LIST OF PAPERS:
1. Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Marie Quinn A, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin JC, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG; TRACERx consortium.; PEACE consortium., Swanton C. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature. 2017 Apr 26;545(7655):446-451. doi: 10.1038/nature22364.
2. Chang W, Brohl AS, Patidar R, Sindiri S, Shern JF, Wei JS, Song YK, Yohe ME, Gryder B, Zhang S, Calzone KA, Shivaprasad N, Wen X, Badgett TC, Miettinen M, Hartman KR, League-Pascual JC, Trahair TN, Widemann BC, Merchant MS, Kaplan RN, Lin JC, Khan J. MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research. Clin Cancer Res. 2016 Aug 1;22(15):3810-20. doi: 10.1158/1078-0432.CCR-15-2717. Epub 2016 Mar 18. PMID: 26994145
3. Arafeh R, Qutob N, Emmanuel R, Keren-Paz A, Madore J, Elkahloun A, Wilmott JS, Gartner JJ, Di Pizio A, Winograd-Katz S, Sindiri S, Rotkopf R, Dutton-Regester K, Johansson P, Pritchard AL, Waddell N, Hill VK, Lin JC, Hevroni Y, Rosenberg SA, Khan J, Ben-Dor S, Niv MY, Ulitsky I, Mann GJ, Scolyer RA, Hayward NK, Samuels Y. Recurrent inactivating RASA2 mutations in melanoma. Nat Genet. 2015 Dec;47(12):1408-10. doi: 10.1038/ng.3427. Epub 2015 Oct 26. PMID: 26502337
4. Yeat NC, Lin C, Sager M, Lin JC. Cancer proteomics: developments in technology, clinical use and commercialization. Expert Rev Proteomics. 2015 Aug;12(4):391-405. doi: 10.1586/14789450.2015.1051969. Epub 2015 Jul 4. Review. PMID: 26145529
5. Sager M, Yeat NC, Pajaro-Van der Stadt S, Lin C, Ren Q, Lin JC. Transcriptomics in cancer diagnostics: developments in technology, clinical research and commercialization. Expert Rev Mol Diagn. 2015;15(12):1589-603. doi: 10.1586/14737159.2015.1105133. Epub 2015 Nov 13. PMID: 26565429
6. Shen T, Pajaro-Van de Stadt SH, Yeat NC, Lin JC. Clinical applications of next generation sequencing in cancer: from panels, to exomes, to genomes. Front Genet. 2015 Jun 17;6:215. doi: 10.3389/fgene.2015.00215. eCollection 2015. Review. PMID: 26136771
7. Shen T, Lee A, Shen C, Lin JC. The long tail and rare disease research: the impact of next-generation sequencing for rare Mendelian disorders. Genet Res (Camb). 2015 Sep 14;97:e15. doi: 10.1017/S0016672315000166. Review. PMID: 26365496
8. Walia V, Prickett TD, Kim JS, Gartner JJ, Lin JC, Zhou M, Rosenberg SA, Elble RC, Solomon DA, Waldman T, Samuels Y. Mutational and functional analysis of the tumor-suppressor PTPRD in human melanoma. Hum Mutat. 2014 Nov;35(11):1301-10. doi: 10.1002/humu.22630. Epub 2014 Sep 10. PMID: 25113440
9. Prickett TD, Zerlanko B, Gartner JJ, Parker SC, Dutton-Regester K, Lin JC, Teer JK, Wei X, Jiang J; NISC Comparative Sequencing Program, Chen G, Davies MA, Gershenwald JE, Robinson W, Robinson S, Hayward NK, Rosenberg SA, Margulies EH, Samuels Y. Somatic mutations in MAP3K5 attenuate its proapoptotic function in melanoma through increased binding to thioredoxin. J Invest Dermatol. 2014 Feb;134(2):452-60. doi: 10.1038/jid.2013.365. Epub 2013 Sep 5. PMID: 24008424
10. Rajasimha HK, Shirol PB, Ramamoorthy P, Hegde M, Barde S, Chandru V, Ravinandan ME, Ramchandran R, Haldar K, Lin JC, Babar IA, Girisha KM, Srinivasan S, Navaneetham D, Battu R, Devarakonda R, Kini U, Vijayachandra K, Verma IC. Organization for rare diseases India (ORDI) - addressing the challenges and opportunities for the Indian rare diseases' community. Genet Res (Camb). 2014 Aug 13;96:e009. doi: 10.1017/S0016672314000111. Review. PMID: 25579084
11. Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK; NISC Comparative Sequencing Program, Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci USA. 2013 Aug 13;110(33):13481-6. doi: 10.1073/pnas.1304227110. Epub 2013 Jul 30.
