Publications

Craig A, Ma L,  Revsine M, Wang L, Heinrich S, Rae Z, Ruchinskas A, Dadkhah K, Do W, Behrens S,  Mehrabadi F, Silveira MD, Dominguez D, Forgues M, Budhu A, Chaisaingmongkol  J, Hernandez J, Davis J, Tran B, Marquardt JU,  Ruchirawat M, Kelly M, Greten T, Wang X. Genome-Wide Profiling of Transcription Factor Activity in Primary Liver Cancer Using Single Cell ATAC Sequencing. http://dx.doi.org/10.2139/ssrn.4466480

Harrington BS, Kamdar R, Ning F, Korrapati S, Caminear MW, Hernandez LF, Butcher D, Edmondson EF, Traficante N, Hendley J; Australian Ovarian Cancer Study; Gough M, Rogers R, Lourie R, Shetty J, Tran B, Elloumi F, Abdelmaksoud A, Madhu ML, Mazan-Mamczarz K, House CD, Hooper JD, Annunziata CM: UGDH promotes tumor-initiating cells and a fibroinflammatory tumor microenvironment in ovarian cancer,(42)1:DOI: 10.1186/s13046-023-02820-z.PMID: 37858159.PMCID: PMC10585874.Published: 2023-10-19.

Osei-Amponsa V, Chandravanshi M, Lu X, Magidson V, Das S,Andresson T, Dyba M, Sabbasani VR, Swenson RE, Fromont C, Shrestha B, Zhao Y, Clapp ME, Chari R, Walters KJ: hRpn13 shapes the proteome and transcriptome through epigenetic factors HDAC8, PADI4, and transcription factor NF-κB p50,DOI: 10.1016/j.molcel.2023.11.035.PMID: 38151017.Published: 2023-12-01.

Kamdar RD, Harrington BS, Attar E, Korrapati S, Shetty J, Zhao Y, Tran B, Wong N, House CD, Annunziata CM: NF-κB signaling modulates miR-452-5p and miR-335-5p expression to functionally decrease epithelial ovarian cancer progression in tumor-initiating cells,24(9):7826,DOI: 10.3390/ijms24097826.PMID: 37175530.PMCID: PMC10178396.Published: 2023-05-24.

Pongor LS, Schultz CW, Rinaldi L, Wangsa D, Redon CE, Takahashi N, Fialkoff G, Desai P, Zhang Y, Burkett S, Hermoni N, Vilk N, Gutin J, Gergely R, Zhao Y, Nichols S, Vilimas R, Sciuto L, Graham C, Caravaca JM, Turan S, Shen T-W, Rajapakse VN, Kumar R, Upadhyay D, Kumar S, Kim YS, Roper N, Tran B, Hewitt SM, Kleiner DE, Aladjem MI, Friedman N, Hager GL, Pommier Y, Ried T, Thomas A: Extrachromosomal DNA amplification contributes to small cell lung cancer heterogeneity and is associated with worse outcomes,13(4):928-949,DOI: 10.1158/2159-8290.CD-22-0796.PMID: 36715552.PMCID: PMC10073312.Published: 2023-04-01.

Budhu A, Pehrsson EC, He A, Goyal L, Kelley RK, Dang H, Xie C, Monge C, Tandon M, Ma L, Revsine M, Kuhlman L, Zhang K, Baiev I, Lamm R, Patel K, Kleiner DE, Hewitt SM, Tran B, Shetty J, Wu X, Zhao Y, Shen TW, Choudhari S, Kriga Y, Ylaya K, Warner AC, Edmondson EF, Forgues M, Greten TF, Wang XW: Tumor biology and immune infiltration define primary liver cancer subsets linked to overall survival after immunotherapy,101052,DOI: 10.1016/j.xcrm.2023.101052.PMID: 37224815.Published: 2023-05-01.

Kamdar RD, Harrington BS, Attar E, Korrapati S, Shetty J, Zhao Y, Tran B, Wong N, House CD, Annunziata CM: NF-κB signaling modulates miR-452-5p and miR-335-3p expression to functionally decrease epithelial ovarian cancer progression in tumor-initiating cells,DOI: 10.3390/ijms24097826.Published: 2023-04-25.

Blech-Hermoni Y, Subedi K, Silver M, Jensen L, Coscia S, Kates MM, Zhao Y, Raley C, Edwards N, Tran B, Ray-Chaudhary A, Pathak P, Mankodi A: Expression of LIM domain-binding 3 (LDB3), a striated muscle Z-band alternatively spliced PDZ-motif protein in the nervous system,13(1):270,DOI: 10.1038/s41598-023-27531-5.PMID: 36609526.PMCID: PMC9822979.Published: 2023-01-01.

Thorell, K., Muñoz-Ramírez, Z.Y., Wang, D. et al. The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes. Nat Commun 14, 8184 (2023). https://doi.org/10.1038/s41467-023-43562-y

Talsania K, Shen TW, Chen X, Jaeger E, Li Z, Chen Z, Chen W, Tran B, Kusko R, Wang L, Pang AWC, Yang Z, Choudhari S, Colgan M, Fang LT, Carroll A, Shetty J, Kriga Y, German O, Smirnova T, Liu T, Li J, Kellman B, Hong K, Hastie AR, Natarajan A, Moshrefi A, Granat A, Truong T, Bombardi R, Mankinen V, Meerzaman D, Mason CE, Collins J , Stahlberg E, Xiao C, Wang C, Xiao W, Zhao Y: Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies,23(1):255,DOI: 10.1186/s13059-022-02816-6.PMID: 36514120.PMCID: PMC9746098.Published: 2022-12-01.

