Genomic Instability and Cancer Genetics Selected Program-Related Publications

Ghaddar B, Biswas A, Harris C, Omary MB, Carpizo DR, Blaser MJ, De S. Tumor microbiome links cellular programs and immunity in pancreatic cancer. Cancer Cell. 2022;40(10):1240-53 e5. doi: 10.1016/j.ccell.2022.09.009. PubMed PMID: 36220074; PMCID: PMC9556978.

Blaser MJ (CMI),
De S (GICG)

Castellano GM, Zeeshan S, Garbuzenko OB, Sabaawy HE, Malhotra J, Minko T, Pine SR. Inhibition of Mtorc1/2 and DNA-PK via CC-115 Synergizes with Carboplatin and Paclitaxel in Lung Squamous Cell Carcinoma. Mol Cancer Ther. 2022;21(9):1381-92. doi: 10.1158/1535-7163.MCT-22-0053. PubMed PMID: 35732569; PMCID: PMC9452486.

Malhotra J (CIPT),
Minko T (CP),
Pine SR (GICG)

Zingg D, Bhin J, Yemelyanenko J, Kas SM, Rolfs F, Lutz C, Lee JK, Klarenbeek S, Silverman IM, Annunziato S, Chan CS, Piersma SR, Eijkman T, Badoux M, Gogola E, Siteur B, Sprengers J, de Klein B, de Goeij-de Haas RR, Riedlinger GM, Ke H, Madison R, Drenth AP, van der Burg E, Schut E, Ganesan S, et al. Truncated FGFR2 is a clinically actionable oncogene in multiple cancers. Nature. 2022;608(7923):609-17. doi: 10.1038/s41586-022-05066-5. PubMed PMID: 35948633; PMCID: PMC9436779.

Chan CS (GICG),
Riedlinger GM (CIPT),
Ganesan S (CIPT)

Wang Y, Liu B, Lu H, Liu J, Romanienko PJ, Montelione GT, Shen Z. SETD4-mediated KU70 methylation suppresses apoptosis. Cell Rep. 2022;39(6):110794. doi: 10.1016/j.celrep.2022.110794. PubMed PMID: 35545041; PMCID: PMC9201767.

Shen Z (GICG)

Mahdi AH, Huo Y, Chen Y, Selenica P, Sharma A, Merritt E, Barnard N, Chan C, Ganesan S, Reis-Filho JS, Weigelt B, De S, Xia B. Loss of the BRCA1-PALB2 interaction accelerates p53-associated tumor development in mice. Genes Dis. 2022;9(3):807-13. doi: 10.1016/j.gendis.2020.08.012. PubMed PMID: 35782971; PMCID: PMC9243321.

Chan C (GICG),
Ganesan S (CIPT),
De S (GICG),
Xia B (GICG)

Madison RW, Hu X, Ramanan V, Xu Z, Huang RSP, Sokol ES, Frampton GM, Schrock AB, Ali SM, Ganesan S, De S. Clustered 8-Oxo-Guanine Mutations and Oncogenic Gene Fusions in Microsatellite-Unstable Colorectal Cancer. JCO Precis Oncol. 2022;6:e2100477. doi: 10.1200/PO.21.00477. PubMed PMID: 35584350; PMCID: PMC9200390.

Ganesan S (CIPT),
De S (GICG)

Yue X, Wang J, Chang CY, Liu J, Yang X, Zhou F, Qiu X, Bhatt V, Guo JY, Su X, Zhang L, Feng Z, Hu W. Leukemia inhibitory factor drives glucose metabolic reprogramming to promote breast tumorigenesis. Cell Death Dis. 2022;13(4):370. doi: 10.1038/s41419-022-04820-x. PubMed PMID: 35440095; PMCID: PMC9018736.

Guo JY (CMI),
Su X (CMI),
Zhang L (CIPT),
Feng Z (GICG),
Hu W (GICG)

Huo Y, Sawant A, Tan Y, Mahdi AH, Li T, Ma H, Bhatt V, Yan R, Coleman J, Dreyfus CF, Guo JY, Mouradian MM, White E, Xia B. Tumor suppressor PALB2 maintains redox and mitochondrial homeostasis in the brain and cooperates with ATG7/autophagy to suppress neurodegeneration. PLoS Genet. 2022;18(4):e1010138. doi: 10.1371/journal.pgen.1010138. PubMed PMID: 35404932; PMCID: PMC9022806.

Guo JY (CMI),
Mouradian MM (CMI), White E (CMI),
Xia B (GICG)

Kreimer A, Ashuach T, Inoue F, Khodaverdian A, Deng C, Yosef N, Ahituv N. Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation. Nat Commun. 2022;13(1):1504. doi: 10.1038/s41467-022-28659-0. PubMed PMID: 35315433; PMCID: PMC8938438.

