Publications

45. Oleksiewicz U et al., “KRAB/TRIM28 preserve self-renewal of human pluripotent stem cells through epigenetic repression of pro-differentiation genes” Stem Cell Reports 2017 17 30486-1.

44. Wiznerowicz M, Shah PK and Andersen, JN “Editorial” Contemp Oncol 2015 19(1A): A78-91.

43. Baniwal SK, Shah PK, Shi Y, Haduong JH, DeClerck YA, Gabet Y and Frenkel B, “Runx2 promotes both osteoblastogenesis and novel osteoclastogenic signals in ST2 mesenchymal progenitor cells” Osteoporosis International 2011.

42. D’Angelo S, .., Shah PK*. “Analysis of mMCC samples identify mechanism of host genomic regulation by merkel cell polyoma virus and biomarkers of response” (In preparation)

41. Naranbhai V, et al. “HLA-A*03 is a predictive biomarker of poor response to immune checkpoint blockade in cancer” Submitted to New England Journal of Medicine

40. D’Angelo S et al., “First-Line avelumab in patients with metastatic merkel cell carcinoma (JAVELIN Merkel 200): primary and biomarker analyses of a single-arm, multicentre phase 2 cohort”. Submitted Journal of ImmunoTherapy of Cancer

39. D’Angelo S et al., “Avelumab in patients with previously treated metastatic Merkel cell carcinoma: long-term data and biomarker analyses from single-arm phase 2 JAVELIN Merkel 200 trial”, Journal of ImmunoTherapy of Cancer 2020 8(1): e000674

38. Vamathavan et al., “Applications of machine learning in drug discovery and development”, Nature Reviews Drug Discovery 2019 18(6): 463-477.

37. Appikonda S et al, “Cross-talk between chromatin acetylation and TRIM24 SUMOylation impacts cell adhesion” J Biol Chem 2018 293(19): 7476-7485.

36. Czerwinska P, Shah PK et al, “TRIM28 regulates cancer stem cell population in breast cancer development” Oncotarget 2017 8(1):863-882.

35. Carugo A et al, “In vivo functional platform targeting patient-derived xenografts identifies WDR5-Myc association as a critical determinant of pancreatic cancer” Cell Rep 2016 16(1): 133-47.

34. Vangamudi B, Shah PK‡, Paul TA‡ et al., “The SMARCA2/4 ATPase domain surpasses the bromodomain as a drug target in SWI/SNF mutant cancers: Insights from cDNA rescue and PFI-3 inhibitor studies” Cancer Res 2015 75(18): 3865-78.

33. Pettazzoni P, Viale A, Shah PK et al., “Genetic events that limit the efficacy of MEK and RTK inhibitor therapies in a mouse model of KRAS-driven pancreatic cancer” Cancer Res 2015 75(6): 1091-101.

32. Oleksiewicz U, Tomczak K, Woropaj J, Markowska M, Stępniak P, Shah PK*. “Computational characterisation of cancer molecular profiles derived using next generation sequencing” Contemp Oncol 2015 19(1A): A78-91.

31. Pathiraja et al., “TRIM24 links glucose metabolism with transformation of human mammary epithelial cells” Oncogene 2014.

30. Li L et al., “Identification and targeting androgen receptor- and c-MyB-regulated DNA damage response pathway in anti-androgen-resistant prostate cancer” Science Signaling 2014 7(326): ra47.

29. Amin SB et al, “Gene Expression Profile Alone Is Inadequate In Predicting Complete Response In Multiple Myeloma” Leukemia 2014.

28. Shah PK‡, Samur MK‡, Wang X, Minvielle S, Magrangeas F, Avet-Loiseau H, Munshi NC and Li C. “Variation and functional consequences of copy number dosage effect in Multiple Myeloma” BMC Genomics 2013 14:672.

27. Wang X et al., “TrF-pathway co-expression analysis reveals distinct transcriptional dysregulation of cell cycle arrest between hyperdiploid and non-hyperdiploid myeloma” Leukemia 2013 1-10.

26. Li Yingxiang et al., “Classify hyperdiploidy status of multiple myeloma patients using gene expression profiles” PLOS ONE 2013 8(3): e58809.

25. Samur MK‡, Yan Z., Wang X, Cao Q, Munshi NC, Li C, and Shah PK‡*, “CanEvolve: A web portal for integrative oncogenomics” PLOS ONE 2013 8(2): e56228.

24. Chauhan D et al., “A small molecule inhibitor of ubiquitin-specific protease-7 induces apoptosis in multiple myeloma cells and overcomes bortezomib resistance.” Cancer Cell. 2012 22(3): 345-58

23. Yan Z, Shah PK et al., “Feed-forward-loops consisting of transcription factors, miRNAs and their target genes explain significant proportion of cancer induced transcriptome changes” Nucleic Acids Research 2012 40(17): e 135.

