
time-multiplexing and ultra-fast response are exploited towards a a reduction
of the physical neu... | [
{
"created": "Wed, 16 Sep 2020 07:52:32 GMT",
"version": "v1"
}
] | 2021-03-30 | [
[
"Skontranis",
"Menelaos",
""
],
[
"Sarantoglou",
"George",
""
],
[
"Deligiannidis",
"Stavros",
""
],
[
"Bogris",
"Adonis",
""
],
[
"Mesaritakis",
"Charis",
""
]
] | We present results of a deep photonic spiking convolutional neural network, based on two-section VCSELs, targeting image classification. Training is based on unsupervised spike-timing dependent plasticity, whereas neuron time-multiplexing and ultra-fast response are exploited towards a a reduction of the physical neuro... |
2302.09151 | Jin Xu | Jin Xu, Gary Geng, Nhan D. Nguyen, Carmen Perena-Cortes, Claire
Samuels, Herbert M. Sauro | SBcoyote: An Extensible Python-Based Reaction Editor and Viewer | null | null | 10.1016/j.biosystems.2023.105001 | null | q-bio.QM q-bio.MN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | SBcoyote is an open-source cross-platform biochemical reaction viewer and
editor released under the liberal MIT license. It is written in Python and uses
wxPython to implement the GUI and the drawing canvas. It supports the
visualization and editing of compartments, species, and reactions. It includes
many options to... | [
{
"created": "Fri, 17 Feb 2023 21:24:44 GMT",
"version": "v1"
},
{
"created": "Mon, 14 Aug 2023 21:43:47 GMT",
"version": "v2"
}
] | 2024-02-14 | [
[
"Xu",
"Jin",
""
],
[
"Geng",
"Gary",
""
],
[
"Nguyen",
"Nhan D.",
""
],
[
"Perena-Cortes",
"Carmen",
""
],
[
"Samuels",
"Claire",
""
],
[
"Sauro",
"Herbert M.",
""
]
] | SBcoyote is an open-source cross-platform biochemical reaction viewer and editor released under the liberal MIT license. It is written in Python and uses wxPython to implement the GUI and the drawing canvas. It supports the visualization and editing of compartments, species, and reactions. It includes many options to s... |
2212.02504 | Jonas Ditz | Jonas C. Ditz, Bernhard Reuter, Nico Pfeifer | COmic: Convolutional Kernel Networks for Interpretable End-to-End
Learning on (Multi-)Omics Data | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Motivation: The size of available omics datasets is steadily increasing with
technological advancement in recent years. While this increase in sample size
can be used to improve the performance of relevant prediction tasks in
healthcare, models that are optimized for large datasets usually operate as
black boxes. In ... | [
{
"created": "Fri, 2 Dec 2022 12:54:27 GMT",
"version": "v1"
},
{
"created": "Wed, 3 May 2023 11:51:34 GMT",
"version": "v2"
}
] | 2023-05-04 | [
[
"Ditz",
"Jonas C.",
""
],
[
"Reuter",
"Bernhard",
""
],
[
"Pfeifer",
"Nico",
""
]
] | Motivation: The size of available omics datasets is steadily increasing with technological advancement in recent years. While this increase in sample size can be used to improve the performance of relevant prediction tasks in healthcare, models that are optimized for large datasets usually operate as black boxes. In hi... |
1504.00959 | Jie Ren | Jie Ren, Kai Song, Minghua Deng, Gesine Reinert, Charles H. Cannon and
Fengzhu Sun | Inference of Markovian Properties of Molecular Sequences from NGS Data
and Applications to Comparative Genomics | accepted by RECOMB-SEQ 2015 | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Next Generation Sequencing (NGS) technologies generate large amounts of short
read data for many different organisms. The fact that NGS reads are generally
short makes it challenging to assemble the reads and reconstruct the original
genome sequence. For clustering genomes using such NGS data, word-count based
alignm... | [
{
"created": "Sat, 4 Apr 2015 00:05:38 GMT",
"version": "v1"
}
] | 2015-04-07 | [
[
"Ren",
"Jie",
""
],
[
"Song",
"Kai",
""
],
[
"Deng",
"Minghua",
""
],
[
"Reinert",
"Gesine",
""
],
[
"Cannon",
"Charles H.",
""
],
[
"Sun",
"Fengzhu",
""
]
] | Next Generation Sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For clustering genomes using such NGS data, word-count based alignmen... |
2010.02993 | Erik Fagerholm | Erik D. Fagerholm, Karl J. Friston, Rosalyn J. Moran, Robert Leech | The principle of stationary action in neural systems | null | null | null | null | q-bio.NC physics.class-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The principle of stationary action is a cornerstone of modern physics,
providing a powerful framework for investigating dynamical systems found in
classical mechanics through to quantum field theory. However, computational
neuroscience, despite its heavy reliance on concepts in physics, is anomalous
in this regard as... | [
{
"created": "Tue, 6 Oct 2020 19:43:55 GMT",
"version": "v1"
}
] | 2020-10-08 | [
[
"Fagerholm",
"Erik D.",
""
],
[
"Friston",
"Karl J.",
""
],
[
"Moran",
"Rosalyn J.",
""
],
[
"Leech",
"Robert",
""
]
] | The principle of stationary action is a cornerstone of modern physics, providing a powerful framework for investigating dynamical systems found in classical mechanics through to quantum field theory. However, computational neuroscience, despite its heavy reliance on concepts in physics, is anomalous in this regard as i... |
2303.16558 | Manh Hong Duong | L. Chen, C. Deng, M. H. Duong and T. A. Han | On the number of equilibria of the replicator-mutator dynamics for noisy
social dilemmas | null | null | null | null | q-bio.PE math.DS | http://creativecommons.org/licenses/by/4.0/ | In this paper, we consider the replicator-mutator dynamics for pairwise
social dilemmas where the payoff entries are random variables. The randomness
is incorporated to take into account the uncertainty, which is inevitable in
