Next-generation diagnostics and disease-gene discovery with the Exomiser
Open accessAbstract
Exomiser is an application that prioritizes genes and variants in next-generation sequencing (NGS) projects for novel disease-gene discovery or differential diagnostics of Mendelian disease. Exomiser comprises a suite of algorithms for prioritizing exome sequences using random-walk analysis of protein interaction networks, clinical relevance and cross-species phenotype comparisons, as well as a wide range of other computational filters for variant frequency, predicted pathogenicity and pedigree analysis. In this protocol, we provide a detailed explanation of how to install Exomiser and use it to prioritize exome sequences in a number of scenarios. Exomiser requires ∼3 GB of RAM and roughly 15-90 s of computing time on a standard desktop computer to analyze a variant call format (VCF) file. Exomiser is freely available for academic use from http://www.sanger.ac.uk/science/tools/exomiser.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
There are limited approaches for phenotype-based diagnosis, and none automatically learn phenotypic and/or genotypic features over patient phenotype terms.
“While deep learning approaches exist for image-based diagnosis10,11, there are limited approaches for phenotype-based diagnosis, and none automatically learn phenotypic and/or genotypic features over patient phenotype terms23–28,44.”
From Few shot learning for phenotype-driven diagnosis of patients with rare genetic diseases (2025) · cites this paper as [24]
The Introduction sections “Alternative analysis packages” and “Overview of analysis with Exomiser” describe phenotype-based diagnostic approaches, including PhenIX’s use of HPO terms and semantic similarity. They do not establish that such approaches are limited in number or that none automatically learns phenotypic or genotypic features from patient phenotype terms. Page numbers are unavailable in our copy. (LLM, conf=0.78)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works
The variant call format and VCFtools
Danecek, P., Auton, A., Abecasis, G. R., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G. A., Marth, G., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,008 · see citing works
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
Wang, K., Li, M., & Hakonarson, H. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq603 · Cited by 14,380 · see citing works
A method and server for predicting damaging missense mutations.
Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R. (2010) · Nature Methods · doi:10.1038/nmeth0410-248 · Cited by 13,194 · see citing works
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,691 · see citing works
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877 · see citing works
Kumar, P., Henikoff, S., & Ng, P. C. (2009) · Nature Protocols · doi:10.1038/nprot.2009.86 · Cited by 6,521 · see citing works
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1094 · Cited by 4,398 · see citing works
MutationTaster2: mutation prediction for the deep-sequencing age
Schwarz, J. M., Cooper, D. N., Schuelke, M., & Seelow, D. (2014) · Nature Methods · doi:10.1038/nmeth.2890 · Cited by 3,652 · see citing works
Gene Ontology Consortium: going forward
The Gene Ontology Consortium (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1179 · Cited by 3,492 · see citing works
MutationTaster evaluates disease-causing potential of sequence alterations
Schwarz, J. M., Rödelsperger, C., Schuelke, M., & Seelow, D. (2010) · Nature Methods · doi:10.1038/nmeth0810-575 · Cited by 2,975 · see citing works
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 · see citing works
Database resources of the National Center for Biotechnology Information
Sayers, E. W., Beck, J., Bolton, E. E., Brister, J., Chan, J., Comeau, D. C., Connor, R., DiCuccio, M., Farrell, C., Feldgarden, M., et al. (2014) · Nucleic Acids Res. · doi:10.1093/nar/gku1130 · Cited by 2,584 · see citing works
