Publications

Alexandru Garaiman, Farhad Nooralahzadeh, Carina Mihai, Nicolas Perez, Nikitas Gkikopoulos, Mike Oliver Becker, Oliver Distler, Michael Krauthammer, Britta Maurer (2022). Vision transformer assisting rheumatologists in screening for capillaroscopy changes in systemic sclerosis: an artificial intelligence model . British Society for Rheumatology.

Kim F. Marquart, Ahmed Allam, Sharan Janjuha, Anna Sintsova, Lukas Villiger, Nina Frey, Michael Krauthammer, Gerald Schwank (2021). Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens. Nature Communications.

Kyriakos Schwarz, Ahmed Allam, Nicolas Perez, Michael Krauthammer (2021). AttentionDDI: Siamese Attention-based Deep Learning method for drug-drug interaction predictions. BMC Bioinformatics.

Egle Ramelyte, Aizhan Tastanova, Zsolt Balázs, Patrick Turko, Ulrike Menzel, Emmanuella Guenova, Christian Beisel, Michael Krauthammer, Mitchell Paul Levesque, Reinhard Dummer (2021). Oncolytic Virotherapy Mediated Anti-Tumor Response: A Single-Cell Perspective. Cancer Cell.

Farhad Nooralahzadeh, Nicolas Perez, Thomas Frauenfelder, Koji Fujimoto, Michael Krauthammer (2021). Progressive Transformer-Based Generation of Radiology Reports. arXiv preprint.

Nikola Biller-Andorno, Andrea Ferrario, Susanne Joebges, Tanja Krones, Federico Massini, Phyllis Barth, Georgios Arampatzis, Michael Krauthammer (2020). AI support for ethical decision-making around resuscitation: proceed with care. medRXiv.

Böhlen, Michael H., Dolmatova, Oksana, Krauthammer, Michael, Mariyagnanaseelan, Alphonse, Stahl, Jonathan, Surbeck, Timo (2020). Iterations for Propensity Score Matching in MonetDB. Advances in Databases and Information Systems. ADBIS 2020. Lecture Notes in Computer Science.

Source Document DOI

Xuefeng Wang, Xiaoqing Yu, Michael Krauthammer, Willy Hugo, Chunzhe Duan, Peter A. Kanetsky, Jamie K. Teer, Zachary J. Thompson, Denise Kalos, Kenneth Y. Tsai, Keiran S.M. Smalley, Vernon K. Sondak, Y Ann Chen, Jose R. Conejo-Garcia (2020). The Association of MUC16 Mutation with Tumor Mutation Burden and Its Prognostic Implications in Cutaneous Melanoma. Cancer Epidemiol Biomarkers Prev.

Martina A Maibach, Ahmed Allam, Matthias P Hilty, Nicolas A Perez Gonzales, Philipp K Buehler, Pedro D Wendel Garcia, Silvio D Brugger, Christoph C Ganter, The CoViD-19 ICU-Research Group Zurich, The RISC-19-ICU Investigators, Michael Krauthammer, Reto A Schuepbach, Jan Bartussek (2020). Timing COVID-19 - Synchronization of longitudinal patient data to the underlying disease progression using CRP as a temporal marker. medRXiv preprint.

Laura Kinkead, Ahmed Allam, Michael Krauthammer (2020). AutoDiscern: Rating the Quality of Online Health Information with Hierarchical Encoder Attention-based Neural Networks. BMC Medical Informatics and Decision Making.

PDF Project DOI

Kevin Lopez, Samah J. Fodeh, Ahmed Allam, Cynthia A. Brandt, Michael Krauthammer (2020). Reducing Annotation Burden Through Multimodal Learning. Front. Big Data.

Ahmed Allam, Matthias Dittberner, Anna Sintsova, Dominique Brodbeck, Michael Krauthammer (2020). Patient Similarity Analysis with Longitudinal Health Data. arXiv preprint.

Vokinger, K. N., Stekhoven, D. J., Michael Krauthammer (2020). Lost in Anonymization — A Data Anonymization Reference Classification Merging Legal and Technical Considerations. The Journal of Law, Medicine & Ethics.

Isabel Alvarado-Cruz, Mariam Mahmoud, Mohammed Khan, Shilin Zhao, Sebastian Oeck, Rithy Meas, Kaylyn Clairmont, Victoria Quintana, Ying Zhu, Angelo Porciuncula, Hailey Wyatt, Shuangge Ma, Yu Shyr, Yong Kong, Patricia M. LoRusso, Daniel Laverty, Zachary D. Nagel, Kurt A. Schalper, Michael Krauthammer, Joann B. Sweasy (2020). Chromatin-Bound PARP1 Correlates with Upregulation of Inflammatory Genes in Response to Long-Term Treatment with Veliparib. bioRXiv preprint.