12. Robbins PF, Lu YC, El-Gamil M, Li YF, Gross C, Gartner J, Lin JC, Teer JK, Cliften P, Tycksen E, Samuels Y, Rosenberg SA. Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells. Nature Medicine. 2013 Jun;19(6):747-52. doi: 10.1038/nm.3161. Epub 2013 May 5.
13. Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Jeong JS, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. Construction of human activity-based phosphorylation networks. Mol Syst Biol. 2013;9:655. doi: 10.1038/msb.2013.12. PMID: 23549483
14. Lee, M, Lin JC. Overcoming the obstacles to returning genomic research results. Genetics Research. 2013 Apr 17:1-6.
15. Dolled-Filhart MP, Lordemann A, Dahl W, Haraksingh RH, Ou-Yang CW, Lin JC. Personalizing rare disease research: how genomics is revolutionizing the diagnosis and treatment of rare disease. Personalized Medicine, November 2012, Vol. 9, 8, 805-819.
16. Dolled-Filhart MP, Lee M Jr, Ou-Yang CW, Haraksingh RR, Lin JC. Computational and bioinformatics frameworks for next-generation whole exome and genome sequencing. Scientific World Journal. Epub 2013 Jan 13.
17. Lordemann A, Danielsson K, Lin JC. Innovative Funding Models for Rare Diseases. Orphan Diseases in the Age of Health 2.0. 2013. Springer
18. Gartner J, Davis S, Wei X, Lin JC, Teer JK, Rosenberg SA, Samuels Y, Trivedi NS, Meltzer PS. Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma. BMC Genomics. 2012 Sep 24;13(1):505.
19. Walia V, Mu EW, Lin JC, Samuels Y. Delving into somatic variation in sporadic melanoma. Pigment Cell Melanoma Res. 2012 Mar;25(2):155-70. doi: 10.1111/j.1755-148X.2012.00976.x. Epub 2012 Feb 13.
20. Prickett TD, Wei X, Cardenas-Navia I, Teer JK, Lin JC, Walia V, Gartner J, Jiang J, Cherukuri PF, Molinolo A, Davies MA, Gershenwald JE, Stemke-Hale K, Rosenberg SA, Margulies EH, Samuels Y. Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma. Nature Genetics. 2011 Sep 25;43(11):1119-26.
21. Gerstung M, Eriksson N, Lin JC, Vogelstein B, Beerenwinkel N. The temporal order of genetic and pathway alterations in tumorigenesis. PLoS One. 2011;6(11):e27136. Epub 2011 Nov 1.
22. Li R, Zhu J, Xie Z, Liao G, Liu J, Chen MR, Hu S, Woodard C, Lin JC, Taverna SD, Desai P, Ambinder RF, Hayward GS, Qian J, Zhu H, Hayward SD. Conserved Herpesvirus Kinases Target the DNA Damage Response Pathway and TIP60 Histone Acetyltransferase to Promote Virus Replication. Cell Host Microbe. 2011 Oct 4;10(4):390-400.