Targeted capture and massively parallel sequencing of 12 human exomes
Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E. E., et al. (2009) · Nature · doi:10.1038/nature08250 · Cited by 2,030 · see citing works
Exome sequencing identifies the cause of a mendelian disorder
Ng, S. B., Buckingham, K. J., Lee, C., Bigham, A. W., Tabor, H. K., Dent, K. M., Huff, C. D., Shannon, P. T., Jabs, E. W., Nickerson, D. A., et al. (2010) · Nature Genetics · doi:10.1038/ng.499 · Cited by 1,957 · see citing works
Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders
Yang, Y.-P., Muzny, D., Reid, J., Bainbridge, M., Willis, A., Ward, P., Braxton, A. A., Beuten, J., Xia, F., Niu, Z., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1306555 · Cited by 1,926 · see citing works
Wright, C., Fitzgerald, T. W., Jones, W., Clayton, S., McRae, J., van Kogelenberg, M., King, D. A., Ambridge, K., Barrett, D. M., Bayzetinova, T., et al. (2015) · The Lancet · doi:10.1016/s0140-6736(14)61705-0 · Cited by 1,794 · see citing works
Diagnostic exome sequencing in persons with severe intellectual disability
de Ligt, J., Willemsen, M. H., van Bon, B. W. M., Kleefstra, T., Yntema, H. G., Kroes, T., Vulto-van Silfhout, A. T., Koolen, D. A., de Vries, P., Gilissen, C., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1206524 · Cited by 1,546 · see citing works
Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing
Yang, Y., Muzny, D. M., Xia, F., Niu, Z., Person, R., Ding, Y., Ward, P., Braxton, A., Wang, M., Buhay, C., et al. (2014) · JAMA · doi:10.1001/jama.2014.14601 · Cited by 1,360 · see citing works
A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
MacArthur, D. G., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., Walter, K., Jostins, L., Habegger, L., Pickrell, J. K., Montgomery, S. B., et al. (2012) · Science · doi:10.1126/science.1215040 · Cited by 1,272 · see citing works
Walking the Interactome for Prioritization of Candidate Disease Genes
Köhler, S., Bauer, S., Horn, D., & Robinson, P. N. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.02.013 · Cited by 1,268 · see citing works
Self-citationCunningham, F., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1010 · Cited by 1,115 · see citing works
The human phenotype ontology: a tool for annotating and analyzing human hereditary disease
Robinson, P. N., Köhler, S., Bauer, S., Seelow, D., Horn, D., & Mundlos, S. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.09.017 · Cited by 1,034 · see citing works
Self-citationThe UCSC Genome Browser database: 2015 update
Rosenbloom, K., Armstrong, J., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) · Nucleic Acids Res. · doi:10.1093/nar/gku1177 · Cited by 1,011 · see citing works
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
Köhler, S., Doelken, S., Mungall, C. J., Bauer, S., Firth, H., Bailleul-Forestier, I., Black, G., Brown, D. L., Brudno, M., Campbell, J., et al. (2013) · Nucleic Acids Res. · doi:10.1093/nar/gkt1026 · Cited by 840 · see citing works
Self-citationWhetzel, P. L., Noy, N. F., Shah, N. H., Alexander, P. R., Nyulas, C. I., Tudorache, T., & Musen, M. A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr469 · Cited by 793 · see citing works
Rare-disease genetics in the era of next-generation sequencing: discovery to translation
Boycott, K. M., Vanstone, M. R., Bulman, D. E., & MacKenzie, A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3555 · Cited by 760 · see citing works
Gene: a gene-centered information resource at NCBI
Brown, G., Hem, V., Katz, K., Ovetsky, M., Wallin, C., Ermolaeva, O. D., Tolstoy, I., Tatusova, T. A., Pruitt, K. D., Maglott, D. R., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1055 · Cited by 706 · see citing works
Clinical Diagnostics in Human Genetics with Semantic Similarity Searches in Ontologies
Köhler, S., Schulz, M. H., Krawitz, P., Bauer, S., Dölken, S., Ott, C. E., Mundlos, C., Horn, D., Mundlos, S., & Robinson, P. N. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.09.003 · Cited by 590 · see citing works
