CSCB - Selected Publications

Hirshfield KM, Tolkunov D, Zhong H, Ali SM, Stein MN, Murphy S, Vig H, Vazquez A, Glod J, Moss RA, Belyi V, Chan CS, Chen S, Goodell L, Foran D, Yelensky R, Palma NA, Sun JX, Miller VA, Stephens PJ, Ross JS, Kaufman H, Poplin E, Mehnert J, Tan AR, Bertino JR, Aisner J, DiPaola RS, Rodriguez-Rodriguez L, Ganesan S. Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers. Oncologist. 2016 Aug 26. PMID:27566247.

Oshima K, Khiabanian H, da Silva-Almeida AC, Tzoneva G, Abate F, Ambesi-Impiombato A, Sanchez-Martin M, Carpenter Z, Penson A, Perez-Garcia A, Eckert C, Nicolas C, Balbin M, Sulis ML, Kato M, Koh K, Paganin M, Basso G, Gastier-Foster JM, Devidas M, Loh ML, Kirschner-Schwabe R, Palomero T, Rabadan R, Ferrando AA. Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia. Proc Natl Acad Sci U S A. 2016 Sep 21. PMID:27655895.

Ai N, Wood RD, Yang E, Welsh WJ. Niclosamide is a Negative Allosteric Modulator of Group I Metabotropic Glutamate Receptors: Implications for Neuropathic Pain. Pharm Res. 2016 Sep 8. PMID:27631130.

Pei S, Minhajuddin M, D'Alessandro A, Nemkov T, Stevens BM, Adane B, Khan N, Hagen FK, Yadav VK, De S, Ashton JM, Hansen KC, Gutman JA, Pollyea DA, Crooks PA, Smith C, Jordan CT. Rational Design of a Parthenolide-based Drug Regimen that Selectively Eradicates Acute Myelogenous Leukemia Stem Cells. J Biol Chem. 2016 Aug 29. PMID:27573247.

Oza J, Ganguly B, Kulkarni A, Ginjala V, Yao M, Ganesan S. A Novel Role of Chromodomain Protein CBX8 in DNA Damage Response. J Biol Chem. 2016 Aug 23. PMID:27555324.

Guo JY, Teng X, Laddha SV, Ma S, Van Nostrand SC, Yang Y, Khor S, Chan CS, Rabinowitz JD, White E. Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells. Genes Dev. 2016 Aug 1;30(15):1704-17. PMID:27516533.

Zheng D, Liu X, Tian B. 3'READS+, a sensitive and accurate method for 3' end sequencing of polyadenylated RNA. RNA. 2016 Oct;22(10):1631-9. PMID:27512124.

Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T, Faltermeier CM, Uzunangelov V, Carlin DE, Fleming DT, Wong CK, Newton Y, Sudha S, Vashisht AA, Huang J, Wohlschlegel JA, Graeber TG, Witte ON, Stuart JM. Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. Cell. 2016 Aug 11;166(4):1041-54. PMID:27499020.

Devany E, Park JY, Murphy MR, Zakusilo G, Baquero J, Zhang X, Hoque M, Tian B, Kleiman FE. Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA. Cell Discov. 2016 Jun 14;2:16013. PMID:27462460.

Lund PK, Verzi MP. Singling Out Intestinal Epithelial Stem Cells. Gastroenterology. 2016 Aug;151(2):228-31. PMID:27374365.

Levine AJ, Puzio-Kuter AM, Chan CS, Hainaut P. The Role of the p53 Protein in Stem-Cell Biology and Epigenetic Regulation. Cold Spring Harb Perspect Med. 2016 Sep 1;6(9). PMID:27352800.

Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362-73. PMID:27335277.

Ganesan S, Rodriguez-Rodriguez L, DiPaola RS. Precision Medicine: Implications for Science and Practice. J Am Coll Surg. 2016 Sep;223(3):433-439. PMID:27321387.

Yadav VK, Smith KS, Flinders C, Mumenthaler SM, De S. Significance of duon mutations in cancer genomes. Sci Rep. 2016 Jun 8;6:27437. PMID:27272679.

Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016 May 25;534(7605):55-62. PMID:27251275.

Spencer KR, Wang J, Silk AW, Ganesan S, Kaufman HL, Mehnert JM. Biomarkers for Immunotherapy: Current Developments and Challenges. Am Soc Clin Oncol Educ Book. 2016;35:e493-503. PMID:27249758.

