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Volume 15; Issue 12
Main
PLoS Computational Biology
Volume 15; Issue 12
PLoS Computational Biology
Volume 15; Issue 12
1
A computational study on the role of glutamate and NMDA receptors on cortical spreading depression using a multidomain electrodiffusion model
Tuttle, Austin
,
Riera Diaz, Jorge
,
Mori, Yoichiro
,
Einevoll, Gaute T.
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 4.66 MB
Your tags:
english, 2019
2
ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest
Li, Jiajin
,
Jew, Brandon
,
Zhan, Lingyu
,
Hwang, Sungoo
,
Coppola, Giovanni
,
Freimer, Nelson B.
,
Sul, Jae Hoon
,
Pertea, Mihaela
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 2.50 MB
Your tags:
english, 2019
3
Representation learning of genomic sequence motifs with convolutional neural networks
Koo, Peter K.
,
Eddy, Sean R.
,
Listgarten, Jennifer
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 3.46 MB
Your tags:
english, 2019
4
The dynamics of motor learning through the formation of internal models
Pierella, Camilla
,
Casadio, Maura
,
Mussa-Ivaldi, Ferdinando A.
,
Solla, Sara A.
,
Haith, Adrian M
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 3.91 MB
Your tags:
english, 2019
5
Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
Janson, Giacomo
,
Grottesi, Alessandro
,
Pietrosanto, Marco
,
Ausiello, Gabriele
,
Guarguaglini, Giulia
,
Paiardini, Alessandro
,
de Groot, Bert L.
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 3.83 MB
Your tags:
english, 2019
6
A novel machine learning based approach for iPS progenitor cell identification
Zhang, Haishan
,
Shao, Ximing
,
Peng, Yin
,
Teng, Yanning
,
Saravanan, Konda Mani
,
Zhang, Huiling
,
Li, Hongchang
,
Wei, Yanjie
,
Zou, Quan
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 3.29 MB
Your tags:
english, 2019
7
Benchmarking network algorithms for contextualizing genes of interest
Hill, Abby
,
Gleim, Scott
,
Kiefer, Florian
,
Sigoillot, Frederic
,
Loureiro, Joseph
,
Jenkins, Jeremy
,
Morris, Melody K.
,
Chen, Luonan
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 2.68 MB
Your tags:
english, 2019
8
Nine quick tips for analyzing network data
Miele, Vincent
,
Matias, Catherine
,
Robin, Stéphane
,
Dray, Stéphane
,
Ouellette, Francis
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 688 KB
Your tags:
english, 2019
9
Stochasticity of replication forks’ speeds plays a key role in the dynamics of DNA replication
Yousefi, Razie
,
Rowicka, Maga
,
Wodarz, Dominik
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 3.43 MB
Your tags:
english, 2019
10
Evidence for a multi-level trophic organization of the human gut microbiome
Wang, Tong
,
Goyal, Akshit
,
Dubinkina, Veronika
,
Maslov, Sergei
,
Tikhonov, Mikhail
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 1.47 MB
Your tags:
english, 2019
11
Protons in small spaces: Discrete simulations of vesicle acidification
Singh, Apeksha
,
Marcoline, Frank V.
,
Veshaguri, Salome
,
Kao, Aimee W.
,
Bruchez, Marcel
,
Mindell, Joseph A.
,
Stamou, Dimitrios
,
Grabe, Michael
,
Krishnan, Yamuna
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 3.44 MB
Your tags:
english, 2019
12
Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs
Wang, Yongcui
,
Chen, Shilong
,
Chen, Luonan
,
Wang, Yong
,
Ioshikhes, Ilya
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 2.93 MB
Your tags:
english, 2019
13
Overlap matrix completion for predicting drug-associated indications
Yang, Mengyun
,
Luo, Huimin
,
Li, Yaohang
,
Wu, Fang-Xiang
,
Wang, Jianxin
,
Wang, Edwin
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 8.71 MB
Your tags:
english, 2019
14
Avoidance of non-localizable obstacles in echolocating bats: A robotic model
Bou Mansour, Carl
,
Koreman, Elijah
,
Steckel, Jan
,
Peremans, Herbert
,
Vanderelst, Dieter
,
Ayers, Joseph
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 4.78 MB
Your tags:
english, 2019
15
Probing neural networks for dynamic switches of communication pathways
Finger, Holger
,
Gast, Richard
,
Gerloff, Christian
,
Engel, Andreas K.
