My Bibliography

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Li D, Jones A, Banerjee S, Engelhardt B. Bayesian Multi-Group Gaussian Process Models for Heterogeneous Group-Structured Data. J Mach Learn Res. 2025;26. PubMed PMID: 41019101; PubMed Central PMCID: PMC12463451.

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Khokhar ES, Brokaw K, Kartje ZJ, Krykbaeva M, Calvo-Roitberg E, Hedger AK, Lee J, Wagh A, Watts JK, Pai AA. CRYPTID-exon: streamlined detection of cryptic exons from RNA-seq data. bioRxiv. 2025 Dec 19;. doi: 10.64898/2025.12.17.694983. PubMed PMID: 41446134; PubMed Central PMCID: PMC12724713.

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Calvo-Roitberg E, Carroll CL, Kim G, Sanabria V, Venev SV, Mick ST, Paquette JD, Uriostegui-Arcos M, Dekker J, Fiszbein A, Pai AA. mRNA initiation and termination are spatially coordinated. Science. 2025 Oct 9;390(6769):eado8279. doi: 10.1126/science.ado8279. Epub 2025 Oct 9. PubMed PMID: 41066574; PubMed Central PMCID: PMC12649799.

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Zhang B, Nyquist S, Jones A, Engelhardt BE, Li D. CONTRASTIVE LINEAR REGRESSION. Ann Appl Stat. 2025 Sep;19(3):1868-1883. doi: 10.1214/24-aoas1977. Epub 2025 Aug 28. PubMed PMID: 41383351; PubMed Central PMCID: PMC12692120.

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Khokhar ES, Brokaw K, Kartje ZJ, Sanabria V, Javeed N, Kumar A, Watts JK, Pai AA. Pervasive noise in human splice site selection. bioRxiv. 2025 Jul 20;. doi: 10.1101/2025.07.16.665169. PubMed PMID: 40791517; PubMed Central PMCID: PMC12338711.

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Davis SM, Hildebrand S, MacMillan HJ, Monopoli KR, Buchwald J, Sousa J, Cooper D, Ly S, Echeverria D, McHugh N, Ferguson C, Coles A, Hariharan VN, O'Reilly D, Tang Q, Furgal R, Yamada K, Alterman JF, Gilbert JW, Knox E, Pineda Y, Weston CN, Baer CE, Pai AA, Khvorova A. Systematic analysis of siRNA and mRNA features impacting fully chemically modified siRNA efficacy. Nucleic Acids Res. 2025 Jun 20;53(12). doi: 10.1093/nar/gkaf479. PubMed PMID: 40548938; PubMed Central PMCID: PMC12205987.

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Peterman EL, Ploessl DS, Love KS, Sanabria V, Daniels RF, Johnstone CP, Godavarti DR, Kabaria SR, Oakes CG, Pai AA, Galloway KE. High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes. Nucleic Acids Res. 2025 Jun 6;53(11). doi: 10.1093/nar/gkaf528. PubMed PMID: 40530694; PubMed Central PMCID: PMC12203911.

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Zhang B, Orning P, Lehman JW, Dinis A, Torres-Ulloa L, Elling R, Kelliher MA, Bertin J, Proulx MK, Goguen JD, Ryan L, Kandasamy RK, Espevik T, Pai AA, Fitzgerald KA, Lien E. Raver1 links Ripk1 RNA splicing to caspase-8-mediated pyroptotic cell death, inflammation, and pathogen resistance. Proc Natl Acad Sci U S A. 2025 Feb 18;122(7):e2420802122. doi: 10.1073/pnas.2420802122. Epub 2025 Feb 13. PubMed PMID: 39946533; PubMed Central PMCID: PMC11848402.

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Harper NW, Birdsall GA, Honeywell ME, Pai AA, Lee MJ. Pol II degradation activates cell death independently from the loss of transcription. bioRxiv. 2025 Jan 14;. doi: 10.1101/2024.12.09.627542. PubMed PMID: 39713309; PubMed Central PMCID: PMC11661175.

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Peterman EL, Ploessl DS, Love KS, Sanabria V, Daniels RF, Johnstone CP, Godavarti DR, Kabaria SR, Oakes CG, Pai AA, Galloway KE. High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes. bioRxiv. 2024 Dec 3;. doi: 10.1101/2024.11.26.625483. PubMed PMID: 39651241; PubMed Central PMCID: PMC11623572.

