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Article

Covering hierarchical dirichlet mixture models on binary data to enhance genomic stratifications in onco-hematology.
Dall'Olio, D. and Sträng, E. and Turki, A.T. and Tettero, J.M. and Barbus, M. and Schulze-Rath, R. and Elicegui, J.M. and Matteuzzi, T. and Merlotti, A. and Carota, L. and Sala, C. and Della Porta, M.G. and Giampieri, E. and Hernández-Rivas, J.M. and Bullinger, L. and Castellani, G.
PLoS Computational Biology 20 (2): e1011299. 2 February 2024

Multiscale networks in multiple sclerosis.
Kennedy, K.E. and Kerlero de Rosbo, N. and Uccelli, A. and Cellerino, M. and Ivaldi, F. and Contini, P. and De Palma, R. and Harbo, H.F. and Berge, T. and Bos, S.D. and Høgestøl, E.A. and Brune-Ingebretsen, S. and de Rodez Benavent, S.A. and Paul, F. and Brandt, A.U. and Bäcker-Koduah, P. and Behrens, J. and Kuchling, J. and Asseyer, S. and Scheel, M. and Chien, C. and Zimmermann, H. and Motamedi, S. and Kauer-Bonin, J. and Saez-Rodriguez, J. and Rinas, M. and Alexopoulos, L.G. and Andorra, M. and Llufriu, S. and Saiz, A. and Blanco, Y. and Martinez-Heras, E. and Solana, E. and Pulido-Valdeolivas, I. and Martinez-Lapiscina, E.H. and Garcia-Ojalvo, J. and Villoslada, P.
PLoS Computational Biology 20 (2): e1010980. February 2024

External mechanical loading overrules cell-cell mechanical communication in sprouting angiogenesis during early bone regeneration.
Dazzi, C. and Mehl, J. and Benamar, M. and Gerhardt, H. and Knaus, P. and Duda, G.N. and Checa, S.
PLoS Computational Biology 19 (11): e1011647. 13 November 2023

Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
Watkins, T.B.K. and Colliver, E.C. and Huska, M.R. and Kaufmann, T.L. and Lim, E.L. and Duncan, C.B. and Haase, K. and Van Loo, P. and Swanton, C. and McGranahan, N. and Schwarz, R.F.
PLoS Computational Biology 19 (10): e1011379. 23 October 2023

Towards reliable quantification of cell state velocities.
Marot-Lassauzaie, V. and Bouman, B.J. and Donaghy, F.D. and Demerdash, Y. and Essers, M.A.G. and Haghverdi, L.
PLoS Computational Biology 18 (9): e1010031. 28 September 2022

Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
Schneider-Lunitz, V. and Ruiz-Orera, J. and Hubner, N. and van Heesch, S.
PLoS Computational Biology 17 (12): e1009658. 8 December 2021

Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.
Dorel, M. and Klinger, B. and Mari, T. and Toedling, J. and Blanc, E. and Messerschmidt, C. and Nadler-Holly, M. and Ziehm, M. and Sieber, A. and Hertwig, F. and Beule, D. and Eggert, A. and Schulte, J.H. and Selbach, M. and Blüthgen, N.
PLoS Computational Biology 17 (11): e1009515. 4 November 2021

On the preservation of vessel bifurcations during flow-mediated angiogenic remodelling.
Edgar, L.T. and Franco, C.A. and Gerhardt, H. and Bernabeu, M.O.
PLoS Computational Biology 17 (2): e1007715. 4 February 2021

A systematic approach to decipher crosstalk in the p53 signaling pathway using single cell dynamics.
Konrath, F. and Mittermeier, A. and Cristiano, E. and Wolf, J. and Loewer, A.
PLoS Computational Biology 16 (6): e1007901. 26 June 2020

DeepWAS: multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning.
Arloth, J. and Eraslan, G. and Andlauer, T.F.M. and Martins, J. and Iurato, S. and Kühnel, B. and Waldenberger, M. and Frank, J. and Gold, R. and Hemmer, B. and Luessi, F. and Nischwitz, S. and Paul, F. and Wiendl, H. and Gieger, C. and Heilmann-Heimbach, S. and Kacprowski, T. and Laudes, M. and Meitinger, T. and Peters, A. and Rawal, R. and Strauch, K. and Lucae, S. and Müller-Myhsok, B. and Rietschel, M. and Theis, F.J. and Binder, E.B. and Mueller, N.S.
PLoS Computational Biology 16 (2): e1007616. 3 February 2020

Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction.
Giese, W. and Milicic, G. and Schröder, A. and Klipp, E.
PLoS Computational Biology 14 (4): e1006075. 9 April 2018

Dynamics and heterogeneity of brain damage in multiple sclerosis.
Kotelnikova, E. and Kiani, N.A. and Abad, E. and Martinez-Lapiscina, E.H. and Andorra, M. and Zubizarreta, I. and Pulido-Valdeolivas, I. and Pertsovskaya, I. and Alexopoulos, L.G. and Olsson, T. and Martin, R. and Paul, F. and Tegnér, J. and Garcia-Ojalvo, J. and Villoslada, P.
PLoS Computational Biology 13 (10): e1005757. 26 October 2017

Feedback, mass conservation and reaction kinetics impact the robustness of cellular oscillations.
Baum, K. and Politi, A.Z. and Kofahl, B. and Steuer, R. and Wolf, J.
PLoS Computational Biology 12 (12): e1005298. 27 December 2016

SMOG 2: A versatile software package for generating structure-based models.
Noel, J.K. and Levi, M. and Raghunathan, M. and Lammert, H. and Hayes, R.L. and Onuchic, J.N. and Whitford, P.C.
PLoS Computational Biology 12 (3): e1004794. 10 March 2016

Changes in postural syntax characterize sensory modulation and natural variation of C. elegans locomotion.
Schwarz, R.F. and Branicky, R. and Grundy, L.J. and Schafer, W.R. and Brown, A.E.X.
PLoS Computational Biology 11 (8): e1004322. 21 August 2015

Spatio-temporal model of endogenous ROS and raft-dependent WNT/β-catenin signaling driving cell fate commitment in human neural progenitor cells.
Haack, F. and Lemcke, H. and Ewald, R. and Rharass, T. and Uhrmacher, A.M.
PLoS Computational Biology 11 (3): e1004106. 20 March 2015

Exploring the miRNA regulatory network using evolutionary correlations.
Obermayer, B. and Levine, E.
PLoS Computational Biology 10 (10): e1003860. 9 October 2014

Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen.
Suratanee, A. and Schaefer, M.H. and Betts, M.J. and Soons, Z. and Mannsperger, H. and Harder, N. and Oswald, M. and Gipp, M. and Ramminger, E. and Marcus, G. and Männer, R. and Rohr, K. and Wanker, E. and Russell, R.B. and Andrade-Navarro, M.A. and Eils, R. and König, R.
PLoS Computational Biology 10 (9): e1003814. 25 September 2014

Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz, R.F. and Trinh, A. and Sipos, B. and Brenton, J.D. and Goldman, N. and Markowetz, F.
PLoS Computational Biology 10 (4): e1003535. 17 April 2014

Distribution of the fittest individuals and the rate of Muller's ratchet in a model with overlapping generations.
Metzger, J.J. and Eule, S.
PLoS Computational Biology 9 (11): e1003303. November 2013

Human monogenic disease genes have frequently functionally redundant paralogs.
Chen, W.H. and Zhao, X.M. and van Noort, V. and Bork, P.
PLoS Computational Biology 9 (5): e1003073. May 2013

Revealing a two-loop transcriptional feedback mechanism in the cyanobacterial circadian clock.
Hertel, S. and Brettschneider, C. and Axmann, I.M.
PLoS Computational Biology 9 (3): e1002966. 14 March 2013

Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.
Schaefer, M.H. and Lopes, T.J.S. and Mah, N. and Shoemaker, J.E. and Matsuoka, Y. and Fontaine, J.F. and Louis-Jeune, C. and Eisfeld, A.J. and Neumann, G. and Perez-Iratxeta, C. and Kawaoka, Y. and Kitano, H. and Andrade-Navarro, M.A.
PLoS Computational Biology 9 (1): e1002860. 3 January 2013

Prediction of drug combinations by integrating molecular and pharmacological data.
Zhao, X.M. and Iskar, M. and Zeller, G. and Kuhn, M. and van Noort, V. and Bork, P.
PLoS Computational Biology 7 (12): e1002323. 29 December 2011

Identifying single copy orthologs in Metazoa.
Creevey, C.J. and Muller, J. and Doerks, T. and Thompson, J.D. and Arendt, D. and Bork, P.
PLoS Computational Biology 7 (12): e1002269. 1 December 2011

Automatic annotation of spatial expression patterns via sparse Bayesian factor models.
Pruteanu-Malinici, I. and Mace, D.L. and Ohler, U.
PLoS Computational Biology 7 (7): e1002098. July 2011

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.
Majoros, W.H. and Ohler, U.
PLoS Computational Biology 6 (12): e1001037. 16 December 2010

