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Torkamani, Ali
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Torkamani, Ali

Faculty Member
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Positions

  • 2017 - Associate Professor (Joint Appointment), Translational Institute , Scripps Research
  • 2017 - Associate Professor (Joint Appointment), Integrative Structural and Computational Biology (ISCB) , Scripps Research
  • 2017 - Associate Professor, Molecular Medicine , Scripps Research
  • 2007 - Faculty Member, Skaggs Graduate School of Chemical and Biological Sciences , Scripps Research
  • 2017 Assistant Professor of MEM (Joint Appointment), Translational Institute , Scripps Research
  • 2017 Assistant Professor of MEM (Joint Appointment), Integrative Structural and Computational Biology (ISCB) , Scripps Research
  • 2017 Assistant Professor of MEM, Molecular Medicine , Scripps Research
  • 2013 - 2017 Assistant Professor of MEM, Integrative Structural and Computational Biology (ISCB) , Scripps Research
  • 2007 - 2017 Assistant Professor, Translational Institute , Scripps Research
  • 2007 - 2012 Assistant Professor of MEM, Molecular and Experimental Medicine (MEM) , Scripps Research
Dr. Ali Torkamani applies a systems biology framework to analysis and integration of numerous types of genomic data, including gene expression, mutation, and epigenetic information.

Research Areas research areas

  • Genetics
  • Genomics
  • Networks

Contact

  • atorkama@scripps.edu

Websites

  • Ali Torkamani, Ph.D.
  • Laboratory Website
  • Publications
  • Research
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Publications

