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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2107.02905 | Meabh MacMahon | M\'eabh MacMahon, Woochang Hwang, Soorin Yim, Eoghan MacMahon,
Alexandre Abraham, Justin Barton, Mukunthan Tharmakulasingam, Paul Bilokon,
Vasanthi Priyadarshini Gaddi, Namshik Han | An in silico drug repurposing pipeline to identify drugs with the
potential to inhibit SARS-CoV-2 replication | 23 pages, 4 figures | Informatics in Medicine Unlocked (2023): 101387 | 10.1016/j.imu.2023.101387 | null | q-bio.QM cs.AI q-bio.MN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Drug repurposing provides an opportunity to redeploy drugs, which ideally are
already approved for use in humans, for the treatment of other diseases. For
example, the repurposing of dexamethasone and baricitinib has played a crucial
role in saving patient lives during the ongoing SARS-CoV-2 pandemic. There
remains a... | [
{
"created": "Mon, 5 Jul 2021 13:08:24 GMT",
"version": "v1"
},
{
"created": "Wed, 23 Nov 2022 15:16:19 GMT",
"version": "v2"
}
] | 2023-11-27 | [
[
"MacMahon",
"Méabh",
""
],
[
"Hwang",
"Woochang",
""
],
[
"Yim",
"Soorin",
""
],
[
"MacMahon",
"Eoghan",
""
],
[
"Abraham",
"Alexandre",
""
],
[
"Barton",
"Justin",
""
],
[
"Tharmakulasingam",
"Mukunthan",
... | Drug repurposing provides an opportunity to redeploy drugs, which ideally are already approved for use in humans, for the treatment of other diseases. For example, the repurposing of dexamethasone and baricitinib has played a crucial role in saving patient lives during the ongoing SARS-CoV-2 pandemic. There remains a n... |
1407.2732 | Thierry Rabilloud | Sarah Triboulet (LCBM - UMR 5249), Catherine Aude-Garcia (LCBM - UMR
5249), Lucie Armand (INAC), Ad\`ele Gerdil (LFP - URA 2453), H\'el\`ene
Diemer (LSMBO-DSA-IPHC), Fabienne Proamer, V\'eronique Collin-Faure (LCBM -
UMR 5249), Aur\'elie Habert (LFP - URA 2453), Jean-Marc Strub
(LSMBO-DSA-IPHC), Daniel Hanau, N... | Analysis of cellular responses of macrophages to zinc ions and zinc
oxide nanoparticles: a combined targeted and proteomic approach | null | Nanoscale 6, 11 (2014) 6102-14 | 10.1039/c4nr00319e | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two different zinc oxide nanoparticles, as well as zinc ions, are used to
study the cellular responses of the RAW 264 macrophage cell line. A proteomic
screen is used to provide a wide view of the molecular effects of zinc, and the
most prominent results are cross-validated by targeted studies. Furthermore,
the alter... | [
{
"created": "Thu, 10 Jul 2014 09:14:09 GMT",
"version": "v1"
}
] | 2014-07-11 | [
[
"Triboulet",
"Sarah",
"",
"LCBM - UMR 5249"
],
[
"Aude-Garcia",
"Catherine",
"",
"LCBM - UMR\n 5249"
],
[
"Armand",
"Lucie",
"",
"INAC"
],
[
"Gerdil",
"Adèle",
"",
"LFP - URA 2453"
],
[
"Diemer",
"Hélène",
"",
"LSMBO-... | Two different zinc oxide nanoparticles, as well as zinc ions, are used to study the cellular responses of the RAW 264 macrophage cell line. A proteomic screen is used to provide a wide view of the molecular effects of zinc, and the most prominent results are cross-validated by targeted studies. Furthermore, the alterat... |
2202.09618 | Fahimeh Palizban | Farshad Noravesh and Fahimeh Palizban | Identifying OCRs in cfDNA WGS Data by Correlation Clustering | 19 pages | null | null | null | q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the recent decade, the emergence of liquid biopsy has significantly
improved cancer monitoring and detection. Dying cells, including those
originating from tumors, shed their DNA into the bloodstream and contribute to
a pool of circulating fragments called cell-free DNA (cfDNA). Identifying the
tissue origin of th... | [
{
"created": "Sat, 19 Feb 2022 14:54:18 GMT",
"version": "v1"
},
{
"created": "Sat, 24 Dec 2022 21:17:48 GMT",
"version": "v2"
}
] | 2022-12-27 | [
[
"Noravesh",
"Farshad",
""
],
[
"Palizban",
"Fahimeh",
""
]
] | In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the bloodstream and contribute to a pool of circulating fragments called cell-free DNA (cfDNA). Identifying the tissue origin of thes... |
2405.00128 | Fanhao Wang | Fanhao Wang, Yuzhe Wang, Laiyi Feng, Changsheng Zhang, Luhua Lai | Target-Specific De Novo Peptide Binder Design with DiffPepBuilder | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite the exciting progress in target-specific de novo protein binder
design, peptide binder design remains challenging due to the flexibility of
peptide structures and the scarcity of protein-peptide complex structure data.
In this study, we curated a large synthetic dataset, referred to as PepPC-F,
from the abund... | [
{
"created": "Tue, 30 Apr 2024 18:24:56 GMT",
"version": "v1"
}
] | 2024-05-02 | [
[
"Wang",
"Fanhao",
""
],
[
"Wang",
"Yuzhe",
""
],
[
"Feng",
"Laiyi",
""
],
[
"Zhang",
"Changsheng",
""
],
[
"Lai",
"Luhua",
""
]
] | Despite the exciting progress in target-specific de novo protein binder design, peptide binder design remains challenging due to the flexibility of peptide structures and the scarcity of protein-peptide complex structure data. In this study, we curated a large synthetic dataset, referred to as PepPC-F, from the abundan... |
0903.0127 | Alain Destexhe | Olivier Marre, Sami El Boustani, Yves Fregnac and Alain Destexhe | Prediction of spatio-temporal patterns of neural activity from pairwise
correlations | Physical Preview Letters (in press, 2009) | Physical Review Letters 102: 138101, 2009. | 10.1103/PhysRevLett.102.138101 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We designed a model-based analysis to predict the occurrence of population
patterns in distributed spiking activity. Using a maximum entropy principle
with a Markovian assumption, we obtain a model that accounts for both spatial
and temporal pairwise correlations among neurons. This model is tested on data
generated ... | [
{
"created": "Sun, 1 Mar 2009 07:59:09 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Marre",
"Olivier",
""
],
[
"Boustani",
"Sami El",
""
],
[
"Fregnac",
"Yves",
""
],
[
"Destexhe",
"Alain",
""
]
] | We designed a model-based analysis to predict the occurrence of population patterns in distributed spiking activity. Using a maximum entropy principle with a Markovian assumption, we obtain a model that accounts for both spatial and temporal pairwise correlations among neurons. This model is tested on data generated wi... |
1602.03093 | Nadav M. Shnerb | Matan Danino, Nadav M. Shnerb, Sandro Azaele, William E. Kunin and
David A. Kessler | The effect of environmental stochasticity on species richness in neutral
communities | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Environmental stochasticity is known to be a destabilizing factor, increasing
abundance fluctuations and extinction rates of populations. However, the
stability of a community may benefit from the differential response of species
to environmental variations due to the storage effect. This paper provides a
systematic ... | [
{
"created": "Tue, 9 Feb 2016 17:48:43 GMT",
"version": "v1"
}
] | 2016-02-10 | [
[
"Danino",
"Matan",
""
],
[
"Shnerb",
"Nadav M.",
""
],
[
"Azaele",
"Sandro",
""
],
[
"Kunin",
"William E.",
""
],
[
"Kessler",
"David A.",
""
]
] | Environmental stochasticity is known to be a destabilizing factor, increasing abundance fluctuations and extinction rates of populations. However, the stability of a community may benefit from the differential response of species to environmental variations due to the storage effect. This paper provides a systematic an... |
1610.07510 | Nicholas Battista | Nicholas A. Battista, Andrea N. Lane, Jiandong Liu, Laura A. Miller | Fluid Dynamics in Heart Development: Effects of Hematocrit and
Trabeculation | 30 pages, 14 figures. arXiv admin note: substantial text overlap with
arXiv:1601.07917 | null | 10.1093/imammb/dqx018 | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent \emph{in vivo} experiments have illustrated the importance of
understanding the hemodynamics of heart morphogenesis. In particular,
ventricular trabeculation is governed by a delicate interaction between
hemodynamic forces, myocardial activity, and morphogen gradients, all of which
are coupled to genetic regul... | [
{
"created": "Mon, 24 Oct 2016 17:55:33 GMT",
"version": "v1"
}
] | 2018-09-19 | [
[
"Battista",
"Nicholas A.",
""
],
[
"Lane",
"Andrea N.",
""
],
[
"Liu",
"Jiandong",
""
],
[
"Miller",
"Laura A.",
""
]
] | Recent \emph{in vivo} experiments have illustrated the importance of understanding the hemodynamics of heart morphogenesis. In particular, ventricular trabeculation is governed by a delicate interaction between hemodynamic forces, myocardial activity, and morphogen gradients, all of which are coupled to genetic regulat... |
1804.11083 | Jicun Wang-Michelitsch | Jicun Wang-Michelitsch, Thomas M Michelitsch | Development of pediatric myeloid leukemia may be related to the
repeatedbone-remodeling during bone-growth | 30 pages, 5 figures | null | null | null | q-bio.CB q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Acute myeloid leukemia (AML) and chronic myeloid leukemia (CML) are two major
formsof leukemia developed from myeloid cells (MCs). To understand why AML and
CML occurin children, we analyzed the causes and the mechanism of cell
transformation of a MC. I. Forthe MCs in marrow cavity, repeated
bone-remodeling during bo... | [
{
"created": "Mon, 30 Apr 2018 08:44:32 GMT",
"version": "v1"
}
] | 2018-05-01 | [
[
"Wang-Michelitsch",
"Jicun",
""
],
[
"Michelitsch",
"Thomas M",
""
]
] | Acute myeloid leukemia (AML) and chronic myeloid leukemia (CML) are two major formsof leukemia developed from myeloid cells (MCs). To understand why AML and CML occurin children, we analyzed the causes and the mechanism of cell transformation of a MC. I. Forthe MCs in marrow cavity, repeated bone-remodeling during bone... |
1107.4572 | Dante Chialvo | Enzo Tagliazucchi, Pablo Balenzuela, Daniel Fraiman, Dante R. Chialvo | Point process analysis of large-scale brain fMRI dynamics | null | null | null | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Functional magnetic resonance imaging (fMRI) techniques have contributed
significantly to our understanding of brain function. Current methods are based
on the analysis of \emph{gradual and continuous} changes in the brain blood
oxygenated level dependent (BOLD) signal. Departing from that approach, recent
work has s... | [
{
"created": "Fri, 22 Jul 2011 16:52:47 GMT",
"version": "v1"
}
] | 2011-07-25 | [
[
"Tagliazucchi",
"Enzo",
""
],
[
"Balenzuela",
"Pablo",
""
],
[
"Fraiman",
"Daniel",
""
],
[
"Chialvo",
"Dante R.",
""
]
] | Functional magnetic resonance imaging (fMRI) techniques have contributed significantly to our understanding of brain function. Current methods are based on the analysis of \emph{gradual and continuous} changes in the brain blood oxygenated level dependent (BOLD) signal. Departing from that approach, recent work has sho... |
2211.11214 | Haitao Lin | Haitao Lin, Yufei Huang, Odin Zhang, Siqi Ma, Meng Liu, Xuanjing Li,
Lirong Wu, Jishui Wang, Tingjun Hou, Stan Z. Li | DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding | 13 pages | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Generating molecules that bind to specific proteins is an important but
challenging task in drug discovery. Previous works usually generate atoms in an
auto-regressive way, where element types and 3D coordinates of atoms are
generated one by one. However, in real-world molecular systems, the
interactions among atoms ... | [
{
"created": "Mon, 21 Nov 2022 07:02:15 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Dec 2022 06:18:09 GMT",
"version": "v2"
},
{
"created": "Sat, 17 Dec 2022 08:29:11 GMT",
"version": "v3"
},
{
"created": "Sun, 14 Jul 2024 06:41:36 GMT",
"version": "v4"
}
] | 2024-07-16 | [
[
"Lin",
"Haitao",
""
],
[
"Huang",
"Yufei",
""
],
[
"Zhang",
"Odin",
""
],
[
"Ma",
"Siqi",
""
],
[
"Liu",
"Meng",
""
],
[
"Li",
"Xuanjing",
""
],
[
"Wu",
"Lirong",
""
],
[
"Wang",
"Jishui",
"... | Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one by one. However, in real-world molecular systems, the interactions among atoms in... |
0902.4417 | Grzegorz A Rempala | Gheorghe Craciun, Casian Pantea, and Grzegorz A. Rempala | A Dimension Reduction Method for Inferring Biochemical Networks | 12 pages and 4 figures | null | null | MCG BBCB Tech Report No 1-09 | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present herein an extension of an algebraic statistical method for
inferring biochemical reaction networks from experimental data, proposed
recently in [3]. This extension allows us to analyze reaction networks that are
not necessarily full-dimensional, i.e., the dimension of their stoichiometric
space is smaller ... | [
{
"created": "Wed, 25 Feb 2009 16:37:32 GMT",
"version": "v1"
}
] | 2009-02-26 | [
[
"Craciun",
"Gheorghe",
""
],
[
"Pantea",
"Casian",
""
],
[
"Rempala",
"Grzegorz A.",
""
]
] | We present herein an extension of an algebraic statistical method for inferring biochemical reaction networks from experimental data, proposed recently in [3]. This extension allows us to analyze reaction networks that are not necessarily full-dimensional, i.e., the dimension of their stoichiometric space is smaller th... |
2305.18804 | Valentina Giunchiglia | Valentina Giunchiglia, Sharon Curtis, Stephen Smith, Naomi Allen, Adam
Hampshire | Neural correlates of cognitive ability and visuo-motor speed: validation
of IDoCT on UK Biobank Data | null | null | null | null | q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Automated online and App-based cognitive assessment tasks are becoming
increasingly popular in large-scale cohorts and biobanks due to advantages in
affordability, scalability and repeatability. However, the summary scores that
such tasks generate typically conflate the cognitive processes that are the
intended focus... | [
{
"created": "Tue, 30 May 2023 07:41:13 GMT",
"version": "v1"
}
] | 2023-05-31 | [
[
"Giunchiglia",
"Valentina",
""
],
[
"Curtis",
"Sharon",
""
],
[
"Smith",
"Stephen",
""
],
[
"Allen",
"Naomi",
""
],
[
"Hampshire",
"Adam",
""
]
] | Automated online and App-based cognitive assessment tasks are becoming increasingly popular in large-scale cohorts and biobanks due to advantages in affordability, scalability and repeatability. However, the summary scores that such tasks generate typically conflate the cognitive processes that are the intended focus o... |
2007.14437 | Javier Alfonso Pinedo Onofre Md Facs | Javier Alfonso Pinedo-Onofre, Euridice Robles-Perez, Erika Sagrario
