Publications

Halaban R, Krauthammer M: RASopathy Gene Mutations in Melanoma. J Invest Dermatol. 2016 Sep; 2016 May 25. PMID: 27236105

Robles-Espinoza CD, Roberts ND, Chen S, Leacy FP, Alexandrov LB, Pornputtapong N, Halaban R, Krauthammer M, Cui R, Timothy Bishop D, Adams DJ: Germline MC1R status influences somatic mutation burden in melanoma. Nat Commun. 2016 Jul 12; 2016 Jul 12. PMID: 27403562

Merlino G, Herlyn M, Fisher DE, Bastian BC, Flaherty KT, Davies MA, Wargo JA, Curiel-Lewandrowski C, Weber MJ, Leachman SA, Soengas MS, McMahon M, Harbour JW, Swetter SM, Aplin AE, Atkins MB, Bosenberg MW, Dummer R, Gershenwald JE, Halpern AC, Herlyn D, Karakousis GC, Kirkwood JM, Krauthammer M, Lo RS, Long GV, McArthur G, Ribas A, Schuchter L, Sosman JA, Smalley KS, Steeg P, Thomas NE, Tsao H, Tueting T, Weeraratna A, Xu G, Lomax R, Martin A, Silverstein S, Turnham T, Ronai ZA: The state of melanoma: challenges and opportunities. Pigment Cell Melanoma Res. 2016 Jul; 2016 Apr 17. PMID: 27087480

Jiang Y, Shi X, Zhao Q, Krauthammer M, Rothberg BE, Ma S: Integrated analysis of multidimensional omics data on cutaneous melanoma prognosis. Genomics. 2016 Jun; 2016 Apr 30. PMID: 27141884

Wang X, Chen M, Yu X, Pornputtapong N, Chen H, Zhang NR, Powers RS, Krauthammer M: Global copy number profiling of cancer genomes. Bioinformatics. 2016 Mar 15; 2015 Nov 16. PMID: 26576652

Holford ME, Krauthammer M: Mutadelic: mutation analysis using description logic inferencing capabilities. Bioinformatics. 2015 Dec 1; 2015 Aug 12. PMID: 26272983

Li Q, Tsuneki M, Krauthammer M, Couture R, Schwartz M, Madri JA: Modulation of Sox10, HIF-1α, Survivin, and YAP by Minocycline in the Treatment of Neurodevelopmental Handicaps following Hypoxic Insult. Am J Pathol. 2015 Sep; 2015 Jul 22. PMID: 26209807

Krauthammer M, Kong Y, Bacchiocchi A, Evans P, Pornputtapong N, Wu C, McCusker JP, Ma S, Cheng E, Straub R, Serin M, Bosenberg M, Ariyan S, Narayan D, Sznol M, Kluger HM, Mane S, Schlessinger J, Lifton RP, Halaban R: Exome sequencing identifies recurrent mutations in NF1 and RASopathy genes in sun-exposed melanomas. Nat Genet. 2015 Sep; 2015 Jul 27. PMID: 26214590

Mimouni M, Krauthammer M, Gershoni A, Mimouni F, Nesher R: Positive Results Bias and Impact Factor in Ophthalmology. Curr Eye Res. 2015; 2014 Sep 8. PMID: 25198281

Kong Y, Krauthammer M, Halaban R: Rare SF3B1 R625 mutations in cutaneous melanoma. Melanoma Res. 2014 Aug. PMID: 24709888

Choi J, Landrette SF, Wang T, Evans P, Bacchiocchi A, Bjornson R, Cheng E, Stiegler AL, Gathiaka S, Acevedo O, Boggon TJ, Krauthammer M, Halaban R, Xu T: Identification of PLX4032-resistance mechanisms and implications for novel RAF inhibitors. Pigment Cell Melanoma Res. 2014 Mar; 2014 Jan 6. PMID: 24283590

Kuhn T, Nagy ML, Luong T, Krauthammer M: Mining images in biomedical publications: Detection and analysis of gel diagrams. J Biomed Semantics. 2014 Feb 25; 2014 Feb 25. PMID: 24568573