,
König, Peter
,
Kumar, Arvind
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 4.46 MB
Your tags:
english, 2019
16
Neuronal population model of globular bushy cells covering unit-to-unit variability
Ashida, Go
,
Heinermann, Helen T.
,
Kretzberg, Jutta
,
Theunissen, Frédéric E.
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 3.92 MB
Your tags:
english, 2019
17
Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways
Medvedev, Kirill E.
,
Kinch, Lisa N.
,
Schaeffer, R. Dustin
,
Grishin, Nick V.
,
Tawfik, Dan S.
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 21.53 MB
Your tags:
english, 2019
18
A computational study on the role of glutamate and NMDA receptors on cortical spreading depression using a multidomain electrodiffusion model
Tuttle, Austin
,
Riera Diaz, Jorge
,
Mori, Yoichiro
,
Einevoll, Gaute T.
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 4.66 MB
Your tags:
2019
19
CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data
Kang, Kai
,
Meng, Qian
,
Shats, Igor
,
Umbach, David M.
,
Li, Melissa
,
Li, Yuanyuan
,
Li, Xiaoling
,
Li, Leping
,
Przytycka, Teresa M.
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 4.25 MB
Your tags:
2019
20
Inferring reaction network structure from single-cell, multiplex data, using toric systems theory
Wang, Shu
,
Lin, Jia-Ren
,
Sontag, Eduardo D.
,
Sorger, Peter K.
,
Mendes, Pedro
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 7.26 MB
Your tags:
2019
21
Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli
Du, Bin
,
Yang, Laurence
,
Lloyd, Colton J.
,
Fang, Xin
,
Palsson, Bernhard O.
,
Wallqvist, Anders
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 2.47 MB
Your tags:
2019
22
Stability of spontaneous, correlated activity in mouse auditory cortex
Betzel, Richard F.
,
Wood, Katherine C.
,
Angeloni, Christopher
,
Neimark Geffen, Maria
,
Bassett, Danielle S.
,
Muller, Lyle
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 6.41 MB
Your tags:
2019
23
Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
Barry, Christopher
,
Schmitz, Matthew T.
,
Argus, Cara
,
Bolin, Jennifer M.
,
Probasco, Mitchell D.
,
Leng, Ning
,
Duffin, Bret M.
,
Steill, John
,
Swanson, Scott
,
McIntosh, Brian E.
,
Stewart, Ron
,
Kendziorsk
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 4.14 MB
Your tags:
2019
24
Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level
Kønig, Simon Mathis
,
Rissler, Vendela
,
Terkelsen, Thilde
,
Lambrughi, Matteo
,
Papaleo, Elena
,
Berezovsky, Igor N.
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 7.60 MB
Your tags:
2019
25
Incomplete information about the partner affects the development of collaborative strategies in joint action
Chackochan, Vinil T.
,
Sanguineti, Vittorio
,
Flack, Jessica C.
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 1.75 MB
Your tags:
2019
26
NUFEB: A massively parallel simulator for individual-based modelling of microbial communities
Li, Bowen
,
Taniguchi, Denis
,
Gedara, Jayathilake Pahala
,
Gogulancea, Valentina
,
Gonzalez-Cabaleiro, Rebeca
,
Chen, Jinju
,
McGough, Andrew Stephen
,
Ofiteru, Irina Dana
,
Curtis, Thomas P.
,
Zuliani, Paolo
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 11.18 MB
Your tags:
2019
27
Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters
Jandrasits, Christine
,
Kröger, Stefan
,
Haas, Walter
,
Renard, Bernhard Y.
,
Kosakovsky Pond, Sergei L.
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 2.71 MB
Your tags:
2019
28
Statistical inference in ensemble modeling of cellular metabolism
Hameri, Tuure
,
Boldi, Marc-Olivier
,
Hatzimanikatis, Vassily
,
Ouzounis, Christos A.
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 3.43 MB
Your tags:
2019
29
Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model
Mittler, John E.
,
Murphy, James T.
,
Stansfield, Sarah E.
,
Peebles, Kathryn C.
,
Gottlieb, Geoffrey S.
,
Abernethy, Neil F.
,
Reid, Molly C.
,
Goodreau, Steven M.
,
Herbeck, Joshua T.
,
Regoes, Roland R.
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 4.99 MB
Your tags:
2019
30
Motion prediction enables simulated MR-imaging of freely moving model organisms
Reischl, Markus
,
Jouda, Mazin
,
MacKinnon, Neil
,
Fuhrer, Erwin
,
Bakhtina, Natalia
,
Bartschat, Andreas
,
Mikut, Ralf
,
Korvink, Jan G.
,
Singh, Rahul
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 8.61 MB
Your tags:
2019
31
ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest
Li, Jiajin
,
Jew, Brandon
,
Zhan, Lingyu
,
Hwang, Sungoo
,
Coppola, Giovanni
,
Freimer, Nelson B.
,
Sul, Jae Hoon
,
Pertea, Mihaela
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 2.50 MB
Your tags:
2019
32
Representation learning of genomic sequence motifs with convolutional neural networks
Koo, Peter K.
,
Eddy, Sean R.
,
Listgarten, Jennifer
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 3.46 MB
Your tags:
2019
33
The dynamics of motor learning through the formation of internal models
Pierella, Camilla
,
Casadio, Maura
,
Mussa-Ivaldi, Ferdinando A.
,
Solla, Sara A.
,
Haith, Adrian M
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 3.91 MB
Your tags:
2019
34
Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
Janson, Giacomo
,
Grottesi, Alessandro
,
Pietrosanto, Marco
,
Ausiello, Gabriele
,
Guarguaglini, Giulia
,
Paiardini, Alessandro
,
de Groot, Bert L.
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 3.83 MB
Your tags:
2019
35
A novel machine learning based approach for iPS progenitor cell identification
Zhang, Haishan
,
Shao, Ximing
,
Peng, Yin
,
Teng, Yanning
,
Saravanan, Konda Mani
,
Zhang, Huiling
,
Li, Hongchang
,
Wei, Yanjie
,
Zou, Quan
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 3.29 MB
Your tags:
2019
36
Benchmarking network algorithms for contextualizing genes of interest
Hill, Abby
,
Gleim, Scott
,
Kiefer, Florian
,
Sigoillot, Frederic
,
Loureiro, Joseph
,
Jenkins, Jeremy
,
Morris, Melody K.
,
Chen, Luonan
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 2.68 MB
Your tags:
2019
37
Nine quick tips for analyzing network data
Miele, Vincent
,
Matias, Catherine
,
Robin, Stéphane
,
Dray, Stéphane
,
Ouellette, Francis
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 688 KB
Your tags:
2019
38
Stochasticity of replication forks’ speeds plays a key role in the dynamics of DNA replication
Yousefi, Razie
,
Rowicka, Maga
,
Wodarz, Dominik
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 3.43 MB
Your tags:
2019
39
Evidence for a multi-level trophic organization of the human gut microbiome
Wang, Tong
,
Goyal, Akshit
,
Dubinkina, Veronika
,
Maslov, Sergei
,
Tikhonov, Mikhail
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 1.47 MB
Your tags:
2019
40
Protons in small spaces: Discrete simulations of vesicle acidification
Singh, Apeksha
,
Marcoline, Frank V.
,
Veshaguri, Salome
,
Kao, Aimee W.
,
Bruchez, Marcel
,
Mindell, Joseph A.
