PLoS Comput Biol

ISSN	1553-7358
ISSN-L	1553-734X
IUID	7f99e6a7f41d4e0fb70a5804edc70ad7
Modified	2020-11-27T13:12:55.603Z
Created	2018-12-03T14:25:39.574Z

PLoS Comput Biol 22 (3) e1014100 [2026-03-00; online 2026-03-18]

Avlant Nilsson DDLS Fellow

PubMed DOI Crossref

HAPP: High-accuracy pipeline for processing deep metabarcoding data.

Sundh J, Granqvist E, Iwaszkiewicz-Eggebrecht E, ..., Andersson AF, Ronquist F

PLoS Comput Biol 21 (11) e1013558 [2025-11-00; online 2025-11-07]

PubMed DOI Crossref

Mouse and human striatal projection neurons compared - somatodendritic arbor, spines and in silico analyses.

Kozlov A, Blazquez-Llorca L, Benavides-Piccione R, ..., DeFelipe J, Grillner S

PLoS Comput Biol 21 (10) e1013569 [2025-10-00; online 2025-10-09]

PubMed DOI Crossref

Competition and cooperation of assembly sequences in recurrent neural networks.

Stöber TM, Lehr AB, Nikzad A, ..., Fyhn M, Kumar A

PLoS Comput Biol 21 (9) e1013403 [2025-09-00; online 2025-09-12]

PubMed DOI Crossref

Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics.

Haloi N, Howard RJ, Lindahl E

PLoS Comput Biol 21 (8) e1013367 [2025-08-00; online 2025-08-11]

PubMed DOI Crossref

Mechanistic modeling of cell viability assays with in silico lineage tracing.

Mutsuddy A, Huggins JR, Amrit AK, ..., Calhoun JC, Birtwistle MR

PLoS Comput Biol 21 (8) e1013156 [2025-08-00; online 2025-08-29]

Cemal Erdem DDLS Fellow

PubMed DOI Crossref

AI-first structural identification of pathogenic protein target interfaces.

Saluri M, Landreh M, Bryant P

PLoS Comput Biol 21 (6) e1013168 [2025-06-00; online 2025-06-26]

DDLS Fellow Patrick Bryant

PubMed DOI Crossref

Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold.

Lidbrink SE, Howard RJ, Haloi N, Lindahl E

PLoS Comput Biol 21 (6) e1013187 [2025-06-00; online 2025-06-27]

PubMed DOI Crossref

Ten simple rules for good model-sharing practices.

Kherroubi Garcia I, Erdmann C, Gesing S, ..., Papin J, Rao Y

PLoS Comput Biol 21 (1) e1012702 [2025-01-00; online 2025-01-10]

PubMed DOI Crossref

Bayesian polynomial neural networks and polynomial neural ordinary differential equations.

Fronk C, Yun J, Singh P, Petzold L

PLoS Comput Biol 20 (10) e1012414 [2024-10-00; online 2024-10-10]

Prashant Singh SciLifeLab Fellow

PubMed DOI Crossref

Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile.

Bryant P, Noé F

PLoS Comput Biol 20 (7) e1012253 [2024-07-00; online 2024-07-25]

DDLS Fellow Patrick Bryant

PubMed DOI Crossref

Scuphr: A probabilistic framework for cell lineage tree reconstruction.

Koptagel H, Jun SH, Hård J, Lagergren J

PLoS Comput Biol 20 (5) e1012094 [2024-05-00; online 2024-05-09]

PubMed DOI Crossref

Ten simple rules for pushing boundaries of inclusion at academic events.

Hall SM, Kochin D, Carne C, ..., Thompson R, Sharan M

PLoS Comput Biol 20 (3) e1011797 [2024-03-00; online 2024-03-01]

PubMed DOI Crossref

Evaluating the utility of brightfield image data for mechanism of action prediction.

