Simon Kasif  PhD.  Principal Investigator 




Jack Minker

Azriel Rosenfeld 


Jack Minker and Azriel Rosenfeld (PhD co-mentors and co-advisors) were both influential scientists and pioneers in Artificial Intelligence (Deductive Database/Logic Programming and Computer Vision respectively). However, what made both of them really special is their HEART.  They followed the old tradition of scientists that cared about broad issues.

Jack Minker was very active in Human Rights. 

Azriel Rosenfeld was very active in more areas that I can list including Rabbinical studies integrating 20th century questions and the Talmud, Mathematical Puzzles, Cognition, Perception, Human Vision and more.


Undergraduate CS Mentors


Zvika Galil

Amir Pnueli

Amiram Yehudai



Past and Present Students that did research with us  (this list does not include thesis committees memberships, academic advisees,  just a list of students or fellows we directly co-mentored in a research project or study leading to a published paper)

  1. Art Delcher, Ph.D. Johns Hopkins University, 1989, M.A. in Mathematics, Johns Hopkins University, now Research Professor Johns Hopkins Medical School.
  2. David Heath, Ph.D. 1992, Johns Hopkins University BS in Electrical Engineering, California Institute of Technology, JHU Wolman Fellow, first position faculty in Johns Hopkins Medical School, Visualization Research in Radiology, established a start-up in medical visualization.
  3. Lewis Stiller, BS in Mathematics, PhD Johns Hopkins University, Ph.D. May 1995, National Defense Fellow, Thesis area: Exploiting Symmetry in Parallel Computation, first position Postdoctoral Fellow, Computer Science Department Berkeley, CA.
  4. Saibal Banerjee, MS Johns Hopkins, PhD with Azriel Rosenfeld, first position IBM Research.
  5. Truxton Fulton BS Cal. Tech, JHU Wolman Fellow, MA 1997 (MS), moved to a start-up.
  6. Scott Weiss, BS in Computer Science, Carnegie-Mellon University, JHU Wolman Fellow, Professor Mount Saint Mary’s University, Champion Jeopardy.
  7. John Bright, PhD Johns Hopkins with Greg Sullivan, first position Google.
  8. David Redish, BS Johns Hopkins, (undergraduate research), PhD CMU, currently Professor University of Arizona.
  9. Phoebe Sengers, BS Johns Hopkins University (undergraduate research), PhD CMU, currently Professor Cornell University.
  10. Sandeep Singhal , BS Johns Hopkins University (undergraduate research), PhD Stanford,  currently Microsoft Research.
  11. Kwabena Boahen, BS Johns Hopkins University (undergraduate research), PhD Cal Tech, currently Professor Biomedical Engineering, Stanford University
  12. Willam Hsu, BS Johns Hopkins University (undergraduate research), PhD Illinois, first position NCSA Urbana, currently professor, Kansas.
  13. Ben Kao, BS in Biomedical Engineering, Duke University, PhD University of Illinois at Chicago, 2004 (co-advised by Pete Nelson), first position start-up.
  14. Deyou Cai, BS, MS, Taichin University and University of Chicago.  (MS)
  15. S. Murthy, (PhD Hopkins with S. Salzberg), senior scientist, IBM Research.
  16. D. Gunopolous, PhD Princeton University with David Dobkin), currently Professor University of Athens.
  17. M.S. Apaydin, intern CRL, PhD Stanford, with J.C. Latombe, first position Duke University.
  18. Baris Suzek, intern CRL, PhD Georgetown, first position Georgetown Protein Database.
  19. Ashutosh Garg,  intern CRL, (PhD Urbana 2002 with Dan Roth and T. Huang),
  20. Joe Szustakowski,  CRL intern, PhD Boston U. 2003 with Zhiping Weng, now Head Biomarker Development, Novartis Research Institute, Vice President, Bristol Meyers Squib.
  21. Tarjei Mikkelsen, CRL intern, BS/MS MIT, PhD Harvard/MIT HST program with Eric Lander (first position Broad Institute of MIT/Harvard and Junior Fellow Harvard), currently Vice President.
  22. Yu Zheng, MS Yale, PhD Boston University 2004 (co-advised by Richard J. Roberts), first position New England Biolabs.
  23. Jeffrey Pelker, BS Boston University (undergraduate research), first position industry.
  24. C.M Ding, PhD Boston University (primary PhD advisor Charles Cantor), Dean Medical School.
  25. John Zhang PhD Boston University 2005 (co-advised by Charles Cantor), first position Center for Advanced Biotechnology BU.
  26. Sharona Washington (co-advised by Kim McKall), MS Boston University.
  27. Dimitri Pervouchine, PhD Moscow U.,  first position research fellow  in CBD, BU
  28. Ulaz Karaoz , PhD Boston University with Zhiping Weng, first position Lawrence Berkeley Lab.
  29. Michael Schaffer, PhD Boston University 2006 (co-advised by Geoff Cooper), 2006, (first position Pfizer Research).
  30. John Rachlin, BS Cornell, PhD Boston University 2006 (co-advised by Charles Cantor and Shang-Hua Teng), first position Aventis/Sanofi Pharma, faculty CS Northeastern University.
