Database resources of the National Center for Biotechnology Information: update

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302

Gene Ontology: tool for the unification of biology

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288

A general method applicable to the search for similarities in the amino acid sequence of two proteins

Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab199 · Cited by 6,187

A gene expression atlas of the central nervous system based on bacterial artificial chromosomes

Gong, S., Zheng, C., Doughty, M. L., Losos, K., Didkovsky, N., Schambra, U. B., Nowak, N. J., Joyner, A., Leblanc, G., Hatten, M. E., et al. (2003) · Nature · doi:10.1038/nature02033 · Cited by 2,108

Reactome knowledgebase of human biological pathways and processes

Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn863 · Cited by 873

NCBI Reference Sequences: current status, policy and new initiatives

Pruitt, K. D., Tatusova, T., Klimke, W., & Maglott, D. R. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn721 · Cited by 736

EcoCyc: A comprehensive view of Escherichia coli biology

Keseler, I. M., Bonavides-Martinez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R. P., Johnson, D. A., Krummenacker, M., Nolan, L. M., Paley, S., Paulsen, I. T., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn751 · Cited by 373

Fast and sensitive protein alignment using DIAMOND

Buchfink, B., Xie, C., & Huson, D. H. (2015) · Nature Methods · doi:10.1038/nmeth.3176 · Cited by 14,201

DAVID: Database for Annotation, Visualization, and Integrated Discovery

Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327

UniProt: the Universal Protein Knowledgebase in 2023

The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bye-A-Jee, H., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1052 · Cited by 7,210

Pfam: the protein families database

Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148

UniProt: the universal protein knowledgebase in 2021

The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1100 · Cited by 6,372

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

Goddard, T. D., Huang, C. C., Meng, E. C., Pettersen, E. F., Couch, G. S., Morris, J. H., & Ferrin, T. E. (2018) · Protein Science · doi:10.1002/pro.3235 · Cited by 5,267

HMMER web server: interactive sequence similarity searching

Finn, R. D., Clements, J., & Eddy, S. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr367 · Cited by 5,952

KEGG for taxonomy-based analysis of pathways and genomes

Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M., & Ishiguro-Watanabe, M. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac963 · Cited by 5,833

PubChem Substance and Compound databases

Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv951 · Cited by 5,436

A draft sequence of the Neandertal genome

Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318

ChEMBL: a large-scale bioactivity database for drug discovery

Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., Light, Y., McGlinchey, S., Michalovich, D., Al-Lazikani, B., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr777 · Cited by 4,382

ClinVar: improving access to variant interpretations and supporting evidence

Landrum, M. J., Lee, J. M., Benson, M., Brown, G. R., Chao, C., Chitipiralla, S., Gu, B., Hart, J., Hoffman, D., Jang, W., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1153 · Cited by 4,196

PubChem in 2021: new data content and improved web interfaces

Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa971 · Cited by 3,953

Alcohol use and burden for 195 countries and territories, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016

Griswold, M. G., Fullman, N., Hawley, C., Arian, N., Zimsen, S. R. M., Tymeson, H. D., Venkateswaran, V., Tapp, A. D., Forouzanfar, M. H., Salama, J. S., et al. (2018) · The Lancet · doi:10.1016/s0140-6736(18)31310-2 · Cited by 3,524

ClinVar: public archive of relationships among sequence variation and human phenotype

Landrum, M. J., Lee, J. M., Riley, G. R., Jang, W., Rubinstein, W. S., Church, D. M., & Maglott, D. R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1113 · Cited by 3,516

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395

PubChem 2023 update

Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac956 · Cited by 3,443

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

Friedländer, M. R., Mackowiak, S. D., Li, N., Chen, W., & Rajewsky, N. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr688 · Cited by 3,207

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

Amberger, J. S., Bocchini, C. A., Schiettecatte, F., Scott, A. F., & Hamosh, A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1205 · Cited by 2,691

