Athma A. Pai, Ph.D. - Publications

2012 Human Genetics University of Chicago, Chicago, IL 

25/34 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
2018 Aguiar D, Cheng LF, Dumitrascu B, Mordelet F, Pai AA, Engelhardt BE. Bayesian nonparametric discovery of isoforms and individual specific quantification. Nature Communications. 9: 1681. PMID 29703885 DOI: 10.1038/S41467-018-03402-W  0.32
2017 Richards AL, Watza D, Findley A, Alazizi A, Wen X, Pai AA, Pique-Regi R, Luca F. Environmental perturbations lead to extensive directional shifts in RNA processing. Plos Genetics. 13: e1006995. PMID 29023442 DOI: 10.1371/Journal.Pgen.1006995  0.68
2016 Pai AA, Baharian G, Pagé Sabourin A, Brinkworth JF, Nédélec Y, Foley JW, Grenier JC, Siddle KJ, Dumaine A, Yotova V, Johnson ZP, Lanford RE, Burge CB, Barreiro LB. Widespread Shortening of 3' Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection. Plos Genetics. 12: e1006338. PMID 27690314 DOI: 10.1371/Journal.Pgen.1006338  1
2015 Pacis A, Tailleux L, Morin AM, Lambourne J, Maclsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, et al. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Research. PMID 26392366 DOI: 10.1101/Gr.192005.115  1
2015 Pai AA, Pritchard JK, Gilad Y. The genetic and mechanistic basis for variation in gene regulation. Plos Genetics. 11: e1004857. PMID 25569255 DOI: 10.1371/Journal.Pgen.1004857  1
2014 Pai AA, Gilad Y. Comparative studies of gene regulatory mechanisms. Current Opinion in Genetics & Development. 29: 68-74. PMID 25215415 DOI: 10.1016/J.Gde.2014.08.010  1
2014 Gallego Romero I, Pai AA, Tung J, Gilad Y. RNA-seq: impact of RNA degradation on transcript quantification. Bmc Biology. 12: 42. PMID 24885439 DOI: 10.1186/1741-7007-12-42  1
2012 Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK. Controls of nucleosome positioning in the human genome. Plos Genetics. 8: e1003036. PMID 23166509 DOI: 10.1371/Journal.Pgen.1003036  1
2012 Pai AA, Cain CE, Mizrahi-Man O, De Leon S, Lewellen N, Veyrieras JB, Degner JF, Gaffney DJ, Pickrell JK, Stephens M, Pritchard JK, Gilad Y. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. Plos Genetics. 8: e1003000. PMID 23071454 DOI: 10.1371/Journal.Pgen.1003000  1
2012 Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, et al. Regulatory element copy number differences shape primate expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 109: 12656-61. PMID 22797897 DOI: 10.1073/Pnas.1205199109  1
2012 Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature. 482: 390-4. PMID 22307276 DOI: 10.1038/Nature10808  1
2012 Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK. Dissecting the regulatory architecture of gene expression QTLs. Genome Biology. 13: R7. PMID 22293038 DOI: 10.1186/Gb-2012-13-1-R7  1
2012 Cusanovich DA, Billstrand C, Zhou X, Chavarria C, De Leon S, Michelini K, Pai AA, Ober C, Gilad Y. The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. Human Molecular Genetics. 21: 2111-23. PMID 22286170 DOI: 10.1093/Hmg/Dds021  1
2012 Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, Gilad Y. Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. Proceedings of the National Academy of Sciences of the United States of America. 109: 1204-9. PMID 22233810 DOI: 10.1073/Pnas.1115761109  1
2011 Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. Plos Genetics. 7: e1001316. PMID 21383968 DOI: 10.1371/Journal.Pgen.1001316  1
2011 Stefflova K, Dulik MC, Barnholtz-Sloan JS, Pai AA, Walker AH, Rebbeck TR. Dissecting the within-Africa ancestry of populations of African descent in the Americas. Plos One. 6: e14495. PMID 21253579 DOI: 10.1371/Journal.Pone.0014495  1
2011 Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biology. 12: R10. PMID 21251332 DOI: 10.1186/Gb-2011-12-1-R10  1
2011 Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Research. 21: 447-55. PMID 21106904 DOI: 10.1101/Gr.112623.110  1