,
Stamou, Dimitrios
,
Grabe, Michael
,
Krishnan, Yamuna
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 3.44 MB
Your tags:
2019
41
Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs
Wang, Yongcui
,
Chen, Shilong
,
Chen, Luonan
,
Wang, Yong
,
Ioshikhes, Ilya
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 2.93 MB
Your tags:
2019
42
Overlap matrix completion for predicting drug-associated indications
Yang, Mengyun
,
Luo, Huimin
,
Li, Yaohang
,
Wu, Fang-Xiang
,
Wang, Jianxin
,
Wang, Edwin
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 8.71 MB
Your tags:
2019
43
Avoidance of non-localizable obstacles in echolocating bats: A robotic model
Bou Mansour, Carl
,
Koreman, Elijah
,
Steckel, Jan
,
Peremans, Herbert
,
Vanderelst, Dieter
,
Ayers, Joseph
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 4.78 MB
Your tags:
2019
44
Probing neural networks for dynamic switches of communication pathways
Finger, Holger
,
Gast, Richard
,
Gerloff, Christian
,
Engel, Andreas K.
,
König, Peter
,
Kumar, Arvind
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 4.46 MB
Your tags:
2019
45
Neuronal population model of globular bushy cells covering unit-to-unit variability
Ashida, Go
,
Heinermann, Helen T.
,
Kretzberg, Jutta
,
Theunissen, Frédéric E.
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 3.92 MB
Your tags:
2019
46
Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways
Medvedev, Kirill E.
,
Kinch, Lisa N.
,
Schaeffer, R. Dustin
,
Grishin, Nick V.
,
Tawfik, Dan S.
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 21.53 MB
Your tags:
2019
47
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection
Yan, Jinyuan
,
Estanbouli, Henri
,
Liao, Chen
,
Kim, Wook
,
Monk, Jonathan M.
,
Rahman, Rayees
,
Kamboj, Mini
,
Palsson, Bernhard O.
,
Qiu, Weigang
,
Xavier, Joao B.
,
Patil, Kiran Raosaheb
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 5.51 MB
Your tags:
2019
48
Chemotaxis in external fields: Simulations for active magnetic biological matter
Codutti, Agnese
,
Bente, Klaas
,
Faivre, Damien
,
Klumpp, Stefan
,
Igoshin, Oleg A
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 2.55 MB
Your tags:
2019
49
Regulatory context drives conservation of glycine riboswitch aptamers
Crum, Matt
,
Ram-Mohan, Nikhil
,
Meyer, Michelle M.
,
Chen, Shi-Jie
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 3.71 MB
Your tags:
english, 2019
50
A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation
Pharris, Matthew C.
,
Patel, Neal M.
,
VanDyk, Tyler G.
,
Bartol, Thomas M.
,
Sejnowski, Terrence J.
,
Kennedy, Mary B.
,
Stefan, Melanie I.
,
Kinzer-Ursem, Tamara L.
,
Jedrzejewski-Szmek, Joanna
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 2.60 MB
Your tags:
2019
51
Interkinetic nuclear movements promote apical expansion in pseudostratified epithelia at the expense of apicobasal elongation
Ferreira, Marina A.
,
Despin-Guitard, Evangeline
,
Duarte, Fernando
,
Degond, Pierre
,
Theveneau, Eric
,
Maini, Philip K.
Journal:
PLoS Computational Biology
Year:
2019
Language:
english
File:
PDF, 2.47 MB
Your tags:
english, 2019
52
Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15
Endo, Akira
,
Uchida, Mitsuo
,
Kucharski, Adam J.
,
Funk, Sebastian
,
Viboud, Cecile
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 1.82 MB
Your tags:
2019
53
Establishment of computational biology in Greece and Cyprus: Past, present, and future
Chasapi, Anastasia
,
Aivaliotis, Michalis
,
Angelis, Lefteris
,
Chanalaris, Anastasios
,
Iliopoulos, Ioannis
,
Kappas, Ilias
,
Karapiperis, Christos
,
Kyrpides, Nikos C.
,
Pafilis, Evangelos
,
Panteris, Elefth
Journal:
PLoS Computational Biology
Year:
2019
File:
PDF, 841 KB
Your tags:
2019
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