practical applications and may arise from different sources such as lack of
data for measur... | [
{
"created": "Wed, 29 Mar 2023 09:27:43 GMT",
"version": "v1"
}
] | 2023-03-30 | [
[
"Chen",
"L.",
""
],
[
"Deng",
"C.",
""
],
[
"Duong",
"M. H.",
""
],
[
"Han",
"T. A.",
""
]
] | In this paper, we consider the replicator-mutator dynamics for pairwise social dilemmas where the payoff entries are random variables. The randomness is incorporated to take into account the uncertainty, which is inevitable in practical applications and may arise from different sources such as lack of data for measurin... |
2101.08111 | Manuel Marques-Pita PhD | Santosh Manicka, Manuel Marques-Pita, Luis M. Rocha | Effective connectivity determines the critical dynamics of biochemical
networks | 22 pages, 7 figures | null | null | null | q-bio.MN nlin.AO | http://creativecommons.org/licenses/by/4.0/ | Living systems operate in a critical dynamical regime -- between order and
chaos -- where they are both resilient to perturbation, and flexible enough to
evolve. To characterize such critical dynamics, the established 'structural
theory' of criticality uses automata network connectivity and node bias (to be
on or off... | [
{
"created": "Wed, 20 Jan 2021 13:16:39 GMT",
"version": "v1"
}
] | 2022-01-28 | [
[
"Manicka",
"Santosh",
""
],
[
"Marques-Pita",
"Manuel",
""
],
[
"Rocha",
"Luis M.",
""
]
] | Living systems operate in a critical dynamical regime -- between order and chaos -- where they are both resilient to perturbation, and flexible enough to evolve. To characterize such critical dynamics, the established 'structural theory' of criticality uses automata network connectivity and node bias (to be on or off) ... |
1903.09567 | Owen Gilbert | Owen M. Gilbert | Natural reward as the fundamental macroevolutionary force | 21 pages, 9 figures, 2 tables. Keywords: invention, entrepreneurship,
innovation, success, progress, advancement | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Darwin's theory of evolution by natural selection does not predict long-term
progress or advancement, nor does it provide a useful way to define or
understand these concepts. Nevertheless, the history of life is marked by major
trends that appear progressive, and seemingly more advanced forms of life have
appeared. T... | [
{
"created": "Fri, 22 Mar 2019 15:50:13 GMT",
"version": "v1"
}
] | 2019-03-25 | [
[
"Gilbert",
"Owen M.",
""
]
] | Darwin's theory of evolution by natural selection does not predict long-term progress or advancement, nor does it provide a useful way to define or understand these concepts. Nevertheless, the history of life is marked by major trends that appear progressive, and seemingly more advanced forms of life have appeared. To ... |
1708.03025 | Zhuolin Qu | Zhuolin Qu, Ling Xue, and James M. Hyman | Modeling the transmission of Wolbachia in mosquitoes for controlling
mosquito-borne diseases | 27 pages, 14 figure; submitted to SIAP | SIAM Journal on Applied Mathematics, 2018 | 10.1137/17M1130800 | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop and analyze an ordinary differential equation model to assess the
potential effectiveness of infecting mosquitoes with the Wolbachia bacteria to
control the ongoing mosquito-borne epidemics, such as dengue fever,
chikungunya, and Zika. Wolbachia is a natural parasitic microbe that stops the
proliferation o... | [
{
"created": "Wed, 9 Aug 2017 22:06:03 GMT",
"version": "v1"
}
] | 2020-08-14 | [
[
"Qu",
"Zhuolin",
""
],
[
"Xue",
"Ling",
""
],
[
"Hyman",
"James M.",
""
]
] | We develop and analyze an ordinary differential equation model to assess the potential effectiveness of infecting mosquitoes with the Wolbachia bacteria to control the ongoing mosquito-borne epidemics, such as dengue fever, chikungunya, and Zika. Wolbachia is a natural parasitic microbe that stops the proliferation of ... |
0711.4937 | Azi Lipshtat | Azi Lipshtat, Sudarshan P. Purushothaman, Ravi Iyengar, Avi Ma'ayan | Functions of Bifans in Context of Multiple Regulatory Motifs in
Signaling Networks | Accepted for publication in the Biophysical Journal | null | 10.1529/biophysj.107.116673 | null | q-bio.MN q-bio.QM q-bio.SC | null | Representation of intracellular signaling networks as directed graphs allows
for the identification of regulatory motifs. Regulatory motifs are groups of
nodes with the same connectivity structure, capable of processing information.
The bifan motif, made of two source nodes directly cross-regulating two target
nodes,... | [
{
"created": "Fri, 30 Nov 2007 14:15:37 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Lipshtat",
"Azi",
""
],
[
"Purushothaman",
"Sudarshan P.",
""
],
[
"Iyengar",
"Ravi",
""
],
[
"Ma'ayan",
"Avi",
""
]
] | Representation of intracellular signaling networks as directed graphs allows for the identification of regulatory motifs. Regulatory motifs are groups of nodes with the same connectivity structure, capable of processing information. The bifan motif, made of two source nodes directly cross-regulating two target nodes, i... |
2401.14651 | Swadesh Pal | Swadesh Pal and Roderick Melnik | Nonlocal Models in Biology and Life Sciences: Sources, Developments, and
Applications | 71 pages | null | null | null | q-bio.QM math-ph math.DS math.MP | http://creativecommons.org/licenses/by-sa/4.0/ | Nonlocality is important in realistic mathematical models of physical and
biological systems at small-length scales. It characterizes the properties of
two individuals located in different locations. This review illustrates
different nonlocal mathematical models applied to biology and life sciences.
