JimmyCheng HoLinMD

PubMed

• Exome sequencing of ABCB5 identifies recurrent melanoma mutations that result in increased proliferative and invasive capacities.
  Sana, G.,Madigan, J. P.,Gartner, J. J.,Fourrez, M.,Lin, J.,Qutob, N.,Narayan, J.,Shukla, S.,Ambudkar, S. V.,Xia, D.,Rosenberg, S. A.,Gottesman, M. M.,Samuels, Y.,Gille...> ;J. Invest. Dermatol.. 2019 Mar 25
• Author Correction: RGS7 is recurrently mutated in melanoma and promotes migration and invasion of human cancer cells.
  Qutob, N.,Masuho, I.,Alon, M.,Emmanuel, R.,Cohen, I.,Di Pizio, A.,Madore, J.,Elkahloun, A.,Ziv, T.,Levy, R.,Gartner, J. J.,Hill, V. K.,Lin, J. C.,Hevroni, Y.,Greenberg...> ;Sci Rep. 2019 Mar 10
• RGS7 is recurrently mutated in melanoma and promotes migration and invasion of human cancer cells.
  Qutob, N.,Masuho, I.,Alon, M.,Emmanuel, R.,Cohen, I.,Di Pizio, A.,Madore, J.,Elkahloun, A.,Ziv, T.,Levy, R.,Gartner, J. J.,Hill, V. K.,Lin, J. C.,Hevroni, Y.,Greenberg...> ;Sci Rep. 2018 Jan 14
• Recurrent inactivating RASA2 mutations in melanoma.
  Arafeh, R.,Qutob, N.,Emmanuel, R.,Keren-Paz, A.,Madore, J.,Elkahloun, A.,Wilmott, J. S.,Gartner, J. J.,Di Pizio, A.,Winograd-Katz, S.,Sindiri, S.,Rotkopf, R.,Dutton-Re...> ;Nat. Genet.. 2015 Oct 27
• Mutational and Functional Analysis of the Tumor-Suppressor PTPRD in Human Melanoma.
  Walia, V.,Prickett, T. D.,Kim, J. S.,Gartner, J. J.,Lin, J. C.,Zhou, M.,Rosenberg, S. A.,Elble, R. C.,Solomon, D. A.,Waldman, T.,Samuels, Y.> ;Hum. Mutat.. 2014 Aug 13
• 12 citations
  Randomized trial of nutrition education added to internet-based information and exercise at the work place for weight loss in a racially diverse population of overweig...
  Andrea Carnie, J Lin, Brittany O. Aicher, Benjamin Leon, Amber B. Courville, Nancy G. Sebring, J. De Jesus, Diane M. DellaValle, B D Fitzpatrick, Gloria Zalos, Tiffany...> ;Nutrition & Diabetes. 2013 Dec 23
• Somatic Mutations in MAP3K5 Attenuate its Pro-Apoptotic Function in Melanoma Through Increased Binding to Thioredoxin.
  Prickett, T. D.,Zerlanko, B.,Gartner, J. J.,Parker, S. C.,Dutton-Regester, K.,Lin, J. C.,Teer, J. K.,Wei, X.,Jiang, J.,Chen, G.,Davies, M. A.,Gershenwald, J. E.,Robins...> ;J. Invest. Dermatol.. 2013 Sep 5
• Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma.
  Gartner, J. J.,Parker, S. C.,Prickett, T. D.,Dutton-Regester, K.,Stitzel, M. L.,Lin, J. C.,Davis, S.,Simhadri, V. L.,Jha, S.,Katagiri, N.,Gotea, V.,Teer, J. K.,Wei, X....> ;Proc. Natl. Acad. Sci. U.S.A.. 2013 Aug 13
• Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells.
  Robbins, P. F.,Lu, Y. C.,El-Gamil, M.,Li, Y. F.,Gross, C.,Gartner, J.,Lin, J. C.,Teer, J. K.,Cliften, P.,Tycksen, E.,Samuels, Y.,Rosenberg, S. A.> ;Nat. Med.. 2013 Jun
• Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma.
  Gartner JJ Davis S Wei X Lin JC Trivedi NS Teer JK Meltzer PS Rosenberg SA Samuels Y > ;BMC Genomics . 2012
• Delving into somatic variation in sporadic melanoma.
  Walia V Mu EW Lin JC Samuels Y > ;Pigment Cell Melanoma Res . 2012 Mar
• 117 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, Vijay Walia, Jared J. Gartner, Jiji Jiang, Praveen F. Cherukuri, Alfredo A. Molinolo, Mi...> ;Nature Genetics. 2011 Nov 1
