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Ph.D. Courant Institute of Mathematical Sciences at New York University, Computer Science (advisor: Dennis Shasha); dissertation on automatic physical database design
M.S. Courant Institute at New York University, Computer Science
B.A. cum laude, University of California at Riverside
1993-present, Research scientist (1994-present) Whitehead Institute, Cambridge MA
1996-present, Bioinformatics consultant (part-time)
1999-2001, Director of intensive, yearly course, Bioinformatics: Writing Software for Genome Research, Cold Spring Harbor Laboratory, New York
1989-1993, Research software engineer (full-time) Software Options, Inc. (DARPA-funded research), Cambridge MA
1988-1989, Graduate assistant/instructor Courant Institute at New York University, New York
2003, University of Amsterdam, Ph.D. committee for Sjoerd Repping: The Reproductive Fitness of the Y Chromosome
1999, 2000, 2001, Cold Spring Harbor Laboratory, New York, organized and directed course Bioinformatics: Writing Software for Genome Research, a yearly intensive course to train researchers in creation and integration of software for genomics, genetics, and molecular biology; covered use of the Unix/Linux operating system, Perl programming, database design, creating dynamic web pages, and analysis of sequence and microarray data
1998, Boston University, master's thesis committee for Rhonda Harrison: A Computer Simulation to Optimize the Effectiveness of Genomic Library Construction and Ordering
1992, International Conference on Very Large Databases, Database Tuning Tutorial (with D. Shasha)
1989, New York University, Courant Institute, Department of Computer Science, taught graduate Special Topics: Parallel Algorithms, Architectures, and Applications (one semester, with D. Shasha)
1988, New York University, Courant Institute, Department of Computer Science, taught undergraduate Introduction to Database Systems (one semester)
1995-1997 Database consultant (part-time) Marble Associates Inc., Boston MA
1986-1988 Database architect and administrator and software engineer (full-time) Prudential-Bache Securities, New York
1983-1986 Information technology specialist and programmer, Chemical Bank, New York
Genomic Studies of Sex Chromosomes. April 2006 to March 2009. Co-PI with D. C. Page. NIH, NHGRI grant R01 HG00275.
Genomic Studies of Sex Chromosomes. March 2003 to March 2006. Co-PI with D. C. Page. NIH, NHGRI grant R01 HG00275.
Genetic Studies of Spermatogenic Failure in Humans. May 2000 to April 2006. Co-PI with D. C. Page. NIH, NICHD grant R01 HD32907.
Genomic Studies of the Y Chromosome. Jan 2000 to Feb 2003. Co-PI with D. C. Page. NIH, NHGRI grant R01 HG00257.
Mapping and Sequencing the Y Chromosome. Jan 1997 to Dec 1999. Co-PI with D. C. Page. NIH, HCHGR grant 2 R01 HG00257-07.
A Freely Sharable Database Management System Designed for Use in Component-Based, Modular, Genome-Informatics Systems. Sept 1995 to Sept 1998. Co-PI with N. Goodman. Department of Energy grant DE-FG02-95ER62101.
Workflow-Management Software for Genome-Laboratory Informatics. May 1996 to April 1999 Co-PI with N. Goodman. NIH, NCHGR grant 1 R01 HG0367-01.