Evans P, Kong Y, Krauthammer M: Computational analysis in cancer exome sequencing. Methods Mol Biol. 2014. PMID: 25030931

Evans P, Avey S, Kong Y, Krauthammer M: Adjusting for background mutation frequency biases improves the identification of cancer driver genes. IEEE Trans Nanobioscience. 2013 Sep; 2013 May 16. PMID: 23694700

Fodeh SJ, Brandt C, Luong TB, Haddad A, Schultz M, Murphy T, Krauthammer M: Complementary ensemble clustering of biomedical data. J Biomed Inform. 2013 Jun; 2013 Feb 27. PMID: 23454721

Li Q, Canosa S, Flynn K, Michaud M, Krauthammer M, Madri JA: Modeling the neurovascular niche: unbiased transcriptome analysis of the murine subventricular zone in response to hypoxic insult. PLoS One. 2013; 2013 Oct 11. PMID: 24146847

Ha BH, Davis MJ, Chen C, Lou HJ, Gao J, Zhang R, Krauthammer M, Halaban R, Schlessinger J, Turk BE, Boggon TJ: Type II p21-activated kinases (PAKs) are regulated by an autoinhibitory pseudosubstrate. Proc Natl Acad Sci U S A. 2012 Oct 2; 2012 Sep 17. PMID: 22988085

Krauthammer M, Kong Y, Ha BH, Evans P, Bacchiocchi A, McCusker JP, Cheng E, Davis MJ, Goh G, Choi M, Ariyan S, Narayan D, Dutton-Regester K, Capatana A, Holman EC, Bosenberg M, Sznol M, Kluger HM, Brash DE, Stern DF, Materin MA, Lo RS, Mane S, Ma S, Kidd KK, Hayward NK, Lifton RP, Schlessinger J, Boggon TJ, Halaban R: Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nat Genet. 2012 Sep; 2012 Jul 29. PMID: 22842228

Holford ME, McCusker JP, Cheung KH, Krauthammer M: A semantic web framework to integrate cancer omics data with biological knowledge. BMC Bioinformatics. 2012 Jan 25; 2012 Jan 25. PMID: 22373303

Kuhn T, Luong T, Krauthammer M: Finding and accessing diagrams in biomedical publications. AMIA Annu Symp Proc. 2012; 2012 Nov 3. PMID: 23304318

Karreth FA, Tay Y, Perna D, Ala U, Tan SM, Rust AG, DeNicola G, Webster KA, Weiss D, Perez-Mancera PA, Krauthammer M, Halaban R, Provero P, Adams DJ, Tuveson DA, Pandolfi PP: In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell. 2011 Oct 14. PMID: 22000016

Xie P, Kranzler HR, Krauthammer M, Cosgrove KP, Oslin D, Anton RF, Farrer LA, Picciotto MR, Krystal JH, Zhao H, Gelernter J: Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence. Biol Psychiatry. 2011 Sep 15; 2011 Jun 17. PMID: 21683344

Chan E, Patel R, Nallur S, Ratner E, Bacchiocchi A, Hoyt K, Szpakowski S, Godshalk S, Ariyan S, Sznol M, Halaban R, Krauthammer M, Tuck D, Slack FJ, Weidhaas JB: MicroRNA signatures differentiate melanoma subtypes. Cell Cycle. 2011 Jun 1; 2011 Jun 1. PMID: 21543894

Tworkoski K, Singhal G, Szpakowski S, Zito CI, Bacchiocchi A, Muthusamy V, Bosenberg M, Krauthammer M, Halaban R, Stern DF: Phosphoproteomic screen identifies potential therapeutic targets in melanoma. Mol Cancer Res. 2011 Jun; 2011 Apr 26. PMID: 21521745

Garla V, Kong Y, Szpakowski S, Krauthammer M: MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions. Bioinformatics. 2011 Feb 1; 2010 Dec 12. PMID: 21149339

Evans P, Krauthammer M: Exploring the use of social media to measure journal article impact. AMIA Annu Symp Proc. 2011; 2011 Oct 22. PMID: 22195090