22. Shah PK‡,*, Huang N‡, Li C* and, “Lessons from a decade of integrating cancer copy number alterations with gene expression profiles” Briefings in Bioinformatics 2011

21. Amin SB, Shah PK, Yan A, Adamia S, Minvielle S, Avet-Loiseau S, Munshi NC and Li C, “The dChip survival analysis module for microarray data” BMC Bioinformatics 2011 12:72.

20. Hua S et al. “Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression”. Mol Syst Biol 2008; 4:188. PMCID: PMC2394496

19. Negre N et al., “A Cis-Regulatory Map of the Drosophila Genome” Nature 2011 471:527-531.

18. Roy S. et al. “Identification of functional elements and regulatory circuits by Drosophila modENCODE” Science 2010 330(6012): 1787-97.

17. Negre N‡, Brown CD‡, Shah PK, Kheradpour P, Morrison CA, Henikoff JG, Feng X, Ahmad K, Russell S, White RA, Stein L, Henikoff S, Kellis M, and White KP. “A comprehensive map of insulator elements for the drosophila genome”. PLoS Genet 2010; 6(1): e1000814. PMCID: PMC2797089

16. Shah PK‡, Tian F‡, Liu X, Negre N, Chen J, Karpenko O, White KP, and Grossman R. “Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks”. Bioinformatics 2009; 25(22): 3001-4. PMCID: PMC2773252

15. Celniker SE et al. “The modENCODE consortium, “unlocking the secrets of the genome”. Nature 2009; 459(7249): 927–30. PMCID: PMC2843545

14. Ling X, Liu Y, Huang Z, Shah PK and Li C. “A graphical article-level metric for intuitive comparison of large-scale literatures” Scientometrics 2016 106(1): 41-50.

13. Shah PK*, and Bork P. “LSAT: learning about alternative transcripts in MEDLINE”. Bioinformatics 2006; 22 (7): 857-65.

12. Shah PK, Jensen LJ, Boue S, and Bork P. “Extraction of transcript diversity from scientific literature”. PLoS Comput Biol 2005; 1(1): e10.

11. Wattarujeekrit T, Shah PK, and Collier N. “PASBio: predicate-argument structures for event extraction in molecular biology”. BMC Bioinformatics 2004; 5:155.

10. Shah PK, Perez-Iratxeta C, Bork P, and Andrade MA. “Information extraction from full text scientific articles: where are the keywords?”. BMC Bioinformatics 2003; 4: 20.

9. Perez-Iratxeta C, Astola N, Ciccarelli FD, Shah PK, Bork P, and Andrade MA. “A protocol for the update of references to scientific literature in biological databases”. Appl Bioinformatics 2003; 2 (3): 189-91.

8. Wang Y, Wu W, Negre NN, White KP, Li C and Shah PK*, “Determinants of antigenicity and specificity for immune response in protein sequences” BMC Bioinformatics 2011 12:251.

7. Shah PK‡, Tripathi L‡, Jensen LJ, Ghanim M, Mason C, Rodrigues V, Furlong E, White KP, Bork P, and Sowdhamini R. “Enhanced function annotations for drosophila serine proteases: a case study for systematic annotation of multi-member gene families”. Gene 2008; 407(1-2): 199–215.

6. Rodrigues AA, Bompada T, Syed M, Shah PK, and Maltsev N. “Evolutionary analysis of enzymes using chisel”. Bioinformatics 2007; 23(22): 2961-8d.

5. Muller A, Schackert HK, Lange B, Ruschoff J, Fuzesi L, Willert J, Burfeind P, Shah PK, Becker H, Epplen JT, and Stemmler S. “A novel MSH2 germline mutation in homozygous state in two brothers with colorectal cancers diagnosed at the age of 11 and 12 years”. Am J Med Genet 2006; 140 (3): 195-9.

4. Campillos M, Doerks T, Shah PK, and Bork P. “Computational characterization of multiple gag-like human proteins”. Trends Genet 2006; 22(11): 585-9.

3. Shah PK, Aloy P, Bork P, and Russell RB. “Structural similarity to bridge sequence space: finding new families on the bridges”. Protein Science 2005; 14 (5): 1305-14.

2. Shah PK, and Sowdhamini R. “Structural understanding of the transmembrane domains of inositol triphosphate receptors and ryanodine receptors towards calcium channeling”. Protein Eng 2001; 14 (11): 867-74.

1. Shah PK, Buslje CM, and Sowdhamini R. “Structural determinants of binding and specificity in transforming growth factor-receptor interactions”. Proteins 2001; 45 (4): 408-20.