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Machine Learning for Healthcare and Life Sciences

Publication

  • Ranit Aharonov, Tal El-Hay, Michal Ozery-Flato, Naama Parush-Shear-Yashuv, Yaara Goldschmidt, Simon Borghs, Jane Chan, Nassim Haddad, Bosny Pierre-Louis, Linda Kalilani "A Data Driven Methodology for Characterizing Subpopulations by Response". In preparation for the journal of biomedical informatics.
  • Devinsky O, Dilley C, Ozery-Flato M, Aharonov R, Goldschmidt Y, Rosen-Zvi M, Clark C, Fritz P, "Changing the approach to treatment choice in epilepsy using big data". Accepted to Epilepsy and Behavior, Dec 2015
  • Chen Yanover, "Modeling the dynamics of the vaginal microbiome", abstract in EMBL conference: The Human Microbiome, 2015
  • The WE CARE consortium. Inger Ekman, Reinhard Busse, Ewout van Ginneken, Chris Van Hoof,, Linde van Ittersum,Ab Klink, Jan A. Kremer, Marisa Miraldo, Anders Olauson, Walter De Raedt, Michal Rosen-Zvi, Valentina Strammiello, Jan Törnell, Karl Swedberg, "Healthcare innovations and improvements in a financially constrained environment." accepted to Lancet. Dec 2015
  • Esther Goldbraich, Zeev Waks, Ariel Farkash, Marco Monti, Michele Torresani, Rossella Bertulli, Paolo Giovanni Casali, Boaz Carmeli: Understanding Deviations from Clinical Practice Guidelines in Adult Soft Tissue Sarcoma. MedInfo 2015
  • Michal Ozery-Flato, Liat Ein-Dor, Hani Neuvirth, Naama Parush, Martin S. Kohn, Jianying Hu, and Ranit Aharonov, A system for identifying and investigating unexpected response to treatment, AMIA Jt Summits Transl Sci Proc. 2015; 2015: 137–141.
  • Falconer E, El-Hay T, Alevras D, Docherty J, Yanover C, Kalton A, Goldschmidt, Rosen-Zvi, Integrated multisystem analysis in a mental health and criminal justice ecosystem. AMIA Annu Symp Proc. 2014 Nov 14;2014:526-33. eCollection 2014.
  • Tal El-Hay, Omer Weissbrod, Elad Eban, Maurizio, Francesca Incardona (2014), Structured Proportional Jump Processes. UAI2014
  • Keira A. Cohen, Tal El-Hay, Kelly L. Wyres, Omer Weissbrod, Tom Conway, Vanisha Munsamy, Max R. O'Donnell, Nesri Padayatchi, Dale Nordenberg, Gail H. Cassell, William R. Bishai and Alexander S. Pym, "Paradoxical Hypersusceptibility To Beta-Lactams In Drug Resistant Clinical Isolates Of M. Tuberculosis: Elucidation Of Molecular Mechanisms By Whole Genome Sequencing", American Journal of Respiratory and Critical Care Medicine, Vol. 189, Meeting Abstracts, 2014
  • Chen Yanover, Natalia Vanetik, Michael Levitt, Rachel Kolodny, and Chen Keasar (2014), "Redundancy-weighting for better inference of protein structural features", Bioinformatics 15;30(16):2295-301.
  • Michal Rosen-Zvi, Lavi Shpigelman, Alan Kalton, Omer Weissbrod, Saheed Akindeinde, Soren Benefeldt, Andrew Bentley, Terry Everett, Joseph Jajinskiji, Emmanuel Kweyu, Chalapathy Neti, Joe Saab, Osamuyimen Stewart, Malcolm Ward, Guo Tong Xie, Estimating the Impact of Prevention Action: A simulation Model of Cervical Cancer Progression, Studies in health technology and informatics 205, 288-292
  • Ozery-Flato M, Parush N, El-Hay T, Visockienė Z, Ryliškytė L, Badarienė J, Solovjova S, Kovaitė M, Navickas R, Laucevičius A. Predictive models for type 2 diabetes onset in middle-aged subjects with the metabolic syndrome. Diabetol Metab Syndr. 2013 Jul 15;5(1):36.
  • Z. Waks, E. Goldbraich, A. Farkash, M. Torresani, R. Bertulli, N. Restifo, P. Locatelli, P. Casali, B. Carmeli, Analyzing the "CareGap": Assessing Gaps in Adherence to Clinical Guidelines in Adult Soft Tissue Sarcoma, European Federation for Medical Informatics 2013, Prague Czech Republic.
  • M. Zazzi, F. Incardona, M. Rosen-Zvi, M. Prosperi, T. Lengauer, A. Altmann, A. Sonnerborg, T. Lavee, E. Schülter, and R. Kaiser (2012). "Predicting Response to Antiretroviral Treatment by Machine Learning: The EuResist Project". Intervirology, 55 pp.123-127
  • N. Parush, T. El-Hay, M. Ozery-Flato, L. Ryliskyte, Z. Visockiene, and A. Laucevicius, "Information-Based Sequential Selection of Clinical Tests in Risk Assessment", European Medical Informatics Conference (MIE), 2012
  • E. Vitkin, H. Neuvirth-Telem, B. Carmeli, A. Shabo, and A. Farkash. "Bringing research to the point of care: Hypergenes project study". European Medical Informatics Conference (MIE) 2012.
  • N Slonim. B Carmeli, A Goldsteen, O keller, C Kent, and R Rinott,"Knowledge-Analytics Synergy in Clinical Decision Support", MIE conference 2012, Pisa Italy
  • R Rinott, M Torresani, R Bertulli, A Goldsteen, P Casali, B Carmeli, N Slonim"Automatic Detection of Inconsistencies between Free Text and Coded data in Sarcoma Discharge letters", MIE conference 2012, Pisa Italy
  • B. Carmeli, P. Casali, A. Goldbraich A. Goldsteen, C. Kent, L. Licitra, P. Locatelli, N. Restifo, R. Rinott, E. Sini, M. Torresani, Z. Waks,"Evicase: An Evidence-Based Case Structuring Approach for Personalized Healthcare",MIE conference 2012, Pisa Italy
  • M. Rosen-Zvi, M. Zazzi, F. Incardona, E. Aharoni, R. Kaiser, T. Lengauer, B. Clotet, A. M. Vandamme, J. C, Schmit A, Sonnerborg, (2011) "Declining differences in treatment outcome among different patient categories in Europe, 1992-2010", 9th European Workshop on HIV & Hepatitis - Treatment Strategies & Antiviral Drug Resistance March 2011, Cyprus.
  • H. Neuvirth, M. Ozery-Flato, J. Laserson, M. Rosen-Zvi, J. Hu, M. S. Kohn, S. Ebadollahi (2011). "Toward personalized care management of patients at risk - The diabetes case study", the 17th ACM SIGKDD international conference on Knowledge discovery and data mining
  • Johnson T, Gaunt TR, Newhouse SJ, Padmanabhan S, Tomaszewski M, Kumari M, Morris RW, Tzoulaki I, O'Brien ET, Poulter NR, Sever P, Shields DC, Thom S, Wannamethee SG, Whincup PH, Brown MJ, Connell JM, Dobson RJ, Howard PJ, Mein CA, Onipinla A, Shaw-Hawkins S, Zhang Y, Smith GD, Day IN, Lawlor DA, Goodall AH; The Cardiogenics Consortium, Fowkes FG, Abecasis GR, Elliott P, Gateva V; The Global BPgen Consortium, Braund PS, Burton PR, Nelson CP, Tobin MD, van der Harst P, Glorioso N, Neuvrith H, Salvi E, Staessen JA, Stucchi A, Devos N, Jeunemaitre X, Plouin PF, Tichet J, Juhanson P, Org E, Putku M, Sõber S, Veldre G, Viigimaa M, Levinsson A, Rosengren A, Thelle DS, Hastie CE, Hedner T, Lee WK, Melander O, Wahlstrand B, Hardy R, Wong A, Cooper JA, Palmen J, Chen L, Stewart AF, Wells GA, Westra HJ, Wolfs MG, Clarke R, Franzosi MG, Goel A, Hamsten A, Lathrop M, Peden JF, Seedorf U, Watkins H, Ouwehand WH, Sambrook J, Stephens J, Casas JP, Drenos F, Holmes MV, Kivimaki M, Shah S, Shah T, Talmud PJ, Whittaker J, Wallace C, Delles C, Laan M, Kuh D, Humphries SE, Nyberg F, Cusi D, Roberts R, Newton-Cheh C, Franke L, Stanton AV, Dominiczak AF, Farrall M, Hingorani AD, Samani NJ,Caulfield MJ, Munroe PB. Blood Pressure Loci Identified with a Gene-Centric Array. Am J Hum Genet. 2011 Dec 9;89(6):688-700. Epub 2011 Nov 17. PubMed PMID: 22100073. IF: 11.680. PubMed PMID: 22100073.