23. Wei X, Moncada-Pazos A, Cal S, Soria-Valles C, Gartner J, Rudloff U, Lin JC; NISC Comparative Sequencing Program, Rosenberg SA, López-Otín C, Samuels Y. Analysis of the disintegrin-metalloproteinases family reveals ADAM29 and ADAM7 are often mutated in melanoma. Hum Mutat. 2011 Jun;32(6):E2148-75. doi: 10.1002/humu.21477. Epub 2011 Feb 24.
24. Wei X, Lin JC, Walia V, Teer JK, Prickett TD, Gartner J, Davis S; NISC Comparative Sequencing Program, Stemke-Hale K, Davies MA, Gershenwald JE, Robinson W, Robinson S, Rosenberg SA, Samuels Y. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nature Genetics. 2011 May;43(5):442-6.
25. Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, Vandenberg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The Genetic Landscape of the Childhood Cancer Medulloblastoma. Science. 2010 Dec 16.
26. Wei X, Prickett TD, Viloria CG, Molinolo A, Lin JC, Cardenas-Navia I, Cruz P; NISC Comparative Sequencing Program, Rosenberg SA, Davies MA, Gershenwald JE, López-Otín C, Samuels Y. Mutational and functional analysis reveals ADAMTS18 metalloproteinase as a novel driver in melanoma. Mol Cancer Res. 2010 Nov;8(11):1513-25.
27. Lin JC. Protein microarrays for cancer diagnostics and therapy. Med Princ Pract. 2010;19(4):247-54.
28. Cárdenas-Navia LI, Cruz P, Lin JC; NISC Comparative Sequencing Program, Rosenberg SA, Samuels Y. (2010) Novel somatic mutations in heterotrimeric G proteins in melanoma. Cancer Biol Ther. 2010 Jul 4;10(1).
29. Lin JC*, Xie Z*, Zhu H and Qian J. (2010) Understanding protein phosphorylation on a systems level. Briefings in Functional Genomics and Proteomics.
30. Hu S, Xie Z, Onishi A, Yu X, Jiang L, Lin JC, Rho HS, Woodard C, Wang H, Jeong JS, Long S, He X, Wade H, Blackshaw S, Qian J, Zhu H. (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell. 2009 Oct 30;139(3):610-22.
31. Prickett TD, Agrawal NS, Wei X, Yates KE, Lin JC, Wunderlich JR, Cronin JC, Cruz P, Rosenberg SA, Samuels Y. (2009) Analysis of the tyrosine kinome in melanoma reveals recurrent mutations in ERBB4. Nature Genetics. 2009 Oct;41(10):1127-32.
32. Blackford A, Serrano OK, Wolfgang CL, Parmigiani G, Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Eshleman JR, Goggins M, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Cameron JL, Olino K, Schulick R, Winter J, Herman JM, Laheru D, Klein AP, Vogelstein B, Kinzler KW, Velculescu VE, Hruban RH. (2009) SMAD4 gene mutations are associated with poor prognosis in pancreatic cancer. Clin Cancer Res. 2009 Jul 15;15(14):4674-9.
33. Wan J, Lin JC, Zack DJ, Qian J. (2009) Relating periodicity of nucleosome organization and gene regulation. Bioinformatics. 2009 May 15.
34. Cronin JC, Wunderlich J, Loftus SK, Prickett TD, Wei X, Ridd K, Vemula S, Burrell AS, Agrawal NS, Lin JC, Banister CE, Buckhaults P, Rosenberg SA, Bastian BC, Pavan WJ, Samuels Y. (2009) Frequent mutations in the MITF pathway in melanoma. Pigment Cell Melanoma Res. 2009 Apr 29.
35. Duncan CG, Leary RJ, Lin JC, Cummins J, Di C, Schaefer CF, Wang TL, Riggins GJ, Edwards J, Bigner D, Kopelovich L, Vogelstein B, Kinzler KW, Velculescu VE, Yan H. (2009) Identification of microbial DNA in human cancer. BMC Med Genomics. 2009 May 8;2:22.