The major focus h... | [
{
"created": "Fri, 26 Jan 2024 05:17:48 GMT",
"version": "v1"
}
] | 2024-01-29 | [
[
"Pal",
"Swadesh",
""
],
[
"Melnik",
"Roderick",
""
]
] | Nonlocality is important in realistic mathematical models of physical and biological systems at small-length scales. It characterizes the properties of two individuals located in different locations. This review illustrates different nonlocal mathematical models applied to biology and life sciences. The major focus has... |
1502.07077 | Flavio Coelho | Joyce de Figueir\'o Santos, Fl\'avio Code\c{c}o Coelho, Pierre
Alexandre Bliman | Behavioral modulation of the coexistence between Apis melifera and
Varroa destructor: A defense against colony colapse disorder? | null | null | 10.1371/journal.pone.0160465 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Colony Collapse Disorder has become a global problem for beekeepers and for
the crops which depend on bee polination. Multiple factors are known to
increase the risk of colony colapse, and the ectoparasitic mite Varroa
destructor that parasitizes honey bees is among the main threats to colony
health. Although this mi... | [
{
"created": "Wed, 25 Feb 2015 08:17:20 GMT",
"version": "v1"
},
{
"created": "Thu, 26 Feb 2015 09:42:26 GMT",
"version": "v2"
}
] | 2020-10-02 | [
[
"Santos",
"Joyce de Figueiró",
""
],
[
"Coelho",
"Flávio Codeço",
""
],
[
"Bliman",
"Pierre Alexandre",
""
]
] | Colony Collapse Disorder has become a global problem for beekeepers and for the crops which depend on bee polination. Multiple factors are known to increase the risk of colony colapse, and the ectoparasitic mite Varroa destructor that parasitizes honey bees is among the main threats to colony health. Although this mite... |
1802.09131 | Tristan Sharp | Tristan A. Sharp, Matthias Merkel, M. Lisa Manning, Andrea J. Liu | Statistical properties of 3D cell geometry from 2D slices | null | null | 10.1371/journal.pone.0209892 | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although cell shape can reflect the mechanical and biochemical properties of
the cell and its environment, quantification of 3D cell shapes within 3D
tissues remains difficult, typically requiring digital reconstruction from a
stack of 2D images. We investigate a simple alternative technique to extract
information ab... | [
{
"created": "Mon, 26 Feb 2018 02:12:39 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Jun 2018 02:04:58 GMT",
"version": "v2"
}
] | 2019-03-06 | [
[
"Sharp",
"Tristan A.",
""
],
[
"Merkel",
"Matthias",
""
],
[
"Manning",
"M. Lisa",
""
],
[
"Liu",
"Andrea J.",
""
]
] | Although cell shape can reflect the mechanical and biochemical properties of the cell and its environment, quantification of 3D cell shapes within 3D tissues remains difficult, typically requiring digital reconstruction from a stack of 2D images. We investigate a simple alternative technique to extract information abou... |
1901.00782 | Julien Renoult | Julien P. Renoult and Tamra C. Mendelson | Processing Bias: Extending Sensory Drive to Include Efficacy and
Efficiency in Information Processing | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Communication signals often comprise an array of colors, lines, spots, notes
or odors that are arranged in complex patterns, melodies or blends. Receiver
perception is assumed to influence preference and thus the evolution of signal
design, but evolutionary biologists still struggle to understand how
perception, pref... | [
{
"created": "Thu, 3 Jan 2019 15:08:55 GMT",
"version": "v1"
}
] | 2019-01-04 | [
[
"Renoult",
"Julien P.",
""
],
[
"Mendelson",
"Tamra C.",
""
]
] | Communication signals often comprise an array of colors, lines, spots, notes or odors that are arranged in complex patterns, melodies or blends. Receiver perception is assumed to influence preference and thus the evolution of signal design, but evolutionary biologists still struggle to understand how perception, prefer... |
1202.4335 | Andr\'es Chavarr\'ia-Krauser | Juliane Claus and Andr\'es Chavarr\'ia-Krauser | Modeling Regulation of Zinc Uptake via ZIP Transporters in Yeast and
Plant Roots | 23 pages including 2 tables and 7 figures | null | 10.1371/journal.pone.0037193 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In yeast (Saccharomyces cerevisiae) and plant roots (Arabidopsis thaliana)
zinc enters the cells via influx transporters of the ZIP family. Since zinc is
both essential for cell function and toxic at high concentrations, tight
regulation is essential for cell viability. We provide new insight into the
underlying mech... | [
{
"created": "Mon, 20 Feb 2012 14:26:48 GMT",
"version": "v1"
}
] | 2015-06-04 | [
[
"Claus",
"Juliane",
""
],
[
"Chavarría-Krauser",
"Andrés",
""
]
] | In yeast (Saccharomyces cerevisiae) and plant roots (Arabidopsis thaliana) zinc enters the cells via influx transporters of the ZIP family. Since zinc is both essential for cell function and toxic at high concentrations, tight regulation is essential for cell viability. We provide new insight into the underlying mechan... |
2405.04734 | Erin Gill | Erin E. Gill, Baofeng Jia, Carmen Lia Murall, Rapha\"el Poujol,
Muhammad Zohaib Anwar, Nithu Sara John, Justin Richardsson, Ashley Hobb,
Abayomi S. Olabode, Alexandru Lepsa, Ana T. Duggan, Andrea D. Tyler, Arnaud
N'Guessan, Atul Kachru, Brandon Chan, Catherine Yoshida, Christina K. Yung,
David Bujold, Dusan And... | The Canadian VirusSeq Data Portal & Duotang: open resources for
SARS-CoV-2 viral sequences and genomic epidemiology | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2
genomes from patient samples to track viral evolution and inform public health
response. Millions of SARS-CoV-2 genome sequences have been deposited in global
public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN -
VirusSeq), a ... | [
{
"created": "Wed, 8 May 2024 00:50:35 GMT",
"version": "v1"
}
] | 2024-05-09 | [
[
"Gill",
"Erin E.",
""
],
[
"Jia",
"Baofeng",
""
],
[
"Murall",
"Carmen Lia",
""
],
[
"Poujol",
"Raphaël",
""
],
[
"Anwar",
"Muhammad Zohaib",
""
],
[
"John",
"Nithu Sara",
""
],
[
"Richardsson",
"Justin",
"... | The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a co... |
2408.07110 | Julian Suk | Julian Suk, Dieuwertje Alblas, Barbara A. Hutten, Albert Wiegman,
