January 2018

Gene expression responses in Halobacterium salinarum exposed to hydrogen peroxide were clustered using the DPGP algorithm. The heatmap displays the proportion of DPGP samples from the Markov chain in which each gene, on the rows and columns, co-clusters with every other gene. Rows and columns were hierarchically clustered by Ward's linkage. The value of the co-clustering proportion scales linearly with intensity (0=black, 1=white). McDowell et al.

Image Credit: Ian McDowell

Editorials

Ten simple rules for biologists learning to program

Maureen A. Carey, Jason A. Papin

PLOS Computational Biology: published January 4, 2018 | https://doi.org/10.1371/journal.pcbi.1005871

Ten simple rules for drawing scientific comics

Jason E. McDermott, Matthew Partridge, Yana Bromberg

PLOS Computational Biology: published January 4, 2018 | https://doi.org/10.1371/journal.pcbi.1005845

Education Articles

The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide

Jigisha Anupama, Margherita Francescatto, Farzana Rahman, Nazeefa Fatima, Dan DeBlasio, Avinash Kumar Shanmugam, Venkata Satagopam, Alberto Santos, Pandurang Kolekar, Magali Michaut, Emre Guney

PLOS Computational Biology: published January 18, 2018 | https://doi.org/10.1371/journal.pcbi.1005802

Assessing an effective undergraduate module teaching applied bioinformatics to biology students

Andreas Madlung

PLOS Computational Biology: published January 11, 2018 | https://doi.org/10.1371/journal.pcbi.1005872

Research Articles

GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies

Runmin Wei, Jingye Wang, Erik Jia, Tianlu Chen, Yan Ni, Wei Jia

PLOS Computational Biology: published January 31, 2018 | https://doi.org/10.1371/journal.pcbi.1005973

Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling

Krzysztof Bartoszek, Marta Majchrzak, Sebastian Sakowski, Anna B. Kubiak-Szeligowska, Ingemar Kaj, Pawel Parniewski

PLOS Computational Biology: published January 31, 2018 | https://doi.org/10.1371/journal.pcbi.1005931

SozRank: A new approach for localizing the epileptic seizure onset zone

Yonathan Murin, Jeremy Kim, Josef Parvizi, Andrea Goldsmith

PLOS Computational Biology: published January 30, 2018 | https://doi.org/10.1371/journal.pcbi.1005953

Metabolic plasticity in synthetic lethal mutants: Viability at higher cost

Francesco Alessandro Massucci, Francesc Sagués, M. Ángeles Serrano

PLOS Computational Biology: published January 30, 2018 | https://doi.org/10.1371/journal.pcbi.1005949

Reactome graph database: Efficient access to complex pathway data

Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marin-Garcia, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D’Eustachio, Henning Hermjakob

PLOS Computational Biology: published January 29, 2018 | https://doi.org/10.1371/journal.pcbi.1005968

The extent of ribosome queuing in budding yeast

Alon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava, Tamir Tuller

PLOS Computational Biology: published January 29, 2018 | https://doi.org/10.1371/journal.pcbi.1005951

Identification of allosteric inhibitors of the ecto-5'-nucleotidase (CD73) targeting the dimer interface

Rahila Rahimova, Simon Fontanel, Corinne Lionne, Lars Peter Jordheim, Suzanne Peyrottes, Laurent Chaloin

PLOS Computational Biology: published January 29, 2018 | https://doi.org/10.1371/journal.pcbi.1005943

Biophysical network modeling of the dLGN circuit: Effects of cortical feedback on spatial response properties of relay cells

Pablo Martínez-Cañada, Milad Hobbi Mobarhan, Geir Halnes, Marianne Fyhn, Christian Morillas, Francisco Pelayo, Gaute T. Einevoll

PLOS Computational Biology: published January 29, 2018 | https://doi.org/10.1371/journal.pcbi.1005930

MUMmer4: A fast and versatile genome alignment system

Guillaume Marçais, Arthur L. Delcher, Adam M. Phillippy, Rachel Coston, Steven L. Salzberg, Aleksey Zimin