Hartford CCR, Shrestha RL, Pongor L, Zhao Y, Chen X, Fromont C, Chaudhary R, Li XL, Pasterczyk KR, Kumar R, Muys BR, Tsitsipatis D, Chari R, Gorospe M, Aladjem MI, Khan J, Basrai MA, Grammatikakis I, Lal A: Context-dependent function of long noncoding RNA PURPL in transcriptome regulation during p53 activation,42(12):e0028922,DOI: 10.1128/mcb.00289-22.PMID: 36342127.PMCID: PMC9753727.Published: 2022-12-15.

Caravaca JM, Mehta M, Gowda S, Tran B: ATAC sequencing protocol for cryopreserved mammalian Cells,12(2):e4294,DOI: 10.21769/BioProtoc.4294.PMID: 35127984.PMCID: PMC8799669.Published: 2022-01-01.

Song NY, Li X, Ma B, Willette-Brown J, Zhu F, Jiang C, Su L, Shetty J, Zhao Y, Shi G, Banerjee S, Wu X, Tran B, Nussinov R, Karin M, Hu Y: IKKα-deficient lung adenocarcinomas generate an immunosuppressive microenvironment by overproducing Treg-inducing cytokines,119(6):DOI: 10.1073/pnas.2120956119.PMID: 35121655.PMCID: PMC8833198.Published: 2022-02-08

Harrington BS, Kamdar R, Ning F, Korrapati S, Caminear MW, Hernandez LF, Butcher D, Edmondson EF, Traficante N, Hendley J, Gough M, Rogers R, Lourie R, Shetty J, Tran B, Elloumi F, Abdelmaksoud A, Lal Nag M, Mazan-Mamczarz K, House CD, Hooper JD, Annunziata CM: UGDH promotes tumor-initiating cells and a fibroinflammatory tumor microenvironment in ovarian cancer,Published: 2022-10-07.

Chang W, Jiao X, Sui H, Goswami S, Sherman BT, Fromont C, Caravaca JM, Tran B, Imamichi T: Complete genome sequence of herpes simplex virus 2 strain G,14(3):DOI: 10.3390/v14030536.PMID: 35336943.Published: 2022-03-01.

Latt KZ, Heymann J, Jessee JH, Rosenberg AZ, Berthier CC, Arazi A, Eddy S, Yoshida T, Zhao Y, Chen V, Nelson GW, Cam M,Kumar P, Mehta M, Kelly MC, Kretzler M, Nephrotic Syndrome Study Network (NEPTUNE)., Accelerating Medicines Partnership in Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium., Ray PE, Moxey-Mims M, Gorman GH, Lechner BL, Regunathan-Shenk R, Raj DS, Susztak K, Winkler CA, Kopp JB: Urine single-cell RNA sequencing in focal segmental glomerulosclerosis reveals inflammatory signatures,7(2):289-304,DOI: 10.1016/j.ekir.2021.11.005.PMID:

Shinzawa M, Moseman EA, Gossa S, Mano Y, Bhattacharya A, Guinter T, Alag A, Chen X, Cam M, McGavern DB, Erman B, Singer A. Reversal of the T cell immune system reveals the molecular basis for T cell lineage fate determination in the thymus. Nat Immunol. 2022 May;23(5):731-742. doi: 10.1038/s41590-022-01187-1. Epub 2022 Apr 29. PMID: 35523960; PMCID: PMC9098387.

Vo T, Brownmiller T, Hall K, Jones T, Choudhari S, Grammatikakis I, Ludwig K, Caplen N, HNRNPH1 destabilizes the G-quadruplex structures formed by G-rich RNA sequences that regulate the alternative splicing of an oncogenic fusion transcript, Nucleic Acids Research, 2022;, gkac409, https://doi.org/10.1093/nar/gkac409

Caceres-Gutierrez RE, Andonegui MA, Oliva-Rico DA, Gonzalez-Barrios R, Luna F, Arriaga-Canon C, Lopez-Saavedra A, Prada D, Castro C, Parmentier L, Diaz-Chavez J, Alfaro-Mora Y, Navarro-Delgado EI, Fabian-Morales E, Tran B, Shetty J, Zhao Y, Alcaraz N, De la Rosa C, Reyes JL, Hedouin S, Hube F, Francastel C, Herrera LA: Proteasome inhibition alters mitotic progression through the upregulation of centromericα-Satellite RNAs,DOI: 10.1111/febs.16261.PMID: 34739170.PMCID: PMC9299679.Published: 2021-11-05.

Zhao Y, Fang LT, Shen T-W, Choudhari S, Talsania K, Chen X, Shetty J, Kriga Y, Tran B, Zhu B, Chen Z, Chen W, Wang C, Jaeger E, Meerzaman D, Lu C, Idler K, Zheng Y, Shi L, Petitjean V, Sultan M, Hung T, Peters E, Drabek J, Vojta P, Maestro R, Gasparotto D, Koks S, Reimann E, Sherer A, Nordlund J, Liljedahl U, Foox J, Mason C, Xiao W: Whole genome and exome sequencing references datasets from a multi-center and cross-platform benchmark study,DOI: 10.1038/s41597-021-01077-5.PMID: 34753956.PMCID: PMC8578599.Published: 2021-11-09.

Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L,  Langenbach K,  de Mars M, Lu C, Idler K, Jacob H, Zheng Y, Ren L, Yu Y, Jaeger E, Schroth G, Abaan O, Talsania K, Lack J, Shen T-W, Chen Z, Stanbouly S, Tran B, Shetty J, Kriga Y, Meerzaman D, Nguyen C, Petitjean V, Sultan M, Cam M, Mehta M, Hung T, Peters E, Kalamegham R, Sahraeian SME, Mohiyuddin M, Guo Y, Yao L, Song L, Lam HYK, Drabek J, Vojta P, Maestro R, Gasparotto D, Koks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Jensen RV, Pirooznia M, Li Z, Xiao C, Sherry ST, Kusko R, Moos M, Donaldson E, Texak Z, Ning B, Tong W, Li J, Duerken-Hughes P, Catalanotti C, Maheshwari S, Shuga J, Liang WS, Keats J, Adkins J, Tassone E, Zismann V, McDaniel T, Trent J, Foox J, Butler D, Mason CE, Hong H, Leming S, Wang C, Xiao W, Somatic Mutation Working Group of Sequencing Quality Control Phase II Cortiumet al:Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing,39(9):1151-1160,DOI: 10.1038/s41587-021-00993-6.PMID: 34504347.PMCID: PMC8532138.Published: 2021-09-09.

Xiao W, Ren L, Chen Z, Fang LT, Zhao Y, Lack J, Guan M, Zhu B, Jaeger E, Kerrigan L, Blomquist TM, Hung T, Sultan M, Idler K, Lu C, Scherer A, Kusko R, Moos M, Xiao C, Sherry ST, Abaan OD, Chen W, Chen X, Nordlund J, Liljedahl U, Maestro R, Polano M, Drabek J, Vojta P, Kõks S, Reimann E, Madala BS, Mercer T, Miller C, Jacob H, Truong T, Moshrefi A, Natarajan A, Granat A, Schroth GP, Kalamegham R, Peters E, Petitjean V, Walton A, Shen TW, Talsania K, Vera CJ, Langenbach K, de Mars M, Hipp JA, Willey JC, Wang J,Shetty J, Kriga Y, Raziuddin A, Tran B, Zheng Y, Yu Y, Cam M, Jailwala P, Nguyen C, Meerzaman D, Chen Q, Yan C, Ernest B, Mehra U, Jensen RV, Jones W, Li JL, Papas BN, Pirooznia M, Chen YC, Seifuddin F, Li Z, Liu X, Resch W, Wang J, Wu L, Yavas G, Miles C, Ning B, Tong W, Mason CE, Donaldson E, Lababidi S, Staudt LM, Tezak Z, Hong H, Wang C, Shi L: Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing,39(9):1141-1150,DOI: 10.1038/s41587-021-00994-5.PMID: 34504346.Published: 2021-09-01.

Yan H, Malik N, Kim YI, He Y, Li M, Dubois W, Liu H, Peat TJ, Nguyen JT, Tseng YC, Ayaz G, Alzamzami W, Chan K, Andresson T, Tessarollo L, Mock BA, Lee MP, Huang J: Fatty acid oxidation is required for embryonic stem cell survival during metabolic stress,e52122,DOI: 10.15252/embr.202052122.PMID: 33950553.Published: 2021-05-01.

Crooks DR, Maio N, Lang M, Ricketts CJ, Vocke CD, Gurram S, Turan S, Kim YY, Cawthon GM, Sohelian F, De Val Alda N, Pfeiffer RM, Jailwala P, Tandon M, Tran B, Fan TWM, Lane AN, Ried T, Wangsa D, Malayeri AA, Merino MJ, Yang Y, Meier JL, Ball MW,  Rouault TA, Srinivasan R, Linehan WM: Mitochondrial DNA alterations underlie an irreversible shift to aerobic glycolysis in fumarate hydratase–deficient renal cancer,14(664):DOI: 10.1126/scisignal.abc4436.PMID: 33402335.Published: 2021-01-05.

Chang W, Jiao X, Sui H, Goswami S, Sherman BT, Fromont C, Caravaca J, Tran B, Imamichi T, Complete Genome Sequence of Herpes Simplex Virus 2 Strain G, Viruses. 2022 Mar; 14(3): 536.

Li D, Schaub N, Guerin T, Bapiro T, Richards F, Chen V, Talsania K, Kumar P, Gilbert D, Schlomer J, Kim S, Sorber R, Teper Y, Bautista W, Palena C, Ock C, Jodrell D, Pate N, Mehta M, Zhao Y,  Kozlov S, Rudloff U: T cell-mediated anti-tumor immunity cooperatively induced by TGFβR1 antagonism and gemcitabine counteracts reformation of the stromal barrier in pancreatic cancer,DOI: 10.1158/1535-7163.MCT-20-0620.PMID: 34376576.Published: 2021-08-10.

Lu X, Sabbasani VR, Osei-Amponsa V, Evans CN, King JC, Tarasov SG, Dyba M, Das S, Chan KC, Schwieters CD, Choudhari S, Fromont C, Zhao Y, Tran B, Chen X, Matsuo H, Andresson T, Chari R, Swenson RE, Tarasova NI, Walters KJ: Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma,DOI: 10.1038/s41467-021-27570-4.Published: 2021-12-16.