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    • Bandres-Ciga, S., Saez-Atienzar, S., Kim, J. J., Makarious, M. B., Faghri, F., Diez-Fairen, M., Iwaki, H., Leonard, H., Botia, J., Ryten, M., Hernandez, D., Gibbs, J. R., et al. Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease Acta Neuropathologica  2020  DOI:10.1007/s00401-020-02181-3  PMID:32601912
    • Deguchi, H., Shukla, M., Hayat, M., Torkamani, A., Elias, D. J., Griffin, J. H. Novel exomic rare variants associated with venous thrombosis British Journal of Haematology  2020  DOI:10.1111/bjh.16613  PMID:32232851
    • Chen, P. B., Black, A. S., Sobel, A. L., Zhao, Y. N., Mukherjee, P., Molparia, B., Moore, N. E., Muench, G. R. A., Wu, J. J., Chen, W. X., Pinto, A. F. M., Maryanoff, B. E., et al. Directed remodeling of the mouse gut microbiome inhibits the development of atherosclerosis Nature Biotechnology  2020  DOI:10.1038/s41587-020-0549-5  PMID:32541956
    • Salfati, E. L., Spencer, E. G., Topol, S. E., Muse, E. D., Rueda, M., Lucas, J. R., Wagner, G. N., Campman, S., Topol, E. J., Torkamani, A. Re-analysis of whole-exome sequencing data uncovers novel diagnostic variants and improves molecular diagnostic yields for sudden death and idiopathic diseases Genome Medicine  2019 11  DOI:10.1186/s13073-019-0702-2  PMID:31847883  PMCID:PMC6916453
    • Kang, S. K., Vanoye, C. G., Misra, S. N., Echevarria, D. M., Calhoun, J. D., O'Connor, J. B., Fabre, K. L., McKnight, D., Demmer, L., Goldenberg, P., Grote, L. E., Thiffault, I., et al. Spectrum of K(V)2.1 dysfunction in KCNB1-associated neurodevelopmental disorders Annals of Neurology  2019  DOI:10.1002/ana.25607  PMID:31600826
    • Dias, R., Torkamani, A. Artificial intelligence in clinical and genomic diagnostics Genome Medicine  2019 11  DOI:10.1186/s13073-019-0689-8  PMID:31744524
    • Torkamani, A., Topol, E. Polygenic risk scores expand to obesity Cell  2019 177:518-520  DOI:10.1016/j.cell.2019.03.051  PMID:31002792
    • Kumar, A., Thomas, S. K., Wong, K. C., Lo Sardo, V., Cheah, D. S., Hou, Y. H., Placone, J. K., Tenerelli, K. P., Ferguson, W. C., Torkamani, A., Topol, E. J., Baldwin, K. K., et al. Mechanical activation of noncoding-RNA-mediated regulation of disease-associated phenotypes in human cardiomyocytes Nature Biomedical Engineering  2019 3:137-146  DOI:10.1038/s41551-018-0344-5
    • Zou, J., Huss, M., Abid, A., Mohammadi, P., Torkamani, A., Telenti, A. A primer on deep learning in genomics Nature Genetics  2019 51:12-18  DOI:10.1038/s41588-018-0295-5  PMID:30478442
    • Deiss, T. C., Vadnais, M., Wang, F., Chen, P. L., Torkamani, A., Mwangi, W., Lefranc, M. P., Criscitiello, M. F., Smider, V. V. Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies Cellular & Molecular Immunology  2019 16:64-75  DOI:10.1038/cmi.2017.117  PMID:29200193  PMCID:PMC6318308
    • Rubanovich, C. K., Cheung, C., Torkamani, A., Bloss, C. S. Physician communication of genomic results in a diagnostic odyssey case series Pediatrics  2019 143:S44-S53  DOI:10.1542/peds.2018-1099I  PMID:30600271
    • Lo Sardo, V., Chubukov, P., Ferguson, W., Kumar, A., Teng, E. L., Duran, M., Zhang, L., Cost, G., Engler, A. J., Urnov, F., Topol, E. J., Torkamani, A., et al. Unveiling the role of the most impactful cardiovascular risk locus through haplotype editing Cell  2018 175:1796-1810  DOI:10.1016/j.cell.2018.11.014  PMID:30528432
    • Pacheu-Grau, D., Callegari, S., Emperador, S., Thompson, K., Aich, A., Topol, S. E., Spencer, E. G., McFarland, R., Ruiz-Pesini, E., Torkamani, A., Taylor, R. W., Montoya, J., et al. Mutations of the mitochondrial carrier translocase channel subunit TIM22 cause early-onset mitochondrial myopathy Human Molecular Genetics  2018 27:4135-4144  DOI:10.1093/hmg/ddy305  PMID:30452684  PMCID:PMC6240735
    • Torkamani, A. Drilling for insight: forecasting phenotype from genotype Trends in Genetics  2018 34:821-822  DOI:10.1016/j.tig.2018.09.001  PMID:30220472