Pe\~na-Mirabal, Jose Amado Hernandez-Carrillo, and Jose Luis Tellez-Becerra | Giant solitary fibrous tumor of the pleura | null | Pinedo-Onofre JA, Robles-P\'erez E, Pe\~na-Mirabal ES,
Hern\'andez-Carrillo JA, T\'ellez-Becerra JL. Tumor fibroso solitario gigante
de la pleura. Cir Cir 2010;78(1):31-43 | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Solitary fibrous tumor is the second primary malignancy of the
pleura and can reach up to 39cm in diameter; to be referred to as giant it must
occupy at least 40% of the affected hemithorax. Although this tumor usually
shows a benign behavior malignancy criteria have been described. The aim of the
study w... | [
{
"created": "Tue, 28 Jul 2020 19:11:45 GMT",
"version": "v1"
}
] | 2020-07-30 | [
[
"Pinedo-Onofre",
"Javier Alfonso",
""
],
[
"Robles-Perez",
"Euridice",
""
],
[
"Peña-Mirabal",
"Erika Sagrario",
""
],
[
"Hernandez-Carrillo",
"Jose Amado",
""
],
[
"Tellez-Becerra",
"Jose Luis",
""
]
] | Background: Solitary fibrous tumor is the second primary malignancy of the pleura and can reach up to 39cm in diameter; to be referred to as giant it must occupy at least 40% of the affected hemithorax. Although this tumor usually shows a benign behavior malignancy criteria have been described. The aim of the study was... |
2407.17286 | Azadeh Hassanpour | Azadeh Hassanpour, Johannes Geibel, Henner Simianer, Antje Rohde,
Torsten Pook | Optimization of breeding program design through stochastic simulation
with evolutionary algorithms | null | null | null | null | q-bio.QM cs.NE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The effective planning and allocation of resources in modern breeding
programs is a complex task. Breeding program design and operational management
have a major impact on the success of a breeding program and changing
parameters such as the number of selected/phenotyped/genotyped individuals will
impact genetic gain... | [
{
"created": "Mon, 22 Jul 2024 21:10:20 GMT",
"version": "v1"
}
] | 2024-07-25 | [
[
"Hassanpour",
"Azadeh",
""
],
[
"Geibel",
"Johannes",
""
],
[
"Simianer",
"Henner",
""
],
[
"Rohde",
"Antje",
""
],
[
"Pook",
"Torsten",
""
]
] | The effective planning and allocation of resources in modern breeding programs is a complex task. Breeding program design and operational management have a major impact on the success of a breeding program and changing parameters such as the number of selected/phenotyped/genotyped individuals will impact genetic gain, ... |
2407.00754 | Yue Wang | Yue Wang, Peng Zheng, Yu-Chen Cheng, Zikun Wang, Aleksandr Aravkin | Gene Regulatory Network Inference with Covariance Dynamics | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Determining gene regulatory network (GRN) structure is a central problem in
biology, with a variety of inference methods available for different types of
data. For a widely prevalent and challenging use case, namely single-cell gene
expression data measured after intervention at multiple time points with
unknown join... | [
{
"created": "Mon, 17 Jun 2024 18:48:35 GMT",
"version": "v1"
}
] | 2024-07-02 | [
[
"Wang",
"Yue",
""
],
[
"Zheng",
"Peng",
""
],
[
"Cheng",
"Yu-Chen",
""
],
[
"Wang",
"Zikun",
""
],
[
"Aravkin",
"Aleksandr",
""
]
] | Determining gene regulatory network (GRN) structure is a central problem in biology, with a variety of inference methods available for different types of data. For a widely prevalent and challenging use case, namely single-cell gene expression data measured after intervention at multiple time points with unknown joint ... |
1106.5386 | Dong-Ping Yang Dong-Ping Yang | Dong-Ping Yang, Hai Lin, Chen-Xu Wu and Jianwei Shuai | Topological conditions of scale-free networks for cooperation to evolve | 4 pages, 4 figures | null | null | null | q-bio.PE cond-mat.stat-mech nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolutionary game theory is employed to study topological conditions of
scale-free networks for the evolution of cooperation. We show that Apollonian
Networks (ANs) are perfect scale-free networks, on which cooperation can spread
to all individuals, even though there are initially only 3 or 4 hubs occupied
by coopera... | [
{
"created": "Mon, 27 Jun 2011 13:19:02 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Jul 2011 08:44:52 GMT",
"version": "v2"
}
] | 2015-03-19 | [
[
"Yang",
"Dong-Ping",
""
],
[
"Lin",
"Hai",
""
],
[
"Wu",
"Chen-Xu",
""
],
[
"Shuai",
"Jianwei",
""
]
] | Evolutionary game theory is employed to study topological conditions of scale-free networks for the evolution of cooperation. We show that Apollonian Networks (ANs) are perfect scale-free networks, on which cooperation can spread to all individuals, even though there are initially only 3 or 4 hubs occupied by cooperato... |
2107.03231 | Arthur Prat-Carrabin | Arthur Prat-Carrabin, Florent Meyniel, Misha Tsodyks and Rava Azeredo
da Silveira | Biases and Variability from Costly Bayesian Inference | 17 pages, 4 figures | Entropy 2021, 23(5), 603 | 10.3390/e23050603 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | When humans infer underlying probabilities from stochastic observations, they
exhibit biases and variability that cannot be explained on the basis of sound,
Bayesian manipulations of probability. This is especially salient when beliefs
are updated as a function of sequential observations. We introduce a
theoretical f... | [
{
"created": "Wed, 7 Jul 2021 14:02:38 GMT",
"version": "v1"
}
] | 2021-07-08 | [
[
"Prat-Carrabin",
"Arthur",
""
],
[
"Meyniel",
"Florent",
""
],
[
"Tsodyks",
"Misha",
""
],
[
"da Silveira",
"Rava Azeredo",
""
]
] | When humans infer underlying probabilities from stochastic observations, they exhibit biases and variability that cannot be explained on the basis of sound, Bayesian manipulations of probability. This is especially salient when beliefs are updated as a function of sequential observations. We introduce a theoretical fra... |
2004.00979 | G\"unter Klambauer | Markus Hofmarcher, Andreas Mayr, Elisabeth Rumetshofer, Peter Ruch,
Philipp Renz, Johannes Schimunek, Philipp Seidl, Andreu Vall, Michael
Widrich, Sepp Hochreiter, G\"unter Klambauer | Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors
using deep neural networks | Additional results added. Various corrections to formulations and
typos | null | null | null | q-bio.BM cs.LG q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Due to the current severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) pandemic, there is an urgent need for novel therapies and drugs.
We conducted a large-scale virtual screening for small molecules that are
potential CoV-2 inhibitors. To this end, we utilized "ChemAI", a deep neural
network trained on mor... | [
{
"created": "Wed, 25 Mar 2020 15:24:09 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Apr 2020 09:10:24 GMT",
"version": "v2"
},
{
"created": "Mon, 17 Aug 2020 15:58:09 GMT",
"version": "v3"
}
] | 2020-08-18 | [
[
"Hofmarcher",
"Markus",
""
],
[
"Mayr",
"Andreas",
""
],
[
"Rumetshofer",
"Elisabeth",
""
],
[
"Ruch",
"Peter",
""
],
[
"Renz",
"Philipp",
""
],
[
"Schimunek",
"Johannes",
""
],
[
"Seidl",
"Philipp",
""
]... | Due to the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there is an urgent need for novel therapies and drugs. We conducted a large-scale virtual screening for small molecules that are potential CoV-2 inhibitors. To this end, we utilized "ChemAI", a deep neural network trained on more ... |
1601.05249 | KaYin Leung | Ka Yin Leung and Odo Diekmann | Dangerous connections: on binding site models of infectious disease
dynamics | null | J Math Biol, 74: 619-671 (2017) | 10.1007/s00285-016-1037-x | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We formulate models for the spread of infection on networks that are amenable
to analysis in the large population limit. We distinguish three different
levels: (1) binding sites, (2) individuals, and (3) the population. In the
tradition of Physiologically Structured Population Models, the formulation
starts on the in... | [
{
"created": "Wed, 20 Jan 2016 12:18:32 GMT",
"version": "v1"
},
{
"created": "Wed, 27 Jan 2016 00:15:51 GMT",
"version": "v2"
}
] | 2017-03-03 | [
[
"Leung",
"Ka Yin",
""
],
[
"Diekmann",
"Odo",
""
]
] | We formulate models for the spread of infection on networks that are amenable to analysis in the large population limit. We distinguish three different levels: (1) binding sites, (2) individuals, and (3) the population. In the tradition of Physiologically Structured Population Models, the formulation starts on the indi... |
2407.09089 | Chun Ka Wong | Chun-Ka Wong, Ali Choo, Eugene C. C. Cheng, Wing-Chun San, Kelvin
Chak-Kong Cheng, Yee-Man Lau, Minqing Lin, Fei Li, Wei-Hao Liang, Song-Yan
Liao, Kwong-Man Ng, Ivan Fan-Ngai Hung, Hung-Fat Tse, Jason Wing-Hon Wong | Lomics: Generation of Pathways and Gene Sets using Large Language Models
for Transcriptomic Analysis | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Interrogation of biological pathways is an integral part of omics data
analysis. Large language models (LLMs) enable the generation of custom pathways
and gene sets tailored to specific scientific questions. These targeted sets
are significantly smaller than traditional pathway enrichment analysis
libraries, reducing... | [
{
"created": "Fri, 12 Jul 2024 08:34:45 GMT",
"version": "v1"
}
] | 2024-07-15 | [
[
"Wong",
"Chun-Ka",
""
],
[
"Choo",
"Ali",
""
],
[
"Cheng",
"Eugene C. C.",
""
],
[
"San",
"Wing-Chun",
""
],
[
"Cheng",
"Kelvin Chak-Kong",
""
],
[
"Lau",
"Yee-Man",
""
],
[
"Lin",
"Minqing",
""
],
[
... | Interrogation of biological pathways is an integral part of omics data analysis. Large language models (LLMs) enable the generation of custom pathways and gene sets tailored to specific scientific questions. These targeted sets are significantly smaller than traditional pathway enrichment analysis libraries, reducing m... |
1610.01949 | Jing Xu | Amanda J. Tan, Dail E. Chapman, Linda S. Hirst, and Jing Xu | Understanding the role of transport velocity in biomotor-powered
microtubule spool assembly | null | Royal Society of Chemistry Advances, 6, 79143-79146 (2016) | 10.1039/C6RA19094D | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We examined the sensitivity of microtubule spools to transport velocity.
Perhaps surprisingly, we determined that the steady-state number and size of
spools remained constant over a seven-fold range of velocities. Our data on the
kinetics of spool assembly further suggest that the main mechanisms underlying
spool gro... | [
{
"created": "Thu, 6 Oct 2016 17:03:56 GMT",
"version": "v1"
}
] | 2016-10-07 | [
[
"Tan",
"Amanda J.",
""
],
[
"Chapman",
"Dail E.",
""
],
[
"Hirst",
"Linda S.",
""
],
[
"Xu",
"Jing",
""
]
] | We examined the sensitivity of microtubule spools to transport velocity. Perhaps surprisingly, we determined that the steady-state number and size of spools remained constant over a seven-fold range of velocities. Our data on the kinetics of spool assembly further suggest that the main mechanisms underlying spool growt... |
2004.13809 | Aneta Polewko-Klim | Aneta Polewko-Klim, Witold R. Rudnicki | Analysis of ensemble feature selection for correlated high-dimensional
RNA-Seq cancer data | 14 pages, 1 table, 29 figure, submitted to International Conference
on Computational Science, Amsterdam 2020 | null | null | null | q-bio.GN cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Discovery of diagnostic and prognostic molecular markers is important and
actively pursued the research field in cancer research. For complex diseases,
this process is often performed using Machine Learning. The current study
compares two approaches for the discovery of relevant variables: by application
of a single ... | [
{
"created": "Tue, 28 Apr 2020 20:38:53 GMT",
"version": "v1"
}
] | 2020-04-30 | [
[
"Polewko-Klim",
"Aneta",
""
],
[
"Rudnicki",
"Witold R.",
""
]
] | Discovery of diagnostic and prognostic molecular markers is important and actively pursued the research field in cancer research. For complex diseases, this process is often performed using Machine Learning. The current study compares two approaches for the discovery of relevant variables: by application of a single fe... |
2002.06514 | Shubhankar Patankar | Shubhankar P. Patankar, Jason Z. Kim, Fabio Pasqualetti, and Danielle
S. Bassett | Path-dependent connectivity, not modularity, consistently predicts
controllability of structural brain networks | 32 pages, 7 figures in main text, and 22 pages, 11 figures in
supplement | null | 10.1162/netn_a_00157 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The human brain displays rich communication dynamics that are thought to be
particularly well-reflected in its marked community structure. Yet, the precise
relationship between community structure in structural brain networks and the
communication dynamics that can emerge therefrom is not well-understood. In
addition... | [
{
"created": "Sun, 16 Feb 2020 06:07:17 GMT",
"version": "v1"
},
{
"created": "Tue, 14 Jul 2020 00:55:45 GMT",
"version": "v2"
},
{
"created": "Fri, 18 Dec 2020 08:49:17 GMT",
"version": "v3"
}
] | 2020-12-23 | [
[
"Patankar",
"Shubhankar P.",
""
],
[
"Kim",
"Jason Z.",
""
],
[
"Pasqualetti",
"Fabio",
""
],
[
"Bassett",
"Danielle S.",
""
]
] | The human brain displays rich communication dynamics that are thought to be particularly well-reflected in its marked community structure. Yet, the precise relationship between community structure in structural brain networks and the communication dynamics that can emerge therefrom is not well-understood. In addition t... |
2008.02475 | Martin Rypdal | Kristoffer Rypdal and Martin Rypdal | A parsimonious description and cross-country analysis of COVID-19
epidemic curve | 27 pages, 14 figures | null | null | null | q-bio.PE physics.soc-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a given country, the cumulative death toll of the first wave of the
COVID-19 epidemic follows a sigmoid curve as a function of time. In most cases,
the curve is well described by the Gompertz function, which is characterized by
two essential parameters, the initial growth rate and the decay rate as the
first epide... | [
{
"created": "Thu, 6 Aug 2020 06:44:18 GMT",
"version": "v1"
}
] | 2020-08-07 | [
[
"Rypdal",
"Kristoffer",
""
],
[
"Rypdal",
"Martin",
""
]
] | In a given country, the cumulative death toll of the first wave of the COVID-19 epidemic follows a sigmoid curve as a function of time. In most cases, the curve is well described by the Gompertz function, which is characterized by two essential parameters, the initial growth rate and the decay rate as the first epidemi... |
1308.5124 | Luke Tweedy | Luke Tweedy, B\"orn Meier, J\"urgen Stephan, Doris Heinrich, Robert G.