Ma L, Wang L, Khatib SA, Chang CW, Heinrich S, Dominguez DA, Forgues M, Candia J, Hernandez MO, Kelly M, Zhao Y, Tran B, Hernandez JM, Davis JL, Kleiner DE, Wood BJ, Greten TF, Wang XW: Single-cell atlas of tumor cell evolution in response to therapy in hepatocellular carcinoma and intrahepatic cholangiocarcinoma,DOI: 10.1016/j.jhep.2021.06.028.PMID: 34216724.Published: 2021-06-01.

Cáceres-Gutiérrez R,  Andonegui M, Oliva-Rico D, González-Barrios R, Luna F, Arriaga-Canon C, López-Saavedra A, Prada D, Castro C, Parmentier L, Díaz-Chávez J, Alfaro-Mora Y, Navarro-Delgado E, Fabian-Morales E, Tran B, Shetty J, Zhao Y, Alcaraz N, Rosa C, Reyes J, Hédouin S, Hubé F, Francastel C, Herrera L. Proteasome inhibition alters mitotic progression through the upregulation of centromeric α-Satellite RNAs. The FEBS Journal, 05 Nov, 2021 https://doi.org/10.1111/febs.16261

Heinrich B, Gertz EM, Schäffer AA, Craig A, Ruf B, Subramanyam V, McVey JC, Diggs LP, Heinrich S, Rosato U, Ma C, Yan C, Hu Y, Zhao Y, Shen TW, Kapoor V, Telford W, Kleiner DE, Stovroff MK, Dhani HS, Kang J, Fishbein T, Wang XW, Ruppin E, Kroemer A, Greten TF, Korangy F. The tumour microenvironment shapes innate lymphoid cells in patients with hepatocellular carcinoma. Gut. 2021 Aug 2:gutjnl-2021-325288. doi: 10.1136/gutjnl-2021-325288

Levin Y, Talsania K, Tran B, Shetty J, Zhao Y, Mehta M: Optimization for sequencing and analysis of degraded FFPE-RNA samples,160 /e61060:10,DOI: 10.3791/61060.PMID: 32568231.Published: 2020-06-08.

Jaynes JM, Sable R, Ronzetti M, Bautista W, Knotts Z, Abisoye-Ogunniyan A, Li D, Calvo R, Dashnyam M, Singh A, Guerin T, White J, Ravichandran S, Kumar P, Talsania K,Chen V, Ghebremedhin A, Karanam B, Bin Salam A, Amin R, Odzorig T, Aiken T, Nguyen V, Bian Y, Zarif JC, de Groot AE,Mehta M, Fan L, Hu X, Simeonov A, Pate N, Abu-Asab M, Ferrer M, Southall N, Ock CY, Zhao Y, Lopez H, Kozlov S,de Val N, Yates CC, Baljinnyam B, Marugan J, Rudloff U: Mannose receptor (CD206) activation in tumor-associated macrophages enhances adaptive and innate antitumor immune responses,12(530):DOI: 10.1126/scitranslmed.aax6337.PMID: 32051227.PMCID: PMC7832040.Published: 2020-02-01.

Ricketts CJ, Vocke CD, Lang M, Chen X, Zhao Y, Tran B, Tandon M, Schmidt LS, Ball MW, Linehan WM: A germline 1;3 translocation disrupting the VHL gene: a novel genetic cause for von Hippel-Lindau,59(1):18-22,DOI: 10.1136/jmedgenet-2020-107308.PMID: 33067352.PMCID: PMC8080673.Published: 2020-10-16.

Dai L, Hallmark L, Boffil De Ros X, Crouch H, Chen S, Shi T, Yang A, Lian C, Zhao Y, Tran B & Shuo Gu. Novel, Abundant Drosha Isoforms are Deficient in miRNA Processing in Cancer Cells.  Jounal RNA Biology. https://doi.org/10.1080/15476286.2020.1813439

Liu J, Tang W, Budhu A, Forgues M, Hernandez M, Candia J, Kim Y, Bowman E, Ambs S, Zhao Y, Tran B, Wu X, Koh C, Surana P, Liang T, Guarnera M, Mann D, Rajaure M, Greten T, Wang Z, Yu H, Wang X . A Viral Exposure Signature Defines Early Onset of Hepatocellular Carcinoma. Cell. June 10, 2020. DOI: 10.1016/j.cell.2020.05.038

Jaynes U, Sable R,  Ronzetti M, Bautista W, Bautista W, Knotts Z, Abisoye-Ogunniyan A, Li D, Calvo R, Dashnyam M, Singh A, Guerin T, White J, Ravichandran S, Kumar P, Talsania K, Chen V, Ghebremedhin A, Karanam B, Sallam A, Amin R, Odzorig T, Aiken T, Nguyen V,  Bian Y, Zarif J,  Groot A, Mehta M, Fan L, Hu X,  Simeonov A, Pate N, Abu-Asab M, Ferrer M, Southall N, Ock C, Zhao Y, Lopez H, Kozlov S, Val N, Yates C, Baljinnyam B, Marugan J, Rudloff U, (2020). Mannose receptor (CD206) activation in tumor-associated macrophages enhances adaptive and innate antitumor immune responses. Science Translational Medicine. 12. 6337. 10.1126/scitranslmed.aax63.

Gutierrez-Escobar AJ, Velaptino B, Borda V, Rabkin CS, Tarazona-Santos E, Cabrer, Cok J, Hooper CC, Jahuira-Arias H, Herrera P, Noureen M, Wang D, Romero-Gallo J, Tran B, Peek, Jr RM, Berg DE, Gilman RH, Camargo MC: Identification of new helicobacter pylori subpopulations in native Americans and mestizos from Peru,11:601839,DOI: 10.3389/fmicb.2020.601839.PMID: 33381095.PMCID: PMC7767971.Published: 2020-01-01.