  • R. Shamir, M. Ozery-Flato, C. Linhart, L. Trachtenbrot and S. Izraeli (2011), "A systematic assessment of associations among chromosomal aberrations in cancer karyotypes", Genome Biology, 12(6):R61.
  • Bigus, J. P. Campbell, M. Carmeli, B. Cefkin, M. Chang, H. Chen-Ritzo, C.-H. Cody, W. F. Ebadollahi, S. Evfimievski, A. Farkash, A. Glissmann, S. Gotz, D. Grandison, T. W. A. Gruhl, D. Haas, P. J. Hsiao, M. J. H. Hsueh, P.-Y. S. Hu, J. Jasinski, J. M. Kaufman, J. H. Kieliszewski, C. A. Kohn, M. S. Knoop, S. E. Maglio, P. P. Mak, R. L. Nelken, H. Neti, C. Neuvirth, H. Pan, Y. Peres, Y. Ramakrishnan, S. Rosen-Zvi, M. Renly, S. Selinger, P. Shabo, A. Sorrentino, R. K. Sun, J. Syeda-Mahmood, T. Tan, W.-C. Tao, Y. Y. Y. Yaesoubi, R. Zhu, X. "Information technology for healthcare transformation",IEEE IBM Centennial issue, IBM Journal of Research and Development 2011
  • R Rinott, B Carmeli, C Kent, D Landau, Y Maman, Y Rubin, N Slonim, "Utilizing Assigned Treatments as Labels for Supervised Machine Learning in Clinical Decision Support", IHI 2011
  • R Rinott, B Carmeli, C Kent, D Landau, Y Maman, Y Rubin, N Slonim, "Prognostic Data-Driven Clinical Decision Support -- Formulation and Implications",MIE Conference 2011
  • E. Aharoni, H. Neuvirth-Telem and S. Rosset (2010). "The Quality Preserving Database: A Computational Framework for Encouraging Collaboration, Enhancing Power and Controlling False Discovery". IEEE/ACM Transactions on Computational Biology and Bioinformatics
  • M. Rosen-Zvi, C. Chemudugunta, T. Griffiths, P. Smyth, and M. Steyvers (2010) "Learning Author-Topic Models from Text Corpora", ACM Transactions on Information Systems, TOIS, 28(1)
  • M. Zazzi, R. Kaiser, A. Sonnerborg, D. Struck, A. Altmann, M. Prosperi, M. Rosen-Zvi, A. Petroczi, Y. Peres, E. Schulter, C. Boucher, F. Brun-Vezinet, R. Harigan, L. Morris, M. Obermeier, C. F. Perno, R. Shafer, A. Vandamme, K. van Laethem, A. Wensing, T. Lengauer, F. Incardona (2010). "Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)". HIV Medicine, 2010
  • M. Zazzi, R. Kaiser, A, Sonnerborg, D, Struck, A, Altmann, M, Prosperi, M, Rosen-Zvi, A, Petroczi, Y, Peres, , E. Schulter, F. Boucher, Brun-Vezinet, PR Harrigan, L. Morris, M. Obermeier, CF. Perno, P. Phanuphak, D. Pillay, RW. Shafer, AM. Vandamme, K. Van Laethem, A.M. Wensing, T. Lengauer, F. Incardona, (2010) "Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study)", 8th European HIV Drug Resistance Workshop, March, Italy.
