Alumni – Benos Lab | Computational & Systems Biology

Postdoctoral Researchers
Graduate Students
Staff
Short term

Postdoctoral Researchers

Sheeraz Akram, PhD \| Research Associate
	Time in Benos’ Lab: 2018-2022 After Benos’ Lab: Superior University, Pakistan, Associate Professor Current Position: Superior University, Pakistan, Associate Professor
Abha Bais, PhD \| Research Associate
	Time in Benos’ Lab: 2008-2011 After Benos’ Lab: UC Berkeley, Postdoctoral fellow Current Position: Ribometrix, Inc, Senior Scientist I Publications (3): Bais, Kaminski, Benos, 2011 Zhang et al, 2011 Coronnello et al, 2012
Claudia Coronnello, PhD \| Postodoctoral Ri.MED Scholar Fellow
	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
	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
	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., 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
	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
	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
	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)
	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 Last known 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
	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
	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
	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 Caparosa^, Sedgwick^, et al, 2019 Sedgewick et al, 2019 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 After Benos’ Lab: Bizowie, Junior Software Developer Current Position: Power Home Remodeling, Software Developer
Arshi Arora, MSc \| Medical Scientist
	Time in Benos’ Lab: 2010-2012 After Benos’ Lab: Memorial Sloan-Kettering Cancer Center, Assistant Research Biostatistician Current Position: Memorial Sloan-Kettering Cancer Center, Res Biostat II Publications (2): Coronnello et al, 2012 Lu et al, 2012
Harry Athanassiou \| Research Programmer
	Time in Benos’ Lab: 2010-2013 After Benos’ Lab: Univ of Pittsburgh, System Programmer / Data Analyst Last known position: Scientific Projects Engineer, Pittsburgh PA Publications (1): Huang, Athanassiou, Benos, 2011
Kevin Bui \| Research Programmer
	Time in Benos’ Lab: 2008 After Benos’ Lab: U Pittsburgh (DBMI),Software Developer Current Position: U Pittsburgh (DBMI), Senior Software Engineer Publications (1): Tchagang et al, 2009
Jessica Cummings \| Research Assistant
	Time in Benos’ Lab: 2003-2007 Current Position: U Pittsburgh (Crit Care Med), 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: University of Palermo, Graduate student Publications (2): Bertolazzi et al, 2020 Bertolazzi et al, 2020b
Heather Kobilnyk, MSc \| MSc Student, CoBB
	Time in Benos’ Lab: Time in Benos’ Lab: 2021 (Fall semester) After Benos’ Lab: Children’s Hospital of Philadelphia, Bioinformatics Engineer Current Position: Children’s Hospital of Philadelphia, Bioinformatics Engineer
Craig Riley, MD \| Pulmonary Fellow, UPMC
	Time in Benos’ Lab: 2018-2019 Current Position: U Penn Health System, Pulmonary Medicine
Yutong Yin \| Graduate Student Researcher, University of Pittsburgh
	Time in Benos’ Lab: 2002-2003 Last known position: Capital One, Principal Quantitative Analyst 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

Sheeraz Akram, PhD \| Research Associate
	Time in Benos’ Lab: 2018-2022 After Benos’ Lab: Superior University, Pakistan, Associate Professor Current Position: Superior University, Pakistan, Associate Professor
Abha Bais, PhD \| Research Associate
	Time in Benos’ Lab: 2008-2011 After Benos’ Lab: UC Berkeley, Postdoctoral fellow Current Position: Ribometrix, Inc, Senior Scientist I Publications (3): Bais, Kaminski, Benos, 2011 Zhang et al, 2011 Coronnello et al, 2012
Claudia Coronnello, PhD \| Postodoctoral Ri.MED Scholar Fellow
	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
	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
	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., 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
	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
	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

Rachel Brower-Sinning, PhD \| PhD Student, CPCB
	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)
	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 Last known 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
	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
	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
	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 Caparosa^, Sedgwick^, et al, 2019 Sedgewick et al, 2019 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