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PLoS Computational Biology, Volume 16
Volume 16, Number 1, January 2020
- Alex Salazar
, Franklin L. Nobrega
, Christine Anyansi
, Cristian Aparicio-Maldonado, Ana Rita Costa
, Anna C. Haagsma
, Anwar Hiralal
, Ahmed Mahfouz
, Rebecca E. McKenzie, Teunke van Rossum
, Stan J. J. Brouns, Thomas Abeel
:
An educational guide for nanopore sequencing in the classroom.
- Anand Pathak
, Nivedita Chatterjee, Sitabhra Sinha
:
Developmental trajectory of Caenorhabditis elegans nervous system governs its structural organization. - Simon Valentin
, Maximilian Harkotte
, Tzvetan Popov:
Interpreting neural decoding models using grouped model reliance. - Filip Melinscak
, Dominik R. Bach
:
Computational optimization of associative learning experiments. - Jeremy M. Chacón
, Allison K. Shaw
, William R. Harcombe
:
Increasing growth rate slows adaptation when genotypes compete for diffusing resources. - Yong Chen, Wentao Ma
:
The origin of biological homochirality along with the origin of life. - Jaideep Joshi
, Åke Brännström
, Ulf Dieckmann:
Emergence of social inequality in the spatial harvesting of renewable public goods. - Henghui Zhu, Hao Liu, Armin Ataei
, Yonatan Munk, Thomas Daniel
, Ioannis Ch. Paschalidis
:
Learning from animals: How to Navigate Complex Terrains. - Vaitea Opuu
, Giuliano Nigro
, Thomas Gaillard
, Emmanuelle Schmitt
, Yves Mechulam
, Thomas Simonson
:
Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power. - Anton M. Unakafov
, Thomas Schultze, Alexander Gail
, Sebastian Möller, Igor Kagan
, Stephan Eule, Fred Wolf
:
Emergence and suppression of cooperation by action visibility in transparent games. - Jake P. Taylor-King
, Asbjørn Nilsen Riseth
, Will Macnair, Manfred Claassen
:
Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming. - Alba Solsona-Berga
, Kaitlin E. Frasier, Simone Baumann-Pickering
, Sean M. Wiggins
, John A. Hildebrand
:
DetEdit: A graphical user interface for annotating and editing events detected in long-term acoustic monitoring data. - Jiwoong Kim, David E. Greenberg
, Reed Pifer
, Shuang Jiang, Guanghua Xiao
, Samuel A. Shelburne, Andrew Y. Koh
, Yang Xie, Xiaowei Zhan
:
VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning. - Tommy Heck
, Diego A. Vargas, Bart Smeets
, Herman Ramon, Paul Van Liedekerke
, Hans Van Oosterwyck
:
The role of actin protrusion dynamics in cell migration through a degradable viscoelastic extracellular matrix: Insights from a computational model. - Manoj Kumar
, Cameron T. Ellis
, Qihong Lu
, Hejia Zhang
, Mihai Capota
, Theodore L. Willke, Peter J. Ramadge, Nicholas B. Turk-Browne, Kenneth A. Norman:
BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis. - Sungrim Seirin-Lee
, Yuhki Yanase, Shunsuke Takahagi
, Michihiro Hide
:
A single reaction-diffusion equation for the multifarious eruptions of urticaria. - Christie A. Bahlai
, Elise F. Zipkin
:
The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations. - Maria Bargués-Ribera
, Chaitanya S. Gokhale
:
Eco-evolutionary agriculture: Host-pathogen dynamics in crop rotations. - Benjamin Allen
, Christine Sample
, Robert Jencks, James Withers, Patricia Steinhagen, Lori Brizuela, Joshua Kolodny
, Darren Parke, Gabor Lippner
, Yulia Dementieva:
Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs. - Josef Tkadlec
, Andreas Pavlogiannis
, Krishnendu Chatterjee, Martin A. Nowak
:
Limits on amplifiers of natural selection under death-Birth updating. - Sayaka Miura
, Koichiro Tamura
, Qiqing Tao
, Louise A. Huuki
, Sergei L. Kosakovsky Pond, Jessica Priest
, Jiamin Deng
, Sudhir Kumar
:
A new method for inferring timetrees from temporally sampled molecular sequences. - Melanie Gerken
, Sergej Kakorin, Kamel Chibani
, Karl-Josef Dietz
:
Computational simulation of the reactive oxygen species and redox network in the regulation of chloroplast metabolism. - Simon D. Angus