  31. Megon Walker PhD Boston University 2006, later Harvard Law, current position Patent Attorney.
  32. Boris Hayete, PhD Boston University with Jim Collins, first position Gene Network Sciences.
  33. J. Faith (PhD with Tim Gardner), PhD Boston University 2008, (first position Washington University), currently Assistant Professor Mount Sinai School of Medicine.
  34. Vera Asodi, (PhD with Noga Alon), BS Tel Aviv University, PhD Tel Aviv University, first position Cal Tech.
  35. Jason Laramie, BS Washington University, PhD Boston University with Meyers, first position Pfizer Research,  Vice President, Novartis.
  36. Andy Tolonen, PhD MIT with Penny Chisholm and George Church, first position Harvard Med, Currently Assistant Professor, France.
  37. Dikla Dotan, (co-advised by Avraham Melkman), BS  and PhD Ben Gurion University, now group leader Microsoft Research.
  38. Evan Snitkin, PhD Boston University with Daniel Segre, first position NIH, currently Assistant Professor Michigan.
  39. Steven Parker, PhD Boston University with Tom Tullius and Margulis at NIH, first position NIH, currently Assistant Professor Michigan.
  40. Adam Gustafson, PhD Boston University with Avi Spira, private industry.
  41. Antonina Mitrofanova, PhD NYU with Bud Mishra, first position Columbia University.
  42. Soo Lee (co-advised by Zhiping Weng and Charles Cantor), PhD Boston University 2009, currently at Harvard Medical School.
  43. Terrence Wu, (co-advised by Isaac Kohane and Tianxi Cai, Harvard Medical School), PhD Boston University 2008, first position Dana Farber, Harvard Medical School.
  44. Henry Li, BS University of Washington, (co-advised with Martin Steffen),  PhD with Jim Collins Boston University, first position Harvard Medical School, Church group.
  45. Naoki Nariyai, BS University of Tokyo, PhD Boston University 2009, currently Assistant Professor, Japan.
  46. Manway Liu, BS MIT, (co-advised by Isaac Kohane and Ron Kahn), PhD Boston University 2010, first position Research Scientist, Novartis Research Institute, currently group leader at Google.
  47. Brian Anton, BS Georgia Tech, (co-advised by Richard J. Roberts) PhD Boston University 2010, first position New England Biolabs.
  48. Emily Palmer, BS Boston University (undergraduate research), currently PhD program in Biomedical Engineering.
  49. Evan Appleton, BS Boston University (undergraduate research), continued to a PhD program in Bioinformatics, currently at Church group at Harvard.
  50. Kevin Tao, BS Duke University (undergraduate research COMBREX).
  51. L. Osmani, BS Boston University (undergraduate research COMBREX), first position MD program University of Illinois Medical School.
  52. Genevieve Housman, BS Boston University (undergraduate research COMBREX),  University of Chicago
  53. Esther Rheinbay, MS MIT (co-advised by Brad Bernstein, Broad Institute), PhD Boston University May 2012, first position Broad Institute of MIT and Harvard, currently assistant professor Harvard Medical School.
  54. Chris Nogiec, BS Boston College, (co-advised by ME Patti, Joslin, Harvard), PhD 2014 Boston University, first position in private market — personal trainer and nutrition, Exercise Research.
  55. Richard Park, BS Brown University, (co-advised by Peter Park, Harvard Medical School),  Finalist in the Illumina iDEA Challenge in 2011.
  56. Clark Freifeld, BS Yale, (co-advisor John Brownstein, Harvard Medical School), PhD Boston University 2014, currently Children’s Hospital & Harvard Medical School, Winner Societal Best Dissertation Award, CTO Start-up, currently faculty CS, Northeastern University.
  57. Lina Faller, PhD Boston University with Daniel Segre 2014, first position NY Genome Center.
  58. Benjamin Allen, PhD Boston University with Mark Kohn, first position postdoc Harvard University, currently Assistant Professor, Emmanuel College.
  59. Irina Glotova, PhD Boston University with James Galagan, first position EMBL.
  60. Kamila Naxerova, BS Heidelberg, PhD with Rakesh Jain, Harvard Medical School 2014,  currently Assistant Professor,  Harvard Medical School.
  61. Andy McMurry, BS Northeastern (co-advised with primary advisors  Ben Reis and Zak Kohane, Harvard Medical School),  Chief Technology Officer. SF.
  62. Yi-Chien (co-advised by Charles DeLisi and Daniel Segre).
  63. Alfred Ramirez, BS MIT, (co-advised by Ron Kahn Harvard Medical School), winner best paper by a graduate student in BME 2017.
  64. Dan Lancour, BS U. Wisconsin (Madison), (co-advised by Mark Crovella and Lindsay Farrer), industry.
  65. Brian Haas (co-advised by Aviv Regev), Broad Institute of Harvard and MIT (group leader).
  66. Nino Lambert (undergraduate research), BS BME, BU.
  67. Catherine Dela Santina (BU, MIT)