    • Torkamani, A., Topol, E. Your genome, on demand MIT Technology Review  2018 121:20-21
    • Torkamani, A., Wineinger, N. E., Topol, E. J. The personal and clinical utility of polygenic risk scores Nature Reviews Genetics  2018 19:581-590  DOI:10.1038/s41576-018-0018-x  PMID:29789686
    • Molparia, B., Schrader, B. N., Cohen, E., Wagner, J. L., Gupta, S. R., Gould, S., Hwynn, N., Spencer, E. G., Torkamani, A. Combined accelerometer and genetic analysis to differentiate essential tremor from Parkinson's disease Peerj  2018 6  DOI:10.7717/peerj.5308  PMID:30042899  PMCID:PMC6055592
    • Muse, E. D., Torkamani, A., Topol, E. J. When genomics goes digital Lancet  2018 391:2405-2405  DOI:10.1038/s41576-018-0018-x  PMID:29916375
    • Molparia, B., Oliveira, G., Wagner, J. L., Spencer, E. G., Torkamani, A. A feasibility study of colorectal cancer diagnosis via circulating tumor DNA derived CNV detection PLoS One  2018 13  DOI:10.1371/journal.pone.0196826  PMID:29791457  PMCID:PMC5965833
    • Tsunemoto, R., Lee, S., Sztics, A., Chubukov, P., Sokolova, I., Blanchard, J. W., Eadel, K. T., Bruggemann, J., Wu, C. L., Torkamani, A., Sanna, P. P., Baldwin, K. K. Diverse reprogramming codes for neuronal identity Nature  2018 557:375-380  DOI:10.1038/s41586-018-0103-5  PMID:29743677
    • Konijeti, G., Molparia, B., Akhtar, E., Wang, X., Chang, J., Lewis, J., Chandrasekaran, A., Groven, S., Oliveira, G., Torkamani, A. P539 Transcriptional changes in mucosal inflammation associated with an autoimmune protocol diet for ulcerative colitis Journal of Crohn's and Colitis  2018 12:S378-S378  DOI:10.1093/ecco-jcc/jjx180.666
    • Konijeti, G. G., Kim, N., Lewis, J. D., Groven, S., Chandrasekaran, A., Grandhe, S., Diamant, C., Singh, E., Oliveira, G., Wang, X. Y., Molparia, B., Torkamani, A. Efficacy of the autoimmune protocol diet for inflammatory bowel disease Inflammatory Bowel Diseases  2017 23:2054-2060  DOI:10.1097/mib.0000000000001221  PMID:28858071  PMCID:PMC5647120
    • Jones, M. C., Topol, S. E., Rueda, M., Oliveira, G., Phillips, T., Spencer, E. G., Torkamani, A. Mutation of WIF1: a potential novel cause of a Nail-Patella-like disorder Genetics in Medicine  2017 19:1179-1183  DOI:10.1038/gim.2017.20  PMID:28383544  PMCID:PMC5629099
    • Muse, E. D., Kramer, E. R., Wang, H. Y., Barrett, P., Parviz, F., Novotny, M. A., Lasken, R. S., Jatkoe, T. A., Oliveira, G., Peng, H. F., Lu, J., Connelly, M. C., et al. A whole blood molecular signature for acute myocardial infarction Scientific Reports  2017 7  DOI:10.1038/s41598-017-12166-0  PMID:28947747  PMCID:PMC5612952
    • Torkamani, A., Andersen, K. G., Steinhubl, S. R., Topol, E. J. High-Definition Medicine Cell  2017 170:828-843  DOI:10.1016/j.cell.2017.08.007  PMID:28841416
    • Rueda, M., Torkamani, A. SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort BMC Bioinformatics  2017 18  DOI:10.1186/s12859-017-1778-6  PMID:28821228  PMCID:PMC5563004
    • Molparia, B., Nichani, E., Torkamani, A. Assessment of circulating copy number variant detection for cancer screening PLoS One  2017 12  DOI:10.1371/journal.pone.0180647  PMID:28686671  PMCID:PMC5501586
    • Torkamani, A. Postmortem genetic testing for sudden unexpected death in reply JAMA-Journal of the American Medical Association  2017 317:321-321  DOI:10.1001/jama.2016.19277  PMID:28114548
    • Lo Sardo, V., Ferguson, W., Erikson, G. A., Topol, E. J., Baldwin, K. K., Torkamani, A. Influence of donor age on induced pluripotent stem cells Nature Biotechnology  2017 35:69-74  DOI:10.1038/nbt.3749  PMID:27941802
    • Boeldt, D. L., Cheung, C., Ariniello, L., Darst, B. F., Topol, S., Schork, N. J., Philis-Tsimikas, A., Torkamani, A., Fortmann, A. L., Bloss, C. S. Patient perspectives on whole-genome sequencing for undiagnosed diseases Personalized Medicine  2017 14:17-25  DOI:10.2217/pme-2016-0050
    • Torkamani, A., Muse, E. D., Spencer, E. G., Rueda, M., Wagner, G. N., Lucas, J. R., Topol, E. J. Molecular autopsy for sudden unexpected death JAMA-Journal of the American Medical Association  2016 316:1492-1494  PMID:27727376
