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Athma A Pai PhD

TitleAssistant Professor
InstitutionUMass Chan Medical School
DepartmentRNA Therapeutics Institute
AddressUMass Chan Medical School
55 Lake Avenue North
Worcester MA 01655
Phone774-455-4681
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentRNA Therapeutics Institute

    InstitutionT.H. Chan School of Medicine
    DepartmentSystems Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiophysical Chemical and Computational Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentMD/PhD Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentSystems Computational and Quantitative Biology


    Collapse Biography 
    Collapse education and training
    University of Pennsylvania, Philadelphia, PA, United StatesBSBiochemistry/Anthropology
    University of Chicago, Chicago, IL, United StatesPHDHuman Genetics
    MIT, Cambridge, MA, United StatesPostdocRNA Genomics

    Collapse Overview 
    Collapse Post Docs

    A postdoctoral position is available to study in this laboratory. Contact Dr. Pai for additional details.


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    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Torres-Ulloa L, Calvo-Roitberg E, Pai AA. Genome-wide kinetic profiling of pre-mRNA 3' end cleavage. RNA. 2024 Feb 16; 30(3):256-270. PMID: 38164598.
      Citations:    Fields:    
    2. 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. 2024 Jan 07. PMID: 38260419.
      Citations:    
    3. Calvo-Roitberg E, Daniels RF, Pai AA. Challenges in identifying mRNA transcript starts and ends from long-read sequencing data. bioRxiv. 2023 Jul 27. PMID: 37546743.
      Citations:    
    4. 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. Proc Natl Acad Sci U S A. 2023 01 03; 120(1):e2213715120. PMID: 36577072.
      Citations: 6     Fields:    Translation:HumansCells
    5. 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 Res. 2022 12 09; 50(22):12657-12673. PMID: 36511872.
      Citations:    Fields:    Translation:HumansCells
    6. 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. Nat Struct Mol Biol. 2022 12; 29(12):1239-1251. PMID: 36482254.
      Citations: 11     Fields:    Translation:Cells
    7. Pai AA, Li YI, Provero P. Editorial: Alternative Polyadenylation in Development and Disease. Front Genet. 2022; 13:936960. PMID: 35846141.
      Citations:    
    8. MacMillan HJ, Kong Y, Calvo-Roitberg E, Alonso LC, Pai AA. High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets. Sci Rep. 2022 05 11; 12(1):7745. PMID: 35546161.
      Citations: 2     Fields:    Translation:Humans
    9. Fiszbein A, McGurk M, Calvo-Roitberg E, Kim G, Burge CB, Pai AA. Widespread occurrence of hybrid internal-terminal exons in human transcriptomes. Sci Adv. 2022 01 21; 8(3):eabk1752. PMID: 35044812.
      Citations: 4     Fields:    Translation:HumansCells
    10. Ibraheim R, Tai PWL, Mir A, Javeed N, Wang J, Rodr?guez TC, Namkung S, Nelson S, Khokhar ES, Mintzer E, Maitland S, Chen Z, Cao Y, Tsagkaraki E, Wolfe SA, Wang D, Pai AA, Xue W, Gao G, Sontheimer EJ. Self-inactivating, all-in-one AAV vectors for precision Cas9 genome editing via homology-directed repair in vivo. Nat Commun. 2021 11 01; 12(1):6267. PMID: 34725353.
      Citations: 31     Fields:    Translation:HumansAnimalsCells
    11. 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, Gernoux G, Mueller C, Gray-Edwards HL, Moser RP, Bishop NC, Jaber SM, Gounis MJ, Sena-Esteves M, Pai AA, DiFiglia M, Aronin N, Khvorova A. A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system. Nat Biotechnol. 2019 08; 37(8):884-894. PMID: 31375812.
      Citations: 69     Fields:    Translation:Animals
    12. Pai AA, Luca F. Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response. Wiley Interdiscip Rev RNA. 2019 01; 10(1):e1503. PMID: 30216698.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    13. 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 Rep. 2018 09 04; 24(10):2553-2560.e5. PMID: 30184490.
      Citations: 22     Fields:    Translation:HumansAnimalsCells
    14. Pai AA, Paggi JM, Yan P, Adelman K, Burge CB. Numerous recursive sites contribute to accuracy of splicing in long introns in flies. PLoS Genet. 2018 08; 14(8):e1007588. PMID: 30148878.
      Citations: 10     Fields:    Translation:AnimalsCells
    15. Aguiar D, Cheng LF, Dumitrascu B, Mordelet F, Pai AA, Engelhardt BE. Bayesian nonparametric discovery of isoforms and individual specific quantification. Nat Commun. 2018 04 27; 9(1):1681. PMID: 29703885.
      Citations: 3     Fields:    Translation:HumansCells
    16. 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. 2017 12 27; 6. PMID: 29280736.
      Citations: 34     Fields:    Translation:AnimalsCells
    17. 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 Genet. 2017 Oct; 13(10):e1006995. PMID: 29023442.