Kreimer A (GICG)

Jasra S, Giricz O, Zeig-Owens R, Pradhan K, Goldfarb DG, Barreto-Galvez A, Silver AJ, Chen J, Sahu S, Gordon-Mitchell S, Choudhary GS, Aluri S, Bhagat TD, Shastri A, Bejan CA, Stockton SS, Spaulding TP, Thiruthuvanathan V, Goto H, Gerhardt J, Haider SH, Veerappan A, Bartenstein M, Nwankwo G, Landgren O, Madireddy A, et al. High burden of clonal hematopoiesis in first responders exposed to the World Trade Center disaster. Nat Med. 2022;28(3):468-71. doi: 10.1038/s41591-022-01708-3. PubMed PMID: 35256801; PMCID: PMC9394171.

Madireddy A (GICG)

Ma H, Kang Z, Foo TK, Shen Z, Xia B. Disrupted BRCA1-PALB2 interaction induces tumor immunosuppression and T-lymphocyte infiltration in HCC through cGAS-STING pathway. Hepatology. 2023;77(1):33-47. doi: 10.1002/hep.32335. PubMed PMID: 35006619; PMCID: PMC9271123.

Shen Z (GICG),
Xia B (GICG)

Zeng Z, Aptekmann AA, Bromberg Y. Decoding the effects of synonymous variants. Nucleic Acids Res. 2021;49(22):12673-91. doi: 10.1093/nar/gkab1159. PubMed PMID: 34850938; PMCID: PMC8682775.

Bromberg Y (GICG)

Koblan LW, Arbab M, Shen MW, Hussmann JA, Anzalone AV, Doman JL, Newby GA, Yang D, Mok B, Replogle JM, Xu A, Sisley TA, Weissman JS, Adamson B, Liu DR Efficient C*G-to-G*C base editors developed using CRISPRi screens, target-library analysis, and machine learning. Nat Biotechnol. 2021;39(11):1414-25. doi: 10.1038/s41587-021-00938-z. PubMed PMID: 34183861; PMCID: PMC8985520.

Adamson B (GICG)

Kwon M, Rubio G, Nolan N, Auteri P, Volmar JA, Adem A, Javidian P, Zhou Z, Verzi MP, Pine SR, Libutti SK. FILIP1L Loss Is a Driver of Aggressive Mucinous Colorectal Adenocarcinoma and Mediates Cytokinesis Defects through PFDN1. Cancer Res. 2021;81(21):5523-39. doi: 10.1158/0008-5472.CAN-21-0897. PubMed PMID: 34417201; PMCID: PMC8563430.

Zhou Z (GICG),
Verzi MP (GICG),
Pine SR (GICG),
Libutti SK (CIPT, GICG)

Hussmann JA, Ling J, Ravisankar P, Yan J, Cirincione A, Xu A, Simpson D, Yang D, Bothmer A, Cotta-Ramusino C, Weissman JS, Adamson B. Mapping the genetic landscape of DNA double-strand break repair. Cell. 2021;184(22):5653-69 e25. doi: 10.1016/j.cell.2021.10.002. PubMed PMID: 34672952; PMCID: PMC9074467.

Adamson B (GICG)

Chen PJ, Hussmann JA, Yan J, Knipping F, Ravisankar P, Chen PF, Chen C, Nelson JW, Newby GA, Sahin M, Osborn MJ, Weissman JS, Adamson B, Liu DR. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell. 2021;184(22):5635-52 e29. doi: 10.1016/j.cell.2021.09.018. PubMed PMID: 34653350; PMCID: PMC8584034.

Adamson B (GICG)

Satas G, Zaccaria S, El-Kebir M, Raphael BJ. DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution. Cell Syst. 2021;12(10):1004-18 e10. doi: 10.1016/j.cels.2021.07.006. PubMed PMID: 34416171; PMCID: PMC8542635.

Raphael BJ (GICG)

Kang Z, Fu P, Alcivar AL, Fu H, Redon C, Foo TK, Zuo Y, Ye C, Baxley R, Madireddy A, Buisson R, Bielinsky AK, Zou L, Shen Z, Aladjem MI, Xia B. BRCA2 associates with MCM10 to suppress PRIMPOL-mediated repriming and single-stranded gap formation after DNA damage. Nat Commun. 2021;12(1):5966. doi: 10.1038/s41467-021-26227-6. PubMed PMID: 34645815; PMCID: PMC8514439.

Madireddy A (GICG),
Shen Z (GICG),
Xia B (GICG)

Tong K, Kothari OA, Haro KS, Panda A, Bandari MM, Carrick JN, Hur JJ, Zhang L, Chan CS, Xing J, Gatza ML, Ganesan S, Verzi MP. SMAD4 is critical in suppression of BRAF-V600E serrated tumorigenesis. Oncogene. 2021;40(41):6034-48. doi: 10.1038/s41388-021-01997-x. PubMed PMID: 34453124; PMCID: PMC8559887.

