Alumni

 


Postdoctoral Researchers

Abha Bais, PhD | Research Associate
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Time in Benos’ Lab: 2008-2011
After Benos’ Lab: UC Berkeley, Postdoctoral fellow
Current Position: Univ of Pittsburgh, Staff Scientist
Publications (3): Bais, Kaminski, Benos, 2011     Zhang et al, 2011     Coronnello et al, 2012
Claudia Coronnello, PhD | Postodoctoral Ri.MED Scholar Fellow
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Time in Benos’ Lab: 2010-2012
After Benos’ Lab: IBIM-CNR (Palermo), Postdoctoral fellow
Current Position: Fondazione RiMED, Senior Scientist in Computational Biology
Publications (6): Coronnello et al, 2012     Coronnello, Benos, 2013     Jain et al, 2013     Osmanbeyoglou et al, 2013     Lu et al, 2013     Edinger et al, 2014
Tridib Dutta, PhD | Postdoctoral fellow
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Time in Benos’ Lab: 2010-2013
Current Position: Absolute Software, Senior Data Scientist
Hyokyeong Lee, PhD | Postdoctoral Fellow
Time in Benos’ Lab: 2014-2017
After Benos’ Lab: Baylor College of Medicine, research associate
Last known position: College of Wooster, Visiting Assistant Professor
Shaun Mahony, PhD | Research Associate
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Time in Benos’ Lab: 2005-2007
After Benos’ Lab: MIT, Research associate
Current Position: Penn State, Associate Professor
Publications (10): Mahony et al, 2005     Mahony et al, 2006     Belov et al, 2006     Mahony, Auron, Benos, 2007a     Mahony, Auron, Benos, 2007b    Mahony, Benos, 2007     Mahony et al, 2007      Mikkelsen et al, 2007     Lu et al, 2007     Zinman et al, 2011
Dimitris Manatakis, PhD | Research Associate
Time in Benos’ Lab: 2015-2018
After Benos’ Lab: Emulate, Inc., Biomedical data scientist
Current Position: Emulate, Inc., Associate Director of Biomedical Data Science
Publications (7): Kitsios et al, 2018     Raghu et al, 2018     Sedgewick et al, 2018     Manatakis*, Raghu*, Benos, 2018     McDonough et al, 2019     Kitsios et al, 2019    Kotok et al, 2020
Klea Panayidou, PhD | Research Associate
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Time in Benos’ Lab: 2015-2016
After Benos’ Lab: Carnegie Mellon University, Postdoctoral fellow
Current Position: European University of Cyprus, Assistant Professor of Biostatistics
Alain Tchagang, PhD | Research Associate
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Time in Benos’ Lab: 2007-2008
After Benos’ Lab: Natl Res Council Canada, Research Scientist
Current Position: Natl Res Council Canada, Research Scientist
Publications (3): Tchagang et al. 2008  Tchagang et al, 2009   Tchagang et al, 2011

 


Graduate Students

Rachel Brower-Sinning, PhD | PhD Student, CPCB
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Thesis title: “On the evolution of microbes: the evolution of genomes with respect to RNA folding” [PDF] Time in Benos’ Lab: 2007-2011
After Benos’ Lab: U Pitt, postdoctoral researcher
Last known position: CMU Software Engineering Institute, Machine Learning Scientist
Publications (2): Brower-Sinning et al, 2009     Zinman et al, 2011
Kristina Buschur, PhD | PhD Student, CPCB
Thesis title: “Unsupervised methods for pattern discovery in high-throughput genomic data” [PDF]

Time in Benos’ Lab: 2012-2019
After Benos’ Lab: Columbia University, T32 Postdoctoral fellow
Current Position: Columbia University, T32 Postdoctoral fellow
Publications (3 – and counting): Sedgewick et al, 2018    Morse et al, 2019   Buschur, Chikina, Benos 2019

David Corcoran, PhD | Grad Student, MSc (Biostatistics), PhD (Human Genetics)
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Thesis title: “Transcriptional Regulation Of MicroRNA Genes And The Regulatory Networks In Which They Participate” [PDF]

Time in Benos’ Lab: 2002-2008
After Benos’ Lab: Duke Univ, Research associate
Current Position: Duke Univ, Founding Director, Omics Data Analysis Core
Publications (8): Corcoran et al, 2005     Workman et al, 2005     Corcoran et al, 2005     Rogulski et al, 2005     Mahony et al, 2007     Benos, Corcoran, Finegold, 2007     Corcoran et al, 2009     Pandit, Corcoran, et al, 2010

Lucas Santana dos Santos, PhD | Grad Student, MSc and PhD (DBMI)
Thesis title: “Computational methods for the functional analysis of  DNA sequence variants” [PDF]

