PMMB People

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The Program in Mathematics and Molecular Biology

PMMB People

PMMB Members

PMMB Member Addresses

PMMB National Fellows

PMMB Fellows in Member Labs

Members

Member	Department	Affiliation	Research Area	Email
Bonnie A. Berger	Mathematics	M.I.T.	Protein Folding	bab@theory.lcs.mit.edu
Partick O.Brown	Biochemistry	Stanford	Gene Function	pbrown@cmgm.stanford.edu
Nicholas R. Cozzarelli	Molecular Biology	Berkeley	DNA Structure	ncozzare@socrates.berkeley.edu
David S. Eisenberg	Chemistry	U.C.L.A.	Protein Determination	david@ewald.mbi.ucla.edu
Vaughan F. R. Jones	Mathematics	Berkeley	Knot Theory/DNA Structure	vfr@math.berkeley.edu
Louis H. Kauffman	Mathematics	U. of Illinois, Chicago	Knot Theory/RNA Structure	kauffman@tigger.cc.uic.edu
Eric S. Lander	Whitehead Institute	M.I.T.	Nucleotide Sequence Analysis	lander@genome.wi.edu
Michael Levitt (Co-Director)	Cellular Biology	Stanford	Protein Dynamics	levitt@cellbio.stanford.edu
Wilma Olson	Chemistry	Rutgers	DNA Topology	olson@rutchem.rutgers.edu
Terry Speed	Statistics	Berkeley	Genome Statistics	terry@stat.berkeley.edu
Sylvia J.Spengler (BWF Director)	Lawrence Berkeley Lab	Berkeley	DNA Array Structure	sylviaj@mh1.lbl.gov
De Witt Sumners (Co-Director, BWF Director)	Mathematics	Florida State	DNA Topology	sumners@math.fsu.edu
Elizabeth Thompson	Statistics	U. of Washington	Statistical Analysis	thompson@stat.washington.edu
Ignacio Tinoco, Jr.	Chemistry	Berkeley	RNA Structure	intinoco@lbl.gov
James C. Wang	Molecular Biology	Harvard	DNA Structure	jcwang@husc.harvard.edu
Michael S. Waterman	Mathematics	U. of So. California	Statistical Analysis	msw@hto.usc.edu
James H. White	Mathematics	U.C.L.A.	DNA Geometry	jhw@math.ucla.edu

PMMB National Fellows

Current

Fellow	Institution	Mentor	Research Area	E-mail
*Ben-Dor, Amir (Post-doctoral)	University of Washington	Prof. Richard Karp	Radiation Hybrid Mapping of the Human Genome	amirbd@csd.cs.technion.ac.il
*Buck, Dorothy (Graduate Student)	University of Texas, Austin	Prof. Makkuni Jayaram	The Topological Aspects of Rearrangement Reactions Involving DNA	dbuck@math.utexas.edu
*Helms, Volkhard (Post-doctoral)	UC, San Diego	Prof. J.A. McCammon	Intramolecular and Supramolecular Protein Motion from Stochastic Dynamics Stimulation	vhelms@chemcca10.ucsd.edu
**Kostov, Konstantin (Post-doctoral)	University of Chicago	Prof. R. Stephen Berry	Statistical Analysis of the Topography and Dynamics of the Potential Energy Surfaces of Proteins and Their Relation to Protein Folding .	kostov@rainbow.uchicago.edu
**Liu, Canwen (Post-doctoral)	Harvard University	Prof. Daniel Jay	Mathematical Modeling of Axon Guidance in Haptotaxis	liu16@husc.harvard.edu
*Ma, Jianpeng (Post-doctoral)	Harvard University	Prof. Martin Karplus	Novel Mathematical Methods for Computing Reaction Paths of the Large Scale Conformational Changes in Protein	jma@tammy.harvard.edu
**McCarthy, Janice (Graduate Student)	Duke University	Prof. Homme Hellinga	Novel Algorithms for Biomolecular Design	janice@acpub.duke.edu
**Richards, Robyn (Graduate Student)	University of Nebraska, Lincoln	Prof. Lawrence J. Parkhurst	Time Dependent Laser Fluorescence Studies of DNA Transcription	rmr@unlgrad1.unl.edu
**Smith, Doug (Graduate Student)	Stanford University	Prof. Steven Chu	Physical Studies of DNA Using Fluorescence Microscopy and Optical Tweezers	des@leland.stanford.edu
*Swigon, David (Graduate Student)	Rutgers University	Prof. Bernard D. Coleman	Theory of the Dependence on Linking Number of the Tertiary Structure of DNA Minicircles with Self-Contact	swigon@jobe.rutgers.edu
**Walker, Wynn (Post-doctoral)	UCLA	Prof.Richard E. Dickerson	Development of Mathematical/Computer Algorithms for the Design of DNA Minor Groove Sequence Reading Molecules	wwalker@biomath.medsch.ucla.edu

* Fellows supported by Burroughs Wellcome Fund
** Fellows supported by National Science Foundation

Past

Fellow	Date of tenure	Mentor and Institution	Research Area	E-mail
Darcy, Isabel	10/01/95-9/30/97	Prof. De Witt Sumners Florida State University	Computation of Strand Passage Metric and Application to Topoisomerase Experiments	darcy@fireant.ma.utexa s.edu
Doerge, Rebecca	8/01/90-12/31/92	Prof. Burce Weir North Carolina State University	Statistical Methods for Locating Quantitive Trait Loci With Molecular Markers
Kang, Hunseung	7/1/95-12/31/96	Prof.Ignacio Tinoco, Jr. University of California at Berkeley	Structure of RNA Pseudoknots in Ribosomal Frameshifting in Mouse Mammary Tumors
Kececioglu, John	11/01/91-10/31/93	Prof. Dan Gusfield University of California, Davis	Algorithms for Assembling Ordered Clone Libraries and Multiple Sequence
Lundstrom, Ron	11/01/90-10/31/92	Prof. Ryk Ward University of Utah	Mathematical Models for Population Surveys of DNA Sequences
Mogilner,Alexander	9/01/95-8/31/96	Prof. George Oster University of California at Berkeley	DNA Motors and Protein Mechanics
Naor, Dalit	11/01/91-10/31/93	Prof. Douglas L. Brutlag Stanford University Medical Center	Combinatorial and Parametric Algorithms for Analyzing Biological Sequences
Nguyen, Trang	9/01/90-8/31/91	Prof. Terrence Speed University of California at Berkeley	Statistical Models and Methods in Molecular Evolution
Olmsted-West, Martha	7/01/92-6/30/94	Prof.Paul Hagerman University of Colorado Health Sciences Center	Distribution of Counterions Around Finite Nucleic Acis Structures
Qian, Hong	9/01/92-8/31/94	Prof. John Hopfield California Institute of Technology	Cooperativity in Neural Networks and Protein Folding Prediction
Ratnanather, Tilak	10/01/94-9/30/96	Prof. Aleksander Popel Johns Hopkins University	The Biophysics of the Substrate Cisternae of the Cochlear Outer Hair Cell
Regan, Jeffrey	9/01/94-8/31/96	Prof. José Onuchic UC San Diego	Further Development of the Theory of Electron Tunneling in Proteins With A Specific Study of the Structure Function Relationship in Azurin, Myoglobin, Cyochrome c and Other Proteins
Warren, Gregory	9/01/95-8/31/97	Prof. Axel Brünger Yale	The Development and Testing of NMR Structure Assessment Techniques
Wukovitz, Stephanie	9/01/95-8/21/97	Prof. Todd Yeates UCLA	An Explanation for the Macromolecular Space Group Frequency Phenomenon
Yooseph, Shibu	9/01/95-8/31/97	Prof. Tandy Warnow University of Pennsylvania	Studying the Notion of Information Extraction from a Set of Evolutionary Trees on a Given Species Set
Zhou, Yaoqi	9/01/95-8/31/96	Prof. Martin Karplus Harvard University	The Molecular Mechanisms of Solute Effects on Protein Stability

PMMB Fellows in Member Labs

Current

Member Laboratory and Institution	Student Name	Support Title	Support Year(s)
Bonnie A. Berger M.I.T.	Tony Eng Lior Patcher	Graduate Student Graduate Student	1997-1998 1997-1998
Nicholas R.Cozzarelli Berkeley	Alexander Alexandrov	Graduate Student	1997-1998
Michael Levitt Stanford	Ram Samudrala	Post-doctoral Student	1997-1998
Wilma Olson Rutgers	Vsevolod Katritch	Post-doctoral Student	1997-1998
Terry Speed Berkeley	Sandrine Dudoit Ru-Fang Yeh	Graduate Student Graduate Student	1997-1998 1997-1998
De Witt Sumners Florida State	Javier Arsuaga Mariel Vazquez	Graduate Student Graduate Student	1997-1998 1997-1998
Elizabeth Thompson U. of Washington	Sharon Browning Beatrix Jones	Graduate Student Graduate Student	1997-1998 1997-1998
Ignacio Tinoco, Jr. Berkeley	Ming Wu	Post-doctoral Student	1997-1998
James H. White U.C.L.A.	Boris Fayn Kai Hu	Post-doctoral Student Graduate Student	1997 1997

Past

Member Laboratory and Institution	Student Name	Support Title	Support Year(s)	Email
Nicholas R.Cozzarelli Berkeley	Roland Kanaar Arkady Khadursky Steve Levene Valentine Rybenkov	Post-doctoral Student Graduate Student Post-doctoral Student Post-doctoral Student	1988-1989 1990-1993/1993-1996 1990-1991 1994-1995
David S.Eisenberg U.C.L.A.	David Bowie Daniel Fischer Danny Rice	Graduate Student Post-doctoral Student Graduate Student	1991-1993 1994-1996 1993-1995
Vaughan F. R.Jones Berkeley	James Deng Hong Liang Said Rida Steve Sawin	Gaduate Student Graduate Student Graduate Student Graduate Student	1990-1991 1990-1991 1990-1991 1990-1991
Eric S. Lander M.I.T.	Tau-Mu Yi	Graduate Student	1990-1992
Michael Levitt Stanford	Miriam Hirschberg Chris Lee Britt Park Mark Gerstein Enoch Huang Jerry Tsai	Graduate Student Graduate Student Gaduate Student Post-doctoral Student Graduate Student Graduate Student	1989-1993 1991-1992 1991-1993/1994-1996 1995-1996 1994-1995 1993-1994
Wilma Olson Rutgers	Ksenija Mihanic Konstantine Kosikov	Graduate Student Graduate Student	1994-1995 1995-1996
De Witt Sumners Florida State	Yuanan Diao Claus Ernst Adam Lucas Isabel Darcy	Post-doctoral Student Post-doctoral Student Graduate Student Graduate Student	1989-1993 1989-1993 1992-1993 1993-1994
Elizabeth Thompson U. of Washington	Simon Heath	Post-doctoral Student	1995-1997
Ignacio Tinoco, Jr. Berkeley	Jennifer Hines Ling Shen Hunseung Kang	Graduate Student Graduate Student Post-doctoral Student	1992-1993 1992-1993 1994-1995
James C. Wang Harvard	Paul Caron Jacqueline Drak Stanley Shaw Thomas Wu Benjamin Tu	Post-doctoral Student Graduate Student Graduate Student Undergraduate Undergraduate	1991-1993 1990-1991 1990-1991 summer 1997 summer 1997
Michael S.Waterman U. of Southern California	Gary Churchill Arndt von Haeseler Martin Vingron	Post-doctoral Student Post-doctoral Student Graduate Student	1988-1990 1990-1991 1991-1993

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