Endres | Distinct cell shapes determine accurate chemotaxis | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The behaviour of an organism often reflects a strategy for coping with its
environment. Such behaviour in higher organisms can often be reduced to a few
stereotyped modes of movement due to physiological limitations, but finding
such modes in amoeboid cells is more difficult as they lack these constraints.
Here, we e... | [
{
"created": "Fri, 23 Aug 2013 13:32:28 GMT",
"version": "v1"
}
] | 2013-08-26 | [
[
"Tweedy",
"Luke",
""
],
[
"Meier",
"Börn",
""
],
[
"Stephan",
"Jürgen",
""
],
[
"Heinrich",
"Doris",
""
],
[
"Endres",
"Robert G.",
""
]
] | The behaviour of an organism often reflects a strategy for coping with its environment. Such behaviour in higher organisms can often be reduced to a few stereotyped modes of movement due to physiological limitations, but finding such modes in amoeboid cells is more difficult as they lack these constraints. Here, we exa... |
q-bio/0608030 | Carla Carvalho | Ekaterini Vourvouhaki, Carla Carvalho, Paulo Aguiar | Model for Osteosarcoma-9 as a Potent Factor in Cell Survivor and
Resistance to Apoptosis | 24 pages, 16 pictures, version accepted for publication in PRE | Phys. Rev. E 76, 011926 (2007) | 10.1103/PhysRevE.76.011926 | DF/IST-5.2007 | q-bio.SC | null | In this paper we use a simple toy model to explore the function of the gene
Osteosarcoma-9. We are in particular interested in understanding the role of
this gene as a potent anti-apoptotic factor. The theoretical description is
constrained by experimental data from induction of apoptosis in cells where
OS-9 is overe... | [
{
"created": "Tue, 15 Aug 2006 19:54:52 GMT",
"version": "v1"
},
{
"created": "Fri, 5 Jan 2007 19:36:18 GMT",
"version": "v2"
},
{
"created": "Wed, 12 Sep 2007 08:48:20 GMT",
"version": "v3"
}
] | 2007-09-12 | [
[
"Vourvouhaki",
"Ekaterini",
""
],
[
"Carvalho",
"Carla",
""
],
[
"Aguiar",
"Paulo",
""
]
] | In this paper we use a simple toy model to explore the function of the gene Osteosarcoma-9. We are in particular interested in understanding the role of this gene as a potent anti-apoptotic factor. The theoretical description is constrained by experimental data from induction of apoptosis in cells where OS-9 is overexp... |
1701.06871 | Colby Long | Colby Long and Laura Kubatko | Identifiability and Reconstructibility of Species Phylogenies Under a
Modified Coalescent | 18 pages, 5 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Coalescent models of evolution account for incomplete lineage sorting by
specifying a species tree parameter which determines a distribution on gene
trees. It has been shown that the unrooted topology of the species tree
parameter of the multispecies coalescent is generically identifiable. Moreover,
a statistically c... | [
{
"created": "Tue, 24 Jan 2017 13:50:30 GMT",
"version": "v1"
}
] | 2017-01-25 | [
[
"Long",
"Colby",
""
],
[
"Kubatko",
"Laura",
""
]
] | Coalescent models of evolution account for incomplete lineage sorting by specifying a species tree parameter which determines a distribution on gene trees. It has been shown that the unrooted topology of the species tree parameter of the multispecies coalescent is generically identifiable. Moreover, a statistically con... |
2209.11199 | Yuuki Matsushita | Yuuki Matsushita, Kunihiko Kaneko | Generic Adaptation by Fast Chaotic Exploration and Slow Feedback
Fixation | 5pages, 6 figures | null | null | null | q-bio.QM nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Living systems adapt to various environmental conditions by changing their
internal states. Inspired by gene expression and epigenetic modification
dynamics, we herein propose a generic mechanism for adaptation by combining
fast oscillatory dynamics and a slower feedback fixation process. Through
extensive model simu... | [
{
"created": "Wed, 21 Sep 2022 15:56:30 GMT",
"version": "v1"
}
] | 2022-09-23 | [
[
"Matsushita",
"Yuuki",
""
],
[
"Kaneko",
"Kunihiko",
""
]
] | Living systems adapt to various environmental conditions by changing their internal states. Inspired by gene expression and epigenetic modification dynamics, we herein propose a generic mechanism for adaptation by combining fast oscillatory dynamics and a slower feedback fixation process. Through extensive model simula... |
2004.10060 | Tommaso Alberti | Tommaso Alberti and Davide Faranda | On the uncertainty of real-time predictions of epidemic growths: a
COVID-19 case study for China and Italy | 24 pages, 6 figures, Preprint submitted to Communications in
Nonlinear Science and Numerical Simulation | null | 10.1016/j.cnsns.2020.105372 | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | While COVID-19 is rapidly propagating around the globe, the need for
providing real-time forecasts of the epidemics pushes fits of dynamical and
statistical models to available data beyond their capabilities. Here we focus
on statistical predictions of COVID-19 infections performed by fitting
asymptotic distributions... | [
{
"created": "Mon, 20 Apr 2020 16:18:57 GMT",
"version": "v1"
}
] | 2020-06-08 | [
[
"Alberti",
"Tommaso",
""
],
[
"Faranda",
"Davide",
""
]
] | While COVID-19 is rapidly propagating around the globe, the need for providing real-time forecasts of the epidemics pushes fits of dynamical and statistical models to available data beyond their capabilities. Here we focus on statistical predictions of COVID-19 infections performed by fitting asymptotic distributions t... |
2401.09490 | Shiyu Wang | Jiayu Chang, Shiyu Wang, Chen Ling, Zhaohui Qin, Liang Zhao | Gene-associated Disease Discovery Powered by Large Language Models | This is the official paper accepted by AAAI 2024 Workshop on Large
Language Models for Biological Discoveries | null | null | null | q-bio.QM cs.IR | http://creativecommons.org/licenses/by/4.0/ | The intricate relationship between genetic variation and human diseases has
been a focal point of medical research, evidenced by the identification of risk
genes regarding specific diseases. The advent of advanced genome sequencing
techniques has significantly improved the efficiency and cost-effectiveness of
detecti... | [
{
"created": "Tue, 16 Jan 2024 21:03:10 GMT",
"version": "v1"
}
] | 2024-01-19 | [
[
"Chang",
"Jiayu",
""
],
[
"Wang",
"Shiyu",
""
],
[
"Ling",
"Chen",
""
],
[
"Qin",
"Zhaohui",
""
],
[
"Zhao",
"Liang",
""
]
] | The intricate relationship between genetic variation and human diseases has been a focal point of medical research, evidenced by the identification of risk genes regarding specific diseases. The advent of advanced genome sequencing techniques has significantly improved the efficiency and cost-effectiveness of detecting... |
1604.01329 | Gao-De Li Dr | Gao-De Li | DNA to DNA transcription might exist in eukaryotic cells | 4 pages | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Till now, in biological sciences, the term, transcription, mainly refers to
DNA to RNA transcription. But our recently published experimental findings
obtained from Plasmodium falciparum strongly suggest the existence of DNA to
DNA transcription in the genome of eukaryotic cells, which could shed some
light on the fu... | [
{
"created": "Tue, 5 Apr 2016 16:56:51 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Apr 2016 19:43:38 GMT",
"version": "v2"
},
{
"created": "Mon, 11 Apr 2016 18:18:15 GMT",
"version": "v3"
},
{
"created": "Wed, 11 May 2016 19:19:45 GMT",
"version": "v4"
},
{
"cre... | 2018-01-30 | [
[
"Li",
"Gao-De",
""
]
] | Till now, in biological sciences, the term, transcription, mainly refers to DNA to RNA transcription. But our recently published experimental findings obtained from Plasmodium falciparum strongly suggest the existence of DNA to DNA transcription in the genome of eukaryotic cells, which could shed some light on the func... |
2310.02152 | Dominik Klepl | Dominik Klepl, Min Wu, Fei He | Graph Neural Network-based EEG Classification: A Survey | 14 pages, 3 figures | null | null | null | q-bio.NC cs.LG q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Graph neural networks (GNN) are increasingly used to classify EEG for tasks
such as emotion recognition, motor imagery and neurological diseases and
disorders. A wide range of methods have been proposed to design GNN-based
classifiers. Therefore, there is a need for a systematic review and
categorisation of these app... | [
{
"created": "Tue, 3 Oct 2023 15:40:03 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Dec 2023 14:30:36 GMT",
"version": "v2"
}
] | 2023-12-21 | [
[
"Klepl",
"Dominik",
""
],
[
"Wu",
"Min",
""
],
[
"He",
"Fei",
""
]
] | Graph neural networks (GNN) are increasingly used to classify EEG for tasks such as emotion recognition, motor imagery and neurological diseases and disorders. A wide range of methods have been proposed to design GNN-based classifiers. Therefore, there is a need for a systematic review and categorisation of these appro... |
2209.06740 | Benjamin Hayden | Benjamin Yost Hayden | The pernicious danger of cortical brain maps | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The parcellation of the primate cerebral cortex into numbered regions, based
on cytoarchitecture, began with the pioneering research of neuroanatomist
Kobrinian Brodmann. While the borders between regions have changed somewhat,
and in some cases continue to be disputed, the idea of dividing the cortex into
distinct n... | [
{
"created": "Wed, 14 Sep 2022 16:05:00 GMT",
"version": "v1"
}
] | 2022-09-15 | [
[
"Hayden",
"Benjamin Yost",
""
]
] | The parcellation of the primate cerebral cortex into numbered regions, based on cytoarchitecture, began with the pioneering research of neuroanatomist Kobrinian Brodmann. While the borders between regions have changed somewhat, and in some cases continue to be disputed, the idea of dividing the cortex into distinct num... |
2406.14432 | Oliver Keatinge Clay | Oliver Keatinge Clay | Inverse population genetic problems with noise: inferring extent and
structure of haplotype blocks from point allele frequencies | 7 pages, 2 figures | null | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A haplotype block, or simply a block, is a chromosomal segment, DNA base
sequence or string that occurs in only a few variants or types in the genomes
of a population of interest, and that has an encapsulated or 'private'
frequency distribution of the string types that is not shared by neighbouring
blocks or regions ... | [
{
"created": "Thu, 20 Jun 2024 15:57:16 GMT",
"version": "v1"
}
] | 2024-06-21 | [
[
"Clay",
"Oliver Keatinge",
""
]
] | A haplotype block, or simply a block, is a chromosomal segment, DNA base sequence or string that occurs in only a few variants or types in the genomes of a population of interest, and that has an encapsulated or 'private' frequency distribution of the string types that is not shared by neighbouring blocks or regions on... |
2104.02603 | Kayode Olumoyin | K.D. Olumoyin, A.Q.M. Khaliq, K.M. Furati | Data-driven deep learning algorithms for time-varying infection rates of
COVID-19 and mitigation measures | Made changes to authors name, F.M. Furati to K.M. Furati | null | 10.3390/epidemiologia2040033 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Epidemiological models with constant parameters may not capture satisfactory
infection patterns in the presence of pharmaceutical and non-pharmaceutical
mitigation measures during a pandemic, since infectiousness is a function of
time. In this paper, an Epidemiology-Informed Neural Network algorithm is
introduced to ... | [
{
"created": "Mon, 5 Apr 2021 16:05:48 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Apr 2021 12:45:55 GMT",
"version": "v2"
},
{
"created": "Fri, 13 May 2022 16:43:08 GMT",
"version": "v3"
}
] | 2022-05-16 | [
[
"Olumoyin",
"K. D.",
""
],
[
"Khaliq",
"A. Q. M.",
""
],
[
"Furati",
"K. M.",
""
]
] | Epidemiological models with constant parameters may not capture satisfactory infection patterns in the presence of pharmaceutical and non-pharmaceutical mitigation measures during a pandemic, since infectiousness is a function of time. In this paper, an Epidemiology-Informed Neural Network algorithm is introduced to le... |
1901.09673 | Robert Marsland III | Robert Marsland III and Wenping Cui and Pankaj Mehta | The Minimum Environmental Perturbation Principle: A New Perspective on
Niche Theory | 56 pages, 6 figures | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fifty years ago, Robert MacArthur showed that stable equilibria optimize
quadratic functions of the population sizes in several important ecological
models. Here, we generalize this finding to a broader class of systems within
the framework of contemporary niche theory, and precisely state the conditions
under which ... | [
{
"created": "Mon, 28 Jan 2019 14:22:48 GMT",
"version": "v1"
},
{
"created": "Tue, 29 Jan 2019 03:56:06 GMT",
"version": "v2"
},
{
"created": "Sat, 20 Apr 2019 00:03:10 GMT",
"version": "v3"
},
{
"created": "Wed, 18 Dec 2019 17:00:29 GMT",
"version": "v4"
}
] | 2019-12-19 | [
[
"Marsland",
"Robert",
"III"
],
[
"Cui",
"Wenping",
""
],
[
"Mehta",
"Pankaj",
""
]
] | Fifty years ago, Robert MacArthur showed that stable equilibria optimize quadratic functions of the population sizes in several important ecological models. Here, we generalize this finding to a broader class of systems within the framework of contemporary niche theory, and precisely state the conditions under which an... |
2205.15020 | Yasamin Kowsari | Yasamin Kowsari, Sanaz Nakhodchi, Davoud Gholamiangonabadi | Gene selection from microarray expression data: A Multi-objective PSO
with adaptive K-nearest neighborhood | null | null | null | null | q-bio.QM cs.AI | http://creativecommons.org/licenses/by/4.0/ | Cancer detection is one of the key research topics in the medical field.
Accurate detection of different cancer types is valuable in providing better
treatment facilities and risk minimization for patients. This paper deals with
the classification problem of human cancer diseases by using gene expression
data. It is ... | [
{
"created": "Fri, 27 May 2022 04:22:10 GMT",
"version": "v1"
}
] | 2022-05-31 | [
[
"Kowsari",
"Yasamin",
""
],
[
"Nakhodchi",
"Sanaz",
""
],
[
"Gholamiangonabadi",
"Davoud",
""
]
] | Cancer detection is one of the key research topics in the medical field. Accurate detection of different cancer types is valuable in providing better treatment facilities and risk minimization for patients. This paper deals with the classification problem of human cancer diseases by using gene expression data. It is pr... |
1309.2686 | Juan Carlos del Alamo | Juan C. Lasheras, BaLdomeRo Alonso-Latorre, Ruedi Meili, Effie
Bastounis, Juan C. del Alamo and Richard A. Firtel | Distribution of Traction Forces and Intracellular Markers Associated
with Shape Changes During Amoeboid Cell Migration | Conference Paper for the Sixth Interdisciplinary Transport Phenomena
Conference: Fluid, Thermal, Biological, Materials and Space Sciences.