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Zhang B, Orning P, Lehman JW, Dinis A, Torres-Ulloa L, Elling R, Kelliher MA, Bertin J, Proulx MK, Ryan L, Kandasamy R, Espevik T, Pai AA, Fitzgerald KA, Lien E. Raver1 links Ripk1 RNA splicing to caspase-8-mediated pyroptotic cell death, inflammation, and pathogen resistance. bioRxiv. 2024 Nov 29;. doi: 10.1101/2024.11.27.625707. PubMed PMID: 39651143; PubMed Central PMCID: PMC11623576.

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Calvo-Roitberg E, Daniels RF, Pai AA. Challenges in identifying mRNA transcript starts and ends from long-read sequencing data. Genome Res. 2024 Nov 20;34(11):1719-1734. doi: 10.1101/gr.279559.124. Review. PubMed PMID: 39567236; PubMed Central PMCID: PMC11610588.

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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. doi: 10.1261/rna.079783.123. PubMed PMID: 38164598; PubMed Central PMCID: PMC10870368.

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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 7;. doi: 10.1101/2024.01.05.574404. PubMed PMID: 38260419; PubMed Central PMCID: PMC10802295.

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Calvo-Roitberg E, Daniels RF, Pai AA. Challenges in identifying mRNA transcript starts and ends from long-read sequencing data. bioRxiv. 2023 Jul 27;. doi: 10.1101/2023.07.26.550536. PubMed PMID: 37546743; PubMed Central PMCID: PMC10402045.

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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 Jan 3;120(1):e2213715120. doi: 10.1073/pnas.2213715120. Epub 2022 Dec 28. PubMed PMID: 36577072; PubMed Central PMCID: PMC9910463.

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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 Dec 9;50(22):12657-12673. doi: 10.1093/nar/gkac1108. PubMed PMID: 36511872; PubMed Central PMCID: PMC9825156.

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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 Dec;29(12):1239-1251. doi: 10.1038/s41594-022-00890-9. Epub 2022 Dec 8. PubMed PMID: 36482254; PubMed Central PMCID: PMC10228515.

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Jones A, Townes FW, Li D, Engelhardt BE. CONTRASTIVE LATENT VARIABLE MODELING WITH APPLICATION TO CASE-CONTROL SEQUENCING EXPERIMENTS. Ann Appl Stat. 2022 Sep;16(3):1268-1291. doi: 10.1214/21-aoas1534. Epub 2022 Jul 19. PubMed PMID: 40994464; PubMed Central PMCID: PMC12456736.

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Pai AA, Li YI, Provero P. Editorial: Alternative Polyadenylation in Development and Disease. Front Genet. 2022;13:936960. doi: 10.3389/fgene.2022.936960. eCollection 2022. PubMed PMID: 35846141; PubMed Central PMCID: PMC9286759.

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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 May 11;12(1):7745. doi: 10.1038/s41598-022-11668-w. PubMed PMID: 35546161; PubMed Central PMCID: PMC9095874.

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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 Jan 21;8(3):eabk1752. doi: 10.1126/sciadv.abk1752. Epub 2022 Jan 19. PubMed PMID: 35044812; PubMed Central PMCID: PMC8769537.

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MacMillan HJ, Kong Y, Calvo-Roitberg E, Alonso LC, Pai AA. High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets. [preprint]. 2022 January. Available from: https://www.biorxiv.org/content/10.1101/2022.01.03.474854v1. doi: 10.1101/2022.01.03.474854.

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Ibraheim R, Tai PWL, Mir A, Javeed N, Wang J, Rodríguez 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 Nov 1;12(1):6267. doi: 10.1038/s41467-021-26518-y. PubMed PMID: 34725353; PubMed Central PMCID: PMC8560862.

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Valton A, Venev SV, Mair B, Khokhar E, Tong AH, Usaj M, Chan KS, Pai AA, Moffat J, Dekker J. A cohesin traffic pattern genetically linked to gene regulation. [preprint]. 2021 July. Available from: https://www.biorxiv.org/content/10.1101/2021.07.29.454218v1. doi: 10.1101/2021.07.29.454218.

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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 Aug;37(8):884-894. doi: 10.1038/s41587-019-0205-0. Epub 2019 Aug 2. PubMed PMID: 31375812; PubMed Central PMCID: PMC6879195.

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Pai AA, Luca F. Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response. Wiley Interdiscip Rev RNA. 2019 Jan;10(1):e1503. doi: 10.1002/wrna.1503. Epub 2018 Sep 14. Review. PubMed PMID: 30216698; PubMed Central PMCID: PMC6294667.

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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 Sep 4;24(10):2553-2560.e5. doi: 10.1016/j.celrep.2018.07.106. PubMed PMID: 30184490; PubMed Central PMCID: PMC6245656.