• 31 citations
  Analysis of the disintegrin-metalloproteinases family reveals ADAM29 and ADAM7 are often mutated in melanoma.
  Xiaomu Wei, Angela Moncada-Pazos, Santiago Cal, Clara Soria-Valles, Jared J. Gartner, Udo Rudloff, Jimmy Lin, Steven A. Rosenberg, Carlos López-Otín, Yardena Samuels> ;Human Mutation. 2011 Jun 1
• 375 citations
  Exome sequencing identifies GRIN2A as frequently mutated in melanoma
  Xiaomu Wei, Vijay Walia, Jimmy Lin, Jamie K. Teer, Todd D. Prickett, Jared J. Gartner, Sean Davis, Nisc Comparative Sequencing Program, Katherine Stemke-Hale, Michael ...> ;Nature Genetics. 2011 May 1
• 44 citations
  Mutational and functional analysis reveals ADAMTS18 metalloproteinase as a novel driver in melanoma.
  Xiaomu Wei, Todd D. Prickett, Cristina G. Viloria, Alfredo A. Molinolo, Jimmy Lin, Isabel Cardenas-Navia, Pedro Cruz, Steven A. Rosenberg, Michael A. Davies, Jeffrey E...> ;Molecular Cancer Research. 2010 Nov 1
• 19 citations
  Novel somatic mutations in heterotrimeric G proteins in melanoma
  L Isabel Cárdenas-Navia, Pedro Cruz, Jimmy Lin, Nisc Comparative Sequencing Program, Steven A. Rosenberg, Yardena Samuels> ;Cancer Biology & Therapy. 2010 Jul 1
• 30 citations
  Understanding protein phosphorylation on a systems level
  Jimmy Lin, Zhi Xie, Heng Zhu, Jiang Qian> ;Briefings in Functional Genomics. 2010 Jan 1
• 266 citations
  Analysis of the Tyrosine Kinome in Melanoma Reveals Recurrent Mutations in ERBB4
  Todd D. Prickett, Neena S Agrawal, Xiaomu Wei, Kristin E. Yates, Jimmy Lin, John R. Wunderlich, Julia C. Cronin, Pedro Cruz, Steven A. Rosenberg, Yardena Samuels> ;Nature Genetics. 2009 Aug 30
• 111 citations
  Frequent mutations in the MITF pathway in melanoma
  Julia C. Cronin, John R. Wunderlich, Stacie K. Loftus, Todd D. Prickett, Xiaomu Wei, Katie Ridd, Swapna S. Vemula, Allison S. Burrell, Neena S Agrawal, Jimmy Lin, Caro...> ;Pigment Cell & Melanoma Research. 2009 Aug 1
• 112 citations
  Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma
  Lavanya H. Palavalli, Todd D. Prickett, John R. Wunderlich, Xiaomu Wei, Allison S. Burrell, Patricia Porter-Gill, Sean Davis, Chenwei Wang, Julia C. Cronin, Neena S Ag...> ;Nature Genetics. 2009 May 1
• 210 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, D. Williams Parsons, Siân Jones, Tobias Sjöblom, Ben Ho Park, Ramon Parsons, Joseph Will...> ;Proceedings of the National Academy of Sciences of the United States of America. 2008 Oct 21
• 4 citations
  Molecular profiling in the age of cancer genomics.
  Jimmy Lin, Meng Li> ;Expert Review of Molecular Diagnostics. 2008 May 1
• 96 citations
  A multidimensional analysis of genes mutated in breast and colorectal cancers
  Jimmy Lin, Christine Gan, Xiaosong Zhang, Siân Jones, Tobias Sjöblom, Laura D. Wood, D. Williams Parsons, Nickolas Papadopoulos, Kenneth W. Kinzler, Bert Vogelstein, G...> ;Genome Research. 2007 Sep 1
• Transcriptional regulatory network prediction
  Jimmy Lin, Donald J. Zack, Jiang Qian> ;Biotechnology & Genetic Engineering Reviews. 2006 Jan 1
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Journal Articles