Ali SM, Hensing T, Schrock AB, Allen J, Sanford E, Gowen K, Kulkarni A, He J, Suh JH, Lipson D, Elvin JA, Yelensky R, Chalmers Z, Chmielecki J, Peled N, Klempner SJ, Firozvi K, Frampton GM, Molina JR, Menon S, Brahmer JR, MacMahon H, Nowak J, Ou SH, Zauderer M, Ladanyi M, Zakowski M, Fischbach N, Ross JS, Stephens PJ, Miller VA, Wakelee H, Ganesan S, Salgia R. Comprehensive Genomic Profiling Identifies a Subset of Crizotinib-Responsive ALK-Rearranged Non-Small Cell Lung Cancer Not Detected by Fluorescence In Situ Hybridization. Oncologist. 2016 Jun;21(6):762-70. PMID:27245569.

Hrdlickova R, Toloue M, Tian B. RNA-Seq methods for transcriptome analysis. Wiley Interdiscip Rev RNA. 2016 May 19. PMID:27198714.

Mehnert JM, Panda A, Zhong H, Hirshfield K, Damare S, Lane K, Sokol L, Stein MN, Rodriguez-Rodriquez L, Kaufman HL, Ali S, Ross JS, Pavlick DC, Bhanot G, White EP, DiPaola RS, Lovell A, Cheng J, Ganesan S. Immune activation and response to pembrolizumab in POLE-mutant endometrial cancer. J Clin Invest. 2016 Jun 1;126(6):2334-40. PMID:27159395.

Paganin M, Buldini B, Germano G, Seganfreddo E, Meglio Ad, Magrin E, Grillo F, Pigazzi M, Rizzari C, Cazzaniga G, Khiabanian H, Palomero T, Rabadan R, Ferrando AA, Basso G. A Case of T-cell Acute Lymphoblastic Leukemia Relapsed As Myeloid Acute Leukemia. Pediatr Blood Cancer. 2016 Sep;63(9):1660-3. PMID:27149388.

Choe KN, Nicolae CM, Constantin D, Imamura Kawasawa Y, Delgado-Diaz MR, De S, Freire R, Smits VA, Moldovan GL. HUWE1 interacts with PCNA to alleviate replication stress. EMBO Rep. 2016 Jun;17(6):874-86. PMID:27146073.

Boregowda RK, Medina DJ, Markert E, Bryan MA, Chen W, Chen S, Rabkin A, Vido MJ, Gunderson SI, Chekmareva M, Foran DJ, Lasfar A, Goydos JS, Cohen-Solal KA. The transcription factor RUNX2 regulates receptor tyrosine kinase expression in melanoma. Oncotarget. 2016 May 17;7(20):29689-707. PMID:27102439.

Wang R, Ganesan S, Zheng XF. Yin and yang of 4E-BP1 in cancer. Cell Cycle. 2016 Jun 2;15(11):1401-2. PMID:27096536.

Wu S, Marie Lutz B, Miao X, Liang L, Mo K, Chang YJ, Du P, Soteropoulos P, Tian B, Kaufman AG, Bekker A, Hu Y, Tao YX. Dorsal root ganglion transcriptome analysis following peripheral nerve injury in mice. Mol Pain. 2016 Mar 11;12. PMID:27030721.

Hintzsche J, Kim J, Yadav V, Amato C, Robinson SE, Seelenfreund E, Shellman Y, Wisell J, Applegate A, McCarter M, Box N, Tentler J, De S, Robinson WA, Tan AC. IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples. J Am Med Inform Assoc. 2016 Jul;23(4):721-30. PMID:27026619.

Gatza ML, Carey LA. Another Breast Cancer Entity Confirmed: Genomics of Invasive Lobular Breast Cancer. J Clin Oncol. 2016 Jun 1;34(16):1838-9. PMID:27022119.

Rodriguez-Rodriguez L, Hirshfield KM, Rojas V, DiPaola RS, Gibbon D, Hellmann M, Isani S, Leiser A, Riedlinger GM, Wagreich A, Ali SM, Elvin JA, Miller VA, Ganesan S. Use of comprehensive genomic profiling to direct point-of-care management of patients with gynecologic cancers. Gynecol Oncol. 2016 Apr;141(1):2-9. PMID:27016222.

