Publications

2021

Olbrich T, Vega-Sendino M, Tillo D, Wu W, Zolnerowich N, Tran A, Domingo C, Franco M, Markiewicz-Potoczny M, Pegoraro G, FitzGerald P, Kruhlak M, Lazzerini-Denchi E, Nora E, Nussenzweig A, Ruiz S

CTCF is a barrier for totipotent 2C-like reprogramming
Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L, Langenbach K, 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, Chen Z, Stanbouly S, Tran B, Shetty J, Kriga Y, Meerzaman D, et al

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
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, K�ks 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
West RR, Calvo KR, Embree LJ, Wang W, Tuschong LM, Bauer TR, Tillo D, Lack J, Droll S, Hsu AP, Holland SM, Hickstein DD

ASXL1 and STAG2 are Common Mutations in GATA2 Deficiency Patients with Bone Marrow Disease and Myelodysplastic Syndrome
Tagawa T, Oh D, Santos J, Dremel S, Mahesh G, Uldrick TS, Yarchoan R, Koparde VN, Ziegelbauer JM

Characterizing expression and regulation of Gamma-Herpesviral circular RNAs
Wan Y, Anastasakis DG, Rodriguez J, Palangat M, Gudla P, Zaki G, Tandon M, Pegoraro G, Chow CC, Hafner M, Larson DR

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection
Wabitsch S, Tandon M, Ruf B, Zhang Q, McCallen JD, McVey JC, Ma C, Green BL, Diggs LP, Heinrich B, Greten TF

Anti-PD-1 in combination with Trametinib suppresses tumor growth and improves survival of intrahepatic cholangiocarcinoma in mice
Baik JY, Liu Z, Jiao D, Kwon HJ, Yan J, Kadigamuwa C, Choe M, Lake R, Kruhlak M, Tandon M, Cai Z, Choksi S, Liu ZG

ZBP1 not RIPK1 mediates tumor necroptosis in breast cancer
Zhang C, Oguz C, Huse S, Xia L, Wu J, Peng YC, Smith M, Chen J, Long CA, Lack J, Su XZ

Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67
Dudley JN, Hong CS, Hawari MA, Shwetar J, Sapp JC, Lack J, Shiferaw H, NISC Comparative Sequencing Program., Johnston JJ, Biesecker LG

Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach
Tewary P, Brooks AD, Xu YM, Wijeratne EMK, Babyak AL, Back TC, Chari R, Evans CN, Henrich CJ, Meyer TJ, Edmondson EF, Prudente de Aquino MT, Kanagasabai T, Shanker A, Gunatilaka AAL, Sayers TJ

Small-Molecule natural product Physachenolide C potentiates immunotherapy efficacy by targeting BET proteins
El Meskini R, Atkinson D, Kulaga A, Abdelmaksoud A, Gumprecht M, Pate N, Hayes S, Oberst M, Kaplan IM, Raber P, Van Dyke T, Sharan SK, Hollingsworth R, Day CP, Merlino G, Ohler ZW

Distinct biomarker profiles and TCR sequence diversity characterize the response to PD-L1 blockade in a mouse melanoma model
Tagawa T, Koparde V, Ziegelbauer JM

Identifying and characterizing virus-encoded circular RNAs
Gardner CL, Pavel-Dinu M, Dobbs K, Bosticardo M, Reardon PK, Lack JB, DeRavin SS, Le K, Bello E, Pala F, Delmonte OM, Malech H, Montel-Hagan A, Crooks G, Acuto O, Porteus MH, Notarangelo LD

Gene editing rescues in vitro T cell development of RAG2-deficient induced pluripotent stem cells in an artificial thymic organoid system
Dorrington MG, Bradfield CJ, Lack JB, Lin B, Liang JJ, Starr T, Ernst O, Gross JL, Sun J, Miller AH, Steele-Mortimer O, Fraser IDC

Type I IFNs facilitate innate immune control of the opportunistic bacteria Burkholderia cenocepacia in the macrophage cytosol
Blazkova J, Huiting ED, Boddapati AK, Shi V, Whitehead EJ, Justement JS, Nordstrom J, Moir S, Lack J, Chun TW

TIGIT expression on CD8+ T cells correlates with higher cytotoxic capacity

CCR Collaborative Bioinformatics Resource

2021

Ask For Help

Upcoming Classes

Recent CCBR Publications

CCBR Staff