Harrison PJ, Gupta A, Rietdijk J, ..., Spjuth O, Sintorn IM

PLoS Comput Biol 19 (7) e1011323 [2023-07-00; online 2023-07-25]

PubMed DOI Crossref

Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach.

Blau C, Yvonnesdotter L, Lindahl E

PLoS Comput Biol 19 (7) e1011255 [2023-07-00; online 2023-07-31]

PubMed DOI Crossref

Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation.

Coulier A, Singh P, Sturrock M, Hellander A

PLoS Comput Biol 18 (12) e1010683 [2022-12-00; online 2022-12-15]

Prashant Singh SciLifeLab Fellow

PubMed DOI Crossref

ToMExO: A probabilistic tree-structured model for cancer progression.

Mohaghegh Neyshabouri M, Lagergren J

PLoS Comput Biol 18 (12) e1010732 [2022-12-00; online 2022-12-05]

PubMed DOI Crossref

A new machine learning method for cancer mutation analysis.

Habibi M, Taheri G

PLoS Comput Biol 18 (10) e1010332 [2022-10-00; online 2022-10-17]

DDLS Fellow Golnaz Taheri

PubMed DOI Crossref

Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin.

Westerlund AM, Sridhar A, Dahl L, ..., Bodnar AY, Delemotte L

PLoS Comput Biol 18 (10) e1010583 [2022-10-00; online 2022-10-07]

Lucie Delemotte SciLifeLab Fellow

PubMed DOI Crossref

De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.

Marco Salas S, Yuan X, Sylven C, ..., Wählby C, Partel G

PLoS Comput Biol 18 (8) e1010366 [2022-08-00; online 2022-08-12]

PubMed DOI Crossref

Ten simple rules for making a software tool workflow-ready.

Brack P, Crowther P, Soiland-Reyes S, ..., Ewels P, Goble C

PLoS Comput Biol 18 (3) e1009823 [2022-03-00; online 2022-03-24]

PubMed DOI Crossref

Survival analysis of pathway activity as a prognostic determinant in breast cancer.

Jeuken GS, Tobin NP, Käll L

PLoS Comput Biol 18 (3) e1010020 [2022-03-00; online 2022-03-28]

PubMed DOI Crossref

gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.

Irrgang ME, Davis C, Kasson PM

PLoS Comput Biol 18 (2) e1009835 [2022-02-00; online 2022-02-14]

PubMed DOI Crossref

Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods.

Jiang R, Singh P, Wrede F, Hellander A, Petzold L

PLoS Comput Biol 18 (1) e1009830 [2022-01-00; online 2022-01-31]

Prashant Singh SciLifeLab Fellow

PubMed DOI Crossref

The evolutionary history of topological variations in the CPA/AT transporters.

Sudha G, Bassot C, Lamb J, ..., Huang Y, Elofsson A

PLoS Comput Biol 17 (8) e1009278 [2021-08-00; online 2021-08-17]

PubMed DOI Crossref

GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction.

Li Z, Jiang K, Qin S, Zhong Y, Elofsson A

PLoS Comput Biol 17 (6) e1009048 [2021-06-00; online 2021-06-03]

PubMed DOI Crossref

Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells.

Erdem C, Lee AV, Taylor DL, Lezon TR

PLoS Comput Biol 17 (6) e1009125 [2021-06-00; online 2021-06-30]

Cemal Erdem DDLS Fellow

PubMed DOI Crossref

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

Kapla J, Rodríguez-Espigares I, Ballante F, Selent J, Carlsson J

PLoS Comput Biol 17 (5) e1008936 [2021-05-00; online 2021-05-13]

Jens Carlsson SciLifeLab Fellow

PubMed DOI Crossref

Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families.

Bassot C, Elofsson A

PLoS Comput Biol 17 (4) e1008798 [2021-04-00; online 2021-04-15]

PubMed DOI Crossref

Machine learning-based investigation of the cancer protein secretory pathway.