Zhang L (CIPT),
Chan CS (GICG),
Gatza ML (GICG),
Ganesan S (CIPT),
Verzi MP (GICG)

Foo TK, Vincelli G, Huselid E, Her J, Zheng H, Simhadri S, Wang M, Huo Y, Li T, Yu X, Li H, Zhao W, Bunting SF, Xia B. ATR/ATM-Mediated Phosphorylation of BRCA1 T1394 Promotes Homologous Recombinational Repair and G(2)-M Checkpoint Maintenance. Cancer Res. 2021;81(18):4676-84. doi: 10.1158/0008-5472.CAN-20-2723. PubMed PMID: 34301763; PMCID: PMC8448966.

Li H (CP),
Bunting SF (GICG),
Xia B (GICG)

Li WV, Zheng D, Wang R, Tian B. MAAPER: model-based analysis of alternative polyadenylation using 3' end-linked reads. Genome Biol. 2021;22(1):222. doi: 10.1186/s13059-021-02429-5. PubMed PMID: 34376236; PMCID: PMC8356463.

Li WV (GICG),
Tian B (GICG)

Etzion-Fuchs A, Todd DA, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021;49(13):e78. doi: 10.1093/nar/gkab356. PubMed PMID: 33999210; PMCID: PMC8287948.

Singh M (GICG)

Liu J, Zhang C, Wang X, Hu W, Feng Z. Tumor suppressor p53 cross-talks with TRIM family proteins. Genes Dis. 2021;8(4):463-74. doi: 10.1016/j.gendis.2020.07.003. PubMed PMID: 34179310; PMCID: PMC8209353.

Hu W (GICG),
Feng Z (GICG)

Chang CY, Wang J, Zhao Y, Liu J, Yang X, Yue X, Wang H, Zhou F, Inclan-Rico JM, Ponessa JJ, Xie P, Zhang L, Siracusa MC, Feng Z, Hu W. Tumor suppressor p53 regulates intestinal type 2 immunity. Nat Commun. 2021;12(1):3371. doi: 10.1038/s41467-021-23587-x. PubMed PMID: 34099671; PMCID: PMC8184793.

Zhang L (CIPT),
Feng Z (GICG),
Hu W (GICG)

Chen L, Luo S, Dupre A, Vasoya RP, Parthasarathy A, Aita R, Malhotra R, Hur J, Toke NH, Chiles E, Yang M, Cao W, Flores J, Ellison CE, Gao N, Sahota A, Su X, Bonder EM, Verzi MP. The nuclear receptor HNF4 drives a brush border gene program conserved across murine intestine, kidney, and embryonic yolk sac. Nat Commun. 2021;12(1):2886. doi: 10.1038/s41467-021-22761-5. PubMed PMID: 34001900; PMCID: PMC8129143.

Gao N (CMI),
Su X (CMI),
Verzi MP (GICG)

Martinez-Zamudio RI, Dewald HK, Vasilopoulos T, Gittens-Williams L, Fitzgerald-Bocarsly P, Herbig U. Senescence-associated beta-galactosidase reveals the abundance of senescent CD8+ T cells in aging humans. Aging Cell. 2021;20(5):e13344. doi: 10.1111/acel.13344. PubMed PMID: 33939265; PMCID: PMC8135084.

Fitzgerald-Bocarsly P (CMI), Herbig U (GICG)

Chan CS, Sun Y, Ke H, Zhao Y, Belete M, Zhang C, Feng Z, Levine AJ, Hu W. Genetic and stochastic influences upon tumor formation and tumor types in Li-Fraumeni mouse models. Life Sci Alliance. 2021;4(3). doi: 10.26508/lsa.202000952. PubMed PMID: 33376133; PMCID: PMC7772779.

Chan CS (GICG),
Feng Z (GICG),
Levine AJ (GICG),
Hu W (GICG)

Domogauer JD, de Toledo SM, Howell RW, Azzam EI. Acquired radioresistance in cancer associated fibroblasts is concomitant with enhanced antioxidant potential and DNA repair capacity. Cell Commun Signal. 2021;19(1):30. doi: 10.1186/s12964-021-00711-4. PubMed PMID: 33637118; PMCID: PMC7912493.

Howell RW (CIPT),
Azzam EI (GICG)

Yuan Z, Gardiner JC, Maggi EC, Huang S, Adem A, Bagdasarov S, Li G, Lee S, Slegowski D, Exarchakis A, Howe JR, Lattime EC, Zang X, Libutti SK. B7 immune-checkpoints as targets for the treatment of neuroendocrine tumors. Endocr Relat Cancer. 2021;28(2):135-49. doi: 10.1530/ERC-20-0337. PubMed PMID: 33410766; PMCID: PMC8486311.

