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Table of Contents

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

Ten simple rules for drawing scientific comics

Jason E. McDermott, Matthew Partridge, Yana Bromberg

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

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

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

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

Yonathan Murin, Jeremy Kim, Josef Parvizi, Andrea Goldsmith

Metabolic plasticity in synthetic lethal mutants: Viability at higher cost

Francesco Alessandro Massucci, Francesc Sagués, M. Ángeles Serrano

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

The extent of ribosome queuing in budding yeast

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

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

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

MUMmer4: A fast and versatile genome alignment system

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

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

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

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

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

Roman Goulard, Jean-Louis Vercher, Stéphane Viollet

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

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

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

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

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

Giulio Di Minin, Andreas Postlmayr, Anton Wutz

The E2.65A 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

Interactions between species introduce spurious associations in microbiome studies

Rajita Menon, Vivek Ramanan, Kirill S. Korolev

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

Takayuki Onojima, Takahiro Goto, Hiroaki Mizuhara, Toshio Aoyagi

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

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

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

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

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

Identifying human diamine sensors for death related putrescine and cadaverine molecules

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

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

Bayesian inference of phylogenetic networks from bi-allelic genetic markers

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

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

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

Robust and efficient coding with grid cells

Lajos Vágó, Balázs B. Ujfalussy

Bowhead: Bayesian modelling of cell velocity during concerted cell migration

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

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

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

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

Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients

Shayna Stein, Rui Zhao, Hiroshi Haeno, Igor Vivanco, Franziska Michor

Probing instructions for expression regulation in gene nucleotide compositions

Chloé Bessière, May Taha, Florent Petitprez, Jimmy Vandel, Jean-Michel Marin, Laurent Bréhélin, Sophie Lèbre, Charles-Henri Lecellier

Model-driven discovery of long-chain fatty acid metabolic reprogramming in heterogeneous prostate cancer cells

Igor Marín de Mas, Esther Aguilar, Erika Zodda, Cristina Balcells, Silvia Marin, Guido Dallmann, Timothy M. Thomson, Balázs Papp, Marta Cascante

Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition

Simon Koplev, Katie Lin, Anders B. Dohlman, Avi Ma’ayan

A systematic atlas of chaperome deregulation topologies across the human cancer landscape

Ali Hadizadeh Esfahani, Angelina Sverchkova, Julio Saez-Rodriguez, Andreas A. Schuppert, Marc Brehme

Improving pairwise comparison of protein sequences with domain co-occurrence

Christophe Menichelli, Olivier Gascuel, Laurent Bréhélin