Zhao Y*, Mehta M*, Walton A*, Talsania K*, Levin Y, Shetty J, Gillanders EM, Tran B, Carrick DM. Robustness of RNA sequencing on older formalin-fixedparaffin-embedded tissue from high-grade ovarian serous adenocarcinomas. PLoS  2019 May 6;14(5): e0216050.

Levin Y^†, Talsania K^†, Tran B, Shetty J*, Zhao Y*, Mehta M*. Optimization for sequencing and analysis of degraded FFPE-RNA samples. JoVE, In Press. (^† Co-first authors; * Co-corresponding authors)

Magen A, Nie J, Ciucci T, Tamoutounour S, Zhao Y, Mehta M, Tran B, McGavern DB, Hannenhalli S, Bosselut R. Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4⁺T Cells. Cell Reports, 2019, 29(10):  3019-3032.e6

The Somatic Mutation Working Group of the SEQC-II consortium, Xiao W, Kusko R, Ren L, Fang F, Shen T, Talsania K, Kriga Y, Shetty J, Tran B, Zhao Y, et al. Towards best practice in cancer mutation detection with whole-genome and whole-exome sequencing.  Nat Biotechnol, 2019. Accepted

Ma L, Hernandez M, Zhao Y, Mehta M, Tran B, Kelly M, Rae Z, Hernandez J, Davis J, Martin S, Kleiner D, Hewitt S, Ylaya K, Wood B, Greten T, Wang X. Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer.  Cancer Cell. 2019 Oct 03.

Jiao X, Sui H, Lyons C, Tran B, Sherman BT, Imamichi T. Complete Genome Sequence of Herpes Simplex Virus 1 Strain McKrae. Microbiol Resour Announc. 2019 Sep 26;8(39).

Vacchio MS, Ciucci T, Gao Y, Watanabe M, Balmaceno-Criss M, McGinty MT, Huang A, Xiao Q, McConkey C, Zhao Y, Shetty J, Tran B, Pepper M, Vahedi G, Jenkins MK,  McGavern DB, Bosselut R. A Thpok-Directed Transcriptional Circuitry Promotes Bcl6 and Maf Expression to Orchestrate T Follicular Helper Differentiation. Immunity.  2019 Sep 17;51(3):465-478.e6. Epub 2019 Aug 15.

Talsania K, Mehta M, Raley C, Kriga Y, Gowda S, Grose C, Drew M, Roberts V, Tai Cheng K, Burkett S, Oeser S, Stephens R, Soppet D, Chen X, Kumar P, German O, Smirnova T, Hautman C, Shetty J, Tran B, Zhao Y, & Esposito D. Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies. Gene, 2019, 10 (2). pii: E79.

Ciucci T, Vacchio MS, Gao Y, Ardori FT, Candia J, Mehta M, Zhao Y, Tran B, Tessarollo L, McGavern D, & Bosselut R. Emergence and functional fitness of memory CD4+ T cells require the transcription factor Thpok. Immunity, 2019, 50(1): 91-105.e4.

Zheng H, Pomyen Y, Hernandez MO, Li C, Livak F, Tang W, Dang H, Greten T, Zhao Y, Mehta M, Levin Y, Shetty J, Tran B, Budhu A, and Wang XW. Single cell analysis reveals cancer stem cell heterogeneities in hepatocellular carcinoma. Hepatology, 2018, 68(1): 127-140.

Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W,  Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396-1407.

Miller ME, Zhang Y, Omidvar V, Sperschneider J, Schwessinger B, Raley C, Palmer JM, Garnica D, Upadhyaya N, Rathjen J, Taylor JM, Park RF, Dodds PN, Hirsch CD, Kianian SF, Figueroa M:De Novo assembly and phasing of dikaryotic genomes from two isolates of puccinia coronata f. sp. avenae, the causal agent of oat crown rust.MBio, 9(1):2018.

Greer YE, Porat-Shliom N, Nagashima K, Stuelten C, Crooks D, Koparde VN, Gilbert SF, Islam C, Ubaldini A, Ji Y, Gattinoni L, Soheilian F, Wang X, Hafner M, Shetty J, Tran B, Jailwala P, Cam M, Lang M, Voeller D, Reinhold WC, Rajapakse V, Pommier Y, Weigert R, Linehan WM, Lipkowitz S. ONC201 kills breast cancer cells in vitro by targeting mitochondria. Oncotarget. 2018 Apr 6;9(26):18454-18479.

Cramer SD, Hixon JA, Andrews C, Porter RJ, Rodrigues GOL, Wu X, Back T, Czarra K, Michael H, Cam M, Chen J, Esposito D, Senkevitch E, Negi V, Aplan PD, Li W, Durum SK. Mutant IL-7Rα and mutant NRas are sufficient to induce murine T cell acute lymphoblastic leukemia. Leukemia. 2018 Aug;32(8):1795-1882.

Shukla A, Zhu J, Kim SY, Hager G, Ruan Y and Hunter KW (2017) Identification of a core inherited metastatic susceptibility network by integrated epigenetic, genetic and chromosomal interaction analysis.  Manuscript in preparation

Carpenter AC, Wohlfert E, Chopp LB, Vacchio MS, Nie J, Zhao Y, Shetty J, Xiao Q, Deng C, Tran B, Cam M, Gaida MM, Belkaid Y, Bosselut R. Control of Regulatory T Cell Differentiation by the Transcription Factors Thpok and LRF.   J Immunol. 2017 Sep 1;199(5): 1716-1728.

