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ORCIDPLoS 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