• Molecular profiling in the age of cancer genomics.  
  Lin JC, Li M, Expert Rev Mol Diagn; 8(3):263-76
• The genomic landscapes of human breast and colorectal cancers.  
  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..., Science; 318(5853):1108-13
• A multidimensional analysis of genes mutated in breast and colorectal cancers.  
  Lin JC, Gan CM, Zhang X, Jones S, Sjöblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, Parmigiani G, Velculescu VE, Genome Res; 17(9):1304-18
• Response to Comments on "The consensus coding sequences of human breast and colorectal cancers".  
  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, Ki..., Science; 317(5844):1500
• 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
• 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
• Characterization of binding sites of eukaryotic transcription factors.  
  Qian J, Lin JC, and Zack D, Genomics Proteomics Bioinformatics; 4(2):67-79
• 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
• The temporal order of genetic and pathway alterations in tumorigenesis.  
  Gerstung M, Eriksson N, Lin JC, Vogelstein B, Beerenwinkel N, PLoS One; 6(11):e27136
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Abstracts/Posters

• 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
• 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
• 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
• Prediction of transcriptional regulatory networks using gene expression data.
  Lin JC, The Seventh Annual International Conference on Computational Biology, Berlin, Germany
• 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
• Toward Deciphering the Genetic Landscape in Melanoma.
  Lin JC, European Society for Medical Oncology (ESMO) 2012 Congress, Vienna, Austria
• Activity-Based Phosphorylation Networks in Humans.
  Lin JC, HUPO 11th Annual World Congress, Boston, MA, USA
• Exome sequencing identifies GRIN2A as frequently mutated in melanoma.
  Lin JC, 26th Annual National MD/PhD Student Conference, Keystone, CO, USA
• Mutational and Functional Analysis Reveals ADAMTS18 Metalloproteinase as a Novel Driver in Melanoma.
  Lin JC, AACR 102nd Annual Meeting 2011, Orlando, Florida, 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
• Breast, Colorectal, Pancreatic, and Glioblostoma Cancer Genome Sequencing.
  Lin JC, 3rd Annual Young Investigator Symposium on Genomics and Bioinformatics, Baltimore, MD, USA
• Glioblastoma and Pancreatic Cancer Genomics.
  Lin JC, Cellular and Molecular Medicine Program Retreat, Baltimore, MD, USA
• Comprehensive Glioblastoma Sequencing Reveals New Disease Subtype.
  Lin JC, 24th Annual National MD/PhD Student Conference, Keystone, CO
• Analysis of the Matrix Metalloproteinase Family Reveals MMP-8 is often mutated in Melanoma.
  Lin JC, AACR 100th Annual Meeting, Denver, CO, 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
• Overview of Computational 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
• Breast and colorectal cancer genomics.
  Lin JC, Cellular and Molecular Medicine Program Retreat, Baltimore, MD, USA
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Lectures

• Medicine without Borders: Innovations for Longer Life and Higher Living Standards. 
  Moscow International Forum for Innovative Development. Moscow, Russia
• Drug repositioning and repurposing for rare and neglected diseases. 
  2nd Annual Drug Repositioning & Indications Discovery Conference. San Francisco, CA, USA
• Open Science and Patient Empowerment Models for Long Tail Diseases. 
  Open Science Summit. Mountain View, CA, USA
• Crowdfunding models for scientific advancement and collaboration. 
  Stanford / Sage Bionetworks BRIDGE Summit. Palo Alto, CA, USA
• Next-generation sequencing technologies and the promise for rare diseases. 
  Multiple locations, 2012
• Protein microarray for cancer diagnostics. 
  Monash Sunway University. Kuala Lumpur, Malaysia
• New Advances in Bioinformatics and Biotechnology in Genetic Medicine. 
  University Malaya. Kuala Lumpur, Malaysia
• Role of cancer genomics and next generation sequencing in the hematologic malignancies. 
  Hospital Ampang. Kuala Lumpur, Malaysia
• Clinical care in the age of cancer genomics. 
  Hospital Ampang. Kuala Lumpur, Malaysia
• A Bottom-up Democratization Approach to Rare Disease Research. 
  Gathering Conference. Dana Point, CA, USA
• Creating a crowdsourced and crowdfunded solution for long tail diseases. 
  Google IdeaBounce. Mountain View, CA, USA
• Rare Genomics Institute: A Social Entrepreneurship Journey. 
  Multiple locations, 2012
• Lessons from Cancer Genomics applied to Rare Genomics. 
  University of Maryland, College Park. College Park, MD, USA
• Exome sequencing of breast, colorectal, pancreatic, and brain cancers. 
  The Georgia Health Sciences University Cancer Center. Augusta, Georgia, USA
• Harnesses the power of the web to give patients suffering from rare diseases a new hope for a cure. 
  Skandalaris Entrepreneurship Center - Washington University in St. Louis
• Genomic studies for Cancer and Rare Diseases. 
  Head & Neck Research Group, Washington University in St. Louis. St. Louis, MO, USA
• Game-changing Paradigms for Rare Diseases. 
  TEDx Gateway Arch Salon. St. Louis, USA
• Enabling heroes for rare diseases – One Family at a Time. 
  TEDxMidWest Salon. Chicago, IL, USA
• Solving Rare Diseases – One Family at a Time. 
  Multiple locations, 2012
• Personalized (n=1) Research for Rare Diseases. 
  Genome, Environment, and Traits (GET) Conference, Harvard Medical School. Boston, MA, USA
• Rare Genomics Institute: Hope for Orphan Diseases. 
  Global Health & Innovation Conference, Yale University. New Haven, CT, USA
• Clinical Generation Sequencing for Cancer and Rare Diseases. 
  Cancer Research UK, University College London. London, England, UK
• Innovation in Healthcare Without Borders. 
  European Commission (European Union). Brussels, Belgium
• 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
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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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