| |
|
January 2003 |
| People |
 |
David Hsu |
| Research |
|
Almost-Delaunay triangulation (Bandyopadhyay) |
| |
|
Surface compression (Isenburg) |
| Student
Profile |
|
Rachel Kolodny |
| |
|
February 2003 |
| Research |
|
The weighted volume derivative of a space filling
diagram (Edelsbrunner, Koehl) |
| Student
Profile |
|
Yusu Wang |
| |
|
March 2003 |
Publications |
|
Identifying structural motifs in proteins (Saha, Singh) |
|
|
Stochastic roadmap simulation: an efficient representation
and algorithm for analyzing molecular motion (Apaydin, Brutlag,
Guestrin, Zhu, Latombe, Varma) |
| |
|
Approximation of protein structure for fast similarity
measures (Lotan, Schwarzer) |
Student
Profile |
|
Andrew Leaver-Fay |
Workshop |
|
Photos from workshop on rigidity & proteins |
| |
|
April 2003 |
Announcements |
|
BioGeometry meeting at Stanford June 2003 |
| |
|
Year 3 annual report |
Student
Profile |
|
Loren Looger |
| |
|
May 2003 |
Meeting |
|
BioGeometry meeting at Stanford June 2003 - Schedule |
People |
|
Johannes Rudolph |
| |
|
Patrice Koehl |
Research |
|
Local squaring functions for multi-atom templates
(Carter, Roach) |
Student Profile |
|
Serkan Apaydin |
| |
|
June 2003 |
Meeting |
|
BioGeometry meeting at Stanford June 2003 - Summary |
Student Summer Projects |
|
Shantanu Sharma, Matt Mian, Andrew Ban, Serkan Apaydin, Itay Lotan, Tammy Bailey, Ben Wong, Ibrahima Mbaye, Kevin Wedderburn, Sewyalew Taddele |
Student
Profile |
|
Andrew Ban |
| |
|
July 2003 |
People |
|
Alex Tropsha |
Research |
|
Four-body statistical potentials (Tropsha, Krishnamoorthy) |
Student
Profile |
|
Andrea Mantler |
| |
|
August 2003 |
Education |
|
SB 228: Computational Structural Biology (Winter 2001; Levitt;
Stanford) |
| |
|
CPS 296: BioGeometric Modeling (Fall 2002; Edelsbrunner; Duke) |
| |
|
COMP 006: Folding: From Paper to Proteins (Fall 2002; Snoeyink;
UNC) |
| |
|
CPS 260: Algorithms in Computational Biology (Fall 2003; Agarwal;
Duke) |
| |
|
COMP 290-079: Applied Optimization in Computational Biology (Fall
2003; Snoeyink; UNC) |
Software |
|
Efficient Monte Carlo simulation of proteins |
| |
|
Stochastic roadmap simulation |
Student
Summer Projects |
|
Shantanu Sharma, Matt Mian |
| |
|
September 2003 |
People |
|
Robert Gdanitz |
Research |
|
Flexible spanners for tracking proximity in folding molecules
(Gao, Guibas, Nguyen) |
Student
Summer Projects |
|
Kevin Wedderburn, Sewyalew Taddele, Ibrahima Mbaye |
| |
|
October 2003 |
| Research |
|
Backbone motion by inverse kinematics for protein design (Leaver-Fay,
Snoeyink) |
| Announcement |
|
BioGeometry meeting at Duke November 2003 |
| Student Profile |
|
Bala Krishnamoorthy |
| |
|
November 2003 |
Meeting |
|
BioGeometry meeting at Duke - November 2003 - Summary |
| |
|
December 2003 |
Research |
|
Protein structural alignment via tetrahedral decomposition (Sharma,
Carter, Roach) |
Student Profile |
|
Itay Lotan |
| |
|
January 2004 |
Research News |
|
Predicting molecular crystal structures (Gdanitz) |
Education |
|
CPS 296.2: Shape Analysis (Spring, 2004; Agawal; Duke) |
| |
|
MEDC 276: Macromolecular Modeling (Annually, Spring; Tropsha;
UNC) |
Student Profile |
|
Vijay Natarajan |
| |
|
February 2004 |
Research |
|
Simplified model for conformational flexibility in small molecule
docking (Headd, Rudolph) |
Research News |
|
Computing high-stringency COGs using Turan graphs (Snoeyink) |
| |
|
March 2004 |
Research |
|
Computing protein structures from electron density maps: the missing
loop problem (Lotan, van den Bedem, Deacon, Latombe) |
Student Profile |
|
Jeff Phillips |
| |
|
April 2004 |
Software |
|
Ciel (Ban) |
| Announcement |
|
BioGeometry meeting at SOCG in Brooklyn June 2004 |
| |
|
May 2004 |
Research |
|
Rigid protein-protein docking (Agarwal, Choi, Edelsbrunner, Rudolph,
Wang) |
Meeting |
|
BioGeometry Meeting at Polytech Univ Brooklyn June 2004 - Schedule |
| |
|
June 2004 |
Meeting |
|
BioGeometry meeting at SoCG in Brooklyn June 2004 - Summary |
Postdoc Profiles |
|
Vicky Choi, Alper Ungor, David Cohen-Steiner |
| |
|
July 2004 |
Student Summer Projects |
|
Albert Chadwick, Martin Jones, Alex Steingart, Hiliary Johnson |
Student Profile |
|
Luke Huan |
| |
|
August 2004 |
Education |
|
CS 273 : Algorithms for Structure and Motion in Biology (Spring 2004; Batzoglou, Guibas, Latombe; Stanford) |
Student Summer Projects |
|
Daniel Evans, Andrew Leaver-Fay, Yuanxin (Leo) Liu, Andrea Mantler, Deepak Bandyopadhyay |
PhD Graduates |
|
Hamish Carr, Rachel Kolodny, Bala Krishnamoorthy, Nabil Mustafa, Vijay Natarajan, Yusu Wang |
| |
|
September 2004 |
Research |
|
Symmetry in protein interfaces (Bailey, Edelsbrunner) |
Meetings |
|
BioGeometry session at PSB '05 - Announcement |
| |
|
PI meeting at PSB '05 - Announcement |
PhD Graduates |
|
Serkan Apaydin, Itay Lotan |
| |
|
October 2004 |
Research |
|
Mining spatial motifs in SCOP families (Huan, Bandyopadhyay) |
People |
|
Homme Helliga |
| |
|
Brian Kuhlman |
Student Profile |
|
Daniel Russel |
| |
|
November 2004 |
Meetings |
|
BioGeometry session and meeting at PSB 2005 in Hawaii January 2005 |
Student Profile |
|
Jeff Headd |
| |
|
December 2004 |
Research |
|
Faster multiple dequence alignment algorithms based on pairwise segmentation (Agarwal, Bilu, Kolodny) |
Student Profile |
|
Xueyi Wang |
| |
|
January 2005 |
Educat'l Outreach |
|
Class at West Caldwell High School |
Student Profile |
|
Dmitriy Morozov |
| |
|
February 2005 |
Research |
|
Persistence algorithm take cubic time in worst case (Morozov) |
|
|
Non-pairwise decomposable solvation models for dynamic programming (Leaver-Fay) |
| |
|
March 2005 |
| |
|
No issue this month |
| |
|
April 2005 |
Research |
|
MAPS: Protein docking interfaces (Ban, Brown, Edelsbrunner, Headd, Rudolph) |
| |
|
May 2005 |
People |
|
PI Awards: Fred Brooks, Herbert Edelsbrunner, Homme Hellinga |
People |
|
New Students: Nathan Marz, Ankur Dhanik |
Student Profile |
|
Madhuwanti Vaidya |
| |
|
June 2005 |
Software |
|
Almost-Delaunay tetrahedra - AlmDel (Bandyopadhyay) |
Research News |
|
New awards (Latombe, Snoeyink, Hellinga) |
Announcement |
|
BioGeometry meeting at NCA&T in August 2005 |
| |
|
July 2005 |
Software |
|
Coresets for shape fitting and kinetic data structures (Agarwal, Yu) |
Meeting |
|
BioGeometry meeting at NCA&T in August 2005: introduction to NCA&T |
| |
|
August 2005 |
Meeting |
|
BioGeometry meeting at NCA&T: report, schedule, photos |
|