Ganguly B, Dolfi SC, Rodriguez-Rodriguez L, Ganesan S, Hirshfield KM. Role of Biomarkers in the Development of PARP Inhibitors. Biomark Cancer. 2016 Mar 9;8(Suppl 1):15-25. PMID:26997874.

Pandya HJ, Park K, Chen W, Goodell LA, Foran DJ, Desai JP. Toward a Portable Cancer Diagnostic Tool Using a Disposable MEMS-Based Biochip. IEEE Trans Biomed Eng. 2016 Jul;63(7):1347-53. PMID:26930673.

Paratala BS, Dolfi SC, Khiabanian H, Rodriguez-Rodriguez L, Ganesan S, Hirshfield KM. Emerging Role of Genomic Rearrangements in Breast Cancer: Applying Knowledge from Other Cancers. Biomark Cancer. 2016 Feb 11;8(Supple 1):1-14. PMID:26917980.

Yadav VK, DeGregori J, De S. The landscape of somatic mutations in protein coding genes in apparently benign human tissues carries signatures of relaxed purifying selection. Nucleic Acids Res. 2016 Mar 18;44(5):2075-84. PMID:26883632.

Groen N, Guvendiren M, Rabitz H, Welsh WJ, Kohn J, de Boer J. Stepping into the omics era: Opportunities and challenges for biomaterials science and engineering. Acta Biomater. 2016 Apr 1;34:133-42. PMID:26876875.

Poczobutt JM, De S, Yadav VK, Nguyen TT, Li H, Sippel TR, Weiser-Evans MC, Nemenoff RA. Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer. J Immunol. 2016 Mar 15;196(6):2847-59. PMID:26873985.

Zhang C, Liu J, Tan C, Yue X, Zhao Y, Peng J, Wang X, Laddha SV, Chan CS, Zheng S, Hu W, Feng Z. microRNA-1827 represses MDM2 to positively regulate tumor suppressor p53 and suppress tumorigenesis. Oncotarget. 2016 Feb 23;7(8):8783-96. PMID:26840028.

Zhang Y, Li Q, Welsh WJ, Moghe PV, Uhrich KE. Micellar and structural stability of nanoscale amphiphilic polymers: Implications for anti-atherosclerotic bioactivity. Biomaterials. 2016 Apr;84:230-40. PMID:26828687.

Rasi S, Khiabanian H, Ciardullo C, Terzi-di-Bergamo L, Monti S, Spina V, Bruscaggin A, Cerri M, Deambrogi C, Martuscelli L, Biasi A, Spaccarotella E, De Paoli L, Gattei V, Foà R, Rabadan R, Gaidano G, Rossi D. Clinical impact of small subclones harboring NOTCH1, SF3B1 or BIRC3 mutations in chronic lymphocytic leukemia. Haematologica. 2016 Apr;101(4):e135-8. PMID:26819056.

Li W, Park JY, Zheng D, Hoque M, Yehia G, Tian B. Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control. BMC Biol. 2016 Jan 22;14:6. PMID:26801249.

Yang Y, Li W, Hoque M, Hou L, Shen S, Tian B, Dynlacht BD. PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation. PLoS Genet. 2016 Jan 14;12(1):e1005794. PMID:26765774.

Zhang C, Liu J, Zhao Y, Yue X, Zhu Y, Wang X, Wu H, Blanco F, Li S, Bhanot G, Haffty BG, Hu W, Feng Z. Glutaminase 2 is a novel negative regulator of small GTPase Rac1 and mediates p53 function in suppressing metastasis. Elife. 2016 Jan 11;5:e10727. PMID:26751560.

Su H, Shen Y, Xing F, Qi X, Hirshfield KM, Yang L, Foran DJ. Robust automatic breast cancer staging using a combination of functional genomics and image-omics. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:7226-9. PMID:26737959.

Ren J, Sadimin ET, Wang D, Epstein JI, Foran DJ, Qi X. Computer aided analysis of prostate histopathology images Gleason grading especially for Gleason score 7. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:3013-6. PMID:26736926.

Wang D, Foran DJ, Ren J, Zhong H, Kim IY, Qi X. Exploring automatic prostate histopathology image Gleason grading via local structure modeling. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:2649-52. PMID:26736836.

