Skip to content

Home Search Authors Pakistan News Saved

SciRah

SciRah does not host or store research papers. Results come live from free, official scholarly APIs, and every paper links back to its original source.

Data sources

OpenAlex
Semantic Scholar
Crossref
CORE
arXiv
PubMed

Privacy policy Terms of service

D. Marks · SciRah

Researcher profile · Semantic Scholar

D. Marks

Share profile

D. Marks — researcher profile on SciRah

h-index: 60
Works: 159
Citations: 30K

Most-cited papers

Disease variant prediction with deep generative models of evolutionary data
J. Frazer, Pascal Notin, Mafalda Dias, Aidan N. Gomez +4 more
2021Nature805 citations Open access
Semantic Scholar
Mutation effects predicted from sequence co-variation
T. Hopf, John Ingraham, F. J. Poelwijk, Charlotta P. I. Schärfe +3 more
2015Nature Biotechnology803 citations Open access
Semantic Scholar
Deep generative models of genetic variation capture the effects of mutations
Adam J. Riesselman, John Ingraham, D. Marks
2018Nature Methods661 citations Open access
Semantic Scholar
Protein design and variant prediction using autoregressive generative models
Jung-Eun Shin, Adam J. Riesselman, Aaron W. Kollasch, C. McMahon +5 more
2021Nature Communications372 citations Open access
Semantic Scholar
A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories
D. Placido, Bo Yuan, J. Hjaltelin, Chunlei Zheng +21 more
2023Nature Medicine319 citations Open access
Semantic Scholar
The EVcouplings Python framework for coevolutionary sequence analysis
T. Hopf, Anna G. Green, B. Schubert, Sophia F. Mersmann +12 more
2018bioRxiv295 citations Open access
Semantic Scholar
Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval
Pascal Notin, Mafalda Dias, J. Frazer, Javier Marchena-Hurtado +3 more
2022International Conference on Machine Learning279 citations Open access
Semantic Scholar
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 +6 more
2018Molecules and Cells257 citations Open access
Semantic Scholar
scPerturb: harmonized single-cell perturbation data
Stefan Peidli, Tessa D. Green, Ci-Yue Shen, Torsten Gross +9 more
2023bioRxiv226 citations Open access
Semantic Scholar
Cryo–electron microscopy structure of the lipid droplet–formation protein seipin
X. Sui, H. Arlt, Kelly P. Brock, Z. W. Lai +5 more
2018bioRxiv181 citations Open access
Semantic Scholar
3D RNA and functional interactions from evolutionary couplings
Caleb Weinreb, Adam J. Riesselman, John Ingraham, Torsten Gross +2 more
2015Cell167 citations Open access
Semantic Scholar
Learning Protein Structure with a Differentiable Simulator
John Ingraham, Adam J. Riesselman, C. Sander, D. Marks
2018International Conference on Learning Representations163 citations
Semantic Scholar
Inferring protein 3D structure from deep mutation scans
Nathan J. Rollins, Kelly P. Brock, F. J. Poelwijk, M. Stiffler +3 more
2019Nature Genetics145 citations Open access
Semantic Scholar
RITA: a Study on Scaling Up Generative Protein Sequence Models
Daniel Hesslow, Niccoló Zanichelli, Pascal Notin, Iacopo Poli +1 more
2022arXiv.org140 citations Open access
Semantic Scholar
Genetic variation in human drug-related genes
Charlotta Schärfe, R. Tremmel, M. Schwab, O. Kohlbacher +1 more
2017Genome Medicine136 citations Open access
Semantic Scholar
Structured states of disordered proteins from genomic sequences
Agnes Toth-Petroczy, P. Palmedo, John Ingraham, T. Hopf +3 more
2016Cell131 citations Open access
Semantic Scholar
CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy.
Bo Yuan, Ci-Yue Shen, Augustin Luna, A. Korkut +3 more
2020Cell Systems120 citations Open access
Semantic Scholar
Structural coordination of polymerization and crosslinking by a SEDS-bPBP peptidoglycan synthase complex
M. Sjodt, P. Rohs, M. Gilman, S. Erlandson +10 more
2020Nature Microbiology117 citations Open access
Semantic Scholar
An Atlas of Variant Effects to understand the genome at nucleotide resolution
D. Fowler, D. J. Adams, A. Gloyn, William C. Hahn +7 more
2023Genome Biology105 citations Open access
Semantic Scholar
Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis
M. Sjodt, Kelly P. Brock, Genevieve S. Dobihal, P. Rohs +10 more
2018Nature104 citations Open access
Semantic Scholar
Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences
Anna G. Green, Hadeer Elhabashy, Kelly P. Brock, Rohan Maddamsetti +2 more
2021Nature Communications103 citations Open access
Semantic Scholar
Coordination of bacterial cell wall and outer membrane biosynthesis
K. R. Hummels, Samuel P. Berry, Zhao-Qi Li, A. Taguchi +4 more
2023Nature88 citations Open access
Semantic Scholar
Rapid generation of potent antibodies by autonomous hypermutation in yeast
Alon Wellner, C. McMahon, M. Gilman, J. Clements +14 more
2021Nature Chemical Biology86 citations Open access
Semantic Scholar
Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact
Melissa A. Chiasson, Nathan J. Rollins, Jason J. Stephany, K. Sitko +8 more
2020bioRxiv82 citations Open access
Semantic Scholar
PDBe-KB: collaboratively defining the biological context of structural data
M. Váradi, S. Anyango, David R. Armstrong, J. Berrisford +67 more
2021Nucleic Acids Res.70 citations Open access
Semantic Scholar
TranceptEVE: Combining Family-specific and Family-agnostic Models of Protein Sequences for Improved Fitness Prediction
Pascal Notin, Lood van Niekerk, Aaron W. Kollasch, D. Ritter +2 more
2022bioRxiv66 citations Open access
Semantic Scholar
Structure and mutagenic analysis of the lipid II flippase MurJ from Escherichia coli
Sanduo Zheng, Lok-To Sham, F. Rubino, Kelly P. Brock +5 more
2018Proceedings of the National Academy of Sciences of the United States of America66 citations Open access
Semantic Scholar
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 +6 more
2018Molecules and Cells60 citations Open access
Semantic Scholar
An in silico method to assess antibody fragment polyreactivity
Edward P. Harvey, Jung-Eun Shin, M. Skiba, Genevieve R. Nemeth +8 more
2022bioRxiv57 citations Open access
Semantic Scholar
All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences
S. Hayat, C. Sander, D. Marks, A. Elofsson
2015Proceedings of the National Academy of Sciences of the United States of America56 citations Open access
Semantic Scholar
Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4
J. M. Nicoludis, Bennett E. Vogt, Anna G. Green, Charlotta P. I. Schärfe +2 more
2016bioRxiv53 citations Open access
Semantic Scholar
Dormant spores sense amino acids through the B subunits of their germination receptors
Lior Artzi, A. Alon, Kelly P. Brock, Anna G. Green +5 more
2021Nature Communications46 citations Open access
Semantic Scholar
Machine learning prediction of enzyme optimum pH
Japheth E. Gado, Matthew W. Knotts, Ada Y. Shaw, D. Marks +3 more
2024bioRxiv45 citations Open access
Semantic Scholar
Accelerating Protein Design Using Autoregressive Generative Models
Jung-Eun Shin, Adam J. Riesselman, Aaron W. Kollasch, C. McMahon +5 more
2019bioRxiv45 citations Open access
Semantic Scholar
Protein structure from experimental evolution
M. Stiffler, F. J. Poelwijk, Kelly P. Brock, Richard R. Stein +6 more
2019bioRxiv45 citations Open access
Semantic Scholar
Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings
B. Schubert, Rohan Maddamsetti, J. Nyman, M. Farhat +1 more
2018Nature Microbiology43 citations Open access
Semantic Scholar
Protein design using structure-based residue preferences
David Ding, Ada Y. Shaw, S. Sinai, Nathan J. Rollins +4 more
2023bioRxiv41 citations Open access
Semantic Scholar
The SpoVA membrane complex is required for dipicolinic acid import during sporulation and export during germination
Yongqiang Gao, Rocio Del Carmen Barajas-Ornelas, J. Amon, Fernando H. Ramírez-Guadiana +5 more
2022Genes & Development39 citations Open access
Semantic Scholar
Coevolution of interacting proteins through non-contacting and non-specific mutations
David Ding, Anna G. Green, Boyuan Wang, T. Lite +3 more
2021Nature Ecology & Evolution39 citations Open access
Semantic Scholar
Rapid generation of potent antibodies by autonomous hypermutation in yeast
Alon Wellner, C. McMahon, M. Gilman, J. Clements +13 more
2020bioRxiv37 citations Open access
Semantic Scholar
Variational Inference for Sparse and Undirected Models
John Ingraham, D. Marks
2016International Conference on Machine Learning35 citations
Semantic Scholar
Non-identifiability and the Blessings of Misspecification in Models of Molecular Fitness
Eli N. Weinstein, Alan N. Amin, J. Frazer, D. Marks
2022bioRxiv31 citations Open access
Semantic Scholar
EVfold.org: Evolutionary Couplings and Protein 3D Structure Prediction
R. Sheridan, R. Fieldhouse, S. Hayat, Yichao Sun +5 more
2015bioRxiv31 citations Open access
Semantic Scholar
The relaxin receptor RXFP1 signals through a mechanism of autoinhibition
S. Erlandson, S. Rawson, James Osei-Owusu, Kelly P. Brock +7 more
2022bioRxiv28 citations Open access
Semantic Scholar
Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis
J. M. Nicoludis, Anna G. Green, Sanket Walujkar, E. May +3 more
2018Proceedings of the National Academy of Sciences of the United States of America28 citations Open access
Semantic Scholar
Deep generative models of genetic variation capture mutation effects
Adam J. Riesselman, John Ingraham, D. Marks
2017bioRxiv28 citations Open access
Semantic Scholar
Population-specific design of de-immunized protein biotherapeutics
B. Schubert, Charlotta P. I. Schärfe, P. Dönnes, T. Hopf +2 more
2017PLoS Comput. Biol.26 citations Open access
Semantic Scholar
Mechanical gating of the auditory transduction channel TMC1 involves the fourth and sixth transmembrane helices
Nurunisa Akyuz, K. D. Karavitaki, Bifeng Pan, Panos I. Tamvakologos +4 more
2022bioRxiv24 citations Open access
Semantic Scholar
Optimal Design of Stochastic DNA Synthesis Protocols based on Generative Sequence Models
Eli N. Weinstein, Alan N. Amin, Will Grathwohl, D. Kassler +2 more
2021bioRxiv24 citations Open access
Semantic Scholar
Natural and designed proteins inspired by extremotolerant organisms can form condensates and attenuate apoptosis in human cells
Mike T. Veling, D. Nguyen, Nicole N. Thadani, Michela E. Oster +9 more
2021bioRxiv22 citations Open access
Semantic Scholar

Frequent co-authors

Invite them to SciRah by sharing their profile.

Kelly P. Brock×15
Invite
Kelly P. Brock — researcher profile on SciRah
C. Sander×12
Invite
C. Sander — researcher profile on SciRah
A. Kruse×11
Invite
A. Kruse — researcher profile on SciRah
T. Hopf×9
Invite
T. Hopf — researcher profile on SciRah

×9

Invite

John Ingraham — researcher profile on SciRah

Anna G. Green×8

Invite

Anna G. Green — researcher profile on SciRah

Adam J. Riesselman×7

Invite

Adam J. Riesselman — researcher profile on SciRah

Jung-Eun Shin×5

Invite

Jung-Eun Shin — researcher profile on SciRah

Nathan J. Rollins×5

Invite

Nathan J. Rollins — researcher profile on SciRah

Pascal Notin×4

Invite

Pascal Notin — researcher profile on SciRah

Joseph K. Min×4

Invite

Joseph K. Min — researcher profile on SciRah

Charlotta P. I. Schärfe×4

Invite

Charlotta P. I. Schärfe — researcher profile on SciRah