Boston University’s Legacy in Computational, Systems and Synthetic Biology

This is an old page that I have not updated in a number of years.

Below I list in random order a few prominent individuals whose paths crossed BU, and who made transformative, prominent or useful computationally centric  contributions to the field of bioinformatics, systems, synthetic or computational biology. This is not a scholarly review. I only mean to provide a sample.  The list is likely to be out of date and incomplete. My apology for the individuals I do not list — its just a matter of time and space and limited knowledge. I hope others will do a more scholarly job tracing the full picture. I also do not list many distinguished biology, chemistry and medicine faculty that played an essential role in advising PhD students and providing them with access to fresh data, scientific understanding and ability to apply their computational thinking to important biology or medicine problems.  These individuals can be found on this web page. I also do not list faculty and staff who made essential administrative, systems support, educational and other contributions to this legacy and are as essential to this transformative initiative as any of the people listed below. (Affiliation can be out of date).

Charles DeLisi – one of the fathers of the Human Genome, recipient of the Presidential Medal for this particular seminal contribution.  He is known for numerous early contributions to Bioinformatics, Computational Biology and Computational Immunology.   His group produced the innovative VISANT system for visualization, mining and searching biological networks. He started the first Bioinformatics PhD Program in the US at Boston University!  He also created the first deep concentration in molecular engineering at BU BME before it became main stream in other BME departments.

Elham Azizi – a young leader in systems biology of cancer (Assistant Professor, Columbia University).

Daniel Beard – leading researcher in Metabolic Modeling and Director of the Virtual Rat Project (Professor at U. Michigan).

Laslo Barabasi – one of the most highly cited authors in biological networks. Laslo and his group observed scale free properties of biological networks and more. He is a former postdoctoral fellow at BU.  Laslo worked with Gene Stanley in Physics.  Gene is a physics pioneer, who started thinking about scale free phenomena in biology and numerous other applications.

Jennifer Beane — made contributions to the bioinformatics of lung cancer (Assistant Professor BU Medical Campus)

Gary Benson – one of the designers (with Mike Waterman)  and developer of the a widely used Tandem Repeat Finder algorithm. Gary ran the second round of the IGERT education program from NSF that supported many students in their first year.

Gyan Bhanot – visiting senior scientist (Professor) who made significant quantitative contributions to cancer systems biology (Professor Rutgers University).

Jadwiga Bienkowska – a pioneer in computational structural biology (Director, Computational Biology Pfizer)

William Blake – made numerous contributions to both academic and industrial synthetic biology (CTO, Sherlock Bioscience).

Mark P. Brynildsen – young leading systems biologist studying bacterial resistance (Assistant Professor at Princeton). He is a former postdoc at BU.

Carlos Camacho – a key contributor to the influential protein docking and protein-protein interaction software systems that came out of BU. Currently Professor of Computational Biology at University of Pittsburgh.

Josh Campbell – Assistant Professor at BU Med,  made important contributions to cancer bioinformatics. 

Charles Cantor — (Professor, BU) is directly or indirectly responsible for a good fraction of the inspiration for some of the best biological science that came out of BU in the DeLisi era. It is virtually impossible to enumerate his life scientific contributions, since he is a true polymath.  Charles Cantor was the key driver behind SQNM developing the first of a kind prenatal non-invasive trisomy detection assay, one of the highest impact clinical deployment of genomics so far.  His work with Dennis Lo is perhaps one of the earliest and the most practically significant clinical contribution of genomics to medicine and led to the explosive area of liquid biopsy. He is one of the fathers of the famous Jukes-Cantor evolutionary analysis, seminal books in Biochemistry, and Genomics, co-inventor of multiple genomic technologies, former director of the Berkeley DOE Genome Center, chair Columbia Biology/Biochemistry, BU BME, and much more.