Mary Ellen Fitzpatrick (System Admin. of CAGT)


Research Scientists and Fellows  (Past and Present)


  1. T. M. Murali, PhD Brown, Senior , Postdoctoral  Fellow,  currently Professor at VPI.
  2. Vladimir Pavlovic, PhD Illinois, Research Scientist, currently  Professor at Rutgers.
  3. Joel Graber, PhD Cornell , Research Scientist, currently  staff scientist in Bar Harbor, JAX LAB.
  4. Richard Beigel, PhD Stanford ,  Visiting Research  Professor
  5. David Goddeau, PhD MIT, Visiting Scientist.
  6. Stan Letovsky, PhD Yale, Visiting Research Professor,  Vice-President, LabCorp
  7. Arthur Liberzon, PhD Weizmann Inst. of Science, postdoctoral fellow, first position at Harvard MIT Broad Institute.
  8. Jason Vertrees,  PhD  U.  Texas, postdoctoral fellow, Senior Vice President.
  9. Michael Molla, PhD University of Wisconsin,  postdoctoral fellow jointly with Tim Gardner and Jim Collins, first position Joslin Diabetes Center and Harvard Medical School.
  10. Revonda Pokrzywa, PhD Virginia Tech, postdoctoral fellow.
  11. Terrence Wu, MD, PhD Boston University, first position Dana Farber, Harvard Medical School.
  12. Ami Levy, PhD Ben Gurion University, first position the Broad Institute of Harvard and MIT.
  13. Jonathan Dreyfuss, PhD Boston University, Joslin Diabetes Center, Harvard Medical School.
  14. Hui Pan, PhD. U. Chicago, Joslin Diabetes Center, Harvard Medical School.



DIRECT  RESEARCH Collaborators  (this list DOES NOT include major consortiums, co-authors on multi-author papers, collaborators on contributed chapters to our book, grant collaborators, consulting, advisory groups and similar) – affiliation at time of collaboration and topic of collaboration)


(In alphabetical order)


David Aha (Navy Research Labs, AI, Machine Learning)

Noga Alon (Tel Aviv/Princeton Institute for Advanced Studies, Network/Graph Theory)

Sol Amar (Boston Medical Center, Microbiome)

Serafim Batzouglou (MIT Genome Center, Computational Biology)

Richard Beigel  (Johns Hopkins University/Yale University, CS Theory and Applications in Biotechnology)

Steven Brenner (Berkeley, Computational Bridges to Biology (COMBREX)

Robert Berwick (MIT, AI)

John Brownstein (Children’s and Harvard Medical School, applications of AI to Public Health)

Brad Bernstein (MGH, Broad Institute and Harvard Medical School. Epigenomics, Cancer)

Dan Brown (MIT Genome Center. Computational Biology)

Allison Burkhart (Joslin Diabetes Center and Harvard Medical School, Diabetes, Metabolic Modeling)

Tianxi Cai (Harvard School of Public Health, Bionformatics / Biostatistics/ Cancer)

Charles Cantor (Sequenom, Biotechnology)

Geoff Cooper (Boston University, Cancer Biology, Gene Regulation)

Jim Collins (Boston University, now MIT)

Mark Crovella (Boston University, Network science)

Susanne Churchill (Harvard Partners, I2B2 Informatics to Bedside)

Simon Dankell (Joslin Diabetes Center and Harvard Medical School)

Charles DeLisi (Boston U., Science Policy, Computational Biology)

David Dobkin (Princeton U., Computational Geometry, Theory)

Josee Dupuis (BU School of Public Health, Genetics/Biostatistics)

Linday Farrer (Boston Medical Center, Human Genetics)

Robert Fleischmann (The Institute for Genomic Research (TIGR), Comparative Genomics)

