About the newsletter
    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