recent publications
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academic article
- Bhatt, I. S., Dias, R., Torkamani, A. Association Analysis of Candidate Gene Polymorphisms and Tinnitus in Young Musicians Otology & Neurotology 2021 42:E1203-E1212 DOI:10.1097/mao.0000000000003279 PMID:34282101
- Muse, E. D., Chen, S. F., Torkamani, A. Monogenic and Polygenic Models of Coronary Artery Disease Current Cardiology Reports 2021 23 DOI:10.1007/s11886-021-01540-0 PMID:34196841 PMCID:PMC8317496
- Chung, W. K., Brothers, K., Bradbury, A., Chanprasert, S., Orlando, L., Torkamani, A., Zierhut, H., Ritchie, M. D., Phillips, M., Schoden, J., Maiese, D., Hendershot, T., et al. Genomic medicine implementation protocols in the PhenX Toolkit: tools for standardized data collection Genetics in Medicine 2021 23:1783-1788 DOI:10.1038/s41436-021-01183-0 PMID:33972721 PMCID:PMC8108409
- Mbala-Kingebeni, P., Pratt, C., Mutafali-Ruffin, M., Pauthner, M. G., Bile, F., Nkuba-Ndaye, A., Black, A., Kinganda-Lusamaki, E., Faye, M., Aziza, A., Diagne, M. M., Mukadi, D., et al. Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease New England Journal of Medicine 2021 384:1240-1247 DOI:10.1056/NEJMoa2024670 PMID:33789012 PMCID:PMC7888312
- Han, Z., Thuy-Boun, P. S., Pfeiffer, W., Vartabedian, V. F., Torkamani, A., Teijaro, J. R., Wolan, D. W. Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome Scientific Reports 2021 11 DOI:10.1038/s41598-021-83875-w PMID:33637779 PMCID:PMC7910532
- Weissbach, S., Sys, S., Hewel, C., Todorov, H., Schweiger, S., Winter, J., Pfenninger, M., Torkamani, A., Evans, D., Burger, J., Everschor-Sitte, K., May-Simera, H. L., et al. Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines BMC Genomics 2021 22 DOI:10.1186/s12864-020-07362-8 PMID:33468057 PMCID:PMC7814447
- Dewan, R., Chia, R., Ding, J. H., Hickman, R. A., Stein, T. D., Abramzon, Y., Ahmed, S., Sabir, M. S., Portley, M. K., Tucci, A., Ibanez, K., Shankaracharya, F. N. U., et al. Article Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis Neuron 2020 109:448-460 DOI:10.1016/j.neuron.2020.11.005 PMID:33242422 PMCID:PMC7864894
- Raisaro, J. L., Marino, F., Troncoso-Pastoriza, J., Beau-Lejdstrom, R., Bellazzi, R., Murphy, R., Bernstam, E. V., Wang, H., Bucalo, M., Chen, Y., Gottlieb, A., Harmanci, A., et al. SCOR: A secure international informatics infrastructure to investigate COVID-19 Journal of the American Medical Informatics Association 2020 27:1721-1726 DOI:10.1093/jamia/ocaa172 PMID:32918447 PMCID:PMC7454652
- 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
- Norgeot, B., Quer, G., Beaulieu-Jones, B. K., Torkamani, A., Dias, R., Gianfrancesco, M., Arnaout, R., Kohane, I. S., Saria, S., Topol, E., Obermeyer, Z., Yu, B., et al. Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist Nature Medicine 2020 26:1320-1324 DOI:10.1038/s41591-020-1041-y PMID:32908275 PMCID:PMC7538196
- 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 38:1288-1297 DOI:10.1038/s41587-020-0549-5 PMID:32541956 PMCID:PMC7641989
- 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