  • E. Vitkin, B. Carmeli, O. Greenshpan, D. Baras, Y. Marmor, "MEDAL: Measuring of Emergency Departments Adaptive Load", MEDINFO 2010
  • Edward Vitkin, Boaz Carmeli, Ohad Greenshpan, Dorit Baras, Yariv Marmor "Neural Networks Application on Emergency Department Load Measurement" SMRLO 2010
  • M. CF Prosperi, A. Altmann, M. Rosen-Zvi, E. Aharoni, G. Borgulya, F. Bazso, A. Sonnerborg, Y. Peres, E. Schuflter, D. Struck, G. Ulivi, F. Incardona, A.-M. Vandamme, J. Vercauteren and M. Zazzi for the EuResist and Virolab study groups, (2009) "Investigation of Expert Rule Bases, Logistic Regression, and Non-Linear Machine Learning Techniques for Predicting Response to Antiretroviral Treatment" Antiviral Therapy, 14: 433-442
  • M. Prosperi, M. Rosen-Zvi, A. Altmann, E. Aharoni, Y. Peres, A. Sonnerborg, F. Incardona, D. Struck, R. Kaiser, M. Zazzi, (2009) "Therapy Optimisation without Genotype Resistance Testing: a Perspective on Treatment History Based Models" Proceedings of the 7th European HIV Drug Resistance Workshop.
  • M. Rosen-Zvi, E. Aharoni, and J. Selbig, (2009) "HIV-1 Drug Resistance Prediction and Therapy Optimization: A Case Study for the Application of Classification and Clustering Methods" M. Biehl et al.: (Eds.): Similarity-Based Clustering, LNAI 5400, pp. 185-201, Springer-Verlag Berlin Heidelberg.
  • A. Altmann, M. Rosen-Zvi, M. Prosperi, E. Aharoni, H. Neuvirth, E. Schulter, J. Buch, D. Struck, Y. Peres, F. Incardona, A. Sonnerborg, R. Kaiser, M. Zazzi, T. Lengauer(2008) "Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy", PLoS ONE 3(10)
  • M. Rosen-Zvi, A. Altmann, M. Prosperi, E. Aharoni, H. Neuvirth, A. Sonnerborg, E. Shulter, D. Struck, Y. Peres, F. Incardona, R. Kaiser, M. Zazzi, T. Lengauer (2008), "Selecting anti-HIV therapies based on a variety of genomic and clinical factors", Accepted for an oral presentation at the ISMB conference/ bioinformatics journal Toronto 2008.
  • A. Altmann, M. Rosen-Zvi, M. Prosperi, E. Aharoni, H. Neuvirth, E. Shulter, J. Buch, Y. Peres, F. Incardona, A. Sonnerborg, R. Kaiser, M. Zazzi, T. Lengauer (2008), "The EuResist approach for predicting response to anti HIV-1 therapy" Accepted for an oral presentation at the 6th European HIV Drug Resistance Workshop, Cascais, Portugal 2008.
  • M. Rosen-Zvi, E. Aharoni, A. Altmann, R. Kaiser, T. Lengauer, H. Neuvirth, M. Prosperi, F. Bazso, F. Incardona, M. Zazzi (2007) EuResist: European data - European interpretation systems, European Journal of Medical Research
  • E. Aharoni, A. Altman, G. Borgulya, R. D'Autilia, F. Incardona, R. Kaiser, C. Kent, T. Lengauer, H. Neuvirth, Y. Peres, A. Petroczi, M. Prosperi, M. Rosenzvi, E. Schulter, T. Sing, A Sonnenborg, R Thompson, M Zazzi, (2007) Integration of viral genomics with clinical data to predict response to anti-HIV treatment. IST-Africa 2007 Conference & Exhibition, May 9-11, 2007, Maputo, Mozambique.
  • Pierre Baldi and Michal Rosen-Zvi. On the relationship between deterministic and probabilistic directed Graphical models: From Bayesian networks to recursive neural networks. Neural Netw. 18, 8 (October 2005), 1080-1086.