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Ali Torkamani, Ph.D. - Publications

Affiliations: 
2008 Biomedical Sciences University of California, San Diego, La Jolla, CA 
Area:
statistical genetics of neuropschiatric disorders
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63 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Chia R, Sabir MS, Bandres-Ciga S, Saez-Atienzar S, Reynolds RH, Gustavsson E, Walton RL, Ahmed S, Viollet C, Ding J, Makarious MB, Diez-Fairen M, Portley MK, Shah Z, Abramzon Y, ... ... Torkamani A, et al. Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture. Nature Genetics. PMID 33589841 DOI: 10.1038/s41588-021-00785-3  0.315
2020 Bandres-Ciga S, Saez-Atienzar S, Kim JJ, Makarious MB, Faghri F, Diez-Fairen M, Iwaki H, Leonard H, Botia J, Ryten M, Hernandez D, Gibbs JR, Ding J, Gan-Or Z, Noyce A, ... ... Torkamani A, et al. Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease. Acta Neuropathologica. PMID 32601912 DOI: 10.1007/S00401-020-02181-3  0.315
2020 Deguchi H, Shukla M, Hayat M, Torkamani A, Elias DJ, Griffin JH. Novel exomic rare variants associated with venous thrombosis. British Journal of Haematology. PMID 32232851 DOI: 10.1111/Bjh.16613  0.322
2019 Salfati EL, Spencer EG, Topol SE, Muse ED, Rueda M, Lucas JR, Wagner GN, Campman S, Topol EJ, 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. 11: 83. PMID 31847883 DOI: 10.1186/S13073-019-0702-2  0.33
2019 Wells A, Heckerman D, Torkamani A, Yin L, Sebat J, Ren B, Telenti A, di Iulio J. Ranking of non-coding pathogenic variants and putative essential regions of the human genome. Nature Communications. 10: 5241. PMID 31748530 DOI: 10.1038/S41467-019-13212-3  0.413
2019 Dias R, Torkamani A. Artificial intelligence in clinical and genomic diagnostics. Genome Medicine. 11: 70. PMID 31744524 DOI: 10.1186/S13073-019-0689-8  0.365
2019 Kumar A, Thomas SK, Wong KC, Lo Sardo V, Cheah DS, Hou YH, Placone JK, Tenerelli KP, Ferguson WC, Torkamani A, Topol EJ, Baldwin KK, Engler AJ. Mechanical activation of noncoding-RNA-mediated regulation of disease-associated phenotypes in human cardiomyocytes. Nature Biomedical Engineering. 3: 137-146. PMID 30911429 DOI: 10.1038/S41551-018-0344-5  0.353
2019 Rubanovich CK, Cheung C, Torkamani A, Bloss CS. Physician Communication of Genomic Results in a Diagnostic Odyssey Case Series. Pediatrics. 143: S44-S53. PMID 30600271 DOI: 10.1542/Peds.2018-1099I  0.353
2018 Lo Sardo V, Chubukov P, Ferguson W, Kumar A, Teng EL, Duran M, Zhang L, Cost G, Engler AJ, Urnov F, Topol EJ, Torkamani A, Baldwin KK. Unveiling the Role of the Most Impactful Cardiovascular Risk Locus through Haplotype Editing. Cell. PMID 30528432 DOI: 10.1016/J.Cell.2018.11.014  0.323
2018 Torkamani A. Drilling for Insight: Forecasting Phenotype from Genotype. Trends in Genetics : Tig. PMID 30220472 DOI: 10.1016/J.Tig.2018.09.001  0.375
2018 Muse ED, Torkamani A, Topol EJ. When genomics goes digital. Lancet (London, England). 391: 2405. PMID 29916375 DOI: 10.1016/S0140-6736(18)31272-8  0.344
2018 Molparia B, Oliveira G, Wagner JL, Spencer EG, Torkamani A. A feasibility study of colorectal cancer diagnosis via circulating tumor DNA derived CNV detection. Plos One. 13: e0196826. PMID 29791457 DOI: 10.1371/Journal.Pone.0196826  0.312
2018 Torkamani A, Wineinger NE, Topol EJ. The personal and clinical utility of polygenic risk scores. Nature Reviews. Genetics. PMID 29789686 DOI: 10.1038/S41576-018-0018-X  0.333
2018 Komori HK, LaMere SA, Hart T, Head SR, Torkamani A, Salomon DR. Microdroplet PCR for Highly Multiplexed Targeted Bisulfite Sequencing. Methods in Molecular Biology (Clifton, N.J.). 1708: 333-348. PMID 29224152 DOI: 10.1007/978-1-4939-7481-8_17  0.334