    • Erikson, G. A., Bodian, D. L., Rueda, M., Molparia, B., Scott, E. R., Scott-Van Zeeland, A. A., Topol, S. E., Wineinger, N. E., Niederhuber, J. E., Topol, E. J., Torkamani, A. Whole-genome sequencing of a healthy aging cohort Cell  2016 165:1002-1011  DOI:10.1016/j.cell.2016.03.022  PMID:27114037  PMCID:PMC4860090
    • Hazen, J. L., Faust, G. G., Rodriguez, A. R., Ferguson, W. C., Shumilina, S., Clark, R. A., Boland, M. J., Martin, G., Chubukov, P., Tsunemoto, R. K., Torkamani, A., Kupriyanov, S., et al. The complete genome sequences, unique mutational spectra, and developmental potency of adult neurons revealed by cloning Neuron  2016 89:1223-1236  DOI:10.1016/j.neuron.2016.02.004  PMID:26948891  PMCID:PMC4795965
    • Sieberts, S. K., Zhu, F., Garcia-Garcia, J., Stahl, E., Pratap, A., Pandey, G., Pappas, D., Aguilar, D., Anton, B., Bonet, J., Eksi, R., Fornes, O., et al. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis Nature Communications  2016 7  DOI:10.1038/ncomms12460  PMID:27549343  PMCID:PMC4996969
    • Xin, J., Mark, A., Afrasiabi, C., Tsueng, G., Juchler, M., Gopal, N., Stupp, G. S., Putman, T. E., Ainscough, B. J., Griffith, O. L., Torkamani, A., Whetzel, P. L., et al. High-performance web services for querying gene and variant annotation Genome Biology  2016 17  DOI:10.1186/s13059-016-0953-9  PMID:27154141  PMCID:PMC4858870
    • Chen, D. H., Meneret, A., Friedman, J. R., Korvatska, O., Gad, A., Bonkowski, E. S., Stessman, H. A., Doummar, D., Mignot, C., Anheim, M., Bernes, S., Davis, M. Y., et al. ADCY5-related dyskinesia: Broader spectrum and genotype-phenotype correlations Neurology  2015 85:2026-2035  DOI:10.1212/WNL.0000000000002058  PMID:26537056  PMCID:PMC4676753
    • Bloss, C. S., Zeeland, A. A. S. V., Topol, S. E., Darst, B. F., Boeldt, D. L., Erikson, G. A., Bethel, K. J., Bjork, R. L., Friedman, J. R., Hwynn, N., Patay, B. A., Pockros, P. J., et al. A genome sequencing program for novel undiagnosed diseases Genetics in Medicine  2015 17:995-1001  DOI:10.1038/gim.2015.21  PMID:25790160  PMCID:PMC4575596
    • Molparia, B., Pham, P. H., Torkamani, A. Symptom-driven idiopathic disease gene identification Genetics in Medicine  2015 17:859-865  DOI:10.1038/gim.2014.202  PMID:25590976  PMCID:PMC4861313
    • Erikson, G. A., Deshpande, N., Kesavan, B. G., Torkamani, A. SG-ADVISER CNV: copy-number variant annotation and interpretation Genetics in Medicine  2015 17:714-718  DOI:10.1038/gim.2014.180  PMID:25521334  PMCID:PMC4886732
    • Pham, P. H., Shipman, W. J., Erikson, G. A., Schork, N. J., Torkamani, A. Scripps Genome ADVISER: annotation and distributed variant interpretation SERver PLoS One  2015 10  DOI:10.1371/journal.pone.0116815  PMID:25706643  PMCID:PMC4338027
    • Topol, E. J., Steinhubl, S. R., Torkamani, A. Digital medical tools and sensors JAMA-Journal of the American Medical Association  2015 313:353-354  DOI:10.1001/jama.2014.17125  PMID:25626031  PMCID:PMC4751024
    • Emamjomeh, A., Goliaei, B., Torkamani, A., Ebrahimpour, R., Mohammadi, N., Parsian, A. Protein-protein interaction prediction by combined analysis of genomic and conservation information Genes & Genetic Systems  2014 89:259-272  PMID:25948120
    • Torkamani, A., Bersell, K., Jorge, B. S., Bjork Jr., R. L., Friedman, J. R., Bloss, C. S., Cohen, J., Gupta, S., Naidu, S., Vanoye, C. G., George Jr., A. L., Kearney, J. A. De novo KCNB1 mutations in epileptic encephalopathy Annals of Neurology  2014 76:529-540  DOI:10.1002/ana.24263  PMID:25164438  PMCID:PMC4192091
    • Belani, R., Oliveira, G., Erikson, G. A., Ra, S., Schechter, M. S., Lee, J. K., Shipman, W. J., Haaser, S. M., Torkamani, A. ASXL1 and DNMT3A mutation in a cytogenetically normal B3 thymoma Oncogenesis  2014 3:e111  DOI:10.1038/oncsis.2014.25  PMID:25000259  PMCID:PMC4150211