Rong Chen – a leading contributor to top docking software and personalized medicine projects, Senior Vice President, SEMA4

Jim Collins — (Professor, BU) pioneered some of the earliest and most popular concepts in modern incarnations of synthetic biology and systems biology. Considered by many  to be one of the fathers of the Engineering Framework for Synthetic Biology (started with increased momentum around 2000).  Some of the developments from his laboratory include the Toggle Switch, Reverse Engineering of Network Algorithms (both with Tim Gardner) and much more. His work is highly cited and he has influenced many biomedical engineers. There are many prominent synthetic biology leaders that were educated in Jim’s laboratory that include:  Tim Gardner, Jef Hastie (UCSD),Mark Brynildsen (Princeton) and many others

Doug Densmore —  (Professor, BU)  is a leading engineering faculty applying engineering design principles to synthetic biology. Doug is a pioneer in taking computer engineering approaches very seriously in the design of biological systems.

Mark DePristo – visiting scientist BU, made pioneering contritions to variant analysis using deep learning, genome analysis and genetics (senior group leader Google)

Chunming Ding —  is a pioneer who is of the key contributors to the seminal work on early detection of DNA in blood, leading to clinically used signatures for prenatal diagnosis of disease (with Charles Cantor  (SQNM) and Dennis Lo in Hong Kong). This early work led to liquid biopsy. Director of the Epigenetics Research Center, Singapore, Dean of Medicine, China.

Jonathan Dreyfuss – the Coordinator of the Systems Biology and Diabetes Core at the Joslin Diabetes Center (Harvard Med).

Eric Francosa – a young leading microbiome expert (Harvard Med). Many prominent papers in top journals.

Brian Haas – a leading bioinformatics scientist and pioneer. Co-author and co-developer of several seminal bioinformatics systems including Trinity.

Rhonda Harrison – the first minority PhD from the Bioinformatics program.

Zhenjun Hu –  (Research Professor, BU)  a key developer and the main architect of the VASANT system at Boston University.  Played an important role in the Database Design for COMBREX.

Jeremiah Faith – one of the leading young scientists in the Microbiome community, (Assistant Professor Mount Sinai, NYC). (Thesis citations > 1400).

Martin Frith – a leading computational biologist with multiple contributions to genome sequence analysis, motif finding, and comparative analysis (Professor University of Tokyo)

James Galagan – (Professor, BU)   – a pioneer in the fields of genomic annotation of fungi (Neospora) and genomic systems biology of TB.

Tim Gardner –  (Professor, BU) with Jim Collins Tim co-pioneered some of the earliest and most influential ideas in synthetic and systems biology including the Toggle Switch and influential papers in Network Reverse Engineering. Tim led or co-led several of the most cited papers from BU in the last 20 years. A radical innovation champion and pioneer! 

Roderic Guigo – one of the leading senior bioinformaticians in Spain and directing a Center.  Very significant and pioneering contributions to bioinformatics of gene splicing. He is a former postdoc at BU.

Jeff Hastie – pioneer in synthetic and systems biologist (Professor of Biomedical Engineering, UCSD). He was a former postdoc at BU.

Farren Isaacs – a leading young synthetic biologist (Assistant Professor Yale U.) Another pioneer.

Evan Johnson –  (Professor, BU)  a leading statistical bioinformatician,  (very highly cited bioinformatics software development with applications to cancer).

Elinor Karlsson – a leading contributor to the dog genome (part of her thesis at BU), (Assistant Professor U. Mass Medical). Currently a leader in Dog Genomics. Another pioneer.

Maxim Frank-Kamenetskii  – (Professor, BU) a very prominent researcher and a legend in the Biophysics of DNA.

Simon Kasif – (Professor, BU) co-developer of Glimmer (a widely used microbial gene finder used to detect a large fraction of genes in all microbial organisms and many important pathogens), co-developer of MUMMER (an early and widely used open access whole genome comparative system, used to detect genome variation responsible for pathogenicity and virulence), helped introduce and popularize Bayesian Networks (Graphical models) in Bioinformatics, Systems Biology, Integrative Biology and In-silico Directed Evolution (Synthetic Biology) (starting 1993), co-pioneered whole genome network gene function prediction, co-introduced Probabilistic Functional Linkage Networks,  helped popularize gene networks signatures for metabolic diseases such as Diabetes and Insulin Resistance, co-founder of COMBREX (with Roberts and Steffen), PI, Bionformatics and Systems Biology Core, Joslin Diabetes Center.

Thomas Kepler – (Professor, BU) made important contributions to immuno-informatics using both systems and predictive methodologies.

Mo Khalil — (Professor, BU)  is a leader in transcription factor engineering and synthetic biology,  also a co-founding associate director of the Design Center.