Joshi S, Tolkunov D, Aviv H, Hakimi AA, Yao M, Hsieh JJ, Ganesan S, Chan CS, White E. The Genomic Landscape of Renal Oncocytoma Identifies a Metabolic Barrier to Tumorigenesis. Cell Rep. 2015 Dec 1;13(9):1895-908. PMID:26655904.

Lee AK, Kulcsar KA, Elliott O, Khiabanian H, Nagle ER, Jones ME, Amman BR, Sanchez-Lockhart M, Towner JS, Palacios G, Rabadan R. De novo transcriptome reconstruction and annotation of the Egyptian rousette bat. BMC Genomics. 2015 Dec 7;16:1033. PMID:26643810.

Levine AJ, Chan CS, Dudgeon C, Puzio-Kuter A, Hainaut P. The Evolution of Tumors in Mice and Humans with Germline p53 Mutations. Cold Spring Harb Symp Quant Biol. 2015;80:139-45. PMID:26642854.

Kurc T, Qi X, Wang D, Wang F, Teodoro G, Cooper L, Nalisnik M, Yang L, Saltz J, Foran DJ. Scalable analysis of Big pathology image data cohorts using efficient methods and high-performance computing strategies. BMC Bioinformatics. 2015 Dec 1;16:399. PMID:26627175.

Faltermeier CM, Drake JM, Clark PM, Smith BA, Zong Y, Volpe C, Mathis C, Morrissey C, Castor B, Huang J, Witte ON. Functional screen identifies kinases driving prostate cancer visceral and bone metastasis. Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):E172-81. PMID:26621741.

Wu Y, Kwon YS, Labib M, Foran DJ, Singer EA. Magnetic Resonance Imaging as a Biomarker for Renal Cell Carcinoma. Dis Markers. 2015;2015:648495. PMID:26609190.

Smith KS, Yadav VK, Pei S, Pollyea DA, Jordan CT, De S. SomVarIUS: somatic variant identification from unpaired tissue samples. Bioinformatics. 2016 Mar 15;32(6):808-13. PMID:26589277.

White E, Mehnert JM, Chan CS. Autophagy, Metabolism, and Cancer. Clin Cancer Res. 2015 Nov 15;21(22):5037-46. PMID:26567363.

da Silva Almeida AC, Abate F, Khiabanian H, Martinez-Escala E, Guitart J, Tensen CP, Vermeer MH, Rabadan R, Ferrando A, Palomero T. The mutational landscape of cutaneous T cell lymphoma and Sézary syndrome. Nat Genet. 2015 Dec;47(12):1465-70. PMID:26551667.

Neve J, Burger K, Li W, Hoque M, Patel R, Tian B, Gullerova M, Furger A. Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation. Genome Res. 2016 Jan;26(1):24-35. PMID:26546131.

Diller DJ, Connell ND, Welsh WJ. Avalanche for shape and feature-based virtual screening with 3D alignment. J Comput Aided Mol Des. 2015 Nov;29(11):1015-24. PMID:26458937.

Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA; TCGA Research Network, Perou CM. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015 Oct 8;163(2):506-19. PMID:26451490.

LaCuran AE, Pegg KM, Liu EM, Bethel CR, Ai N, Welsh WJ, Bonomo RA, Oelschlaeger P. Elucidating the Role of Residue 67 in IMP-Type Metallo-β-Lactamase Evolution. Antimicrob Agents Chemother. 2015 Dec;59(12):7299-307. PMID:26369960.

Chen W, Brandes Z, Roy R, Chekmareva M, Pandya HJ, Desai JP, Foran DJ. Robot-Guided Atomic Force Microscopy for Mechano-Visual Phenotyping of Cancer Specimens. Microsc Microanal. 2015 Oct;21(5):1224-35. PMID:26343283.

Yang Y, Del Re DP, Nakano N, Sciarretta S, Zhai P, Park J, Sayed D, Shirakabe A, Matsushima S, Park Y, Tian B, Abdellatif M, Sadoshima J. miR-206 Mediates YAP-Induced Cardiac Hypertrophy and Survival. Circ Res. 2015 Oct 23;117(10):891-904. PMID:26333362.