Isabel Alvarado-Cruz, Mariam Mahmoud, Mohammed Khan, Shilin Zhao, Sebastian Oeck, Rithy Meas, Kaylyn Clairmont, Victoria Quintana, Ying Zhu, Angelo Porciuncula, Hailey Wyatt, Shuangge Ma, Yu Shyr, Yong Kong, Patricia M. LoRusso, Daniel Laverty, Zachary D. Nagel, Kurt A. Schalper, Michael Krauthammer, Joann B. Sweasy (2020). Chromatin-Bound PARP1 Correlates with Upregulation of Inflammatory Genes in Response to Long-Term Treatment with Veliparib.. bioRxiv.

Arwen E. Frick-Cheng, Anna Sintsova, Sara N. Smith, Michael Krauthammer, Kathryn A. Eaton, Harry L. T. Mobley (2020). The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model. bioRXiv preprint.

Ahmed Allam, Michael Krauthammer, Mate Nagy, George Thoma (2019). Neural networks versus Logistic regression for 30 days all-cause readmission prediction. Scientific Reports.

PDF Project DOI

R Halaban, A Bacchiocchi, R Straub, J Cao, M Sznol, D Narayan, Ahmed Allam, M Krauthammer, T S Mansour (2019). A novel anti-melanoma SR C-family kinase inhibitor. Oncotarget.

Connor Sweetnam, Simone Mocellin, Michael Krauthammer, Nathaniel Knopf, Robert Baertsch, Jeff Shrager (2018). Prototyping a precision oncology 3.0 rapid learning platform. BMC bioinformatics.

Michael Krauthammer (2018). Unraveling the etiology of primary malignant melanoma of the esophagus. Journal of Thoracic Disease.

Ahmed Allam, Michael Krauthammer (2017). PySeqLab: an open source Python package for sequence labeling and segmentation. Bioinformatics (Oxford, England).

Rossitza Lazova, Natapol Pornputtapong, Ruth Halaban, Marcus Bosenberg, Yalai Bai, Hao Chai, Michael Krauthammer (2017). Spitz nevi and Spitzoid melanomas: exome sequencing and comparison with conventional melanocytic nevi and melanomas.. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc.

Ahmed Allam, Peter J. Schulz, Michael Krauthammer (2017). Toward automated assessment of health Web page quality using the DISCERN instrument. Journal of the American Medical Informatics Association.

Roxanne Wadia, Mark Shifman, Forrest L Levin, Luis Marenco, Cynthia A Brandt, Kei-Hoi Cheung, Tamar Taddei, Michael Krauthammer (2017). A Clinical Decision Support System for Monitoring Post-Colonoscopy Patient Follow-Up and Scheduling.. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Chandra Sekhar Boddupalli, Noffar Bar, Krishna Kadaveru, Michael Krauthammer, Natopol Pornputtapong, Zifeng Mai, Stephan Ariyan, Deepak Narayan, Harriet Kluger, Yanhong Deng, Rakesh Verma, Rituparna Das, Antonella Bacchiocchi, Ruth Halaban, Mario Sznol, Madhav V Dhodapkar, Kavita M Dhodapkar (2016). Interlesional diversity of T cell receptors in melanoma with immune checkpoints enriched in tissue-resident memory T cells.. JCI insight.

Ruth Halaban, Michael Krauthammer (2016). RASopathy Gene Mutations in Melanoma.. The Journal of investigative dermatology.

Carla Daniela Robles-Espinoza, Nicola D Roberts, Shuyang Chen, Finbarr P Leacy, Ludmil B Alexandrov, Natapol Pornputtapong, Ruth Halaban, Michael Krauthammer, Rutao Cui, D Timothy Bishop, David J Adams (2016). Germline MC1R status influences somatic mutation burden in melanoma.. Nature communications.

Yu Jiang, Xingjie Shi, Qing Zhao, Michael Krauthammer, Bonnie E Gould Rothberg, Shuangge Ma (2016). Integrated analysis of multidimensional omics data on cutaneous melanoma prognosis.. Genomics.