Publications |
top printable CV (PDF) home |
L. Kaaij-Visser, H. Westerveld, C. Korver, S. van Daalen, S. Hoving, S. Rozen, F. van der Veen, S. Repping "Y-chromosome gr/gr deletions: is there a phenotype?" submitted (2008)
J. F. Hughes, H. Skaletsky, S. Rozen, R. K. Wilson, D. C. Page "Has the chimpanzee Y chromosome been sequenced?" Nat. Genetics, 38(8):853-854 (2006) [ PDF ]
S. Repping, S. K. M. van Daalen, L. G. Brown, C. M. Korver, J. Lange, J. D. Marszalek, T. Pyntikova, F. van der Veen, H. Skaletsky, D. C. Page, S. Rozen. "High mutation rates have driven extensive structural polymorphism among human Y chromosomes." Nat. Genetics, 38(4):463-467 (2006) [ PDF and Sup. info ]
A. Ballabio, D. Nelson, S. Rozen. "Genetics of disease, The sex chromosomes and human disease, Editorial overview" Curr. Opin. Genet. Dev. 16:1-4 (2006) [ PDF ]
J. F. Hughes, H. Skaletsky, T. Pyntikova, P. J. Minx, T. Graves, S. Rozen, R. K. Wilson, D. C. Page. "Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee." Nature, 437:101-104 (2005) [ PDF ]
S. Rozen, M. E. Cudkowicz, M. Bogdanov, W. R. Matson, B. S. Kristal, C. Beecher, S. Harrison, P. Vouros, J. Flarakos, K. Vigneau-Callahan, T. D. Matson, K. M. Newhall, M. F. Beal, R. H. Brown, Jr., R. Kaddurah-Daouk. "Metabolomic analysis and signatures in motor neuron disease." Metabolomics, 1(2):101-108 (2005) [ PDF ]
S. Repping, C. M. Korver, R. D. Oates, S. Silber, F. van der Veen, D. C. Page, S. Rozen. "Are sequence family variants useful for identifying deletions in the human Y chromosome?" Am. J. Hum. Genet. 75(3):514-517 (2004) [ PDF ]
S. Repping, S. K. M. van Daalen, C. M. Korver, L. G. Brown, J. D. Marszalek, J. Gianotten, R. D. Oates, S. Silber, F. van der Veen, D. C. Page, S. Rozen. "A family of human Y chromosomes has dispersed throughout Northern Eurasia despite a 1.8 Mb deletion in the Azoospermia Factor c region." Genomics, 83(6):1046-1052 (2004) [ PDF ]
S. Repping, H. Skaletsky, L. Brown, S. K. M. van Daalen, C. M. Korver, T. Pyntikova, T. Kuroda-Kawaguchi, J. W. A. de Vries, R. D. Oates, S. Silber, F. van der Veen, D. C. Page, S. Rozen. "Polymorphism for a 1.6-Mb deletion of the human Y chromosome persists through balance between recurrent mutation and haploid selection." Nat. Genetics, 35(3):247-251 (2003) [ PDF ] and [ Sup. info ]
S. Rozen, H. Skaletsky, J. D. Marszalek, P. J. Minx, H.S. Cordum, R. H. Waterston, R. K. Wilson, D. C. Page. "Abundant gene conversion between arms of massive palindromes in human and ape Y chromosomes." Nature, 19(6942):873-876 (2003) [ PDF ]
H. Skaletsky, T. Kuroda-Kawaguchi, P. J. Minx, H. S. L. Hillier, L. G. Brown, S. Repping, T. Pyntikova, J. Ali, K. Delahunty, H. Du, G. Fewell, G. Fulton, T. Graves, S.-F. Hou P. Latrielle, R. Leonard, R. Maupin, T. Miner, W. Nash, C. Nguyen, P. Ozersky, K. Pepin, S. Rock, T. Rohlfing, K. Scott, C. Stoneking, C. Strong, A. Tin-Wollam, R. H. Waterston, R. K. Wilson, S. Rozen, D. C. Page. "The male-specific region of the human Y chromosome: A mosaic of discrete sequence classes." Nature, 19(6942):825-837 (2003) [ PDF ] [ Sup. info ]
S. Repping, H. Skaletsky, J. Lange, S. Silber, F. van der Veen, R. D. Oates, D. C. Page, S. Rozen. "Recombination between palindromes P5 and P1 on the human Y chromosome causes massive deletions and spermatogenic failure". Am. J. Hum. Genet. 71(4):906-922 (2002) [ PDF ]
T. Kuroda-Kawaguchi, H. Skaletsky, L. G. Brown, P. J. Minx, H. S. Cordum, R. H. Waterston, R. K. Wilson, S. Silber, R. Oates, S. Rozen, D. C. Page. "The human Y chromosome's AZFc region features massive palindromes, uniform recurrent deletions, and testis gene families." Nat. Genetics, 29(3):279-286 (2001) [ PDF ]
C. Tilford, T. Kuroda-Kawaguchi, H. Skaletsky, S. Rozen, L. G. Brown, M. Rosenberg, J. D. McPherson, K. Wylle, M. Sekhon, T. A. Kucaba, R. H. Waterston, D. C. Page. "A physical map of the human Y chromosome." Nature, 409:943-945 (2001) [ PDF ]
E. Drenkard, B. G. Richter, S. Rozen, L. M. Stutius, N. A. Angell, M. Mindrinos, R. J. Cho, P. J. Oefner, R. W. Davis, F. M. Ausubel. "A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis." Plant Physiol. 124(4):1483-1492 (2000) [ PDF ]
C. Sun, H. Skaletsky, S. Rozen, J. Gromoll, E. Nieschlag, R. Oates, D. C. Page. "Deletion of azoospermia factor a (AZFa) region of human Y chromosome caused by recombination between HERV15 proviruses." Hum. Mol. Genet. 9(15):2291-2296 (2000) [ PDF ]
S. Rozen, H. Skaletsky. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz, S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386 [ PDF ]
N. Goodman, S. Rozen, L. Stein. "LabBase: data and workflow management for large scale biological research." In S. Letovsky, ed. Bioinformatics: Databases and Systems. Kluwer Academic Publishers, Norwell, MA, 1999.