Volterra. Italy. October 4-9, (2009) | Int J. Trans. Phenomena, Vol 12, 1-2, pp 3-12, 2011 | null | null | q-bio.CB q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During migration, amoeboid cells perform a cycle of quasi-periodic repetitive
events (motility cycle). the cell length and the strain energy exchanged with
the substrate oscillate in time with an average frequency, f, on top of which
are imposed smaller random fluctuations. the fact that a considerable portion
of the... | [
{
"created": "Tue, 10 Sep 2013 23:02:19 GMT",
"version": "v1"
}
] | 2013-09-12 | [
[
"Lasheras",
"Juan C.",
""
],
[
"Alonso-Latorre",
"BaLdomeRo",
""
],
[
"Meili",
"Ruedi",
""
],
[
"Bastounis",
"Effie",
""
],
[
"del Alamo",
"Juan C.",
""
],
[
"Firtel",
"Richard A.",
""
]
] | During migration, amoeboid cells perform a cycle of quasi-periodic repetitive events (motility cycle). the cell length and the strain energy exchanged with the substrate oscillate in time with an average frequency, f, on top of which are imposed smaller random fluctuations. the fact that a considerable portion of the c... |
2106.01455 | Tobias Wenzel | Anna Pryszlak, Tobias Wenzel, Kiley West Seitz, Falk Hildebrand, Ece
Kartal, Marco Raffaele Cosenza, Vladimir Benes, Peer Bork, Christoph Merten | Enrichment of gut microbiome strains for cultivation-free genome
sequencing using droplet microfluidics | 18 pages incl. references, 4 main figures and one supplementary
figure | Cell Reports Methods 12/2021 | 10.1016/j.crmeth.2021.100137 | null | q-bio.GN physics.bio-ph q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | We report a droplet microfluidic method to target and sort individual cells
directly from complex microbiome samples, and to prepare these cells for bulk
whole genome sequencing without cultivation. We characterize this approach by
recovering bacteria spiked into human stool samples at a ratio as low as 1:250
and by ... | [
{
"created": "Wed, 2 Jun 2021 20:24:10 GMT",
"version": "v1"
}
] | 2022-02-01 | [
[
"Pryszlak",
"Anna",
""
],
[
"Wenzel",
"Tobias",
""
],
[
"Seitz",
"Kiley West",
""
],
[
"Hildebrand",
"Falk",
""
],
[
"Kartal",
"Ece",
""
],
[
"Cosenza",
"Marco Raffaele",
""
],
[
"Benes",
"Vladimir",
""
]... | We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples, and to prepare these cells for bulk whole genome sequencing without cultivation. We characterize this approach by recovering bacteria spiked into human stool samples at a ratio as low as 1:250 and by su... |
2005.08842 | Ji-Seon Bang | Ji-Seon Bang, Ji-Hoon Jeong, and Dong-Ok Won | Classification of Visual Perception and Imagery based EEG Signals Using
Convolutional Neural Networks | Submitted to IEEE 9th International Winter Conference on
Brain-Computer Interface (BCI 2021) | null | null | null | q-bio.NC eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, visual perception (VP) and visual imagery (VI) paradigms are
investigated in several brain-computer interface (BCI) studies. VP and VI are
defined as a changing of brain signals when perceiving and memorizing visual
information, respectively. These paradigms could be alternatives to the
previous visual-base... | [
{
"created": "Fri, 15 May 2020 05:29:21 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Dec 2020 08:16:40 GMT",
"version": "v2"
},
{
"created": "Tue, 8 Dec 2020 02:17:39 GMT",
"version": "v3"
},
{
"created": "Fri, 5 Feb 2021 07:00:59 GMT",
"version": "v4"
}
] | 2021-02-08 | [
[
"Bang",
"Ji-Seon",
""
],
[
"Jeong",
"Ji-Hoon",
""
],
[
"Won",
"Dong-Ok",
""
]
] | Recently, visual perception (VP) and visual imagery (VI) paradigms are investigated in several brain-computer interface (BCI) studies. VP and VI are defined as a changing of brain signals when perceiving and memorizing visual information, respectively. These paradigms could be alternatives to the previous visual-based ... |
2208.00649 | Akira Kinjo | Eden Tian Hwa Ng and Akira R. Kinjo | Computational Modelling of Plasticity-Led Evolution | 20 pages, 2 tables, 1 box | Biophysical Reviews, volume 14, pages 1359-1367 (2022) | 10.1007/s12551-022-01018-5 | null | q-bio.PE q-bio.MN | http://creativecommons.org/licenses/by-sa/4.0/ | Plasticity-led evolution is a form of evolution where a change in the
environment induces novel traits via phenotypic plasticity, after which the
novel traits are genetically accommodated over generations under the novel
environment. This mode of evolution is expected to resolve the problem of
gradualism (i.e., evolu... | [
{
"created": "Mon, 1 Aug 2022 07:14:58 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Sep 2022 05:56:12 GMT",
"version": "v2"
},
{
"created": "Fri, 4 Nov 2022 07:01:44 GMT",
"version": "v3"
},
{
"created": "Mon, 19 Dec 2022 02:51:18 GMT",
"version": "v4"
}
] | 2023-01-18 | [
[
"Ng",
"Eden Tian Hwa",
""
],
[
"Kinjo",
"Akira R.",
""
]
] | Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This mode of evolution is expected to resolve the problem of gradualism (i.e., evoluti... |
2101.05221 | Arie Horowitz | Arie Horowitz | Membrane Trafficking of Integral Cell Junction Proteins and its
Functional Consequences | 34 pages; 6 figures | null | null | null | q-bio.SC | http://creativecommons.org/licenses/by/4.0/ | Though membrane trafficking of cell junction proteins has been studied
extensively for more than two decades, the accumulated knowledge remains
fragmentary. The goal of this review is to synthesize published studies on the
membrane trafficking of the five major junction transmembrane proteins:
claudins, occludin, and... | [
{
"created": "Wed, 13 Jan 2021 17:34:56 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Jan 2021 15:50:26 GMT",
"version": "v2"
},
{
"created": "Mon, 25 Jan 2021 16:19:55 GMT",
"version": "v3"
},
{
"created": "Thu, 11 Feb 2021 01:51:47 GMT",
"version": "v4"
},
{
"c... | 2021-04-13 | [
[
"Horowitz",
"Arie",
""
]
] | Though membrane trafficking of cell junction proteins has been studied extensively for more than two decades, the accumulated knowledge remains fragmentary. The goal of this review is to synthesize published studies on the membrane trafficking of the five major junction transmembrane proteins: claudins, occludin, and j... |
1402.5984 | Melanie JI Muller PhD | Melanie JI Muller, Beverly I Neugeboren, David R Nelson, Andrew W
Murray | Genetic drift opposes mutualism during spatial population expansion | 12 pages main text, 20 pages SI | Proc. Natl. Acad. Sci. USA 111, 1037-1042 (2014) | 10.1073/pnas.1313285111 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mutualistic interactions benefit both partners, promoting coexistence and
genetic diversity. Spatial structure can promote cooperation, but spatial
expansions may also make it hard for mutualistic partners to stay together,
since genetic drift at the expansion front creates regions of low genetic and
species diversit... | [
{
"created": "Mon, 24 Feb 2014 21:15:27 GMT",
"version": "v1"
}
] | 2014-02-26 | [
[
"Muller",
"Melanie JI",
""
],
[
"Neugeboren",
"Beverly I",
""
],
[
"Nelson",
"David R",
""
],
[
"Murray",
"Andrew W",
""
]
] | Mutualistic interactions benefit both partners, promoting coexistence and genetic diversity. Spatial structure can promote cooperation, but spatial expansions may also make it hard for mutualistic partners to stay together, since genetic drift at the expansion front creates regions of low genetic and species diversity.... |
1002.1558 | Andrea Veglio | A. Veglio, A. Gamba, M. Nicodemi, F. Bussolino, G. Serini | A symmetry breaking mechanism for epithelial cell polarization | 7 pages, 6 figures | Physical Review E 80 (3), 031919 (2009) | 10.1103/PhysRevE.80.031919 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In multicellular organisms, epithelial cells form layers separating
compartments responsible for different physiological functions. At the early
stage of epithelial layer formation, each cell of an aggregate defines an inner
and an outer side by breaking the symmetry of its initial state, in a process
known as epithe... | [
{
"created": "Mon, 8 Feb 2010 09:53:55 GMT",
"version": "v1"
}
] | 2010-02-09 | [
[
"Veglio",
"A.",
""
],
[
"Gamba",
"A.",
""
],
[
"Nicodemi",
"M.",
""
],
[
"Bussolino",
"F.",
""
],
[
"Serini",
"G.",
""
]
] | In multicellular organisms, epithelial cells form layers separating compartments responsible for different physiological functions. At the early stage of epithelial layer formation, each cell of an aggregate defines an inner and an outer side by breaking the symmetry of its initial state, in a process known as epitheli... |
0812.0025 | Stefan Legewie | Stefan Legewie, Dennis Dienst, Annegret Wilde, Hanspeter Herzel and
Ilka M. Axmann | Small RNAs Establish Delays and Temporal Thresholds in Gene Expression | null | Biophys J. 2008 Oct;95(7):3232-8 | 10.1529/biophysj.108.133819 | null | q-bio.MN q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Non-coding RNAs are crucial regulators of gene expression in prokaryotes and
eukaryotes, but it remains poorly understood how they affect the dynamics of
transcriptional networks. We analyzed the temporal characteristics of the
cyanobacterial iron stress response by mathematical modeling and quantitative
experimental... | [
{
"created": "Fri, 28 Nov 2008 22:30:47 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Legewie",
"Stefan",
""
],
[
"Dienst",
"Dennis",
""
],
[
"Wilde",
"Annegret",
""
],
[
"Herzel",
"Hanspeter",
""
],
[
"Axmann",
"Ilka M.",
""
]
] | Non-coding RNAs are crucial regulators of gene expression in prokaryotes and eukaryotes, but it remains poorly understood how they affect the dynamics of transcriptional networks. We analyzed the temporal characteristics of the cyanobacterial iron stress response by mathematical modeling and quantitative experimental a... |
2405.18760 | Irina Mizeva | Irina A. Mizeva, Natalia P. Podolyan, Oleg V. Mamontov, Anastasiia V.
Sakovskaia, and Alexei A. Kamshilin | Local nature of 0.1 Hz oscillations in microcirculation is confirmed by
imaging photoplethysmography | 25 pages, 5 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Low-frequency oscillations in the human circulatory system is important for
basic physiology and practical applications in clinical medicine. Our objective
was to study which mechanism (central or local) is responsible for changes in
blood flow fluctuations at around 0.1 Hz. We used the method of imaging
photoplethys... | [
{
"created": "Wed, 29 May 2024 04:58:05 GMT",
"version": "v1"
}
] | 2024-05-30 | [
[
"Mizeva",
"Irina A.",
""
],
[
"Podolyan",
"Natalia P.",
""
],
[
"Mamontov",
"Oleg V.",
""
],
[
"Sakovskaia",
"Anastasiia V.",
""
],
[
"Kamshilin",
"Alexei A.",
""
]
] | Low-frequency oscillations in the human circulatory system is important for basic physiology and practical applications in clinical medicine. Our objective was to study which mechanism (central or local) is responsible for changes in blood flow fluctuations at around 0.1 Hz. We used the method of imaging photoplethysmo... |
2312.00691 | Christophe Magnani | Christophe Magnani and Lee E. Moore | Power spectral analysis of voltage-gated channels in neurons | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | This article develops a fundamental insight into the behavior of neuronal
membranes, focusing on their responses to stimuli measured with power spectra
in the frequency domain. It explores the use of linear and nonlinear (quadratic
sinusoidal analysis) approaches to characterize neuronal function. It further
delves i... | [
{
"created": "Fri, 1 Dec 2023 16:17:17 GMT",
"version": "v1"
}
] | 2023-12-04 | [
[
"Magnani",
"Christophe",
""
],
[
"Moore",
"Lee E.",
""
]
] | This article develops a fundamental insight into the behavior of neuronal membranes, focusing on their responses to stimuli measured with power spectra in the frequency domain. It explores the use of linear and nonlinear (quadratic sinusoidal analysis) approaches to characterize neuronal function. It further delves int... |
1111.3062 | Didier Sornette | Ivan Osorio, Alexey Lyubushin, Didier Sornette | Automated Seizure Detection: Unrecognized Challenges, Unexpected
Insights | 27 pages with 8 figures and 2 tables | Epilepsy & Behavior 22, S7-S17 (2011) | 10.1016/j.yebeh.2011.09.011 | null | q-bio.NC physics.med-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of epileptology's fundamental aims is the formulation of a universal,
internally consistent seizure definition. To assess this aim's feasibility,
three signal analysis methods were applied to a seizure time series and
performance comparisons were undertaken among them and with respect to a
validated algorithm. On... | [
{
"created": "Sun, 13 Nov 2011 21:10:40 GMT",
"version": "v1"
}
] | 2011-11-15 | [
[
"Osorio",
"Ivan",
""
],
[
"Lyubushin",
"Alexey",
""
],
[
"Sornette",
"Didier",
""
]
] | One of epileptology's fundamental aims is the formulation of a universal, internally consistent seizure definition. To assess this aim's feasibility, three signal analysis methods were applied to a seizure time series and performance comparisons were undertaken among them and with respect to a validated algorithm. One ... |
2004.01714 | George Mohler | George Mohler, Frederic Schoenberg, Martin B. Short, Daniel Sledge | Analyzing the World-Wide Impact of Public Health Interventions on the
Transmission Dynamics of COVID-19 | null | null | 10.13140/RG.2.2.32817.12642 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze changes in the reproduction number, R, of COVID-19 in response to
public health interventions. Our results indicate that public health measures
undertaken in China reduced R from 1.5 in January to 0.4 in mid-March 2020.