Eric Kolaczyk – (Professor, BU) is a leader in the statistics of networks  and author of the first book in this area with many applications to network biology.

Mark Kon – (Professor, BU) co-advised a number of PhD students in Bioinformatics, introducing machine learning rigor into their software and data analysis.

Dima Kozakov – a leading contributor to several high performing docking systems developed at BU and a highly cited researcher (Assoc. Professor, Stonybrook).

Rick Lathrop – Protein Engineering (Professor U. C. Irvine). Rick was a former postdoc at BU.

Henry Lee – Leader in Antibiotic Resistance, Fast Evolution, Non-model organisms

Manway Liu – did pioneering work on application of network biology to diabetes and aging research, (co-developer of GNEA),  former group head Google (life sciences, currently a VP.

Joseph Lehar – visiting scientist, made significant contributions to the Computational Biology of Combinatorial Drug Treatment.  Vice President. Co-led some of the earliest applications of computation in combinatorial drug design in industry.

Stan Letovsky – visiting scientist, a leading industrial computational biologist, a pioneer in bionformatics,  VP for Bioinformatics in several Boston area start-ups. Most recently leading the development of Precision Medicine at LabCorp.  Also co-introduced Probabilistic Functional Linkage Networks with Simon Kasif.

Arthur Liberzon – leading the Geneset Annotation group at the Broad Institute, which supports the GSEA algorithm.  Arthur was a former postdoctoral fellow at BU who co-developed GNEA.

Pankaj Mehta – (Professor, BU)  a leading researcher in physical biology.

Jill Mesirov — adjunct professor and former VP and senior Director of Bioinformatics at the Broad Institute.  Co-advised some of the most influential PhD theses in Bioinformatics at BU. Jill is a senior contributor to GSEA, director of Gene Pattern, and the Broad Genome Browser and is a highly visible and influential Senior Bioinformatician with numerous seminal contributions such as GSEA and others.

Michael Molla — former Director of Bioinformatics at the Joslin Diabetes Center and Harvard Medical School. Michael was a former postdoc at BU.

Stefano Monti – (Professor, BU)  made important contributions to gene expression analysis and a leading contributor to the informatics of carcinogenicity!

T.M. Murali – Professor of Systems Biology at VPI and Co-Director of the Systems Biology of the Tissue Engineering Center.  Prof. Murali was a former postdoctoral fellow at BU and a leading researcher in analysis of protein-protein interaction networks.

Naoki Nariai – important contributions to using Bayes Networks in Data Integration and Protein Function Prediction in Aging Research, Assistant Professor Japan.

Richard Park – important contributions to genome visualization, finalist in the Illumina Genome Visualization Competition.

Steve Parker – important contribution to understanding of selection in non-coding regions in the human genome and later Diabetes research  (Assistant Professor Michigan)

Vladimir Pavlovic – Professor of Biomedical Engineering at Rutgers  and expert on the applications of Bayes networks to genomics. Vladimir was a former research scientist at BU.

Alfred Ramirez – in his PhD Alfred did pioneering work in applications of network biology to Diabetes and Obesity.

Tim Reddy – made important contributions to transcriptional regulation and transcriptional understanding of metabolic diseases, (Professor Duke University).

Esther Rheinbay – in her thesis at BU (co-advised by Brad Bernstein (Broad) and Simon Kasif) she co-envisioned reprogramming cancer stem cells along the malignancy axis. She accomplished this feat working with Mario Suva (now Assistant Professor at Harvard Medical School and MGH) using both computational and experimental techniques. Esther is now an Assistant Professor at Harvard Medical School.  

Richard Roberts – (Distinguished Professor, BU)  Nobel Laureate for discovery of splicing!  Father of REBASE.  One of the fathers of COMBREX. Co-advisor for a number of PhD students at BU.  One of the leading scientists in the area of DNA methyltransferases and DNA restriction systems.  Major activist in the Open Access movement. Introduced both the NAR Database Server and NAR Webserver issues. Co-founder of the Ocean Genome Legacy Foundation (with Sidney Brenner), co-founder COMBREX (with Kasif and Steffen).  Rich put Bioinformatics databases on the map, predicting the scientific impact such databases (Flybase, Kegg, EcoCyc, Genbank, Ensembl, etc) would have on biology.  One of the greatest humanitarians and activists among world class scientists.