36. Blackford A, Parmigiani G, Kensler TW, Wolfgang C, Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Eshleman JR, Goggins M, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Klein A, Cameron JL, Olino K, Schulick R, Winter J, Vogelstein B, Velculescu VE, Kinzler KW, Hruban RH. (2009) Genetic mutations associated with cigarette smoking in pancreatic cancer. Cancer Res. 2009 Apr 15;69(8):3681-8.
37. Palavalli LH, Prickett TD, Wunderlich JR, Wei X, Burrell AS, Porter-Gill P, Davis S, Wang C, Cronin JC, Agrawal NS, Lin JC, Westbroek W, Hoogstraten-Miller S, Molinolo AA, Fetsch P, Filie AC, O'Connell MP, Banister CE, Howard JD, Buckhaults P, Weeraratna AT, Brody LC, Rosenberg SA, Samuels Y. (2009) Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma. Nature Genetics. 2009 Mar 29.
38. Jones S, Hruban RH, Kamiyama M, Borges M, Zhang X, Parsons DW, Lin JC, Palmisano E, Brune K, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Parmigiani G, Kern SE, Velculescu VE, Kinzler KW, Vogelstein B, Eshleman JR, Goggins M, Klein AP. (2009) Exomic Sequencing Identifies PALB2 as a Pancreatic Cancer Susceptibility Gene. Science. 2009 Apr 10;324(5924):217.
39. Parmigiani G, Boca S, Lin JC, Kinzler KW, Velculescu V, Vogelstein B. (2009) Design and analysis issues in genome-wide somatic mutation studies of cancer. Genomics.
40. Leary RJ, Lin JC, Cummins J, Boca S, Wood LD, Parsons DW, Jones S, Sjöblom T, Park BH, Parsons R, Willis J, Dawson D, Willson JK, Nikolskaya T, Nikolsky Y, Kopelovich L, Papadopoulos N, Pennacchio LA, Wang TL, Markowitz SD, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. (2008) Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16224-9.
41. Lin JC*, Jones S*, Zhang X*, Parsons DW*, Leary RJ*, Angenendt P*, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. (2008) Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008 Sep 26;321(5897): 1801-6.
42. Lin JC*, Parsons DW*, Jones S*, Zhang X*, Leary RJ*, Angenendt P*, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA Jr, Hartigan J, Smith DR, Strausberg RL, Marie SK, Shinjo SM, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. (2008) An integrated genomic analysis of human glioblastoma multiforme. Science. 2008 Sep 26;321(5897):1807-12.
43. Yu X, Lin JC, Zack DJ, Mendell JT, Qian J. (2008) Analysis of regulatory network topology reveals functionally distinct classes of microRNAs. Nucleic Acids Res. 2008 Nov;36(20):6494-503.
44. Lin JC, Li M. (2008) Molecular profiling in the age of cancer genomics. Expert Rev Mol Diagn. 2008 May;8(3):263-76.
45. Lin JC*, Wood LD*, Parsons DW*, Jones S*, Sjöblom T*, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. (2007) The genomic landscapes of human breast and colorectal cancers. Science. 2007 Nov 16;318(5853):1108-13.
46. Lin JC, Gan CM, Zhang X, Jones S, Sjöblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, Parmigiani G, Velculescu VE. (2007) A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res. 2007 Sep;17(9):1304-18.
47. Parmigiani G., Lin JC, Boca SM, Sjoblom T, Jones S, Wood LD, Parsons DW, Barber TD, , Buckhaults P, Markowitz SD, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. (2007) Response to Comments on "The consensus coding sequences of human breast and colorectal cancers". Science. 2007 Sep 14;317(5844):1500.