Hodson DJ, Shaffer AL, Xiao W, Wright GW, Schmitz R, Phelan JD, Yang Y, Webster DE, Rui L, Kohlhammer H, Nakagawa M, Waldmann TA, Staudt LM.  Regulation of normal B cell differentiation and malignant B cell survival by OCT2.  Proc Natl Acad Sci 2016 113:E2039-E2046.

Thompson, Bethtrice; Varticovski, Lyuba; Baek, Songjoon; et al. Hager GL. Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation. PLOS ONE   Volume: 11   Issue: 2

Yang Y, Kelly P, Shaffer AL, Schmitz R, Liu X, Huang DW, Webster D, Young RM, Yoo H, Nakagawa M, Ceribelli M, Wright GW, Yang Y, Zhao H, Yu X, Xu W, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza L, Staudt LM.  Targeting non-proteolytic protein ubiquitination for the treatment of diffuse large B cell lymphoma.  Cancer Cell 2016 29:494-507.

Kuschal C, Botta E, Orioli D, Digiovanna JJ, Seneca S, Keymolen K, Tamura D, Heller E, Khan SG, Caligiuri G, Lanzafame M, Nardo T, Ricotti R, Peverali FA, Stephens R, Zhao Y, Lehmann AR, Baranello L, Levens D, Kraemer KH, Stefanini M. GTF2E2 Mutations Destabilize the General Transcription Factor Complex TFIIE in Individuals with DNA Repair-Proficient Trichothiodystrophy.  Am J Hum Genet. 2016 Apr 7;98(4):627-42.

Liang M, Raley C, Zheng X, Kutty G, Gogineni E, Sherman BT, Sun Q, Chen X,  Skelly T, Jones K, Stephens R, Zhou B, Lau W, Johnson C, Imamichi T, Jiang M, Dewar R, Lempicki RA, Tran B, Kovacs JA, Huang DW. Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads. BioData Min. 2016 Apr 5; 9:13.

Huang DW, Raley C, Jiang MK, Zheng X, Liang D, Rehman MT, Highbarger HC, Jiao X, Sherman B, Ma L, Chen X, Skelly T, Troyer J, Stephens R, Imamichi T, Pau A, Lempicki RA, Tran B, Nissley D, Lane HC, Dewar RL. Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level.   J Data Mining Genomics Proteomics. 2016Jan;7(1). pii: 182. Epub 2015 Nov 8.

Ma L, Chen Z, Huang da W, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA. Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts. Nat Commun. 2016 Feb 22;7:10740.

Rui L, Drennan AC, Ceribelli M, Zhu F, Wright GW, Xiao W, Grindle KM, Lu L, Hodson DJ, Zhao H, Xu W, Yang Y, Staudt LM.  Epigenetic gene regulation by Janus kinase 1 in diffuse large B cell lymphoma. Proc Natl Acad Sci, in press, 2016.

Smith OK, Kim RG, Fu H, Martin M, Utani K, Zhang Y, Marks AB, Lalande M, Chamberlaine S, Libbrecht MW, Bouhassira EE, Ryan MC, Noble WC, Aladjem MI. Distinct Epigenetic Features of Differentiation-Regulated Replication Origins. Epigenetics and Chromatin 9:18. 2016.

Zhang Y, Huang L, Fu H, Smith OK, Lin CM, Utani K, Rao M, Reinhold WC, Redon CE, Ryan  M, Kim RG, You Y, Hanna H, Boisclair  Y, Long  Q, Aladjem  MI. A Replicator-Specific Binding Protein Essential For Site-Specific Initiation of DNA Replication in Mammalian Cells. Nat. Commun. 7:11748. 2016.

Ceribelli M, Hou EZ, Kelly PN, Huang DW, Ganapathi K, Evbuomwan MO, Pittaluga S, Shaffer AL, Wright G, Marcucci G, Forman SJ, Xiao W, Guha R, Zhang X, Ferrer M, Chaperot L, Plumas L, Jaffe ES, Thomas CJ, Reizis B, Staudt LM.  A druggable TCF4- and BRD4-dependent transcriptional network sustains malignancy in blastic plasmacytoid dendritic cell neoplasm.  Cancer Cell 2016, in press.

Zhang M, Lykke-Andersen S, Zhu B, Xiao W, Hoskins JW, Jermusyk A, Zhang X, Rost L, Collins I, Jia J, Parikh H, Zhang T, Song L, Zhu B, Zhou W, Matters GL, Kurtz RC, Yeager M, Jensen TH, Brown KM, Bamlet WR, TCGA Research Network, Chanock S, Chatterjee N, Wolpin BM, Smith J, Olson SH, Petersen GM, Shi J, Amundadottir LT. Characterizing cis-regulatory variation in the transcriptome of histologically normal and tumor-derived pancreatic tissues. 2016: Gut

Doran AG, Wong K, Flint J, Adams DJ, Hunter KW* and Keane TM* (2016) Deep genome sequencing and variation analysis of 13 inbred mouse strains find novel missense mutations in essential DNA repair pathway genes.  Genome Biology, 17:167.

Zhang S, Zhu I, Deng T, Furusawa T, Rochman M, Vacchio MS, Bosselut R, Yamane A, Casellas R, Landsman D, Bustin M.  HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells. Nucleic Acids Res. 2016 Sep 6;44(15):7144-58. 