Pandya HJ, Park K, Chen W, Chekmareva MA, Foran DJ, Desai JP. Simultaneous MEMS-based electro-mechanical phenotyping of breast cancer. Lab Chip. 2015;15(18):3695-706. PMID:26224116.

Bjørklund SS, Kristensen VN, Seiler M, Kumar S, Alnæs GI, Ming Y, Kerrigan J, Naume B, Sachidanandam R, Bhanot G, Børresen-Dale AL, Ganesan S. Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas. BMC Cancer. 2015 Jul 17;15:524. PMID:26183823.

Goodwin JF, Kothari V, Drake JM, Zhao S, Dylgjeri E, Dean JL, Schiewer MJ, McNair C, Jones JK, Aytes A, Magee MS, Snook AE, Zhu Z, Den RB, Birbe RC, Gomella LG, Graham NA, Vashisht AA, Wohlschlegel JA, Graeber TG, Karnes RJ, Takhar M, Davicioni E, Tomlins SA, Abate-Shen C, Sharifi N, Witte ON, Feng FY, Knudsen KE. DNA-PKcs-Mediated Transcriptional Regulation Drives Prostate Cancer Progression and Metastasis. Cancer Cell. 2015 Jul 13;28(1):97-113. PMID:26175416.

Garcia CA, Baron JM, Beckwith BA, Brodsky V, Dighe AS, Gudewicz TM, Kim JY, Klepeis VE, Lane WJ, Lee RE, Levy BP, Mahowald MA, Mandelker D, McClintock DS, Quinn AM, Rao LK, Riedlinger GM, Rudolf J, Gilbertson JR. Environmental components and methods for engaging pathology residents in informatics training. J Pathol Inform. 2015 Jun 29;6:42. PMID:26167386.

Hu J, Verzi MP, Robinson AS, Tang PL, Hua LL, Xu SM, Kwok PY, Black BL. Endothelin signaling activates Mef2c expression in the neural crest through a MEF2C-dependent positive-feedback transcriptional pathway. Development. 2015 Aug 15;142(16):2775-80. PMID:26160899.

Dai W, Li W, Hoque M, Li Z, Tian B, Makeyev EV. A post-transcriptional mechanism pacing expression of neural genes with precursor cell differentiation status. Nat Commun. 2015 Jul 6;6:7576. PMID:26144867.

Silva GO, He X, Parker JS, Gatza ML, Carey LA, Hou JP, Moulder SL, Marcom PK, Ma J, Rosen JM, Perou CM. Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer. Breast Cancer Res Treat. 2015 Jul;152(2):347-56. PMID:26109346.

Pfister NT, Fomin V, Regunath K, Zhou JY, Zhou W, Silwal-Pandit L, Freed-Pastor WA, Laptenko O, Neo SP, Bargonetti J, Hoque M, Tian B, Gunaratne J, Engebraaten O, Manley JL, Børresen-Dale AL, Neilsen PM, Prives C. Mutant p53 cooperates with the SWI/SNF chromatin remodeling complex to regulate VEGFR2 in breast cancer cells. Genes Dev. 2015 Jun 15;29(12):1298-315. PMID:26080815.

Das S, Yu S, Sakamori R, Vedula P, Feng Q, Flores J, Hoffman A, Fu J, Stypulkowski E, Rodriguez A, Dobrowolski R, Harada A, Hsu W, Bonder EM, Verzi MP, Gao N. Rab8a vesicles regulate Wnt ligand delivery and Paneth cell maturation at the intestinal stem cell niche. Development. 2015 Jun 15;142(12):2147-62. PMID:26015543.

Xu J, Xiang L, Wang G, Ganesan S, Feldman M, Shih NN, Gilmore H, Madabhushi A. Sparse Non-negative Matrix Factorization (SNMF) based color unmixing for breast histopathological image analysis. Comput Med Imaging Graph. 2015 Dec;46 Pt 1:20-9. PMID:25958195.

Young CD, Zimmerman LJ, Hoshino D, Formisano L, Hanker AB, Gatza ML, Morrison MM, Moore PD, Whitwell CA, Dave B, Stricker T, Bhola NE, Silva GO, Patel P, Brantley-Sieders DM, Levin M, Horiates M, Palma NA, Wang K, Stephens PJ, Perou CM, Weaver AM, O'Shaughnessy JA, Chang JC, Park BH, Liebler DC, Cook RS, Arteaga CL. Activating PIK3CA Mutations Induce an Epidermal Growth Factor Receptor (EGFR)/Extracellular Signal-regulated Kinase (ERK) Paracrine Signaling Axis in Basal-like Breast Cancer. Mol Cell Proteomics. 2015 Jul;14(7):1959-76. PMID:25953087.

Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S. Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Nucleic Acids Res. 2015 Jun 23;43(11):5307-17. PMID:25934800.

Li W, You B, Hoque M, Zheng D, Luo W, Ji Z, Park JY, Gunderson SI, Kalsotra A, Manley JL, Tian B. Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genet. 2015 Apr 23;11(4):e1005166. PMID:25906188.

Abdelhamid DS, Zhang Y, Lewis DR, Moghe PV, Welsh WJ, Uhrich KE. Tartaric acid-based amphiphilic macromolecules with ether linkages exhibit enhanced repression of oxidized low density lipoprotein uptake. Biomaterials. 2015 Jun;53:32-9. PMID:25890704.

Teh JL, Shah R, La Cava S, Dolfi SC, Mehta MS, Kongara S, Price S, Ganesan S, Reuhl KR, Hirshfield KM, Karantza V, Chen S. Metabotropic glutamate receptor 1 disrupts mammary acinar architecture and initiates malignant transformation of mammary epithelial cells. Breast Cancer Res Treat. 2015 May;151(1):57-73. PMID:25859923.

Martin AA, Tomasini M, Kholodovych V, Gu L, Sommerfeld SD, Uhrich KE, Murthy NS, Welsh WJ, Moghe PV. Carbohydrate-derived amphiphilic macromolecules: a biophysical structural characterization and analysis of binding behaviors to model membranes. J Funct Biomater. 2015 Apr 8;6(2):171-91. PMID:25855953.

Ai N, Wood RD, Welsh WJ. Identification of Nitazoxanide as a Group I Metabotropic Glutamate Receptor Negative Modulator for the Treatment of Neuropathic Pain: An In Silico Drug Repositioning Study. Pharm Res. 2015 Aug;32(8):2798-807. PMID:25762088.

Emmett KJ, Lee A, Khiabanian H, Rabadan R. High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants. PLoS Curr. 2015 Feb 9;7. PMID:25737802.

Selmecki AM, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson AL, De S, Kishony R, Michor F, Dowell R, Pellman D. Polyploidy can drive rapid adaptation in yeast. Nature. 2015 Mar 19;519(7543):349-52. PMID:25731168.

Yadav A, Radhakrishnan A, Bhanot G, Sinha H. Differential regulation of antagonistic pleiotropy in synthetic and natural populations suggests its role in adaptation. G3 (Bethesda). 2015 Feb 23;5(5):699-709. PMID:25711830.

Khiabanian H, Carpenter Z, Kugelman J, Chan J, Trifonov V, Nagle E, Warren T, Iversen P, Bavari S, Palacios G, Rabadan R. Viral diversity and clonal evolution from unphased genomic data. BMC Genomics. 2014;15 Suppl 6:S17. PMID:25573168.

Glod J, Song M, Sharma A, Tyagi R, Rhodes RH, Weissmann DJ, Roychowdhury S, Khan A, Kane MP, Hirshfield K, Ganesan S, DiPaola RS, Rodriguez-Rodriguez L. Next generation sequencing as an aid to diagnosis and treatment of an unusual pediatric brain cancer. J Pers Med. 2014 Jul 15;4(3):402-11. PMID:25563358.

Pimenta EM, De S, Weiss R, Feng D, Hall K, Kilic S, Bhanot G, Ganesan S, Ran S, Barnes BJ. IRF5 is a novel regulator of CXCL13 expression in breast cancer that regulates CXCR5(+) B- and T-cell trafficking to tumor-conditioned media. Immunol Cell Biol. 2015 May-Jun;93(5):486-99. PMID:25533286.

Wang J, Khiabanian H, Rossi D, Fabbri G, Gattei V, Forconi F, Laurenti L, Marasca R, Del Poeta G, Foà R, Pasqualucci L, Gaidano G, Rabadan R. Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia. Elife. 2014 Dec 11;3. PMID:25496728.

