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† Indicates co-senior authors
underline Indicates Lab Members

[71] Enhanced detection and genotyping of disease-associated tandem repeats using hmmstr and targeted long-read sequencing.
Van Deynze K, Mumm C, Maltby CJ, Switzenberg JA, Todd PK, Boyle AP. submitted 2024.
 
 
[70] Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration.
Crone B, Boyle AP. bioRxiv 2024.
   
 
[69] Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders.
Lee S, McAfee JC, Sharp RR, Clarke D, Gerstein MB, Boyle AP, Sullivan PF, Love MI, Won H. submitted 2023.
 
 
[68] Organ-specific prioritization and annotation of non-coding regulatory variants in the human genome.
Zhao N, Dong S, Boyle AP. bioRxiv 2023.
       
 
[67] EGL-43 and FOS-1 directly activate synaptic genes and coordinate mRNA export with transcription.
Yee C, Xiao Y, Chen H, Reddy A, Xu R, Medwig-Kinney T, Zhang W, Boyle AP, Xiang YK, Matus DQ, Shen K. submitted 2023.
 
 
[66] Explain-seq: an end-to-end pipeline from training to interpretation of sequence-based deep learning models.
Zhao N, Wang S, Huang Q, Dong S, Boyle AP. bioRxiv 2023.
       
 
[65] Quantitative assessment of association between noncoding variants and transcription factor binding.
Ouyang N, Boyle AP. bioRxiv 2022.
       
 
[64] DNA methylation directs nucleosome positioning in RNA-mediated transcriptional silencing.
Rothi MH, Sethuraman S, Dolata J, Boyle AP, Wierzbicki AT. bioRxiv 2020.
       
 
[63] The Impact of Genomic Variation on Function (IGVF) Consortium.
IGVF Consortium. Nature, Accepted 2024.
       
 
[62] CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.
The Critical Assessment of Genome Interpretation Consortium. Genome Biology 2024, 25:53. PMID: 38389099.
       
 
[61] HaplotagLR: an efficient and configurable utility for haplotagging long reads.
Holmes MJ, Mahjour B, Castro CP, Farnum GA, Diehl AG, Boyle AP. PLoS ONE 2024, 19(3):1–15. PMID: 38478504.
       
 
[60] Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants.
McAfee JC, Lee S, Lee J, Bell JL, Krupa O, Davis J, Insigne K, Bond ML, Zhao N, Boyle AP, Phanstiel DH, Love MI, Stein JL, Ruzicka WB, Davila-Velderrain J, Kosuri S, Won H. Cell Genomics 2023, 3:100404. PMID: 37868037.
       
 
[59] Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1.
Moritz L, Schon SB, Rabbani M, Sheng Y, Agrawal R, Glass-Klaiber J, Sultan C, M CJ, Clements J, Baldwin MR, Diehl AG, Boyle AP, O'Brien PJ, Ragunathan K, Hu YC, Kelleher NL, Nandakumar J, Li JZ, Orwig KE, Redding S, Hammoud SS. Nature Structural & Molecular Biology 2023. PMID: 37460896.
       
 
[58] Challenges in screening for de novo noncoding variants contributing to genetically complex phenotypes.
Castro CP, Diehl AG, Boyle AP. Human Genetics and Genomics Advances 2023, 4(3):100210. PMID: 37305558.
       
 
[57] OnRamp: rapid nanopore plasmid validation.
Mumm C, Drexel ML, McDonald TL, Diehl AG, Switzenberg JA, Boyle AP. Genome Research 2023, 33(5):741–749. PMID: 37156622.
       
 
[56] Annotating and prioritizing human non-coding variants with RegulomeDB v.2.
*Dong S, *Zhao N, Spragins E, Kagda MS, Li M, Assis PR, Jolanki O, Luo Y, Cherry JM, †Boyle AP, †Hitz BC. Nature Genetics 2023, 55(5):724–726. PMID: 37173523.
       
 
[55] SEMplMe: A tool for integrating DNA methylation effects in transcription factor binding affinity predictions.
Nishizaki SS, Boyle AP. BMC Bioinformatics 2022, 23:317. PMID: 35927613.
       
 
[54] Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.
Qin T, Lee C, Li S, Cavalcante RG, Orchard P, Yao H, Zhang H, Wang S, Patil S, Boyle AP, Sartor MA. Genome Biology 2022, 23:105. PMID: 35473573.
       