PLOS Computational Biology: published January 26, 2018 | https://doi.org/10.1371/journal.pcbi.1005944

The role of spatial heterogeneity in the evolution of local and global infections of viruses

Koich Saeki, Akira Sasaki

PLOS Computational Biology: published January 25, 2018 | https://doi.org/10.1371/journal.pcbi.1005952

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations

Jagdish Suresh Patel, Celeste J. Brown, F. Marty Ytreberg, Deborah L. Stenkamp

PLOS Computational Biology: published January 24, 2018 | https://doi.org/10.1371/journal.pcbi.1005974

Sequence determinants of protein phase behavior from a coarse-grained model

Gregory L. Dignon, Wenwei Zheng, Young C. Kim, Robert B. Best, Jeetain Mittal

PLOS Computational Biology: published January 24, 2018 | https://doi.org/10.1371/journal.pcbi.1005941

Modeling visual-based pitch, lift and speed control strategies in hoverflies

Roman Goulard, Jean-Louis Vercher, Stéphane Viollet

PLOS Computational Biology: published January 23, 2018 | https://doi.org/10.1371/journal.pcbi.1005894

What drives the perceptual change resulting from speech motor adaptation? Evaluation of hypotheses in a Bayesian modeling framework

Jean-François Patri, Pascal Perrier, Jean-Luc Schwartz, Julien Diard

PLOS Computational Biology: published January 22, 2018 | https://doi.org/10.1371/journal.pcbi.1005942

Static length changes of cochlear outer hair cells can tune low-frequency hearing

Nikola Ciganović, Rebecca L. Warren, Batu Keçeli, Stefan Jacob, Anders Fridberger, Tobias Reichenbach

PLOS Computational Biology: published January 19, 2018 | https://doi.org/10.1371/journal.pcbi.1005936

A mathematical model for IL-6-mediated, stem cell driven tumor growth and targeted treatment

Fereshteh Nazari, Alexander T. Pearson, Jacques Eduardo Nör, Trachette L. Jackson

PLOS Computational Biology: published January 19, 2018 | https://doi.org/10.1371/journal.pcbi.1005920

Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis

Samhita P. Banavar, Carlos Gomez, Michael Trogdon, Linda R. Petzold, Tau-Mu Yi, Otger Campàs

PLOS Computational Biology: published January 18, 2018 | https://doi.org/10.1371/journal.pcbi.1005940

A theory of how active behavior stabilises neural activity: Neural gain modulation by closed-loop environmental feedback

Christopher L. Buckley, Taro Toyoizumi

PLOS Computational Biology: published January 17, 2018 | https://doi.org/10.1371/journal.pcbi.1005926

HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cells

Giulio Di Minin, Andreas Postlmayr, Anton Wutz

PLOS Computational Biology: published January 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005950

The E^2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors

Ravi Kumar Verma, Ara M. Abramyan, Mayako Michino, R. Benjamin Free, David R. Sibley, Jonathan A. Javitch, J. Robert Lane, Lei Shi

PLOS Computational Biology: published January 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005948

Interactions between species introduce spurious associations in microbiome studies

Rajita Menon, Vivek Ramanan, Kirill S. Korolev

PLOS Computational Biology: published January 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005939

A dynamical systems approach for estimating phase interactions between rhythms of different frequencies from experimental data

Takayuki Onojima, Takahiro Goto, Hiroaki Mizuhara, Toshio Aoyagi

PLOS Computational Biology: published January 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005928

Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance

Jacob C. Kimmel, Amy Y. Chang, Andrew S. Brack, Wallace F. Marshall

PLOS Computational Biology: published January 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005927

Interrupting behaviour: Minimizing decision costs via temporal commitment and low-level interrupts

Kevin Lloyd, Peter Dayan

PLOS Computational Biology: published January 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005916

A model for cooperative gating of L-type Ca²⁺ channels and its effects on cardiac alternans dynamics