, Jonathan Newton
:
Collaboration leads to cooperation on sparse networks. - Jennifer Hannig
, Hendrik Schäfer
, Jörg Ackermann, Marie Hebel, Tim Schäfer
, Claudia Döring
, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch
:
Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma. - Amadeus Maes
, Mauricio Barahona
, Claudia Clopath
:
Learning spatiotemporal signals using a recurrent spiking network that discretizes time. - Veena Padmanaban
, Yohannes Tsehay
, Kevin J. Cheung, Andrew J. Ewald, Joel S. Bader
:
Between-tumor and within-tumor heterogeneity in invasive potential. - Edward W. Huang
, Ameya Bhope
, Jing Lim
, Saurabh Sinha
, Amin Emad
:
Tissue-guided LASSO for prediction of clinical drug response using preclinical samples. - Christopher A. Lavender
, Andrew J. Shapiro
, Frank S. Day, David C. Fargo
:
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets. - Rasmus S. Petersen
, Andrea Colins Rodriguez
, Mathew H. Evans, Dario Campagner, Michaela S. E. Loft:
A system for tracking whisker kinematics and whisker shape in three dimensions. - Erinija Pranckeviciene
, Sergey Hosid
, Nathan Liang
, Ilya Ioshikhes
:
Nucleosome positioning sequence patterns as packing or regulatory. - Daan H. de Groot
, Josephus Hulshof, Bas Teusink
, Frank J. Bruggeman
, Robert Planqué
:
Elementary Growth Modes provide a molecular description of cellular self-fabrication. - Sean M. Cascarina
, Mikaela R. Elder
, Eric D. Ross
:
Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome. - Rocío Vega
, Manuel Carretero
, Rui D. M. Travasso
, Luis L. Bonilla
:
Notch signaling and taxis mechanisms regulate early stage angiogenesis: A mathematical and computational model. - Tomasz Konopka
, Damian Smedley:
Incremental data integration for tracking genotype-disease associations. - Roger J. W. Hill
, Pasquale F. Innominato, Francis Lévi, Annabelle Ballesta:
Optimizing circadian drug infusion schedules towards personalized cancer chronotherapy. - Subhodh Kotekal, Jason N. MacLean
:
Recurrent interactions can explain the variance in single trial responses. - Yichao Han
, Fuzhong Zhang
:
Heterogeneity coordinates bacterial multi-gene expression in single cells. - Jordan A. Berg
, Jonathan R. Belyeu
, Jeffrey T. Morgan
, Yeyun Ouyang
, Alex J. Bott
, Aaron R. Quinlan, Jason Gertz
, Jared Rutter:
XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data.
Volume 16, Number 2, February 2020
- Veronika Cheplygina, Felienne Hermans
, Casper J. Albers
, Natalia Z. Bielczyk
, Ionica Smeets
:
Ten simple rules for getting started on Twitter as a scientist. - John S. Tregoning
, Jason E. McDermott
:
Ten Simple Rules to becoming a principal investigator.
- Janine Arloth
, Gökcen Eraslan, Till F. M. Andlauer
, Jade Martins
, Stella Iurato, Brigitte Kühnel, Melanie Waldenberger, Josef Frank, Ralf Gold, Bernhard Hemmer, Felix Luessi, Sandra Nischwitz, Friedemann Paul
, Heinz Wiendl, Christian Gieger, Stefanie Heilmann-Heimbach, Tim Kacprowski
, Matthias Laudes, Thomas Meitinger, Annette Peters
, Rajesh Rawal, Konstantin Strauch, Susanne Lucae, Bertram Müller-Myhsok, Marcella Rietschel
, Fabian J. Theis, Elisabeth B. Binder, Nikola S. Müller
:
DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning. - Nadim A. A. Atiya
, Arkady Zgonnikov
, Denis O'Hora
, Martin Schoemann
, Stefan Scherbaum
, KongFatt Wong-Lin
:
Changes-of-mind in the absence of new post-decision evidence. - Collins Assisi
, Mark Stopfer, Maxim Bazhenov
:
Optimality of sparse olfactory representations is not affected by network plasticity. - Hadar Levi-Aharoni
, Oren Shriki
, Naftali Tishby:
Surprise response as a probe for compressed memory states. - Flavia Corsi, Richard Lavery
, Elodie Laine
, Alessandra Carbone
:
Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties. - Aleksandr Ianevski
, Sanna Timonen
, Alexander Kononov
, Tero Aittokallio
