Claus O. Wilke

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 40 papers. Top paper: “Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs”.

Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs

PLoS Biology(2020)10.1371/journal.pbio.3000627

N/A

0DataRank · unranked

65 citations

Riddhiman K. Garge, A Teufel, Claus O. Wilke, Aashiq H. Kachroo, Edward M. Marcotte +1 more

A Comprehensive Coexpression Network Analysis in Vibrio cholerae

mSystems(2020)10.1128/msystems.00550-20

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0DataRank · unranked

12 citations

Claus O. Wilke, Bryan W. Davies, Cory D. DuPai

TsrA Regulates Virulence and Intestinal Colonization in Vibrio cholerae

mSphere(2020)10.1128/msphere.01014-20

N/A

0DataRank · unranked

4 citations

Ashley L. Cunningham, Aaron R. Conrado, Claus O. Wilke, Bryan W. Davies, Cory D. DuPai

BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.13.094805

N/A

0DataRank · unranked

11 citations

Claus O. Wilke, Adam J. Hockenberry

A systematic analysis of the beta hairpin motif in the Protein Data Bank

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.28.359612

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0DataRank · unranked

4 citations

Bryan W. Davies, Claus O. Wilke, Cory D. DuPai

Uncovering modeling features of viral replication dynamics from high-throughput single-cell virology experiments

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.09.195925

N/A

0DataRank · unranked

2 citations

Wu Liu, Jeremy A. Draghi, Craig E. Cameron, Claus O. Wilke, A Teufel

Site-specific amino acid distributions follow a universal shape

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.05.238493

N/A

0DataRank · unranked

0 citations

Claus O. Wilke, Mackenzie M. Johnson

Generating complex patterns of gene expression without regulatory circuits

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.25.398248

N/A

0DataRank · unranked

0 citations

Alexis M. Hill, Claus O. Wilke, Adam J. Hockenberry, Sahil B. Shah

BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains

PeerJ(2021)10.7717/peerj.11396

N/A

0DataRank · unranked

334 citations

Claus O. Wilke, Adam J. Hockenberry

A systematic analysis of the beta hairpin motif in the Protein Data Bank

Protein Science(2021)10.1002/pro.4020

N/A

0DataRank · unranked

39 citations

Bryan W. Davies, Claus O. Wilke, Cory D. DuPai

Modeling poliovirus replication dynamics from live time-lapse single-cell imaging data

Scientific Reports(2021)10.1038/s41598-021-87694-x

N/A

0DataRank · unranked

4 citations

Wu Liu, Jeremy A. Draghi, Craig E. Cameron, Claus O. Wilke, A Teufel

Virulent but not temperate bacteriophages display hallmarks of rapid translation initiation

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.21.440840

N/A

0DataRank · unranked

1 citations

David C. Weaver, Claus O. Wilke, Adam J. Hockenberry

Learning the local landscape of protein structures with convolutional neural networks

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.19.456994

N/A

0DataRank · unranked

0 citations

Daniel J. Diaz, James M. Loy, Andrew D. Ellington, Claus O. Wilke, Anastasiya V. Kulikova

Generating dynamic gene expression patterns without the need for regulatory circuits

PLoS ONE(2022)10.1371/journal.pone.0268883

N/A

0DataRank · unranked

3 citations

Alexis M. Hill, Claus O. Wilke, Adam J. Hockenberry, Sahil B. Shah

Designing β-hairpin peptide macrocycles for antibiotic potential

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.21.497034

N/A

0DataRank · unranked

0 citations

Cory D. DuPai, T. Jeffrey Cole, Gillian Davidson, Kyra E. Groover, Claus O. Wilke +2 more

Recombination rate inference via deep learning is limited by sequence diversity

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.01.498489

N/A

0DataRank · unranked

0 citations

Claus O. Wilke, Mackenzie M. Johnson

Using machine learning to predict the effects and consequences of mutations in proteins

Current Opinion in Structural Biology(2023)10.1016/j.sbi.2022.102518

N/A

0DataRank · unranked

57 citations

Anastasiya V. Kulikova, Andrew D. Ellington, Claus O. Wilke, Daniel J. Diaz

Two sequence- and two structure-based ML models have learned different aspects of protein biochemistry

Scientific Reports(2023)10.1038/s41598-023-40247-w

N/A

0DataRank · unranked

13 citations

Daniel J. Diaz, Tianlong Chen, T. Jeffrey Cole, Andrew D. Ellington, Claus O. Wilke +1 more

Using alternative SMILES representations to identify novel functional analogues in chemical similarity vector searches

Patterns(2023)10.1016/j.patter.2023.100865

N/A

0DataRank · unranked

11 citations

Aaron L. Feller, Claus O. Wilke, Andrew D. Ellington, Clayton W. Kosonocky

Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases

Molecular Biology and Evolution(2023)10.1093/molbev/msad189

N/A

0DataRank · unranked

2 citations

Adam J. Hockenberry, Matthew J. McGuffie, Luiz Carlos Vieira, Claus O. Wilke, Mackenzie M. Johnson

Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.28.551017

N/A

0DataRank · unranked

5 citations

Luiz Carlos Vieira, Claus O. Wilke, Bryan W. Davies, Justin R. Randall

Semantic search using protein large language models detects class II microcins in bacterial genomes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.15.567263

N/A

0DataRank · unranked

5 citations

Jennifer K. Parker, Bryan W. Davies, Claus O. Wilke, Anastasiya V. Kulikova

Two sequence- and two structure-based ML models have learned different aspects of protein biochemistry

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.20.533508

N/A

0DataRank · unranked

4 citations

Daniel J. Diaz, Tianlong Chen, T. Jeffrey Cole, Andrew D. Ellington, Claus O. Wilke +1 more

Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity

Research Square(2023)10.21203/rs.3.rs-3280212/v1

N/A

0DataRank · unranked

1 citations

Justin R. Randall, Luiz Ângelo Vieira, Claus O. Wilke, Bryan W. Davies

Growth-dependent gene expression variation influences the strength of codon usage biases

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.14.532645

N/A

0DataRank · unranked

0 citations

Adam J. Hockenberry, Matthew J. McGuffie, Luiz Carlos Vieira, Claus O. Wilke, Mackenzie M. Johnson

Deep mutational scanning and machine learning for the analysis of antimicrobial-peptide features driving membrane selectivity

Nature Biomedical Engineering(2024)10.1038/s41551-024-01243-1

N/A

0DataRank · unranked

37 citations

Luiz Carlos Vieira, Claus O. Wilke, Bryan W. Davies, Justin R. Randall

Mining patents with large language models elucidates the chemical function landscape

Digital Discovery(2024)10.1039/d4dd00011k

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0DataRank · unranked

12 citations

Claus O. Wilke, Edward M. Marcotte, Andrew D. Ellington, Clayton W. Kosonocky

A computational model for bacteriophage ϕX174 gene expression

PLoS ONE(2024)10.1371/journal.pone.0313039

N/A

0DataRank · unranked

5 citations

Tanvi Ingle, Claus O. Wilke, Alexis M. Hill

Single-Cell Virology: On-Chip, Quantitative Characterization of the Dynamics of Virus Spread from One Single Cell to Another

Viruses(2024)10.3390/v16111659

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0DataRank · unranked

3 citations

Claus O. Wilke, Jamie J. Arnold, Mohamad S. Sotoudegan, Craig E. Cameron, Wu Liu

Medium-sized protein language models perform well at transfer learning on realistic datasets

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.22.624936

N/A

0DataRank · unranked

11 citations

Morgan L. Handojo, Claus O. Wilke, Luiz Carlos Vieira

Modeling and measuring how codon usage modulates the relationship between burden and yield during protein overexpression in bacteria

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.28.625058

N/A

0DataRank · unranked

1 citations

Alexis M. Hill, Claus O. Wilke, Jeffrey E. Barrick, Cameron T. Roots

A computational model for bacteriophage ϕ X174 gene expression

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.22.586356

N/A

0DataRank · unranked

0 citations

Tanvi Ingle, Claus O. Wilke, Alexis M. Hill

Single-cell virology: On-chip, quantitative characterization of the dynamics of virus spread from one single cell to another

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.25.615011

N/A

0DataRank · unranked

0 citations

Claus O. Wilke, Jamie J. Arnold, Mohamad S. Sotoudegan, Craig E. Cameron, Wu Liu

Single-Cell Virology: On-Chip, Quantitative Characterization of the Dynamics of Virus Spread from One Single Cell to Another

UNC Libraries(2024)10.17615/vfex-6c92

N/A

0DataRank · unranked

0 citations

Jamie J. Arnold, Mohamad S. Sotoudegan, Wu Liu, Claus O. Wilke, Craig E. Cameron

Peptide-Aware Chemical Language Model Successfully Predicts Membrane Diffusion of Cyclic Peptides

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.4c01441

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0DataRank · unranked

22 citations

Claus O. Wilke, Aaron L. Feller

Medium-sized protein language models perform well at transfer learning on realistic datasets

Scientific Reports(2025)10.1038/s41598-025-05674-x

N/A

0DataRank · unranked

22 citations

Morgan L. Handojo, Claus O. Wilke, Luiz Carlos Vieira

Antibacterial microcins are ubiquitous and functionally diverse across bacterial communities

Nature Communications(2025)10.1038/s41467-025-61151-z

N/A

0DataRank · unranked

9 citations

Aaron L. Feller, Richard Gu, Simon Sanchez-Paiva, Bethany C. Perez, Angela C. O’Donnell +6 more

Codon usage modulates the relationship between the burden and yield of protein overexpression

Journal of Biological Engineering(2025)10.1186/s13036-025-00521-z

N/A

0DataRank · unranked

8 citations

Alexis M. Hill, Claus O. Wilke, Jeffrey E. Barrick, Cameron T. Roots

p2smi: A toolkit enabling SMILES generation and property analysis for noncanonical and cyclized peptides

The Journal of Open Source Software(2025)10.21105/joss.08319

N/A

0DataRank · unranked

1 citations

Claus O. Wilke, Aaron L. Feller

A fold switch regulates conformation of an alphavirus virus RNA-dependent RNA polymerase

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.18.676892

N/A

0DataRank · unranked

1 citations

Sean M. Braet, Luiz Carlos Vieira, Ibrahim M. Moustafa, David W. Gohara, Julie Fecko +8 more