JimmyCheng HoLinMD

PubMed

• 211 citations
  Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers
  Rebecca J. Leary, Jimmy Lin, Jordan M. Cummins, Simina M. Boca, Laura D. Wood
  Proceedings of the National Academy of Sciences of the United States of America. 2008-10-21
• 121 citations
  Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma
  Todd D. Prickett, Xiaomu Wei, Isabel Cardenas-Navia, Jamie K. Teer, Jimmy Lin
  Nature Genetics. 2011-11-01
• 374 citations
  Exome sequencing identifies GRIN2A as frequently mutated in melanoma
  Xiaomu Wei, Vijay Walia, Jimmy Lin, Jamie K. Teer, Todd D. Prickett
  Nature Genetics. 2011-05-01

Journal Articles

• Characterization of binding sites of eukaryotic transcription factors.  
  Qian J, Lin JC, and Zack D, Genomics Proteomics Bioinformatics; 4(2):67-79
• Statistical Methods for the Analysis of Cancer Genome Sequencing Data.  
  Parmigiani G, Lin JC, Boca, S., Sjoblom T, Kinzler K, Velculescu VE, and Vogelstein B, Working Paper 126
• Limits to the Human Cancer Genome Project?  
  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..., Science; 315(5813): 764-5
• Genome-wide mutational analyses of breast and colorectal cancers.  
  Lin JC, Sjoblom T, Discov Med; 7(37):13-9
• A Systems Biology Approach to Integrative Comparative Genomics.  
  Lin JC, Qian J, Expert Review in Proteomics; 4(1):107-19
• Significant of candidate cancer genes assessed by the CaMP score.  
  Parmigiani G, Lin JC, Sjoblom T, Kinzler K, Vogelstein B, and Velculescu VE, Working Paper 126
• The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT.  
  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, Nat Biotechnol; 24(12):1573-80
• Bioinformatics in Public Health.  
  Lin JC, Schmitt J, Encyclopedic Reference of Public Health
• The consensus coding sequences of human breast and colorectal cancers.  
  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..., Science; 314(5797):268-74
• Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues.  
  Yu X, Lin JC, Zack DJ, Qian J, Nucleic Acids Res; 34(17):4925-36
• Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.  
  Yu X, Lin JC, Zack DJ, Qian J, BMC Bioinformatics; 8(1):437
• Genome-wide prediction of transcription factor interactions in S. cerevisiae.  
  Yu X, Masuda T, Lin JC, Zack D, Qian J, Nucleic Acids Res; 34(3):917-27
• Transcriptional regulatory network prediction.  
  Lin JC, Zack DJ, Qian J, Biotechnol Genet Eng Rev; 22:45-62
• Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.  
  Qian J, Lin JC, Luscombe NM, Yu H, Gerstein M, Bioinformatics; 19(15):1917-26
• GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.  
  Lin JC, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M, Nucleic Acids Res; 30(20):4574-82
• Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds.  
  Hegyi H, Lin JC, Greenbaum D, Gerstein M, Proteins; 47(2):126-41
• Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.  
  Qian J, Dolled-Filhart M, Lin JC, Yu H, Gerstein M, J Mol Biol; 314(5):1053-66
• PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole- genome expression and interaction information.  
  Qian J, Stenger B, Wilson CA, Lin JC, Jansen R, Teichmann SA, Park J, Krebs WG, Yu H, Alexandrov V, Echols N, Gerstein M, Nucleic Acids Res; 29(8):1750-64
• Protein folds in the worm genome.  
  Gerstein M, Lin JC, Hegyi H, Pac Symp Biocomput; 30-41
• Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels.  
  Lin JC, Gerstein M, Genome Res; 10(6):808-18
• Exomic Sequencing Identifies PALB2 as a Pancreatic Cancer Susceptibility Gene.  
  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, Velcules..., Science; 324(5924):217
• Conserved Herpesvirus Kinases Target the DNA Damage Response Pathway and TIP60 Histone Acetyltransferase to Promote Virus Replication.  
  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, Cell Host Microbe; 10(4):390-400
• The Genetic Landscape of the Childhood Cancer Medulloblastoma.  
  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, Ger..., Science
• Protein microarrays for cancer diagnostics and therapy.  
  Lin JC, Med Princ Pract; 19(4):247-54
• Understanding protein phosphorylation on a systems level.  
  Lin JC, Xie Z, Zhu H and Qian J, Briefings in Functional Genomics and Proteomics
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Abstracts/Posters