, Anil K. Giri
:
SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy. - Antoine Allard
, M. Ángeles Serrano
:
Navigable maps of structural brain networks across species. - Ana Moyano
, Gila Lustig, Hylton E. Rodel
, Tibor Antal, Alex Sigal
:
Interference with HIV infection of the first cell is essential for viral clearance at sub-optimal levels of drug inhibition. - Brian Lang
, Jack Kuipers
, Benjamin Misselwitz
, Niko Beerenwinkel:
Predicting colorectal cancer risk from adenoma detection via a two-type branching process model. - Florent Le Möel
, Antoine Wystrach
:
Opponent processes in visual memories: A model of attraction and repulsion in navigating insects' mushroom bodies. - Manuel Stritt
, Anna Stalder, Enrico Vezzali
:
Orbit Image Analysis: An open-source whole slide image analysis tool. - Alice E. Milne
, Timothy R. Gottwald, Stephen Parnell
, Vasthi Alonso Chávez
, Frank van den Bosch:
What makes or breaks a campaign to stop an invading plant pathogen? - Kaeser Md. Sabrin
, Yongbin Wei, Martijn P. van den Heuvel
, Constantine Dovrolis
:
The hourglass organization of the Caenorhabditis elegans connectome. - Susanne Reimering
, Sebastian Muñoz, Alice C. McHardy
:
Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic. - Marion F. Sauer
, Alexander M. Sevy
, James E. Crowe Jr.
, Jens Meiler
:
Multi-state design of flexible proteins predicts sequences optimal for conformational change. - Paul Hager, Hans-Werner Mewes
, Meino Rohlfs
, Christoph Klein, Tim Jeske
:
SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases. - Shubham Tripathi
, Priyanka Chakraborty, Herbert Levine
, Mohit Kumar Jolly:
A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells. - Ernesto Segredo-Otero, Rafael Sanjuán
:
The role of spatial structure in the evolution of viral innate immunity evasion: A diffusion-reaction cellular automaton model. - Xiangying Sun, Zhezhen Wang
, Johnathon M. Hall
, Carlos Perez-Cervantes
, Alexander J. Ruthenburg
, Ivan P. Moskowitz
, Michael Gribskov
, Xinan Holly Yang
:
Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq. - Daniel Majoral
, Ajmal Zemmar
, Raul Vicente
:
A model for time interval learning in the Purkinje cell. - Simon Dirmeier
, Christopher Dächert
, Martijn van Hemert
, Ali Tas
, Natacha S. Ogando
, Frank J. M. van Kuppeveld
, Ralf Bartenschlager
, Lars Kaderali
, Marco Binder
, Niko Beerenwinkel:
Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation. - Shuang Song
, Wei Jiang
, Lin Hou
, Hongyu Zhao
:
Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies. - Eric C. Dykeman
:
A stochastic model for simulating ribosome kinetics in vivo. - Paco Derouault
, Jasmine Chauzeix, David Rizzo, Federica Miressi, Corinne Magdelaine, Sylvie Bourthoumieu, Karine Durand
, Hélène Dzugan, Jean Feuillard, Franck Sturtz, Stéphane Mérillou, Anne-Sophie Lia
:
CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer. - Lu Li
, Massimo Lai, Stephen Cole
, Nicolas Le Novère, Stuart J. Edelstein
:
Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies. - Pegah Kassraian-Fard
, Michael Pfeiffer, Roman Bauer
:
A generative growth model for thalamocortical axonal branching in primary visual cortex. - Christoffer Flensburg
, Tobias Sargeant
, Alicia Oshlack
, Ian J. Majewski
:
SuperFreq: Integrated mutation detection and clonal tracking in cancer. - Qian-Yuan Tang
, Kunihiko Kaneko:
Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis. - Giulio Bondanelli
, Srdjan Ostojic
:
Coding with transient trajectories in recurrent neural networks. - Jordan Douglas
, Richard Kingston
, Alexei J. Drummond:
Bayesian inference and comparison of stochastic transcription elongation models. - Kosuke Hamazaki
, Hiroyoshi Iwata
:
RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method. - Pol Kennel, Jules Dichamp, Corinne Barreau, Christophe Guissard
, Lise Teyssedre, Jacques Rouquette, Julien Colombelli