Christoph Brune, Pim van Ooij and Jelmer M. Wolterink | Physics-informed graph neural networks for flow field estimation in
carotid arteries | Preprint. Under Review | null | null | null | q-bio.QM cs.LG physics.flu-dyn | http://creativecommons.org/licenses/by/4.0/ | Hemodynamic quantities are valuable biomedical risk factors for
cardiovascular pathology such as atherosclerosis. Non-invasive, in-vivo
measurement of these quantities can only be performed using a select number of
modalities that are not widely available, such as 4D flow magnetic resonance
imaging (MRI). In this wor... | [
{
"created": "Tue, 13 Aug 2024 13:09:28 GMT",
"version": "v1"
}
] | 2024-08-15 | [
[
"Suk",
"Julian",
""
],
[
"Alblas",
"Dieuwertje",
""
],
[
"Hutten",
"Barbara A.",
""
],
[
"Wiegman",
"Albert",
""
],
[
"Brune",
"Christoph",
""
],
[
"van Ooij",
"Pim",
""
],
[
"Wolterink",
"Jelmer M.",
""
... | Hemodynamic quantities are valuable biomedical risk factors for cardiovascular pathology such as atherosclerosis. Non-invasive, in-vivo measurement of these quantities can only be performed using a select number of modalities that are not widely available, such as 4D flow magnetic resonance imaging (MRI). In this work,... |
0805.3588 | Vladimir Ivancevic | Vladimir G. Ivancevic | Human-Robot Biodynamics | 20 pages, 11 figures, Latex | null | null | null | q-bio.OT q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper presents the scientific body of knowledge behind the Human
Biodynamics Engine (HBE), a human motion simulator developed on the concept of
Euclidean motion group SE(3), with 270 active degrees of freedom,
force-velocity-time muscular mechanics and two-level neural control -
formulated in the fashion of nonl... | [
{
"created": "Fri, 23 May 2008 06:55:30 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Jun 2008 02:51:28 GMT",
"version": "v2"
},
{
"created": "Fri, 18 Jul 2008 05:05:47 GMT",
"version": "v3"
}
] | 2008-07-18 | [
[
"Ivancevic",
"Vladimir G.",
""
]
] | This paper presents the scientific body of knowledge behind the Human Biodynamics Engine (HBE), a human motion simulator developed on the concept of Euclidean motion group SE(3), with 270 active degrees of freedom, force-velocity-time muscular mechanics and two-level neural control - formulated in the fashion of nonlin... |
q-bio/0506042 | Van M. Savage jr | Van M. Savage and Geoffrey B. West | Towards a Quantitative, Metabolic Theory for Mammalian Sleep | 20 pages, 4 figures | null | null | null | q-bio.OT | null | Sleep is one of the most noticeable and widespread phenomena occurring in
multicellular animals. Nevertheless, no consensus for a theory of its origins
has emerged. In particular, no explicit, quantitative theory exists that
elucidates or distinguishes between the myriad hypotheses proposed for sleep.
Here, we develo... | [
{
"created": "Thu, 30 Jun 2005 04:34:16 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Savage",
"Van M.",
""
],
[
"West",
"Geoffrey B.",
""
]
] | Sleep is one of the most noticeable and widespread phenomena occurring in multicellular animals. Nevertheless, no consensus for a theory of its origins has emerged. In particular, no explicit, quantitative theory exists that elucidates or distinguishes between the myriad hypotheses proposed for sleep. Here, we develop ... |
1801.01856 | Glenn Webb Dr | Pierre Magal, Glenn F. Webb, and Yixiang Wu | Spatial Spread of Epidemic Diseases in Geographical Settings: Seasonal
Influenza Epidemics in Puerto Rico | 18 pages, 13 figures | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deterministic models are developed for the spatial spread of epidemic
diseases in geographical settings. The models are focused on outbreaks that
arise from a small number of infected hosts imported into sub-regions of the
geographical settings. The goal is to understand how spatial heterogeneity
influences the trans... | [
{
"created": "Fri, 5 Jan 2018 18:05:14 GMT",
"version": "v1"
}
] | 2018-01-08 | [
[
"Magal",
"Pierre",
""
],
[
"Webb",
"Glenn F.",
""
],
[
"Wu",
"Yixiang",
""
]
] | Deterministic models are developed for the spatial spread of epidemic diseases in geographical settings. The models are focused on outbreaks that arise from a small number of infected hosts imported into sub-regions of the geographical settings. The goal is to understand how spatial heterogeneity influences the transmi... |
2102.04301 | Khaled Khleifat Dr | H.A Qaralleh, M.O. Al-Limoun, A. Khlaifat, K.M. Khleifat, N.
Al-Tawarah, K.Y. Alsharafa, H.A. Abu-Harirah | Antibacterial and antibiofilm activities of a traditional herbal formula
against respiratory infection causing bacteria | 8 pages, 4 tables, 2 figures | Antibacterial and Antibiofilm Activities of a Traditional Herbal
Formula against Respiratory Infection Causing Bacteria. Trop J Nat Prod Res.
2020; 4(9):527-534 | 10.26538/tjnpr/v4i9.6 | null | q-bio.OT | http://creativecommons.org/publicdomain/zero/1.0/ | The plants, Althaea officinalis, Tilia cordata and Psidium guaja have been
used traditionally to treat respiratory infection symptoms. Flowers of A.
officinalis and leaves of T. cordata and P. guaja have been used to treat
cough, sore throat, catarrh, oral and pharyngeal mucosa irritation. Therefore,
this study was d... | [
{
"created": "Tue, 19 Jan 2021 20:34:55 GMT",
"version": "v1"
}
] | 2021-02-09 | [
[
"Qaralleh",
"H. A",
""
],
[
"Al-Limoun",
"M. O.",
""
],
[
"Khlaifat",
"A.",
""
],
[
"Khleifat",
"K. M.",
""
],
[
"Al-Tawarah",
"N.",
""
],
[
"Alsharafa",
"K. Y.",
""
],
[
"Abu-Harirah",
"H. A.",
""
]
] | The plants, Althaea officinalis, Tilia cordata and Psidium guaja have been used traditionally to treat respiratory infection symptoms. Flowers of A. officinalis and leaves of T. cordata and P. guaja have been used to treat cough, sore throat, catarrh, oral and pharyngeal mucosa irritation. Therefore, this study was des... |
1603.03752 | Luca Ferreri | Luca Ferreri and Paolo Bajardi and Mario Giacobini | Non-systemic transmission of tick-borne diseases: a network approach | 15 pages, 4 figures, to be published in Communications in Nonlinear
Science and Numerical Simulation | Communications in Nonlinear Science and Numerical Simulations,
Volume 39, October 2016, pages 149-155 | 10.1016/j.cnsns.2016.02.034 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tick-Borne diseases can be transmitted via non-systemic (NS) transmission.