Drug-induced regulation of target expression.
Iskar, M. and Campillos, M. and Kuhn, M. and Jensen, L.J. and van Noort, V. and Bork, P.
PLoS Computational Biology 6 (9): e1000925. 9 September 2010

Calcium signals driven by single channel noise.
Skupin, A. and Kettenmann, H. and Falcke, M.
PLoS Computational Biology 6 (8): e1000870. 5 August 2010

Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.
Xu, A.G. and He, L. and Li, Z. and Xu, Y. and Li, M. and Fu, X. and Yan, Z. and Yuan, Y. and Menzel, C. and Li, N. and Somel, M. and Hu, H. and Chen, W. and Paeaebo, S. and Khaitovich, P.
PLoS Computational Biology 6 (7): e1000843. 1 July 2010

TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.
Wiebe, N.J.P. and Meyer, I.M.
PLoS Computational Biology 6 (6): e1000823. 24 June 2010

New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
Petretto, E. and Bottolo, L. and Langley, S.R. and Heinig, M. and McDermott-Roe, C. and Sarwar, R. and Pravenec, M. and Huebner, N. and Aitman, T.J. and Cook, S.A. and Richardson, S.
PLoS Computational Biology 6 (4): e1000737. 8 April 2010

Tipping the balance: robustness of tip cell selection, migration and fusion in angiogenesis.
Bentley, K. and Mariggi, G. and Gerhardt, H. and Bates, P.A.
PLoS Computational Biology 5 (10): e1000549. 30 October 2009

Detection of alpha-rod protein repeats using a neural network and application to huntingtin.
Palidwor, G.A. and Shcherbinin, S. and Huska, M.R. and Rasko, T. and Stelzl, U. and Arumughan, A. and Foulle, R. and Porras, P. and Sanchez-Pulido, L. and Wanker, E.E. and Andrade-Navarro, M.A.
PLoS Computational Biology 5 (3): e1000304. 13 March 2009

Computational lipidology: predicting lipoprotein density profiles in human blood plasma.
Huebner, K. and Schwager, T. and Winkler, K. and Reich, J.G. and Holzhuetter, H.G.
PLoS Computational Biology 4 (5): e1000079. 23 May 2008

Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events.
Holste, D. and Ohler, U.
PLoS Computational Biology 4 (1): e21. 25 January 2008

SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework.
Meyer, I.M. and Miklos, I.
PLoS Computational Biology 3 (8): e149. 10 August 2007

Enhancer responses to similarly distributed antagonistic gradients in development.
Zinzen, R.P. and Papatsenko, D.
PLoS Computational Biology 3 (5): e84. 11 May 2007

Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes.
Suyama, M. and Harrington, E. and Bork, P. and Torrents, D.
PLoS Computational Biology 2 (6): e76 (627-636). 30 June 2006

Recognition of unknown conserved alternatively spliced exons.
Ohler, U. and Shomron, N. and Burge, C.B.
PLoS Computational Biology 1 (2): 113-122. July 2005

Extraction of transcript diversity from scientific literature.
Shah, P.K. and Jensen, L.J. and Boue, S. and Bork, P.
PLoS Computational Biology 1 (1): e10. 24 June 2005

microRNA target predictions across seven Drosophila species and comparison to mammalian targets.
Grün, D. and Wang, Y.L. and Langenberger, D. and Gunsalus, K.C. and Rajewsky, N.
PLoS Computational Biology 1 (1): e13. June 2005

Review

Ten simple rules for implementing open and reproducible research practices after attending a training course.
Heise, V. and Holman, C. and Lo, H. and Lyras, E.M. and Adkins, M.C. and Aquino, M.R.J. and Bougioukas, K.I. and Bray, K.O. and Gajos, M. and Guo, X. and Hartling, C. and Huerta-Gutierrez, R. and Jindrová, M. and Kenney, J.P.M. and Kępińska, A.P. and Kneller, L. and Lopez-Rodriguez, E. and Mühlensiepen, F. and Richards, A. and Richards, G. and Siebert, M. and Smith, J.A. and Smith, N. and Stransky, N. and Tarvainen, S. and Valdes, D.S. and Warrington, K.L. and Wilpert, N.M. and Witkowska, D. and Zaneva, M. and Zanker, J. and Weissgerber, T.L.
PLoS Computational Biology 19 (1): e1010750. 5 January 2023

Editorial

Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication".
Chen, W.H. and Zhao, X.M. and van Noort, V. and Bork, P.
PLoS Computational Biology 10 (7): e1003758. 31 July 2014