Saghaleyni R, Sheikh Muhammad A, Bangalore P, Nielsen J, Robinson JL

PLoS Comput Biol 17 (4) e1008898 [2021-04-00; online 2021-04-05]

PubMed DOI Crossref

Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes.

Asplund-Samuelsson J, Hudson EP

PLoS Comput Biol 17 (2) e1008742 [2021-02-00; online 2021-02-08]

Paul Hudson SciLifeLab Fellow

PubMed DOI Crossref

Ten simple rules for annotating sequencing experiments.

Stevens I, Mukarram AK, Hörtenhuber M, ..., Rung J, Daub CO

PLoS Comput Biol 16 (10) e1008260 [2020-10-00; online 2020-10-05]

PubMed DOI Crossref

Inferring tumor progression in large datasets.

Mohaghegh Neyshabouri M, Jun SH, Lagergren J

PLoS Comput Biol 16 (10) e1008183 [2020-10-00; online 2020-10-09]

PubMed DOI Crossref

A framework to assess the quality and impact of bioinformatics training across ELIXIR.

Gurwitz KT, Singh Gaur P, Bellis LJ, ..., Morgan SL, Rustici G

PLoS Comput Biol 16 (7) e1007976 [2020-07-00; online 2020-07-23]

PubMed DOI Crossref

Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity.

Jaiteh M, Rodríguez-Espigares I, Selent J, Carlsson J

PLoS Comput Biol 16 (3) e1007680 [2020-03-00; online 2020-03-13]

Jens Carlsson SciLifeLab Fellow

PubMed DOI Crossref

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.

Jansen C, Ramirez RN, El-Ali NC, ..., Conesa A, Mortazavi A

PLoS Comput Biol 15 (11) e1006555 [2019-11-00; online 2019-11-04]

PubMed DOI Crossref

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals.

Bruce NJ, Narzi D, Trpevski D, ..., Carloni P, Hellgren Kotaleski J

PLoS Comput Biol 15 (10) e1007382 [2019-10-00; online 2019-10-30]

PubMed DOI Crossref

Why do eukaryotic proteins contain more intrinsically disordered regions?

Basile W, Salvatore M, Bassot C, Elofsson A

PLoS Comput Biol 15 (7) e1007186 [2019-07-00; online 2019-07-22]

PubMed DOI Crossref

How good are pathogenicity predictors in detecting benign variants?

Niroula A, Vihinen M

PLoS Comput Biol 15 (2) e1006481 [2019-02-00; online 2019-02-11]

Abhishek Niroula DDLS Fellow

PubMed DOI Crossref

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems.

Elofsson A, Hess B, Lindahl E, ..., van der Spoel D, Wallqvist A

PLoS Comput Biol 15 (1) e1006649 [2019-01-00; online 2019-01-17]

PubMed DOI Crossref

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.

Wang H, Marcišauskas S, Sánchez BJ, ..., Nielsen J, Kerkhoven EJ

PLoS Comput Biol 14 (10) e1006541 [2018-10-00; online 2018-10-18]

PubMed DOI Crossref

Effect of Ca2+ on the promiscuous target-protein binding of calmodulin.

Westerlund AM, Delemotte L

PLoS Comput Biol 14 (4) e1006072 [2018-04-00; online 2018-04-03]

Affiliated researcher Lucie Delemotte SciLifeLab Fellow

PubMed DOI Crossref

Dynamics and heterogeneity of brain damage in multiple sclerosis.

Kotelnikova E, Kiani NA, Abad E, ..., Garcia-Ojalvo J, Villoslada P

PLoS Comput Biol 13 (10) e1005757 [2017-10-00; online 2017-10-26]

PubMed DOI Crossref

LASSIM-A network inference toolbox for genome-wide mechanistic modeling.

Magnusson R, Mariotti GP, Köpsén M, ..., Tjärnberg A, Gustafsson M

PLoS Comput Biol 13 (6) e1005608 [2017-06-00; online 2017-06-22]

PubMed DOI Crossref

Fast and general tests of genetic interaction for genome-wide association studies.

