Dr Thomas Hopf is a scientific consultant and PhD-trained computational biologist with expertise in data science, method development, and software development. He is passionate about understanding biology through large dataset analysis to improve diagnostics and therapies for human diseases.
Dr Hopf has a strong background in data science and software development, with a focus on computational biology and bioinformatics. He has worked with world-renowned scientists at the forefront of computational biology since 2011, contributing to research published in leading journals such as Nature Biotechnology, Cell, and eLIFE.
He currently works as a scientific consultant, offering research consultation, performing research, and developing scientific software for clients in the life and data sciences.
Dr Hopf's research interests include protein interactions, genetic variation, deep mutational scanning, and structure prediction. He has co-authored several publications in prestigious journals, including:
Although his exact educational background is unclear, Dr Hopf's affiliation with Harvard Medical School and the Department of Systems Biology indicates a strong educational foundation in the field of computational biology and bioinformatics.
Thomas A. Hopf
Scientific Consultant
N/A
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:u5HHmVD_uO8C
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:qjMakFHDy7sC
Protein structure prediction from sequence variation DS Marks, TA Hopf, C Sander Nature biotechnology 30 (11), 1072-1080, 2012 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:9yKSN-GCB0IC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:8d8msizDQcsC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:6ZxmRoH8BuwC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:u-x6o8ySG0sC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:rmuvC79q63oC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:_5tno0g5mFcC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:sNmaIFBj_lkC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:_axFR9aDTf0C
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:IRz6iEL74y4C
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:_FM0Bhl9EiAC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:Ri6SYOTghG4C
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:XvxMoLDsR5gC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:kh2fBNsKQNwC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:DUooU5lO8OsC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:UeHWp8X0CEIC
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 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:9pM33mqn1YgC
PDBe-KB: collaboratively defining the biological context of structural data
Nucleic acids research 50 (D1), D534-D542, 2022 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:OTTXONDVkokC
Evfold. org: Evolutionary couplings and protein 3d structure prediction R Sheridan, RJ Fieldhouse, S Hayat, Y Sun, Y Antipin, L Yang, T Hopf, … biorxiv, 021022, 2015 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=dK2eepUAAAAJ&citationforview=dK2eepUAAAAJ:bz8QjSJIRt4C
Debora Marks googlescholarauthorid deboramarks.md:qFmoeNkAAAAJ
Chris Sander googlescholarauthorid chrissander.md:4R7_wW8AAAAJ
Charlotta Scharfe googlescholarauthorid charlottascharfe.md:fCmpyIYAAAAJ
John Ingraham googlescholarauthorid johningraham.md:qBarioAAAAAJ
Anna G. Green googlescholarauthorid annag._green.md:o9rcausAAAAJ
Burkhard Rost googlescholarauthorid burkhardrost.md:BP3ofxcAAAAJ
Andrea Pagnani googlescholarauthorid andreapagnani.md:EWJYRncAAAAJ
Riccardo Zecchina googlescholarauthorid riccardozecchina.md:fNOReswAAAAJ
Frank Poelwijk googlescholarauthorid frankpoelwijk.md:QeJfCXUAAAAJ
Michael Springer googlescholarauthorid michaelspringer.md:pJrcQwEAAAAJ
Oliver Kohlbacher googlescholarauthorid oliverkohlbacher.md:8sb5XNIAAAAJ
Benjamin Schubert googlescholarauthorid benjaminschubert.md:D2wEjisAAAAJ
Agnes Toth-Petroczy googlescholarauthorid agnestoth-petroczy.md:7KjpSCgAAAAJ
Matúš Kalaš googlescholarauthorid matúškalaš.md:bcEzXSQAAAAJ
Richard Benton googlescholarauthorid richardbenton.md:PlPUMesAAAAJ
Gaetano T Montelione, Constellation… googlescholarauthorid gaetanotmontelione,constellation….md:mrtpF44AAAAJ
Maximilian Hecht googlescholarauthorid maximilianhecht.md:Hk104ucAAAAJ
Peter Hönigschmid googlescholarauthorid peterhönigschmid.md:Y-Z2O0kAAAAJ
Stefan Seemayer googlescholarauthorid stefanseemayer.md:22b2apQAAAAJ
Denis Krompass googlescholarauthorid deniskrompass.md:xEnt2TEAAAAJ
Youtube Title: OUT AND ABOUT / THOMAS HOPF
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Youtube Channel Name: Out And About South West Florida
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OUT AND ABOUT / THOMAS HOPF
Youtube Title: Thomas Hopf & Mik Quantius Live at De Audio Plant, 14.03.2013
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Thomas Hopf & Mik Quantius Live at De Audio Plant, 14.03.2013
Youtube Title: THOMAS HOPF // OUT AND ABOUT
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Youtube Channel Name: Out And About South West Florida
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THOMAS HOPF // OUT AND ABOUT
Youtube Title: Hummingbird—Sam & Tom in Göttingen, Germany 22.02.19
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Hummingbird—Sam & Tom in Göttingen, Germany 22.02.19
Youtube Title: THOMAS HOPF / OUT AND ABOUT
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Youtube Channel Name: Out And About South West Florida
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THOMAS HOPF / OUT AND ABOUT
Youtube Title: Lessons From Seminary - Avis Blake-Thomas, Chris Hopf, and Daymond Wilkins
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Youtube Channel Name: Dallas Theological Seminary
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Lessons From Seminary - Avis Blake-Thomas, Chris Hopf, and Daymond Wilkins
Youtube Title: THOMAS HOPF OUT AND ABOUT 2
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Youtube Channel Name: Engel & Völkers Cape Coral
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THOMAS HOPF OUT AND ABOUT 2
Youtube Title: Eric Weinstein on why Neil deGrasse Tyson is not a Great Physicist #joerogan #jre #shorts
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Youtube Channel Name: MicrodosingOfWisdom
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Eric Weinstein on why Neil deGrasse Tyson is not a Great Physicist #joerogan #jre #shorts
Youtube Title: Mik Quantius with Thomas Hopf live at Tiefgrund, Berlin, 2013
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Youtube Channel Name: fastermilesanhourcom
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Mik Quantius with Thomas Hopf live at Tiefgrund, Berlin, 2013
Youtube Title: Putin flirts, Putin sigma rule, Putin body language #sigma #confidence #bodylanguage #putin #shorts
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Youtube Channel Name: Leadership and Confidence.
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Putin flirts, Putin sigma rule, Putin body language #sigma #confidence #bodylanguage #putin #shorts
Youtube Title: The New York New York Duo
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Youtube Channel Name: Tom Black
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The New York New York Duo
Youtube Title: Dagora & Thomas Hopf soundchecking @ de Audio Plant
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Dagora & Thomas Hopf soundchecking @ de Audio Plant
Youtube Title: Hopf - S/T (Full Album)
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Youtube Channel Name: Aumega Project
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Hopf - S/T (Full Album)
Youtube Title: Hopf - Dr. O'blivion’s Nightmare (Full Album)
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Youtube Channel Name: Aumega Project
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Hopf - Dr. O'blivion’s Nightmare (Full Album)
Youtube Title: Rare opportunity on Sanibel
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Youtube Channel Name: SWFL360
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Rare opportunity on Sanibel
Youtube Title: BE DANGEROUS/BE GOOD! Motivational Speech
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Youtube Channel Name: UnknownWisdom
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BE DANGEROUS/BE GOOD! Motivational Speech
Youtube Title: ANDREW TATE SAYS THIS ABOUT CRYPTO FUTURE #shorts
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Youtube Channel Name: TATE ONLY
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ANDREW TATE SAYS THIS ABOUT CRYPTO FUTURE #shorts