Deng T, Zhu ZI, Zhang S, Postnikov Y, Huang D, Horsch M, Furusawa T, Beckers J, Rozman J, Klingenspor M, Amarie O, Graw J, Rathkolb B, Wolf E, Adler T, Busch DH, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, van der Velde A, Tessarollo L, Ovcherenko I, Landsman D, Bustin M. Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers. Genome Res. 2015 Sep;25(9):1295-308.

Deng T, Zhu ZI, Zhang S, Leng F, Cherukuri S, Hansen L, Mariño-Ramírez L, Meshorer E, Landsman D, Bustin M. HMGN1 modulates nucleosome occupancy and DNase I hypersensitivity at the CpG island promoters of embryonic stem cells. Mol Cell Biol. 2013 Aug;33(16):3377-89. 

Bai L, Yang H, Hu Y, Shukla, A, Ha, N-H, Doran A, Faraji F, Goldberger N, Lee M, Keane T and Hunter KW. (2016)An integrated genome-wide systems genetics screen for breast cancer susceptibility genes.  PLoS Genetics.

Ha N-H, Long J, Cai Q, Shu X-O and Hunter KW. The circadian rhythm gene Arntl2 is a metastasis susceptibility gene for estrogen receptor-negative breast cancer.  PLoS Genetics, 12(9) e1006267. The article highlighted by the journal (Siracusa and Bussard, PLoS Genetics 12(9) e1006299).

Kim J, Sturgill D, Tran AD, Sinclair DA, Oberdoerffer P. Controlled DNA double-strand break induction in mice reveals post-damage transcriptome stability. Nucleic Acids Res. 2016 Apr 20;44(7):e64. 

Khurana S, Kruhlak MJ, Kim J, Tran AD, Liu J, Nyswaner K, Shi L, Jailwala P, Sung MH, Hakim O, Oberdoerffer P. A macrohistone variant links dynamic chromatin compaction to BRCA1-dependent genome maintenance. Nucleic Acids Res. 2016 Apr 20;44(7):e64.

Young RM, Wu T, Schmitz T, Dawood M, Xiao W, Phelan JD, Xu W, Menard L, Meffre E, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza L, Staudt LM.  Survival of human lymphoma cells requires B cell receptor engagement by self-antigens.  Proc Natl Acad Sci 2015 112:13447-54.

Manna S, Kim JK, Baugé C, Cam M, Zhao Y, Shetty J, Vacchio MS, Castro E, Tran B, Tessarollo L, Bosselut R. Histone H3 Lysine 27 demethylases Jmjd3 and Utx are required for T-cell differentiation. Nat Commun. 2015;6:8152

Miles, George; Zhao, Yongmei; Levin, Yelena; et al. Multiplex Tissue and Clinical Proteomics By Next-Generation Sequencing Conference: 104th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Location: Boston, MA Date: MAR 21-27, 2015

Fu H, Martin MM, Regairaz M, Huang L, You Y, Lin CM, Ryan M, Kim R, Shimura T, Pommier Y, Aladjem MI. The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage. Nature Communications 6:6746. 2015.

Bartholdy B, Mukhopadhyay R, Lajugie J, Aladjem MI, Bouhassira EE. Allele-specific analysis of DNA replication origins in mammalian cells. Nat Commun.6:7051. 2015.

Schmitz R, Ceribelli M, Pitaluga S, Wright G, and Staudt LM.  Oncogenic mechanisms in Burkitt lymphoma. Cold Spring Harb Perspect Med. 2014 4:1-13.

Yang Y, Schmitz R, Mitala J, Whiting A, Xiao W, Ceribelli M, Wright G, Zhao H, Yang Y, Xu W, Rosenwald A, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Wiestner A, Kruhlak MJ, Iwai K, Bernal F, Staudt LM.  Essential role of the linear ubiquitin chain assembly complex in lymphoma revealed by rare germline polymorphisms.  Cancer Discovery 2014 4:480-93.

Yudkin D, Hayward B, Aladjem MI, Kumari D, Usdin K. Chromosome fragility and the abnormal replication of the FMR1 locus in Fragile X syndrome. Hum Mol Genet, 23:2940-52. 2014.

Mukhopadhyay R, Lajugie J, Fourel N, Selzer A, Schizas M, Bartholdy B, Mar J, Lin CM, Martin MM, Ryan M, Aladjem MI, Bouhassira EE. Allele-specific genome-wide profiling in human primary erythroblasts reveals replication program organization. PLoS Genetics 10(5): e1004319. 2014.

Hoskins JW, Jia J, Flandez M, Parikh H, Xiao W, Collins I, Emmanuel MA, Ibrahim A, Powell J, Zhang L, Malats N, Bamlet WR, Petersen GM, Real FX, Amundadottir LT. Transcriptome analysis of pancreatic cancer reveals a tumor suppressor function for HNF1A. Carcinogenesis 2014; 35(12): 2670-2678.

Yi, Ming; Zhao, Yongmei; Jia, Li; et al. Performance comparison of SNP detection tools with Illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data. NAR Volume: 42. Issue: 12  Article Number: e101

Muppidi JR, Schmitz R, Green JA, Xiao W, Larsen AB, Braun SE, An J, Xu Y, Rosenwald A, Ott G, Gascoyne RD, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Vaidehi N, Staudt LM*, Cyster JG*.  Loss of signaling via Gα13 in germinal center B cell-derived lymphoma.  Nature 2014 516: 254-8.