Xu S, Krauthammer M: A new pivoting and iterative text detection algorithm for biomedical images. J Biomed Inform. 2010 Dec; 2010 Sep 29. PMID: 20887803

Tilleman H, Hakim V, Novikov O, Liser K, Nashelsky L, Di Salvio M, Krauthammer M, Scheffner O, Maor I, Mayseless O, Meir I, Kayam G, Sela-Donenfeld D, Simeone A, Brodski C: Bmp5/7 in concert with the mid-hindbrain organizer control development of noradrenergic locus coeruleus neurons. Mol Cell Neurosci. 2010 Sep; 2010 May 21. PMID: 20493948

Halaban R, Zhang W, Bacchiocchi A, Cheng E, Parisi F, Ariyan S, Krauthammer M, McCusker JP, Kluger Y, Sznol M: PLX4032, a selective BRAF(V600E) kinase inhibitor, activates the ERK pathway and enhances cell migration and proliferation of BRAF melanoma cells. Pigment Cell Melanoma Res. 2010 Apr; 2010 Feb 10. PMID: 20149136

Rubinstein JC, Tran N, Ma S, Halaban R, Krauthammer M: Genome-wide methylation and expression profiling identifies promoter characteristics affecting demethylation-induced gene up-regulation in melanoma. BMC Med Genomics. 2010 Feb 9; 2010 Feb 9. PMID: 20144234

Gould Rothberg BE, Berger AJ, Molinaro AM, Subtil A, Krauthammer MO, Camp RL, Bradley WR, Ariyan S, Kluger HM, Rimm DL: Melanoma prognostic model using tissue microarrays and genetic algorithms. J Clin Oncol. 2009 Dec 1; 2009 Nov 2. PMID: 19884546

Tran N, Alves P, Ma S, Krauthammer M: Enriching PubMed related article search with sentence level co-citations. AMIA Annu Symp Proc. 2009 Nov 14; 2009 Nov 14. PMID: 20351935

Tran N, Michel G, Krauthammer M, Shiffman RN: Embedding the guideline elements model in web ontology language. AMIA Annu Symp Proc. 2009 Nov 14; 2009 Nov 14. PMID: 20351934

McCusker JP, Phillips JA, González Beltrán A, Finkelstein A, Krauthammer M: Semantic web data warehousing for caGrid. BMC Bioinformatics. 2009 Oct 1; 2009 Oct 1. PMID: 19796399

Shivakumar P, Krauthammer M: Structural similarity assessment for drug sensitivity prediction in cancer. BMC Bioinformatics. 2009 Sep 17; 2009 Sep 17. PMID: 19761571

Koga Y, Pelizzola M, Cheng E, Krauthammer M, Sznol M, Ariyan S, Narayan D, Molinaro AM, Halaban R, Weissman SM: Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Res. 2009 Aug; 2009 Jun 2. PMID: 19491193

Szpakowski S, McCusker J, Krauthammer M: Using semantic web technologies to annotate and align microarray designs. Cancer Inform. 2009; 2009 May 13. PMID: 24904201

Halaban R, Krauthammer M, Pelizzola M, Cheng E, Kovacs D, Sznol M, Ariyan S, Narayan D, Bacchiocchi A, Molinaro A, Kluger Y, Deng M, Tran N, Zhang W, Picardo M, Enghild JJ: Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications. PLoS One. 2009; 2009 Feb 23. PMID: 19234609

Nath AK, Krauthammer M, Li P, Davidov E, Butler LC, Copel J, Katajamaa M, Oresic M, Buhimschi I, Buhimschi C, Snyder M, Madri JA: Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects. PLoS One. 2009; 2009 Jan 19. PMID: 19156209

Xu S, McCusker J, Krauthammer M: Exploring the use of image text for biomedical literature retrieval. AMIA Annu Symp Proc. 2008 Nov 6; 2008 Nov 6. PMID: 18999241

Pelizzola M, Koga Y, Urban AE, Krauthammer M, Weissman S, Halaban R, Molinaro AM: MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Res. 2008 Oct; 2008 Sep 2. PMID: 18765822

