Pai Lab Publications
Publications
Read Our Publications
| # | Authors | Title | Journal | Year | |
|---|---|---|---|---|---|
| 48 | 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 sequencing data | bioRxiv | 2025 | |
| 47 | Calvo-Roitberg E, Lehman JL, Tam E, Elhajjajy S, Engelhardt BE, Pai AA | SPARK: in-silico simulations for benchmarking nascent RNA sequencing experiments | bioRxiv | 2025 | |
| 46 | 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 | |
| 45 | Schooley A, Venev SV, Aksenova V, Lehman JW, Navarrete E, Pai AA, Dasso M, Dekker J | Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm | Nature Cell Biology | 2025 | |
| 44 | Calvo-Roitberg E*, Carroll CL*, Kim GY, 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 | |
| 43 | Harper NW, Birdsall GA, Honeywell ME, Ward KM, Pai AA, Lee MJ | RNA PolII inhibition activates cell death independently from the loss of transcription | Cell | 2025 | |
| 42 | Davis, SM, Hildebrand S, MacMillan H, Monopoli KR, Sousa J, Cooper D, Ly S, Echeverria D, Mchugh N, Ferguson C, Coles A, Hariharan VN, O’Reilly D, Tang Q, Furgal R, Buchwald J, Yamada K, Gilbert J, Knox E, Alterman J, Pineda Y, Weston CN, Baer C, Pai AA, Khvorova A | Guidelines for Designing Therapeutic siRNA | Nucleic Acids Research | 2025 | |
| 41 | Peterman EL, Ploessl DS, Love KS, Sanabria V, Daniels RF, Johnstone CP, Godavarti DR, Kabaria SR, Pai AA, Galloway KE | High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes | Nucleic Acids Research | 2025 | |
| 40 | 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 | RaverI links RipkI RNA splicing to caspase-8-mediated pyroptotic cell death, inflammation, and pathogen resistance | PNAS | 2025 | |
| 39 | Calvo-Roitberg E, Daniels RF, Pai AA | Challenges in identifying mRNA transcript starts and ends from long-read sequencing data | Genome Research | 2024 | |
| 38 | Torres-Ulloa L, Calvo-Roitberg E, Pai AA | Genome-wide kinetic profiling of pre-mRNA 3’ end cleavage | RNA | 2024 | |
| 37 | Vierbuchen T, Agarwal S, Johnson J, Galia L, Lei X, Stein K, Olagnier D, Gaede K, Herzmann C, Holm CK, Heine H, Pai AA, Hall AO, Hoebe K, Fitzgerald KA | The lncRNA LUCAT1 is elevated in inflammatory disease and retrains inflammation by regulating the splicing and stability of NR4A1 | PNAS | 2023 | |
| 36 | Wang F, Calvo-Roitberg E, Rembetsy-Brown JM, Fang M, Sousa J, Krishnamurthy PM, Lee J, Green MR, Pai AA, Watts JK | Intron-targeting antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects | Nucleic Acids Research | 2022 | |
| 35 | Valton AL, Venev SV, Mair B, Khokhar ES, Tong AY, Usaj M, Chan KSK, Pai AA, Moffat J, Dekker J | A cohesion traffic pattern genetically linked to gene regulation | Nature Structural Molecular Biology | 2022 | |
| 34 | Pai AA*, Li YI*, Provero P* | Editorial: Alternative polyadenylation in development and disease | Frontiers in Genetics | 2022 | |
| 33 | MacMillan H*, Kong Y*, Calvo-Roitberg E, Alonso LC, Pai AA. | High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets | Scientific Reports | 2022 | |
| 32 | Fiszbein A, McGurk M, Calvo-Roitberg E, Kim GY, Burge CB, Pai AA | Widespread occurrence of hybrid internal-terminal exons in human transcriptomes | Science Advances | 2022 | |
| 31 | Ibraheim R, Tai PWL, Mir A, Javeed N, Wang J, Rodriquez T, Nelson S, Khokhar E, Mintzer E, Maitland S, Cao Y, Tsagkaraki E, Wolfe SA, Wang D, Pai AA, Xue W, Gao G, Sontheimer EJ | Precision Cas9 Genome Editing in vivo with All-in-one, Self-targeting AAV Vectors | Nature Communications | 2021 | |
| 30 | 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 | Nature Biotechnology | 2019 | |
| 29 | Pai AA and Luca F | Environmental influences on RNA processing: biochemical, molecular, and genetic regulators of cellular response | WIREs RNA | 2018 | |
| 28 | 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 | 2018 | |
| 27 | Pai AA*, Paggi JM*, Yan P, Adelman K, Burge CB | Numerous recursive sites contribute to accuracy of splicing of long introns in flies | PLOS Genetics | 2018 | |