, Anne Lorsignol
, Louis Casteilla, Franck Plouraboué
:
From whole-organ imaging to in-silico blood flow modeling: A new multi-scale network analysis for revisiting tissue functional anatomy. - Joël R. Pradines, Victor Farutin
, Nicholas A. Cilfone
, Abouzar Ghavami
, Elma Kurtagic, Jamey Guess
, Anthony M. Manning
, Ishan Capila
:
Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein. - Jong Hoon Lee
, Xiaoqin Wang, Daniel Bendor
:
The role of adaptation in generating monotonic rate codes in auditory cortex. - Chieh Lin
, Jun Ding
, Ziv Bar-Joseph:
Inferring TF activation order in time series scRNA-Seq studies. - Aleksandr Kovaltsuk
, Matthew I. J. Raybould
, Wing Ki Wong
, Claire Marks
, Sebastian Kelm
, James Snowden
, Johannes Trück
, Charlotte M. Deane
:
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice. - Bruno Junior Neves
, Rodolpho C. Braga
, Vinicius M. Alves
, Marília N. N. Lima
, Gustavo C. Cassiano
, Eugene N. Muratov
, Fabio T. M. Costa
, Carolina Horta Andrade
:
Deep Learning-driven research for drug discovery: Tackling Malaria. - W. Jeffrey Johnston
, Stephanie E. Palmer
, David J. Freedman:
Nonlinear mixed selectivity supports reliable neural computation. - Andrei Yu. Zinovyev
, Urszula Czerwinska
, Laura Cantini
, Emmanuel Barillot
, Klaus M. Frahm
, Dima L. Shepelyansky
:
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. - Florian Ott
, Dimitrije Markovic
, Alexander Strobel
, Stefan J. Kiebel
:
Dynamic integration of forward planning and heuristic preferences during multiple goal pursuit. - Lauren Castro
, Trevor Bedford, Lauren Ancel Meyers
:
Early prediction of antigenic transitions for influenza A/H3N2. - Stefan Sellman
, Michael J. Tildesley, Christopher L. Burdett, Ryan S. Miller
, Clayton Hallman, Colleen Webb, Uno Wennergren, Katie Portacci, Tom Lindström
:
Realistic assumptions about spatial locations and clustering of premises matter for models of foot-and-mouth disease spread in the United States. - Toshinori Namba
, Shuji Ishihara
:
Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells. - Hao Hong
, Shuai Jiang
, Hao Li, Guifang Du, Yu Sun
, Huan Tao
, Cheng Quan
, Chenghui Zhao
, Ruijiang Li
, Wanying Li, Xiaoyao Yin
, Yangchen Huang, Cheng Li, Hebing Chen
, Xiaochen Bo
:
DeepHiC: A generative adversarial network for enhancing Hi-C data resolution. - Nadine S. Schaadt
, Ralf Schönmeyer, Germain Forestier
, Nicolas Brieu, Peter Braubach
, Katharina Nekolla, Michael Meyer-Hermann
, Friedrich Feuerhake
:
Graph-based description of tertiary lymphoid organs at single-cell level. - Natacha Comandante-Lou
, Mehwish Khaliq
, Divya Venkat, Mohan Manikkam
, Mohammad Fallahi-Sichani
:
Phenotype-based probabilistic analysis of heterogeneous responses to cancer drugs and their combination efficacy. - Daniel B. Reeves
, Yunda Huang, Elizabeth R. Duke
, Bryan T. Mayer, E. Fabian Cardozo-Ojeda
, Florencia A. Boshier, David A. Swan
, Morgane Rolland, Merlin L. Robb, John R. Mascola
, Myron S. Cohen, Lawrence Corey
, Peter B. Gilbert, Joshua T. Schiffer
:
Mathematical modeling to reveal breakthrough mechanisms in the HIV Antibody Mediated Prevention (AMP) trials. - Muhammad Ali Al-Radhawi
, David Angeli, Eduardo D. Sontag
:
A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks. - Kael Dai
, Juan Hernando
, Yazan N. Billeh
, Sergey L. Gratiy
, Judit Planas
, Andrew P. Davison
, Salvador Dura-Bernal
, Padraig Gleeson
, Adrien Devresse
, Benjamin K. Dichter
, Michael Gevaert
, James Gonzalo King
, Werner Van Geit
, Arseny V. Povolotsky, Eilif Müller
, Jean-Denis Courcol
, Anton Arkhipov
:
The SONATA data format for efficient description of large-scale network models. - Franziska Hörhold, David Eisel, Marcus Oswald, Amol Kolte, Daniela Röll, Wolfram Osen, Stefan B. Eichmüller
, Rainer König
:
Reprogramming of macrophages employing gene regulatory and metabolic network models. - Jieyun Bai, Andy Lo, Patrick A. Gladding
