Ravi Sachidanandam
Computer Scientist
Ph.D., University of Pennsylvania, 1994
(Condensed Matter Physics)
Sequence analysis, RNAi, splicing, phylogeny, simulations, modelling, genetic
networks
email sachidan@cshl.edu, phone (516) 367-8864
There has been a "paradigm shift" in biological research, caused by the sequencing
of the genomes of several organisms and a corresponding acceleration of the
pace of discovery. This turn of events has provided people with training in
physical sciences, like myself, an opportunity to explore the challenges posed
by the deluge of data, and to devise novel solutions to these challenges.
One of our interests is the analysis of genomics data. We are developing algorithms
and software that will be useful in many genomics applications, including:
the rapid detection and mapping of features within genome sequences; the correlation
of large-scale genome organization with function and the analysis of microarray data.
Other interests include understanding miRNA and siRNA targetting, splicing
and factors determining splicing efficiency, phylogeny,
simulation and modelling of cellular processes and behavior of
genetic networks.
This work depends on close collaborations with bench scientists at Cold Spring Harbor Laboratory and elsewhere, both to identify interesting problems and to test ideas.
Please visit Ravi's home page. |
Selected Publications
A resource for large-scale RNA-interference-based screens in mammals
Abstract
Patrick J. Paddison, Jose M. Silva, Douglas S. Conklin, Mike Schlabach, Mamie
Li, Shola Aruleba, Vivekanand Balija, Andy O'Shaughnessy, Lidia Gnoj, Kim
Scobie, Kenneth Chang, Thomas Westbrook, Michele Cleary, Ravi Sachidanandam,
W. Richard McCombie, Stephen J. Elledge and Gregory J. Hannon
Nature. 2004 Mar 25;428(6981):427-31
From Silencing to Gene Expression: Real-Time Analysis in Single Cells
Abstract
Susan M. Janicki, Toshiro Tsukamoto, Simone E. Salghetti, William P. Tansey,
Ravi Sachidanandam, Kannanganattu V. Prasanth, Thomas Ried, Yaron Shav-Tal,
Edouard Bertrand, Robert H. Singer, and David L. Spector
Cell, Vol. 116, 683-698, March 5, 2004
Free energy lights the path toward more effective RNAi.
Abstract
Silva JM, Sachidanandam R, Hannon GJ.
Nature Genetics 2003 Dec;35(4):303-5
Intrinsic differences between authentic and cryptic 5' splice sites
Abstract
Roca X, Sachidanandam R, Krainer AR.
Nucleic Acids Res. 2003 Nov 1;31(21):6321-33.
A 3.9-Centimorgan-Resolution Human Single-Nucleotide Polymorphism Linkage Map
and Screening Set
Abstract
Tara C. Matise, Ravi Sachidanandam, Andrew G. Clark, Leonid Kruglyak, Ellen
Wijsman, Jerzy Kakol, Steven Buyske, Buena Chui, Patrick Cohen, Claudia de
Toma, Margaret Ehm, Stephen Glanowski, Chunsheng He, Jeremy Heil, Kyriacos
Markianos, Ivy McMullen, Margaret A. Pericak-Vance, Arkadiy Silbergleit, Lincoln
Stein, Michael Wagner, Alexander F. Wilson, Jeffrey D. Winick, Emily S. Winn-Deen,
Carl T. Yamashiro, Howard M. Cann, Eric Lai, and Arthur L. Holden
Am J Hum Genet. 2003 Aug;73(2):271-84. Epub 2003 Jul03
Chromosome-wide distribution of haplotype blocks and the role of recombination
hotspots
Abstract
Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Donaldson M, Studebaker
J, Ankener WM, Alfisi SV, Camisa A, Kuo F, Faith JJ, Pazorov V, Bhatti HA,
Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler
JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Scott KE, Varde SA, Broxholme
J, Abecasis GR, Boyce-Jacino M and Cardon LR.
Nat Genet. 2003 Mar;33(3):382-7. Epub 2003 Feb 18.
Classification of VH1-like Dual Specificity Phosphatases.
Abstract--to be added
Chen H, Faith JJ, Sachidanandam R, Tonks NK.
(manuscript in prep)
Lightweight Genome Viewer.
Abstract
Faith JJ and Sachidanandam R.
lwgv at Source forge
Genomics: more than the sum of the parts.
Abstract
Rabinowicz PD, Sachidanandam R.
Genome Res. 2002 Jul;12(7):1015-6.
Comparative genomics between rice and Arabidopsis shows scant collinearity
in gene order.
Abstract
Liu H, Sachidanandam R, Stein L.
Genome Res. 2001 Dec 11(12):2020-6
A map of human genome sequence variation containing 1.42 million single nucleotide
polymorphisms.
Abstract
Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry
S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice
CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook
L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman
B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin
J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D.
Nature. 2001 Feb 15, 409(6822):928-33
A high-resolution radiation hybrid map of the human genome draft sequence.
Abstract
Olivier M, Aggarwal A, Allen J, Almendras AA, Bajorek ES, Beasley EM, Brady
SD, Bushard JM, Bustos VI, Chu A, Chung TR, De Witte A, Denys ME, Dominguez
R, Fang NY, Foster BD, Freudenberg RW, Hadley D, Hamilton LR, Jeffrey TJ, Kelly
L, Lazzeroni L, Levy MR, Lewis SC, Liu X, Lopez FJ, Louie B, Marquis JP, Martinez
RA, Matsuura MK, Misherghi NS, Norton JA, Olshen A, Perkins SM, Perou AJ, Piercy
C, Piercy M, Qin F, Reif T, Sheppard K, Shokoohi V, Smick GA, Sun WL, Stewart
EA, Fernando J, Tejeda, Tran NM, Trejo T, Vo NT, Yan SC, Zierten DL, Zhao S,
Sachidanandam R, Trask BJ, Myers RM, Cox DR.
Science. 2001 Feb 16, 291 (5507):1298-302
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