Article

Stochastic model of IP3-induced Ca2+ spiking of HEK293 cells.
Azzoni, Caterina ORCID: https://orcid.org/0009-0009-4926-3534, Jüttner, Rene ORCID: https://orcid.org/0000-0003-3565-0698, Sporbert, Anje ORCID: https://orcid.org/0000-0002-3738-1295, Gotthardt, Michael ORCID: https://orcid.org/0000-0003-1788-3172, Roderick, H. Llewelyn and Falcke, Martin ORCID: https://orcid.org/0000-0001-7137-1114
PLoS Computational Biology 21 (8): e1013322. August 2025

Quantitative modeling of signaling in aggressive B cell lymphoma unveils conserved core network.
Klinger, B. ORCID: https://orcid.org/0000-0003-0242-1506, Rausch, I., Siebert, A. ORCID: https://orcid.org/0000-0001-6588-8547, Kutz, H., Kruse, V., Kirchner, M. ORCID: https://orcid.org/0000-0002-7049-534X, Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, Kieser, A. ORCID: https://orcid.org/0000-0003-0783-1950, Blüthgen, N. ORCID: https://orcid.org/0000-0002-0171-7447 and Kube, D. ORCID: https://orcid.org/0000-0001-7760-525X
PLoS Computational Biology 20 (10): e1012488. 1 October 2024

Covering hierarchical dirichlet mixture models on binary data to enhance genomic stratifications in onco-hematology.
Dall'Olio, D. ORCID: https://orcid.org/0000-0003-0196-6870, Sträng, E., Turki, A.T., Tettero, J.M., Barbus, M., Schulze-Rath, R. ORCID: https://orcid.org/0000-0003-4589-7213, Elicegui, J.M., Matteuzzi, T., Merlotti, A. ORCID: https://orcid.org/0000-0002-3648-2828, Carota, L., Sala, C. ORCID: https://orcid.org/0000-0002-4889-1047, Della Porta, M.G., Giampieri, E., Hernández-Rivas, J.M., Bullinger, L. ORCID: https://orcid.org/0000-0002-5890-5510 and Castellani, G.
PLoS Computational Biology 20 (2): e1011299. 2 February 2024

Multiscale networks in multiple sclerosis.
Kennedy, K.E. ORCID: https://orcid.org/0000-0001-5551-7304, Kerlero de Rosbo, N., Uccelli, A., Cellerino, M., Ivaldi, F., Contini, P., De Palma, R., Harbo, H.F., Berge, T., Bos, S.D., Høgestøl, E.A. ORCID: https://orcid.org/0000-0001-8446-2111, Brune-Ingebretsen, S., de Rodez Benavent, S.A., Paul, F. ORCID: https://orcid.org/0000-0002-6378-0070, Brandt, A.U. ORCID: https://orcid.org/0000-0002-9768-014X, Bäcker-Koduah, P., Behrens, J., Kuchling, J. ORCID: https://orcid.org/0000-0002-7981-2073, Asseyer, S., Scheel, M., Chien, C. ORCID: https://orcid.org/0000-0001-8280-9513, Zimmermann, H. ORCID: https://orcid.org/0000-0002-0276-8051, Motamedi, S. ORCID: https://orcid.org/0000-0002-6897-5387, Kauer-Bonin, J., Saez-Rodriguez, J., Rinas, M., Alexopoulos, L.G., Andorra, M., Llufriu, S., Saiz, A., Blanco, Y., Martinez-Heras, E., Solana, E., Pulido-Valdeolivas, I., Martinez-Lapiscina, E.H., Garcia-Ojalvo, J. ORCID: https://orcid.org/0000-0002-3716-7520 and Villoslada, P. ORCID: https://orcid.org/0000-0002-8735-6119
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. ORCID: https://orcid.org/0000-0002-5435-0554, Mehl, J., Benamar, M., Gerhardt, H. ORCID: https://orcid.org/0000-0002-3030-0384, Knaus, P., Duda, G.N. and Checa, S. ORCID: https://orcid.org/0000-0002-1444-5858
PLoS Computational Biology 19 (11): e1011647. 13 November 2023

Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
Watkins, T.B.K. ORCID: https://orcid.org/0000-0001-7414-737X, Colliver, E.C., Huska, M.R. ORCID: https://orcid.org/0000-0002-0912-745X, Kaufmann, T.L. ORCID: https://orcid.org/0000-0003-4374-1338, Lim, E.L., Duncan, C.B. ORCID: https://orcid.org/0000-0003-3127-228X, Haase, K. ORCID: https://orcid.org/0000-0002-0944-5618, Van Loo, P., Swanton, C., McGranahan, N. and Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268
PLoS Computational Biology 19 (10): e1011379. 23 October 2023

Towards reliable quantification of cell state velocities.
Marot-Lassauzaie, V. ORCID: https://orcid.org/0000-0002-8362-9634, Bouman, B.J. ORCID: https://orcid.org/0000-0003-1259-5040, Donaghy, F.D. ORCID: https://orcid.org/0000-0001-6892-0186, Demerdash, Y., Essers, M.A.G. and Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170
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. ORCID: https://orcid.org/0000-0002-3980-3789, Ruiz-Orera, J. ORCID: https://orcid.org/0000-0002-8317-0034, Hubner, N. ORCID: https://orcid.org/0000-0002-1218-6223 and van Heesch, S. ORCID: https://orcid.org/0000-0001-9593-1980
PLoS Computational Biology 17 (12): e1009658. 8 December 2021

Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.
Dorel, M. ORCID: https://orcid.org/0000-0002-1663-2075, Klinger, B. ORCID: https://orcid.org/0000-0003-0242-1506, Mari, T. ORCID: https://orcid.org/0000-0001-6011-9386, Toedling, J. ORCID: https://orcid.org/0000-0003-1471-1295, Blanc, E. ORCID: https://orcid.org/0000-0002-4369-0254, Messerschmidt, C. ORCID: https://orcid.org/0000-0001-8632-656X, Nadler-Holly, M., Ziehm, M. ORCID: https://orcid.org/0000-0001-7074-4054, Sieber, A. ORCID: https://orcid.org/0000-0001-6588-8547, Hertwig, F. ORCID: https://orcid.org/0000-0003-4784-6516, Beule, D. ORCID: https://orcid.org/0000-0002-3284-0632, Eggert, A., Schulte, J.H. ORCID: https://orcid.org/0000-0003-0671-1201, Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751 and Blüthgen, N. ORCID: https://orcid.org/0000-0002-0171-7447
PLoS Computational Biology 17 (11): e1009515. 4 November 2021

On the preservation of vessel bifurcations during flow-mediated angiogenic remodelling.
Edgar, L.T., Franco, C.A. ORCID: https://orcid.org/0000-0002-2861-3883, Gerhardt, H. ORCID: https://orcid.org/0000-0002-3030-0384 and Bernabeu, M.O. ORCID: https://orcid.org/0000-0002-6456-3756
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. ORCID: https://orcid.org/0000-0002-6843-6252, Mittermeier, A. ORCID: https://orcid.org/0000-0001-8439-4307, Cristiano, E., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Loewer, A. ORCID: https://orcid.org/0000-0002-8819-3040
PLoS Computational Biology 16 (6): e1007901. 26 June 2020

DeepWAS: multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning.
Arloth, J. ORCID: https://orcid.org/0000-0003-1139-3308, Eraslan, G., Andlauer, T.F.M., Martins, J. ORCID: https://orcid.org/0000-0001-6528-8947, Iurato, S., Kühnel, B., Waldenberger, M., Frank, J., Gold, R., Hemmer, B., Luessi, F., Nischwitz, S., Paul, F. ORCID: https://orcid.org/0000-0002-6378-0070, Wiendl, H., Gieger, C., Heilmann-Heimbach, S., Kacprowski, T. ORCID: https://orcid.org/0000-0002-5393-2413, Laudes, M., Meitinger, T., Peters, A., Rawal, R., Strauch, K., Lucae, S., Müller-Myhsok, B., Rietschel, M. ORCID: https://orcid.org/0000-0002-5236-6149, Theis, F.J., Binder, E.B. and Mueller, N.S. ORCID: https://orcid.org/0000-0001-8659-4548
PLoS Computational Biology 16 (2): e1007616. 3 February 2020

Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction.
Giese, W. ORCID: https://orcid.org/0000-0003-0872-0929, Milicic, G., 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., Kiani, N.A., Abad, E., Martinez-Lapiscina, E.H., Andorra, M., Zubizarreta, I., Pulido-Valdeolivas, I., Pertsovskaya, I., Alexopoulos, L.G., Olsson, T., Martin, R., Paul, F. ORCID: https://orcid.org/0000-0002-6378-0070, Tegnér, J., 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. ORCID: https://orcid.org/0000-0001-7256-0566, Politi, A.Z. ORCID: https://orcid.org/0000-0003-4788-0933, Kofahl, B., Steuer, R. and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
PLoS Computational Biology 12 (12): e1005298. 27 December 2016