Database resources of the national center for biotechnology information

Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1112 · Cited by 2,812

ClinVar: public archive of interpretations of clinically relevant variants

Landrum, M. J., Lee, J. M., Benson, M., Brown, G., Chao, C., Chitipiralla, S., Gu, B., Hart, J., Hoffman, D., Hoover, J., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1222 · Cited by 2,758

NCBI Taxonomy: a comprehensive update on curation, resources and tools

Schoch, C. L., Ciufo, S., Domrachev, M., Hotton, C. L., Kannan, S., Khovanskaya, R., Leipe, D., Mcveigh, R., O’Neill, K., Robbertse, B., et al. (2020) · Database · doi:10.1093/database/baaa062 · Cited by 2,635

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303

METLIN—a metabolite mass spectral database

Smith, C. A., Maille, G. O., Want, E. J., Qin, C., Trauger, S. A., Brandon, T. R., Custodio, D. E., Abagyan, R., & Siuzdak, G. (2005) · Therapeutic Drug Monitoring · doi:10.1097/01.ftd.0000179845.53213.39 · Cited by 2,226

ChIP–seq: advantages and challenges of a maturing technology

Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

Darnell, J. C., Van Driesche, S. J., Zhang, C., Hung, K. Y. S., Mele, A., Fraser, C. E., Stone, E. F., Chen, C., Fak, J. J., Chi, S. W., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.013 · Cited by 2,072

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

Castro-Mondragon, J. A., Riudavets-Puig, R., Rauluseviciute, I., Berhanu Lemma, R., Turchi, L., Blanc-Mathieu, R., Lucas, J., Boddie, P., Khan, A., Manosalva Pérez, N., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1113 · Cited by 1,935

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0012-7 · Cited by 1,882

Expansion of the Gene Ontology knowledgebase and resources

The Gene Ontology Consortium (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1108 · Cited by 1,850

A protocol for generating a high-quality genome-scale metabolic reconstruction

Thiele, I., & Palsson, B. Ø. (2010) · Nature Protocols · doi:10.1038/nprot.2009.203 · Cited by 1,789

Reactome: a database of reactions, pathways and biological processes

Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1018 · Cited by 1,751

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

Rawlings, N. D., Barrett, A. J., Thomas, P. D., Huang, X., Bateman, A., & Finn, R. D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1134 · Cited by 1,749

The Controversial Role of Human Gut Lachnospiraceae

Vacca, M., Celano, G., Calabrese, F. M., Portincasa, P., Gobbetti, M., & De Angelis, M. (2020) · Microorganisms · doi:10.3390/microorganisms8040573 · Cited by 1,688

UniRef: comprehensive and non-redundant UniProt reference clusters

Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R., & Wu, C. H. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm098 · Cited by 1,613

A census of human transcription factors: function, expression and evolution

Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A., & Luscombe, N. M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2538 · Cited by 1,573

A copy number variation morbidity map of developmental delay

Cooper, G. M., Coe, B. P., Girirajan, S., Rosenfeld, J. A., Vu, T. H., Baker, C., Williams, C., Stalker, H., Hamid, R., Hannig, V., et al. (2011) · Nature Genetics · doi:10.1038/ng.909 · Cited by 1,351

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

Kind, T., & Fiehn, O. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-105 · Cited by 1,201

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

Dührkop, K., Shen, H., Meusel, M., Rousu, J., & Böcker, S. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1509788112 · Cited by 1,190

CDD: a Conserved Domain Database for protein classification

Marchler-Bauer, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki069 · Cited by 1,156

Pathway Commons, a web resource for biological pathway data

Cerami, E. G., Gross, B. E., Demir, E., Rodchenkov, I., Babur, O., Anwar, N., Schultz, N., Bader, G. D., & Sander, C. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1039 · Cited by 1,101

Interpretation of Shotgun Proteomic Data

Nesvizhskii, A. I., & Aebersold, R. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r500012-mcp200 · Cited by 1,025

ClinVar: improvements to accessing data

Landrum, M. J., Chitipiralla, S., Brown, G. R., Chen, C., Gu, B., Hart, J., Hoffman, D., Jang, W., Kaur, K., Liu, C., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz972 · Cited by 994