Daisuke Sato, Rose E. Dixon, Luis F. Santana, Manuel F. Navedo

PLOS Computational Biology: published January 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005906

Clustering gene expression time series data using an infinite Gaussian process mixture model

Ian C. McDowell, Dinesh Manandhar, Christopher M. Vockley, Amy K. Schmid, Timothy E. Reddy, Barbara E. Engelhardt

PLOS Computational Biology: published January 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005896

Modeling the assembly order of multimeric heteroprotein complexes

Lenna X. Peterson, Yoichiro Togawa, Juan Esquivel-Rodriguez, Genki Terashi, Charles Christoffer, Amitava Roy, Woong-Hee Shin, Daisuke Kihara

PLOS Computational Biology: published January 12, 2018 | https://doi.org/10.1371/journal.pcbi.1005937

A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition

Talia Zeppelin, Lucy Kate Ladefoged, Steffen Sinning, Xavier Periole, Birgit Schiøtt

PLOS Computational Biology: published January 12, 2018 | https://doi.org/10.1371/journal.pcbi.1005907

Identifying human diamine sensors for death related putrescine and cadaverine molecules

Cristina Izquierdo, José C. Gómez-Tamayo, Jean-Christophe Nebel, Leonardo Pardo, Angel Gonzalez

PLOS Computational Biology: published January 11, 2018 | https://doi.org/10.1371/journal.pcbi.1005945

Disentangling and modeling interactions in fish with burst-and-coast swimming reveal distinct alignment and attraction behaviors

Daniel S. Calovi, Alexandra Litchinko, Valentin Lecheval, Ugo Lopez, Alfonso Pérez Escudero, Hugues Chaté, Clément Sire, Guy Theraulaz

PLOS Computational Biology: published January 11, 2018 | https://doi.org/10.1371/journal.pcbi.1005933

Bayesian inference of phylogenetic networks from bi-allelic genetic markers

Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M. Meudt, Luay Nakhleh

PLOS Computational Biology: published January 10, 2018 | https://doi.org/10.1371/journal.pcbi.1005932

Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission

Wesley Wong, Edward A. Wenger, Daniel L. Hartl, Dyann F. Wirth

PLOS Computational Biology: published January 9, 2018 | https://doi.org/10.1371/journal.pcbi.1005923

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

Zixuan Cang, Lin Mu, Guo-Wei Wei

PLOS Computational Biology: published January 8, 2018 | https://doi.org/10.1371/journal.pcbi.1005929

Robust and efficient coding with grid cells

Lajos Vágó, Balázs B. Ujfalussy

PLOS Computational Biology: published January 8, 2018 | https://doi.org/10.1371/journal.pcbi.1005922

Bowhead: Bayesian modelling of cell velocity during concerted cell migration

Mathias Engel, James Longden, Jesper Ferkinghoff-Borg, Xavier Robin, Gaye Saginc, Rune Linding

PLOS Computational Biology: published January 8, 2018 | https://doi.org/10.1371/journal.pcbi.1005900

Cardinal features of involuntary force variability can arise from the closed-loop control of viscoelastic afferented muscles

Akira Nagamori, Christopher M. Laine, Francisco J. Valero-Cuevas

PLOS Computational Biology: published January 8, 2018 | https://doi.org/10.1371/journal.pcbi.1005884

A neural network model for the orbitofrontal cortex and task space acquisition during reinforcement learning

Zhewei Zhang, Zhenbo Cheng, Zhongqiao Lin, Chechang Nie, Tianming Yang

PLOS Computational Biology: published January 4, 2018 | https://doi.org/10.1371/journal.pcbi.1005925

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

Alyaa M. Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard O. Palsson, Nathan E. Lewis, Neema Jamshidi

PLOS Computational Biology: published January 4, 2018 | https://doi.org/10.1371/journal.pcbi.1005895

Cover

Similarity in gene expression trajectories as evaluated by the Dirichlet process Gaussian Process (DPGP) clustering algorithm

Editorials

Education Articles

Research Articles