This occurs when tick gets the infection by co-feeding with infected ticks on
the same host resulting in a direct pathogen transmission between the vectors,
without infecting the host. This transmission is peculiar, as it does not
require any ... | [
{
"created": "Fri, 11 Mar 2016 20:38:14 GMT",
"version": "v1"
}
] | 2017-07-11 | [
[
"Ferreri",
"Luca",
""
],
[
"Bajardi",
"Paolo",
""
],
[
"Giacobini",
"Mario",
""
]
] | Tick-Borne diseases can be transmitted via non-systemic (NS) transmission. This occurs when tick gets the infection by co-feeding with infected ticks on the same host resulting in a direct pathogen transmission between the vectors, without infecting the host. This transmission is peculiar, as it does not require any sy... |
1503.02117 | Tatiana Tatarinova | Konstantin Kozlov, Dmitry Chebotarov, Mehedi Hassan, Martin Triska,
Petr Triska, Pavel Flegontov, Tatiana Tatarinova | Differential Evolution Approach to Detect Recent Admixture | presented at ISMB 2014, VariSIG | BMC Genomics 2015, 16(Suppl 8):S9 | 10.1186/1471-2164-16-S8-S9 | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The genetic structure of human populations is extraordinarily complex and of
fundamental importance to studies of anthropology, evolution, and medicine.
As increasingly many individuals are of mixed origin, there is an unmet need
for tools that can infer multiple origins. Misclassification of such
individuals can l... | [
{
"created": "Sat, 7 Mar 2015 01:43:14 GMT",
"version": "v1"
}
] | 2015-08-26 | [
[
"Kozlov",
"Konstantin",
""
],
[
"Chebotarov",
"Dmitry",
""
],
[
"Hassan",
"Mehedi",
""
],
[
"Triska",
"Martin",
""
],
[
"Triska",
"Petr",
""
],
[
"Flegontov",
"Pavel",
""
],
[
"Tatarinova",
"Tatiana",
""
... | The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools that can infer multiple origins. Misclassification of such individuals can lead ... |
0904.1365 | Simon Mitternacht | Anders Irb\"ack, Simon Mitternacht, Sandipan Mohanty | An effective all-atom potential for proteins | null | PMC Biophysics 2009, 2:2 | null | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We describe and test an implicit solvent all-atom potential for simulations
of protein folding and aggregation. The potential is developed through studies
of structural and thermodynamic properties of 17 peptides with diverse
secondary structure. Results obtained using the final form of the potential are
presented fo... | [
{
"created": "Wed, 8 Apr 2009 16:05:27 GMT",
"version": "v1"
}
] | 2009-04-09 | [
[
"Irbäck",
"Anders",
""
],
[
"Mitternacht",
"Simon",
""
],
[
"Mohanty",
"Sandipan",
""
]
] | We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for ... |
2303.11833 | Hyunseung Kim | Hyunseung Kim (1), Haeyeon Choi (2), Dongju Kang (1), Won Bo Lee (1),
Jonggeol Na (2) ((1) Seoul National University, (2) Ewha Womans University) | Materials Discovery with Extreme Properties via Reinforcement
Learning-Guided Combinatorial Chemistry | 18 pages, 8 figures | Chemical Science, 2024 | 10.1039/D3SC05281H | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The goal of most materials discovery is to discover materials that are
superior to those currently known. Fundamentally, this is close to
extrapolation, which is a weak point for most machine learning models that
learn the probability distribution of data. Herein, we develop reinforcement
learning-guided combinatoria... | [
{
"created": "Tue, 21 Mar 2023 13:21:43 GMT",
"version": "v1"
},
{
"created": "Tue, 7 May 2024 15:07:34 GMT",
"version": "v2"
}
] | 2024-05-08 | [
[
"Kim",
"Hyunseung",
"",
"Seoul National University"
],
[
"Choi",
"Haeyeon",
"",
"Ewha Womans University"
],
[
"Kang",
"Dongju",
"",
"Seoul National University"
],
[
"Lee",
"Won Bo",
"",
"Seoul National University"
],
[
"Na",
"... | The goal of most materials discovery is to discover materials that are superior to those currently known. Fundamentally, this is close to extrapolation, which is a weak point for most machine learning models that learn the probability distribution of data. Herein, we develop reinforcement learning-guided combinatorial ... |
1206.0959 | Mary Ann Blaetke | Mary Ann Bl\"atke, Anna Dittrich, Christian Rohr, Monika Heiner, Fred
Schaper, Wolfgang Marwan | JAK/STAT signalling - an executable model assembled from
molecule-centred modules demonstrating a module-oriented database concept for
systems- and synthetic biology | 54 pages, 12 figures, 2 tables | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/3.0/ | We describe a molecule-oriented modelling approach based on a collection of
Petri net models organized in the form of modules into a prototype database
accessible through a web interface. The JAK/STAT signalling pathway with the
extensive cross-talk of its components is selected as case study. Each Petri
net module r... | [
{
"created": "Tue, 5 Jun 2012 15:21:49 GMT",
"version": "v1"
}
] | 2012-06-06 | [
[
"Blätke",
"Mary Ann",
""
],
[
"Dittrich",
"Anna",
""
],
[
"Rohr",
"Christian",
""
],
[
"Heiner",
"Monika",
""
],
[
"Schaper",
"Fred",
""
],
[
"Marwan",
"Wolfgang",
""
]
] | We describe a molecule-oriented modelling approach based on a collection of Petri net models organized in the form of modules into a prototype database accessible through a web interface. The JAK/STAT signalling pathway with the extensive cross-talk of its components is selected as case study. Each Petri net module rep... |
1901.11246 | Michael B\"orsch | Anika Westphal, Hendrik Sielaff, Stefanie Reuter, Thomas Heitkamp,
Ralf Mrowka, Michael B\"orsch | Ligand-induced oligomerization of the human GPCR neurotensin receptor 1
monitored in living HEK293T cells | 12 pages, 5 figures | null | null | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that
can be expressed in HEK293T cells by stable transfection. Its ligand is a
13-amino-acid peptide that binds with nanomolar affinity from the extracellular