They also suggest, however, the limitations of isolation, quarantine, and
large-scale a... | [
{
"created": "Fri, 3 Apr 2020 16:05:20 GMT",
"version": "v1"
}
] | 2020-04-07 | [
[
"Mohler",
"George",
""
],
[
"Schoenberg",
"Frederic",
""
],
[
"Short",
"Martin B.",
""
],
[
"Sledge",
"Daniel",
""
]
] | We analyze changes in the reproduction number, R, of COVID-19 in response to public health interventions. Our results indicate that public health measures undertaken in China reduced R from 1.5 in January to 0.4 in mid-March 2020. They also suggest, however, the limitations of isolation, quarantine, and large-scale att... |
1309.5078 | Jacob Scott | Jacob G. Scott, Alexander G. Fletcher, Philip K. Maini, Alexander R.
A. Anderson and Philip Gerlee | A filter-flow perspective of hematogenous metastasis offers a
non-genetic paradigm for personalized cancer therapy | pre-publication draft, 2 figures, 2 tables | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Research into mechanisms of hematogenous metastasis has largely become
genetic in focus, attempting to understand the molecular basis of `seed-soil'
relationships. Preceeding this biological mechanism is the physical process of
dissemination of circulating tumour cells (CTCs). We utilize a `filter-flow'
paradigm to s... | [
{
"created": "Thu, 19 Sep 2013 19:35:21 GMT",
"version": "v1"
}
] | 2013-09-20 | [
[
"Scott",
"Jacob G.",
""
],
[
"Fletcher",
"Alexander G.",
""
],
[
"Maini",
"Philip K.",
""
],
[
"Anderson",
"Alexander R. A.",
""
],
[
"Gerlee",
"Philip",
""
]
] | Research into mechanisms of hematogenous metastasis has largely become genetic in focus, attempting to understand the molecular basis of `seed-soil' relationships. Preceeding this biological mechanism is the physical process of dissemination of circulating tumour cells (CTCs). We utilize a `filter-flow' paradigm to sho... |
1211.0349 | Anyou Wang | Anyou Wang | Systematically Dissecting the Global Mechanism of miRNA Functions in
Pluripotent Stem Cells | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | MicroRNAs (miRNAs) critically modulate stem cell properties like
pluripotency, but the fundamental mechanism remains largely unknown. This study
systematically analyzes multiple-omics data and builds a systems physical
network including genome-wide interactions between miRNAs and their targets to
reveal the systems m... | [
{
"created": "Fri, 2 Nov 2012 02:17:01 GMT",
"version": "v1"
},
{
"created": "Wed, 12 Dec 2012 03:09:57 GMT",
"version": "v2"
},
{
"created": "Sun, 10 Feb 2013 23:54:59 GMT",
"version": "v3"
},
{
"created": "Fri, 19 Apr 2013 18:41:37 GMT",
"version": "v4"
},
{
"cr... | 2014-08-14 | [
[
"Wang",
"Anyou",
""
]
] | MicroRNAs (miRNAs) critically modulate stem cell properties like pluripotency, but the fundamental mechanism remains largely unknown. This study systematically analyzes multiple-omics data and builds a systems physical network including genome-wide interactions between miRNAs and their targets to reveal the systems mec... |
2104.11364 | Elana Fertig | Anne E Carpenter, Casey S Greene, Piero Carnici, Benilton S Carvalho,
Michiel de Hoon, Stacey Finley, Kim-Anh Le Cao, Jerry SH Lee, Luigi
Marchionni, Suzanne Sindi, Fabian J Theis, Gregory P Way, Jean YH Yang, Elana
J Fertig | A field guide to cultivating computational biology | null | null | null | null | q-bio.OT cs.CY | http://creativecommons.org/licenses/by-sa/4.0/ | Biomedical research centers can empower basic discovery and novel therapeutic
strategies by leveraging their large-scale datasets from experiments and
patients. This data, together with new technologies to create and analyze it,
has ushered in an era of data-driven discovery which requires moving beyond the
tradition... | [
{
"created": "Fri, 23 Apr 2021 01:24:21 GMT",
"version": "v1"
}
] | 2021-04-26 | [
[
"Carpenter",
"Anne E",
""
],
[
"Greene",
"Casey S",
""
],
[
"Carnici",
"Piero",
""
],
[
"Carvalho",
"Benilton S",
""
],
[
"de Hoon",
"Michiel",
""
],
[
"Finley",
"Stacey",
""
],
[
"Cao",
"Kim-Anh Le",
""
... | Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered in an era of data-driven discovery which requires moving beyond the traditional... |
1705.09374 | Michael Margaliot | Yoram Zarai and Alexander Ovseevich and Michael Margaliot | Optimal Translation Along a Circular mRNA | null | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ribosome flow model on a ring (RFMR) is a deterministic model for
translation of a circularized mRNA. We derive a new spectral representation for
the optimal steady-state production rate and the corresponding optimal
steady-state ribosomal density in the RFMR. This representation has several
important advantages.... | [
{
"created": "Thu, 25 May 2017 21:43:50 GMT",
"version": "v1"
}
] | 2017-05-29 | [
[
"Zarai",
"Yoram",
""
],
[
"Ovseevich",
"Alexander",
""
],
[
"Margaliot",
"Michael",
""
]
] | The ribosome flow model on a ring (RFMR) is a deterministic model for translation of a circularized mRNA. We derive a new spectral representation for the optimal steady-state production rate and the corresponding optimal steady-state ribosomal density in the RFMR. This representation has several important advantages. F... |
0712.0613 | Michael Plank | A. James and M. J. Plank | On fitting power laws to ecological data | null | null | null | null | q-bio.QM | null | Heavy-tailed or power-law distributions are becoming increasingly common in
biological literature. A wide range of biological data has been fitted to
distributions with heavy tails. Many of these studies use simple fitting
methods to find the parameters in the distribution, which can give highly
misleading results. T... | [
{
"created": "Tue, 4 Dec 2007 21:09:59 GMT",
"version": "v1"
}
] | 2007-12-06 | [
[
"James",
"A.",
""
],
[
"Plank",
"M. J.",
""
]
] | Heavy-tailed or power-law distributions are becoming increasingly common in biological literature. A wide range of biological data has been fitted to distributions with heavy tails. Many of these studies use simple fitting methods to find the parameters in the distribution, which can give highly misleading results. The... |
1209.0176 | Anna-Sophie Fiston-Lavier | Anna-Sophie Fiston-Lavier, Charles E. Vejnar and Hadi Quesneville | Transposable element sequence evolution is influenced by gene context | 36 pages, 4 figures, 2 supplementary figures) | null | null | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Transposable elements (TEs) in eukaryote genomes are
quantitatively the main components affecting genome size, structure and
expression. The dynamics of their insertion and deletion depend on diverse
factors varying in strength and nature along the genome. We address here how TE
sequence evolution is affe... | [
{
"created": "Sun, 2 Sep 2012 13:38:37 GMT",
"version": "v1"
},
{
"created": "Sun, 24 Nov 2013 16:30:17 GMT",
"version": "v2"
}
] | 2013-11-26 | [
[
"Fiston-Lavier",
"Anna-Sophie",
""
],
[
"Vejnar",
"Charles E.",
""
],
[
"Quesneville",
"Hadi",
""
]
] | Background: Transposable elements (TEs) in eukaryote genomes are quantitatively the main components affecting genome size, structure and expression. The dynamics of their insertion and deletion depend on diverse factors varying in strength and nature along the genome. We address here how TE sequence evolution is affect... |
1911.07788 | Haitham Qaralleh | Mohammad Jaafreh, Haitham Qaralleh, Muhamad O. Al-limoun | Biological Value of Centaurea damascena: Minireview | 8 pages. arXiv admin note: substantial text overlap with
arXiv:1911.02243 | Journal of basic and applied Research in Biomedicine, 2019, 5(2):
99-106 | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The family Asteraceae include large number of Centaurea species which have
been applied in folk medicine. One of the family Asteraceae members is the
Centaurea damascena which authentically been tested for its antibacterial
activity. The aim of the study was to discuss antibacterial activities of
essential oil compos... | [
{
"created": "Thu, 14 Nov 2019 11:34:34 GMT",
"version": "v1"
}
] | 2019-11-19 | [
[
"Jaafreh",
"Mohammad",
""
],
[
"Qaralleh",
"Haitham",
""
],
[
"Al-limoun",
"Muhamad O.",
""
]
] | The family Asteraceae include large number of Centaurea species which have been applied in folk medicine. One of the family Asteraceae members is the Centaurea damascena which authentically been tested for its antibacterial activity. The aim of the study was to discuss antibacterial activities of essential oil composit... |
2101.03125 | Olivier Besson M.W. | Olivier Besson, Herv\'e Mugnier, Aur\'elien Neveux, Ga\"elle Rey,
Sully Vitry | Bee Cluster 3D: A system to monitor the temperature in a hive over time | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A new system, Bee Cluster 3D, allowing the study of the time evolution of the
3D temperature distribution in a bee hive is presented. This system can be used
to evaluate the cluster size and the location of the queen during winter. In
summer, the device can be used to quantify the size of the brood nest and the
breed... | [
{
"created": "Fri, 8 Jan 2021 17:39:00 GMT",
"version": "v1"
}
] | 2021-01-11 | [
[
"Besson",
"Olivier",
""
],
[
"Mugnier",
"Hervé",
""
],
[
"Neveux",
"Aurélien",
""
],
[
"Rey",
"Gaëlle",
""
],
[
"Vitry",
"Sully",
""
]
] | A new system, Bee Cluster 3D, allowing the study of the time evolution of the 3D temperature distribution in a bee hive is presented. This system can be used to evaluate the cluster size and the location of the queen during winter. In summer, the device can be used to quantify the size of the brood nest and the breedin... |
1701.04967 | Shiwei Yan | Shuxia Liu, Yizhao Geng, and Shiwei Yan | Structural Effects and Competition Mechanisms Targeting the Interactions
between p53 and Mdm2 for Cancer Therapy | 9 pages, 8 figures | null | null | null | q-bio.MN physics.bio-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | About half of human cancers show normal TP53 gene and aberrant overexpression
of Mdm2 and/or MdmX. This fact promotes a promising cancer therapeutic strategy
which targeting the interactions between p53 and Mdm2/MdmX. For developing the
inhibitors to disrupt the p53-Mdm2/MdmX interactions, we systematically
investiga... | [
{
"created": "Wed, 18 Jan 2017 06:48:31 GMT",
"version": "v1"
}
] | 2017-01-25 | [
[
"Liu",
"Shuxia",
""
],
[
"Geng",
"Yizhao",
""
],
[
"Yan",
"Shiwei",
""
]
] | About half of human cancers show normal TP53 gene and aberrant overexpression of Mdm2 and/or MdmX. This fact promotes a promising cancer therapeutic strategy which targeting the interactions between p53 and Mdm2/MdmX. For developing the inhibitors to disrupt the p53-Mdm2/MdmX interactions, we systematically investigate... |
0705.1019 | Shenbing Kuang | Shenbing Kuang, Jiafu Wang, Ting Zeng, Aiyin Cao | Theoretical Analysis of Subthreshold Oscillatory Behaviors in Nonlinear
Autonomous Systems | 4 pages, 2 figures | null | null | null | q-bio.QM | null | We have developed a linearization method to investigate the subthreshold
oscillatory behaviors in nonlinear autonomous systems. By considering firstly
the neuronal system as an example, we show that this theoretical approach can
predict quantitatively the subthreshold oscillatory activities, including the
damping coe... | [
{
"created": "Tue, 8 May 2007 00:48:55 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Kuang",
"Shenbing",
""
],
[
"Wang",
"Jiafu",
""
],
[
"Zeng",
"Ting",
""
],
[
"Cao",
"Aiyin",
""
]
] | We have developed a linearization method to investigate the subthreshold oscillatory behaviors in nonlinear autonomous systems. By considering firstly the neuronal system as an example, we show that this theoretical approach can predict quantitatively the subthreshold oscillatory activities, including the damping coeff... |
2311.16317 | Niket Thakkar | Niket Thakkar and Mike Famulare | A generating function perspective on the transmission forest | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | In a previous paper, we showed that a compartmental stochastic process model
of SARS-CoV-2 transmission could be fit to time series data and then
reinterpreted as a collection of interacting branching processes drawn from a
dynamic degree distribution. We called this reinterpretation a transmission
forest. This paper... | [
{
"created": "Mon, 27 Nov 2023 21:06:07 GMT",
"version": "v1"
}
] | 2023-11-29 | [
[
"Thakkar",
"Niket",
""
],
[
"Famulare",
"Mike",
""
]
] | In a previous paper, we showed that a compartmental stochastic process model of SARS-CoV-2 transmission could be fit to time series data and then reinterpreted as a collection of interacting branching processes drawn from a dynamic degree distribution. We called this reinterpretation a transmission forest. This paper b... |
2003.07764 | Amirhossein Sadeghi Manesh | AmirHosein Sadeghimanesh and Matthew England | Polynomial Superlevel Set Representation of the Multistationarity Region
of Chemical Reaction Networks | 27 pages, 9 figures | BMC Bioinformatics, 23 Article number 391, 2022 | 10.1186/s12859-022-04921-6 | null | q-bio.MN math.AG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we introduce a new representation for the multistationarity
region of a reaction network, using polynomial superlevel sets. The advantages
of using this polynomial superlevel set representation over the already
existing representations (cylindrical algebraic decompositions, numeric
sampling, rectangular... | [
{
"created": "Tue, 17 Mar 2020 15:27:05 GMT",
"version": "v1"
},
{
"created": "Mon, 12 Sep 2022 11:13:28 GMT",
"version": "v2"
}
] | 2022-09-29 | [
[
"Sadeghimanesh",
"AmirHosein",
""
],
[
"England",
"Matthew",
""
]
] | In this paper we introduce a new representation for the multistationarity region of a reaction network, using polynomial superlevel sets. The advantages of using this polynomial superlevel set representation over the already existing representations (cylindrical algebraic decompositions, numeric sampling, rectangular d... |
1110.1803 | Claus Metzner | Claus Metzner, Patrick Krauss and Ben Fabry | Poresizes in random line networks | 5 pages, 3 figures, paper draft, to be extended | null | null | null | q-bio.QM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many natural fibrous networks with fiber diameters much smaller than the
average poresize can be described as three-dimensional (3D) random line
networks. We consider here a `Mikado' model for such systems, consisting of
straight line segments of equal length, distributed homogeneously and
isotropically in space. Fir... | [
{
"created": "Sun, 9 Oct 2011 07:28:26 GMT",
"version": "v1"
}
] | 2011-10-11 | [
[
"Metzner",
"Claus",
""
],
[
"Krauss",
"Patrick",
""
],
[
"Fabry",
"Ben",
""
]
] | Many natural fibrous networks with fiber diameters much smaller than the average poresize can be described as three-dimensional (3D) random line networks. We consider here a `Mikado' model for such systems, consisting of straight line segments of equal length, distributed homogeneously and isotropically in space. First... |
2201.01830 | Diego Martinez | Bingfan Zhang, Jordan Weil, Antonio Beita Guerra, Pramir Maharjan,
Katie Hilton, Nawin Suesuttajit, Diego A. Martinez, and Craig N. Coon | Egg shell quality and bone status as affected by environmental
temperature, Ca and non-phytate P intake and in vitro limestone solubility in
Single-Comb White Leghorn hens | null | International Journal of Poultry Science (2020) 19: 219-231 | 10.3923/ijps.2020.219.231 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Environmental temperature (ET) often changes the nutrient intake/output for
layers. Changing feed formulations based on ET may need to be utilized to
obtain optimum performance, shell quality and bone status. This study was
conducted to investigate the effects of temperature, Ca intake, non-phytate P
(NPP) intake and... | [
{
"created": "Wed, 5 Jan 2022 21:22:33 GMT",
"version": "v1"
}
] | 2022-01-07 | [
[
"Zhang",
"Bingfan",
""
],
[
"Weil",
"Jordan",
""
],
[
"Guerra",
"Antonio Beita",
""
],
[
"Maharjan",
"Pramir",
""
],
[
"Hilton",
"Katie",
""
],
[
"Suesuttajit",
"Nawin",
""
],
[
"Martinez",
"Diego A.",
""
... | Environmental temperature (ET) often changes the nutrient intake/output for layers. Changing feed formulations based on ET may need to be utilized to obtain optimum performance, shell quality and bone status. This study was conducted to investigate the effects of temperature, Ca intake, non-phytate P (NPP) intake and i... |
2312.13745 | Francisco Meseguer | Francisco Meseguer and Fernando Ramiro-Manzano | The neuron as a temporal electroacoustic medium | 16 pages, 4 figures | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human brain is one of the most complex and intriguing scientific topics.
