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ORCIDPLoS Computational Biology, Volume 15
Volume 15, Number 1, January 2019
- Arne Elofsson
, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist:
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. - Fran Lewitter, Philip E. Bourne, Teresa K. Attwood:
Ten Simple Rules for avoiding and resolving conflicts with your colleagues. - Christopher J. Lortie:
Ten simple rules for writing statistical book reviews.
- Fatma Z. Guerfali, Dhafer Laouini, Abdellatif Boudabous, Fredj Tekaia:
Designing and running an advanced Bioinformatics and genome analyses course in Tunisia.
- Joel Ostblom, Emanuel J. P. Nazareth, Mukul Tewary, Peter W. Zandstra:
Context-explorer: Analysis of spatially organized protein expression in high-throughput screens. - Song-Yao Zhang, Shaowu Zhang, Xiaonan Fan, Jia Meng, Yidong Chen, Shou-Jiang Gao, Yufei Huang:
Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. - Mehrdad Salmasi, Alex Loebel, Stefan Glasauer, Martin Stemmler:
Short-term synaptic depression can increase the rate of information transfer at a release site. - Anna C. Sales, Karl J. Friston, Matthew W. Jones, Anthony E. Pickering, Rosalyn J. Moran:
Locus Coeruleus tracking of prediction errors optimises cognitive flexibility: An Active Inference model. - Jignesh H. Parmar, Pedro Mendes:
A computational model to understand mouse iron physiology and disease. - Fabien Vinckier, Lionel Rigoux, Irma T. Kurniawan, Chen Hu, Sacha Bourgeois-Gironde, Jean Daunizeau, Mathias Pessiglione:
Sour grapes and sweet victories: How actions shape preferences. - Tomasz Wojdyla, Hrishikesh Mehta, Taly Glaubach, Roberto Bertolusso, Marta Iwanaszko, Rosemary Braun, Seth J. Corey, Marek Kimmel:
Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia. - Raji Viswanathan, J. Eduardo Fajardo, Gabriel Steinberg, Matthew Haller, András Fiser:
Protein - protein binding supersites. - Sathyavani Malyala, Yizhu Zhang, Jasiel O. Strubbe, Jason N. Bazil:
Calcium phosphate precipitation inhibits mitochondrial energy metabolism. - Matías Fuentealba, Handan Melike Dönertas, Rhianna Williams, Johnathan Labbadia, Janet M. Thornton, Linda Partridge:
Using the drug-protein interactome to identify anti-ageing compounds for humans. - Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuñiga, Jared Broddrick, Karsten Zengler, Bernhard O. Palsson:
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. - Douglas K. Brubaker, Elizabeth A. Proctor, Kevin M. Haigis, Douglas A. Lauffenburger:
Computational translation of genomic responses from experimental model systems to humans. - Deena M. A. Gendoo, Robert E. Denroche, Amy Zhang, Nikolina Radulovich, Gun Ho Jang, Mathieu Lemire, Sandra Fischer, Dianne Chadwick, Ilinca M. Lungu, Emin Ibrahimov, Ping-Jiang Cao, Lincoln D. Stein, Julie M. Wilson, John M. S. Bartlett, Ming-Sound Tsao, Neesha Dhani, David Hedley, Steven Gallinger, Benjamin Haibe-Kains:
Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer. - Guohua Shen, Tomoyasu Horikawa, Kei Majima, Yukiyasu Kamitani:
Deep image reconstruction from human brain activity. - Yuan-Hao Hsu, Claire Churchhouse, Tune H. Pers, Josep M. Mercader, Andres Metspalu, Krista Fischer, Kristen Fortney, Eric K. Morgen, Clicerio Gonzalez, Maria E. Gonzalez, Tõnu Esko, Joel Hirschhorn:
PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data. - Zachary R. Fox, Brian Munsky:
The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments. - Dheeraj Dube, Navjeet Ahalawat, Himanshu Khandelia, Jagannath Mondal, Surajit Sengupta:
On identifying collective displacements in apo-proteins that reveal eventual binding pathways. - Ada W. C. Yan, Sophie G. Zaloumis, Julie A. Simpson, James M. McCaw:
Sequential infection experiments for quantifying innate and adaptive immunity during influenza infection. - Abdul-Saboor Sheikh, Nicol S. Harper, Jakob Drefs, Yosef Singer, Zhenwen Dai, Richard E. Turner, Jörg Lücke:
STRFs in primary auditory cortex emerge from masking-based statistics of natural sounds. - Keesha E. Erickson, Oleksii S. Rukhlenko, MD Shahinuzzaman, Kalina P. Slavkova, Yen Ting Lin, Ryan Suderman, Edward C. Stites, Marian Anghel, Richard G. Posner, Dipak Barua, Boris N. Kholodenko, William S. Hlavacek:
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. - Alejandra Gonzalez, Shadi Jafari, Alberto Zenere, Mattias Alenius, Claudio Altafini:
Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila. - Carlos Alquezar-Baeta, Silvia Gimeno-Martos, Sara Miguel-Jiménez, Pilar Santolaria, Jesús Yániz, Inmaculada Palacín, Adriana Casao, José Álvaro Cebrián-Pérez, Teresa Muiño-Blanco, Rosaura Pérez-Pé:
OpenCASA: A new open-source and scalable tool for sperm quality analysis. - David J. Haw, Derek A. T. Cummings, Justin Lessler, Henrik Salje, Jonathan M. Read, Steven Riley:
Differential mobility and local variation in infection attack rate. - Wayne Adams, James N. Graham, Xuchen Han, Hermann Riecke:
Top-down inputs drive neuronal network rewiring and context-enhanced sensory processing in olfaction. - Rafael D'Andrea, Maria A. Riolo, Annette Ostling:
Generalizing clusters of similar species as a signature of coexistence under competition. - Debmalya Chakrabarty, Mounya Elhilali:
A Gestalt inference model for auditory scene segregation. - Carmen Lía Murall, Robert Jackson, Ingeborg Zehbe, Nathalie Boulle, Michel Segondy, Samuel Alizon:
Epithelial stratification shapes infection dynamics. - Dayanne M. Castro, Nicholas R. de Veaux, Emily R. Miraldi, Richard Bonneau:
Multi-study inference of regulatory networks for more accurate models of gene regulation. - David Hodgson, Andrew D. Rowan, Francesco Falciani, Carole J. Proctor:
Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli. - Anika Küken, Jeanne M. O. Eloundou-Mbebi, Georg Basler, Zoran Nikoloski:
Cellular determinants of metabolite concentration ranges. - Xiaohu Hu, Yibo Wang, Amanda Hunkele, Davide Provasi, Gavril W. Pasternak, Marta Filizola:
Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis. - Debolina Sarkar, Thomas J. Mueller, Deng Liu, Himadri B. Pakrasi, Costas D. Maranas:
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism. - Joseph D. Monaco, Rose M. De Guzman, Hugh T. Blair, Kechen Zhang:
Spatial synchronization codes from coupled rate-phase neurons. - Timothy Majarian, Robert F. Murphy, Seema S. Lakdawala:
Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization. - Margot C. Bjoring, C. Daniel Meliza:
A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex. - Jordan J. Clark, Mark L. Benson, Richard D. Smith, Heather A. Carlson:
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. - Alessandro Di Stefano, Marialisa Scatà, Supreeta Vijayakumar, Claudio Angione, Aurelio La Corte, Pietro Liò:
Social dynamics modeling of chrono-nutrition. - Sulav Duwal, Laura Dickinson, Saye Khoo, Max von Kleist:
Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis. - Itay Katzir, Murat Cokol, Bree B. Aldridge, Uri Alon:
Prediction of ultra-high-order antibiotic combinations based on pairwise interactions. - Laurent Mombaerts, Alberto Carignano, Fiona C. Robertson, Timothy J. Hearn, Jin Junyang, David P. Hayden, Zoe Rutterford, Carlos T. Hotta, Katherine E. Hubbard, Marti Ruiz C. Maria, Ye Yuan, Matthew A. Hannah, Jorge M. Gonçalves, Alex Webb:
Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator. - Dimitrije Markovic, Andrea M. F. Reiter, Stefan J. Kiebel:
Predicting change: Approximate inference under explicit representation of temporal structure in changing environments.