Lattime EC (CMI),
Libutti SK (CIPT, GICG)

Chen L, Cao W, Aita R, Aldea D, Flores J, Gao N, Bonder EM, Ellison CE, Verzi MP. Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4. Cell Rep. 2021;34(4):108679. doi: 10.1016/j.celrep.2020.108679. PubMed PMID: 33503426; PMCID: PMC7899294.

Gao N (CMI),
Verzi MP (GICG)

Jalloul N, Gomy I, Stokes S, Gusev A, Johnson BE, Lindeman NI, Macconaill L, Ganesan S, Garber JE, Khiabanian H. Germline Testing Data Validate Inferences of Mutational Status for Variants Detected From Tumor-Only Sequencing. JCO Precis Oncol. 2021;5. doi: 10.1200/PO.21.00279. PubMed PMID: 34820595; PMCID: PMC8608266.

Ganesan S (CIPT), Khiabanian H (GICG)

Zhang C, Liu J, Wang J, Zhang T, Xu D, Hu W, Feng Z. The Interplay Between Tumor Suppressor p53 and Hypoxia Signaling Pathways in Cancer. Front Cell Dev Biol. 2021;9:648808. doi: 10.3389/fcell.2021.648808. PubMed PMID: 33681231; PMCID: PMC7930565.

Hu W (GICG),
Feng Z (GICG)

Lu H, Ye C, Liu J, Rabson AB, Verzi M, De S, Shen Z. Requirement of Bccip for the Regeneration of Intestinal Progenitors. Am J Pathol. 2021;191(1):66-78. doi: 10.1016/j.ajpath.2020.09.009. PubMed PMID: 33039352; PMCID: PMC7857062.

Verzi M (GICG),
De S (GICG),
Shen Z (GICG)

Ye C, Liu B, Lu H, Liu J, Rabson AB, Jacinto E, Pestov DG, Shen Z. BCCIP is required for nucleolar recruitment of eIF6 and 12S pre-rRNA production during 60S ribosome biogenesis. Nucleic Acids Res. 2020;48(22):12817-32. doi: 10.1093/nar/gkaa1114. PubMed PMID: 33245766; PMCID: PMC7736804.

Jacinto E (CMI),
Pestov DG (GICG),
Shen Z (GICG)

Rahem SM, Epsi NJ, Coffman FD, Mitrofanova A. Genome-wide analysis of therapeutic response uncovers molecular pathways governing tamoxifen resistance in ER+ breast cancer. EBioMedicine. 2020;61:103047. doi: 10.1016/j.ebiom.2020.103047. PubMed PMID: 33099086; PMCID: PMC7585053.

Mitrofanova A (GICG)

Zhang C, Liu J, Xu D, Zhang T, Hu W, Feng Z. Gain-of-function mutant p53 in cancer progression and therapy. J Mol Cell Biol. 2020;12(9):674-87. doi: 10.1093/jmcb/mjaa040. PubMed PMID: 32722796; PMCID: PMC7749743.

Hu W (GICG),
Feng Z (GICG)

Yu S, Balasubramanian I, Laubitz D, Tong K, Bandyopadhyay S, Lin X, Flores J, Singh R, Liu Y, Macazana C, Zhao Y, Béguet-Crespel F, Patil K, Midura-Kiela MT, Wang D, Yap GS, Ferraris RP, Wei Z, Bonder EM, Häggblom MM, Zhang L, Douard V, Verzi MP, Cadwell K, Kiela PR, Gao N. Paneth Cell-Derived Lysozyme Defines the Composition of Mucolytic Microbiota and the Inflammatory Tone of the Intestine. Immunity. 2020;53(2):398-416 e8. doi: 10.1016/j.immuni.2020.07.010. PubMed PMID: 32814028; PMCID: PMC7461615.

Zhang L (CIPT),
Verzi MP (GICG),
Gao N (CMI)

Replogle JM, Norman TM, Xu A, Hussmann JA, Chen J, Cogan JZ, Meer EJ, Terry JM, Riordan DP, Srinivas N, Fiddes IT, Arthur JG, Alvarado LJ, Pfeiffer KA, Mikkelsen TS, Weissman JS, Adamson B. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Nat Biotechnol. 2020;38(8):954-61. doi: 10.1038/s41587-020-0470-y. PubMed PMID: 32231336; PMCID: PMC7416462.

Adamson B (GICG)

Wang H, Wang J, Zhao Y, Zhang X, Liu J, Zhang C, Haffty B, Verzi M, Zhang L, Gao N, Feng Z, Hu W. LIF is essential for ISC function and protects against radiation-induced gastrointestinal syndrome. Cell Death Dis. 2020;11(7):588. doi: 10.1038/s41419-020-02790-6. PubMed PMID: 32719388; PMCID: PMC7385639.

