I am an MD/PhD student working on applications of machine learning techniques to basic problems in genetics and biochemistry. My thesis was supervised by Raul Rabadan and focused on computational approaches to the genomics of clonal evolution. As part of this work I co-developed pipelines for detecting oncogenic gene fusions and oncoviruses from RNA sequencing of human cancers. I also developed a novel computational framework for the visualization and statistical analysis of tumor and viral evolution. The approach built on recent mathematical progress in modeling phylogenetic tree spaces. I continue to be interested in basic cancer and viral genetics, as well as emerging approaches for directing the evolution of synthetic genomes.
Before beginning the MD/PhD program I received my BA in physics and MS in biomedical engineering from Columbia. During that period of five years I worked with Szabolcs Marka's experimental astrophysics lab, searching for gravitational waves in the LIGO data stream; Eric Kandel's neurobiology lab, studying the non-proteolytic role of ubiquitination in long-term memory and synaptic plasticity; and Paul Sajda's laboratory for intelligent imaging and neural computing, augmenting human performance in visual classification tasks via EEG-based brain-computer interfacing.
** member of the HPN-DREAM Consortium
* indicates equal author contributions
Zairis S, Margalit DN, Royce TJ, Powlis WD, Tishler RB, Schoenfeld JD. Prospective analysis of radiation oncology image and plan-driven peer review for head and neck cancer. Head & Neck. 2017 Aug;39(8):1603-1608.
Pappas K, Xu J, Zairis S, Resnick-Silverman L, Abate F, Steinbach N, Ozturk S, Saal LH, Su T, Cheung P, Schmidt H, Aaronson SA, Hibshoosh H, Manfredi JJ, Rabadan R, Parsons R. p53 maintains baseline expression of multiple tumor suppressor genes. Mol Cancer Res. 2017 May 8. pii: molcanres.0089.2017.
Abate F, da Silva-Almeida AC, Zairis S, Robles-Valero J, Couronne L, Khiabanian H, Quinn SA, Kim MY, Laginestra MA, Kim C, Fiore D, Bhagat G, Piris MA, Campo E, Lossos IS, Bernard OA, Inghirami G, Pileri S, Bustelo XR, Rabadan R, Ferrando AA, Palomero T. Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas. Proc Natl Acad Sci U S A. 2017 Jan 24;114(4):764-769.
Zairis S, Khiabanian H, Blumberg AJ, Rabadan R. Genomic data analysis in tree spaces. arXiv 2016 Jul 25;1607.07503.
Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362-73.
Wang J, Cazzato E, Ladewig E, Frattini V, Rosenbloom DI, Zairis S, Abate F, Liu Z, Elliott O, Shin YJ, Lee JK, Lee IH, Park WY, Eoli M, Blumberg AJ, Lasorella A, Nam DH, Finocchiaro G, Iavarone A, Rabadan R. Clonal evolution of glioblastoma under therapy. Nat Genet. 2016 Jul;48(7):768-76
Anzalone AV, Lin AJ, Zairis S, Rabadan R, Cornish VW. Reprogramming eukaryotic translation with ligand-responsive synthetic RNA switches. Nat Methods. 2016 May;13(5):453-458.
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium**, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Inferring causal molecular networks: empirical assessment through a community-based effort. Nat Methods. 2016 Apr;13(4):310-8.
Abate F, Ambrosio MR, Mundo L, Laginestra MA, Fuligni F, Rossi M, Zairis S, Gazaneo S, De Falco G, Lazzi S, Bellan C, Rocca BJ, Amato T, Marasco E, Etebari M, Ogwang M, Calbi V, Ndede I, Patel K, Chumba D, Piccaluga PP, Pileri S, Leoncini L, Rabadan R. Distinct viral and mutational spectrum of endemic Burkitt lymphoma. PLoS Pathog. 2015 Oct 15;11(10):e1005158.
Zairis S, Khiabanian H, Blumberg AJ, Rabadan R. Moduli spaces of phylogenetic trees describing tumor evolution. Lect Notes Comput Sc. 2014 8609:528-539.
Abate F*, Zairis S*, Ficarra E, Acquaviva A, Wiggins CH, Frattini V, Lasorella A, Iavarone A, Inghirami G, Rabadan R. Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. BMC Syst Biol. 2014 Sep 4;8:97.
Gansell AR, Van de Meent JW, Zairis S, Wiggins CH. Stylistic clusters and the Syrian/South Syrian tradition of first-millennium BCE Levantine ivory carvings: a machine learning approach. J Archaeol Sci. 2014 Apr;44:194-205.
Pavlopoulos E, Trifilieff P, Chevaleyre V, Fioriti L, Zairis S, Pagano A, Malleret G, Kandel ER. Neuralized1 activates CPEB3: a function of non-proteolytic ubiquitin in synaptic plasticity and memory storage. Cell. 2011 Dec 9;147(6):1369-83.
Nature Reviews Neuroscience "Highlight Research Article" 2012 February (Issue 13; page 73).
Lightman M, Thurkal J, Dwyer J, Grossman R, Kalmus P, Matone L, Rollins J, Zairis S, Marka S. Prospects of gravitational wave data mining and exploration via evolutionary computing. J Phys Conf Ser. 2006;32:58-65.