2019 (2)
Neural networks versus Logistic regression for 30 days all-cause readmission prediction. Allam, A.; Nagy, M.; Thoma, G.; and Krauthammer, M. Scientific Reports, 9(1): 9277. 2019.
Neural networks versus Logistic regression for 30 days all-cause readmission prediction [link]Paper   doi   bibtex   abstract
A novel anti-melanoma SR C-family kinase inhibitor. Halaban, R; Bacchiocchi, A; Straub, R; Cao, J; Sznol, M; Narayan, D; Allam, A; Krauthammer, M; and Mansour, T S Oncotarget, 10(23): 2237–2251. mar 2019.
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  2018 (2)
Prototyping a precision oncology 3.0 rapid learning platform. Sweetnam, C.; Mocellin, S.; Krauthammer, M.; Knopf, N.; Baertsch, R.; and Shrager, J. BMC bioinformatics, 19(1): 341. sep 2018.
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Unraveling the etiology of primary malignant melanoma of the esophagus. Krauthammer, M. apr 2018.
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  2017 (4)
PySeqLab: an open source Python package for sequence labeling and segmentation. Allam, A.; and Krauthammer, M. Bioinformatics (Oxford, England), 33(21): 3497–3499. jul 2017.
PySeqLab: an open source Python package for sequence labeling and segmentation [link]Paper   doi   bibtex   abstract
Toward automated assessment of health Web page quality using the DISCERN instrument. Allam, A.; Schulz, P. J.; and Krauthammer, M. Journal of the American Medical Informatics Association, 24(3): 481–487. 2017.
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A Clinical Decision Support System for Monitoring Post-Colonoscopy Patient Follow-Up and Scheduling. Wadia, R.; Shifman, M.; Levin, F. L; Marenco, L.; Brandt, C. A; Cheung, K.; Taddei, T.; and Krauthammer, M. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, 2017: 295–301. 2017.
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Spitz nevi and Spitzoid melanomas: exome sequencing and comparison with conventional melanocytic nevi and melanomas. Lazova, R.; Pornputtapong, N.; Halaban, R.; Bosenberg, M.; Bai, Y.; Chai, H.; and Krauthammer, M. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 30(5): 640–649. may 2017.
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  2016 (8)
The state of melanoma: Challenges and opportunities. G., M.; M., H.; D.E., F.; B.C., B.; K.T., F.; M.A., D.; J.A., W.; C., C.; M.J., W.; S.A., L.; M.S., S.; M., M.; J.W., H.; S.M., S.; A.E., A.; M.B., A.; M.W., B.; R., D.; J.E., G.; A.C., H.; D., H.; G.C., K.; J.M., K.; M., K.; R.S., L.; G.V., L.; G., M.; A., R.; L., S.; J.A., S.; K.S., S.; P., S.; N.E., T.; H., T.; T., T.; A., W.; G., X.; R., L.; A., M.; S., S.; and T., T. Pigment Cell and Melanoma Research, 29(4): no pagination. 2016.
The state of melanoma: Challenges and opportunities [link]Paper   bibtex   abstract
Controlling testing volume for respiratory viruses using machine learning and text mining. Mai, M. V; and Krauthammer, M. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2016: 1910–1919. 2016.
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Interlesional diversity of T cell receptors in melanoma with immune checkpoints enriched in tissue-resident memory T cells. Boddupalli, C. S.; Bar, N.; Kadaveru, K.; Krauthammer, M.; Pornputtapong, N.; Mai, Z.; Ariyan, S.; Narayan, D.; Kluger, H.; Deng, Y.; Verma, R.; Das, R.; Bacchiocchi, A.; Halaban, R.; Sznol, M.; Dhodapkar, M. V; and Dhodapkar, K. M JCI insight, 1(21): e88955. dec 2016.
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Future perspectives in melanoma research : Meeting report from the "Melanoma Bridge". Napoli, December 1st-4th 2015. Ascierto, P. A; Agarwala, S.; Botti, G.; Cesano, A.; Ciliberto, G.; Davies, M. A; Demaria, S.; Dummer, R.; Eggermont, A. M; Ferrone, S.; Fu, Y. X.; Gajewski, T. F; Garbe, C.; Huber, V.; Khleif, S.; Krauthammer, M.; Lo, R. S; Masucci, G.; Palmieri, G.; Postow, M.; Puzanov, I.; Silk, A.; Spranger, S.; Stroncek, D. F; Tarhini, A.; Taube, J. M; Testori, A.; Wang, E.; Wargo, J. A; Yee, C.; Zarour, H.; Zitvogel, L.; Fox, B. A; Mozzillo, N.; Marincola, F. M; and Thurin, M. nov 2016.