Haffty B (CIPT),
Verzi M (GICG),
Zhang L (CIPT),
Gao N (CMI),
Feng Z (GICG),
Hu W (GICG)

Panda A, Yadav A, Yeerna H, Singh A, Biehl M, Lux M, Schulz A, Klecha T, Doniach S, Khiabanian H, Ganesan S, Tamayo P, Bhanot G. Tissue- and development-stage-specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples. Nucleic Acids Res. 2020;48(13):7079-98. doi: 10.1093/nar/gkaa485. PubMed PMID: 32525984; PMCID: PMC7367157.

Khiabanian H (GICG), Ganesan S (CIPT),
Bhanot G (GICG)

Kobren SN, Chazelle B, Singh M. PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. Cell Syst. 2020;11(1):63-74 e7. doi: 10.1016/j.cels.2020.06.005. PubMed PMID: 32711844; PMCID: PMC7493809.

Singh M (GICG)

Yue X, Wu F, Wang J, Kim K, Santhamma B, Dileep KV, Zhang KYJ, Viswanadhapalli S, Vadlamudi RK, Ahmed G, Feng Z, Nickisch K, Hu W. EC330, a small-molecule compound, is a potential novel inhibitor of LIF signaling. J Mol Cell Biol. 2020;12(6):477-80. doi: 10.1093/jmcb/mjaa008. PubMed PMID: 32221559; PMCID: PMC7333478.

Feng Z (GICG),
Hu W (GICG)

Hristov BH, Chazelle B, Singh M. uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes. Cell Syst. 2020;10(6):470-9 e3. doi: 10.1016/j.cels.2020.05.008. PubMed PMID: 32684276; PMCID: PMC7821437.

Singh M (GICG)

Lu H, Ye C, Feng X, Liu J, Bhaumik M, Xia B, Liu C, Shen Z. Spontaneous Development of Hepatocellular Carcinoma and B-Cell Lymphoma in Mosaic and Heterozygous Brca2 and Cdkn1a Interacting Protein Knockout Mice. Am J Pathol. 2020;190(6):1175-87. doi: 10.1016/j.ajpath.2020.01.020. PubMed PMID: 32201259; PMCID: PMC7280756.

Xia B (GICG),
Liu C (CIPT),
Shen Z (GICG)

Liu J, Zhang C, Wu H, Sun XX, Li Y, Huang S, Yue X, Lu SE, Shen Z , Su X, White E, Haffty BG, Hu W, Feng Z. Parkin ubiquitinates phosphoglycerate dehydrogenase to suppress serine synthesis and tumor progression. J Clin Invest. 2020;130(6):3253-69. doi: 10.1172/JCI132876. PubMed PMID: 32478681; PMCID: PMC7260041.

Shen Z (GICG),
Su X (CMI),
White E (CMI),
Haffty BG (CIPT),
Hu W (GICG),
Feng Z (GICG)

Yue X, Wu F, Li Y, Liu J, Boateng M, Mandava K, Zhang C, Feng Z, Gao J, Hu W. Gain of function mutant p53 protein activates AKT through the Rac1 signaling to promote tumorigenesis. Cell Cycle. 2020;19(11):1338-51. doi: 10.1080/15384101.2020.1749790. PubMed PMID: 32275841; PMCID: PMC7469461.

Feng Z (GICG),
Hu W (GICG)

Loh JW, Guccione C, Di Clemente F, Riedlinger G, Ganesan S, Khiabanian H. All-FIT: allele-frequency-based imputation of tumor purity from high-depth sequencing data. Bioinformatics. 2020;36(7):2173-80. doi: 10.1093/bioinformatics/btz865. PubMed PMID: 31750888; PMCID: PMC7141867.

Riedlinger G (CIPT), Ganesan S (CIPT), Khiabanian H (GICG)

Singh A, Pandey M, Nandakumar D, Raney KD, Yin YW, Patel SS. Excessive excision of correct nucleotides during DNA synthesis explained by replication hurdles. EMBO J. 2020;39(6):e103367. doi: 10.15252/embj.2019103367. PubMed PMID: 32037587; PMCID: PMC7073461.

Patel SS (GICG)

Chen L, Vasoya RP, Toke NH, Parthasarathy A, Luo S, Chiles E, Flores J, Gao N, Bonder EM, Su X, Verzi MP. HNF4 Regulates Fatty Acid Oxidation and Is Required for Renewal of Intestinal Stem Cells in Mice. Gastroenterology. 2020;158(4):985-99 e9. doi: 10.1053/j.gastro.2019.11.031. PubMed PMID: 31759926; PMCID: PMC7062567.

Gao N (CMI),
Su X (CMI),
Verzi MP (GICG)

Przytycki PF, Singh M. Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations. Cell Syst. 2020;10(2):193-203 e4. doi: 10.1016/j.cels.2020.01.002. PubMed PMID: 32078798; PMCID: PMC7457951.

