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Athma A. Pai, Ph.D. - Publications

Affiliations: 
2012 Human Genetics University of Chicago, Chicago, IL 
Area:
Olfaction
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36 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
2024 Calvo-Roitberg E, Carroll CL, Venev SV, Kim G, Mick ST, Dekker J, Fiszbein A, Pai AA. mRNA initiation and termination are spatially coordinated. Biorxiv : the Preprint Server For Biology. PMID 38260419 DOI: 10.1101/2024.01.05.574404  0.35
2023 Torres-Ulloa L, Calvo-Roitberg E, Pai AA. Genome-wide kinetic profiling of pre-mRNA 3' end cleavage. Rna (New York, N.Y.). PMID 38164598 DOI: 10.1261/rna.079783.123  0.322
2022 Vierbuchen T, Agarwal S, Johnson JL, Galia L, Lei X, Stein K, Olagnier D, Gaede KI, Herzmann C, Holm CK, Heine H, Pai A, O'Hara Hall A, Hoebe K, Fitzgerald KA. The lncRNA LUCAT1 is elevated in inflammatory disease and restrains inflammation by regulating the splicing and stability of NR4A2. Proceedings of the National Academy of Sciences of the United States of America. 120: e2213715120. PMID 36577072 DOI: 10.1073/pnas.2213715120  0.327
2022 Wang F, Calvo-Roitberg E, Rembetsy-Brown JM, Fang M, Sousa J, Kartje ZJ, Krishnamurthy PM, Lee J, Green MR, Pai AA, Watts JK. G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects. Nucleic Acids Research. PMID 36511872 DOI: 10.1093/nar/gkac1108  0.355
2022 Valton AL, Venev SV, Mair B, Khokhar ES, Tong AHY, Usaj M, Chan K, Pai AA, Moffat J, Dekker J. A cohesin traffic pattern genetically linked to gene regulation. Nature Structural & Molecular Biology. PMID 36482254 DOI: 10.1038/s41594-022-00890-9  0.318
2022 MacMillan HJ, Kong Y, Calvo-Roitberg E, Alonso LC, Pai AA. High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets. Scientific Reports. 12: 7745. PMID 35546161 DOI: 10.1038/s41598-022-11668-w  0.323
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  0.406
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  0.423
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  0.316
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  0.415
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  0.439
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  0.489
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  0.447
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  0.462
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  0.392
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  0.408
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  0.602
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  0.677
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  0.636
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  0.606
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  0.602
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  0.724
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  0.741
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  0.714
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  0.668
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  0.734
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  0.612
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  0.64
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  0.658
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  0.651
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  0.601
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  0.651
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  0.709
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  0.316
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  0.624
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  0.319
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