Sequence-free identification of enhancers identifies conserved patterns of chromatin.
Gafur J, Lang OW, Lai WKM.
Submitted 2024.

Adversarial Robustness and Explainability of Machine Learning Models.
Gafur J, Goddard S, Lai WKM.
Practice and Experience in Advanced Research Computing 2024, https://doi.org/10.1145/3626203.3670522

Multi-dimensional analyses identify genes of high priority for pancreatic cancer research.
Nwosu ZC, Giza H, Nassif M, Charlestin V, Menjivar RE, Kim D, Kemp SB, Lai WKM, Loveless I, Steele NG, Hu J, Hu B, Wang S, Magliano MP, Lyssiotis CA.
JCI Insight (accepted) 2024, https://www.biorxiv.org/content/10.1101/2021.05.28.446056v2

GenoPipe: identifying the genotype of origin within (epi)genomic datasets.
Lang O, Srivastava D, Pugh BF, Lai WKM.
Nucleic Acids Research 2023, Nucleic Acids Research 51 (22), 12054-12068. PMID: 37933851; PMCID: PMC10711449.

Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin.
Arora S, Yang J, Akiyama T, James DQ, Morrissey A, Blanda TR, Badjatia N, Lai WKM, Ko MSH, Pugh BF, Mahony S.
bioArxiv 2023, https://doi.org/10.1101/2023.10.06.561228

ScriptManager: an interactive platform for reducing barriers to genomics analysis.
Lang O, Pugh BF, Lai WKM.
Practice and Experience in Advanced Research Computing 2022, https://doi.org/10.1145/3491418.3535161

An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters.
Mittal C, Lang O, Lai WKM, Pugh BF.
Genome Research 2022, 36(17-18):985-1001. PMID: 36302553 PMCID: PMC9732905

Genome-wide promoter assembly in E. coli measured at single-base resolution.
John J, Jabbar J, Badjatia N, Rossi MJ, Lai WKM, Pugh BF.
Genome Research 2022, 32(5):878-892. PMID: 35483960 PMCID: PMC9104697

PEGR: a flexible management platform for reproducible epigenomic and genomic research.
Shao D, Kellogg G, Nematbakhsh A, Kuntala PK, Mahony S, Pugh BF, Lai WKM.
Genome Biology 2022, 19;23(1):99. PMID: 35440038 PMCID: PMC9016988

STENCIL: A web templating engine for visualizing and sharing life science datasets.
Sun Q, Nematbakhsh A, Kuntala PK, Kellogg G, Pugh BF, Lai WKM.
PLoS Computational Biology. 2022 Feb 9;18(2):e1009859. doi: 10.1371/journal.pcbi.1009859. PMID: 35139076; PMCID: PMC8863220.

Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae.
Zhao T, Vvedenskaya IO, Lai WKM, Basu S, Pugh BF, Nickels BE, Kaplan CD.
eLife. 2021, 10:e71013. doi:10.7554/eLife.71013. PMID: 34652274; PMCID: PMC8589449.

A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.
Lai WKM, Mariani L, Rothschild G, Smith ER, Venters BJ, Blanda TR, Kuntala PK, Bocklund K, Mairose J, Dweikat SN, Mistretta K, Rossi MJ, James D, Anderson JT, Phanor SK, Zhang W, Zhao Z, Shah AP, Novitzky K, McAnarney E, Keogh MC, Shilatifard A, Basu U, Bulyk ML, Pugh BF.
Genome Research. 2021, 31(9):1663-1679. doi: 10.1101/gr.275472.121. PMID: 34426512; PMCID: PMC8415381.

A high-resolution protein architecture of the budding yeast genome.
Rossi MJ, Kuntala PK, Lai WKM, Yamada N, Badjatia N, Mittal C, Kuzu G, Bocklund K, Farrell NP, Blanda TR, Mairose JD, Basting AV, Mistretta KS, Rocco DJ, Perkinson ES, Kellogg GD, Mahony S, Pugh BF.
Nature. 2021, 592(7853):309-314. doi: 10.1038/s41586-021-03314-8. PMID: 33692541; PMCID: PMC8035251.

Acute stress drives global repression through two independent RNA polymerase II stalling events in Saccharomyces.
Badjatia N, Rossi MJ, Bataille AR, Mittal C, Lai WKM, Pugh BF.
Cell Reports. 2021, 34(3):108640. doi: 10.1016/j.celrep.2020.108640. PMID: 33472084; PMCID: PMC7879390.

Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae.
Qiu C, Jin H, Vvedenskaya I, Vvedenskaya I, Llenas JA, Zhao T, Malik I, Visbisky AM, Schwartz SL, Cui P, Čabart P, Han KH, Lai WKM, Metz RP, Johnson CD, Sze SH, Pugh BF, Nickels BE, Kaplan CD.
Genome Biology. 2020, 21(1):132. doi: 10.1186/s13059-020-02040-0. PMID: 32487207; PMCID: PMC7265651.

Characterizing protein-DNA binding event subtypes in ChIP-exo data.
Yamada N, Lai WKM, Farrell N, Pugh BF, Mahony S.
Bioinformatics. 2019, 35(6):903-913. doi: 10.1093/bioinformatics/bty703. PMID: 30165373; PMCID: PMC6419906.