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Germline MC1R status influences somatic mutation burden in melanoma. Robles-Espinoza, C. D.; Roberts, N. D; Chen, S.; Leacy, F. P; Alexandrov, L. B; Pornputtapong, N.; Halaban, R.; Krauthammer, M.; Cui, R.; Timothy Bishop, D; and Adams, D. J Nature communications, 7: 12064. jul 2016.
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RASopathy Gene Mutations in Melanoma. Halaban, R.; and Krauthammer, M. The Journal of investigative dermatology, 136(9): 1755–1759. sep 2016.
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Integrated analysis of multidimensional omics data on cutaneous melanoma prognosis. Jiang, Y.; Shi, X.; Zhao, Q.; Krauthammer, M.; Rothberg, B. E G.; and Ma, S. Genomics, 107(6): 223–230. jun 2016.
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Global copy number profiling of cancer genomes. Wang, X.; Chen, M.; Yu, X.; Pornputtapong, N.; Chen, H.; Zhang, N. R; Powers, R S.; and Krauthammer, M. Bioinformatics (Oxford, England), 32(6): 926–928. mar 2016.
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  2015 (4)
Mutadelic: mutation analysis using description logic inferencing capabilities. Holford, M. E; and Krauthammer, M. Bioinformatics (Oxford, England), 31(23): 3742–3747. dec 2015.
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Exome sequencing identifies recurrent mutations in NF1 and RASopathy genes in sun-exposed melanomas. Krauthammer, M.; Kong, Y.; Bacchiocchi, A.; Evans, P.; Pornputtapong, N.; Wu, C.; McCusker, J. P; Ma, S.; Cheng, E.; Straub, R.; Serin, M.; Bosenberg, M.; Ariyan, S.; Narayan, D.; Sznol, M.; Kluger, H. M; Mane, S.; Schlessinger, J.; Lifton, R. P; and Halaban, R. Nature genetics, 47(9): 996–1002. sep 2015.
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Modulation of Sox10, HIF-1alpha, Survivin, and YAP by Minocycline in the Treatment of Neurodevelopmental Handicaps following Hypoxic Insult. Li, Q.; Tsuneki, M.; Krauthammer, M.; Couture, R.; Schwartz, M.; and Madri, J. A The American journal of pathology, 185(9): 2364–2378. sep 2015.
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Genomic Classification of Cutaneous Melanoma. Cell, 161(7): 1681–1696. jun 2015.
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  2014 (4)
Computational analysis in cancer exome sequencing. Evans, P.; Kong, Y.; and Krauthammer, M. Methods in molecular biology (Clifton, N.J.), 1176: 219–227. 2014.
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Rare SF3B1 R625 mutations in cutaneous melanoma. Kong, Y.; Krauthammer, M.; and Halaban, R. Melanoma research, 24(4): 332–334. aug 2014.
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Mining images in biomedical publications: Detection and analysis of gel diagrams. Kuhn, T.; Nagy, M. L.; Luong, T.; and Krauthammer, M. Journal of biomedical semantics, 5(1): 10. feb 2014.
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Identification of PLX4032-resistance mechanisms and implications for novel RAF inhibitors. Choi, J.; Landrette, S. F; Wang, T.; Evans, P.; Bacchiocchi, A.; Bjornson, R.; Cheng, E.; Stiegler, A. L; Gathiaka, S.; Acevedo, O.; Boggon, T. J; Krauthammer, M.; Halaban, R.; and Xu, T. Pigment cell & melanoma research, 27(2): 253–262. mar 2014.
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  2013 (4)
Modeling the neurovascular niche: unbiased transcriptome analysis of the murine subventricular zone in response to hypoxic insult. Li, Q.; Canosa, S.; Flynn, K.; Michaud, M.; Krauthammer, M.; and Madri, J. A PloS one, 8(10): e76265. 2013.