2011 Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. Correction: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines Genome Biology. 12. DOI: 10.1186/Gb-2011-12-6-405  1
2010 Pickrell JK, Pai AA, Gilad Y, Pritchard JK. Noisy splicing drives mRNA isoform diversity in human cells. Plos Genetics. 6: e1001236. PMID 21151575 DOI: 10.1371/Journal.Pgen.1001236  1
2010 Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 464: 768-72. PMID 20220758 DOI: 10.1038/Nature08872  1
2009 Stefflova K, Dulik MC, Pai AA, Walker AH, Zeigler-Johnson CM, Gueye SM, Schurr TG, Rebbeck TR. Evaluation of group genetic ancestry of populations from Philadelphia and Dakar in the context of sex-biased admixture in the Americas. Plos One. 4: e7842. PMID 19946364 DOI: 10.1371/Journal.Pone.0007842  1
2009 Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics (Oxford, England). 25: 3207-12. PMID 19808877 DOI: 10.1093/Bioinformatics/Btp579  1
2008 Gokcumen O, Dulik MC, Pai AA, Zhadanov SI, Rubinstein S, Osipova LP, Andreenkov OV, Tabikhanova LE, Gubina MA, Labuda D, Schurr TG. Genetic variation in the enigmatic Altaian Kazakhs of South-Central Russia: insights into Turkic population history. American Journal of Physical Anthropology. 136: 278-93. PMID 18322915 DOI: 10.1002/Ajpa.20802  1
2006 McDaniell R, Warthen DM, Sanchez-Lara PA, Pai A, Krantz ID, Piccoli DA, Spinner NB. NOTCH2 mutations cause Alagille syndrome, a heterogeneous disorder of the notch signaling pathway American Journal of Human Genetics. 79: 169-173. PMID 16773578 DOI: 10.1086/505332  1
Low-probability matches
2018 Pai AA, Luca F. Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response. Wiley Interdisciplinary Reviews. Rna. e1503. PMID 30216698 DOI: 10.1002/Wrna.1503  0.04
2019 Alterman JF, Godinho BMDC, Hassler MR, Ferguson CM, Echeverria D, Sapp E, Haraszti RA, Coles AH, Conroy F, Miller R, Roux L, Yan P, Knox EG, Turanov AA, King RM, ... ... Pai AA, et al. A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system. Nature Biotechnology. 37: 884-894. PMID 31375812 DOI: 10.1038/S41587-019-0205-0  0.01
2018 Didiot MC, Ferguson CM, Ly S, Coles AH, Smith AO, Bicknell AA, Hall LM, Sapp E, Echeverria D, Pai AA, DiFiglia M, Moore MJ, Hayward LJ, Aronin N, Khvorova A. Nuclear Localization of Huntingtin mRNA Is Specific to Cells of Neuronal Origin. Cell Reports. 24: 2553-2560.e5. PMID 30184490 DOI: 10.1016/J.Celrep.2018.07.106  0.01
2018 Pai AA, Paggi JM, Yan P, Adelman K, Burge CB. Numerous recursive sites contribute to accuracy of splicing in long introns in flies. Plos Genetics. 14: e1007588. PMID 30148878 DOI: 10.1371/Journal.Pgen.1007588  0.01
2017 Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB. The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture. Elife. 6. PMID 29280736 DOI: 10.7554/Elife.32537  0.01
2016 Chen Y, Pai AA, Herudek J, Lubas M, Meola N, Järvelin AI, Andersson R, Pelechano V, Steinmetz LM, Jensen TH, Sandelin A. Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nature Genetics. PMID 27455346 DOI: 10.1038/Ng.3616  0.01
2013 Gupta M, Pai AA, Bhattacharya A, Ramachandra R, Sawarappa R, Mohapatra S, Kanoi A. Anterior plagiocephaly in an atypical case of apert syndrome. World Journal of Plastic Surgery. 2: 115-8. PMID 25489515  0.01
2013 Gupta M, Pai AA, Setty RR, Sawarappa R, Majumdar BK, Banerjee T, Kanoi A, Bhattacharya A. Perforator plus fasciocutaneous flaps in the reconstruction of post-burn flexion contractures of the knee joint. Journal of Clinical and Diagnostic Research : Jcdr. 7: 896-901. PMID 23814737 DOI: 10.7860/JCDR/2013/5324.2968  0.01
2017 Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB. Author response: The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture Elife. DOI: 10.7554/Elife.32537.022  0
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