2017 Boeldt DL, Cheung C, Ariniello L, Darst BF, Topol S, Schork NJ, Philis-Tsimikas A, Torkamani A, Fortmann AL, Bloss CS. Patient perspectives on whole-genome sequencing for undiagnosed diseases. Personalized Medicine. 14: 17-25. PMID 29749824 DOI: 10.2217/Pme-2016-0050  0.536
2017 Deiss TC, Vadnais M, Wang F, Chen PL, Torkamani A, Mwangi W, Lefranc MP, Criscitiello MF, Smider VV. Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies. Cellular & Molecular Immunology. PMID 29200193 DOI: 10.1038/Cmi.2017.117  0.304
2017 Rueda M, Wagner JL, Phillips TC, Topol SE, Muse ED, Lucas JR, Wagner GN, Topol EJ, Torkamani A. Molecular Autopsy for Sudden Death in the Young: Is Data Aggregation the Key? Frontiers in Cardiovascular Medicine. 4: 72. PMID 29181379 DOI: 10.3389/Fcvm.2017.00072  0.396
2017 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. 18: 373. PMID 28821228 DOI: 10.1186/S12859-017-1778-6  0.346
2016 Erikson GA, Bodian DL, Rueda M, Molparia B, Scott ER, Scott-Van Zeeland AA, Topol SE, Wineinger NE, Niederhuber JE, Topol EJ, Torkamani A. Whole-Genome Sequencing of a Healthy Aging Cohort. Cell. PMID 27114037 DOI: 10.1016/J.Cell.2016.03.022  0.368
2016 Hazen JL, Faust GG, Rodriguez AR, Ferguson WC, Shumilina S, Clark RA, Boland MJ, Martin G, Chubukov P, Tsunemoto RK, Torkamani A, Kupriyanov S, Hall IM, Baldwin KK. The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning. Neuron. PMID 26948891 DOI: 10.1016/J.Neuron.2016.02.004  0.334
2015 Bloss CS, Zeeland AA, Topol SE, Darst BF, Boeldt DL, Erikson GA, Bethel KJ, Bjork RL, Friedman JR, Hwynn N, Patay BA, Pockros PJ, Scott ER, Simon RA, Williams GW, ... ... Torkamani A, et al. A genome sequencing program for novel undiagnosed diseases. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 25790160 DOI: 10.1038/Gim.2015.21  0.548
2015 Pham PH, Shipman WJ, Erikson GA, Schork NJ, Torkamani A. Scripps Genome ADVISER: Annotation and Distributed Variant Interpretation SERver. Plos One. 10: e0116815. PMID 25706643 DOI: 10.1371/Journal.Pone.0116815  0.528
2015 Molparia B, Pham PH, Torkamani A. Symptom-driven idiopathic disease gene identification. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 25590976 DOI: 10.1038/Gim.2014.202  0.398
2015 Erikson GA, Deshpande N, Kesavan BG, Torkamani A. SG-ADVISER CNV: copy-number variant annotation and interpretation. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 17: 714-8. PMID 25521334 DOI: 10.1038/Gim.2014.180  0.379
2014 Torkamani A, Bersell K, Jorge BS, Bjork RL, Friedman JR, Bloss CS, Cohen J, Gupta S, Naidu S, Vanoye CG, George AL, Kearney JA. De novo KCNB1 mutations in epileptic encephalopathy. Annals of Neurology. 76: 529-40. PMID 25164438 DOI: 10.1002/Ana.24263  0.314
2014 Chen YZ, Friedman JR, Chen DH, Chan GC, Bloss CS, Hisama FM, Topol SE, Carson AR, Pham PH, Bonkowski ES, Scott ER, Lee JK, Zhang G, Oliveira G, Xu J, ... ... Torkamani A, et al. Gain-of-function ADCY5 mutations in familial dyskinesia with facial myokymia. Annals of Neurology. 75: 542-9. PMID 24700542 DOI: 10.1002/Ana.24119  0.483
2014 Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, ... ... Torkamani A, 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. 15: R53. PMID 24667040 DOI: 10.1186/Gb-2014-15-3-R53  0.415
2014 Scott-Van Zeeland AA, Bloss CS, Tewhey R, Bansal V, Torkamani A, Libiger O, Duvvuri V, Wineinger N, Galvez L, Darst BF, Smith EN, Carson A, Pham P, Phillips T, Villarasa N, et al. Evidence for the role of EPHX2 gene variants in anorexia nervosa. Molecular Psychiatry. 19: 724-32. PMID 23999524 DOI: 10.1038/Mp.2013.91  0.72
2013 Paliwal A, Temkin AM, Kerkel K, Yale A, Yotova I, Drost N, Lax S, Nhan-Chang CL, Powell C, Borczuk A, Aviv A, Wapner R, Chen X, Nagy PL, Schork N, ... ... Torkamani A, et al. Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation. Plos Genetics. 9: e1003622. PMID 24009515 DOI: 10.1371/Journal.Pgen.1003622  0.496
