| # | Title | Journal | Year | Citations |
|---|
| 1 | Fitting a mixture model by expectation maximization to discover motifs in biopolymers | Proceedings | 1994 | 2,298 |
| 2 | Robust Object Tracking with Online Multiple Instance Learning | IEEE Transactions on Pattern Analysis and Machine Intelligence | 2011 | 1,766 |
| 3 | De novo identification of repeat families in large genomes | Bioinformatics | 2005 | 1,590 |
| 4 | The Diploid Genome Sequence of an Individual Human | PLoS Biology | 2007 | 1,491 |
| 5 | ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees | BMC Bioinformatics | 2018 | 1,451 |
| 6 | Experimental Security Analysis of a Modern Automobile | BMC Bioinformatics | 2010 | 1,217 |
| 7 | Best practices for analysing microbiomes | Nature Reviews Microbiology | 2018 | 1,138 |
| 8 | Whole-Genome Patterns of Common DNA Variation in Three Human Populations | Science | 2005 | 1,074 |
| 9 | SUN: A Bayesian framework for saliency using natural statistics | Journal of Vision | 2008 | 1,003 |
| 10 | Spectral grouping using the nystrom method | IEEE Transactions on Pattern Analysis and Machine Intelligence | 2004 | 994 |
| 11 | MS-GF+ makes progress towards a universal database search tool for proteomics | Nature Communications | 2014 | 945 |
| 12 | The Transporter Classification Database (TCDB): recent advances | Nucleic Acids Research | 2016 | 711 |
| 13 | Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome | Movement Disorders | 2017 | 649 |
| 14 | PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling | Analytical Chemistry | 2005 | 615 |
| 15 | Microbiome-wide association studies link dynamic microbial consortia to disease | Nature | 2016 | 595 |
| 16 | Telomere-to-telomere assembly of a complete human X chromosome | Nature | 2020 | 549 |
| 17 | On the complexity of the parity argument and other inefficient proofs of existence | Journal of Computer and System Sciences | 1994 | 531 |
| 18 | Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity | Nature | 2017 | 530 |
| 19 | Integrative approaches for finding modular structure in biological networks | Nature Reviews Genetics | 2013 | 512 |
| 20 | How to apply de Bruijn graphs to genome assembly | Nature Biotechnology | 2011 | 470 |
| 21 | On the Complexity of Cooperative Solution Concepts | Mathematics of Operations Research | 1994 | 451 |
| 22 | Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases | Journal of Proteome Research | 2008 | 426 |
| 23 | Localizing Parts of Faces Using a Consensus of Exemplars | IEEE Transactions on Pattern Analysis and Machine Intelligence | 2013 | 406 |
| 24 | Localizing parts of faces using a consensus of exemplars | IEEE Transactions on Pattern Analysis and Machine Intelligence | 2011 | 401 |
| 25 | The Transporter Classification Database: recent advances | Nucleic Acids Research | 2009 | 391 |
| 26 | Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information | MSystems | 2018 | 376 |
| 27 | Adaptive computing on the grid using AppLeS | IEEE Transactions on Parallel and Distributed Systems | 2003 | 348 |
| 28 | Circular ecDNA promotes accessible chromatin and high oncogene expression | Nature | 2019 | 343 |
| 29 | Shortest paths without a map | Theoretical Computer Science | 1991 | 325 |
| 30 | Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution | Proceedings of the National Academy of Sciences of the United States of America | 2003 | 322 |
| 31 | Semantic Annotation and Retrieval of Music and Sound Effects | IEEE Transactions on Audio Speech and Language Processing | 2008 | 312 |
| 32 | Dynamic Node Creation in Backpropagation Networks | Connection Science | 1989 | 302 |
| 33 | Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes | Genome Research | 2003 | 302 |
| 34 | Balance Trees Reveal Microbial Niche Differentiation | MSystems | 2017 | 284 |
| 35 | Fusobacterium nucleatum promotes colorectal cancer by inducing Wnt/β‐catenin modulator Annexin A1 | EMBO Reports | 2019 | 283 |
| 36 | The value of prior knowledge in discovering motifs with MEME | Proceedings | 1995 | 279 |
| 37 | Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers | Nature Genetics | 2020 | 273 |
| 38 | Discovery and revision of Arabidopsis genes by proteogenomics | Proceedings of the National Academy of Sciences of the United States of America | 2008 | 268 |
| 39 | Context based object categorization: A critical survey | Computer Vision and Image Understanding | 2010 | 259 |
| 40 | Color-to-Grayscale: Does the Method Matter in Image Recognition? | PLoS ONE | 2012 | 240 |
| 41 | SUN: Top-down saliency using natural statistics | Visual Cognition | 2009 | 230 |
| 42 | The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search | Molecular and Cellular Proteomics | 2010 | 226 |
| 43 | Stochastic gradient descent with differentially private updates | Molecular and Cellular Proteomics | 2013 | 226 |
| 44 | Interkingdom metabolic transformations captured by microbial imaging mass spectrometry | Proceedings of the National Academy of Sciences of the United States of America | 2012 | 220 |
| 45 | Does Trypsin Cut Before Proline? | Journal of Proteome Research | 2008 | 217 |
| 46 | Word sense disambiguation for free-text indexing using a massive semantic network | Journal of Proteome Research | 1993 | 208 |
| 47 | Complete genomic and epigenetic maps of human centromeres | Science | 2022 | 204 |
| 48 | Efficient Garbling from a Fixed-Key Blockcipher | Science | 2013 | 202 |
| 49 | Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission | Nature | 2022 | 200 |
| 50 | Learning Visual Clothing Style with Heterogeneous Dyadic Co-Occurrences | Nature | 2015 | 199 |