Frånberg M, Strawbridge RJ, Hamsten A, ..., Lagergren J, Sennblad B

PLoS Comput Biol 13 (6) e1005556 [2017-06-00; online 2017-06-06]

PubMed DOI Crossref

Ten simple rules for surviving an interdisciplinary PhD.

Demharter S, Pearce N, Beattie K, ..., Deane CM, Knapp B

PLoS Comput Biol 13 (5) e1005512 [2017-05-00; online 2017-05-25]

DDLS Fellow Nicholas Pearce

PubMed DOI Crossref

Human behavioral complexity peaks at age 25.

Gauvrit N, Zenil H, Soler-Toscano F, Delahaye JP, Brugger P

PLoS Comput Biol 13 (4) e1005408 [2017-04-00; online 2017-04-13]

PubMed DOI Crossref

Sequence dependency of canonical base pair opening in the DNA double helix.

Lindahl V, Villa A, Hess B

PLoS Comput Biol 13 (4) e1005463 [2017-04-00; online 2017-04-03]

PubMed DOI Crossref

High GC content causes orphan proteins to be intrinsically disordered.

Basile W, Sachenkova O, Light S, Elofsson A

PLoS Comput Biol 13 (3) e1005375 [2017-03-00; online 2017-03-29]

PubMed DOI Crossref

Role of DARPP-32 and ARPP-21 in the Emergence of Temporal Constraints on Striatal Calcium and Dopamine Integration.

Nair AG, Bhalla US, Hellgren Kotaleski J

PLoS Comput Biol 12 (9) e1005080 [2016-09-00; online 2016-09-01]

PubMed DOI Crossref

Computational Cancer Biology: An Evolutionary Perspective.

Beerenwinkel N, Greenman CD, Lagergren J

PLoS Comput Biol 12 (2) e1004717 [2016-02-00; online 2016-02-04]

PubMed DOI Crossref

The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel.

Yazdi S, Stein M, Elinder F, Andersson M, Lindahl E

PLoS Comput Biol 12 (1) e1004704 [2016-01-00; online 2016-01-11]

PubMed DOI Crossref

Improved contact predictions using the recognition of protein like contact patterns.

Skwark MJ, Raimondi D, Michel M, Elofsson A

PLoS Comput Biol 10 (11) e1003889 [2014-11-00; online 2014-11-06]

PubMed DOI Crossref

Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes

Zelezniak A, Sheridan S, Patil KR

PLoS Comput Biol 10 (4) e1003572 [2014-04-24; online 2014-04-24]

Aleksej Zelezniak SciLifeLab Fellow

PubMed DOI Crossref

Comparative analysis of RNA families reveals distinct repertoires for each domain of life.

Hoeppner MP, Gardner PP, Poole AM

PLoS Comput Biol 8 (11) e1002752 [2012-11-01; online 2012-11-01]

PubMed DOI Crossref

Molecular mechanism for the dual alcohol modulation of Cys-loop receptors.

Murail S, Howard RJ, Broemstrup T, ..., Trudell JR, Lindahl E

PLoS Comput Biol 8 (10) e1002710 [2012-10-04; online 2012-10-04]

PubMed DOI Crossref

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

Agren R, Bordel S, Mardinoglu A, ..., Nookaew I, Nielsen J

PLoS Comput Biol 8 (5) e1002518 [2012-05-17; online 2012-05-17]

Adil Mardinoglu SciLifeLab Fellow

PubMed DOI Crossref

Computational mass spectrometry-based proteomics.

Käll L, Vitek O

PLoS Comput Biol 7 (12) e1002277 [2011-12-00; online 2011-12-01]

PubMed DOI Crossref

Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes

Zelezniak A, Pers TH, Soares S, Patti ME, Patil KR

PLoS Comput Biol 6 (4) e1000729 [2010-04-01; online 2010-04-01]

Aleksej Zelezniak SciLifeLab Fellow

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