2013 Choi NM, Loguercio S, Verma-Gaur J, Degner SC, Torkamani A, Su AI, Oltz EM, Artyomov M, Feeney AJ. Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies. Journal of Immunology (Baltimore, Md. : 1950). 191: 2393-402. PMID 23898036 DOI: 10.4049/Jimmunol.1301279  0.337
2013 Schork AJ, Thompson WK, Pham P, Torkamani A, Roddey JC, Sullivan PF, Kelsoe JR, O'Donovan MC, Furberg H, Schork NJ, Andreassen OA, Dale AM. All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs. Plos Genetics. 9: e1003449. PMID 23637621 DOI: 10.1371/Journal.Pgen.1003449  0.546
2012 Torkamani A, Pham P, Libiger O, Bansal V, Zhang G, Scott-Van Zeeland AA, Tewhey R, Topol EJ, Schork NJ. Clinical implications of human population differences in genome-wide rates of functional genotypes. Frontiers in Genetics. 3: 211. PMID 23125845 DOI: 10.3389/Fgene.2012.00211  0.73
2012 Verma-Gaur J, Torkamani A, Schaffer L, Head SR, Schork NJ, Feeney AJ. 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. 109: 17004-9. PMID 23027941 DOI: 10.1073/Pnas.1208398109  0.445
2012 Tewhey R, Cannavino CR, Leake JA, Bansal V, Topol EJ, Torkamani A, Bradley JS, Schork NJ. Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300. Bmc Genomics. 13: 508. PMID 23009684 DOI: 10.1186/1471-2164-13-508  0.694
2012 Malyshev DA, Dhami K, Quach HT, Lavergne T, Ordoukhanian P, Torkamani A, Romesberg FE. 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. 109: 12005-10. PMID 22773812 DOI: 10.1073/Pnas.1205176109  0.327
2012 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 (Baltimore, Md. : 1950). 188: 2305-15. PMID 22287713 DOI: 10.4049/Jimmunol.1103484  0.46
2012 Torkamani A, Schork NJ. Background gene expression networks significantly enhance drug response prediction by transcriptional profiling. The Pharmacogenomics Journal. 12: 446-52. PMID 21826086 DOI: 10.1038/Tpj.2011.35  0.462
2012 Friedman AJ, Torkamani A, Verkhivker G, Schork NJ. From coding variant to structure and function insight Proteomics Research Journal. 3: 395-405.  0.376
2011 Sebastiani P, Riva A, Montano M, Pham P, Torkamani A, Scherba E, Benson G, Milton JN, Baldwin CT, Andersen S, Schork NJ, Steinberg MH, Perls TT. Whole genome sequences of a male and female supercentenarian, ages greater than 114 years. Frontiers in Genetics. 2: 90. PMID 22303384 DOI: 10.3389/Fgene.2011.00090  0.561
2011 Torkamani A, Scott-Van Zeeland AA, Topol EJ, Schork NJ. Annotating individual human genomes. Genomics. 98: 233-41. PMID 21839162 DOI: 10.1016/J.Ygeno.2011.07.006  0.548
2011 Zhang H, Torkamani A, Jones TM, Ruiz DI, Pons J, Lerner RA. 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. 108: 13456-61. PMID 21825149 DOI: 10.1073/Pnas.1111218108  0.317
2011 Komori HK, LaMere SA, Torkamani A, Hart GT, Kotsopoulos S, Warner J, Samuels ML, Olson J, Head SR, Ordoukhanian P, Lee PL, Link DR, Salomon DR. Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Research. 21: 1738-45. PMID 21757609 DOI: 10.1101/Gr.116863.110  0.302
2011 Degner SC, Verma-Gaur J, Wong TP, Bossen C, Iverson GM, Torkamani A, Vettermann C, Lin YC, Ju Z, Schulz D, Murre CS, Birshtein BK, Schork NJ, Schlissel MS, Riblet R, 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. 108: 9566-71. PMID 21606361 DOI: 10.1073/Pnas.1019391108  0.452
2011 Cheng J, Torkamani A, Grover RK, Jones TM, Ruiz DI, Schork NJ, Quigley MM, Hall FW, Salomon DR, Lerner RA. Ectopic B-cell clusters that infiltrate transplanted human kidneys are clonal. Proceedings of the National Academy of Sciences of the United States of America. 108: 5560-5. PMID 21415369 DOI: 10.1073/Pnas.1101148108  0.44
2011 Tewhey R, Bansal V, Torkamani A, Topol EJ, Schork NJ. The importance of phase information for human genomics. Nature Reviews. Genetics. 12: 215-23. PMID 21301473 DOI: 10.1038/Nrg2950  0.712
