Ali Torkamani, Ph.D. - Publications

Affiliations: 
2008 Biomedical Sciences University of California, San Diego, La Jolla, CA 
Area:
statistical genetics of neuropschiatric disorders

59 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
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  0.32
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  0.76
2016 Lo Sardo V, Ferguson W, Erikson GA, Topol EJ, Baldwin KK, Torkamani A. Influence of donor age on induced pluripotent stem cells. Nature Biotechnology. PMID 27941802 DOI: 10.1038/nbt.3749  0.44
2016 Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, ... ... Torkamani A, et al. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications. 7: 12460. PMID 27549343 DOI: 10.1038/ncomms12460  0.76
2016 Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, et al. High-performance web services for querying gene and variant annotation. Genome Biology. 17: 91. PMID 27154141 DOI: 10.1186/s13059-016-0953-9  0.76
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  0.76
2015 Chen DH, Méneret A, Friedman JR, Korvatska O, Gad A, Bonkowski ES, Stessman HA, Doummar D, Mignot C, Anheim M, Bernes S, Davis MY, Damon-Perrière N, Degos B, Grabli D, ... ... Torkamani A, et al. ADCY5-related dyskinesia: Broader spectrum and genotype-phenotype correlations. Neurology. PMID 26537056 DOI: 10.1212/WNL.0000000000002058  0.76
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  0.76
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  0.76
2015 Topol EJ, Steinhubl SR, Torkamani A. Digital medical tools and sensors. Jama. 313: 353-4. PMID 25626031 DOI: 10.1001/jama.2014.17125  0.76
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  0.76
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  0.76
2014 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. 89: 259-72. PMID 25948120 DOI: 10.1266/ggs.89.259  0.76
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  0.76
2014 Larman HB, Scott ER, Wogan M, Oliveira G, Torkamani A, Schultz PG. Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay. Nucleic Acids Research. 42: 9146-57. PMID 25063296 DOI: 10.1093/nar/gku636  0.76
2014 Belani R, Oliveira G, Erikson GA, Ra S, Schechter MS, Lee JK, Shipman WJ, Haaser SM, Torkamani A. ASXL1 and DNMT3A mutation in a cytogenetically normal B3 thymoma. Oncogenesis. 3: e111. PMID 25000259 DOI: 10.1038/oncsis.2014.25  0.76
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  0.76
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  0.76
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  0.76
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  0.76
2013 Wang F, Ekiert DC, Ahmad I, Yu W, Zhang Y, Bazirgan O, Torkamani A, Raudsepp T, Mwangi W, Criscitiello MF, Wilson IA, Schultz PG, Smider VV. Reshaping antibody diversity. Cell. 153: 1379-93. PMID 23746848 DOI: 10.1016/j.cell.2013.04.049  0.76
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  0.76
2012 Shih HY, Verma-Gaur J, Torkamani A, Feeney AJ, Galjart N, Krangel MS. 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. 109: E3493-502. PMID 23169622 DOI: 10.1073/pnas.1214131109  0.76
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  0.76
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  0.76
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  0.76
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  0.76
2012 Cheng J, Torkamani A, Peng Y, Jones TM, Lerner RA. Plasma membrane associated transcription of cytoplasmic DNA. Proceedings of the National Academy of Sciences of the United States of America. 109: 10827-31. PMID 22711823 DOI: 10.1073/pnas.1208716109  0.76
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  0.76
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  0.76
2012 Friedman AJ, Torkamani A, Verkhivker G, Schork NJ. From coding variant to structure and function insight Proteomics Research Journal. 3: 395-405.  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
2011 Vlad G, King J, Chang CC, Liu Z, Friedman RA, Torkamani AA, Suciu-Foca N. Gene profile analysis of CD8(+) ILT3-Fc induced T suppressor cells. Human Immunology. 72: 107-14. PMID 20974207 DOI: 10.1016/j.humimm.2010.10.012  0.76
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  0.76
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  0.76
2010 Chang CC, Vlad G, D'Agati VD, Liu Z, Zhang QY, Witkowski P, Torkamani AA, Stokes MB, Ho EK, Cortesini R, Suciu-Foca N. BCL6 is required for differentiation of Ig-like transcript 3-Fc-induced CD8+ T suppressor cells. Journal of Immunology (Baltimore, Md. : 1950). 185: 5714-22. PMID 20935202 DOI: 10.4049/jimmunol.1001732  0.76
2010 Ota M, Duong BH, Torkamani A, Doyle CM, Gavin AL, Ota T, Nemazee D. Regulation of the B cell receptor repertoire and self-reactivity by BAFF. Journal of Immunology (Baltimore, Md. : 1950). 185: 4128-36. PMID 20817867 DOI: 10.4049/jimmunol.1002176  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
2008 Torkamani A, Schork NJ. Predicting functional regulatory polymorphisms. Bioinformatics (Oxford, England). 24: 1787-92. PMID 18562267 DOI: 10.1093/bioinformatics/btn311  0.76
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  0.76
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  0.76
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  0.76
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