Simplified ChIP-exo assays.
Rossi MJ, Lai WKM, Pugh BF.
Nature Communications. 2018, 9(1):2842. doi: 10.1038/s41467-018-05265-7. PMID: 30030442; PMCID: PMC6054642.

Genome-wide determinants of sequence-specific DNA binding of general regulatory factors.
Rossi MJ, Lai WKM, Pugh BF.
Genome Research. 2018, 28(4):497-508. doi: 10.1101/gr.229518.117. PMID: 29563167; PMCID: PMC5880240.

Understanding nucleosome dynamics and their links to gene expression and DNA replication.
Lai WKM, Pugh BF.
Nature Reviews Molecular Cell Biology. 2017, 18(9):548-562. doi: 10.1038/nrm.2017.47. EPMID: 28537572; PMCID: PMC5831138.

Correspondence: DNA shape is insufficient to explain binding.
Rossi MJ, Lai WKM, Pugh BF.
Nature Communications. 2017, 8:15643. doi: 10.1038/ncomms15643. Erratum in: Nat Commun. 2017 Jun 05;8:15723. PMID: 28580956; PMCID: PMC5465349.

Genome-wide uniformity of human ‘open’ pre-initiation complexes.
Lai WKM, Pugh BF.
Genome Research. 2017, 27(1):15-26. doi: 10.1101/gr.210955.116. PMID: 27927716; PMCID: PMC5204339.

Chromatin mediation of a transcriptional memory effect in yeast.
Paul E, Tirosh I, Lai W, Buck MJ, Palumbo MJ, Morse RH.
G3: Genes|Genomes|Genetics. 2015, 5(5):829-38. doi: 10.1534/g3.115.017418. PMID: 25748434; PMCID: PMC4426369.

Iron-responsive chromatin remodelling and MAPK signalling enhance adhesion in Candida albicans.
Puri S, Lai WKM, Rizzo JM, Buck MJ, Edgerton M.
Molecular Microbiology. 2014, 93(2):291-305. doi: 10.1111/mmi.12659. PMID: 24889932; PMCID: PMC4107033.

An integrative approach to understanding the combinatorial histone code at functional elements.
Lai WKM, Buck MJ.
Bioinformatics. 2013, 29(18):2231-7. doi: 10.1093/bioinformatics/btt382. PMID: 23821650.PMCID: PMC4107033.

Chromatin architectures at fission yeast transcriptional promoters and replication origins.
Givens RM, Lai WKM, Rizzo JM, Bard JE, Mieczkowski PA, Leatherwood J, Huberman JA, Buck MJ.
Nucleic Acids Research. 2012, 40(15):7176-89. doi: 10.1093/nar/gks351. PMID: 22573177; PMCID: PMC3424540.

ArchTEx: accurate extraction and visualization of next-generation sequence data.
Lai WKM, Bard JE, Buck MJ.
Bioinformatics. 2012, 28(7):1021-3. doi: 10.1093/bioinformatics/bts063. PMID: 22302569.

ArchAlign: coordinate-free chromatin alignment reveals novel architectures.
Lai WKM, Buck MJ.
Genome Biology. 2010, 11(12):R126. doi: 10.1186/gb-2010-11-12-r126. PMID: 21182771; PMCID: P

Genome-wide search identifies Ccnd2 as a direct transcriptional target of Elf5 in mouse mammary gland.
Escamilla-Hernandez R, Chakrabarti R, Romano RA, Smalley K, Zhu QQ Lai W Halfon MS Buck MJ Sinha S.
BMC Molecular Biology. 2010, 11:68. doi: 10.1186/1471-2199-11-68. PMID: 20831799 PMCID: PMC2949602

Gene expression analysis of hepatic roles in cause and development of diabetes in Goto-Kakizaki rats.
Almon RR, DuBois DC, Lai W, Xue B, Nie J, Jusko WJ.
Journal of Endocrinology. 2009, 11:68. doi: 10.1186/1471-2199-11-68. PMID: 20831799 PMCID: PMC2949602

Relationships between Circadian Rhythms and Modulation of Gene Expression by Glucocorticoids in Skeletal Muscle.
Almon RR, Yang E, Lai W, Androulakis IP, Ghimbovschi S, Hoffman EP, Jusko WJ, DuBois DC.
American Journal of Physiology-Regulatory, Integrative and Comparative Physiology. 2008, 295(4):R1031-47. doi: 10.1152/ajpregu.90399.2008. PMID: 18667713 PMCID: PMC2576101

Circadian variations in rat liver gene expression: relationships to drug actions.
Almon RR, Yang E, Lai W, Androulakis IP, DuBois DC, Jusko WJ.
Journal of Pharmacology and Experimental Therapeutics. 2008, 26(3):700-16. doi: 10.1124/jpet.108.140186. PMID: 18562560 PMCID: PMC2561907

Corticosteroid-regulated Genes in Rat Kidney: Mining Time Series Data.
Almon RR, Lai W, DuBois DC, Jusko WJ.
American Journal of Physiology-Endocrinology and Metabolism. 2005, 289(5):E870-82. doi: 10.1152/ajpendo.00196.2005. PMID: 15985454 PMCID: PMC3752664