Thomas A. Hopf

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Debora MarksSystems Biology, Harvard Medical School, Broad Institute of Harvard and MITVerified email at hms.harvard.edu
Chris SanderHarvard Medical School, Broad Institute, MGH, Dana-Farber Cancer Institute, Memorial Sloan KetteringVerified email at sanderlab.org
Charlotta ScharfePrincipal Data Scientist, F. Hoffmann-La Roche, SwitzerlandVerified email at roche.com
John IngrahamGenerate Biomedicines, IncVerified email at csail.mit.edu
Anna G. GreenAssistant Professor, Manning College of Information and Computer Sciences, UMass, AmherstVerified email at umass.edu
Burkhard RostProfessor of Computer Science, Technical University MunichVerified email at tum.de
Andrea PagnaniProfessor at DISAT - Politecnico di Torino, and PI at the IIGMVerified email at polito.it
Riccardo Zecchinaprofessor, theoretical physics, Bocconi UniversityVerified email at unibocconi.it
Frank PoelwijkGenerate Biomedicines LLCVerified email at generatebiomedicines.com
Michael Springerharvard medical schoolVerified email at hms.harvard.edu
Oliver KohlbacherProfessor for Applied Bioinformatics, University of TübingenVerified email at uni-tuebingen.de
Benjamin SchubertGroup Leader, ICB@Helmholtz Center MunichVerified email at helmholtz-muenchen.de
Agnes Toth-PetroczyMPI of Molecular Cell Biology and Genetics and Center for Systems Biology DresdenVerified email at mpi-cbg.de
Matúš KalašSenior Engineer / Infrastructure Scientist, Department of Informatics, University of BergenVerified email at uib.no
Richard BentonUniversity of LausanneVerified email at unil.ch
Gaetano T Montelione, Constellation...Rensselaer Polytechnic InstituteVerified email at rpi.edu
Maximilian HechtAmazon.com Inc.Verified email at rostlab.org
Peter HönigschmidDepartment of Genome-Oriented Bioinformatics, TUM, WeihenstephanVerified email at wzw.tum.de
Stefan SeemayerComputational Biologist at BASF SEVerified email at seemayer.de
Denis KrompassSiemens AGVerified email at siemens.com

Thomas A. Hopf

Scientific Consultant

Verified email at thomashopf.com

Computational Biology


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
Protein 3D structure computed from evolutionary sequence variation DS Marks, LJ Colwell, R Sheridan, TA Hopf, A Pagnani, R Zecchina, ... PloS one 6 (12), e28766, 2011	1285	2011
A large-scale evaluation of computational protein function prediction P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, ... Nature methods 10 (3), 221-227, 2013	1126	2013
Protein structure prediction from sequence variation DS Marks, TA Hopf, C Sander Nature biotechnology 30 (11), 1072-1080, 2012	725	2012
Mutation effects predicted from sequence co-variation TA Hopf, JB Ingraham, FJ Poelwijk, CPI Schärfe, M Springer, C Sander, ... Nature biotechnology 35 (2), 128-135, 2017	706	2017
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues D Wang, B Eraslan, T Wieland, B Hallström, T Hopf, DP Zolg, J Zecha, ... Molecular systems biology 15 (2), e8503, 2019	691	2019
Three-dimensional structures of membrane proteins from genomic sequencing TA Hopf, LJ Colwell, R Sheridan, B Rost, C Sander, DS Marks Cell 149 (7), 1607-1621, 2012	601	2012
Sequence co-evolution gives 3D contacts and structures of protein complexes TA Hopf, CPI Schärfe, JP Rodrigues, AG Green, O Kohlbacher, C Sander, ... elife 3, e03430, 2014	545	2014
A systematic p53 mutation library links differential functional impact to cancer mutation pattern and evolutionary conservation E Kotler, O Shani, G Goldfeld, M Lotan-Pompan, O Tarcic, A Gershoni, ... Molecular cell 71 (1), 178-190. e8, 2018	295	2018
The EVcouplings Python framework for coevolutionary sequence analysis TA Hopf, AG Green, B Schubert, S Mersmann, CPI Schärfe, JB Ingraham, ... Bioinformatics 35 (9), 1582-1584, 2019	248	2019
Meltome atlas—thermal proteome stability across the tree of life A Jarzab, N Kurzawa, T Hopf, M Moerch, J Zecha, N Leijten, Y Bian, ... Nature methods 17 (5), 495-503, 2020	229	2020
FreeContact: fast and free software for protein contact prediction from residue co-evolution L Kaján, TA Hopf, M Kalaš, DS Marks, B Rost BMC bioinformatics 15, 1-6, 2014	195	2014
Structured states of disordered proteins from genomic sequences A Toth-Petroczy, P Palmedo, J Ingraham, TA Hopf, B Berger, C Sander, ... Cell 167 (1), 158-170. e12, 2016	152	2016
Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors TA Hopf, S Morinaga, S Ihara, K Touhara, DS Marks, R Benton Nature communications 6 (1), 6077, 2015	147	2015
Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis M Sjodt, K Brock, G Dobihal, PDA Rohs, AG Green, TA Hopf, AJ Meeske, ... Nature 556 (7699), 118-121, 2018	139	2018
Protein structure determination by combining sparse NMR data with evolutionary couplings Y Tang, YJ Huang, TA Hopf, C Sander, DS Marks, GT Montelione Nature methods 12 (8), 751-754, 2015	87	2015
Quantification and discovery of sequence determinants of protein‐per‐mRNA amount in 29 human tissues B Eraslan, D Wang, M Gusic, H Prokisch, BM Hallström, M Uhlén, ... Molecular systems biology 15 (2), e8513, 2019	80	2019
Homology-based inference sets the bar high for protein function prediction T Hamp, R Kassner, S Seemayer, E Vicedo, C Schaefer, D Achten, F Auer, ... BMC bioinformatics 14, 1-10, 2013	66	2013
Decrypting drug actions and protein modifications by dose-and time-resolved proteomics J Zecha, FP Bayer, S Wiechmann, J Woortman, N Berner, J Müller, ... Science 380 (6640), 93-101, 2023	58	2023
Quantification of the effect of mutations using a global probability model of natural sequence variation TA Hopf, JB Ingraham, FJ Poelwijk, M Springer, C Sander, DS Marks arXiv preprint arXiv:1510.04612, 2015	43	2015
PDBe-KB: collaboratively defining the biological context of structural data Nucleic acids research 50 (D1), D534-D542, 2022	42	2022

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