2011 Bansal V, Libiger O, Torkamani A, Schork NJ. An application and empirical comparison of statistical analysis methods for associating rare variants to a complex phenotype. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 76-87. PMID 21121035  0.476
2010 Kerkel K, Schupf N, Hatta K, Pang D, Salas M, Kratz A, Minden M, Murty V, Zigman WB, Mayeux RP, Jenkins EC, Torkamani A, Schork NJ, Silverman W, Croy BA, et al. Altered DNA methylation in leukocytes with trisomy 21. Plos Genetics. 6: e1001212. PMID 21124956 DOI: 10.1371/Journal.Pgen.1001212  0.477
2010 Bansal V, Libiger O, Torkamani A, Schork NJ. Statistical analysis strategies for association studies involving rare variants. Nature Reviews. Genetics. 11: 773-85. PMID 20940738 DOI: 10.1038/Nrg2867  0.562
2010 Torkamani A, Dean B, Schork NJ, Thomas EA. Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia. Genome Research. 20: 403-12. PMID 20197298 DOI: 10.1101/Gr.101956.109  0.447
2010 Lahiry P, Torkamani A, Schork NJ, Hegele RA. Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nature Reviews. Genetics. 11: 60-74. PMID 20019687 DOI: 10.1038/Nrg2707  0.496
2009 Dixit A, Yi L, Gowthaman R, Torkamani A, Schork NJ, Verkhivker GM. Sequence and structure signatures of cancer mutation hotspots in protein kinases. Plos One. 4: e7485. PMID 19834613 DOI: 10.1371/Journal.Pone.0007485  0.505
2009 Torkamani A, Schork NJ. Pathway and network analysis with high-density allelic association data. Methods in Molecular Biology (Clifton, N.J.). 563: 289-301. PMID 19597792 DOI: 10.1007/978-1-60761-175-2_16  0.481
2009 Torkamani A, Schork NJ. Identification of rare cancer driver mutations by network reconstruction. Genome Research. 19: 1570-8. PMID 19574499 DOI: 10.1101/Gr.092833.109  0.493
2009 Torkamani A, Schork NJ. Prestige centrality-based functional outlier detection in gene expression analysis. Bioinformatics (Oxford, England). 25: 2222-8. PMID 19549629 DOI: 10.1093/Bioinformatics/Btp388  0.47
2009 Dixit A, Torkamani A, Schork NJ, 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. 96: 858-74. PMID 19186126 DOI: 10.1016/J.Bpj.2008.10.041  0.468
2009 Torkamani A, Verkhivker G, Schork NJ. Cancer driver mutations in protein kinase genes. Cancer Letters. 281: 117-27. PMID 19081671 DOI: 10.1016/J.Canlet.2008.11.008  0.509
2008 Mossé YP, Laudenslager M, Longo L, Cole KA, Wood A, Attiyeh EF, Laquaglia MJ, Sennett R, Lynch JE, Perri P, Laureys G, Speleman F, Kim C, Hou C, Hakonarson H, ... Torkamani A, et al. Identification of ALK as a major familial neuroblastoma predisposition gene. Nature. 455: 930-5. PMID 18724359 DOI: 10.1038/Nature07261  0.502
2008 Torkamani A, Topol EJ, Schork NJ. Pathway analysis of seven common diseases assessed by genome-wide association. Genomics. 92: 265-72. PMID 18722519 DOI: 10.1016/J.Ygeno.2008.07.011  0.545
2008 Torkamani A, Kannan N, Taylor SS, Schork NJ. Congenital disease SNPs target lineage specific structural elements in protein kinases. Proceedings of the National Academy of Sciences of the United States of America. 105: 9011-6. PMID 18579784 DOI: 10.1073/Pnas.0802403105  0.508
2008 Torkamani A, Schork NJ. Predicting functional regulatory polymorphisms. Bioinformatics (Oxford, England). 24: 1787-92. PMID 18562267 DOI: 10.1093/Bioinformatics/Btn311  0.528
2008 Torkamani A, Schork NJ. Prediction of cancer driver mutations in protein kinases. Cancer Research. 68: 1675-82. PMID 18339846 DOI: 10.1158/0008-5472.Can-07-5283  0.489
2007 Torkamani A, Schork NJ. Accurate prediction of deleterious protein kinase polymorphisms. Bioinformatics (Oxford, England). 23: 2918-25. PMID 17855419 DOI: 10.1093/Bioinformatics/Btm437  0.544
2007 Torkamani A, Schork NJ. Distribution analysis of nonsynonymous polymorphisms within the human kinase gene family. Genomics. 90: 49-58. PMID 17498919 DOI: 10.1016/J.Ygeno.2007.03.006  0.529
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