Self-citationLiu, X., Jian, X., & Boerwinkle, E. (2013) · Human Mutation · doi:10.1002/humu.22376 · Cited by 580 · see citing works
Soden, S. E., Saunders, C., Willig, L. K., Farrow, E., Smith, L. D., Petrikin, J. E., LePichon, J.-B., Miller, N., Thiffault, I., Dinwiddie, D. L., et al. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3010076 · Cited by 528 · see citing works
Deep phenotyping for precision medicine
Robinson, P. N. (2012) · Human Mutation · doi:10.1002/humu.22080 · Cited by 471 · see citing works
Self-citationHagman, K. D. F., Shahmirzadi, L., El‐Khechen, D., Powis, Z., Chao, E., Davis, B. T., Baxter, R. M., Zeng, W., Mroske, C., Parra, M. C., et al. (2014) · Genetics in Medicine · doi:10.1038/gim.2014.154 · Cited by 469 · see citing works
Disease gene identification strategies for exome sequencing
Gilissen, C., Hoischen, A., Brunner, H. G., & Veltman, J. A. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2011.258 · Cited by 460 · see citing works
O'Rawe, J., Jiang, T., Sun, G., Wu, Y., Wang, W., Hu, J., Bodily, P., Tian, L., Hakonarson, H. H., Johnson, W. E., et al. (2013) · Genome Medicine · doi:10.1186/gm432 · Cited by 443 · see citing works
Computational tools for prioritizing candidate genes: boosting disease gene discovery
Moreau, Y., & Tranchevent, L.-C. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3253 · Cited by 417 · see citing works
The modular nature of genetic diseases
Oti, M., & Brunner, H. G. (2006) · Clinical Genetics · doi:10.1111/j.1399-0004.2006.00708.x · Cited by 411 · see citing works
Rath, A., Olry, A., Dhombres, F., Brandt, M., Urbero, B., & Aymé, S. (2012) · Human Mutation · doi:10.1002/humu.22078 · Cited by 367 · see citing works
The National Institutes of Health Undiagnosed Diseases Program: insights into rare diseases
Gahl, W. A., Markello, T. C., Toro, C., Fajardo, K. F., Sincan, M., Gill, F., Carlson-Donohoe, H., Gropman, A., Pierson, T. M., Golas, G., et al. (2012) · Genetics in Medicine · doi:10.1038/gim.0b013e318232a005 · Cited by 291 · see citing works
Shashi, V., McConkie‐Rosell, A., Rosell, B., Schoch, K., Kasturi, V. G., McDonald, M., Jiang, Y., Xie, P., Need, A. C., & Goldstein, D. B. (2013) · Genetics in Medicine · doi:10.1038/gim.2013.99 · Cited by 290 · see citing works
Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation
Washington, N. L., Haendel, M. A., Mungall, C., Ashburner, M., Westerfield, M., & Lewis, S. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000247 · Cited by 277 · see citing works
Self-citationThe Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
Blake, J. A., Bult, C. J., Kadin, J. A., Richardson, J. E., Eppig, J. T., & the Mouse Genome Database Group (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1008 · Cited by 263 · see citing works
Koscielny, G., Yaikhom, G., Iyer, V., Meehan, T. F., Morgan, H., Atienza-Herrero, J., Blake, A., Chen, C.-K., Easty, R., Fenza, A. D., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt977 · Cited by 262 · see citing works
Self-citationŻemojtel, T., Köhler, S., Mackenroth, L., Jäger, M., Hecht, J., Krawitz, P. M., Graul-Neumann, L. M., Doelken, S. C., Ehmke, N., Spielmann, M., et al. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3009262 · Cited by 256 · see citing works
Self-citationPhenoTips: Patient Phenotyping Software for Clinical and Research Use
Gîrdea, M., Dumitriu, S., Fiume, M., Bowdin, S. C., Boycott, K. M., Chénier, S., Chitayat, D. A., Faghfoury, H., Meyn, M. S., Ray, P. N., et al. (2013) · Human Mutation · doi:10.1002/humu.22347 · Cited by 250 · see citing works
Li, M., Gui, H., Kwan, J. S. H., Bao, S., & Sham, P. C. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1257 · Cited by 247 · see citing works
A probabilistic disease-gene finder for personal genomes.Preprint
Yandell, M., Huff, C., Hu, H., Singleton, M., Moore, B., Xing, J.-C., Jorde, L., & Reese, M. G. (2011) · Genome Research · doi:10.1101/gr.123158.111 · Cited by 210 · see citing works