 
[53] SquiggleNet: real-time, direct classification of nanopore signals.
Bao Y, Wadden J, Erb-Downward JR, Ranjan P, Zhou W, McDonald TL, Mills RE, Boyle AP, Dickson RP, Blaauw D, Welch JD. Genome Biology 2021, 22:298. PMID: 34706748.
       
 
[52] Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome.
Dong S, Boyle AP. Nucleic Acids Research 2021, 50:e6–e6. PMID: 34648033.
       
 
[51] Cas9 targeted enrichment of mobile elements using nanopore sequencing.
*McDonald TL, *Zhou W, Castro CP, Mumm C, Switzenberg JA, †Mills RE, †Boyle AP. Nature Communications 2021, 12:3586. PMID: 34117247.
       
 
[50] The inducible lac operator-repressor system is functional in zebrafish cells.
*Nishizaki SS, *McDonald TL, Farnum GA, Holmes MJ, Drexel ML, Switzenberg JA, Boyle AP. Frontiers in Genetics 2021, 12. PMID: 34220959.
       
 
[49] F-Seq2: improving the feature density based peak caller with dynamic statistics.
Zhao N, Boyle AP. NAR Genomics and Bioinformatics 2021, 3. PMID: 33655209.
       
 
[48] Broad noncoding transcription suggests genome surveillance by RNA polymerase V.
*Tsuzuki M, *Sethuraman S, Coke AN, Rothi MH, Boyle AP, Wierzbicki AT. Proceedings of the National Academy of Sciences 2020, 117(48):30799–30804. PMID: 33199612.
       
 
[47] MapGL: Inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony.
Diehl AG, Boyle AP. BMC Bioinformatics 2020, 21:416. PMID: 32962625.
       
 
[46] Perspectives on ENCODE.
The ENCODE Project Consortium. Nature 2020, 583(7818):693–698. PMID: 32728248.
       
 
[45] Expanded encyclopaedias of DNA elements in the human and mouse genomes.
The ENCODE Project Consortium. Nature 2020, 583(7818):699–710. PMID: 32728249.
       
 
[44] TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.
Ouyang N, Boyle AP. Genome Research 2020, 30:1040–1046. PMID: 32660981.
       
 
[43] Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes.
Diehl AG, Ouyang N, Boyle AP. Nature Communications 2020, 11:1796. PMID: 32286261.
       
 
[42] Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions.
Lee CT, Cavalcante RG, Lee C, Qin T, Patil S, Wang S, Tsai Z, Boyle AP, Sartor MA. NAR Genomics and Bioinformatics 2020, 2. PMID: 32051932.
       
 
[41] Predicting the effects of SNPs on transcription factor binding affinity.
Nishizaki SS, Ng N, Dong S, Porter RS, Morterud C, Williams C, Asman C, Switzenberg JA, Boyle AP. Bioinformatics 2019, 50:2434. PMID: 31373606.
       
 
[40] CGIMP: Real-time exploration and covariate projection for self-organizing map datasets.
Diehl AG, Boyle AP. Journal of Open Source Software 2019, 4(39):1520.
       
 
[39] The ENCODE Blacklist: Identification of Problematic Regions of the Genome.
Amemiya HM, †Kundaje A, †Boyle AP. Scientific Reports 2019, 9:9354. PMID: 31249361.
       
 
[38] Predicting functional variants in enhancer and promoter elements using RegulomeDB.
Dong S, Boyle AP. Human Mutation 2019, 33(8):831. PMID: 31228310.
       
 
[37] Integration of Multiple Epigenomic Marks Improves Prediction of Variant Impact in Saturation Mutagenesis Reporter Assay.
Shigaki D, Adato O, Adhikar AN, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar DP, Schubach M, Xiong C, Yan Z, Boyle AP, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, Beer MA. Human mutation 2019, 33(8):831. PMID: 31106481.
       
 
[36] Cell specificity of regulatory annotations and their genetic effects on gene expression.
Varshney A, VanRenterghem H, Orchard P, †Boyle AP, †Stitzel ML, †Ucar D, Parker SC. Genetics 2019, 211(2):549–562. PMID: 30593493.
       
 
[35] Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.
Diehl AG, Boyle AP. Nucleic Acids Research 2018, 46(4):1878–1894. PMID: 29361190.
       