, Martin K. Stiles
, Vadim V. Fedorov, Jichao Zhao
:
In silico investigation of the mechanisms underlying atrial fibrillation due to impaired Pitx2. - Daniel E. Hurtado
, Javiera Jilberto
, Grigory Panasenko:
Non-ohmic tissue conduction in cardiac electrophysiology: Upscaling the non-linear voltage-dependent conductance of gap junctions. - Cristina Vaghi
, Anne Rodallec, Raphaelle Fanciullino, Joseph Ciccolini
, Jonathan Mochel
, Michalis Mastri
, Clair Poignard
, John M. L. Ebos
, Sébastien Benzekry
:
Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors. - Julia A. K. Chartove
, Michelle M. McCarthy, Benjamin R. Pittman-Polletta, Nancy J. Kopell:
A biophysical model of striatal microcircuits suggests gamma and beta oscillations interleaved at delta/theta frequencies mediate periodicity in motor control. - Michael I. Love
, Charlotte Soneson
, Peter F. Hickey
, Lisa K. Johnson
, N. Tessa Pierce
, Lori A. Shepherd
, Martin Morgan, Rob Patro
:
Tximeta: Reference sequence checksums for provenance identification in RNA-seq. - Rok Grah
, Tamar Friedlander
:
The relation between crosstalk and gene regulation form revisited. - Chuang Liu, Junfei Zhao, Weiqiang Lu, Yao Dai, Jennifer Hockings
, Yadi Zhou, Ruth Nussinov
, Charis Eng, Feixiong Cheng
:
Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6, 700 cancer genomes. - Jill Gallaher
, Susan Christine Massey
, Andrea Hawkins-Daarud
, Sonal S. Noticewala
, Russell C. Rockne
, Sandra K. Johnston, Luis Gonzalez-Cuyar
, Joseph Juliano
, Orlando Gil, Kristin R. Swanson
, Peter D. Canoll, Alexander R. A. Anderson
:
From cells to tissue: How cell scale heterogeneity impacts glioblastoma growth and treatment response. - Isaac Fradkin
, Casimir J. H. Ludwig
, Eran Eldar
, Jonathan D. Huppert
:
Doubting what you already know: Uncertainty regarding state transitions is associated with obsessive compulsive symptoms. - Joshua B. Moskowitz
, Daniel J. Gale
, Jason P. Gallivan
, Daniel M. Wolpert
, J. Randall Flanagan
:
Human decision making anticipates future performance in motor learning. - Bastien Berret
, Frédéric Jean
:
Stochastic optimal open-loop control as a theory of force and impedance planning via muscle co-contraction. - Lenka Stejskal
, William D. Lees
, David S. Moss, Machaela Palor
, Richard J. Bingham
, Adrian J. Shepherd
, Joe Grove
:
Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein.
Volume 16, Number 3, March 2020
- Ana Arnal
, Irene Epifanio
, Pablo Gregori
, Vicente Martínez
:
Ten Simple Rules for organizing a non-real-time web conference. - Judit Kumuthini
, Michael Chimenti
, Sven Nahnsen, Alexander Peltzer
, Rebone Meraba, Ross McFadyen, Gordon Wells, Deanne M. Taylor
, Mark Maienschein-Cline, Jian-Liang Li
, Jyothi Thimmapuram
, Radha Murthy-Karuturi
, Lyndon Zass
:
Ten simple rules for providing effective bioinformatics research support.
- Marijn van Vliet
:
Seven quick tips for analysis scripts in neuroimaging.
- Jason C. Hyun
, Erol S. Kavvas
, Jonathan M. Monk
, Bernhard O. Palsson
:
Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. - Barbara Bravi
, Riccardo Ravasio, Carolina Brito, Matthieu Wyart
:
Direct coupling analysis of epistasis in allosteric materials. - Daniel Priego-Espinosa
, Alberto Darszon
, Adán Guerrero
, Ana Laura González-Cota, Takuya Nishigaki, Gustavo Martinez-Mekler
, Jorge Carneiro
:
Modular analysis of the control of flagellar Ca2+-spike trains produced by CatSper and CaV channels in sea urchin sperm. - Elba Raimúndez-Álvarez
, Simone Keller, Gwen Zwingenberger, Karolin Ebert
, Sabine Hug
, Fabian J. Theis
, Dieter Maier, Birgit Luber
, Jan Hasenauer
:
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines. - Sebastian M. Bernasek
, Nicolás Peláez
, Richard W. Carthew, Neda Bagheri
, Luis A. Nunes Amaral
:
Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila.