| # | Title | Journal | Year | Citations |
|---|
| 1 | The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design | Journal of Chemical Theory and Computation | 2017 | 1,032 |
| 2 | Minimum Information about a Biosynthetic Gene cluster | Nature Chemical Biology | 2015 | 715 |
| 3 | Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies | PLoS Computational Biology | 2009 | 587 |
| 4 | SLC transporters as therapeutic targets: emerging opportunities | Nature Reviews Drug Discovery | 2015 | 584 |
| 5 | Dysbiosis of the Gut Microbiota Is Associated with HIV Disease Progression and Tryptophan Catabolism | Science Translational Medicine | 2013 | 578 |
| 6 | A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics | Cell | 2014 | 573 |
| 7 | The Metabolic Profile of Tumors Depends on Both the Responsible Genetic Lesion and Tissue Type | Cell Metabolism | 2012 | 553 |
| 8 | Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells | Nature Cell Biology | 2011 | 529 |
| 9 | Ballistocardiography and Seismocardiography: A Review of Recent Advances | IEEE Journal of Biomedical and Health Informatics | 2015 | 529 |
| 10 | Macromolecular modeling and design in Rosetta: recent methods and frameworks | Nature Methods | 2020 | 513 |
| 11 | ModBase, a database of annotated comparative protein structure models, and associated resources | Nucleic Acids Research | 2011 | 506 |
| 12 | Clinical Pharmacogenetics Implementation Consortium Guidelines for Thiopurine Methyltransferase Genotype and Thiopurine Dosing | Clinical Pharmacology and Therapeutics | 2011 | 504 |
| 13 | Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments | Biophysical Journal | 2013 | 489 |
| 14 | BDDCS, the Rule of 5 and drugability | Advanced Drug Delivery Reviews | 2016 | 475 |
| 15 | FoXS: a web server for rapid computation and fitting of SAXS profiles | Nucleic Acids Research | 2010 | 474 |
| 16 | Massively parallel functional dissection of mammalian enhancers in vivo | Nature Biotechnology | 2012 | 468 |
| 17 | FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles | Nucleic Acids Research | 2016 | 427 |
| 18 | SNX27 mediates retromer tubule entry and endosome-to-plasma membrane trafficking of signalling receptors | Nature Cell Biology | 2011 | 408 |
| 19 | Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations | Nature | 2013 | 405 |
| 20 | Synthetic biology to access and expand nature's chemical diversity | Nature Reviews Microbiology | 2016 | 393 |
| 21 | Cholangiocarcinomas can originate from hepatocytes in mice | Journal of Clinical Investigation | 2012 | 385 |
| 22 | A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens | Cell | 2019 | 379 |
| 23 | Protein Structure Modeling with MODELLER | Methods in Molecular Biology | 2017 | 376 |
| 24 | Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing | Cell | 2020 | 371 |
| 25 | Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice | Nature | 2012 | 364 |
| 26 | Clinical Pharmacogenetics Implementation Consortium Guidelines for Thiopurine Methyltransferase Genotype and Thiopurine Dosing: 2013 Update | Clinical Pharmacology and Therapeutics | 2013 | 304 |
| 27 | Single-cell mutation analysis of clonal evolution in myeloid malignancies | Nature | 2020 | 304 |
| 28 | Reconstructing the Population Genetic History of the Caribbean | PLoS Genetics | 2013 | 296 |
| 29 | Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments | Nature Chemical Biology | 2013 | 272 |
| 30 | A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity | Genome Research | 2017 | 244 |
| 31 | The Role of BCS (Biopharmaceutics Classification System) and BDDCS (Biopharmaceutics Drug Disposition Classification System) in Drug Development | Journal of Pharmaceutical Sciences | 2013 | 242 |
| 32 | Malaria eradication within a generation: ambitious, achievable, and necessary | Lancet, The | 2019 | 240 |
| 33 | Mouse liver repopulation with hepatocytes generated from human fibroblasts | Nature | 2014 | 232 |
| 34 | CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency | Science | 2019 | 230 |
| 35 | Decoding enhancers using massively parallel reporter assays | Genomics | 2015 | 208 |
| 36 | Glucose Sensor O-GlcNAcylation Coordinates with Phosphorylation to Regulate Circadian Clock | Cell Metabolism | 2013 | 206 |
| 37 | 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update | Acta Crystallographica Section D: Structural Biology | 2017 | 205 |
| 38 | Coding exons function as tissue-specific enhancers of nearby genes | Genome Research | 2012 | 202 |
| 39 | Association of busulfan exposure with survival and toxicity after haemopoietic cell transplantation in children and young adults: a multicentre, retrospective cohort analysis | Lancet Haematology,the | 2016 | 197 |
| 40 | A Genome-Wide Association Study Identifies Novel Loci for Paclitaxel-Induced Sensory Peripheral Neuropathy in CALGB 40101 | Clinical Cancer Research | 2012 | 183 |
| 41 | The Drug Transporter−Metabolism Alliance: Uncovering and Defining the Interplay | Molecular Pharmaceutics | 2009 | 176 |
| 42 | Improvements to Robotics-Inspired Conformational Sampling in Rosetta | PLoS ONE | 2013 | 176 |
| 43 | Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin | Pharmacogenetics and Genomics | 2010 | 175 |
| 44 | MicroRNA-21 is a potential link between non-alcoholic fatty liver disease and hepatocellular carcinoma via modulation of the HBP1-p53-Srebp1c pathway | Gut | 2016 | 162 |
| 45 | Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data | Nature Genetics | 2022 | 156 |
| 46 | The UCSF-FDA TransPortal: A Public Drug Transporter Database | Clinical Pharmacology and Therapeutics | 2012 | 155 |
| 47 | MODBASE, a database of annotated comparative protein structure models and associated resources | Nucleic Acids Research | 2009 | 154 |
| 48 | Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution | Nature Communications | 2019 | 152 |
| 49 | RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning | Nucleic Acids Research | 2023 | 152 |
| 50 | Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment | Proteins: Structure, Function and Bioinformatics | 2016 | 148 |