| 26 | Aguiar D, Cheng L, Dumitrascu B, Mordelet F, Pai AA, Engelhardt BE | BIISQ: Bayesian nonparametric discovery of Isoforms and Individual Specific Quantification from RNA-seq data | Nature Communications | 2018 | |
| 25 | 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 | |
| 24 | 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 | 2017 | |
| 23 | Pai AA*, Baharian G*, Sabourin AP, Brinkworth JF, Nedelec Y, Foley JW, Grenier JC, Siddle KJ, Dumaine A, Yotova Y, 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 response to infection | PLOS Genetics | 2016 | |
| 22 | 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 | 2016 | |
| 21 | Pacis A, Tailleux L, Amorim A, Lambourne J, MacIssac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai AA, Tung J, He C, Pastinen T, Kobor MS, Pique-Regi R, Gilad Y, Barreiro LB | Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells | Genome Research | 2015 | |
| 20 | Pai AA, Pritchard JK, Gilad Y | The genetic and mechanistic basis for variation in gene regulation | PLOS Genetics | 2015 | |
| 19 | Pai AA and Gilad, Y | Comparative studies of gene regulatory mechanisms | Current Opinions in Genetics and Development | 2014 | |
| 18 | Gallego Romero I, Pai AA, Tung J, Gilad Y | Impact of RNA degradation on measurements of gene expression | BMC Biology | 2014 | |
| 17 | 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 | 2012 | |
| 16 | Pai AA, Cain CE, Man O, Veyrieras J-B, De Leon S, Lewellen N, 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 | 2012 | |
| 15 | 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 | PNAS | 2012 | |
| 14 | 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 | 2012 | |
| 13 | Degner JF*, Pai AA*, Pique-Regi R*, Veyrieras J-B, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, †Gilad Y, †Pritchard JK | DNaseI sensitivity QTLs are a major determinant of human expression variation | Nature | 2012 | |
| 12 | Gaffney DJ, Veyrieras J-B, 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 | 2012 | |
| 11 | Barreiro LB*, Tailleux L*, Pai AA, Gicquel B, Marioni JC, Gilad Y | Deciphering the genetic architecture of immune responses to Mycobacterium tuberculosis infection | PNAS | 2012 | |
| 10 | 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 | 2011 | |
| 9 | 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 samples | Genome Biology | 2011 | |
| 8 | Stefflova K, Dulik MC, Barnholtz-Sloan JS, Pai AA, Walker AH, Rebbeck T | Dissecting the Within-Africa Ancestry of Populations of African Descent in the Americas | PLOS One | 2011 | |
| 7 | 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 | 2011 | |
| 6 | Pickrell JK, Pai AA, Gilad Y, Pritchard JK | Noisy splicing drives mRNA isoform diversity in human cells | PLOS Genetics | 2010 | |
| 5 | Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J-B, Stephens M, Gilad Y, and Pritchard JK | Understanding mechanisms underlying gene expression variation in humans with RNA sequencing | Nature | 2010 | |
| 4 | Stefflova K, Dulik MC, Pai AA, Walker AH, Zeigler-Johnson C, Gueye SM, Schurr TG, and Rebbeck T | Evaluation of group genetic ancestry of populations from Philadelphia and Dakar in the context of sex-biased admixture in the Americas | PLOS One | 2009 | |
| 3 | Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, and Pritchard JK | Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. | Bioinformatics | 2009 | |
| 2 | Gokcumen O, Dulik MC, Pai AA, Zhadanov SI, Rubenstein S, Osipova LP, Andreenkov OV, Tabikhanova LE, Gubina MA, Labuda D, and Schurr TG | Genetic variation in the enigmatic Altaian Kazakhs of South-Central Russia: insights into Turkic population history | American Jounal of Physical Anthropology | 2008 | |
| 1 | McDaniell R, Warthen DM, Sanchez-Lara PA, Pai A, Krantz ID, Piccoli DA, and Spinner NB | NOTCH2 mutations cause Alagille syndrome, a heterogeneous disorder of the notch signaling pathway | American Jounal of Human Genetics | 2006 |