    • Chen, Y. Z., Friedman, J. R., Chen, D. H., Chan, G. C. K., Bloss, C. S., Hisama, F. M., Topol, S. E., Carson, A. R., Pham, P. H., Bonkowski, E. S., Scott, E. R., Lee, J. K., et al. Gain-of-function ADCY5 mutations in familial dyskinesia with facial myokymia Annals of Neurology  2014 75:542-549  DOI:10.1002/ana.24119  PMID:24700542  PMCID:PMC4457323
    • Brownstein, C. A., Beggs, A. H., Homer, N., Merriman, B., Neupert, P., Wang, J. J., Yu, T. W., Flannery, K. C., DeChene, E. T., Towne, M. C., Savage, S. K., Price, E. N., Holm, I. A., Luquette, L. J., et al. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge Genome Biology  2014 15:R53  DOI:10.1186/gb-2014-15-3-r53  PMID:24667040  PMCID:PMC4073084
    • Scott-Van Zeeland, A. A., Bloss, C. S., Tewhey, R., Bansal, V., Torkamani, A., Libiger, O., Duvvuri, V., Wineinger, N., Galvez, L., Darst, B. F., Smith, E. N., Carson, A., et al. Evidence for the role of EPHX2 gene variants in anorexia nervosa Molecular Psychiatry  2014 19:724-732  DOI:10.1038/mp.2013.91  PMID:23999524  PMCID:PMC3852189
    • Larman, H. B., Scott, E. R., Wogan, M., Oliveira, G., Torkamani, A., Schultz, P. G. Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay Nucleic Acids Research  2014 42:9146-9157  DOI:10.1093/nar/gku636  PMID:25063296  PMCID:PMC4132746
    • Choi, N. M., Loguercio, S., Verma-Gaur, J., Degner, S. C., Torkamani, A., Su, A. I., Oltz, E. M., Artyomov, M., Feeney, A. J. Deep sequencing of the murine Igh repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies Journal of Immunology  2013 191:2393-2402  DOI:10.4049/jimmunol.1301279  PMID:23898036  PMCID:PMC3778908
    • Wang, F., Ekiert, D. C., Ahmad, I., Yu, W., Zhang, Y., Bazirgan, O., Torkamani, A., Raudsepp, T., Mwangi, W., Criscitiello, M. F., Wilson, I. A., Schultz, P. G., et al. Reshaping antibody diversity Cell  2013 153:1379-1393  DOI:10.1016/j.cell.2013.04.049  PMID:23746848  PMCID:PMC4007204
    • Schork, A. J., Thompson, W. K., Pham, P., Torkamani, A., Roddey, J. C., Sullivan, P. F., Kelsoe, J. R., O'Donovan, M. C., Furberg, H., The Tobacco & Genetics Consortium, The Bipolar Disorder Psychiatric Genomics Consortium, Schizophrenia Psychiatric Genomics Consortium, et al. All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs PLoS Genetics  2013 9:e1003449  DOI:10.1371/journal.pgen.1003449  PMID:23637621  PMCID:PMC3636284
    • Shih, H. Y., Verma-Gaur, J., Torkamani, A., Feeney, A. J., Galjart, N., Krangel, M. S. Tcra gene recombination is supported by a Tcra enhancer- and CTCF-dependent chromatin hub Proceedings of the National Academy of Sciences of the United States of America  2012 109:E3493-E3502  DOI:10.1073/pnas.1214131109  PMID:23169622  PMCID:PMC3528579
    • Verma-Gaur, J., Torkamani, A., Schaffer, L., Head, S. R., Schork, N. J., Feeney, A. J. Noncoding transcription within the Igh distal V-H region at pair elements affects the 3d structure of the Igh locus in pro-B cells Proceedings of the National Academy of Sciences of the United States of America  2012 109:17004-17009  DOI:10.1073/pnas.1208398109  PMID:23027941  PMCID:PMC3479473
    • Torkamani, A., Schork, N. J. Background gene expression networks significantly enhance drug response prediction by transcriptional profiling Pharmacogenomics Journal  2012 12:446-452  DOI:10.1038/tpj.2011.35  PMID:21826086  PMCID:PMC4846279
    • Tewhey, R., Cannavino, C. R., Leake, J. A. D., Bansal, V., Topol, E. J., Torkamani, A., Bradley, J. S., Schork, N. J. Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300 BMC Genomics  2012 13:508  DOI:10.1186/1471-2164-13-508  PMID:23009684  PMCID:PMC3598774
    • Malyshev, D. A., Dhami, K., Quach, H. T., Lavergne, T., Ordoukhanian, P., Torkamani, A., Romesberg, F. E. Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet Proceedings of the National Academy of Sciences of the United States of America  2012 109:12005-12010  DOI:10.1073/pnas.1205176109  PMID:22773812  PMCID:PMC3409741