Time in Benos’ Lab: 2010-2017
After Benos’ Lab: UPMC Lab, Bioinformatics scientist
Current Position: Assistant Professor and Director of Bioinformatics, Northwestern University
Publications (4): Mao et al, 2013     Chandran et al, 2015     Bahreini et al, 2016     Kulkami et al, 2017

Grace T. Huang, PhD | PhD Student, CPCB
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Thesis title: “An Integrated, Module-based Biomarker Discovery Framework” [PDF]

Time in Benos’ Lab: 2008-2013
After Benos’ Lab: PopSugar, Data scientist
Current Position: Netflix, Manager of Research/Machine Learning Engineering
Publications (5): Huang, Athanassiou, Benos, 2011     Zinman et al, 2011     Huang et al, 2013     Huang et al, 2015     Pociask et al, 2017

Sabah Kadri, PhD | PhD Student, CPCB
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Thesis title: “microRNA regulation in development” [PDF]

Time in Benos’ Lab: 2008-2012
After Benos’ Lab: Broad Institute, Associate computational biologist
Current Position: AbbVie, Director of Computational Genomics
Publications (2): Kadri, Hinman, Benos, 2009     Kadri, Hinman, Benos, 2011
Personal web page: Sabah Kadri, PhD

Vineet Raghu, PhD | PhD student, Pitt CS
Thesis title: “A Computational Pipeline for Graphical Modeling of Integrated Biomedical Data” [PDF]

Time in Benos’ Lab: 2015-2019
After Benos’ Lab: Harvard University / MGH, T32 Postdoctoral fellow
Current Position: Harvard University / MGH, Instructor of Radiology
Publications (11 – and counting): Huang et al, 2015     Raghu et al, 2018     Raghu et al, 2018b     Raghu et al. 2018c     Manatakis*, Raghu*, Benos, 2018   Sedgewick et al, 2019   Raghu et al, 2019   Xe et al, 2020   Raghu et al, 2020   Fuccello et al. 2020  Raghu et al 2021

Andrew J. Sedgewick, PhD | PhD student, CPCB
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Thesis title: “Graphical models for de novo and pathway-based network prediction over multi- modal high-throughput biological data” [PDF]

Time in Benos’ Lab: 2012-2016
After Benos’ Lab: NantOmics LLC, Bioinformatics specialist
Current Position: Tempus Labs, Senior Computational Systems Biologist
Publications (4): Sedgewick et al, 2016     Sedgewick et al, 2018     Caparosa*, Sedgwick*, et al, 2018     Abecassis*, Sedgewick* et al. 2019

Shu (Eric) Wang | Tsinghua scholar
Time in Benos’ Lab: 2016-2018
Last known position: Tsinghua University, MD student
Haopu Yang | Tsinghua scholar
Time in Benos’ Lab: 2019-2021
Current position: Tsinghua University, MD student
Publications (4): Yang et al, 2020   Kitsios et al, 2020   Valenzi et al. 2021  Kitsios et al. 2021

 


Staff

Neha Abraham | Research Programmer
Time in Benos’ Lab: 2017-2018
Current Position: Innovative Supply Solutions, Software Engineer
Arshi Arora, MSc | Medical Scientist
ArshiArora100X142 Time in Benos’ Lab: 2010-2012
Current Position: Memorial Sloan-Kettering Cancer Center, Res Biostat II
Publications (2): Coronnello et al, 2012     Lu et al, 2012
Harry Athanassiou | Research Programmer
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Time in Benos’ Lab: 2010-2013
Last known position: Scientific Projects Engineer, Pittsburgh PA
Publications (1): Huang, Athanassiou, Benos, 2011
Kevin Bui | Research Programmer
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Time in Benos’ Lab: 2008
Current Position: DBMI, Senior Software Engineer
Publications (1): Tchagang et al, 2009
Jessica Cummings | Research Assistant
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Time in Benos’ Lab: 2003-2007
Current Position: U Pittsburgh, Senior Research Specialist (Res  IV)
Publications (1; as Jessica Dominick): Corcoran et al, 2005

 


Short term

Giorgio Bertolazzi | Visiting Graduate student, University of Palermo
Time in Benos’ Lab: Jan-Jun 2019
Last known position: Graduate student, University of  Palermo
Publications (2): Bertolazzi et al, 2020   Bertolazzi et al, 2020b
Craig  Riley, MD | Pulmonary Fellow, UPMC
Time in Benos’ Lab: 2018-2019
Current Position: Pulmonary Medicine, U Penn Health System
Yutong Yin | Graduate Student Researcher, University of Pittsburgh
Time in Benos’ Lab: 2002-2003
Last known position: Principal Quantitative Analyst, Capital One
Publications (1): Workman et al, 2005
Grace Zhang | MD student volunteer, University of Pittsburgh
Time in Benos’ Lab: Summer 2018
Current Position: UCSF, Internal Medicine Resident