48. Yu X, Lin JC, Zack DJ, Qian J. (2007) Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors. BMC Bioinformatics. 2007 Nov 9;8(1):437
49. Parmigiani G, Lin JC, Boca, S., Sjoblom T, Kinzler K, Velculescu VE, and Vogelstein B. (2007) “Statistical Methods for the Analysis of Cancer Genome Sequencing Data” (October 2007). Johns Hopkins University, Dept. of Biostatistics Working Papers. Working Paper 126.
50. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin JC, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. (2007) Limits to the Human Cancer Genome Project? Science. 2007 Feb 9;315(5813): 764-5.
51. Lin JC, Sjoblom T. (2007) Genome-wide mutational analyses of breast and colorectal cancers. Discov Med. 2007 Feb;7(37):13-9.
52. Lin JC, Qian J. (2007) A Systems Biology Approach to Integrative Comparative Genomics. Expert Review in Proteomics. 2007 Feb;4(1):107-19.
53. Parmigiani G, Lin JC, Sjoblom T, Kinzler K, Vogelstein B, and Velculescu VE, Significant of candidate cancer genes assessed by the CaMP score (December 2006). Johns Hopkins University, Dept. of Biostatistics Working Papers. Working Paper 126.
54. Lin JC*, Bettegowda C*,Huang X*,Cheong I,Kohli M,Szabo S,Zhang X,Diaz D,Velculescu V, Parmigiani G,Kinzler K,Vogelstein B, Zhou S. (2006) The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT. Nature Biotechnology. 2006 Dec;24(12):1573-80.
55. Lin JC, Schmitt J. (2006) "Bioinformatics in Public Health" Encyclopedic Reference of Public Health.
56. Sjoblom T*, Jones S*, Wood LD*, Parsons DW*, Lin JC, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. (2006) The consensus coding sequences of human breast and colorectal cancers. Science. 2006 Oct 13;314(5797):268-74.
57. Yu X, Lin JC, Zack DJ, Qian J. (2006) Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res. 2006;34(17):4925-36.
58. Qian J, Lin JC, and Zack D. (2006) Characterization of binding sites of eukaryotic transcription factors. Genomics Proteomics Bioinformatics. 2006 May;4(2):67-79.
59. Yu X, Masuda T, Lin JC, Zack D, Qian J. (2006) Genome-wide prediction of transcription factor interactions in S. cerevisiae. Nucleic Acids Res. 2006 Feb 6;34(3):917-27.
60. Lin JC, Zack DJ, Qian J. (2006) Transcriptional regulatory network prediction. (2006) Biotechnol Genet Eng Rev. 2006;22:45-62.
61. Lin JC, Yamashita K, Tokumaru Y, Xiao Y, Son C, Hoque M, Mori M, Sidransky D. (2004) Comprehensive identification of novel tumor-specific and conserved epigenetically silenced genes in human cancers using modified pharmacological unmasking microarray. ACP Annual Session 2004 Medical Student Abstract Competition (Winner).
62. Qian J, Lin JC, Luscombe NM, Yu H, Gerstein M. (2003) Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics. 2003 Oct 12;19(15):1917-26.
63. Lin JC, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M. (2002) GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Res. 2002 Oct 15;30(20):4574-82.
64. Hegyi H, Lin JC, Greenbaum D, Gerstein M. (2002) Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds. Proteins. 2002 May 1;47(2):126-41.
65. Qian J, Dolled-Filhart M, Lin JC, Yu H, Gerstein M. (2001) Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J Mol Biol. 2001 Dec 14;314(5):1053-66.
66. Qian J, Stenger B, Wilson CA, Lin JC, Jansen R, Teichmann SA, Park J, Krebs WG, Yu H, Alexandrov V, Echols N, Gerstein M. (2001) PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Nucleic Acids Res. 2001 Apr 15;29(8):1750-64.
67. Gerstein M, Lin JC, Hegyi H. (2000) Protein folds in the worm genome. Pac Symp Biocomput. 2000;:30-41.
68. Lin JC, Gerstein M. (2000) Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res. 2000 Jun;10(6):808-18.