Ceribelli M, Kelly P, Shaffer AL, Wright G, Yang Y, Mathews-Griner LA, Guha R, Shinn P, Keller JM, Liu D, Patel PR, Ferrer M, Joshi S, Nerle S, Sandy P, Normant E, Thomas CJ, Staudt LM.  Blockade of oncogenic IkB kinase activity in ABC DLBCL by small molecule BET protein inhibitors.  Proc Natl Acad Sci 2014 111:11365-70.Nakagawa M, Schmitz R, Xiao W, Goldman CK, Xu W, Yang Y, Yu X, Waldmann TA, Staudt LM.  Gain-of-function CCR4 mutations in adult T-cell leukemia/lymphoma.J Exp Med 2014 211:2497-2505.

Xiao W, Tran B, Staudt LM, Schmitz R. High-throughput RNA sequencing in B-cell lymphomas. Methods Mol Biol 2013 971:295-312.

Jia J, Parikh H, Xiao W, Hoskins JW, Pflicke H, Liu X, Collins I, Zhou W, Wang Z, Powell J, Thorgeirsson SS, Rudloff U, Petersen GM, Amundadottir LT.  An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer. BMC Med Genomics 2013; 6:33.

Fu YP, Kohaar I, Rothman N, Earl J, Figueroa JD, Ye Y, Malats N, Tang W, Liu L, Garcia-Closas M, Muchmore B, Chatterjee N, Tarway M, Kogevinas M, Porter-Gill P, Baris D, Mumy A, Albanes D, Purdue MP, Hutchinson A, Carrato A, Tardón A, Serra C, García-Closas R, Lloreta J, Johnson A, Schwenn M, Karagas MR, Schned A, Diver WR, Gapstur SM, Thun MJ, Virtamo J, Chanock SJ, Fraumeni JF Jr, Silverman DT, Wu X, Real FX, Prokunina-Olsson L. Common genetic variants in the PSCA gene influence gene expression and bladder cancer risk. Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4974-9.

Swaminathan, Sanjay; Hu, Xiaojun; Zheng, Xin; et al. Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   Volume: 434   Issue: 2   Pages: 228-234.

Fu H, Maunakea AK, Martin MM, Huang L, Zhang Y, Ryan M, Kim R, Lin CM, Zhao K, Aladjem MI. Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle. PLoS Genet. 9:e1003542. 2013.

Snow AL, Xiao W, Stinson JR, Lu W, Chaigne-Delalande B, Zheng L, Pittaluga S, Matthews HF, Schmitz R, Jhavar S, Kuchen S, Kardava L, Wang W, Lamborn IT, Jing H, Raffeld M, Moir S, Fleisher TA, Staudt LM, Su HC, Lenardo MJ.  Congenital B cell lymphocytosis explained by novel germline CARD11 mutations.  J Exp Med 2012 209:2247-61.

Grontved L, Hager GL. Impact of chromatin structure on PR signaling: Transition from local to global analysis. Mol Cell Endocrinol. 357, 30-36.

Li M¹, He Y, Dubois W, Wu X, Shi J, Huang J.  Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells, Molecular Cell (2012)

Yang Y, Shaffer AL, Emre NCT, Ceribelli M, Wright G, Xiao W, Powell J, Platig J, Kohlhammer H, Young RM, Zhao H, Yang Y, Xu W, Balasubramanian S, Buggy JJ, Mathews LA, Shinn P, Guha R, Ferrer M, Thomas C, Staudt LM. Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma.  Cancer Cell 2012 21:723–737.

Koh Y, Wu X, Ferris AL, Matreyek KA, Smith SJ, Lee K, KewalRamani VN, Hughes SH, Engelman A:  Differential effects of human immunodeficiency virus type 1 capsid and cellular factors nucleoporin 153 and ledgf/p75 on the efficiency and specificity of viral DNA integration. Journal of Virology. 2012. 

Wang H, Jurado KA, Wu X, Shun MC, Li X, Ferris AL, Smith SJ, Patel PA, Fuchs JR, Cherepanov P, Kvaratskheila M, Hughes SH, Engelman A: Hrp2 determines the efficiency and specificity of hiv-1 integration in ledgf/p75 knockout cells but does not contribute to the antiviral activity of a potent ledgf/p75-binding site integrase inhibitor. Nucleic acids research. 2012.

Schmitz R, Young RM, Cerribeli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson D, Buras E, Lu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Muller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Fisher RI , Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM.  Pathogenetic mechanisms and therapeutic targets in Burkitt lymphoma from structural and functional genomics. Nature 2012 490:116-20.

Grontved L, Bandle R, John S, Baek S, Chung H-J, Liu Y, Aguilera G, Oberholtzer C, Hager GL, Levens D: Rapid genome-scale mapping of chromatin accessibility in tissue. Epigenetics Chromatin 2012 Jun 26;5(1):10.

Ngo VN, Young RM, Schmitz R, Jhavar S, Xiao W, Lim KH, Kohlhammer H, Xu W, Yang Y, Zhao H, Shaffer AL, Romesser P, Wright G, Powell J, Rosenwald A, Muller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Fisher RI , Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Staudt LM.  Oncogenically active MYD88 mutations in human lymphoma.  Nature 2011 470:115-119.Martin MM, Ryan M, Kim R, Zakas AL, Fu H, Lin CM, Reinhold WC, Davis SR, Bilke S, Liu H, Doroshow JH, Reimers MA, Valenzuela MS, Pommier Y, Meltzer PS, Aladjem MI. Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Research 21: 1822-1832.  2011.