Singh M (GICG)

Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, Reimand J, Raphael BJ, et al. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2020;11(1):729. doi: 10.1038/s41467-020-14367-0. PubMed PMID: 32024854; PMCID: PMC7002574.

Raphael BJ (GICG)

Omene C, Ma L, Moore J, Ouyang H, Illa-Bochaca I, Chou W, Patel MS, Sebastiano C, Demaria S, Mao JH, Karagoz K, Gatza ML, Barcellos-Hoff MH. Aggressive Mammary Cancers Lacking Lymphocytic Infiltration Arise in Irradiated Mice and Can Be Prevented by Dietary Intervention. Cancer Immunol Res. 2020;8(2):217-29. doi: 10.1158/2326-6066.CIR-19-0253. PubMed PMID: 31831632; PMCID: PMC7002223.

Omene C (CIPT),
Gatza ML (GICG)

King MR, Petry S. Phase separation of TPX2 enhances and spatially coordinates microtubule nucleation. Nat Commun. 2020;11(1):270. doi: 10.1038/s41467-019-14087-0. PubMed PMID: 31937751; PMCID: PMC6959270.

Petry S (GICG)

Sharma A, Merritt E, Hu X, Cruz A, Jiang C, Sarkodie H, Zhou Z, Malhotra J, Riedlinger GM, De S. Non-Genetic Intra-Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics in Lung Tumors. Cell Rep. 2019;29(8):2164-74 e5. doi: 10.1016/j.celrep.2019.10.045. PubMed PMID: 31747591; PMCID: PMC6952742.

Malhotra J (CIPT),
Riedlinger GM (CIPT),
De S (GICG)

Laddha SV, da Silva EM, Robzyk K, Untch BR, Ke H, Rekhtman N, Poirier JT, Travis WD, Tang LH, Chan CS. Integrative Genomic Characterization Identifies Molecular Subtypes of Lung Carcinoids. Cancer Res. 2019;79(17):4339-47. doi: 10.1158/0008-5472.CAN-19-0214. PubMed PMID: 31300474; PMCID: PMC6733269.

Chan CS (GICG)

Myers MA, Satas G, Raphael BJ. CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples. Cell Syst. 2019;8(6):514-22 e5. doi: 10.1016/j.cels.2019.05.010. PubMed PMID: 31229560; PMCID: PMC7263382.

Raphael BJ (GICG)

Singh A, Bhanot G, Khiabanian H. TuBA: Tunable biclustering algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer. Gigascience. 2019;8(6). doi: 10.1093/gigascience/giz064. PubMed PMID: 31216036; PMCID: PMC6582332.

Bhanot G (GICG), Khiabanian H (GICG)

Chen L, Toke NH, Luo S, Vasoya RP, Fullem RL, Parthasarathy A, Perekatt AO, Verzi MP. A reinforcing HNF4-SMAD4 feed-forward module stabilizes enterocyte identity. Nat Genet. 2019;51(5):777-85. doi: 10.1038/s41588-019-0384-0. PubMed PMID: 30988513; PMCID: PMC6650150.

Perekatt AO (GICG),
Verzi MP (GICG)

Simhadri S, Vincelli G, Huo Y, Misenko S, Foo TK, Ahlskog J, Sørensen CS, Oakley GG, Ganesan S, Bunting SF, Xia B. PALB2 connects BRCA1 and BRCA2 in the G2/M checkpoint response. Oncogene. 2019;38(10):1585-96. doi: 10.1038/s41388-018-0535-2. PubMed PMID: 30337689; PMCID: PMC6408219.

Ganesan S (CIPT),
Bunting SF (GICG),
Xia B (GICG)

Lee YS, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, Kristensen VN, Dolinski K, Theesfeld CL, Troyanskaya OG. A Computational Framework for Genome-wide Characterization of the Human Disease Landscape. Cell Syst. 2019;8(2):152-62 e6. doi: 10.1016/j.cels.2018.12.010. PubMed PMID: 30685436; PMCID: PMC7374759.

Troyanskaya OG (GICG)

Riedlinger G, Hadigol M, Khiabanian H, Ganesan S. Association of JAK2-V617F Mutations Detected by Solid Tumor Sequencing With Coexistent Myeloproliferative Neoplasms. JAMA Oncol. 2019;5(2):265-7. doi: 10.1001/jamaoncol.2018.6286. PubMed PMID: 30605212; PMCID: PMC6439565.

Riedlinger G (CIPT), Khiabanian H (GICG), Ganesan S (CIPT)

Balaparya A, De S. Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data. Nat Genet. 2018;50(12):1626-8. doi: 10.1038/s41588-018-0219-4. PubMed PMID: 30250123; PMCID: PMC6952740.