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Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications. McCusker, J. P; Lebo, T.; Krauthammer, M.; and McGuinness, D. L Data integration in the life sciences : ... International Workshop, DILS ... : proceedings. DILS (Conference), 7970: 105–112. jul 2013.
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Adjusting for background mutation frequency biases improves the identification of cancer driver genes. Evans, P.; Avey, S.; Kong, Y.; and Krauthammer, M. IEEE transactions on nanobioscience, 12(3): 150–157. sep 2013.
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Complementary ensemble clustering of biomedical data. Fodeh, S. J.; Brandt, C.; Luong, T. B.; Haddad, A.; Schultz, M.; Murphy, T.; and Krauthammer, M. Journal of biomedical informatics, 46(3): 436–443. jun 2013.
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  2012 (5)
A semantic web framework to integrate cancer omics data with biological knowledge. Holford, M. E; McCusker, J. P; Cheung, K.; and Krauthammer, M. BMC Bioinformatics, 13(S1): S10. jan 2012.
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Finding and accessing diagrams in biomedical publications. Kuhn, T.; Luong, T.; and Krauthammer, M. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2012: 468–474. 2012.
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Type II p21-activated kinases (PAKs) are regulated by an autoinhibitory pseudosubstrate. Ha, B. H.; Davis, M. J; Chen, C.; Lou, H. J.; Gao, J.; Zhang, R.; Krauthammer, M.; Halaban, R.; Schlessinger, J.; Turk, B. E; and Boggon, T. J Proceedings of the National Academy of Sciences of the United States of America, 109(40): 16107–16112. oct 2012.
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Enhancing Clustering by Exploiting Complementary Data Modalities in the Medical Domain. Fodeh, S. J.; Haddad, A.; Brandt, C.; Schultz, M.; and Krauthammer, M. IFIP advances in information and communication technology, 381: 357–367. sep 2012.
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Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Krauthammer, M.; Kong, Y.; Ha, B. H.; Evans, P.; Bacchiocchi, A.; McCusker, J. P; Cheng, E.; Davis, M. J; Goh, G.; Choi, M.; Ariyan, S.; Narayan, D.; Dutton-Regester, K.; Capatana, A.; Holman, E. C; Bosenberg, M.; Sznol, M.; Kluger, H. M; Brash, D. E; Stern, D. F; Materin, M. A; Lo, R. S; Mane, S.; Ma, S.; Kidd, K. K; Hayward, N. K; Lifton, R. P; Schlessinger, J.; Boggon, T. J; and Halaban, R. Nature genetics, 44(9): 1006–1014. sep 2012.
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  2011 (6)
Exploring the use of social media to measure journal article impact. Evans, P.; and Krauthammer, M. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2011: 374–381. 2011.
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In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Karreth, F. A; Tay, Y.; Perna, D.; Ala, U.; Tan, S. M.; Rust, A. G; DeNicola, G.; Webster, K. A; Weiss, D.; Perez-Mancera, P. A; Krauthammer, M.; Halaban, R.; Provero, P.; Adams, D. J; Tuveson, D. A; and Pandolfi, P. P. Cell, 147(2): 382–395. oct 2011.
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Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence. Xie, P.; Kranzler, H. R; Krauthammer, M.; Cosgrove, K. P; Oslin, D.; Anton, R. F; Farrer, L. A; Picciotto, M. R; Krystal, J. H; Zhao, H.; and Gelernter, J. Biological psychiatry, 70(6): 528–536. sep 2011.
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MicroRNA signatures differentiate melanoma subtypes. 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, F. J; and Weidhaas, J. B. Cell cycle (Georgetown, Tex.), 10(11): 1845–1852. jun 2011.
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Phosphoproteomic screen identifies potential therapeutic targets in melanoma. Tworkoski, K.; Singhal, G.; Szpakowski, S.; Zito, C. I.; Bacchiocchi, A.; Muthusamy, V.; Bosenberg, M.; Krauthammer, M.; Halaban, R.; and Stern, D. F Molecular cancer research : MCR, 9(6): 801–812. jun 2011.
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MU2A–reconciling the genome and transcriptome to determine the effects of base substitutions. Garla, V.; Kong, Y.; Szpakowski, S.; and Krauthammer, M. Bioinformatics (Oxford, England), 27(3): 416–418. feb 2011.