• Analysis of the Matrix Metalloproteinase Family Reveals MMP-8 is often mutated in Melanoma.
  Lin JC, AACR 100th Annual Meeting, Denver, CO, USA
• Prediction of transcriptional regulatory networks using gene expression data.
  Lin JC, The Seventh Annual International Conference on Computational Biology, Berlin, Germany
• The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT.
  Lin JC, Delta Omega Honorary Society in Public Health Poster Session, Baltimore, MD, USA
• Statistical and computational methods for large-scale sequencing of cancer genomes.
  Lin JC, Delta Omega Honorary Society in Public Health Poster Session, Baltimore, MD, USA
• A multidimensional analysis of genes mutated in breast and colorectal cancers.
  Lin JC, First RECOMB Satellite Workshop on Computational Cancer Biology, Center for Algorithmic and Systems Biology, UCSD / Calit2, San Diego, CA, USA
• Breast and colorectal cancer genomics.
  Lin JC, Cellular and Molecular Medicine Program Retreat, Baltimore, MD, USA
• Computational Methods for Cancer Genome Sequencing.
  Lin JC, 2nd Annual Young Investigator Symposium on Genomics and Bioinformatics, Baltimore, MD, USA
• Overview of Computational Cancer Genomics.
  Lin JC, Cellular and Molecular Medicine Program Retreat, Baltimore, MD, USA
• Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses.
  Lin JC, Johns Hopkins Graduate Student Association Poster Competition, Baltimore, MD, USA
• Comprehensive identification of novel tumor-specific and conserved epigenetically silenced genes in human cancers using modified pharmacological unmasking microarray.
  Lin JC, Yamashita K, Tokumaru Y, Xiao Y, Son C, Hoque M, Mori M, Sidransky D, ACP Annual Session, 2004 Medical Student Abstract Competition
• Comprehensive Glioblastoma Sequencing Reveals New Disease Subtype.
  Lin JC, 24th Annual National MD/PhD Student Conference, Keystone, CO
• Glioblastoma and Pancreatic Cancer Genomics.
  Lin JC, Cellular and Molecular Medicine Program Retreat, Baltimore, MD, USA
• Breast, Colorectal, Pancreatic, and Glioblostoma Cancer Genome Sequencing.
  Lin JC, 3rd Annual Young Investigator Symposium on Genomics and Bioinformatics, Baltimore, MD, USA
• Global genomic analyses reveal core signaling pathways in human pancreatic cancers and PALB2 as a Pancreatic Cancer Susceptibility Gene.
  Lin JC, Systems Biology Approaches to Cancer and Metabolic Disease, Karolinska Instituet, Stockholm, Sweden
• Mutational and Functional Analysis Reveals ADAMTS18 Metalloproteinase as a Novel Driver in Melanoma.
  Lin JC, AACR 102nd Annual Meeting 2011, Orlando, Florida, USA
• Exome sequencing identifies GRIN2A as frequently mutated in melanoma.
  Lin JC, 26th Annual National MD/PhD Student Conference, Keystone, CO, USA
• Activity-Based Phosphorylation Networks in Humans.
  Lin JC, HUPO 11th Annual World Congress, Boston, MA, USA
• Toward Deciphering the Genetic Landscape in Melanoma.
  Lin JC, European Society for Medical Oncology (ESMO) 2012 Congress, Vienna, Austria
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Lectures