Singleton, M., Guthery, S. L., Voelkerding, K. V., Chen, K., Kennedy, B., Margraf, R. L., Durtschi, J., Eilbeck, K. L., Reese, M. G., Jorde, L. B., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.03.010 · Cited by 186 · see citing works
Three-stage quality control strategies for DNA re-sequencing data
Guo, Y. P., Ye, F., Sheng, Q., Clark, T. A., & Samuels, D. C. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbt069 · Cited by 178 · see citing works
DeNovoGear: de novo indel and point mutation discovery and phasing
Ramu, A., Noordam, M. J., Schwartz, R. S., Wüster, A., Hurles, M. E., Cartwright, R. A., & Conrad, D. F. (2013) · Nature Methods · doi:10.1038/nmeth.2611 · Cited by 172 · see citing works
The Characterization of Twenty Sequenced Human Genomes
Pelak, K., Shianna, K., Ge, D., Maia, J., Zhu, M., Smith, J. P., Cirulli, E., Fellay, J., Dickson, S., Gumbs, C., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001111 · Cited by 168 · see citing works
eXtasy: variant prioritization by genomic data fusion
Sifrim, A., Popovic, D. D., Tranchevent, L.-C., Ardeshirdavani, A., Sakai, R., Könings, P., Vermeesch, J. R., Aerts, J. A., Moor, B. D., & Moreau, Y. (2013) · Nature Methods · doi:10.1038/nmeth.2656 · Cited by 163 · see citing works
Phen-Gen: combining phenotype and genotype to analyze rare disorders
Javed, A., Agrawal, S., & Ng, P. C. (2014) · Nature Methods · doi:10.1038/nmeth.3046 · Cited by 143 · see citing works
Li, M., Kwan, J. S. H., Bao, S., Yang, W., Ho, S., Song, Y., & Sham, P. C. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003143 · Cited by 139 · see citing works
PhenoDigm: analyzing curated annotations to associate animal models with human diseases
Smedley, D. P., Oellrich, A., Köhler, S., et al. (2013) · Database · doi:10.1093/database/bat025 · Cited by 137 · see citing works
Self-citationThe Ontology Lookup Service: bigger and better
Cote, R., Reisinger, F., Martens, L., Barsnes, H., Vizcaíno, J. A., & Hermjakob, H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq331 · Cited by 136 · see citing works
Requena, T., Cabrera, S., Martín‐Sierra, C., Price, S. D., Lysakowski, A., & Lopez-Escamez, J. A. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu524 · Cited by 128 · see citing works
York platelet syndrome is a CRAC channelopathy due to gain-of-function mutations in STIM1
Markello, T. C., Chen, D., Kwan, J. Y., Horkayne‐Szakaly, I., Morrison, A., Šimáková, O., Marić, I., Lozier, J. N., Cullinane, A. R., Kilo, T., et al. (2014) · Molecular Genetics and Metabolism · doi:10.1016/j.ymgme.2014.12.307 · Cited by 113 · see citing works
Self-citationBone, W. P., Washington, N. L., Buske, O. J., Adams, D. R., Davis, J., Draper, D. D., Flynn, E. D., Gîrdea, M., Godfrey, R. A., Golas, G. A., et al. (2015) · Genetics in Medicine · doi:10.1038/gim.2015.137 · Cited by 103 · see citing works
Self-citationStrategies for exome and genome sequence data analysis in disease‐gene discovery projects
Robinson, P. N., Krawitz, P. M., & Mundlos, S. (2011) · Clinical Genetics · doi:10.1111/j.1399-0004.2011.01713.x · Cited by 98 · see citing works
Self-citationSmedley, D. P., Köhler, S., Czeschik, J. C., Amberger, J. S., Bocchini, C. A., Hamosh, A., Veldboer, J., Żemojtel, T., & Robinson, P. N. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu508 · Cited by 97 · see citing works
Self-citationA Novel Null Homozygous Mutation Confirms CACNA2D2 as a Gene Mutated in Epileptic Encephalopathy
Pippucci, T., Parmeggiani, A., Palombo, F., Maresca, A., Angius, A., Crisponi, L., Cucca, F., Liguori, R., Valentino, M. L., Seri, M., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0082154 · Cited by 93 · see citing works
Entity/quality-based logical definitions for the human skeletal phenome using PATO
Gkoutos, G. V., Mungall, C., Doelken, S. C., Ashburner, M., Lewis, S., Hancock, J. M., Schofield, P. N., Köhler, S., & Robinson, P. N. (2009) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/iembs.2009.5333362 · Cited by 85 · see citing works