Ketone bodies as signaling metabolites

Newman, J. C., & Verdin, E. (2014) · Trends in Endocrinology & Metabolism · doi:10.1016/j.tem.2013.09.002 · Cited by 966

Identification of a Molecular Signaling Network that Regulates a Cellular Necrotic Cell Death Pathway

Hitomi, J., Christofferson, D. E., Ng, A., Yao, J., Degterev, A., Xavier, R. J., & Yuan, J. (2008) · Cell · doi:10.1016/j.cell.2008.10.044 · Cited by 989

Disease Ontology: a backbone for disease semantic integration

Schriml, L. M., Arze, C., Nadendla, S., Chang, Y.-W. W., Mazaitis, M., Felix, V., Feng, G., & Kibbe, W. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr972 · Cited by 929

A side effect resource to capture phenotypic effects of drugs

Kuhn, M., Campillos, M., Letunic, I., Jensen, L. J., & Bork, P. (2010) · Molecular Systems Biology · doi:10.1038/msb.2009.98 · Cited by 899

The NCBI BioSystems database

Geer, L. Y., Marchler-Bauer, A., Geer, R. C., Han, L., He, J., He, S., Liu, C., Shi, W., & Bryant, S. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp858 · Cited by 875

Gateways to the FANTOM5 promoter level mammalian expression atlas

Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., et al. (2015) · Genome Biology · doi:10.1186/s13059-014-0560-6 · Cited by 871

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Asnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16366-7 · Cited by 869

BRENDA, the ELIXIR core data resource in 2021: new developments and updates

Chang, A., Jeske, L., Ulbrich, S., Hofmann, J., Koblitz, J., Schomburg, I., Neumann-Schaal, M., Jahn, D., & Schomburg, D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1025 · Cited by 789

An integrative approach to ortholog prediction for disease-focused and other functional studies

Hu, Y., Flockhart, I., Vinayagam, A., Bergwitz, C., Berger, B., Perrimon, N., & Mohr, S. E. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-357 · Cited by 848

Molecular diversity of midbrain development in mouse, human, and stem cells

La Manno, G., Gyllborg, D., Codeluppi, S., Nishimura, K., Salto, C., Zeisel, A., Borm, L. E., Stott, S. R. W., Toledo, E. M., Villaescusa, J. C., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.027 · Cited by 835

Database Resources of the National Center for Biotechnology Information

Coordinators, N. R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1071 · Cited by 817

The Cellosaurus, a Cell-Line Knowledge Resource

Bairoch, A. (2018) · Journal of Biomolecular Techniques JBT · doi:10.7171/jbt.18-2902-002 · Cited by 807

Meta-analysis of age-related gene expression profiles identifies common signatures of aging

de Magalhães, J. P., Curado, J., & Church, G. M. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp073 · Cited by 737

PANTHER version 10: expanded protein families and functions, and analysis tools

Mi, H., Poudel, S., Muruganujan, A., Casagrande, J. T., & Thomas, P. D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1194 · Cited by 770

Coexpression Analysis of Human Genes Across Many Microarray Data Sets

Lee, H. K., Hsu, A. K., Sajdak, J., Qin, J., & Pavlidis, P. (2004) · Genome Research · doi:10.1101/gr.1910904 · Cited by 770

The ctenophore genome and the evolutionary origins of neural systems

Moroz, L. L., Kocot, K. M., Citarella, M. R., Dosung, S., Norekian, T. P., Povolotskaya, I. S., Grigorenko, A. P., Dailey, C., Berezikov, E., Buckley, K. M., et al. (2014) · Nature · doi:10.1038/nature13400 · Cited by 716

NCBI Reference Sequences: current status, policy and new initiatives

Pruitt, K. D., Tatusova, T., Klimke, W., & Maglott, D. R. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn721 · Cited by 736

The BioPAX community standard for pathway data sharing

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745

Ensembl 2024

Harrison, P. W., Amode, M. R., Austine-Orimoloye, O., Azov, A. G., Barba, M., Barnes, I., Becker, A., Bennett, R., Berry, A., Bhai, J., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad1049 · Cited by 742

MicroRNA-Mediated Feedback and Feedforward Loops Are Recurrent Network Motifs in Mammals

Tsang, J., Zhu, J., & van Oudenaarden, A. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.05.018 · Cited by 740

CAMP R3 : a database on sequences, structures and signatures of antimicrobial peptides: Table 1.