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  2010 (3)
A new pivoting and iterative text detection algorithm for biomedical images. Xu, S.; and Krauthammer, M. Journal of Biomedical Informatics, 43(6): 924–931. dec 2010.
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PLX4032, a selective BRAF(V600E) kinase inhibitor, activates the ERK pathway and enhances cell migration and proliferation of BRAF melanoma cells. Halaban, R.; Zhang, W.; Bacchiocchi, A.; Cheng, E.; Parisi, F.; Ariyan, S.; Krauthammer, M.; McCusker, J. P; Kluger, Y.; and Sznol, M. Pigment cell & melanoma research, 23(2): 190–200. apr 2010.
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Genome-wide methylation and expression profiling identifies promoter characteristics affecting demethylation-induced gene up-regulation in melanoma. Rubinstein, J. C; Tran, N.; Ma, S.; Halaban, R.; and Krauthammer, M. BMC medical genomics, 3: 4. feb 2010.
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  2009 (9)
Genome-wide screen of promoter methylation identifies novel markers in melanoma. Koga, Y; M, P.; E, C.; M, K.; M, S.; S, A.; D, N.; AM, M.; R, H.; and SM., W. Genome Research, 19(8): ––. aug 2009.
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Melanoma prognostic model using tissue microarrays and genetic algorithms. Gould Rothberg, B. E; Berger, A. J; Molinaro, A. M; Subtil, A.; Krauthammer, M. O; Camp, R. L; Bradley, W. R; Ariyan, S.; Kluger, H. M; and Rimm, D. L Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 27(34): 5772–5780. dec 2009.
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Semantic web data warehousing for caGrid. McCusker, J. P; Phillips, J. A; Gonzalez Beltran, A.; Finkelstein, A.; and Krauthammer, M. BMC bioinformatics, 10 Suppl 10: S2. oct 2009.
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Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications. 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.; and Enghild, J. J PloS one, 4(2): e4563. 2009.
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Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects. Nath, A. K; Krauthammer, M.; Li, P.; Davidov, E.; Butler, L. C; Copel, J.; Katajamaa, M.; Oresic, M.; Buhimschi, I.; Buhimschi, C.; Snyder, M.; and Madri, J. A PloS one, 4(1): e4221. 2009.
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Using semantic web technologies to annotate and align microarray designs. Szpakowski, S.; McCusker, J.; and Krauthammer, M. Cancer informatics, 8: 65–73. 2009.
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Enriching PubMed related article search with sentence level co-citations. Tran, N.; Alves, P.; Ma, S.; and Krauthammer, M. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2009: 650–654. nov 2009.
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Embedding the guideline elements model in web ontology language. Tran, N.; Michel, G.; Krauthammer, M.; and Shiffman, R. N AMIA ... Annual Symposium proceedings. AMIA Symposium, 2009: 645–649. nov 2009.
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Structural similarity assessment for drug sensitivity prediction in cancer. Shivakumar, P.; and Krauthammer, M. BMC Bioinformatics, 10(S9): S17. sep 2009.
Structural similarity assessment for drug sensitivity prediction in cancer [link]Paper   doi   bibtex   abstract
  2008 (5)
Exploring the use of image text for biomedical literature retrieval. Xu, S.; McCusker, J.; and Krauthammer, M. AMIA ... Annual Symposium proceedings. AMIA Symposium,1186. nov 2008.
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Introducing meta-services for biomedical information extraction. Leitner, F.; Krallinger, M.; Rodriguez-Penagos, C.; Hakenberg, J.; Plake, C.; Kuo, C.; Hsu, C.; Tsai, R. T.; Hung, H.; Lau, W. W; Johnson, C. A; Saetre, R.; Yoshida, K.; Chen, Y. H.; Kim, S.; Shin, S.; Zhang, B.; Baumgartner, W. A J.; Hunter, L.; Haddow, B.; Matthews, M.; Wang, X.; Ruch, P.; Ehrler, F.; Ozgur, A.; Erkan, G.; Radev, D. R; Krauthammer, M.; Luong, T.; Hoffmann, R.; Sander, C.; and Valencia, A. Genome biology, 9 Suppl 2: S6. 2008.