Self-citationKöhler, S., Doelken, S. C., Ruef, B. J., Bauer, S., Washington, N. L., Westerfield, M., Gkoutos, G. V., Schofield, P. N., Smedley, D. P., Lewis, S., et al. (2013) · F1000Research · doi:10.12688/f1000research.2-30.v2 · Cited by 83 · see citing works
Self-citationSmith, K. R., Bromhead, C. J., Hildebrand, M. S., Shearer, A. E., Lockhart, P. J., Najmabadi, H., Leventer, R. J., McGillivray, G., Amor, D. J., Smith, R. J., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-r85 · Cited by 81 · see citing works
Jannovar: A Java Library for Exome Annotation
Jäger, M., Wang, K., Bauer, S., Smedley, D. P., Krawitz, P. M., & Robinson, P. N. (2014) · Human Mutation · doi:10.1002/humu.22531 · Cited by 77 · see citing works
Self-citationHe, Z., O’Roak, B. J., Smith, J. D., Wang, G. T., Hooker, S. E., Santos‐Cortez, R. L. P., Li, B., Kan, M., Krumm, N., Nickerson, D. A., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.11.021 · Cited by 73 · see citing works
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio
Slyke, C. E. V., Bradford, Y. M., Westerfield, M., & Haendel, M. A. (2014) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-5-12 · Cited by 68 · see citing works
Self-citationMasino, A. J., DeChene, E. T., Dulik, M. C., et al. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-248 · Cited by 59 · see citing works
Finding Disease Variants in Mendelian Disorders By Using Sequence Data: Methods and Applications
Ionita‐Laza, I., Makarov, V., Yoon, S. C., Raby, B. A., Buxbaum, J. D., Nicolae, D. L., & Lin, X. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.003 · Cited by 46 · see citing works
Alemán, A., Garcia‐García, F., Salavert, F., Medina, I., & Dopazo, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku407 · Cited by 40 · see citing works
Coutant, S., Cabot, C., Lefebvre, A., Léonard, M., Prieur-Gaston, É., Campion, D., Thierry Lecroq, B., & Dauchel, H. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-s14-s9 · Cited by 30 · see citing works
Sifrim, A., Houdt, J. V., Tranchevent, L., Nowakowska, B., Sakai, R., Pavlopoulos, G., Devriendt, K., Vermeesch, J., Moreau, Y., & Aerts, J. (2012) · Genome Medicine · doi:10.1186/gm374 · Cited by 29 · see citing works
Lee, I., Lee, K., Hsing, M., Choe, Y., Park, J., Kim, S. H., Bohn, J. M., Neu, M. B., Hwang, K., Green, R. C., et al. (2014) · Human Mutation · doi:10.1002/humu.22520 · Cited by 23 · see citing works
Phenomics and the Interpretation of Personal Genomes
Petrovski, S., & Goldstein, D. B. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3010272 · Cited by 16 · see citing works
The influence of disease categories on gene candidate predictions from model organism phenotypes
Oellrich, A., Koehler, S., Washington, N. L., Sanger Mouse Genetic Project, Mungall, C., Lewis, S., Haendel, M. A., Robinson, P. N., & Smedley, D. P. (2014) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-5-s1-s4 · Cited by 13 · see citing works
Self-citationCorpas, M. (2013) · Source Code for Biology and Medicine · doi:10.1186/1751-0473-8-13 · Cited by 10 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [78]Washington NL How good is your phenotyping? Methods for quality assessment Proceedings of Phenotype Day 2014@ISMB 2014 http://phenoday2014.bio-lark.org/pdf/6.pdf 2014
Cited by
Sorted by citations
100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care — Preliminary Report
The 100, 0. G. P. P. I. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2035790 · Cited by 716 · see citing works
Mungall, C. J., McMurry, J. A., Köhler, S., Balhoff, J. P., Borromeo, C., Brush, M., Carbon, S., Conlin, T., Dunn, N., Engelstad, M., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1128 · Cited by 441 · see citing works
Self-citationSmedley, D., Schubach, M., Jacobsen, J. O. B., Köhler, S., Zemojtel, T., Spielmann, M., Jäger, M., Hochheiser, H., Washington, N. L., McMurry, J. A., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.07.005 · Cited by 283 · see citing works
Self-citationDeelen, P., van Dam, S., Herkert, J. C., Karjalainen, J. M., Brugge, H., Abbott, K. M., van Diemen, C. C., van der Zwaag, P. A., Gerkes, E. H., Zonneveld-Huijssoon, E., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10649-4 · Cited by 138 · see citing works
AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature
Birgmeier, J., Haeussler, M., Deisseroth, C. A., Steinberg, E. H., Jagadeesh, K. A., Ratner, A. J., Guturu, H., Wenger, A. M., Diekhans, M. E., Stenson, P. D., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aau9113 · Cited by 118 · see citing works
Network analysis reveals rare disease signatures across multiple levels of biological organization
Buphamalai, P., Kokotovic, T., Nagy, V., & Menche, J. (2021) · Nature Communications · doi:10.1038/s41467-021-26674-1 · Cited by 95 · see citing works
Jagadeesh, K. A., Birgmeier, J., Guturu, H., Deisseroth, C. A., Wenger, A. M., Bernstein, J. A., & Bejerano, G. (2019) · Genetics in Medicine · doi:10.1038/s41436-018-0072-y · Cited by 56 · see citing works
AI-MARRVEL — A Knowledge-Driven AI System for Diagnosing Mendelian Disorders
Mao, D., Liu, C., Wang, L., AI-Ouran, R., Deisseroth, C., Pasupuleti, S., Kim, S. Y., Li, L., Rosenfeld, J. A., Meng, L., et al. (2024) · NEJM AI · doi:10.1056/aioa2300009 · Cited by 51 · see citing works
A Census of Disease Ontologies
Haendel, M. A., McMurry, J. A., Relevo, R., Mungall, C. J., Robinson, P. N., & Chute, C. G. (2018) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-080917-013459 · Cited by 49 · see citing works
Self-citationVIPdb, a genetic variant impact predictor database
Hu, Z., Yu, C., Furutsuki, M., Andreoletti, G., Ly, M., Hoskins, R., Adhikari, A. N., & Brenner, S. E. (2019) · Human Mutation · doi:10.1002/humu.23858 · Cited by 37 · see citing works
Few shot learning for phenotype-driven diagnosis of patients with rare genetic diseases
Alsentzer, E., Li, M. M., Kobren, S. N., Noori, A., Undiagnosed Diseases Network, Kohane, I. S., & Zitnik, M. (2025) · npj Digital Medicine · doi:10.1038/s41746-025-01749-1 · Cited by 54 · see citing works
Simulation of undiagnosed patients with novel genetic conditions
Alsentzer, E., Finlayson, S. G., Li, M. M., Undiagnosed Diseases Network, Kobren, S. N., & Kohane, I. S. (2023) · Nature Communications · doi:10.1038/s41467-023-41980-6 · Cited by 10 · see citing works
InpherNet accelerates monogenic disease diagnosis using patients’ candidate genes’ neighbors
Yoo, B., Birgmeier, J., Bernstein, J. A., & Bejerano, G. (2021) · Genetics in Medicine · doi:10.1038/s41436-021-01238-2 · Cited by 4 · see citing works
- Authors
- Smedley, D., Jacobsen, J. O. B., Jäger, M., Köhler, S., Holtgrewe, M., Schubach, M., Siragusa, E., Zemojtel, T., Buske, O. J., Washington, N. L., Bone, W. P., Haendel, M. A., & Robinson, P. N.
- Affiliations
- Wellcome Sanger Institute (GB)
- Berlin-Brandenburger Centrum für Regenerative Therapien (DE)
- Charité – Universitätsmedizin Berlin (DE)
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE)
- University of Toronto (CA)
- Lawrence Berkeley National Laboratory (US)
- National Institutes of Health (US)
- Oregon Health & Science University (US)
- Corresponding author
- Robinson, Peter N
- ORCID
- Venue
- Nature Protocols
- Published
- 2015-11-12
- Volume
- 10
- Issue
- 12
- Pages
- 2004-2015
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- PMC
- PMC5467691
- OpenAlex
- W2246559112
- Cited by
- 445
- References
- 78
- Citations by year
- 2026: 62 · 2025: 47 · 2024: 60 · 2023: 46 · 2022: 56 · 2021: 36 · 2020: 33 · 2019: 44 · 2018: 26 · 2017: 18 · 2016: 14 · 2015: 2
- FWCI
- 14.14
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Protocols (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (R24OD011883)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Exomiser, disease gene discovery, monogenic disorders, differential diagnosis, variant prioritization, exome sequencing, protein-protein interaction network, variant pathogenicity prediction, pedigree analysis
- MeSH terms
- Genetic Testing, Humans, Software, Sequence Analysis, DNA, High-Throughput Nucleotide Sequencing, Exome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