Waghu, F. H., Barai, R. S., Gurung, P., & Idicula-Thomas, S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1051 · Cited by 715

Large-scale genome-wide meta-analysis of polycystic ovary syndrome suggests shared genetic architecture for different diagnosis criteria

Day, F., Karaderi, T., Jones, M. R., Meun, C., He, C., Drong, A., Kraft, P., Lin, N., Huang, H., Broer, L., et al. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007813 · Cited by 619

The UCSC Genome Browser database: 2014 update

Karolchik, D., Barber, G. P., Casper, J., Clawson, H., Cline, M. S., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1168 · Cited by 670

Drug–target interaction prediction: databases, web servers and computational models

Chen, X., Yan, C. C., Zhang, X., Zhang, X., Dai, F., Yin, J., & Zhang, Y. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbv066 · Cited by 658

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

Sharova, L. V., Sharov, A. A., Nedorezov, T., Piao, Y., Shaik, N., & Ko, M. S. H. (2009) · DNA Research · doi:10.1093/dnares/dsn030 · Cited by 591

The immune epitope database 2.0

Vita, R., Zarebski, L., Greenbaum, J. A., Emami, H., Hoof, I., Salimi, N., Damle, R., Sette, A., & Peters, B. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1004 · Cited by 631

A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease

Brehme, M., Voisine, C., Rolland, T., Wachi, S., Soper, J. H., Zhu, Y., Orton, K., Villella, A., Garza, D., Vidal, M., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.09.042 · Cited by 584

Minimum information requested in the annotation of biochemical models (MIRIAM)

Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1156 · Cited by 622

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1492 · Cited by 588

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

Xie, C., & Tammi, M. T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-80 · Cited by 582

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

McPherson, A., Hormozdiari, F., Zayed, A., Giuliany, R., Ha, G., Sun, M. G. F., Griffith, M., Heravi Moussavi, A., Senz, J., Melnyk, N., et al. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001138 · Cited by 557

Network-based approach to prediction and population-based validation of in silico drug repurposing

Cheng, F., Desai, R. J., Handy, D. E., Wang, R., Schneeweiss, S., Barabási, A.-L., & Loscalzo, J. (2018) · Nature Communications · doi:10.1038/s41467-018-05116-5 · Cited by 552

TreeFam: a curated database of phylogenetic trees of animal gene families

Li, H. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj118 · Cited by 523

A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart

Kalsotra, A., Xiao, X., Ward, A. J., Castle, J. C., Johnson, J. M., Burge, C. B., & Cooper, T. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809045105 · Cited by 508

Chapter 12: Human Microbiome Analysis

Morgan, X. C., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002808 · Cited by 496

The Sequence Read Archive: a decade more of explosive growth

Katz, K., Shutov, O., Lapoint, R., Kimelman, M., Brister, J. R., & O’Sullivan, C. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1053 · Cited by 424

Big data and artificial intelligence modeling for drug discovery

Zhu, H. (2020) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010919-023324 · Cited by 455

De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)

Wang, Z., Fang, B., Chen, J., Zhang, X., Luo, Z., Huang, L., Chen, X., & Li, Y. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-726 · Cited by 433

The Edinburgh human metabolic network reconstruction and its functional analysis

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The Airway Microbiota in Cystic Fibrosis: A Complex Fungal and Bacterial Community—Implications for Therapeutic Management

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CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator

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Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

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The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans

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Assembly Properties of the Human Immunodeficiency Virus Type 1 CA Protein

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