SMOG 2: A versatile software package for generating structure-based models.
Noel, J.K. ORCID: https://orcid.org/0000-0003-3168-6036, Levi, M., Raghunathan, M., Lammert, H., Hayes, R.L., 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. ORCID: https://orcid.org/0000-0001-9155-4268, Branicky, R., Grundy, L.J., 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., Lemcke, H., Ewald, R., 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. ORCID: https://orcid.org/0000-0002-9116-630X 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., Schaefer, M.H., Betts, M.J., Soons, Z., Mannsperger, H., Harder, N., Oswald, M., Gipp, M., Ramminger, E., Marcus, G., Männer, R., Rohr, K., Wanker, E. ORCID: https://orcid.org/0000-0001-8072-1630, Russell, R.B., Andrade-Navarro, M.A. ORCID: https://orcid.org/0000-0001-6650-1711, Eils, R. and König, R.
PLoS Computational Biology 10 (9): e1003814. 25 September 2014

Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Trinh, A., Sipos, B., Brenton, J.D., 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. ORCID: https://orcid.org/0000-0001-6813-4425 and Eule, S.
PLoS Computational Biology 9 (11): e1003303. November 2013

Sensitive detection of viral transcripts in human tumor transcriptomes.
Schelhorn, S.E., Fischer, M., Tolosi, L., Altmüller, J. ORCID: https://orcid.org/0000-0003-4372-1521, Nürnberg, P., Pfister, H., Lengauer, T. and Berthold, F.
PLoS Computational Biology 9 (10): e1003228. 3 October 2013

Human monogenic disease genes have frequently functionally redundant paralogs.
Chen, W.H., Zhao, X.M., van Noort, V. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
PLoS Computational Biology 9 (5): e1003073. May 2013

Revealing a two-loop transcriptional feedback mechanism in the cyanobacterial circadian clock.
Hertel, S., 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., Lopes, T.J.S., Mah, N. ORCID: https://orcid.org/0000-0002-1240-8076, Shoemaker, J.E., Matsuoka, Y., Fontaine, J.F. ORCID: https://orcid.org/0000-0002-1101-4091, Louis-Jeune, C., Eisfeld, A.J., Neumann, G., Perez-Iratxeta, C., Kawaoka, Y., Kitano, H. and Andrade-Navarro, M.A. ORCID: https://orcid.org/0000-0001-6650-1711
PLoS Computational Biology 9 (1): e1002860. 3 January 2013

Prediction of drug combinations by integrating molecular and pharmacological data.
Zhao, X.M., Iskar, M., Zeller, G., Kuhn, M., van Noort, V. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
PLoS Computational Biology 7 (12): e1002323. 29 December 2011

Identifying single copy orthologs in Metazoa.
Creevey, C.J., Muller, J., Doerks, T., Thompson, J.D., Arendt, D. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
PLoS Computational Biology 7 (12): e1002269. 1 December 2011

Automatic annotation of spatial expression patterns via sparse Bayesian factor models.
Pruteanu-Malinici, I., Mace, D.L. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
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. ORCID: https://orcid.org/0000-0002-0881-3116
PLoS Computational Biology 6 (12): e1001037. 16 December 2010

Drug-induced regulation of target expression.
Iskar, M., Campillos, M., Kuhn, M., Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, van Noort, V. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
PLoS Computational Biology 6 (9): e1000925. 9 September 2010