The most established theory on neuronal communication is a pure electrical
model based on the propagation of intracell cationic charges along the neurons.
Here we propose a complementary model based on two properties of brain
communication: ... | [
{
"created": "Thu, 21 Dec 2023 11:29:15 GMT",
"version": "v1"
},
{
"created": "Mon, 25 Mar 2024 16:06:48 GMT",
"version": "v2"
}
] | 2024-03-26 | [
[
"Meseguer",
"Francisco",
""
],
[
"Ramiro-Manzano",
"Fernando",
""
]
] | The human brain is one of the most complex and intriguing scientific topics. The most established theory on neuronal communication is a pure electrical model based on the propagation of intracell cationic charges along the neurons. Here we propose a complementary model based on two properties of brain communication: A)... |
2210.04479 | Alessandro Casa | Maria Frizzarin, Giulio Visentin, Alessandro Ferragina, Elena Hayes,
Antonio Bevilacqua, Bhaskar Dhariyal, Katarina Domijan, Hussain Khan,
Georgiana Ifrim, Thach Le Nguyen, Joe Meagher, Laura Menchetti, Ashish Singh,
Suzy Whoriskey, Robert Williamson, Martina Zappaterra, Alessandro Casa | Classification of cow diet based on milk mid infrared spectra: a data
analysis competition at the "International workshop of spectroscopy and
chemometrics 2022" | 27 pages, 9 figures | null | null | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by/4.0/ | In April 2022, the Vistamilk SFI Research Centre organized the second edition
of the "International Workshop on Spectroscopy and Chemometrics - Applications
in Food and Agriculture". Within this event, a data challenge was organized
among participants of the workshop. Such data competition aimed at developing a
predi... | [
{
"created": "Mon, 10 Oct 2022 08:08:55 GMT",
"version": "v1"
}
] | 2022-10-11 | [
[
"Frizzarin",
"Maria",
""
],
[
"Visentin",
"Giulio",
""
],
[
"Ferragina",
"Alessandro",
""
],
[
"Hayes",
"Elena",
""
],
[
"Bevilacqua",
"Antonio",
""
],
[
"Dhariyal",
"Bhaskar",
""
],
[
"Domijan",
"Katarina",
... | In April 2022, the Vistamilk SFI Research Centre organized the second edition of the "International Workshop on Spectroscopy and Chemometrics - Applications in Food and Agriculture". Within this event, a data challenge was organized among participants of the workshop. Such data competition aimed at developing a predict... |
1902.02875 | Christian Klos | Christian Klos, Yaroslav Felipe Kalle Kossio, Sven Goedeke, Aditya
Gilra, and Raoul-Martin Memmesheimer | Dynamical learning of dynamics | null | Phys. Rev. Lett. 125, 088103 (2020) | 10.1103/PhysRevLett.125.088103 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The ability of humans and animals to quickly adapt to novel tasks is
difficult to reconcile with the standard paradigm of learning by slow synaptic
weight modification. Here we show that fixed-weight neural networks can learn
to generate required dynamics by imitation. After appropriate weight
pretraining, the networ... | [
{
"created": "Thu, 7 Feb 2019 23:00:54 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Nov 2019 21:43:02 GMT",
"version": "v2"
},
{
"created": "Tue, 25 Aug 2020 11:35:22 GMT",
"version": "v3"
}
] | 2020-08-26 | [
[
"Klos",
"Christian",
""
],
[
"Kossio",
"Yaroslav Felipe Kalle",
""
],
[
"Goedeke",
"Sven",
""
],
[
"Gilra",
"Aditya",
""
],
[
"Memmesheimer",
"Raoul-Martin",
""
]
] | The ability of humans and animals to quickly adapt to novel tasks is difficult to reconcile with the standard paradigm of learning by slow synaptic weight modification. Here we show that fixed-weight neural networks can learn to generate required dynamics by imitation. After appropriate weight pretraining, the networks... |
q-bio/0405020 | Laszlo Papp | Stan Bumble | The Orchestral Analog of Molecular Biology | 17 pages, 8 figures | null | null | null | q-bio.MN | null | Signal processing (SP) techniques convert DNA and protein sequences into
information that lead to successful drug discovery. One must, however, be aware
about the difference between information and entropy1. Eight other physical
properties of DNA and protein segments are suggested for SP analysis other than
ones alre... | [
{
"created": "Wed, 26 May 2004 00:07:10 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bumble",
"Stan",
""
]
] | Signal processing (SP) techniques convert DNA and protein sequences into information that lead to successful drug discovery. One must, however, be aware about the difference between information and entropy1. Eight other physical properties of DNA and protein segments are suggested for SP analysis other than ones alread... |
1701.00648 | Wilhelm Braun | Wilhelm Braun and R\"udiger Thul | Sign-changes as a universal concept in first-passage time calculations | 7 pages, 6 figures. Accepted for publication in Phys. Rev. E | null | 10.1103/PhysRevE.95.012114 | null | q-bio.NC physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | First-passage time problems are ubiquitous across many fields of study
including transport processes in semiconductors and biological synapses,
evolutionary game theory and percolation. Despite their prominence,
first-passage time calculations have proven to be particularly challenging.
Analytical results to date hav... | [
{
"created": "Tue, 3 Jan 2017 11:06:40 GMT",
"version": "v1"
}
] | 2017-02-01 | [
[
"Braun",
"Wilhelm",
""
],
[
"Thul",
"Rüdiger",
""
]
] | First-passage time problems are ubiquitous across many fields of study including transport processes in semiconductors and biological synapses, evolutionary game theory and percolation. Despite their prominence, first-passage time calculations have proven to be particularly challenging. Analytical results to date have ... |
1610.01404 | Yuri Shestopaloff | Yuri K. Shestopaloff | Why cells grow and divide? General growth mechanism and how it defines
cells' growth, reproduction and metabolic properties | 37 pages, 13 figures, 3 tables | Biophysical Reviews and Letters, 2015, 10(4), 209-256 | 10.1142/S1793048015500113 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a general growth mechanism, which acts at cellular level and
above (organs, systems and whole organisms). Using its mathematical
representation, the growth equation, we study the growth and division
mechanisms of amoeba and fission yeast Schizosaccharomyces pombe. We show how
this mechanism, together with... | [
{
"created": "Wed, 5 Oct 2016 13:17:37 GMT",
"version": "v1"
}
] | 2016-10-06 | [
[
"Shestopaloff",
"Yuri K.",
""
]
] | We consider a general growth mechanism, which acts at cellular level and above (organs, systems and whole organisms). Using its mathematical representation, the growth equation, we study the growth and division mechanisms of amoeba and fission yeast Schizosaccharomyces pombe. We show how this mechanism, together with b... |
1107.4220 | Vladimir Chechetkin R. | G.I. Kravatskaya, Y.V. Kravatsky, V.R. Chechetkin, V.G. Tumanyan | Coexistence of different base periodicities in prokaryotic genomes as
related to DNA curvature, supercoiling, and transcription | 23 pages, 6 figures, 2 tables | null | 10.1016/j.ygeno.2011.06.006 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyzed the periodic patterns in E. coli promoters and compared the
distributions of the corresponding patterns in promoters and in the complete
genome to elucidate their function. Except the three-base periodicity,
coincident with that in the coding regions and growing stronger in the region
downstream from the ... | [
{
"created": "Thu, 21 Jul 2011 10:03:27 GMT",
"version": "v1"
}
] | 2011-07-22 | [
[
"Kravatskaya",
"G. I.",
""
],
[
"Kravatsky",
"Y. V.",
""
],
[
"Chechetkin",
"V. R.",
""
],
[
"Tumanyan",
"V. G.",
""
]
] | We analyzed the periodic patterns in E. coli promoters and compared the distributions of the corresponding patterns in promoters and in the complete genome to elucidate their function. Except the three-base periodicity, coincident with that in the coding regions and growing stronger in the region downstream from the tr... |
1909.00585 | R\'obert Juh\'asz | R. Juh\'asz and B. Oborny | Percolation theory suggests some general features in range margins
across environmental gradients | 17 pages, 5 figures | Ecological Complexity 42, 100814 (2020) | 10.1016/j.ecocom.2020.100814 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The margins within the geographic range of species are often specific in
terms of ecological and evolutionary processes, and can strongly influence the
species' reaction to climate change. One of the frequently observed features at
range margins is fragmentation, caused internally by population dynamics or
externally... | [
{
"created": "Mon, 2 Sep 2019 07:52:25 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Feb 2020 08:04:30 GMT",
"version": "v2"
}
] | 2020-02-28 | [
[
"Juhász",
"R.",
""
],
[
"Oborny",
"B.",
""
]
] | The margins within the geographic range of species are often specific in terms of ecological and evolutionary processes, and can strongly influence the species' reaction to climate change. One of the frequently observed features at range margins is fragmentation, caused internally by population dynamics or externally b... |
2111.09402 | Caden Lin | Caden Lin | A Novel Compartmental Approach to Modeling COVID-19 Disease Dynamics and
Analyzing the Effect of Common Preventative Measures | 25 pages, 14 figures | null | null | null | q-bio.PE physics.soc-ph stat.AP | http://creativecommons.org/licenses/by/4.0/ | As of December 2020, the COVID-19 pandemic has infected over 75 million
people, making it the deadliest pandemic in modern history. This study develops
a novel compartmental epidemiological model specific to the SARS-CoV-2 virus
and analyzes the effect of common preventative measures such as testing,
quarantine, soci... | [
{
"created": "Wed, 17 Nov 2021 21:16:19 GMT",
"version": "v1"
}
] | 2021-11-19 | [
[
"Lin",
"Caden",
""
]
] | As of December 2020, the COVID-19 pandemic has infected over 75 million people, making it the deadliest pandemic in modern history. This study develops a novel compartmental epidemiological model specific to the SARS-CoV-2 virus and analyzes the effect of common preventative measures such as testing, quarantine, social... |
2012.15750 | Samiya Alkhairy | Samiya A Alkhairy, Christopher A Shera | An analytic physically motivated model of the mammalian cochlea | 17 pages, 12 figures. Published in JASA | The Journal of the Acoustical Society of America, 145(1), 45-60
(2019) | 10.1121/1.5084042 | null | q-bio.TO cs.SD eess.AS eess.SP q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop an analytic model of the mammalian cochlea. We use a mixed
physical-phenomenological approach by utilizing existing work on the physics of
classical box-representations of the cochlea, and behavior of recent
data-derived wavenumber estimates. Spatial variation is incorporated through a
single independent v... | [
{
"created": "Fri, 25 Dec 2020 00:26:22 GMT",
"version": "v1"
}
] | 2021-08-20 | [
[
"Alkhairy",
"Samiya A",
""
],
[
"Shera",
"Christopher A",
""
]
] | We develop an analytic model of the mammalian cochlea. We use a mixed physical-phenomenological approach by utilizing existing work on the physics of classical box-representations of the cochlea, and behavior of recent data-derived wavenumber estimates. Spatial variation is incorporated through a single independent var... |
2407.16580 | Jacob Sumner | Jacob Sumner, Grace Meng, Naomi Brandt, Alex T. Grigas, Andr\'es
C\'ordoba, Mark D. Shattuck, Corey S. O'Hern | Assessment of scoring functions for computational models of
protein-protein interfaces | 21 pages, 7 figures | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | A goal of computational studies of protein-protein interfaces (PPIs) is to
predict the binding site between two monomers that form a heterodimer. The
simplest version of this problem is to rigidly re-dock the bound forms of the
monomers, which involves generating computational models of the heterodimer and
then scori... | [
{
"created": "Tue, 23 Jul 2024 15:36:47 GMT",
"version": "v1"
}
] | 2024-07-24 | [
[
"Sumner",
"Jacob",
""
],
[
"Meng",
"Grace",
""
],
[
"Brandt",
"Naomi",
""
],
[
"Grigas",
"Alex T.",
""
],
[
"Córdoba",
"Andrés",
""
],
[
"Shattuck",
"Mark D.",
""
],
[
"O'Hern",
"Corey S.",
""
]
] | A goal of computational studies of protein-protein interfaces (PPIs) is to predict the binding site between two monomers that form a heterodimer. The simplest version of this problem is to rigidly re-dock the bound forms of the monomers, which involves generating computational models of the heterodimer and then scoring... |
2204.10672 | Anna Lewis | Madelyn Mauro, Danielle S. Allen, Bege Dauda, Santiago J. Molina,
Benjamin M. Neale, Anna C. F. Lewis | A systematic review of guidelines for the use of race, ethnicity, and
ancestry reveals widespread consensus but also points of ongoing disagreement | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | The use of population descriptors like race, ethnicity, and ancestry in
science, medicine and public health has a long, complicated, and at times dark
history, particularly for genetics, given the field's perceived importance for
understanding between-group differences. The historical and potential harms
that come wi... | [
{
"created": "Thu, 21 Apr 2022 14:01:00 GMT",
"version": "v1"
}
] | 2022-04-25 | [
[
"Mauro",
"Madelyn",
""
],
[
"Allen",
"Danielle S.",
""
],
[
"Dauda",
"Bege",
""
],
[
"Molina",
"Santiago J.",
""
],
[
"Neale",
"Benjamin M.",
""
],
[
"Lewis",
"Anna C. F.",
""
]
] | The use of population descriptors like race, ethnicity, and ancestry in science, medicine and public health has a long, complicated, and at times dark history, particularly for genetics, given the field's perceived importance for understanding between-group differences. The historical and potential harms that come with... |
0805.3861 | Vladimir Ivancevic | Vladimir G. Ivancevic and Eugene V. Aidman | Life-Space Foam: a Medium for Motivational and Cognitive Dynamics | 25 pages, 2 figures, elsart | Physica A 382, 616-630, (2007) | 10.1016/j.physa.2007.04.025 | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | General stochastic dynamics, developed in a framework of Feynman path
integrals, have been applied to Lewinian field--theoretic psychodynamics,
resulting in the development of a new concept of life--space foam (LSF) as a
natural medium for motivational and cognitive psychodynamics. According to LSF
formalisms, the cl... | [
{
"created": "Mon, 26 May 2008 02:21:45 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Ivancevic",
"Vladimir G.",
""
],
[
"Aidman",
"Eugene V.",
""
]
] | General stochastic dynamics, developed in a framework of Feynman path integrals, have been applied to Lewinian field--theoretic psychodynamics, resulting in the development of a new concept of life--space foam (LSF) as a natural medium for motivational and cognitive psychodynamics. According to LSF formalisms, the clas... |
q-bio/0607045 | Krzysztof Malarz | K.Malarz | The risk of extinction - the mutational meltdown or the overpopulation | RevTex4, 5 pages, 4 figures (8 eps files) | Theory Biosci. 125 (2007) 147 | 10.1016/j.thbio.2006.08.001 | null | q-bio.PE | null | The phase diagrams survival-extinction for the Penna model with parameters:
(mutations rate)-(birth rate), (mutation rate)-(harmful mutations threshold),
(harmful mutation threshold)-(minimal reproduction age) are presented. The
extinction phase may be caused by either mutational meltdown or overpopulation.
When the ... | [
{
"created": "Tue, 25 Jul 2006 13:38:41 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Malarz",
"K.",
""
]
] | The phase diagrams survival-extinction for the Penna model with parameters: (mutations rate)-(birth rate), (mutation rate)-(harmful mutations threshold), (harmful mutation threshold)-(minimal reproduction age) are presented. The extinction phase may be caused by either mutational meltdown or overpopulation. When the Ve... |
2311.08735 | Ha-Na Jo | Ha-Na Jo, Young-Seok Kweon, Gi-Hwan Shin, Heon-Gyu Kwak, Seong-Whan
Lee | Neurophysiological Response Based on Auditory Sense for Brain Modulation
Using Monaural Beat | Accepted to EMBC 2023 | null | null | null | q-bio.NC cs.HC | http://creativecommons.org/licenses/by/4.0/ | Brain modulation is a modification process of brain activity through external
stimulations. However, which condition can induce the activation is still
unclear. Therefore, we aimed to identify brain activation conditions using 40
Hz monaural beat (MB). Under this stimulation, auditory sense status which is
determined... | [
{
"created": "Wed, 15 Nov 2023 06:57:56 GMT",
"version": "v1"
}
] | 2023-11-16 | [
[
"Jo",
"Ha-Na",
""
],
[
"Kweon",
"Young-Seok",
""
],
[
"Shin",
"Gi-Hwan",
""
],
[
"Kwak",
"Heon-Gyu",
""
],
[
"Lee",
"Seong-Whan",
""
]
] | Brain modulation is a modification process of brain activity through external stimulations. However, which condition can induce the activation is still unclear. Therefore, we aimed to identify brain activation conditions using 40 Hz monaural beat (MB). Under this stimulation, auditory sense status which is determined b... |
1904.07952 | Linda Wang | Linda Wang | Response of Selective Attention in Middle Temporal Area | 9 pages, preprint | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The primary visual cortex processes a large amount of visual information,
however, due to its large receptive fields, when multiple stimuli fall within
one receptive field, there are computational problems. To solve this problem,
the visual system uses selective attention, which allocates resources to a
specific spat... | [
{
"created": "Tue, 16 Apr 2019 20:04:32 GMT",
"version": "v1"
}
] | 2019-04-18 | [
[
"Wang",
"Linda",
""
]
] | The primary visual cortex processes a large amount of visual information, however, due to its large receptive fields, when multiple stimuli fall within one receptive field, there are computational problems. To solve this problem, the visual system uses selective attention, which allocates resources to a specific spatia... |
2110.06078 | Charlotte Caucheteux | Charlotte Caucheteux, Alexandre Gramfort, Jean-R\'emi King | Model-based analysis of brain activity reveals the hierarchy of language
in 305 subjects | Accepted to EMNLP 2021 (Findings) | Findings of the Association for Computational Linguistics (EMNLP
2021) | null | null | q-bio.NC cs.AI cs.CL cs.LG | http://creativecommons.org/licenses/by/4.0/ | A popular approach to decompose the neural bases of language consists in
correlating, across individuals, the brain responses to different stimuli (e.g.
regular speech versus scrambled words, sentences, or paragraphs). Although
successful, this `model-free' approach necessitates the acquisition of a large
and costly ... | [
{
"created": "Tue, 12 Oct 2021 15:30:21 GMT",
"version": "v1"
}
] | 2023-03-21 | [
[
"Caucheteux",
"Charlotte",
""
],
[
"Gramfort",
"Alexandre",
""
],
[
"King",
"Jean-Rémi",
""
]
] | A popular approach to decompose the neural bases of language consists in correlating, across individuals, the brain responses to different stimuli (e.g. regular speech versus scrambled words, sentences, or paragraphs). Although successful, this `model-free' approach necessitates the acquisition of a large and costly se... |
2006.13471 | Sergio Verduzco-Flores | Sergio Verduzco-Flores, William Dorrell, Erik DeSchutter | A differential Hebbian framework for biologically-plausible motor
control | 35 pages, 10 figures. Appendix: 9 pages, 2 figures | Neural Networks (2022) 150:237-258 | 10.1016/j.neunet.2022.03.002 | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we explore a neural control architecture that is both
biologically plausible, and capable of fully autonomous learning. It consists
of feedback controllers that learn to achieve a desired state by selecting the
errors that should drive them. This selection happens through a family of
differential Hebbia... | [
{
"created": "Wed, 24 Jun 2020 04:25:27 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Apr 2021 01:12:46 GMT",
"version": "v2"
},
{
"created": "Thu, 11 Nov 2021 02:24:39 GMT",
"version": "v3"
},
{
"created": "Wed, 2 Feb 2022 03:50:52 GMT",
"version": "v4"
}
] | 2022-03-23 | [
[
"Verduzco-Flores",
"Sergio",
""
],
[
"Dorrell",
"William",
""
],
[
"DeSchutter",
"Erik",
""
]
] | In this paper we explore a neural control architecture that is both biologically plausible, and capable of fully autonomous learning. It consists of feedback controllers that learn to achieve a desired state by selecting the errors that should drive them. This selection happens through a family of differential Hebbian ... |
1904.09061 | Jingwei Liu | Jingwei Liu | Random Fragments Classification of Microbial Marker Clades with
Multi-class SVM and N-Best Algorithm | 17 pages, 59 figurea | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Microbial clades modeling is a challenging problem in biology based on
microarray genome sequences, especially in new species gene isolates discovery
and category. Marker family genome sequences play important roles in describing
specific microbial clades within species, a framework of support vector machine
(SVM) ba... | [
{
"created": "Fri, 19 Apr 2019 03:21:48 GMT",
"version": "v1"
}
] | 2019-04-22 | [
[
"Liu",
"Jingwei",
""
]
] | Microbial clades modeling is a challenging problem in biology based on microarray genome sequences, especially in new species gene isolates discovery and category. Marker family genome sequences play important roles in describing specific microbial clades within species, a framework of support vector machine (SVM) base... |
1812.06317 | Nikita Pospelov | K.Anokhin, V.Avetisov, A.Gorsky, S.Nechaev, N.Pospelov, O.Valba | Spectral peculiarity and criticality of the human connectome | null | null | null | null | q-bio.NC cond-mat.dis-nn physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have performed the comparative spectral analysis of structural connectomes
for various organisms using open-access data. Our analysis indicates several
new peculiar features of the human connectome. We found that the spectral
density of human connectome has the maximal deviation from the spectral density
of the ra... | [
{
"created": "Sat, 15 Dec 2018 16:28:02 GMT",
"version": "v1"
}
] | 2018-12-18 | [
[
"Anokhin",
"K.",
""
],
[
"Avetisov",
"V.",
""
],
[
"Gorsky",
"A.",
""
],
[
"Nechaev",
"S.",
""
],
[
"Pospelov",
"N.",
""
],
[
"Valba",
"O.",
""
]
] | We have performed the comparative spectral analysis of structural connectomes for various organisms using open-access data. Our analysis indicates several new peculiar features of the human connectome. We found that the spectral density of human connectome has the maximal deviation from the spectral density of the rand... |
2402.10516 | Yiheng Zhu | Yiheng Zhu, Zitai Kong, Jialu Wu, Weize Liu, Yuqiang Han, Mingze Yin,
Hongxia Xu, Chang-Yu Hsieh and Tingjun Hou | Generative AI for Controllable Protein Sequence Design: A Survey | 9 pages | null | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | The design of novel protein sequences with targeted functionalities underpins
a central theme in protein engineering, impacting diverse fields such as drug
discovery and enzymatic engineering. However, navigating this vast
combinatorial search space remains a severe challenge due to time and financial
constraints. Th... | [
{
"created": "Fri, 16 Feb 2024 09:05:02 GMT",
"version": "v1"
}
] | 2024-02-19 | [
[
"Zhu",
"Yiheng",
""
],
[
"Kong",
"Zitai",
""
],
[
"Wu",
"Jialu",
""
],
[
"Liu",
"Weize",
""
],
[
"Han",
"Yuqiang",
""
],
[
"Yin",
"Mingze",
""
],
[
"Xu",
"Hongxia",
""
],
[
"Hsieh",
"Chang-Yu",
... | The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial search space remains a severe challenge due to time and financial constraints. This... |
0711.2001 | Demian Battaglia | Demian Battaglia, Nicolas Brunel and David Hansel | Temporal decorrelation of collective oscillations in neural networks
with local inhibition and long-range excitation | 4 pages, 5 figures. accepted for publication in Physical Review
Letters | null | 10.1103/PhysRevLett.99.238106 | null | q-bio.NC cond-mat.dis-nn nlin.CD | null | We consider two neuronal networks coupled by long-range excitatory
interactions. Oscillations in the gamma frequency band are generated within
each network by local inhibition. When long-range excitation is weak, these
oscillations phase-lock with a phase-shift dependent on the strength of local
inhibition. Increasin... | [
{
"created": "Tue, 13 Nov 2007 15:01:34 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Battaglia",
"Demian",
""
],
[
"Brunel",
"Nicolas",
""
],
[
"Hansel",
"David",
""
]
] | We consider two neuronal networks coupled by long-range excitatory interactions. Oscillations in the gamma frequency band are generated within each network by local inhibition. When long-range excitation is weak, these oscillations phase-lock with a phase-shift dependent on the strength of local inhibition. Increasing ... |
q-bio/0605042 | Tobias Reichenbach | Tobias Reichenbach, Mauro Mobilia, and Erwin Frey | Coexistence versus extinction in the stochastic cyclic Lotka-Volterra
model | 12 pages, 9 figures, minor corrections | Phys. Rev. E 74, 051907 (2006) | 10.1103/PhysRevE.74.051907 | LMU-ASC 38/06 | q-bio.PE cond-mat.stat-mech physics.bio-ph | null | Cyclic dominance of species has been identified as a potential mechanism to
maintain biodiversity, see e.g. B. Kerr, M. A. Riley, M. W. Feldman and B. J.