Daniel Segre — (Professor, BU) is a visible metabolic network researcher. Developed the COMET system for community modeling of metabolic networks and formerly co-developed the widely cited MOMMA algorithm for metabolic networks. 

Temple Smith – (Professor, BU) is  a Bioinformatics Pioneer and one of the two fathers of the  seminal and very famous Smith-Waterman local alignment algorithm and a leading contributor to many other early insights in the field.

Chris Sander – visiting scientist, one of the early pioneers in Computational Biology.  No introduction needed but he made seminal contributions to structure alignment algorithms and protein secondary structure prediction among others. Chris also mentored many of the leading computational biologists in the world.

Michael Schaffer – important early contributions to integrative analysis and the first PhD student at BU to combine serious experimental and computational research in his own work, leading a whole generation of others that followed this paradigm.

Aravind Subramanian – one of the fathers of the widely used Gene Set Enrichment Analysis (GSEA) which was part of his PhD thesis at BU with Jill Mesirov. GSEA is one of the most widely used systems biology tools in the field with over 20000 citations !  Currently heading CMAP at the Broad. Both are considered seminal developments in Bioinformatics.  A pioneer. 

Evan Snitkin – one of the leading young scientists in the Microbiome community (Assistant Professor U. Michigan).

Gene Stanley -(Professor, BU)  is a leading physicist. Highly insightful papers on long range DNA interactions (mentored both Barabasi and Tamayo listed here). Gene inspired a whole generation of researchers doing research on scale free phenomena and network science with spillovers to biology.

Joseph D. Szustakowsk – member of Human Genome Project  (as a student)) and a contributor to structural Bioinformatics at BU (both software and new principles), Vice President, Translational Medicine Bioinformatics, Informatics and Predictive Sciences, Bristol-Myers Squibb.

Pablo Tamayo – the joint first author of some of the earliest and most influential gene expression papers from the MIT Genome center.  Pavlo is a former postdoc at BU. Now Professor at UCSD.

Itai Yanai – first PhD student in Bioinformatics at BU, tenured at the Technion and now Director of the Comp. Biology Institute at NYU.  Itai’s work is focusing on evolutionary systems biology, a fundamental and relatively understudied area.

Sandor Vajda —   (Professor, BU) is a senior and influential researcher in protein-small molecule docking and protein-protein docking systems, one of the fathers of the CAPRI competition.

Megan Walker – the second minority PhD and also the first lawyer (Harvard Law).  Megan pioneered Active Learning applications to biology research at Boston University and the early use of AI for molecular drug design! Today, application of AI to drug design is all the rage. Megon proposed this research in 2002 or even earlier. A true pioneer!

Zhiping Weng — made numerous important contributions to transcriptional genome regulation, one of the key computational leaders of the ENCODE project and now a director of a the Computational Biology program at U. Mass. Medical. Her work is exceptionally well cited and having impact in two different fields (structural biology of proteins and identification of transcriptional elements in both the Drosophila and Human Genomes). 

Wilson Wong – (Professor, BU) is a leader in synthetic biology, immune cell reprogramming and more. Another champion of radical innovation.

Yu Zheng — important early contributions to integration of networks with genomic data, developed several important new technologies for epigenomics and directed evolution (Group Leader NEB, Currently Director at  Foundation Medicine)

Brandon Xia –  (Professor, BU), leader in evolutionary analysis of PPI networks.

A long list of former alumni that are leading industrial units in the US is available below. Among many this list includes Enoch Huang (visiting scientist and a group Leader at Pfizer Research Discovery Center), Jason Laramie (VP, G), Boris Hayette (Gene Network Sciences), Boris Shaknowitz (president of a start-up), Joseph Szustakowski (Vice President of Translational Bioinformatics at Brystol-Meyers) and many others.

Other alumni are profiled on this site.

Important Boston University Staff.

Caroline Lyman (executive director of the program)

David King (director of graduate office)

Johanna (runs the systems biology seminar!)

Tom Tullius  (Chemistry, Bioinfo. Program Director).

Scott Mohr (Chemistry, Graduate program Director).