Xuefeng Wang, Mengjie Chen, Xiaoqing Yu, Natapol Pornputtapong, Hao Chen, Nancy R Zhang, R Scott Powers, Michael Krauthammer (2016). Global copy number profiling of cancer genomes.. Bioinformatics (Oxford, England).

Merlino G., Herlyn M., Fisher D.E., Bastian B.C., Flaherty K.T., Davies M.A., Wargo J.A., Curiel-Lewandrowski C., Weber M.J., Leachman S.A., Soengas M.S., Mcmahon M., Harbour J.W., Swetter S.M., Aplin A.E., Atkins M.B., Bosenberg M.W., Dummer R., Gershenwald J.E., Halpern A.C., Herlyn D., Karakousis G.C., Kirkwood J.M., Krauthammer M., Lo R.S., Long G.V., Mcarthur G., Ribas A., Schuchter L., Sosman J.A., Smalley K.S., Steeg P., Thomas N.E., Tsao H., Tueting T., Weeraratna A., Xu G., Lomax R., Martin A., Silverstein S., Turnham T. (2016). The state of melanoma: Challenges and opportunities. Pigment Cell and Melanoma Research.

Mark V Mai, Michael Krauthammer (2016). Controlling testing volume for respiratory viruses using machine learning and text mining.. AMIA … Annual Symposium proceedings. AMIA Symposium.

Matthew E Holford, Michael Krauthammer (2015). Mutadelic: mutation analysis using description logic inferencing capabilities.. Bioinformatics (Oxford, England).

Qi Li, Masayuki Tsuneki, Michael Krauthammer, Rachael Couture, Michael Schwartz, Joseph A Madri (2015). Modulation of Sox10, HIF-1alpha, Survivin, and YAP by Minocycline in the Treatment of Neurodevelopmental Handicaps following Hypoxic Insult.. The American journal of pathology.

Yong Kong, Michael Krauthammer, Ruth Halaban (2014). Rare SF3B1 R625 mutations in cutaneous melanoma.. Melanoma research.

Jaehyuk Choi, Sean F Landrette, Tiffany Wang, Perry Evans, Antonella Bacchiocchi, Robert Bjornson, Elaine Cheng, Amy L Stiegler, Symon Gathiaka, Orlando Acevedo, Titus J Boggon, Michael Krauthammer, Ruth Halaban, Tian Xu (2014). Identification of PLX4032-resistance mechanisms and implications for novel RAF inhibitors.. Pigment cell & melanoma research.

Tobias Kuhn, Mate Levente Nagy, Thaibinh Luong, Michael Krauthammer (2014). Mining images in biomedical publications: Detection and analysis of gel diagrams.. Journal of biomedical semantics.

Perry Evans, Yong Kong, Michael Krauthammer (2014). Computational analysis in cancer exome sequencing.. Methods in molecular biology (Clifton, N.J.).

Perry Evans, Stefan Avey, Yong Kong, Michael Krauthammer (2013). Adjusting for background mutation frequency biases improves the identification of cancer driver genes.. IEEE transactions on nanobioscience.

James P McCusker, Timothy Lebo, Michael Krauthammer, Deborah L McGuinness (2013). Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications.. Data integration in the life sciences : … International Workshop, DILS … : proceedings. DILS (Conference).

Samah Jamal Fodeh, Cynthia Brandt, Thai Binh Luong, Ali Haddad, Martin Schultz, Terrence Murphy, Michael Krauthammer (2013). Complementary ensemble clustering of biomedical data.. Journal of biomedical informatics.

Qi Li, Sandra Canosa, Kelly Flynn, Michael Michaud, Michael Krauthammer, Joseph A Madri (2013). Modeling the neurovascular niche: unbiased transcriptome analysis of the murine subventricular zone in response to hypoxic insult.. PloS one.

Byung Hak Ha, Matthew J Davis, Catherine Chen, Hua Jane Lou, Jia Gao, Rong Zhang, Michael Krauthammer, Ruth Halaban, Joseph Schlessinger, Benjamin E Turk, Titus J Boggon (2012). Type II p21-activated kinases (PAKs) are regulated by an autoinhibitory pseudosubstrate.. Proceedings of the National Academy of Sciences of the United States of America.

Samah Jamal Fodeh, Ali Haddad, Cynthia Brandt, Martin Schultz, Michael Krauthammer (2012). Enhancing Clustering by Exploiting Complementary Data Modalities in the Medical Domain.. IFIP advances in information and communication technology.

Tobias Kuhn, ThaiBinh Luong, Michael Krauthammer (2012). Finding and accessing diagrams in biomedical publications.. AMIA … Annual Symposium proceedings. AMIA Symposium.