- Correction: clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets.
- Notice of Republication: Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects.
Volume 15, Number 2, February 2019
- PLOS Computational Biology 2018 Reviewer and Editorial Board Thank You.
- Ana Julia Velez Rueda, Guillermo I. Benítez, Julia Marchetti, Marcia Anahi Hasenahuer, María Silvina Fornasari, Nicolas Palopoli, Gustavo D. Parisi:
Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools.
- Dave Osthus, Ashlynn R. Daughton, Reid Priedhorsky:
Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited. - Sabine Koch, Fabian Kohrs, Patrick Lahmann, Thomas Bissinger, Stefan Wendschuh, Dirk Benndorf, Udo Reichl, Steffen Klamt:
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. - Stephanie L. Barnes, Nathan M. Belliveau, William T. Ireland, Justin B. Kinney, Rob Phillips:
Mapping DNA sequence to transcription factor binding energy in vivo. - Honda Naoki, Ryutaro Akiyama, Dini Wahyu Kartika Sari, Shin Ishii, Yasumasa Bessho, Takaaki Matsui:
Noise-resistant developmental reproducibility in vertebrate somite formation. - Ahmed A. Metwally, Philip S. Yu, Derek Reiman, Yang Dai, Patricia W. Finn, David L. Perkins:
Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks. - Limeng Pu, Rajiv Gandhi Govindaraj, Jeffrey Mitchell Lemoine, Hsiao-Chun Wu, Michal Brylinski:
DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. - David V. McLeod, Troy Day:
Social evolution under demographic stochasticity. - Wan Yang, Juan Li, Jeffrey Shaman:
Characteristics of measles epidemics in China (1951-2004) and implications for elimination: A case study of three key locations. - Robert Marsland III, Cui Wenping, Joshua Goldford, Alvaro Sanchez, Kirill S. Korolev, Pankaj Mehta:
Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities. - Amin Allahyar, Joske Ubels, Jeroen de Ridder:
A data-driven interactome of synergistic genes improves network-based cancer outcome prediction. - Nathan A. Dunn, Deepak R. Unni, Colin M. Diesh, Monica C. Munoz-Torres, Nomi L. Harris, Eric Yao, Helena Rasche, Ian H. Holmes, Christine G. Elsik, Suzanna E. Lewis:
Apollo: Democratizing genome annotation. - Lior Tiroshi, Joshua A. Goldberg:
Population dynamics and entrainment of basal ganglia pacemakers are shaped by their dendritic arbors. - Simon N. Weber, Henning Sprekeler:
A local measure of symmetry and orientation for individual spikes of grid cells. - Daniel Toker, Friedrich T. Sommer:
Information integration in large brain networks. - Aleix Lafita, Spencer Bliven, Andreas Prlic, Dmytro Guzenko, Peter W. Rose, Anthony R. Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael L. Heuer, Matt Larson, Stephen K. Burley, Jose M. Duarte:
BioJava 5: A community driven open-source bioinformatics library. - Abhishek Niroula, Mauno Vihinen:
How good are pathogenicity predictors in detecting benign variants? - Matthew Ruffalo, Roby Thomas, Jian Chen, Adrian V. Lee, Steffi Oesterreich, Ziv Bar-Joseph:
Network-guided prediction of aromatase inhibitor response in breast cancer. - Qingtian Zhang, Xiaolin Hu, Bo Hong, Bo Zhang:
A hierarchical sparse coding model predicts acoustic feature encoding in both auditory midbrain and cortex. - Nicholas Rogers, John Hermiz, Mehran Ganji, Erik J. Kaestner, Kivilcim Kiliç, Lorraine Hossain, Martin Thunemann, Daniel R. Cleary, Bob S. Carter, David Barba, Anna Devor, Eric Halgren, Shadi A. Dayeh, Vikash Gilja:
Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components. - Julien Moukhtar, Alain Trubuil, Katia Belcram, David Legland, Zhor Khadir, Aurélie Urbain, Jean-Christophe Palauqui, Philippe Andrey:
Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos. - Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe, Rosalind M. Eggo, W. John Edmunds:
Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15. - Damien G. Hicks, Terence P. Speed, Mohammed Yassin, Sarah M. Russell:
Maps of variability in cell lineage trees. - Yangchun Frank Chen, Yu Xia:
Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes. - Nitzan Shahar, Tobias U. Hauser, Michael Moutoussis, Rani Moran, Mehdi Keramati, Raymond J. Dolan:
Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling. - Giuseppe Passucci, Megan E. Brasch, James H. Henderson, Vasily Zaburdaev, M. Lisa Manning:
Identifying the mechanism for superdiffusivity in mouse fibroblast motility. - Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison J. Miller, Anne Fennell, Qin Ma:
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis. - Nico M. Franz, Lukas J. Musher, Joseph W. Brown, Shizhuo Yu, Bertram Ludäscher:
Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion. - Ardi Tampuu, Tambet Matiisen, H. Freyja Ólafsdóttir, Caswell Barry, Raul Vicente:
Efficient neural decoding of self-location with a deep recurrent network. - Rachel Marceau West, Wenbin Lu, Daniel M. Rotroff, Mélaine A. Kuenemann, Sheng-Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger-Reif, Denis Fourches, Jung-Ying Tzeng:
Identifying individual risk rare variants using protein structure guided local tests (POINT). - Ivar Grytten, Knut D. Rand, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve:
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. - Masayuki Maeda, Hideaki Yamashita:
A numerical approach for a discrete Markov model for progressing drug resistance of cancer. - He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov, Feixiong Cheng:
A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications. - Muhammad Ali Al-Radhawi, Domitilla Del Vecchio, Eduardo D. Sontag:
Multi-modality in gene regulatory networks with slow promoter kinetics. - Koichiro Uriu, Hajime Tei:
A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks. - Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao:
Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. - Daniel Rüdiger, Sascha Young Kupke, Tanja Laske, Pawel Zmora, Udo Reichl:
Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions. - David G. P. van IJzendoorn, Karoly Szuhai, Inge H. Briaire-de Bruijn, Marie Kostine, Marieke L. Kuijjer, Judith V. M. G. Bovée:
Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas. - David Aagten-Murphy, Paul M. Bays:
Independent working memory resources for egocentric and allocentric spatial information. - Tyler Funnell, Allen W. Zhang, Diljot Grewal, Steven McKinney, Ali Bashashati, Yi Kan Wang, Sohrab P. Shah:
Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models. - Nir Even-Chen, Blue Sheffer, Saurabh Vyas, Stephen I. Ryu, Krishna V. Shenoy:
Structure and variability of delay activity in premotor cortex. - Anita T. Layton, Harold E. Layton:
A computational model of epithelial solute and water transport along a human nephron. - Tuan Pham, Julie S. Haas:
Electrical synapses regulate both subthreshold integration and population activity of principal cells in response to transient inputs within canonical feedforward circuits. - Simona Olmi, Spase Petkoski, Maxime Guye, Fabrice Bartolomei, Viktor K. Jirsa:
Controlling seizure propagation in large-scale brain networks. - Stephen Woloszynek, Zhengqiao Zhao, Jian Chen, Gail L. Rosen:
16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses. - Cornelia Metzig, Oliver Ratmann, Daniela Bezemer, Caroline Colijn:
Phylogenies from dynamic networks. - Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance:
CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis. - Sarah C. Kramer, Jeffrey Shaman:
Development and validation of influenza forecasting for 64 temperate and tropical countries. - Jorge Fernandez-de-Cossío-Diaz, Roberto Mulet:
Maximum entropy and population heterogeneity in continuous cell cultures. - Gao Wang, Bo Peng:
Script of Scripts: A pragmatic workflow system for daily computational research. - Moritz Möller, Rafal Bogacz:
Learning the payoffs and costs of actions. - Chiara Damiani, Davide Maspero, Marzia Di Filippo, Riccardo Colombo, Dario Pescini, Alex Graudenzi, Hans V. Westerhoff, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri:
Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. - Sen Pei, Mark A. Cane, Jeffrey Shaman:
Predictability in process-based ensemble forecast of influenza. - Shayne M. Plourde, Prativa Amom, Michelle Tan, Adriana T. Dawes, Anna A. Dobritsa:
Changes in morphogen kinetics and pollen grain size are potential mechanisms of aberrant pollen aperture patterning in previously observed and novel mutants of Arabidopsis thaliana. - Alejandro Tabas, Martin Andermann, Valeria Schuberth, Helmut Riedel, Emili Balaguer-Ballester, André Rupp:
Modeling and MEG evidence of early consonance processing in auditory cortex. - Moritz Hoffmann, Christoph Fröhner, Frank Noé:
ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics.
- Dariusz Matlak, Ewa Szczurek:
Correction: Epistasis in genomic and survival data of cancer patients.
Volume 15, Number 3, March 2019
- Tomasz Miksa, Stephanie Renee Simms, Daniel Mietchen, Sarah Jones:
Ten principles for machine-actionable data management plans.
- Chad M. Glen, Melissa L. Kemp, Eberhard O. Voit:
Agent-based modeling of morphogenetic systems: Advantages and challenges. - Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng:
Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.
- Colton J. Lloyd, Zachary A. King, Troy E. Sandberg, Ying Hefner, Connor A. Olson, Patrick V. Phaneuf, Edward J. O'Brien, Jon G. Sanders, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory Humphrey, Rob Knight, Adam M. Feist:
The genetic basis for adaptation of model-designed syntrophic co-cultures. - Jingyu Zhang, Hengyu Chen, Ruoyan Li, David A. Taft, Guang Yao, Fan Bai, Jianhua Xing:
Spatial clustering and common regulatory elements correlate with coordinated gene expression. - Joshua H. Goldwyn, Michiel W. H. Remme, John Rinzel:
Soma-axon coupling configurations that enhance neuronal coincidence detection. - Marc de Kamps, Mikkel E. Lepperød, Yi Ming Lai:
Computational geometry for modeling neural populations: From visualization to simulation. - Joshua G. A. Cashaback, Christopher K. Lao, Dimitrios J. Palidis, Susan K. Coltman, Heather R. McGregor, Paul L. Gribble:
The gradient of the reinforcement landscape influences sensorimotor learning. - Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora:
Genesis of the αβ T-cell receptor. - Marieke Rohde, Kenichi Narioka, Jochen J. Steil, Lina K. Klein, Marc O. Ernst:
Goal-related feedback guides motor exploration and redundancy resolution in human motor skill acquisition. - Mohamed Mounir, Marta Lucchetta, Tiago Chedraoui Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo:
New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx. - Karin Münch, Richard Münch, Rebekka Biedendieck, Dieter Jahn, Johannes Müller:
Evolutionary model for the unequal segregation of high copy plasmids. - David R. Berg, Chetan Offord, Iris Kemler, Matthew K. Ennis, Lawrence Chang, George F. Paulik, Zeljko Bajzer, Claudia Neuhauser, David Dingli:
In vitro and in silico multidimensional modeling of oncolytic tumor virotherapy dynamics. - Maor Grinberg, Tomer Orevi, Nadav Kashtan:
Bacterial surface colonization, preferential attachment and fitness under periodic stress. - Songting Li, Nan Liu, Li Yao, Xiaohui Zhang, Douglas Zhou, David Cai:
Determination of effective synaptic conductances using somatic voltage clamp. - Florian Eberhardt, Andreas V. M. Herz, Stefan Häusler:
Tuft dendrites of pyramidal neurons operate as feedback-modulated functional subunits. - Yuri Kheifetz, Markus Scholz:
Modeling individual time courses of thrombopoiesis during multi-cyclic chemotherapy. - Jonathan B. Dingwell, Joseph P. Cusumano:
Humans use multi-objective control to regulate lateral foot placement when walking. - Robert John Holash, Brian MacIntosh:
A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell. - Maxim V. Shapovalov, Slobodan Vucetic, Roland L. Dunbrack Jr.:
A new clustering and nomenclature for beta turns derived from high-resolution protein structures. - Enrico Riccardi, Eva C. van Mastbergen, William Wiley Navarre, Jocelyne Vreede:
Predicting the mechanism and rate of H-NS binding to AT-rich DNA. - Joanne K. Liu, Colton J. Lloyd, Mahmoud M. Al-Bassam, Ali Ebrahim, Ji-Nu Kim, Connor A. Olson, Alexander Aksenov, Pieter C. Dorrestein, Karsten Zengler:
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. - Yujie Ye, Xin Kang, Jordan Bailey, Chunhe Li, Tian Hong:
An enriched network motif family regulates multistep cell fate transitions with restricted reversibility. - Solveig Engebretsen, Kenth Engø-Monsen, Arnoldo Frigessi, Birgitte Freiesleben de Blasio:
A theoretical single-parameter model for urbanisation to study infectious disease spread and interventions. - Ramu Anandakrishnan, Robin T. Varghese, Nicholas Kinney, Harold R. Garner:
Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations. - Alfredo Rago, Kostas Kouvaris, Tobias Uller, Richard A. Watson:
How adaptive plasticity evolves when selected against. - Paul Van Liedekerke, Johannes Neitsch, Tim Johann, Kevin Alessandri, Pierre Nassoy, Dirk Drasdo:
Quantitative cell-based model predicts mechanical stress response of growing tumor spheroids over various growth conditions and cell lines. - Agustin Lage-Castellanos, Giancarlo Valente, Elia Formisano, Federico De Martino:
Methods for computing the maximum performance of computational models of fMRI responses. - Lilith K. Whittles, Peter J. White, Xavier Didelot:
A dynamic power-law sexual network model of gonorrhoea outbreaks. - Giovanni Marini, Giorgio Guzzetta, Cecilia Marques-Toledo, Mauro Teixeira, Roberto Rosà, Stefano Merler:
Effectiveness of Ultra-Low Volume insecticide spraying to prevent dengue in a non-endemic metropolitan area of Brazil. - Andrea Avena-Koenigsberger, Xiaoran Yan, Artemy Kolchinsky, Martijn P. van den Heuvel, Patric Hagmann, Olaf Sporns:
A spectrum of routing strategies for brain networks. - Fangzhou Shen, Renliang Sun, Jie Yao, Jian Li, Qian Liu, Nathan D. Price, Chenguang Liu, Zhuo Wang:
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling. - Pei-Chi Yang, Shweta Purawat, Pek U. Ieong, Mao-Tsuen Jeng, Kevin R. DeMarco, Igor Vorobyov, Andrew D. McCulloch, Ilkay Altintas, Rommie E. Amaro, Colleen E. Clancy:
A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. - Rodoniki Athanasiadou, Benjamin Neymotin, Nathan Brandt, Wei Wang, Lionel A. Christiaen, David Gresham, Daniel Tranchina:
A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory. - Bernardo P. de Almeida, André F. Vieira, Joana Paredes, Mónica Bettencourt-Dias, Nuno L. Barbosa-Morais:
Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome. - Margaret P. Chapman, Tyler T. Risom, Anil Aswani, Ellen M. Langer, Rosalie C. Sears, Claire J. Tomlin:
Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer.