Carnegie Mellon University

The Merck Computational Biology and Chemistry Program

"Bio-Chem Bits" Schedules

Summer 2003

Date Presenter Topic/Reference
June 10, 2003 Kuok Chiang Kim, Daniel Kleinbaum, Ruben Valas Descriptions of Research Goals
June 19, 2003 Ling Wang, Julia Conde-Adorno, Yenixsa Rivera Sierra Descriptions of Research Goals
June 26, 2003 Brian Frezza Description of Research Goals
June 26, 2003 Xiang Chen Nearest neighbour algorithm for predicting protein subcellular location by comining functional domain composition and pseudo-amino acid composition, Y.-D. Cai and K.-C. Chou , Biochem. Biophys. Res. Commun. 305: 407-411 (2003) [Download PDF Reprint]
July 3, 2003 Kuok Chiang Kim Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle, K. C. Chen, A.Csikasz-Nagy, B. Gyorffy, J. Val, B. Novak, and J.J. Tyson, Mol. Biol. Cell. 11: 369-391 (2000) [Download PDF Reprint]
July 3, 2003 Ruben Valas A Robust Method for Determining the Magnitude of the Fully Asymmetric Alignment Tensor of Oriented Macromolecules in the Absence of Structural Information, G. M. Clore, A. M. Gronenborn, and A. Bax, J. Magnetic Resonance 133: 216-221 (1998)
July 10, 2003 Daniel Kleinbaum Mining Protein Sequences for Motifs, G. Narasimhan, C. Bu, Y. Gao, X. Wang, N. Xu, and K. Mathee, J. Comp. Biol. 9: 707-720 (2002) [Download PDF Reprint]
July 10, 2003 Ling Wang Simple Networks for Spike-Timing Based Computation, with Application to Olfactory Processing, C. D. Brody and J. J. Hopfield, Neuron 37: 843-852 (2003) [Download PDF Reprint]
July 17, 2003 Julianna Conde Adorno An HMM model for coiled-coil domains and a comparison with PSSM-based predictions, M. Delorenzi and T. Speed, Bioinformatics 18: 617-625(2002) [Download PDF Reprint]
July 17, 2003 Yenixsa Rivera Sierra A heuristic managing errors for DNA sequencing, J. Blazewicz, P. Formanowicz, F. Guinand, and M. Kasprzak, Bioinformatics 18: 652-660 (2002) [Download PDF Reprint]
July 24, 2003 Brian Frezza Comparative Evaluation of 11 Scoring Functions for Molecular Docking, R. Wang, Y. Lu, and S. Wang, J. Med. Chem. 46: 2287-2303 (2003) [Download PDF Reprint]
July 24, 2003 Narayanan Raghupathy Recent Segmental Duplications in the Human Genome, J.A. Bailey, Z. Gu, R.A. Clark, K. Reinert, R.V. Samonte, S. Schwartz, M.D. Adams, E.W. Myers, P.W. Li, and E.E. Eichler, Science 297: 1003-1007 (2002) [Download PDF Reprint]

Spring 2003 Sessions

Date Presenter/Group Topic/Reference
February 18, 2003Kai Huang/Murphy groupFeature Reduction for Improved Recognition of Subcellular Location Patterns in Fluorescence Microscope Images
February 18, 2003Arun Krishaswamy/Minden groupQuantitative Image Analysis of Difference Gel Electrophoresis Gel Images
March 18, 2003Zhenzhen Kou/Murphy groupPanel Label Extraction from Online Biological Journal Articles
March 18, 2003Benjamin Janesko/Yaron groupLocal Methods for Including Electron Correlation in Large System
April 15, 2003Aimee Tomlinson/Yaron groupComputational optimization of the INDO/SCI excited-state algorithm for predicting the photophysics of large systems
April 15, 2003Radu Stefan Niculescu/Mitchell groupMachine Learning Approaches to fMRI data
May 6, 2003Angela Liu/Yaron groupEffects of Disorder on the Photophysics of Organic Semiconductors
May 6, 2003Swati Manjari/Kim groupContinuum Models of Solvation: The Ups and Downs in a Cavity

Summer 2002

Date Presenter Topic/Reference
June 17, 2002 Craig Gallek, Neil Halelamien, Richard Wang, Oliver Wojtyna Descriptions of Research Goals
June 20, 2002 Dr. David Yaron New Approaches to Semiempirical Quantum Chemistry
June 27, 2002 Craig Gallek "Visualization of Two-Body Electron Densities and Wave Functions of Magnetic Molecules", D. Yamaki, Y. Kitagawa, H. Nagao, M. Nakano, Y. Yoshioka, and K. Yamaguchi, International Journal of Quantum Chemistry 75:645-654 (1999) [Download PDF Reprint]
June 27, 2002 Neil Halelamien "What is a moment? Transient synchrony as a collective mechanism for spatiotemporal integration", J. J. Hopfield and C. D. Brady, Proc. Natl. Acad. Sci. U.S.A. 98:1282-1287 (2001) [Download PDF Reprint]
July 11, 2002 Richard Wang "Toward information extraction: Identifying protein names from biological papers", K. Fukuda, T. Tsunoda, A. Tamura, and T. Takagi, Proc. of the Pacific Symposium on Biocomputing '98 (PSB-98), pp707-718 (1998)
"Automatic Construction of Knowledge Base from Biological Papers"Y. Ohta, Y. Yamamoto, T. Okazaki, I. Uchiyama, and T. Takagi, Proc. of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB-97), pp218-225 (1997)
"Development of Information Extraction Tool: Toward Construction of Protein-Protein Interaction Database", T. Okazaki-Ohta, and T. Takagi, Proc. of the 9th Workshop on Genome Informatics, (1998)
July 11, 2002 Oliver Wojtyna "Molecular Feature Mining in HIV Data", S. Kramer, L. De Raedt, and C. Helma, Proceedings of the Seventh ACM SIGKDD International conference on Knowledge discovery and data mining, pp. 136-143 (2001)
July 18, 2002 Dr. Eric Ahrens In Vivo Magnetic Resonance Microscopy in Animal Models
July 25, 2002 CALD KDD Project Presentation: Matteo Matteucci Learning Rich Neural Network Topologies

Summer 2001

Date Presenter Topic Reference
June 7, 2001 Dr. Robert F. Murphy Phylogenetic Tree Construction "Timing the Ancestor of the HIV-1 Pandemic Strains" by B. Korber, M. Muldoon, J. Theiler, F. Gao, R. Gupta, A. Lapedes, B. H. Hahn, S. Wolinsky, and T. Bhattacharyz, Science 288:1789-1796 (2000) [Download PDF Reprint]
June 14, 2001 Jennifer Airone, Craig Gallek, Matthew Kofke Descriptions of Research Goals
June 21, 2001 Courtney Davis, Gregory Porreca Descriptions of Research Goals
June 28, 2001 Dr. Gordon Rule Computational aspects of rational HIV drug design
July 5, 2001 Jennifer Airone Pharmokinetic Modeling "Optimizing Drug Regimens in Cancer Chemotherapy by an Efficacy-Toxicity Mathematical Model" by A. Iliadis and D. Barbolosi, Computers in Biomedical Research 33:211-226 (2000)
July 5, 2001 Craig Gallek Ant Colony Optimization "Inspiration for optimization from social insect behaviour" by E. Bonabeau, M. Dorigo, and G. Theraulaz, Nature 406:39-42 (2000)
July 12, 2001 Matthew Kofke Structure similarity "PEPCAT - A new tool for conformational analysis of peptides" by M.F. O'Donohue, E. Miasian, S.J. Leach, A.W. Burgess, and H.R. Treutlein, Journal of Computational Chemistry 21:446-461 (2000)
July 19, 2001 Courtney Davis Molecular Computing "Molecular Computation of Solutions to Combinatorial Problems" by Leonard M. Adleman, Science 266:1021-1023
July 19, 2001 Gregory Porreca Protein structure prediction "Predicting protein-protein interactions from primary structure" by Joel R. Bock and David A. Gough, Bioinformatics 17:455-460 (2001)
July 26, 2001 Dr. David Yaron Semi-empirical Molecular Dynamics Simulations

Summer 2000

Date Presenter Topic Reference
June 8, 2000 Dr. Ramamoorthi Ravi Protein Database Searching using Hidden Markov Models "Hidden Markov Models in Computational Biology: Applications to Protein Modeling" by Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjölander and David Haussler, J. Mol. Biol. 235:1501-1531 (1994) [Download PDF Reprint from idealibrary.com]
June 15, 2000 Danny Lam, Jennifer Lin, Anushka Nethisinghe, Bjarni Halldórsson Descriptions of Research Goals
June 22, 2000 Dr. Ramamoorthi Ravi Hidden Markov Models
June 29, 2000 Jennifer Lin Gene Structure Prediction "Gene Structure Prediction by Spliced Alignment of Genomic DNA with Protein Sequences: Increased Accuracy by Differential Splice Site Scoring" by Jonathan Usuka and Volker Brendel, J. Mol. Biol. 297: 1075-1085 (2000)[Download PDF Reprint from idealibrary.com]
July 6, 2000 Anushka Nethisinghe Protein Structure Prediction "Neural networks for protein structure prediction: hype or hit?" by Burkhard Rost [View text from embl-heidelberg]
July 6, 2000 Bjarni Halldórsson Generalizing from a Tree "Weights for Data Related by a Tree" by Stephen F. Altschul, Raymond J. Carroll and David J. Lipman, J. Mol. Biol. 207, 647-653 (1989)
July 20, 2000 Danny Lam Importance of Hydrophobicity in Force Field Calculations for Ligand Docking "Hydrogen Bonding, Hydrophobic Interactions, and Failure of the Rigid Receptor Hypothesis" by Andrew M. Davis and Simon J. Teague, Angew. Chem. Int. Ed. 38, 736-749 (1999)
July 20, 2000 Adrienne Wells Modeling Tumor Escape "Self-organization and competition in the immune response to cancer invasion: a phase-orientated computational model of oncogenesis" by Sorinel Adrian Oprisan, Aurel Ardelean and Petre T. Frangopol, Bioinformatics 16, 96-100 (2000)
August 3, 2000 Dr. Raul Valdes-Perez Automated Elucidation of Chemical Pathways

"Proposed Methodological Improvement in the Elucidation of Chemical Reaction Mechanisms Based on Chemist-Computer Interaction" by A.V. Zeigarnik, R.E. Valdes-Perez, and B.S. White, Journal of Chemical Education 77, 214 (2000) [View text]

"How Hard is Mechanism Elucidation in Catalysis? Combinatorial Analysis of C1 Chemistry" by R.E. Valdes-Perez and A.V. Zeigarnik, Journal of Chemical Information and Computer Sciences 40, 833-838 (2000) [View text]

Summer 1999

Date Presenter Topic Reference(s) Summary Links
May 27, 1999 Dr. Robert Murphy Sequence alignment by dynamic programming "A general method applicable to the search for similarities in the amino acid sequence of two proteins" by Saul B. Needleman and Christian D. Wunsch, J. Mol. Biol. 48:443-453 (1970) Summary
June 3, 1999 Dr. Frederick Lanni Image restoration by deconvolution "Visualization of single RNA transcripts in situ" by Andrea M. Femino, Frederic S. Fay, Kevin Fogarty, and Robert H. Singer, Science 280:585-590 (1998)
"Diffraction and Resolving Power" by J. L. Harris, J. Opt. Soc. Am. 54:931-936 (1964)
June 10, 1999 Dr. Mark Craven Models of transcription regulation "Modeling regulatory networks with weight matrices" by D. C. Weaver, C. T. Workman, and G.D. Stormo, Pacific Symposium on Biocomputing 4:112-123 (1999) Summary
July 1, 1999 Ryle Goodrich Predicting subcellular locations of protein from sequence "Protein subcellular location prediction" by Kuo-Chen Chou and David W. Elrod, Protein Engineering 12:107-118 (1999) MEDLINE abstract
July 8, 1999 Chris Mason Optimal pairwise alignment of protein structures "Protein structure comparison by alignment of distance matrices" by Liisa Holm and Chris Sander, J. Mol. Biol. 233:123-138 MEDLINE abstract
July 8, 1999 Matt Vieta Tracking objects in image sequences "Frequency-domain motion estimation using a complex lapped transform" by Robert W. Young and Nick G. Kingsbury, IEEE Trans. Image Process. 2:2-16
July 15, 1999 Kiarri Kershaw Automated annotation of protein function "Automatic extraction of keywords from scientific text: application to the knowlege domain of protein families" by Miguel A. Andrade and Alfonso Valencia, Bioinformatics 14:600-607 MEDLINE abstract
July 15, 1999 Dan Vogel Ab initio molecular energy prediction "Gaussian-1 theory: A general procedure for prediction of molecular energies" by John A. Pople, Martin Head-Gordon, Douglas J. Fox, Krishnan Raghavachari, and Larry A. Curtiss, J. Chem. Phys. 90:5622-5629
July 22, 1999 Dr. Gordon Rule Structure refinement "Molecular dynamics: Applications to proteins" by M. Karplus, A.T. Brünger, R. Elber, and J. Kuriyan, Cold Spring Harbor Symp. Quant. Biol. 52:381-390
"Crystallographic refinement by simulated annealing: Application to a 2.8 Å resolution structure of aspartate aminotransferase" by Axel T. Brünger, J. Mol. Biol. 203:803-816 		MEDLINE abstract


MEDLINE abstract