R. G. Steen,..., S. Rozen, ..., H. J. Jacob. "A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat genome." Genome Res. 9 (advance electronic publication) (1999) [ PDF ]
J. T.- L. Wang, T. G. Marr, S. Rozen, D. Shasha, B. A. Shapiro, G.-W. Chirn, Z. Wang, K. Zhang. "Pattern discovery and classification in biosequences." In J. T.-L. Wang, B. A. Shapiro, D. Shasha, eds. Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications. Oxford University Press, 1999, pages 55-74 [ PDF ]
J. T.- L. Wang, S. Rozen, B. A. Shapiro, D. Shasha, Z. Wang, M. Yin. "New techniques for DNA sequence classification." J. Comp. Bio. 6:209-218 (1999) [ PDF ]
P. Deloukas,..., S. Rozen,..., D. R. Bently. "A physical map of 30,000 human genes." Science, 282(5389):744-746 (1998) [ PDF ]
D. Wang, ..., S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, E. S. Lander. "Large-scale identification, mapping and genotyping of single nucleotide polymorphisms in the human genome." Science, 280:1077-1082 (1998) [ PDF ]
N. Goodman, S. Rozen, L .D. Stein. "The LabFlow System for Workflow Management in Large Scale Biology Research Laboratories." Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB), 6:69-77 (1998) [ PDF ]
N. Goodman, S. Rozen, L. D. Stein, A. G. Smith. "The LabBase System for Data Management in Large Scale Biology Research Laboratories." Bioinformatics, 14(7):562-574 (1998) [ PDF ]
N. Kenmochi, T. Kawaguchi, S. Rozen, E. Davis, N. Goodman, T.J. Hudson, T. Tanaka, D.C. Page. "A map of 75 human ribosomal protein genes." Genome Res. 8(5):509-523 (1998) [ PDF ]
R. Saxena, L. G. Brown, T. Hawkins, R. K. Alagappan, H. Skaletsky, M. P. Reeve, R. Reijo, S. Rozen, M. B. Dinulos, C. M. Disteche, D. C. Page." The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned." Nat. Genetics, 14(3):292-299 (1996) [ PDF ]
G. D. Schuler, ...,S. Rozen, ..., T. J. Hudson. "A gene map of the human genome." Science, 274(5287):540-546 (1996) [ DOI ]
A. J. Bonner, A. Shrufi, S. Rozen. "LabFlow-1: A database benchmark for high-throughput workflow management." In Proceedings of the International Conference on Extending Database Technology (EDBT) (1996) Acceptance ratio 31/178 [ PDF ]
A. J. Bonner, A. Shrufi, S. Rozen. "Database requirements for workflow management in a high-throughput genome laboratory." NSF Workshop on Workflow and Process Automation in Information Systems: State-of-the-art and Future Directions (1996) [ PDF ]
L. Stein, S. Rozen, N. Goodman. "Managing laboratory workflow with LabBase." In Proceedings of the 1994 Conference on Computers in Medicine (CompMed94), World Scientific Publishing Company (1996) [ PDF ]
A. J. Bonner, A. Shrufi, S. Rozen. "Benchmarking object-oriented DBMSs for workflow management." OOPSLA'95 Workshop on Object Database Behavior, Benchmarks, and Performance. Austin, Texas. (1995) [ PDF ]
T. J. Hudson et al. "An STS-based map of the human genome." Science, 270:1945-954 (1995)
R. Reijo, T-Y Lee, P. Salo, R. Alagappan, L. G. Brown, M. Rosenberg, S. Rozen, T. Jaffe, D. Straus, O. Hovatta, A. de la Chapelle, S. Sibler, D. C. Page. "Diverse spermatogenic defects in humans caused by overlapping de novo Y deletions encompassing a novel RNA-binding protein gene." Nat. Genetics, 10:383-393 (1995) [ PDF ]
S. Rozen, L. Stein, N. Goodman. "LabBase: A database to manage laboratory data in a large-scale genome-mapping project." IEEE Engineering in Medicine and Biology, 14:702-709 (1995) [ PDF ]
N. Goodman, S. Rozen, L. Stein. "Requirements for a Deductive Query Language in the MapBase Genome-Mapping Database." In R. Ramakrishnan, ed. Applications of Logic Databases, Kluwer, 1994, pages 259-278 [ PDF ]