side to NTSR1. Ligand binding induces conformational changes that trigger the
intracel... | [
{
"created": "Thu, 31 Jan 2019 07:38:07 GMT",
"version": "v1"
}
] | 2019-02-01 | [
[
"Westphal",
"Anika",
""
],
[
"Sielaff",
"Hendrik",
""
],
[
"Reuter",
"Stefanie",
""
],
[
"Heitkamp",
"Thomas",
""
],
[
"Mrowka",
"Ralf",
""
],
[
"Börsch",
"Michael",
""
]
] | The human neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that can be expressed in HEK293T cells by stable transfection. Its ligand is a 13-amino-acid peptide that binds with nanomolar affinity from the extracellular side to NTSR1. Ligand binding induces conformational changes that trigger the intracellu... |
1706.07789 | Peter Hufton | Peter G. Hufton, Yen Ting Lin, and Tobias Galla | Phenotypic switching of populations of cells in a stochastic environment | 17 pages, 6 figures | null | 10.1088/1742-5468/aaa78e | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In biology phenotypic switching is a common bet-hedging strategy in the face
of uncertain environmental conditions. Existing mathematical models often focus
on periodically changing environments to determine the optimal phenotypic
response. We focus on the case in which the environment switches randomly
between discr... | [
{
"created": "Fri, 23 Jun 2017 17:52:32 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Jan 2018 17:42:23 GMT",
"version": "v2"
}
] | 2018-03-14 | [
[
"Hufton",
"Peter G.",
""
],
[
"Lin",
"Yen Ting",
""
],
[
"Galla",
"Tobias",
""
]
] | In biology phenotypic switching is a common bet-hedging strategy in the face of uncertain environmental conditions. Existing mathematical models often focus on periodically changing environments to determine the optimal phenotypic response. We focus on the case in which the environment switches randomly between discret... |
1801.08085 | Meysam Golmohammadi | Vinit Shah, Eva von Weltin, Silvia Lopez, James Riley McHugh, Lily
Veloso, Meysam Golmohammadi, Iyad Obeid and Joseph Picone | The Temple University Hospital Seizure Detection Corpus | Under review in Frontiers in Neuroscience | null | null | null | q-bio.QM eess.SP q-bio.NC stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce the TUH EEG Seizure Corpus (TUSZ), which is the largest open
source corpus of its type, and represents an accurate characterization of
clinical conditions. In this paper, we describe the techniques used to develop
TUSZ, evaluate their effectiveness, and present some descriptive statistics on
the resultin... | [
{
"created": "Wed, 3 Jan 2018 01:16:26 GMT",
"version": "v1"
}
] | 2018-01-25 | [
[
"Shah",
"Vinit",
""
],
[
"von Weltin",
"Eva",
""
],
[
"Lopez",
"Silvia",
""
],
[
"McHugh",
"James Riley",
""
],
[
"Veloso",
"Lily",
""
],
[
"Golmohammadi",
"Meysam",
""
],
[
"Obeid",
"Iyad",
""
],
[
... | We introduce the TUH EEG Seizure Corpus (TUSZ), which is the largest open source corpus of its type, and represents an accurate characterization of clinical conditions. In this paper, we describe the techniques used to develop TUSZ, evaluate their effectiveness, and present some descriptive statistics on the resulting ... |
q-bio/0411043 | Lucilla de Arcangelis | Lucilla de Arcangelis, Hans J. Herrmann and Carla Perrone-Capano | Activity-dependent brain model explaining EEG spectra | null | null | null | null | q-bio.NC | null | Most brain models focus on associative memory or calculation capability,
experimentally inaccessible using physiological methods. Here we present a
model explaining a basic feature of electroencephalograms (EEG). Our model is
based on an electrical network with threshold firing and plasticity of synapses
that reprodu... | [
{
"created": "Tue, 23 Nov 2004 17:56:16 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"de Arcangelis",
"Lucilla",
""
],
[
"Herrmann",
"Hans J.",
""
],
[
"Perrone-Capano",
"Carla",
""
]
] | Most brain models focus on associative memory or calculation capability, experimentally inaccessible using physiological methods. Here we present a model explaining a basic feature of electroencephalograms (EEG). Our model is based on an electrical network with threshold firing and plasticity of synapses that reproduce... |
q-bio/0412049 | Carlos Escudero | Carlos Escudero | Particle Statistics and Population Dynamics | null | null | 10.1016/j.physa.2005.02.021 | null | q-bio.PE cond-mat.stat-mech q-bio.QM | null | We study a master equation system modelling a population dynamics problem in
a lattice. The problem is the calculation of the minimum size of a refuge that
can protect a population from hostile external conditions, the so called
critical patch size problem. We analize both cases in which the particles are
considered ... | [
{
"created": "Thu, 30 Dec 2004 11:15:37 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Escudero",
"Carlos",
""
]
] | We study a master equation system modelling a population dynamics problem in a lattice. The problem is the calculation of the minimum size of a refuge that can protect a population from hostile external conditions, the so called critical patch size problem. We analize both cases in which the particles are considered fe... |
0807.4040 | Florian Hartig | Florian Hartig and Martin Drechsler | The time horizon and its role in multiple species conservation planning | 8 pages, 5 figures. Minor changes to v1. This version corredponds to
the final publication in Biological Conservation | Biological Conservation, 2008, 141, 2625-2631 | 10.1016/j.biocon.2008.07.028 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Survival probability within a certain time horizon T is a common measure of
population viability. The choice of T implicitly involves a time preference,
similar to economic discounting: Conservation success is evaluated at the time
horizon T, while all effects that occur later than T are not considered.