 
[34] Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development.
Nielsen JB, Fritsche LG, Zhou W, Teslovich TM, Holmen OL, Gustafsson S, Gabrielsen ME, Schmidt EM, Beaumont R, Wolford BN, Lin M, Brummett CM, Preuss MH, Refsgaard L, Bottinger EP, Graham SE, Surakka I, Chu Y, Skogholt AH, Dalen H, Boyle AP, Oral H, Herron TJ, Kitzman J, Jalife J, Svendsen JH, Olesen MS, Njølstad I, Løchen ML, Baras A, Gottesman O, Marcketta A, O'Dushlaine C, Ritchie MD, Wilsgaard T, Loos RJF, Frayling TM, Boehnke M, Ingelsson E, Carey DJ, Dewey FE, Kang HM, Abecasis GR, Hveem K, Willer CJ. American Journal of Human Genetics 2017, 102:103–115. PMID: 29290336.
       
 
[33] A proximity-based graph clustering method for the identification and application of transcription factor clusters.
Spadafore M, Najarian K, Boyle AP. BMC Bioinformatics 2017, 18:530. PMID: 29187152.
       
 
[32] Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve.
*Yang B, *Zhou W, *Jiao J, Nielsen JB, Mathis MR, Heydarpour M, Lettre G, Folkersen L, Prakash S, Schurmann C, Fritsche L, Farnum GA, Lin M, Othman M, Hornsby W, Driscoll A, Levasseur A, Thomas M, Farhat L, Dubé MP, Isselbacher EM, Franco-Cereceda A, Guo Dc, Bottinger EP, Deeb GM, Booher A, Kheterpal S, Chen YE, Kang HM, Kitzman J, Cordell HJ, Keavney BD, Goodship JA, Ganesh SK, Abecasis G, Eagle KA, Boyle AP, Loos RJF, †Eriksson P, †Tardif JC, †Brummett CM, †Milewicz DM, †Body SC, †Willer CJ. Nature Communications 2017, 8:15481. PMID: 28541271.
       
 
[31] Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms.
Nishizaki SS, Boyle AP. Trends in Genetics 2017, 33:34–45. PMID: 27939749.
       
 
[30] Deciphering ENCODE.
Diehl AG, Boyle AP. Trends in Genetics 2016, 32(4):238–249. PMID: 26962025.
       
 
[29] Mango: A bias correcting ChIA-PET analysis pipeline.
Phanstiel DH, Boyle AP, Heidari N, Snyder MP. Bioinformatics 2015. PMID: 26034063.
       
 
[28] Principles of regulatory information conservation between mouse and human.
*Cheng Y, *Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, †Hardison RC, †Snyder MP. Nature 2014, 515(7527):371–375. PMID: 25409826.
       
 
[27] A comparative encyclopedia of DNA elements in the mouse genome.
*Yue F, *Cheng Y, *Breschi A, *Vierstra J, *Wu W, *Ryba T, *Sandstrom R, *Ma Z, *Davis C, *Pope BD, *Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse ENCODE Consortium. Nature 2014, 515(7527):355–364. PMID: 25409824.
       
 
[26] Comparative analysis of regulatory information and circuits across distant species.
*Boyle AP, *Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, †White KP, †Kellis M, †Snyder M. Nature 2014, 512(7515):453–456. PMID: 25164757.
       
 
[25] Regulatory analysis of the C. elegans genome with spatiotemporal resolution.
Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M. Nature 2014, 512(7515):400–405. PMID: 25164749.
       
 
[24] Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures.
Phanstiel DH, Boyle AP, Araya CL, Snyder MP. Bioinformatics 2014. PMID: 24903420.
       
 
[23] Dynamic trans-acting factor colocalization in human cells.
*Xie D, *Boyle AP, *Wu L, Kawli T, Zhai J, Snyder M. Cell 2013, 155(3):713–724. PMID: 24243024.
       
 
[22] Extensive variation in chromatin states across humans.
*Kasowski M, *Kyriazopoulou-Panagiotopoulou S, *Grubert F, *Zaugg JB, *Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Science 2013, 342(6159):750–752. PMID: 24136358.
       
 
[21] Annotation of functional variation in personal genomes using RegulomeDB.
Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. Genome Research 2012, 22(9):1790–1797. PMID: 22955989.
       
 
[20] Linking disease associations with regulatory information in the human genome.
Schaub MA, Boyle AP, Kundaje A, †Batzoglou S, †Snyder M. Genome Research 2012, 22(9):1748–1759. PMID: 22955986.
       
 
[19] An integrated encyclopedia of DNA elements in the human genome.
The ENCODE Project Consortium. Nature 2012, 489(7414):57–74. PMID: 22955616.
       
 
[18] Architecture of the human regulatory network derived from ENCODE data.
*Gerstein MB, *Kundaje A, *Hariharan M, *Landt SG, *Yan KK, *Cheng C, *Mu XJ, *Khurana E, *Rozowsky J, *Alexander R, *Min R, *Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Nature 2012, 489(7414):91–100. PMID: 22955619.
       
 
[17] Personal omics profiling reveals dynamic molecular and medical phenotypes.
*Chen R, *Mias GI, *Li-Pook-Than J, *Jiang L, Lam HYK, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M. Cell 2012, 148(6):1293–1307. PMID: 22424236.
       
 
[16] Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
*Song L, *Zhang Z, *Grasfeder LL, *Boyle AP, *Giresi PG, *Lee B, *Sheffield NC, Graff S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, †Birney E, †Iyer VR, †Crawford GE, †Lieb JD, †Furey TS. Genome Research 2011, 21(10):1757–1767. PMID: 21750106.
       
 
[15] A user's guide to the encyclopedia of DNA elements (ENCODE).
The ENCODE Project Consortium. PLoS Biology 2011, 9(4):e1001046. PMID: 21526222.
       
 
[14] High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Boyle AP, Song L, Lee B, London D, Keefe D, Birney E, Iyer VR, †Crawford GE, †Furey TS. Genome Research 2011, 21:456–464. PMID: 21106903.
       
 
[13] Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.
*Stitzel ML, *Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SCJ, Boyle AP, Scott LJ, Margulies EH, Boehnke M, Furey TS, Crawford GE, Collins FS. Cell Metabolism 2010, 12(5):443–455. PMID: 21035756.
       
 
[12] Heritable individual-specific and allele-specific chromatin signatures in humans.
McDaniell R, Lee B, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, †Crawford GE, †Iyer VR, †Birney E. Science 2010, 328(5975):235–239. PMID: 20299549.
         
 
[11] Evidence-ranked motif identification.
Georgiev S, Boyle AP, Jayasurya K, Mukherjee S, Ohler U. Genome Biology 2010, 11(2):R19. PMID: 20156354.
       
 
[10] Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain.
Babbitt CC, Fedrigo O, Pfefferle AD, Boyle AP, Horvath JE, Furey TS, Wray GA. Genome Biology and Evolution 2010, 2:67–79. PMID: 20333225.
       
 
[9] DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2.
Xu X, Tsumagari K, Sowden J, Tawil R, Boyle AP, Song L, Furey TS, Crawford GE, Ehrlich M. Nucleic Acids Research 2009, 37(22):7381–7393. PMID: 19820107.
       
 
[8] High-resolution mapping studies of chromatin and gene regulatory elements.
Boyle AP, Furey TS. Epigenomics 2009, 1(2):319–329. PMID: 20514362.
       
 
[7] F-Seq: a feature density estimator for high-throughput sequence tags.
Boyle AP, Guinney J, Crawford GE, Furey TS. Bioinformatics 2008, 24(21):2537–2538. PMID: 18784119.
       
 
[6] High-resolution mapping and characterization of open chromatin across the genome.
Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, †Furey TS, †Crawford GE. Cell 2008, 132(2):311–322. PMID: 18243105.
       
 
[5] Identification of regulatory elements in archaea using self-organizing maps.
Boyle AP, Boyle JA, Bridges SM. In Proc RECOMB 2004.
   
 
[4] Global analysis of microbial translation initiation regions.
Boyle AP, Boyle JA. In Journal of the Mississippi Academy of Sciences, Volume 48 2003:138–150.
     
 
[3] Clustering of archael gene regulatory regions.
Boyle AP, Bridges S. In FASEB Journal, Volume 17 2003:A985–A985.
 
 
[2] Visualization of aligned genomic open reading frame data.
Boyle AP, Boyle JA. Biochemistry and Molecular Biology Education 2003, 31:64–68.
     
 
[1] Interactive clustering for exploration of genomic data.
Wan X, Boyle JA, Bridges SM, Boyle AP. In Proceedings of the Artificial Neural Networks in Engineering Conference, Volume 12, St. Louis, MO 2002:753–758.