• Cancer Genomics: Past, Present, Future. 
  School of Biomedicine, Health Sciences University of Mongolia. Ulaanbaatar, Mongolia
• Clinical Generation Sequencing: Hope for Patients with Cancer and Rare Diseases. 
  National Cancer Institute, National Institutes of Health. Gaithersburg, MD, USA
• Rare Genomics Institute: Impacting Rare Diseases, One Family at a Time. 
  Q Conference. Washington, DC, USA
• Rare Genomics Institute: Crowdfunding Innovation in Rare Diseases. 
  TED 2012. Long Beach, CA, USA
• Rare Genomics Institute. 
  Praxis Social Entrepreneurship Accelerator. Los Angeles, CA, USA
• Cancer Genome Sequencing: Past, Present, and Future. 
  Johns Hopkins MD/PhD Program Annual Retreat. Hershey, PA, USA
• Rare Genomics Institute: Empower Communities. Accelerating Research. 
  Rare Disease Roundtable. Palisades, NY, USA
• Cancer Exome Sequencing of Breast, Colorectal, Pancreatic, and Brain Cancers. 
  National Cancer Center of Mongolia. Ulaanbaatar, Mongolia
• Research Ethics: The American Experience. 
  Bioethics Committee, Health Sciences University of Mongolia. Ulaanbaatar, Mongolia
• Emerging Sequencing Technologies: First-, Second-, and Third-Generations. 
  Mongolia Academy of Sciences. Ulaanbaatar, Mongolia
• Overview of Cancer Genomics: Past, Present, Future. 
  Mongolia International University. Ulaanbaatar, Mongolia
• Cancer Therapeutics in the Age of Cancer Genomics. 
  School of Biomedicine, Health Sciences University of Mongolia. Ulaanbaatar, Mongolia
• Innovation in Healthcare Without Borders. 
  European Commission (European Union). Brussels, Belgium
• DNA Sequencing Technologies. 
  School of Biomedicine, Health Sciences University of Mongolia. Ulaanbaatar, Mongolia
• Rare Genomics Institute: Genome-wide Sequencing for Rare Diseases. 
  Multiple locations, 2011
• Microfinancing Genomic Sequencing of Rare Diseases. 
  Multiple locations, 2011
• Exome sequencing identifies GRIN2A as frequently mutated in melanoma. 
  26th Annual National MD/PhD Student Conference. Keystone, CO, USA
• Lessons From Sequencing the Genomes of Breast, Colorectal, Pancreatic, and Brain Cancers. 
  Johns Hopkins Cellular and Molecular Medicine Thesis Defense. Baltimore, MD, USA
• Lessons from Sequencing Cancer Exomes of Breast, Colon, Pancreas, and Brain– A Personal Journey. 
  Multiple locations, 2010
• Lessons from Sequencing Four Cancer Genomes. 
  Johns Hopkins Cellular and Molecular Medicine Lunch Seminar. Baltimore, MD, USA
• The consensus coding sequences of human breast and colorectal cancers. 
  Johns Hopkins School of Public Health Expressionist Seminar Series. Baltimore, MD, USA
• A multidimensional analysis of genes mutated in breast and colorectal cancers. 
  Multiple locations, 2007
• Comprehensive identification of novel tumor-specific and conserved epigenetically silenced genes in human cancers using modified pharmacological unmasking microarray. 
  American College Physicians Annual Session, New Orleans, LA, USA
• Rare Genomics Institute: A Social Entrepreneurship Journey. 
  Multiple locations, 2012
• Drug repositioning and repurposing for rare and neglected diseases. 
  2nd Annual Drug Repositioning & Indications Discovery Conference. San Francisco, CA, USA
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Other

• Genetic Alterations in Isocitrate Dehydrogenase and the Other Genes in Malignant Glioma. 
  Lin JC, Chinese Patient Application No. 200980138651.4
• Consensus Coding Sequences of Human Breast and Colorectal Cancers. 
  Lin JC, US Patent Application 2010/0316995
• Genomic Landscapes of Human Breast and Colorectal Cancers. 
  Lin JC, US Patent Application 2009/0123928
• Consensus Coding Sequences of Human Breast and Colorectal Cancers. 
  Lin JC, WO Patent Application 2008/021288 A3R4
• Genomic Landscapes of Human Breast and Colorectal Cancers. 
  Lin JC, WO Patent Application 2009/049166 A3R4
• Pathways Underlying Pancreatic Tumorigenesis and an Hereditary Pancreatic Cancer Gene. 
  Lin JC, WO Patent Application 2010/028098 A4R1
• Genetic Alterations in Isocitrate Dehydrogenase and the Other Genes in Malignant Glioma. 
  Lin JC, WO Patent Application 2010/028099 A1
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