      Citations: 16     Fields:    Translation:HumansCells
    18. Pai AA, Baharian G, Pag? Sabourin A, Brinkworth JF, N?d?lec 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 Genet. 2016 Sep; 12(9):e1006338. PMID: 27690314.
      Citations: 49     Fields:    
    19. Chen Y, Pai AA, Herudek J, Lubas M, Meola N, J?rvelin AI, Andersson R, Pelechano V, Steinmetz LM, Jensen TH, Sandelin A. Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nat Genet. 2016 09; 48(9):984-94. PMID: 27455346.
      Citations: 47     Fields:    Translation:HumansCells
    20. Pacis A, Tailleux L, Morin AM, Lambourne J, MacIsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, Tung J, Pastinen T, Kobor MS, Pique-Regi R, Gilad Y, Barreiro LB. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015 Dec; 25(12):1801-11. PMID: 26392366.
      Citations: 104     Fields:    Translation:HumansCells
    21. Pai AA, Pritchard JK, Gilad Y. The genetic and mechanistic basis for variation in gene regulation. PLoS Genet. 2015 Jan; 11(1):e1004857. PMID: 25569255.
      Citations: 81     Fields:    Translation:HumansCells
    22. Pai AA, Gilad Y. Comparative studies of gene regulatory mechanisms. Curr Opin Genet Dev. 2014 Dec; 29:68-74. PMID: 25215415.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    23. Gallego Romero I, Pai AA, Tung J, Gilad Y. RNA-seq: impact of RNA degradation on transcript quantification. BMC Biol. 2014 May 30; 12:42. PMID: 24885439.
      Citations: 190     Fields:    Translation:HumansCells
    24. Gupta M, Pai AA, Bhattacharya A, Ramachandra R, Sawarappa R, Mohapatra S, Kanoi A. Anterior plagiocephaly in an atypical case of apert syndrome. World J Plast Surg. 2013 Jun; 2(2):115-8. PMID: 25489515.
      Citations:    
    25. 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 Genet. 2012; 8(11):e1003036. PMID: 23166509.
      Citations: 158     Fields:    Translation:HumansCells
    26. 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 Genet. 2012; 8(10):e1003000. PMID: 23071454.
      Citations: 64     Fields:    Translation:HumansCells
    27. 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, Lee C. Regulatory element copy number differences shape primate expression profiles. Proc Natl Acad Sci U S A. 2012 Jul 31; 109(31):12656-61. PMID: 22797897.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    28. 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. 2012 Feb 05; 482(7385):390-4. PMID: 22307276.
      Citations: 380     Fields:    Translation:HumansCells
    29. 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 Biol. 2012 Jan 31; 13(1):R7. PMID: 22293038.
      Citations: 125     Fields:    Translation:HumansCells
    30. 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. Hum Mol Genet. 2012 May 01; 21(9):2111-23. PMID: 22286170.
      Citations: 34     Fields:    Translation:HumansCells
    31. 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. Proc Natl Acad Sci U S A. 2012 Jan 24; 109(4):1204-9. PMID: 22233810.
      Citations: 143     Fields:    Translation:HumansCells
    32. 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 Genet. 2011 Feb; 7(2):e1001316. PMID: 21383968.
      Citations: 108     Fields:    Translation:HumansAnimalsCells
    33. 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 Biol. 2011; 12(1):R10. PMID: 21251332.
      Citations: 482     Fields:    Translation:HumansCells
    34. 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. 2011 Jan 06; 6(1):e14495. PMID: 21253579.
      Citations: 24     Fields:    Translation:Humans
    35. Pickrell JK, Pai AA, Gilad Y, Pritchard JK. Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet. 2010 Dec 09; 6(12):e1001236. PMID: 21151575.
      Citations: 167     Fields:    Translation:HumansCells
    36. 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 Res. 2011 Mar; 21(3):447-55. PMID: 21106904.
      Citations: 332     Fields:    Translation:HumansCells
    37. 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. 2010 Apr 01; 464(7289):768-72. PMID: 20220758.
      Citations: 769     Fields:    Translation:HumansCells
    38. 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. 2009 Nov 25; 4(11):e7842. PMID: 19946364.
      Citations: 18     Fields:    Translation:HumansCells
    39. 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. 2009 Dec 15; 25(24):3207-12. PMID: 19808877.
      Citations: 277     Fields:    Translation:HumansCells
    40. 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. Am J Phys Anthropol. 2008 Jul; 136(3):278-93. PMID: 18322915.
      Citations: 15     Fields:    Translation:Humans
    41. 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. Am J Hum Genet. 2006 Jul; 79(1):169-73. PMID: 16773578.
      Citations: 275     Fields:    Translation:HumansCells
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