M. Bohannan [Nature {\bf 418}, 171 (2002)] and B. Kirkup and M. A. Riley
[Nature {\bf 428}, 412 (2004)]. Through analytical methods supported by
numerical simulatio... | [
{
"created": "Wed, 24 May 2006 17:45:31 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Jun 2006 17:55:25 GMT",
"version": "v2"
},
{
"created": "Thu, 5 Oct 2006 12:06:46 GMT",
"version": "v3"
}
] | 2007-05-23 | [
[
"Reichenbach",
"Tobias",
""
],
[
"Mobilia",
"Mauro",
""
],
[
"Frey",
"Erwin",
""
]
] | Cyclic dominance of species has been identified as a potential mechanism to maintain biodiversity, see e.g. B. Kerr, M. A. Riley, M. W. Feldman and B. J. M. Bohannan [Nature {\bf 418}, 171 (2002)] and B. Kirkup and M. A. Riley [Nature {\bf 428}, 412 (2004)]. Through analytical methods supported by numerical simulations... |
0905.4468 | Tina Toni | Tina Toni, Michael P. H. Stumpf | Parameter inference and model selection in signaling pathway models | Book chapter for Topics in Computational Biology Methods in Molecular
Biology Series, Humana Press, 2009 | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To support and guide an extensive experimental research into systems biology
of signaling pathways, increasingly more mechanistic models are being developed
with hopes of gaining further insight into biological processes. In order to
analyse these models, computational and statistical techniques are needed to
estimat... | [
{
"created": "Wed, 27 May 2009 16:35:40 GMT",
"version": "v1"
}
] | 2009-05-28 | [
[
"Toni",
"Tina",
""
],
[
"Stumpf",
"Michael P. H.",
""
]
] | To support and guide an extensive experimental research into systems biology of signaling pathways, increasingly more mechanistic models are being developed with hopes of gaining further insight into biological processes. In order to analyse these models, computational and statistical techniques are needed to estimate ... |
1801.06452 | Qinbing Fu | Qinbing Fu and Cheng Hu and Shigang Yue | Collision Selective Visual Neural Network Inspired by LGMD2 Neurons in
Juvenile Locusts | null | null | null | null | q-bio.NC cs.CV cs.RO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For autonomous robots in dynamic environments mixed with human, it is vital
to detect impending collision quickly and robustly. The biological visual
systems evolved over millions of years may provide us efficient solutions for
collision detection in complex environments. In the cockpit of locusts, two
Lobula Giant M... | [
{
"created": "Fri, 22 Dec 2017 00:34:55 GMT",
"version": "v1"
}
] | 2018-01-22 | [
[
"Fu",
"Qinbing",
""
],
[
"Hu",
"Cheng",
""
],
[
"Yue",
"Shigang",
""
]
] | For autonomous robots in dynamic environments mixed with human, it is vital to detect impending collision quickly and robustly. The biological visual systems evolved over millions of years may provide us efficient solutions for collision detection in complex environments. In the cockpit of locusts, two Lobula Giant Mov... |
2302.10599 | Mengjie Chen | Mengjie Chen | The construction of ceRNAs network reveals the prognostic
characteristics of prostate cancer | in Chinese language | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | The dysregulation of transcripts is characterized as one of the main
mechanisms in tumor pathogenesis. The recent discovery developed a new
hypothesis, competitive endogenous RNAs (ceRNAs), which could regulate other
RNA transcripts via competing for their shared miRNAs. The interaction of
elements in ceRNAs network ... | [
{
"created": "Tue, 21 Feb 2023 11:06:55 GMT",
"version": "v1"
}
] | 2023-02-22 | [
[
"Chen",
"Mengjie",
""
]
] | The dysregulation of transcripts is characterized as one of the main mechanisms in tumor pathogenesis. The recent discovery developed a new hypothesis, competitive endogenous RNAs (ceRNAs), which could regulate other RNA transcripts via competing for their shared miRNAs. The interaction of elements in ceRNAs network wa... |
1106.4628 | Jiapu Zhang | Jiapu Zhang | The nature of the infectious agents: PrP models of resistant species to
prion diseases (dog, rabbit and horses) | This paper is an Invited and Accepted Book Chapter for "Prions and
Prion Diseases: New Developments (J.M. Verdier Eds.), NOVA Publishers, 2012,
ISBN 1621000273." | Prions and Prion Diseases: New Developments (J.M. Verdier Eds.),
NOVA Science Publishers, 2012, ISBN 978-1-61942-768-6, Chapter 2, pages 41-48 | null | null | q-bio.BM physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Prion diseases are invariably fatal and highly infectious neurodegenerative
diseases affecting humans and animals. By now there have not been some
effective therapeutic approaches to treat all these prion diseases. In 2008,
canine mammals including dogs (canis familials) were the first time
academically reported to b... | [
{
"created": "Thu, 23 Jun 2011 05:16:40 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Apr 2012 08:29:16 GMT",
"version": "v2"
}
] | 2012-10-16 | [
[
"Zhang",
"Jiapu",
""
]
] | Prion diseases are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. By now there have not been some effective therapeutic approaches to treat all these prion diseases. In 2008, canine mammals including dogs (canis familials) were the first time academically reported to be ... |
1809.01722 | Hau-tieng Wu | Yu-Ting Lin, Yu-Lun Lo, Chen-Yun Lin, Hau-Tieng Wu, Martin G. Frasch | Unexpected sawtooth artifact in beat-to-beat pulse transit time measured
from patient monitor data | null | null | 10.1371/journal.pone.0221319 | null | q-bio.QM cs.LG eess.SP physics.data-an stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Object: It is increasingly popular to collect as much data as possible in the
hospital setting from clinical monitors for research purposes. However, in this
setup the data calibration issue is often not discussed and, rather, implicitly
assumed, while the clinical monitors might not be designed for the data
analysis... | [
{
"created": "Mon, 27 Aug 2018 17:35:09 GMT",
"version": "v1"
},
{
"created": "Fri, 9 Aug 2019 14:41:54 GMT",
"version": "v2"
}
] | 2019-09-17 | [
[
"Lin",
"Yu-Ting",
""
],
[
"Lo",
"Yu-Lun",
""
],
[
"Lin",
"Chen-Yun",
""
],
[
"Wu",
"Hau-Tieng",
""
],
[
"Frasch",
"Martin G.",
""
]
] | Object: It is increasingly popular to collect as much data as possible in the hospital setting from clinical monitors for research purposes. However, in this setup the data calibration issue is often not discussed and, rather, implicitly assumed, while the clinical monitors might not be designed for the data analysis p... |
2202.02849 | Ian Wong | Alex M. Hruska and Haiqian Yang and Susan E. Leggett and Ming Guo and
Ian Y. Wong | Mechanobiology of Collective Cell Migration in 3D Microenvironments | null | null | null | null | q-bio.CB physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Tumor cells invade individually or in groups, mediated by mechanical
interactions between cells and their surrounding matrix. These multicellular
dynamics are reminiscent of leader-follower coordination and
epithelial-mesenchymal transitions (EMT) in tissue development, which may occur
via dysregulation of associated... | [
{
"created": "Sun, 6 Feb 2022 20:48:57 GMT",
"version": "v1"
},
{
"created": "Sun, 26 Jun 2022 22:12:32 GMT",
"version": "v2"
}
] | 2022-06-28 | [
[
"Hruska",
"Alex M.",
""
],
[
"Yang",
"Haiqian",
""
],
[
"Leggett",
"Susan E.",
""
],
[
"Guo",
"Ming",
""
],
[
"Wong",
"Ian Y.",
""
]
] | Tumor cells invade individually or in groups, mediated by mechanical interactions between cells and their surrounding matrix. These multicellular dynamics are reminiscent of leader-follower coordination and epithelial-mesenchymal transitions (EMT) in tissue development, which may occur via dysregulation of associated m... |
0803.0483 | Tao Hu | Tao Hu, B. I. Shklovskii | Theory of DNA translocation through narrow ion channels and nanopores
with charged walls | 3 pages, 1 figure | Phys. Rev. E 78, 032901 (2008) | 10.1103/PhysRevE.78.032901 | null | q-bio.SC cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Translocation of a single stranded DNA through genetically engineered
$\alpha$-hemolysin channels with positively charged walls is studied. It is
predicted that transport properties of such channels are dramatically different
from neutral wild type $\alpha$-hemolysin channel. We assume that the wall
charges compensat... | [
{
"created": "Tue, 4 Mar 2008 16:45:26 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Jun 2008 00:08:17 GMT",
"version": "v2"
}
] | 2008-09-10 | [
[
"Hu",
"Tao",
""
],
[
"Shklovskii",
"B. I.",
""
]
] | Translocation of a single stranded DNA through genetically engineered $\alpha$-hemolysin channels with positively charged walls is studied. It is predicted that transport properties of such channels are dramatically different from neutral wild type $\alpha$-hemolysin channel. We assume that the wall charges compensate ... |
2004.12053 | Daniel Mas Montserrat | Daniel Mas Montserrat, Arvind Kumar, Carlos Bustamante, Alexander
Ioannidis | Addressing Ancestry Disparities in Genomic Medicine: A Geographic-aware
Algorithm | null | null | null | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With declining sequencing costs a promising and affordable tool is emerging
in cancer diagnostics: genomics. By using association studies, genomic variants
that predispose patients to specific cancers can be identified, while by using
tumor genomics cancer types can be characterized for targeted treatment.
However, a... | [
{
"created": "Sat, 25 Apr 2020 04:32:16 GMT",
"version": "v1"
}
] | 2020-04-28 | [
[
"Montserrat",
"Daniel Mas",
""
],
[
"Kumar",
"Arvind",
""
],
[
"Bustamante",
"Carlos",
""
],
[
"Ioannidis",
"Alexander",
""
]
] | With declining sequencing costs a promising and affordable tool is emerging in cancer diagnostics: genomics. By using association studies, genomic variants that predispose patients to specific cancers can be identified, while by using tumor genomics cancer types can be characterized for targeted treatment. However, a s... |
1210.7083 | Thomas Pfeil | Thomas Pfeil, Andreas Gr\"ubl, Sebastian Jeltsch, Eric M\"uller, Paul
M\"uller, Mihai A. Petrovici, Michael Schmuker, Daniel Br\"uderle, Johannes
Schemmel, Karlheinz Meier | Six networks on a universal neuromorphic computing substrate | 21 pages, 9 figures | Front. Neurosci. 7:11 (2013) | 10.3389/fnins.2013.00011 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this study, we present a highly configurable neuromorphic computing
substrate and use it for emulating several types of neural networks. At the
heart of this system lies a mixed-signal chip, with analog implementations of
neurons and synapses and digital transmission of action potentials. Major
advantages of this ... | [
{
"created": "Fri, 26 Oct 2012 09:51:03 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Dec 2012 00:13:53 GMT",
"version": "v2"
},
{
"created": "Wed, 9 Jan 2013 14:19:14 GMT",
"version": "v3"
},
{
"created": "Thu, 21 Feb 2013 16:55:08 GMT",
"version": "v4"
}
] | 2013-04-08 | [
[
"Pfeil",
"Thomas",
""
],
[
"Grübl",
"Andreas",
""
],
[
"Jeltsch",
"Sebastian",
""
],
[
"Müller",
"Eric",
""
],
[
"Müller",
"Paul",
""
],
[
"Petrovici",
"Mihai A.",
""
],
[
"Schmuker",
"Michael",
""
],
[... | In this study, we present a highly configurable neuromorphic computing substrate and use it for emulating several types of neural networks. At the heart of this system lies a mixed-signal chip, with analog implementations of neurons and synapses and digital transmission of action potentials. Major advantages of this em... |
1112.4694 | Jakob Bj\"ornberg | Jakob E. Bj\"ornberg, Tom Britton, Erik I. Broman, Eviatar Natan | A stochastic model for virus growth in a cell population | 18 pages, 1 figure | null | null | null | q-bio.CB math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A stochastic model for the growth of a virus in a cell population is
introduced. The virus has two ways of spreading: either by allowing its host
cell to live on and duplicate, or else by multiplying in large numbers within
the host cell such that the host cell finally bursts and the viruses then have
the chance to e... | [
{
"created": "Tue, 20 Dec 2011 14:16:19 GMT",
"version": "v1"
},
{
"created": "Mon, 29 Oct 2012 13:57:40 GMT",
"version": "v2"
}
] | 2012-10-30 | [
[
"Björnberg",
"Jakob E.",
""
],
[
"Britton",
"Tom",
""
],
[
"Broman",
"Erik I.",
""
],
[
"Natan",
"Eviatar",
""
]
] | A stochastic model for the growth of a virus in a cell population is introduced. The virus has two ways of spreading: either by allowing its host cell to live on and duplicate, or else by multiplying in large numbers within the host cell such that the host cell finally bursts and the viruses then have the chance to ent... |
1204.1995 | Johannes Wollbold | Johannes Wollbold | Attribute Exploration of Gene Regulatory Processes | 111 pages, 9 figures, file size 2.1 MB, PhD thesis University of
Jena, Germany, Faculty of Mathematics and Computer Science, 2011. Online
available at http://www.db-thueringen.de/servlets/DocumentServlet?id=19601 | null | null | null | q-bio.MN cs.CE cs.LO math.LO | http://creativecommons.org/licenses/by/3.0/ | This thesis aims at the logical analysis of discrete processes, in particular
of such generated by gene regulatory networks. States, transitions and
operators from temporal logics are expressed in the language of Formal Concept
Analysis. By the attribute exploration algorithm, an expert or a computer
program is enabl... | [
{
"created": "Mon, 9 Apr 2012 21:23:04 GMT",
"version": "v1"
}
] | 2012-04-11 | [
[
"Wollbold",
"Johannes",
""
]
] | This thesis aims at the logical analysis of discrete processes, in particular of such generated by gene regulatory networks. States, transitions and operators from temporal logics are expressed in the language of Formal Concept Analysis. By the attribute exploration algorithm, an expert or a computer program is enabled... |
1510.08397 | J. C. Phillips | J. C. Phillips | Bioinformatic Scaling of Allosteric Interactions in Biomedical Isozymes | 12 pages, 5 figures | null | 10.1016/j.physa.2016.03.038 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Allosteric (long-range) interactions can be surprisingly strong in proteins
of biomedical interest. Here we use bioinformatic scaling to connect prior
results on nonsteroidal anti-inflammatory drugs to promising new drugs that
inhibit cancer cell metabolism. Many parallel features are apparent, which
explain how even... | [
{
"created": "Mon, 19 Oct 2015 01:49:22 GMT",
"version": "v1"
}
] | 2016-05-04 | [
[
"Phillips",
"J. C.",
""
]
] | Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit cancer cell metabolism. Many parallel features are apparent, which explain how even o... |
0904.2668 | Siew-Ann Cheong | Siew-Ann Cheong, Paul Stodghill, David J. Schneider, Samuel W.
Cartinhour, and Christopher R. Myers | The Context Sensitivity Problem in Biological Sequence Segmentation | IEEEtran class, 39 pages, 20 figures | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we describe the context sensitivity problem encountered in
partitioning a heterogeneous biological sequence into statistically homogeneous
segments. After showing signatures of the problem in the bacterial genomes of
Escherichia coli K-12 MG1655 and Pseudomonas syringae DC3000, when these are
segmented... | [
{
"created": "Fri, 17 Apr 2009 10:02:26 GMT",
"version": "v1"
}
] | 2009-04-20 | [
[
"Cheong",
"Siew-Ann",
""
],
[
"Stodghill",
"Paul",
""
],
[
"Schneider",
"David J.",
""
],
[
"Cartinhour",
"Samuel W.",
""
],
[
"Myers",
"Christopher R.",
""
]
] | In this paper, we describe the context sensitivity problem encountered in partitioning a heterogeneous biological sequence into statistically homogeneous segments. After showing signatures of the problem in the bacterial genomes of Escherichia coli K-12 MG1655 and Pseudomonas syringae DC3000, when these are segmented u... |
2311.10321 | David Black | David Black, Declan Byrne, Anna Walke, Sidong Liu, Antonio Di leva,
Sadahiro Kaneko, Walter Stummer, Septimiu Salcudean, Eric Suero Molina | Towards Machine Learning-based Quantitative Hyperspectral Image Guidance
for Brain Tumor Resection | 22 pages, 8 figures | null | null | null | q-bio.TO cs.LG eess.IV | http://creativecommons.org/licenses/by/4.0/ | Complete resection of malignant gliomas is hampered by the difficulty in
distinguishing tumor cells at the infiltration zone. Fluorescence guidance with
5-ALA assists in reaching this goal. Using hyperspectral imaging, previous work
characterized five fluorophores' emission spectra in most human brain tumors.
In this... | [
{
"created": "Fri, 17 Nov 2023 04:15:27 GMT",
"version": "v1"
},
{
"created": "Fri, 24 Nov 2023 19:59:28 GMT",
"version": "v2"
}
] | 2023-11-28 | [
[
"Black",
"David",
""
],
[
"Byrne",
"Declan",
""
],
[
"Walke",
"Anna",
""
],
[
"Liu",
"Sidong",
""
],
[
"Di leva",
"Antonio",
""
],
[
"Kaneko",
"Sadahiro",
""
],
[
"Stummer",
"Walter",
""
],
[
"Salcu... | Complete resection of malignant gliomas is hampered by the difficulty in distinguishing tumor cells at the infiltration zone. Fluorescence guidance with 5-ALA assists in reaching this goal. Using hyperspectral imaging, previous work characterized five fluorophores' emission spectra in most human brain tumors. In this p... |
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