Lance Fortnow (U. Chicago, NEC Research, CS Theory)

David Goddeau (CRL, Computational Biology)

Tim Gardner (Boston University, Systems Biology, Synthetic Biology)

Allison Goldfine  (Joslin and Harvard Medical School, Systems Biology of Diabetes)

Dimitris Gunopulous (IBM Research, Almaden, Data Mining)

Russ Greiner (U. Alberta, Machine Learning and applications)

Adam Grove (NEC Research, Princeton, Graphical Models)

Bob Grossman (University of Chicago, Distributed Data Mining )

Nurit Haspell (U. Mass, Bioinformatics)

Alan Herbert (Boston Medical School, Human Genetics)

Tom Huang (Urbana, Human Centered Computing Initiatives at NSF)

Rakesh Jain (MGH and Harvard Medical School, Cancer)

Peter Karp (SRI, Computational Bridges to Experiments)

Ronald Kahn (Joslin Diabetes Center and Harvard Medical School, Systems Biology of Diabetes and Wellness).

Isaac Kohane (Harvard Medical School, Medical Informatics, Systems Biology, Bioinformatics, Applications of AI to Medicine)

Madhur Kohli (IBM Research, Parallel Logic Programming)

Sek Won Kong (Childrens’ Hospital – Harvard Medical School, Systems Biology)

Eric Kolaczyk (Boston University, Biostatistics/Bioinformatics)

Rao Kosaraju (Johns Hopkins, CS Theory and Algorithms)

Eric Lander (MIT Genome Center, Human Genome Project)

Stan Letovsky (Harvard Medical School and Boston University, AI applications in Computational Biology)

Jie Liang (UIC, Computational Biology)

Beth Logan (CRL, Applications of Machine Learning to Computational Biology)

Kim McKall (BU Biology, Gene Function Prediction)

Avraham Melkman (Ben Gurion University, Applications of CS to Computational Biology)

Jack Minker (PhD Advisor, Parallel Logic Programming)

Bud Mishra (NYU, Computational Biology)

Marcelo Mori (Joslin Diabetes Center and Harvard Medical School, Systems Biology of Diabetes)

Pedro Moreno (CRL, Applications of Machine Learning to Computational Biology)

TM Murali (Virginia Tech)

Peter Nelson (UIC, AI)

Peter Park (Harvard Medical School, Computational Biology)

ME Patti (Joslin and Harvard Medical School, Systems Biology of Diabetes, Metabolic Networks)

Vladimir Pavlovic (CRL, applications of graphical models and AI to Genomics)

Judea Pearl (UCLA, Graphical Models, AI)

Roy Perlis (Harvard Medical School)

Norbert Perrimone (Harvard Medical School, Flybase)

Daria Prilutski (Harvard Med, Bioinformatics)

Aviv Regev (MIT/Broad Institute, Genomics)

John Reif (Duke U., CS Theory, AI)

Richard Roberts (New England BioLabs, Computational Biology, Bacterial Genomics,  Computational Bridges to Experiments, Transforming Biology)

Azriel Rosenfeld (U. Maryland, PhD co-advisor and co-mentor, Computer Vision, Parallel Computing, Cognitive Analysis)

Stuart Russell (Berkeley, Learning Complex Behaviors Initiative/Symposium, AI Journal)

Steven Salzberg (TIGR/Johns Hopkins, AI, Machine Learning, Computational Biology)

David Searls (Smith Kline Beacham, Computational Biology Book)

Roded Sharan (Tel Aviv University, Computational Biology)

Deepak Sherlekar (University of Maryland, Graph Separators and Satisfiability)

David Sinclair (Harvard Medical School, Aging, short genes)

Hamilton Smith (Celera/Hopkins, early Bioinformatics)

Martin Steffen (Harvard Medical School, Computational Bridges to Experiments, Systems Biology)

Shamil Sunyaev (Harvard Genetics / Harvard Medical School, Human Genetics)

Gregory Sullivan (Johns Hopkins University, CS Theory and Algorithms)

Mario Suva (MGH/Broad Institute of MIT and Harvard, Epigenomics, Cancer Reprogramming)

Herve Tettelin (The Institute for Genomic Research, Biotechnology)

Yu-Hua Tseng (Harvard Medical School/Joslin, Systems Biology of Diabetes and Obesity)

John Tullai (Boston University Biology, Systems Biology of Cancer, Gene Regulation)

David Waltz (NEC Research, Princeton, AI)

LJ Wei (Harvard School of Public Health, Biostatistics)

Zhiping Weng (Boston U., Computational Biology, Bioinformatics)

Owen White (The Institute for Genomic Research, Gene Identification, Computational Biology)