De S (GICG)

Razdan N, Vasilopoulos T, Herbig U. Telomere dysfunction promotes transdifferentiation of human fibroblasts into myofibroblasts. Aging Cell. 2018;17(6):e12838. doi: 10.1111/acel.12838. PubMed PMID: 30244523; PMCID: PMC6260909.

Herbig U (GICG)

Paratala BS, Chung JH, Williams CB, Yilmazel B, Petrosky W, Williams K, Schrock AB, Gay LM, Lee E, Dolfi SC, Pham K, Lin S, Yao M, Kulkarni A, DiClemente F, Liu C, Rodriguez-Rodriguez L, Ganesan S, Ross JS, Ali SM, Leyland-Jones B, Hirshfield KM. RET rearrangements are actionable alterations in breast cancer. Nat Commun. 2018;9(1):4821. doi: 10.1038/s41467-018-07341-4. PubMed PMID: 30446652; PMCID: PMC6240119.

Liu C (CIPT),
Rodriguez-Rodriguez L (CIPT),
Ganesan S (CIPT),
Hirshfield KM (GICG)

Yao V, Kaletsky R, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG. An integrative tissue-network approach to identify and test human disease genes. Nat Biotechnol. 2018. doi: 10.1038/nbt.4246. PubMed PMID: 30346941; PMCID: PMC7021177

Troyanskaya OG (GICG)

Devarkar SC, Schweibenz B, Wang C, Marcotrigiano J, Patel SS. RIG-I Uses an ATPase-Powered Translocation-Throttling Mechanism for Kinetic Proofreading of RNAs and Oligomerization. Mol Cell. 2018;72(2):355-68 e4. doi: 10.1016/j.molcel.2018.08.021. PubMed PMID: 30270105; PMCID: PMC6434538.

Patel SS (GICG)

Chan CS, Laddha SV, Lewis PW, Koletsky MS, Robzyk K, Da Silva E, Torres PJ, Untch BR, Li J, Bose P, Chan TA, Klimstra DS, Allis CD, Tang LH. ATRX, DAXX or MEN1 mutant pancreatic neuroendocrine tumors are a distinct alpha-cell signature subgroup. Nat Commun. 2018;9(1):4158. doi: 10.1038/s41467-018-06498-2. PubMed PMID: 30315258; PMCID: PMC6185985.

Chan CS (GICG)

Perekatt AO, Shah PP, Cheung S, Jariwala N, Wu A, Gandhi V, Kumar N, Feng Q, Patel N, Chen L, Joshi S, Zhou A, Taketo MM, Xing J, White E, Gao N, Gatza ML, Verzi MP. SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium. Cancer Res. 2018;78(17):4878-90. doi: 10.1158/0008-5472.CAN-18-0043. PubMed PMID: 29986996; PMCID: PMC6125228.

Perekatt AO (GICG),
White E (CMI),
Gao N (CMI),
Gatza ML (GICG),
Verzi MP (GICG)

Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nat Genet. 2018;50(8):1171-9. doi: 10.1038/s41588-018-0160-6. PubMed PMID: 30013180; PMCID: PMC6094955.

Troyanskaya OG (GICG)

Mahdi AH, Huo Y, Tan Y, Simhadri S, Vincelli G, Gao J, Ganesan S, Xia B. Evidence of Intertissue Differences in the DNA Damage Response and the Pro-oncogenic Role of NF-kappaB in Mice with Disengaged BRCA1-PALB2 Interaction. Cancer Res. 2018;78(14):3969-81. doi: 10.1158/0008-5472.CAN-18-0388. PubMed PMID: 29739757; PMCID: PMC6050088.

Ganesan S (CIPT),
Xia B (GICG)

Severson EA, Riedlinger GM, Connelly CF, Vergilio JA, Goldfinger M, Ramkissoon S, Frampton GM, Ross JS, Fratella-Calabrese A, Gay L, Ali S, Miller V, Elvin J, Hadigol M, Hirshfield KM, Rodriguez-Rodriguez L, Ganesan S, Khiabanian H. Detection of clonal hematopoiesis of indeterminate potential in clinical sequencing of solid tumor specimens. Blood. 2018;131(22):2501-5. doi: 10.1182/blood-2018-03-840629. PubMed PMID: 29678827; PMCID: PMC5981171.

Riedlinger GM (CIPT),
Hirshfield KM (GICG),
Rodriguez-Rodriguez L (CIPT),
Ganesan S (CIPT),
Khiabanian H (GICG)

Sharma A, Jiang C, De S. Dissecting the sources of gene expression variation in a pan-cancer analysis identifies novel regulatory mutations. Nucleic Acids Res. 2018;46(9):4370-81. doi: 10.1093/nar/gky271. PubMed PMID: 29672706; PMCID: PMC5961375.