Matthew E Holford, James P McCusker, Kei-Hoi Cheung, Michael Krauthammer (2012). A semantic web framework to integrate cancer omics data with biological knowledge. BMC Bioinformatics.

Florian A Karreth, Yvonne Tay, Daniele Perna, Ugo Ala, Shen Mynn Tan, Alistair G Rust, Gina DeNicola, Kaitlyn A Webster, Dror Weiss, Pedro A Perez-Mancera, Michael Krauthammer, Ruth Halaban, Paolo Provero, David J Adams, David A Tuveson, Pier Paolo Pandolfi (2011). In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma.. Cell.

Pingxing Xie, Henry R Kranzler, Michael Krauthammer, Kelly P Cosgrove, David Oslin, Raymond F Anton, Lindsay A Farrer, Marina R Picciotto, John H Krystal, Hongyu Zhao, Joel Gelernter (2011). Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence.. Biological psychiatry.

Kathryn Tworkoski, Garima Singhal, Sebastian Szpakowski, Christina Ivins Zito, Antonella Bacchiocchi, Viswanathan Muthusamy, Marcus Bosenberg, Michael Krauthammer, Ruth Halaban, David F Stern (2011). Phosphoproteomic screen identifies potential therapeutic targets in melanoma.. Molecular cancer research : MCR.

Elcie Chan, Rajeshvari Patel, Sunitha Nallur, Elena Ratner, Antonella Bacchiocchi, Kathleen Hoyt, Sebastian Szpakowski, Sirie Godshalk, Stephan Ariyan, Mario Sznol, Ruth Halaban, Michael Krauthammer, David Tuck, Frank J Slack, Joanne Barnes Weidhaas (2011). MicroRNA signatures differentiate melanoma subtypes.. Cell cycle (Georgetown, Tex.).

Vijay Garla, Yong Kong, Sebastian Szpakowski, Michael Krauthammer (2011). MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions.. Bioinformatics (Oxford, England).

Perry Evans, Michael Krauthammer (2011). Exploring the use of social media to measure journal article impact.. AMIA … Annual Symposium proceedings. AMIA Symposium.

Songhua Xu, Michael Krauthammer (2010). A new pivoting and iterative text detection algorithm for biomedical images. Journal of Biomedical Informatics.

Ruth Halaban, Wengeng Zhang, Antonella Bacchiocchi, Elaine Cheng, Fabio Parisi, Stephan Ariyan, Michael Krauthammer, James P McCusker, Yuval Kluger, Mario Sznol (2010). PLX4032, a selective BRAF(V600E) kinase inhibitor, activates the ERK pathway and enhances cell migration and proliferation of BRAF melanoma cells.. Pigment cell & melanoma research.

Jill C Rubinstein, Nam Tran, Shuangge Ma, Ruth Halaban, Michael Krauthammer (2010). Genome-wide methylation and expression profiling identifies promoter characteristics affecting demethylation-induced gene up-regulation in melanoma.. BMC medical genomics.

Bonnie E Gould Rothberg, Aaron J Berger, Annette M Molinaro, Antonio Subtil, Michael O Krauthammer, Robert L Camp, William R Bradley, Stephan Ariyan, Harriet M Kluger, David L Rimm (2009). Melanoma prognostic model using tissue microarrays and genetic algorithms.. Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Nam Tran, Pedro Alves, Shuangge Ma, Michael Krauthammer (2009). Enriching PubMed related article search with sentence level co-citations.. AMIA … Annual Symposium proceedings. AMIA Symposium.

Nam Tran, George Michel, Michael Krauthammer, Richard N Shiffman (2009). Embedding the guideline elements model in web ontology language.. AMIA … Annual Symposium proceedings. AMIA Symposium.

James P McCusker, Joshua A Phillips, Alejandra Gonzalez Beltran, Anthony Finkelstein, Michael Krauthammer (2009). Semantic web data warehousing for caGrid.. BMC bioinformatics.

Pavithra Shivakumar, Michael Krauthammer (2009). Structural similarity assessment for drug sensitivity prediction in cancer. BMC Bioinformatics.

Y Koga, Pelizzola M, Cheng E, Krauthammer M, Sznol M, Ariyan S, Narayan D, Molinaro AM, Halaban R, Weissman SM. (2009). Genome-wide screen of promoter methylation identifies novel markers in melanoma.. Genome Research.