N. Goodman, S. Rozen, L. Stein. "Building a laboratory information system around a C++-based object-oriented DBMS." In Proceedings of the 20th International Conference on Very Large Data Bases (1994) [ PDF ]
S. Rozen, L. Stein, N. Goodman. "Constructing a domain-specific DBMS using a persistent object system." In Sixth International Workshop on Persistent Object Systems (1994) Acceptance ratio 27/56 [ PDF ]
L. Stein, A. Marquis, E. Dredge, M. P. Reeve, M. Daly, S. Rozen, N. Goodman. "Splicing UNIX into a genome mapping laboratory." In USENIX Summer 1994 Technical Conference, pages 221-229 (1994) [ PDF ]
S. Rozen. "Automating Physical Database Design: An Extensible Approach." Ph.D. thesis, Courant Institute of Mathematical Sciences, New York University (Mar 1993), 124 pages [ PDF ]
S. Rozen, D. Shasha. "A framework for automating physical database design." In Proceedings of the 17th International Conference on Very Large Data Bases, pages 401-411 (1991) Acceptance ratio 59/323 [ PDF ]
S. Rozen, D. Shasha. "Rationale and design of BULK." In Proceedings of the Third International Workshop on Database Programming Languages, pages 71-85 (1991) [ PDF ]
S. Rozen, D. Shasha. "Using a relational system on Wall Street: The good, the bad, the ugly, and the ideal." Communications of the ACM, 32:8 988-994 (1989) [ PDF ]
The Mammalian Y Chromosome Sequencing Consortium. "Sequencing and Annotating New Mammalian Y Chromosomes A White Paper Proposal, July 2006." A proposal to the National Human Genome Research Institute, National Institutes of Health [ PDF ]
S. Rozen, H. J. Skaletsky. "Primer3: A software component for picking PCR primers." 1996-present. Source code available at https://sourceforge.net/project/showfiles.php?group_id=112461; public WWW server at http://fokker.wi.mit.edu/primer3/input.htm
S. Rozen, L. Stein, N. Goodman. "LabBase User Manual." (1997) 21 pages [ PDF ]
S. Rozen, et al. "Workflow Adapter Module: Draft Specification." Technical report (1997)
N. Goodman, S. Rozen, L. Stein. "Database-and Workflow-Management Challenges Posed by the Human Genome Project." Technical Report (1995) 31 pages [ PDF ]
N. Goodman, S. Rozen. "A Freely Sharable Database Management System Designed for Use in Component-Based, Modular Genome Informatics Systems." From a proposal to the Department of Energy (1994) 22 pages [ PDF ]
S. Rozen, M. J. Daly, M.-P. Reeve, N. Goodman. "GENOME-MAP: Real-World Test Data and Queries for Logic Databases." Technical Report (1994) 7 pages [ PDF and data ]
S. Rozen, D. Shasha. "Automating physical database design: A general approach and its evaluation." (1993) 51 pages [ PDF ]
M. Karr, W. G. Morris, S. Rozen. "Global optimization for a coagulating code generator: Final technical report." Software Options, Inc., Technical Report (1991) 7 pages [ PDF ]
W. G. Morris, S. Rozen. "Interim report on E-L/CCG benchmarks." Technical Report SOI-01-90, Software Options, Inc. (1991) 40 pages [ PDF ]
Other Activities |
top publications printable CV (PDF) home |
Issue editor for Current Opinion in Genetics and Development, vol. 16, issue 16, "Genetics of disease, The sex chromosomes and human disease" with A. Ballabio and D. Nelson, 2006
Referee for
Study section reviewer for
GenomeCanada (2006)
National Cancer Institute/NIH, Metabolomics for Early Cancer Detection (2005)
Organized and taught yearly intensive course to train researchers in the basics of creating integrated software for genomics, genetics, and molecular biology: Bioinformatics: Writing Software for Genome Research, 1999, 2000, 2001, Cold Spring Harbor Laboratory, New York
Wrote and maintain the Primer3 program for PCR primer design (with H. Skaletsky) 1996-present
Metabolomics Society, member of Scientific Board, 2005-present
Last updated 2008-05-20 http://purl.com/STEVEROZEN/ rozen@wi.mit.edu