De S (GICG)

Thawani A, Kadzik RS, Petry S. XMAP215 is a microtubule nucleation factor that functions synergistically with the gamma-tubulin ring complex. Nat Cell Biol. 2018;20(5):575-85. doi: 10.1038/s41556-018-0091-6. PubMed PMID: 29695792; PMCID: PMC5926803.

Petry S (GICG)

Panja S, Hayati S, Epsi NJ, Parrott JS, Mitrofanova A. Integrative (epi) Genomic Analysis to Predict Response to Androgen-Deprivation Therapy in Prostate Cancer. EBioMedicine. 2018;31:110-21. doi: 10.1016/j.ebiom.2018.04.007. PubMed PMID: 29685789; PMCID: PMC6013754.

Mitrofanova A (GICG)

El-Kebir M, Satas G, Raphael BJ. Inferring parsimonious migration histories for metastatic cancers. Nat Genet. 2018;50(5):718-26. doi: 10.1038/s41588-018-0106-z. PubMed PMID: 29700472; PMCID: PMC6103651.

Raphael BJ (GICG)

Zhao Y, Wu L, Yue X, Zhang C, Wang J, Li J, Sun X, Zhu Y, Feng Z, Hu W. A polymorphism in the tumor suppressor p53 affects aging and longevity in mouse models. Elife. 2018;7. doi: 10.7554/eLife.34701. PubMed PMID: 29557783; PMCID: PMC5906094.

Feng Z (GICG),
Hu W (GICG)

Khiabanian H, Hirshfield KM, Goldfinger M, Bird S, Stein M, Aisner J, Toppmeyer D, Wong S, Chan N, Dhar K, Gheeya J, Vig H, Hadigol M, Pavlick D, Ansari S, Ali S, Xia B, Rodriguez-Rodriguez L, Ganesan S. Inference of Germline Mutational Status and Evaluation of Loss of Heterozygosity in High-Depth, Tumor-Only Sequencing Data. JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.17.00148. PubMed PMID: 30246169; PMCID: PMC6148761.

Khiabanian H (GICG),
Hirshfield KM (GICG),
Aisner J (CIPT),
Toppmeyer D (CIPT),
Chan N (CIPT),
Xia B (GICG),
Rodriguez-Rodriguez L (CIPT),
Ganesan S (CIPT)

Tong K, Pellón-Cárdenas O, Sirihorachai VR, Warder BN, Kothari OA, Perekatt AO, Fokas EE, Fullem RL, Zhou A, Thackray JK, Tran H, Zhang L, Xing J, Verzi MP. Degree of Tissue Differentiation Dictates Susceptibility to BRAF-Driven Colorectal Cancer. Cell Rep. 2017;21(13):3833-45. doi: 10.1016/j.celrep.2017.11.104. PubMed PMID: 29281831; PMCID: PMC5747303.

Perekatt AO (GICG),
Zhang L (CIPT),
Verzi MP (GICG)

Morgan KM, Fischer BS, Lee FY, Shah JJ, Bertino JR, Rosenfeld J, Singh A, Khiabanian H, Pine SR. Gamma Secretase Inhibition by BMS-906024 Enhances Efficacy of Paclitaxel in Lung Adenocarcinoma. Mol Cancer Ther. 2017;16(12):2759-69. doi: 10.1158/1535-7163.MCT-17-0439. PubMed PMID: 28978720; PMCID: PMC5716926.

Bertino JR (CP),
Khiabanian H (GICG),
Pine SR (GICG)

Liu J, Zhang C, Zhao Y, Yue X, Wu H, Huang S, Chen J, Tomsky K, Xie H, Khella CA, Gatza ML, Xia D, Gao J, White E, Haffty BG, Hu W, Feng Z. Parkin targets HIF-1alpha for ubiquitination and degradation to inhibit breast tumor progression. Nat Commun. 2017;8(1):1823. doi: 10.1038/s41467-017-01947-w. PubMed PMID: 29180628; PMCID: PMC5703960.

Gatza ML (GICG),
White E (CMI),
Haffty BG (CIPT),
Hu W (GICG),
Feng Z (GICG)

Patel DS, Misenko SM, Her J, Bunting SF. BLM helicase regulates DNA repair by counteracting RAD51 loading at DNA double-strand break sites. J Cell Biol. 2017;216(11):3521-34. doi: 10.1083/jcb.201703144. PubMed PMID: 28912125; PMCID: PMC5674892.

Bunting SF (GICG)

Smith KS, Liu LL, Ganesan S, Michor F, De S. Nuclear topology modulates the mutational landscapes of cancer genomes. Nat Struct Mol Biol. 2017;24(11):1000-6. doi: 10.1038/nsmb.3474. PubMed PMID: 28967881; PMCID: PMC5744871.

Ganesan S (CIPT),
De S (GICG)