Rozen, Steve

Research Interests:

Our laboratory works in the areas of genome-scale biology, bioinformatics, and human genetics. We apply advanced computational and quantitative analysis to genome-scale data in pursuit of the most
interesting and important biological questions.

Our laboratory works in the areas of genome-scale biology, bioinformatics, and human genetics. We apply advanced computational and quantitative analysis to genome-scale data in pursuit of the most
interesting and important biological questions.

In genome-scale-biology and bioinformatics, we develop approaches for analyzing and interpreting high-dimensional, genome-scale data sets, such as those generated by gene-expression arrays and metabolic profiling. Technologies for generating genome-scale data are improving exponentially and are increasingly central in biological research. Our goal is to use genome-scale data to gain new insights into biological processes in health and in disease.

Selected Publications:

S. Rozen. "Defending Male Fertility" (Perspective). Sci. Transl. Med. 3:92ps31 (2011)

X. Han, S. Rozen, S. H. Boyle, C. Hellegers, H. Cheng, J. R. Burke, K. A. Welsh-Bohmer, P. M. Doraiswamy, R. Kaddurah-Daouk. "Metabolomics in early Alzheimer's disease: identification of altered plasma sphingolipidome using shotgun lipidomics." PLoS One. 6: e21643 (2011) [ PDF ] IF 4.3

L. Goh, G. B. Chen, I. Cutcutache, B. Low, B. T. Teh, S. Rozen, P. Tan. "Assessing matched normal and tumor pairs in next-generation sequencing studies." PLoS One. 6:e17810 (2011) [ PDF ] IF 4.3

I. B. Tan, I. Cutcutache, Z. J. Zang, J. Iqbal, S. F. Yap, W. Hwang, W.-T. Lim, B. T. Teh, S. Rozen, E.-H. Tan, and P. Tan "Fanconi's anemia in adulthood: Chemoradiation-induced bone marrow failure and a novel FANCA mutation identified by targeted deep sequencing." J. Clin. Oncol. Epub e591-e594 (2011) IF 17.8

Z. J. Zang, C. K. Ong, I. Cutcutache, W. Yu, S. L. Zhang, D. Huang, L. D. Ler, K. Dykema, A. Gan, J. Tao, S. Lim , Y. Liu, P. A. Futreal, H. Grabsch, K. A. Furge, L. K. Goh, S. Rozen*, B. T. Teh*, P. Tan*. "Genetic and structural variation in the gastric cancer kinome revealed through targeted deep sequencing." Cancer Res. 71:29-39 (2011) (* = corresponding author) IF 7.5

R. Kaddurah-Daouk, S. Rozen, W. Matson, X. Han, C. M. Hulette, J. R. Burke, P. M. Doraiswamy, K. A. Welsh-Bohmer. "Metabolomic changes in autopsy-confirmed Alzheimer's disease." Alzheimers Dement. 7:309-317 (2011) IF 4.6

D. Bellott , H.Skaletsky , T. Pyntikova , E. Mardis , T. A. Graves , C. Kremitzki , L. Brown , S. Rozen, W. C. Warren , R. K. Wilson, D. C. Page. "Convergent Evolution of Chicken Z and Human X Chromosomes by Expansion and Gene Acquisition." Nature 466:612-616 (2010) IF 31.4

J. F. Hughes, H. Skaletsky, T. Pyntikova, T. A. Graves, P. J. Minx, R. S. Fulton, S. D. McGrath, W. C. Warren, D. P. Locke, E. R. Mardis, S. K. M. van Daalen, S. Repping, C. Friedman, B. J. Trask, S. Rozen, R. K. Wilson, David C. Page. "Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content." Nature. 463:536-539 (2010) [ Sup. info ] IF 31.4

S. Rozen, J. D. Marszalek, R. K. Alagappan, H. Skaletsky, D. C. Page. "Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection." Am. J. Hum. Genet. 85:923-928 (2009) [ PDF ] [ Sup. info ] IF 10.2

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

P. Mannelli, A. Patkar, S.Rozen, W. Matson, R. Krishnan, R. Kaddurah-Daouk. "Opioid use affects antioxidant activity and purine metabolism: preliminary results." Hum. Psychopharmacol. 24:666-675 (2009) [ PDF ]

A. A. Patkar, S. Rozen, P. Mannelli, W. Matson, C. Pae, K. R. Krishnan, R. Kaddurah-Daouk. "Alterations in tryptophan and purine metabolism in cocaine addiction: A metabolomic study." Psychopharmacology (Berl)., 206:479-489 (2009) [ PDF ] IF 3.7

L. Visser, G. H. Westerveld, C. M. Korver, S. K. M. van Daalen, S. E. Hovingh, S. Rozen, F. van der Veen, S. Repping. "Y chromosome gr/gr deletions are a risk factor for low semen quality." Hum. Reprod. 24:2667-2673 (2009) [ PDF ] IF 3.8

J. K. Yao, G. G. Dougherty Jr, R. D. Reddy, M. S. Keshavan, D. M. Montrose, W. R. Matson, S. Rozen, R. R. Krishnan, J. McEvoy, R. Kaddurah-Daouk. "Altered interactions of tryptophan metabolites in first-episode neuroleptic-naive patients with schizophrenia." Mol. Psychiatry, Epub ahead of print, doi: 10.1038/mp.2009.33 (2009) [ DOI ] IF 12.5

J. F. Hughes, H. Skaletsky, S. Rozen, R. K. Wilson, D. C. Page "Has the chimpanzee Y chromosome been sequenced?" Nature Genetics, 38(8):853-854 (2006)

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." Nature Genetics, 38(4):463-467 (2006)

A. Ballabio, D. Nelson, S. Rozen. "Genetics of disease, The sex chromosomes and human disease, Editorial overview" Current Opinion in Genetics & Development 16:1-4 (2006)

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)

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)

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?" American Journal of Human Genetics 75(3):514-517 (2004)

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)

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." Nature Genetics, 35(3):247-251 (2003)

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)

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)

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". American Journal of Human Genetics 71(4):906-922 (2002)

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." Nature Genetics, 29(3):279-286 (2001)

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)

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 rabidopsis." Plant Physiology. 124(4):1483-1492 (2000)

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." Human Molecular Genetics 9(15):2291-2296 (2000)

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

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)

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." Nature Genetics, 14(3):292-299 (1996)

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

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)

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)

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." Nature Genetics, 10:383-393 (1995)

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)

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)

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

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

S. Rozen, D. Shasha. "Rationale and design of BULK." In Proceedings of the Third International Workshop on Database Programming Languages, pages 71-85 (1991)

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)