    • Cheng, J. L., Torkamani, A., Peng, Y. J., Jones, T. M., Lerner, R. A. Plasma membrane associated transcription of cytoplasmic DNA Proceedings of the National Academy of Sciences of the United States of America  2012 109:10827-10831  DOI:10.1073/pnas.1208716109  PMID:22711823  PMCID:PMC3390847
    • Aoki-Ota, M., Torkamani, A., Ota, T., Schork, N., Nemazee, D. Skewed primary Igκ repertoire and V-J joining in C57BL/6 mice: implications for recombination accessibility and receptor editing Journal of Immunology  2012 188:2305-2315  DOI:10.4049/jimmunol.1103484  PMID:22287713  PMCID:PMC3288532
    • Torkamani, A., Scott-Van Zeeland, A. A., Topol, E. J., Schork, N. J. Annotating individual human genomes Genomics  2011 98:233-241  DOI:10.1016/j.ygeno.2011.07.006  PMID:21839162  PMCID:PMC4074010
    • Komori, H. K., LaMere, S. A., Torkamani, A., Hart, G. T., Kotsopoulos, S., Warner, J., Samuels, M. L., Olson, J., Head, S. R., Ordoukhanian, P., Lee, P. L., Link, D. R., et al. Application of microdroplet pcr for large-scale targeted bisulfite sequencing Genome Research  2011 21:1738-1745  DOI:10.1101/gr.116863.110  PMID:21757609  PMCID:PMC3202290
    • Zhang, H. K., Torkamani, A., Jones, T. M., Ruiz, D. I., Pons, J., Lerner, R. A. Phenotype-information-phenotype cycle for deconvolution of combinatorial antibody libraries selected against complex systems Proceedings of the National Academy of Sciences of the United States of America  2011 108:13456-13461  DOI:10.1073/pnas.1111218108  PMID:21825149  PMCID:PMC3158238
    • Degner, S. C., Verma-Gaur, J., Wong, T. P., Bossen, C., Iverson, G. M., Torkamani, A., Vettermann, C., Lin, Y. C., Ju, Z. L., Schulz, D., Murre, C. S., Birshtein, B. K., et al. CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells Proceedings of the National Academy of Sciences of the United States of America  2011 108:9566-9571  DOI:10.1073/pnas.1019391108  PMID:21606361  PMCID:PMC3111298
    • Pazirandeh, A., Torkamani, A., Taheri, A. Design and simulation of a neutron source based on an electron linear accelerator for bnct of skin melanoma Applied Radiation and Isotopes  2011 69:749-755  DOI:10.1016/j.apradiso.2011.01.035  PMID:21334211
    • Cheng, J. L., Torkamani, A., Grover, R., Jones, T. M., Ruiz, D. I., Schork, N. J., Quigley, M. M., Hall, F. W., Salomon, D. R., Lerner, R. A. Ectopic B-cell clusters that infiltrate transplanted human kidneys are clonal Proceedings of the National Academy of Sciences of the United States of America  2011 108:5560-5565  DOI:10.1073/pnas.1101148108  PMID:21415369  PMCID:PMC3078383
    • Tewhey, R., Bansal, V., Torkamani, A., Topol, E. J., Schork, N. J. The importance of phase information for human genomics Nature Reviews Genetics  2011 12:215-223  DOI:10.1038/nrg2950  PMID:21301473  PMCID:PMC3753045
    • Vlad, G., King, J., Chang, C. C., Liu, Z. R., Friedman, R. A., Torkamani, A. A., Suciu-Foca, N. Gene profile analysis of cd8(+) ilt3-fc induced t suppressor cells Human Immunology  2011 72:107-114  DOI:10.1016/j.humimm.2010.10.012  PMID:20974207
    • Bansal, V., Libiger, O., Torkamani, A., Schork, N. J. An application and empirical comparison of statistical analysis methods for associating rare variants to a complex phenotype Pacific Symposium on Biocomputing  2011 76-87  DOI:10.1142/9789814335058_0009  PMID:21121035
    • Chang, C. C., Vlad, G., D'Agati, V. D., Liu, Z. R., Zhang, Q. Y., Witkowski, P., Torkamani, A. A., Stokes, M. B., Ho, E. K., Cortesini, R., Suciu-Foca, N. Bcl6 is required for differentiation of ig-like transcript 3-fc-induced cd8(+) t suppressor cells Journal of Immunology  2010 185:5714-5722  DOI:10.4049/jimmunol.1001732  PMID:20935202
    • Kerkel, K., Schupf, N., Hatta, K., Pang, D., Salas, M., Kratz, A., Minden, M., Murty, V., Zigman, W. B., Mayeux, R. P., Jenkins, E. C., Torkamani, A., et al. Altered DNA methylation in leukocytes with trisomy 21 PLoS Genetics  2010 6:e1001212  DOI:10.1371/journal.pgen.1001212  PMID:21124956  PMCID:PMC2987931
    • Bansal, V., Libiger, O., Torkamani, A., Schork, N. J. Statistical analysis strategies for association studies involving rare variants Nature Reviews Genetics  2010 11:773-785  DOI:10.1038/nrg2867  PMID:20940738  PMCID:PMC3743540
