CIS 4930 / CIS 6930: Recent Advances in Bioinformatics

Reading List

Group A
  1. Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan: SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. ISMB/ECCB (Supplement of Bioinformatics) 2007: 359-366
  2. Jayesh Pandey, Mehmet Koyutürk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam, Ananth Grama: Functional annotation of regulatory pathways. ISMB/ECCB (Supplement of Bioinformatics) 2007: 377-386
  3. Mustafa Kirac, Gultekin Özsoyoglu: Protein Function Prediction Based on Patterns in Biological Networks. RECOMB 2008: 197-213
  4. Allister Bernard, David S. Vaughn, Alexander J. Hartemink: Reconstructing the Topology of Protein Complexes. RECOMB 2007: 32-46
  5. Eilon Sharon, Eran Segal: A Feature-Based Approach to Modeling Protein-DNA Interactions. RECOMB 2007: 77-91
  6. Joshua A. Grochow, Manolis Kellis: Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking. RECOMB 2007: 92-106
  7. Hiroyuki Kuwahara, Chris J. Myers: Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. RECOMB 2007: 166-180
  8. Marcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Müller: Identifying functional modules in protein-protein interaction networks: an integrated exact approach. ISMB 2008: 223-231
  9. Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph: Protein complex identification by supervised graph local clustering. ISMB 2008: 250-268
  10. Olivia Sanchez-Graillet, Massimo Poesio: Negation of protein-protein interactions: analysis and extraction. ISMB/ECCB (Supplement of Bioinformatics) 2007: 424-432
  11. Markus W. Covert, Nan Xiao, Tiffany J. Chen and Jonathan R. Karr: Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli, Bioinformatics 2008 24(18):2044-2050
Group B
  1. Xiaoyu Chen, Timothy R. Hughes, Quaid Morris: RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. ISMB/ECCB (Supplement of Bioinformatics) 2007: 72-79
  2. Tien-ho Lin, Naftali Kaminski, Ziv Bar-Joseph: Alignment and classification of time series gene expression in clinical studies. ISMB 2008: 147-155
  3. Yue Lu, Sing-Hoi Sze: Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences. RECOMB 2007: 283-295
  4. Bin Ma, Xiaoming Sun: More Efficient Algorithms for Closest String and Substring Problems. RECOMB 2008: 396-409
  5. Maxim Kalaev, Vineet Bafna, Roded Sharan: Fast and Accurate Alignment of Multiple Protein Networks. RECOMB 2008: 246-256
  6. Janina Reeder, Jens Reeder, Robert Giegerich: Locomotif: from graphical motif description to RNA motif search. ISMB/ECCB (Supplement of Bioinformatics) 2007: 392-400
  7. Yanay Ofran, Venkatesh Mysore, Burkhard Rost: Prediction of DNA-binding residues from sequence. ISMB/ECCB (Supplement of Bioinformatics) 2007: 347-353
Group C
  1. Sohrab P. Shah, Wan L. Lam, Raymond T. Ng, Kevin P. Murphy: Modeling recurrent DNA copy number alterations in array CGH data. ISMB/ECCB (Supplement of Bioinformatics) 2007: 450-458
  2. Travis J. Wheeler, John D. Kececioglu: Multiple alignment by aligning alignments. ISMB/ECCB (Supplement of Bioinformatics) 2007: 559-568
  3. Yiqun Cao, Tao Jiang, Thomas Girke: A maximum common substructure-based algorithm for searching and predicting drug-like compounds. ISMB 2008: 366-374
  4. Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial: Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. ISMB 2008: 41-49
  5. Yoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge, Wataru Honda, Minoru Kanehisa: Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. ISMB 2008: 232-240
  6. Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye: Computation of Median Gene Clusters. RECOMB 2008: 331-345
  7. Yanxin Shi, Fan Guo, Wei Wu, Eric P. Xing: GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH Data. RECOMB 2007: 151-165
  8. Yuval Inbar, Dina Schneidman-Duhovny, Oranit Dror, Ruth Nussinov, Haim J. Wolfson: Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules. RECOMB 2007: 412-429
  9. Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev: Automatic genome-wide reconstruction of phylogenetic gene trees. ISMB/ECCB (Supplement of Bioinformatics) 2007: 549-558

Tamer Kahveci
Last modified: Wed Mar 4 14:54:47 EST 2009