Xu S, McCusker J, Krauthammer M: Yale Image Finder (YIF): a new search engine for retrieving biomedical images. Bioinformatics. 2008 Sep 1; 2008 Jul 9. PMID: 18614584

Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA Jr, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A: Introducing meta-services for biomedical information extraction. Genome Biol. 2008; 2008 Sep 1. PMID: 18834497

Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L: Overview of BioCreative II gene normalization. Genome Biol. 2008; 2008 Sep 1. PMID: 18834494

Smith A, Cheung K, Krauthammer M, Schultz M, Gerstein M: Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. Bioinformatics. 2007 Nov 15; 2007 Oct 7. PMID: 17923450

Tran N, Luong T, Krauthammer M: Mapping terms to UMLS concepts of the same semantic type. AMIA Annu Symp Proc. 2007 Oct 11; 2007 Oct 11. PMID: 18694233

Gelernter J, Panhuysen C, Weiss R, Brady K, Poling J, Krauthammer M, Farrer L, Kranzler HR: Genomewide linkage scan for nicotine dependence: identification of a chromosome 5 risk locus. Biol Psychiatry. 2007 Jan 1; 2006 Nov 1. PMID: 17081504

Nielsen DA, Leidner M, Haynes C, Krauthammer M, Kreek MJ: The BiolAD-DB system : an informatics system for clinical and genetic data. Mol Diagn Ther. 2007. PMID: 17286447

Paek H, Kogan Y, Thomas P, Codish S, Krauthammer M: Shallow semantic parsing of randomized controlled trial reports. AMIA Annu Symp Proc. 2006. PMID: 17238412

Kogan Y, Collier N, Pakhomov S, Krauthammer M: Towards semantic role labeling & IE in the medical literature. AMIA Annu Symp Proc. 2005. PMID: 16779072

Krauthammer M, Nenadic G: Term identification in the biomedical literature. J Biomed Inform. 2004 Dec. PMID: 15542023

Krauthammer M, Kaufmann CA, Gilliam TC, Rzhetsky A: Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. Proc Natl Acad Sci U S A. 2004 Oct 19; 2004 Oct 7. PMID: 15471992

Iossifov I, Krauthammer M, Friedman C, Hatzivassiloglou V, Bader JS, White KP, Rzhetsky A: Probabilistic inference of molecular networks from noisy data sources. Bioinformatics. 2004 May 22; 2004 Feb 10. PMID: 14871876

Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboué PA, Weng W, Wilbur WJ, Hatzivassiloglou V, Friedman C: GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform. 2004 Feb. PMID: 15016385

Johnson SB, Campbell DA, Krauthammer M, Tulipano PK, Medonca EA, Friedman C, Hripcsak G: A native XML database design for clinical document research. AMIA Annu Symp Proc. 2003. PMID: 14728388

Krauthammer M, Kra P, Iossifov I, Gomez SM, Hripcsak G, Hatzivassiloglou V, Friedman C, Rzhetsky A: Of truth and pathways: chasing bits of information through myriads of articles. Bioinformatics. 2002. PMID: 12169554

Krauthammer M, Johnson SB, Hripcsak G, Campbell DA, Friedman C: Representing nested semantic information in a linear string of text using XML. Proc AMIA Symp. 2002. PMID: 12463856

Friedman C, Kra P, Yu H, Krauthammer M, Rzhetsky A: GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics. 2001. PMID: 11472995

Krauthammer M, Hripcsak G: A knowledge model for the interpretation and visualization of NLP-parsed discharged summaries. Proc AMIA Symp. 2001. PMID: 11825207

Krauthammer M, Rzhetsky A, Morozov P, Friedman C: Using BLAST for identifying gene and protein names in journal articles. Gene. 2000 Dec 23. PMID: 11163982

Rzhetsky A, Koike T, Kalachikov S, Gomez SM, Krauthammer M, Kaplan SH, Kra P, Russo JJ, Friedman C: A knowledge model for analysis and simulation of regulatory networks. Bioinformatics. 2000 Dec. PMID: 11159331