Calcium signals driven by single channel noise.
Skupin, A., Kettenmann, H. ORCID: https://orcid.org/0000-0001-8208-0291 and Falcke, M. ORCID: https://orcid.org/0000-0001-7137-1114
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., He, L., Li, Z., Xu, Y., Li, M., Fu, X., Yan, Z., Yuan, Y., Menzel, C., Li, N., Somel, M., Hu, H., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, 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. ORCID: https://orcid.org/0000-0002-4048-3479
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., Bottolo, L., Langley, S.R., Heinig, M. ORCID: https://orcid.org/0000-0002-5612-1720, McDermott-Roe, C., Sarwar, R., Pravenec, M. ORCID: https://orcid.org/0000-0001-9197-5871, Huebner, N. ORCID: https://orcid.org/0000-0002-1218-6223, Aitman, T.J., 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., Mariggi, G., Gerhardt, H. ORCID: https://orcid.org/0000-0002-3030-0384 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., Shcherbinin, S., Huska, M.R. ORCID: https://orcid.org/0000-0002-0912-745X, Rasko, T., Stelzl, U. ORCID: https://orcid.org/0000-0003-2500-3585, Arumughan, A., Foulle, R., Porras, P. ORCID: https://orcid.org/0000-0002-8429-8793, Sanchez-Pulido, L., Wanker, E.E. ORCID: https://orcid.org/0000-0001-8072-1630 and Andrade-Navarro, M.A. ORCID: https://orcid.org/0000-0001-6650-1711
PLoS Computational Biology 5 (3): e1000304. 13 March 2009

Computational lipidology: predicting lipoprotein density profiles in human blood plasma.
Huebner, K., Schwager, T., Winkler, K., 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. ORCID: https://orcid.org/0000-0002-0881-3116
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. ORCID: https://orcid.org/0000-0002-4048-3479 and Miklos, I.
PLoS Computational Biology 3 (8): e149. 10 August 2007

Enhancer responses to similarly distributed antagonistic gradients in development.
Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102 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., Harrington, E., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X and Torrents, D.
PLoS Computational Biology 2 (6): e76 (627-636). 30 June 2006

Recognition of unknown conserved alternatively spliced exons.
Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, 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., Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, Boue, S. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
PLoS Computational Biology 1 (1): e10. 24 June 2005

microRNA target predictions across seven Drosophila species and comparison to mammalian targets.
Grün, D., Wang, Y.L., Langenberger, D., Gunsalus, K.C. and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
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. ORCID: https://orcid.org/0000-0002-5625-4128, Holman, C. ORCID: https://orcid.org/0000-0002-8075-2821, Lo, H. ORCID: https://orcid.org/0000-0003-4808-6440, Lyras, E.M. ORCID: https://orcid.org/0000-0003-3269-0854, Adkins, M.C. ORCID: https://orcid.org/0000-0002-3173-9479, Aquino, M.R.J. ORCID: https://orcid.org/0000-0002-3989-1221, Bougioukas, K.I. ORCID: https://orcid.org/0000-0002-6533-1391, Bray, K.O. ORCID: https://orcid.org/0000-0002-3990-2429, Gajos, M. ORCID: https://orcid.org/0000-0002-6731-3736, Guo, X. ORCID: https://orcid.org/0000-0002-3023-2449, Hartling, C., Huerta-Gutierrez, R. ORCID: https://orcid.org/0000-0002-0882-9695, Jindrová, M. ORCID: https://orcid.org/0000-0002-9924-6427, Kenney, J.P.M. ORCID: https://orcid.org/0000-0002-6507-7063, Kępińska, A.P. ORCID: https://orcid.org/0000-0002-3232-6289, Kneller, L. ORCID: https://orcid.org/0000-0002-4463-6831, Lopez-Rodriguez, E., Mühlensiepen, F. ORCID: https://orcid.org/0000-0001-8571-7286, Richards, A., Richards, G. ORCID: https://orcid.org/0000-0003-0233-0153, Siebert, M. ORCID: https://orcid.org/0000-0003-4385-5773, Smith, J.A. ORCID: https://orcid.org/0000-0003-2634-0268, Smith, N. ORCID: https://orcid.org/0000-0001-6320-3946, Stransky, N. ORCID: https://orcid.org/0000-0002-0872-5220, Tarvainen, S. ORCID: https://orcid.org/0000-0003-3669-5716, Valdes, D.S. ORCID: https://orcid.org/0000-0002-1309-5147, Warrington, K.L. ORCID: https://orcid.org/0000-0003-3206-8002, Wilpert, N.M. ORCID: https://orcid.org/0000-0001-9453-8335, Witkowska, D. ORCID: https://orcid.org/0000-0002-8197-7301, Zaneva, M. ORCID: https://orcid.org/0000-0003-3569-931X, Zanker, J. ORCID: https://orcid.org/0000-0001-6925-3987 and Weissgerber, T.L. ORCID: https://orcid.org/0000-0002-7490-2600
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., Zhao, X.M., van Noort, V. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
PLoS Computational Biology 10 (7): e1003758. 31 July 2014