Despite the o... | [
{
"created": "Fri, 25 Jul 2008 10:07:52 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Sep 2008 14:50:13 GMT",
"version": "v2"
}
] | 2008-09-26 | [
[
"Hartig",
"Florian",
""
],
[
"Drechsler",
"Martin",
""
]
] | Survival probability within a certain time horizon T is a common measure of population viability. The choice of T implicitly involves a time preference, similar to economic discounting: Conservation success is evaluated at the time horizon T, while all effects that occur later than T are not considered. Despite the obv... |
1001.0653 | Enrico Carlon | J. Hooyberghs, P. Van Hummelen, E. Carlon | The effects of mismatches on hybridization in DNA microarrays:
determination of nearest neighbor parameters | 31 pages, 5 figures | Nucleic Acid Research 37, e53 (2009) | 10.1093/nar/gkp109 | null | q-bio.BM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quantifying interactions in DNA microarrays is of central importance for a
better understanding of their functioning. Hybridization thermodynamics for
nucleic acid strands in aqueous solution can be described by the so-called
nearest-neighbor model, which estimates the hybridization free energy of a
given sequence as... | [
{
"created": "Tue, 5 Jan 2010 09:09:18 GMT",
"version": "v1"
}
] | 2010-01-06 | [
[
"Hooyberghs",
"J.",
""
],
[
"Van Hummelen",
"P.",
""
],
[
"Carlon",
"E.",
""
]
] | Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest-neighbor model, which estimates the hybridization free energy of a given sequence as a... |
2401.08004 | Tinghe Zhang | Ting-He Zhang, Sumin Jo, Michelle Zhang, Kai Wang, Shou-Jiang Gao and
Yufei Huang | Understanding YTHDF2-mediated mRNA Degradation By m6A-BERT-Deg | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | N6-methyladenosine (m6A) is the most abundant mRNA modification within
mammalian cells, holding pivotal significance in the regulation of mRNA
stability, translation, and splicing. Furthermore, it plays a critical role in
the regulation of RNA degradation by primarily recruiting the YTHDF2 reader
protein. However, th... | [
{
"created": "Mon, 15 Jan 2024 23:15:55 GMT",
"version": "v1"
}
] | 2024-01-17 | [
[
"Zhang",
"Ting-He",
""
],
[
"Jo",
"Sumin",
""
],
[
"Zhang",
"Michelle",
""
],
[
"Wang",
"Kai",
""
],
[
"Gao",
"Shou-Jiang",
""
],
[
"Huang",
"Yufei",
""
]
] | N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation, and splicing. Furthermore, it plays a critical role in the regulation of RNA degradation by primarily recruiting the YTHDF2 reader protein. However, the ... |
1409.6384 | Alejandro Ochoa | Alejandro Ochoa, John D. Storey, Manuel Llin\'as, and Mona Singh | Beyond the E-value: stratified statistics for protein domain prediction | 31 pages, 8 figures, does not include supplementary files | null | 10.1371/journal.pcbi.1004509 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | E-values have been the dominant statistic for protein sequence analysis for
the past two decades: from identifying statistically significant local sequence
alignments to evaluating matches to hidden Markov models describing protein
domain families. Here we formally show that for "stratified" multiple
hypothesis testi... | [
{
"created": "Tue, 23 Sep 2014 01:27:56 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Mar 2015 19:57:37 GMT",
"version": "v2"
}
] | 2016-02-17 | [
[
"Ochoa",
"Alejandro",
""
],
[
"Storey",
"John D.",
""
],
[
"Llinás",
"Manuel",
""
],
[
"Singh",
"Mona",
""
]
] | E-values have been the dominant statistic for protein sequence analysis for the past two decades: from identifying statistically significant local sequence alignments to evaluating matches to hidden Markov models describing protein domain families. Here we formally show that for "stratified" multiple hypothesis testing... |
1006.0480 | Vern Williams MR | Vernon Williams | Mathematical Demonstration of Darwinian Theory of Evolution | Keywords: eye evolution, computer eye simulation, simulation of
Darwin's Theory | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Darwin's book, Origin of the Species has been a source of public controversy
for more than hundred and fifty years. Court cases and mountains of words have
not dispelled this controversy. In this paper, a quantitative approach using
simple mathematics shows that the concept of evolution by natural selection
using onl... | [
{
"created": "Thu, 3 Jun 2010 10:32:07 GMT",
"version": "v1"
}
] | 2010-06-04 | [
[
"Williams",
"Vernon",
""
]
] | Darwin's book, Origin of the Species has been a source of public controversy for more than hundred and fifty years. Court cases and mountains of words have not dispelled this controversy. In this paper, a quantitative approach using simple mathematics shows that the concept of evolution by natural selection using only ... |
0911.2021 | Stefano Allesina | Stefano Allesina | Predicting trophic relations in ecological networks: a test of the
Allometric Diet Breadth Model | 28 pages, 3 figures, 4 tables | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Few of food web theory hypotheses/predictions can be readily tested using
empirical data. An exception is represented by simple probabilistic models for
food web structure, for which the likelihood has been derived. Here I test the
performance of a more complex model for food web structure that is grounded in
the all... | [
{
"created": "Tue, 10 Nov 2009 22:29:43 GMT",
"version": "v1"
}
] | 2009-11-12 | [
[
"Allesina",
"Stefano",
""
]
] | Few of food web theory hypotheses/predictions can be readily tested using empirical data. An exception is represented by simple probabilistic models for food web structure, for which the likelihood has been derived. Here I test the performance of a more complex model for food web structure that is grounded in the allom... |
2109.14751 | Young Joon Suh | Young Joon Suh (1), Mrinal Pandey (1), Jeffrey E Segall (2), Mingming
Wu (1) ((1) Department of Biological and Environmental Engineering, Cornell
University, Ithaca, NY, USA (2) Anatomy and Structural Biology, Albert
Einstein College of Medicine, Bronx, NY, USA) | Tumor Spheroid Chemotaxis in Epidermal Growth Factor Gradients Revealed
by a 3D Microfluidic Device | 12 pages, 4 figures, and 3 supplementary figures | null | 10.1088/1478-3975/ac54c7 | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | Epidermal growth factor (EGF), a potent cytokine, is known to promote tumor
invasion both in vivo and in vitro. Previously, we observed that single breast
tumor cells (MDA-MB-231 cell line) embedded within a 3D collagen matrix
displayed enhanced motility but no discernible chemotaxis in the presence of
linear EGF gra... | [
{
"created": "Wed, 29 Sep 2021 22:53:21 GMT",
"version": "v1"
}
] | 2022-03-23 | [
[
"Suh",
"Young Joon",
""
],
[
"Pandey",
"Mrinal",
""
],
[
"Segall",
"Jeffrey E",
""
],
[
"Wu",
"Mingming",
""
]
] | Epidermal growth factor (EGF), a potent cytokine, is known to promote tumor invasion both in vivo and in vitro. Previously, we observed that single breast tumor cells (MDA-MB-231 cell line) embedded within a 3D collagen matrix displayed enhanced motility but no discernible chemotaxis in the presence of linear EGF gradi... |
1911.03221 | Valentin Thorey | Antoine Guillot, Fabien Sauvet, Emmanuel H During and Valentin Thorey | Dreem Open Datasets: Multi-Scored Sleep Datasets to compare Human and
Automated sleep staging | 10 pages, journal submitted | null | null | null | q-bio.QM cs.LG eess.SP stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sleep stage classification constitutes an important element of sleep disorder
diagnosis. It relies on the visual inspection of polysomnography records by
trained sleep technologists. Automated approaches have been designed to
alleviate this resource-intensive task. However, such approaches are usually
compared to a s... | [
{
"created": "Thu, 31 Oct 2019 16:12:43 GMT",
"version": "v1"
},
{
"created": "Tue, 12 Nov 2019 17:21:23 GMT",
"version": "v2"
},
{
"created": "Mon, 2 Mar 2020 16:53:12 GMT",
"version": "v3"
},
{
"created": "Mon, 27 Apr 2020 09:45:45 GMT",
"version": "v4"
}
] | 2020-04-28 | [
[
"Guillot",
"Antoine",
""
],
[
"Sauvet",
"Fabien",
""
],
[
"During",
"Emmanuel H",
""
],
[
"Thorey",
"Valentin",
""
]
] | Sleep stage classification constitutes an important element of sleep disorder diagnosis. It relies on the visual inspection of polysomnography records by trained sleep technologists. Automated approaches have been designed to alleviate this resource-intensive task. However, such approaches are usually compared to a sin... |
2402.02520 | Linn\'ea Gyllingberg | Linn\'ea Gyllingberg, Yu Tian, and David J.T. Sumpter | A minimal model of cognition based on oscillatory and reinforcement
processes | null | null | null | null | q-bio.NC cs.SI math.DS nlin.AO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Building mathematical models of brains is difficult because of the sheer
complexity of the problem. One potential starting point is through basal
cognition, which give abstract representation of a range of organisms without
central nervous systems, including fungi, slime moulds and bacteria. We propose
one such model... | [
{
"created": "Sun, 4 Feb 2024 15:08:02 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Jun 2024 14:45:47 GMT",
"version": "v2"
}
] | 2024-06-14 | [
[
"Gyllingberg",
"Linnéa",
""
],
[
"Tian",
"Yu",
""
],
[
"Sumpter",
"David J. T.",
""
]
] | Building mathematical models of brains is difficult because of the sheer complexity of the problem. One potential starting point is through basal cognition, which give abstract representation of a range of organisms without central nervous systems, including fungi, slime moulds and bacteria. We propose one such model, ... |
1906.05556 | Sungchan Kim | Sungchan Kim, Jong Hyuk Byun and Il Hyo Jung | Global Stability of an SEIR Epidemic Model where Empirical Distribution
of Incubation Period has Approximated by Coxian Distribution | null | Adv Differ Equ (2019) 2019: 469 | 10.1186/s13662-019-2405-9 | null | q-bio.PE math.DS physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, we have developed a Coxian distributed SEIR model in
incorporating an empirical incubation period. We show that the global dynamics
are completely determined by a basic reproduction number. An application of the
Coxian distributed SEIR model using data of an empirical incubation period is
explored. The ... | [
{
"created": "Thu, 13 Jun 2019 09:10:29 GMT",
"version": "v1"
},
{
"created": "Mon, 19 Aug 2019 11:54:48 GMT",
"version": "v2"
}
] | 2019-11-20 | [
[
"Kim",
"Sungchan",
""
],
[
"Byun",
"Jong Hyuk",
""
],
[
"Jung",
"Il Hyo",
""
]
] | In this work, we have developed a Coxian distributed SEIR model in incorporating an empirical incubation period. We show that the global dynamics are completely determined by a basic reproduction number. An application of the Coxian distributed SEIR model using data of an empirical incubation period is explored. The mo... |
1505.07170 | Cesar F. Caiafa | Cesar F. Caiafa and Franco Pestilli | Sparse multiway decomposition for analysis and modeling of diffusion
imaging and tractography | 19 pages, 1 table, 9 figures | null | null | null | q-bio.QM math.NA stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The number of neuroimaging data sets publicly available is growing at fast
rate. The increase in availability and resolution of neuroimaging data requires
modern approaches to signal processing for data analysis and results
validation. We introduce the application of sparse multiway decomposition
methods (Caiafa and ... | [
{
"created": "Wed, 27 May 2015 01:21:37 GMT",
"version": "v1"
}
] | 2015-05-28 | [
[
"Caiafa",
"Cesar F.",
""
],
[
"Pestilli",
"Franco",
""
]
] | The number of neuroimaging data sets publicly available is growing at fast rate. The increase in availability and resolution of neuroimaging data requires modern approaches to signal processing for data analysis and results validation. We introduce the application of sparse multiway decomposition methods (Caiafa and Ci... |
2011.00485 | Marco Wiering | Xiangxie Zhang, Ben Beinke, Berlian Al Kindhi and Marco Wiering | Comparing Machine Learning Algorithms with or without Feature Extraction
for DNA Classification | 17 pages | null | null | null | q-bio.OT cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | The classification of DNA sequences is a key research area in bioinformatics
as it enables researchers to conduct genomic analysis and detect possible
diseases. In this paper, three state-of-the-art algorithms, namely
Convolutional Neural Networks, Deep Neural Networks, and N-gram Probabilistic
Models, are used for t... | [
{
"created": "Sun, 1 Nov 2020 12:04:54 GMT",
"version": "v1"
}
] | 2020-11-03 | [
[
"Zhang",
"Xiangxie",
""
],
[
"Beinke",
"Ben",
""
],
[
"Kindhi",
"Berlian Al",
""
],
[
"Wiering",
"Marco",
""
]
] | The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural Networks, Deep Neural Networks, and N-gram Probabilistic Models, are used for the... |
1010.1191 | Thomas Adams | Thomas Adams \ast (1), Graeme Ackland (1), Glenn Marion (2) and Colin
Edwards (3) ((1) School of Physics and Astronomy, The University of
Edinburgh, (2) Biomathematics and Statistics Scotland,(3) Forest Research,
Northern Research Station) | Effects of local interaction and dispersal on the dynamics of
size-structured populations | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Traditional approaches to ecosystem modelling have relied on spatially
homogeneous approximations to interaction, growth and death. More recently,
spatial interaction and dispersal have also been considered. While these leads
to certain changes in community dynamics, their effect is sometimes fairly
minimal, and demo... | [
{
"created": "Wed, 6 Oct 2010 16:28:11 GMT",
"version": "v1"
}
] | 2010-10-07 | [
[
"\\ast",
"Thomas Adams",
""
],
[
"Ackland",
"Graeme",
""
],
[
"Marion",
"Glenn",
""
],
[
"Edwards",
"Colin",
""
]
] | Traditional approaches to ecosystem modelling have relied on spatially homogeneous approximations to interaction, growth and death. More recently, spatial interaction and dispersal have also been considered. While these leads to certain changes in community dynamics, their effect is sometimes fairly minimal, and demogr... |
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