    • Ota, M., Duong, B. H., Torkamani, A., Doyle, C. M., Gavin, A. L., Ota, T., Nemazee, D. Regulation of the B cell receptor repertoire and self-reactivity by BAFF Journal of Immunology  2010 185:4128-4136  DOI:10.4049/jimmunol.1002176  PMID:20817867  PMCID:PMC3263398
    • Torkamani, A., Dean, B., Schork, N. J., Thomas, E. A. Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia Genome Research  2010 20:403-412  DOI:10.1101/gr.101956.109  PMID:20197298  PMCID:PMC2847743
    • Lahiry, P., Torkamani, A., Schork, N. J., Hegele, R. A. Kinase mutations in human disease: Interpreting genotype-phenotype relationships Nature Reviews Genetics  2010 11:60-74  DOI:10.1038/nrg2707  PMID:20019687
    • Dixit, A., Yi, L., Gowthaman, R., Torkamani, A., Schork, N. J., Verkhivker, G. M. Sequence and structure signatures of cancer mutation hotspots in protein kinases PLoS One  2009 4:e7485  DOI:10.1371/journal.pone.0007485  PMID:19834613  PMCID:PMC2759519
    • Torkamani, A., Schork, N. J. Identification of rare cancer driver mutations by network reconstruction Genome Research  2009 19:1570-1578  DOI:10.1101/gr.092833.109  PMID:19574499  PMCID:PMC2752121
    • Torkamani, A., Schork, N. J. Prestige centrality-based functional outlier detection in gene expression analysis Bioinformatics  2009 25:2222-2228  DOI:10.1093/bioinformatics/btp388  PMID:19549629  PMCID:PMC2800353
    • Torkamani, A., Verkhivker, G., Schork, N. J. Cancer driver mutations in protein kinase genes Cancer Letters  2009 281:117-127  DOI:10.1016/j.canlet.2008.11.008  PMID:19081671  PMCID:PMC2905872
    • Dixit, A., Torkamani, A., Schork, N. J., Verkhivker, G. Computational modeling of structurally conserved cancer mutations in the ret and met kinases: The impact on protein structure, dynamics, and stability Biophysical Journal  2009 96:858-874  DOI:10.1016/j.bpj.2008.10.041  PMID:19186126  PMCID:PMC2716637
    • Torkamani, A., Topol, E. J., Schork, N. J. Pathway analysis of seven common diseases assessed by genome-wide association Genomics  2008 92:265-272  DOI:10.1016/j.ygeno.2008.07.011  PMID:18722519  PMCID:PMC2602835
    • Mosse, Y. P., Laudenslager, M., Longo, L., Cole, K. A., Wood, A., Attiyeh, E. F., Laquaglia, M. J., Sennett, R., Lynch, J. E., Perri, P., Laureys, G., Speleman, F., et al. Identification of alk as a major familial neuroblastoma predisposition gene Nature  2008 455:930-935  DOI:10.1038/nature07261  PMID:18724359  PMCID:PMC2672043
    • Torkamani, A., Schork, N. J. Predicting functional regulatory polymorphisms Bioinformatics  2008 24:1787-1792  DOI:10.1093/bioinformatics/btn311  PMID:18562267  PMCID:PMC2732211
    • Torkamani, A., Kannan, N., Taylor, S. S., Schork, N. J. Congenital disease snps target lineage specific structural elements in protein kinases Proceedings of the National Academy of Sciences of the United States of America  2008 105:9011-9016  DOI:10.1073/pnas.0802403105  PMID:18579784  PMCID:PMC2449356
    • Torkamani, A., Schork, N. J. Prediction of cancer driver mutations in protein kinases Cancer Research  2008 68:1675-1682  DOI:10.1158/0008-5472.can-07-5283  PMID:18339846
    • Torkamani, A., Schork, N. J. Accurate prediction of deleterious protein kinase polymorphisms Bioinformatics  2007 23:2918-2925  DOI:10.1093/bioinformatics/btm437  PMID:17855419
    • Torkamani, A., Schork, N. J. Distribution analysis of nonsynonymous polymorphisms within the human kinase gene family Genomics  2007 90:49-58  DOI:10.1016/j.ygeno.2007.03.006  PMID:17498919
    • Meyer, T. W., Walther, J. L., Pagtalunan, M. E., Martinez, A. W., Torkamani, A., Fong, P. D., Recht, N. S., Robertson, C. R., Hostetter, T. H. The clearance of protein-bound solutes by hemofiltration and hemodiafiltration Kidney International  2005 68:867-877  DOI:10.1111/j.1523-1755.2005.00469.x  PMID:16014068
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Research