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Overview of BioCreative II gene normalization. Morgan, A. A; Lu, Z.; Wang, X.; Cohen, A. M; Fluck, J.; Ruch, P.; Divoli, A.; Fundel, K.; Leaman, R.; Hakenberg, J.; Sun, C.; Liu, H.; Torres, R.; Krauthammer, M.; Lau, W. W; Liu, H.; Hsu, C.; Schuemie, M.; Cohen, K B.; and Hirschman, L. Genome biology, 9 Suppl 2: S3. 2008.
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MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Pelizzola, M.; Koga, Y.; Urban, A. E.; Krauthammer, M.; Weissman, S.; Halaban, R.; and Molinaro, A. M Genome research, 18(10): 1652–1659. oct 2008.
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Yale Image Finder (YIF): a new search engine for retrieving biomedical images. Xu, S.; McCusker, J.; and Krauthammer, M. Bioinformatics (Oxford, England), 24(17): 1968–1970. sep 2008.
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  2007 (4)
Mapping terms to UMLS concepts of the same semantic type. Tran, N.; Luong, T.; and Krauthammer, M. AMIA ... Annual Symposium proceedings. AMIA Symposium,1136. oct 2007.
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Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. Smith, A.; Cheung, K.; Krauthammer, M.; Schultz, M.; and Gerstein, M. Bioinformatics (Oxford, England), 23(22): 3073–3079. nov 2007.
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The BiolAD-DB system : an informatics system for clinical and genetic data. Nielsen, D. A; Leidner, M.; Haynes, C.; Krauthammer, M.; and Kreek, M. J. Molecular diagnosis & therapy, 11(1): 15–19. 2007.
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Genomewide linkage scan for nicotine dependence: identification of a chromosome 5 risk locus. Gelernter, J.; Panhuysen, C.; Weiss, R.; Brady, K.; Poling, J.; Krauthammer, M.; Farrer, L.; and Kranzler, H. R Biological psychiatry, 61(1): 119–126. jan 2007.
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  2006 (1)
Shallow semantic parsing of randomized controlled trial reports. Paek, H.; Kogan, Y.; Thomas, P.; Codish, S.; and Krauthammer, M. AMIA ... Annual Symposium proceedings. AMIA Symposium,604–608. 2006.
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  2005 (1)
Towards semantic role labeling & IE in the medical literature. Kogan, Y.; Collier, N.; Pakhomov, S.; and Krauthammer, M. AMIA ... Annual Symposium proceedings. AMIA Symposium,410–414. 2005.
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  2004 (4)
Term identification in the biomedical literature. Krauthammer, M.; and Nenadic, G. Journal of biomedical informatics, 37(6): 512–526. dec 2004.
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Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. Krauthammer, M.; Kaufmann, C. A; Gilliam, T C.; and Rzhetsky, A. Proceedings of the National Academy of Sciences of the United States of America, 101(42): 15148–15153. oct 2004.
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GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. Rzhetsky, A.; Iossifov, I.; Koike, T.; Krauthammer, M.; Kra, P.; Morris, M.; Yu, H.; Duboue, P. A.; Weng, W.; Wilbur, W J.; Hatzivassiloglou, V.; and Friedman, C. Journal of biomedical informatics, 37(1): 43–53. feb 2004.
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Probabilistic inference of molecular networks from noisy data sources. Iossifov, I.; Krauthammer, M.; Friedman, C.; Hatzivassiloglou, V.; Bader, J. S; White, K. P; and Rzhetsky, A. Bioinformatics (Oxford, England), 20(8): 1205–1213. may 2004.
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  2003 (1)
A native XML database design for clinical document research. Johnson, S B; Campbell, D A; Krauthammer, M; Tulipano, P K; Medonca, E A; Friedman, C; and Hripcsak, G AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium,883. 2003.
A native XML database design for clinical document research. [link]Paper   bibtex   abstract
  2002 (2)
Of truth and pathways: Chasing bits of information through myriads of articles. Krauthammer, M.; Kra, P.; Iossifov, I.; Gomez, S. M.; Hripcsak, G.; Hatzivassiloglou, V.; Friedman, C.; and Rzhetsky, A. Bioinformatics, 18(SUPPL. 1): S249––257. 2002.
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Representing nested semantic information in a linear string of text using XML. Krauthammer, M.; Johnson, S. B; Hripcsak, G.; Campbell, D. A; and Friedman, C. Proceedings. AMIA Symposium,405–409. 2002.
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