San Roman AK, Aronson BE, Krasinski SD, Shivdasani RA, Verzi MP. Transcription factors GATA4 and HNF4A control distinct aspects of intestinal homeostasis in conjunction with transcription factor CDX2. J Biol Chem. 2015 Jan 16;290(3):1850-60. PMID:25488664.

Stein MN, Hirshfield KM, Zhong H, Singer EA, Ali SM, Ganesan S. Response to crizotinib in a patient with MET-mutant papillary renal cell cancer after progression on tivantinib. Eur Urol. 2015 Feb;67(2):353-4. PMID:25457019.

Osimitz TG, Welsh WJ, Ai N, Toole C. Polyester monomers lack ability to bind and activate both androgenic and estrogenic receptors as determined by in vitro and in silico methods. Food Chem Toxicol. 2015 Jan;75:128-38. PMID:25455886.

Ai N, Welsh WJ, Santhanam U, Hu H, Lyga J. Novel virtual screening approach for the discovery of human tyrosinase inhibitors. PLoS One. 2014 Nov 26;9(11):e112788. PMID:25426625.

Di Giammartino DC, Li W, Ogami K, Yashinskie JJ, Hoque M, Tian B, Manley JL. RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3' UTRs. Genes Dev. 2014 Oct 15;28(20):2248-60. PMID:25319826.

Ariffin H, Hainaut P, Puzio-Kuter A, Choong SS, Chan AS, Tolkunov D, Rajagopal G, Kang W, Lim LL, Krishnan S, Chen KS, Achatz MI, Karsa M, Shamsani J, Levine AJ, Chan CS. Whole-genome sequencing analysis of phenotypic heterogeneity and anticipation in Li-Fraumeni cancer predisposition syndrome. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15497-501. PMID:25313051.

Lee A, Khiabanian H, Kugelman J, Elliott O, Nagle E, Yu GY, Warren T, Palacios G, Rabadan R. Transcriptome reconstruction and annotation of cynomolgus and African green monkey. BMC Genomics. 2014 Oct 3;15:846. PMID:25277458.

Pandya HJ, Chen W, Goodell LA, Foran DJ, Desai JP. Mechanical phenotyping of breast cancer using MEMS: a method to demarcate benign and cancerous breast tissues. Lab Chip. 2014 Dec 7;14(23):4523-32. PMID:25267099.

Shaknovich R, De S, Michor F. Epigenetic diversity in hematopoietic neoplasms. Biochim Biophys Acta. 2014 Dec;1846(2):477-84. PMID:25240947.

Zheng D, Tian B. RNA-binding proteins in regulation of alternative cleavage and polyadenylation. Adv Exp Med Biol. 2014;825:97-127. PMID:25201104.

Zhang C, Liu J, Wang X, Wu R, Lin M, Laddha SV, Yang Q, Chan CS, Feng Z. MicroRNA-339-5p inhibits colorectal tumorigenesis through regulation of the MDM2/p53 signaling. Oncotarget. 2014 Oct 15;5(19):9106-17. PMID:25193859.

Kurosaki T, Li W, Hoque M, Popp MW, Ermolenko DN, Tian B, Maquat LE. A post-translational regulatory switch on UPF1 controls targeted mRNA degradation. Genes Dev. 2014 Sep 1;28(17):1900-16. PMID:25184677.

Tereshchenko IV, Zhong H, Chekmareva MA, Kane-Goldsmith N, Santanam U, Petrosky W, Stein MN, Ganesan S, Singer EA, Moore D, Tischfield JA, DiPaola RS. ERG and CHD1 heterogeneity in prostate cancer: use of confocal microscopy in assessment of microscopic foci. Prostate. 2014 Nov;74(15):1551-9. PMID:25175909.

Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; Cancer Genome Atlas Research Network, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014 Sep 8;26(3):319-30. PMID:25155756.

Qi X, Wang D, Rodero I, Diaz-Montes J, Gensure RH, Xing F, Zhong H, Goodell L, Parashar M, Foran DJ, Yang L. Content-based histopathology image retrieval using CometCloud. BMC Bioinformatics. 2014 Aug 26;15:287. PMID:25155691.

Hormoz S, Bhanot G, Biehl M, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Dayarian A. Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets. Bioinformatics. 2015 Feb 15;31(4):492-500. PMID:25152231.

 

 

 

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