research overview

  • Networks, Genetics and Genomics

    Our goal is to understand genetic mechanisms of human disease by analyzing genetic and genomic data of many types in a systems biology framework. Due to the large amount of data generated by modern high-throughput genomic technologies, it can be difficult to differentiate real biological signals from noise in different disease states, however, by considering the data as a set of connected signals organized in networks and pathways, we are able to identify consistent perturbations across biological networks and gain insight into the mechanisms underlying human disease. By identifying the genetic mechanisms of human disease, we can begin to propose strategies for disease prevention.

    Our work focuses on the genetic mechanisms of cancer and neuropsychiatric diseases through strong collaborations with other faculty, but the methods are amenable to any human diseases or even to studying other organisms. We focus on integrating mutation, gene expression, and epigenetic data, and believe that disease mechanisms, or basic signaling processes, can only be fully understood in the context of the whole biological system.

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Teaching

advisees

  • graduate advising relationship

    • Chen, Shang-Fu, Ph.D.  candidate, 2019 -
    • Chubukov, Pavel A, Ph.D.  candidate, 2012 - 2018
    • Molparia, Bhuvan, Ph.D.  candidate, 2014 - 2018
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Background

education and training

  • Ph.D. in Biomedical Sciences, University of California, San Diego 2008
  • B.S. in Chemistry, Stanford University 2003
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Contact

full name

  • Ali Torkamani

geographic location

  • Scripps California 

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