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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 Aug;14(8):e1007588. doi: 10.1371/journal.pgen.1007588. eCollection 2018 Aug. PubMed PMID: 30148878; PubMed Central PMCID: PMC6110457.

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Aguiar D, Cheng LF, Dumitrascu B, Mordelet F, Pai AA, Engelhardt BE. Bayesian nonparametric discovery of isoforms and individual specific quantification. Nat Commun. 2018 Apr 27;9(1):1681. doi: 10.1038/s41467-018-03402-w. PubMed PMID: 29703885; PubMed Central PMCID: PMC5923247.

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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 Dec 27;6. doi: 10.7554/eLife.32537. PubMed PMID: 29280736; PubMed Central PMCID: PMC5762160.

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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. doi: 10.1371/journal.pgen.1006995. eCollection 2017 Oct. PubMed PMID: 29023442; PubMed Central PMCID: PMC5667937.

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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 Genet. 2016 Sep;12(9):e1006338. doi: 10.1371/journal.pgen.1006338. eCollection 2016 Sep. PubMed PMID: 27690314; PubMed Central PMCID: PMC5045211.

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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. Nat Genet. 2016 Sep;48(9):984-94. doi: 10.1038/ng.3616. Epub 2016 Jul 25. PubMed PMID: 27455346; PubMed Central PMCID: PMC5008441.

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McDowell I, Pai A, Guo C, Vockley C, Brown C, Reddy T, Engelhardt B. Many long intergenic non-coding RNAs distally regulate mRNA gene expression levels. [preprint]. 2016 March. doi: 10.1101/044719.

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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. doi: 10.1101/gr.192005.115. Epub 2015 Sep 21. PubMed PMID: 26392366; PubMed Central PMCID: PMC4665002.

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Pai AA, Pritchard JK, Gilad Y. The genetic and mechanistic basis for variation in gene regulation. PLoS Genet. 2015 Jan;11(1):e1004857. doi: 10.1371/journal.pgen.1004857. eCollection 2015 Jan. PubMed PMID: 25569255; PubMed Central PMCID: PMC4287341.

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Pai AA, Gilad Y. Comparative studies of gene regulatory mechanisms. Curr Opin Genet Dev. 2014 Dec;29:68-74. doi: 10.1016/j.gde.2014.08.010. Epub 2014 Sep 16. Review. PubMed PMID: 25215415; PubMed Central PMCID: PMC4258459.

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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. doi: 10.1186/1741-7007-12-42. PubMed PMID: 24885439; PubMed Central PMCID: PMC4071332.

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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. doi: 10.1371/journal.pgen.1003036. Epub 2012 Nov 15. PubMed PMID: 23166509; PubMed Central PMCID: PMC3499251.

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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. doi: 10.1371/journal.pgen.1003000. Epub 2012 Oct 11. PubMed PMID: 23071454; PubMed Central PMCID: PMC3469421.

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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. doi: 10.1073/pnas.1205199109. Epub 2012 Jul 13. PubMed PMID: 22797897; PubMed Central PMCID: PMC3411951.

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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 5;482(7385):390-4. doi: 10.1038/nature10808. PubMed PMID: 22307276; PubMed Central PMCID: PMC3501342.

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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. doi: 10.1186/gb-2012-13-1-r7. PubMed PMID: 22293038; PubMed Central PMCID: PMC3334587.

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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 1;21(9):2111-23. doi: 10.1093/hmg/dds021. Epub 2012 Jan 27. PubMed PMID: 22286170; PubMed Central PMCID: PMC3315207.

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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. doi: 10.1073/pnas.1115761109. Epub 2012 Jan 10. PubMed PMID: 22233810; PubMed Central PMCID: PMC3268270.

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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. doi: 10.1371/journal.pgen.1001316. Epub 2011 Feb 24. PubMed PMID: 21383968; PubMed Central PMCID: PMC3044686.

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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. doi: 10.1186/gb-2011-12-1-r10. Epub 2011 Jan 20. PubMed PMID: 21251332; PubMed Central PMCID: PMC3091299.

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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 6;6(1):e14495. doi: 10.1371/journal.pone.0014495. PubMed PMID: 21253579; PubMed Central PMCID: PMC3017210.

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Pickrell JK, Pai AA, Gilad Y, Pritchard JK. Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet. 2010 Dec 9;6(12):e1001236. doi: 10.1371/journal.pgen.1001236. PubMed PMID: 21151575; PubMed Central PMCID: PMC3000347.