Sebastian Szpakowski, James McCusker, Michael Krauthammer (2009). Using semantic web technologies to annotate and align microarray designs.. Cancer informatics.

Anjali K Nath, Michael Krauthammer, Puyao Li, Eugene Davidov, Lucas C Butler, Joshua Copel, Mikko Katajamaa, Matej Oresic, Irina Buhimschi, Catalin Buhimschi, Michael Snyder, Joseph A Madri (2009). Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects.. PloS one.

Ruth Halaban, Michael Krauthammer, Mattia Pelizzola, Elaine Cheng, Daniela Kovacs, Mario Sznol, Stephan Ariyan, Deepak Narayan, Antonella Bacchiocchi, Annette Molinaro, Yuval Kluger, Min Deng, Nam Tran, Wengeng Zhang, Mauro Picardo, Jan J Enghild (2009). Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications.. PloS one.

Songhua Xu, James McCusker, Michael Krauthammer (2008). Exploring the use of image text for biomedical literature retrieval.. AMIA … Annual Symposium proceedings. AMIA Symposium.

Mattia Pelizzola, Yasuo Koga, Alexander Eckehart Urban, Michael Krauthammer, Sherman Weissman, Ruth Halaban, Annette M Molinaro (2008). MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment.. Genome research.

Songhua Xu, James McCusker, Michael Krauthammer (2008). Yale Image Finder (YIF): a new search engine for retrieving biomedical images.. Bioinformatics (Oxford, England).

Andrew Smith, Kei Cheung, Michael Krauthammer, Martin Schultz, Mark Gerstein (2007). Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.. Bioinformatics (Oxford, England).

Nam Tran, ThaiBinh Luong, Michael Krauthammer (2007). Mapping terms to UMLS concepts of the same semantic type.. AMIA … Annual Symposium proceedings. AMIA Symposium.

David A Nielsen, Marty Leidner, Chad Haynes, Michael Krauthammer, Mary Jeanne Kreek (2007). The BiolAD-DB system : an informatics system for clinical and genetic data.. Molecular diagnosis & therapy.

Joel Gelernter, Carolien Panhuysen, Roger Weiss, Kathleen Brady, James Poling, Michael Krauthammer, Lindsay Farrer, Henry R Kranzler (2007). Genomewide linkage scan for nicotine dependence: identification of a chromosome 5 risk locus.. Biological psychiatry.

Hyung Paek, Yacov Kogan, Prem Thomas, Seymour Codish, Michael Krauthammer (2006). Shallow semantic parsing of randomized controlled trial reports.. AMIA … Annual Symposium proceedings. AMIA Symposium.

Yacov Kogan, Nigel Collier, Serguei Pakhomov, Michael Krauthammer (2005). Towards semantic role labeling & IE in the medical literature.. AMIA … Annual Symposium proceedings. AMIA Symposium.

Michael Krauthammer, Goran Nenadic (2004). Term identification in the biomedical literature.. Journal of biomedical informatics.

Michael Krauthammer, Charles A Kaufmann, T Conrad Gilliam, Andrey Rzhetsky (2004). Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease.. Proceedings of the National Academy of Sciences of the United States of America.

Ivan Iossifov, Michael Krauthammer, Carol Friedman, Vasileios Hatzivassiloglou, Joel S Bader, Kevin P White, Andrey Rzhetsky (2004). Probabilistic inference of molecular networks from noisy data sources.. Bioinformatics (Oxford, England).

Andrey Rzhetsky, Ivan Iossifov, Tomohiro Koike, Michael Krauthammer, Pauline Kra, Mitzi Morris, Hong Yu, Pablo Ariel Duboue, Wubin Weng, W John Wilbur, Vasileios Hatzivassiloglou, Carol Friedman (2004). GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.. Journal of biomedical informatics.

S B Johnson, D A Campbell, M Krauthammer, P K Tulipano, E A Medonca, C Friedman, G Hripcsak (2003). A native XML database design for clinical document research.. AMIA … Annual Symposium proceedings / AMIA Symposium. AMIA Symposium.

Michael Krauthammer, Stephen B Johnson, George Hripcsak, David A Campbell, Carol Friedman (2002). Representing nested semantic information in a linear string of text using XML.. Proceedings. AMIA Symposium.

Michael Krauthammer, Pauline Kra, Ivan Iossifov, Shawn M. Gomez, George Hripcsak, Vasileios Hatzivassiloglou, Carol Friedman, Andrey Rzhetsky (2002). Of truth and pathways: Chasing bits of information through myriads of articles. Bioinformatics.