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Journal Club

In our weekly group meetings we discuss recent papers in our area. Below is the list of papers we have discussed so far.




3/18/2014 Andrei Considering Unknown Unknowns - Reconstruction of Non-confoundable Causal Relations in Biological Networks
Mohammad Javad Sadeh, Giusi Moffa, Rainer Spang
RECOMB, 2013
2/18/2014 Mahmudul TALE: A Tool for Approximate Large Graph Matching
Yuanyuan Tian, Jignesh M. Pate
ICDE, 2008
2/4/2014 Haitham An optimal algorithm for building the majority rule consensus tree
Jesper Jansson, Chuanqi Shen, and Wing-Kin Sung
Research in Computational Molecular Biology*. Springer Berlin Heidelberg, 2013
1/21/2014 Andrei Going the Distance for Protein Function Prediction: A New Distance Metric for Protein Interaction Networks
Mengfei Cao, Hao Zhang, Jisoo Park, Noah M. Daniels, Mark E. Crovella, Lenore J. Cowen, Benjamin Hescott
11/14/2013 Mahmudul CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways
Gamze Abaka, Turker Biyikoglu and Cesim Erten
10/28/2013 Haitham A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks
Alexander lan, Michal Ziv-Ukelson and Esti Yeger-Lotem
10/14/2013 Ryan An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees
Yufeng Wu
9/9/2013 Andrei NP-MuScL: Unsupervised global prediction of interaction networks from multiple data sources
Kriti Puniyani and Eric P. Xing
RECOMB 2013.
5/22/2013 Mahmudul Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
Raja Jothi et al.
Molecular Systems Biology. August 2009.
5/1/2013 Gunhan Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
Noa Novershtern, Aravind Subramanian et al.
Cell. 2011 January, Pages 296-309
1/23/2013 Saad Utilizing RNA-Seq data for de novo coexpression network inference
Ovidiu D. Iancu, Sunita Kawane, Daniel Bottomly, Robert Searles, Robert Hitzemann and Shannon McWeeney
Bioinformatics, Vol. 28, Nr. 12 (2012)
12/11/2012 Mahmudul Ballast: A Ball-based Algorithm for Structural Motifs
Lu He, Fabio Vandin, Gopal Pandurangan and Chris Bailey-Kellogg
11/27/2012 Gunhan
Inferring gene functions from metabolic reactions
11/13/2012 Gunhan A single source k-shortest paths algorithm to infer regulatory pathways in a gene network
Yu-Keng Shih and Srinivasan Parthasarathy
ISMB 2012
10/30/2012 Haitham Finding Maximum Colorful Subtrees in practice
Imran Rauf, Florian Rasche, Franois Nicolas and Sebastian Boecker
4/4/2012 Haitham Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks
Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan
Journal of Computational Biology March 2006, 13(2): 133-144. doi:10.1089/cmb.2006.13.133.
2/22/2012 Mahmudul Kavosh: a new algorithm for finding network motifs
Zahra RM Kashani, Hayedeh Ahrabian, Elahe Elahi, Abbas Nowzari-Dalini, Elnaz S Ansari, Sahar Asadi, Shahin Mohammadi, Falk Schreiber and Ali Masoudi-Nejad
BMC Bioinformatics BMC Bioinformatics 2009, 10:318 doi:10.1186/1471-2105-10-318
2/8/2012 Serdar Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data
Christian Bender, Frauke Henjes, Holger Frohlichh, Stefan Wiemann, Ulrike Korf and Tim Beissbarth
OUP Bioinformatics Bioinformatics (2010) 26 (18): i596-i602. doi: 10.1093/bioinformatics/btq385
1/25/2012 Gunhan SING: Subgraph search In Non-homogeneous Graphs
Raffaele Di Natale, Alfredo Ferro, Rosalba Giugno, Misael Mongiovi, Alfredo Pulvirenti1and Dennis Shasha
BMC Bioinformatics 2010, 11:96 doi:10.1186/1471-2105-11-96
4/20/2011 Guliz Global alignment of multiple protein interaction networks with application to functional orthology detection
Rohit Singh, Jinbo Xu, and Bonnie Berger
PNAS 2008 105 (35) 12763-12768; published ahead of print August 25, 2008 (PNAS)
4/13/2011 Gunhan Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut
Mark D. M. Leiserson, Diana Tatar, Lenore J. Cowen, and Benjamin J. Hescott
In Proceedings of the 15th Annual international conference on Research in computational molecular biology (RECOMB'11), Vineet Bafna and S. Cenk Sahinalp (Eds.). Springer-Verlag, Berlin, Heidelberg, 154-167. (ACM Digital Library)
4/6/2011 Nirmalya Time Varying Dynamic Bayesian Network for Nonstationary Events Modeling and Online Inference
Zhaowen Wang; Kuruog?lu, E.E.; Xiaokang Yang; Yi Xu; Huang, T.S.
Signal Processing, IEEE Transactions on , vol.59, no.4, pp.1553-1568, April 2011 (IEEExplore)
3/30/2011 Ferhat Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework
Yoshihiro Yamanishi, Masaaki Kotera, Minoru Kanehisa, and Susumu Goto
Bioinformatics (2010) 26(12): i246-i254 (Bioinformatics)
3/23/2011 Gokhan Among-site rate variation and its impact on phylogenetic analyses
Ziheng Yang
Trends in Ecology & Evolution, Volume 11, Issue 9, September 1996, Pages 367-372 (ScienceDirect)
3/16/2011 Guliz Conserved pathways within bacteria and yeast as revealed by global protein network alignment
Brian P. Kelley, Roded Sharan, Richard M. Karp, Taylor Sittler, David E. Root, Brent R. Stockwell, and Trey Ideker
PNAS 2003 100 (20) 11394-11399; published ahead of print September 22, 2003 (PNAS)
3/2/2011 Gunhan Algorithm Engineering for Color-Coding with Applications to Signaling Pathway Detection
Falk Huffner, Sebastian Wernicke, Thomas Zichner
Algorithmica, Volume 52, Number 2, 114-132, (SpringerLink)
2/2/2011 Gokhan Evolutionary trees from DNA sequences: A maximum likelihood approach
Joseph Felsenstein
J Mol Evol(1981) 17:368-376 (PDF)
10/19/2010 Nirmalya Cross-species queries of large gene expression databases
Hai-Son Le, Zoltan N. Oltvai and Ziv Bar-Joseph
Bioinformatics. 2010 Aug 11;26(19):2416-2423. (PDF)
10/12/2010 Gunhan Biomolecular network motif counting and discovery by color coding
Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Cenk Sahinalp
ISMB 2008, Toronto, Canada (PDF)
09/28/2010 Ferhat Network motifs: theory and experimental approaches
Uri Alon
Nature Reviews Genetics Volume 8, June 2007, Pages 450-461. (PDF)
09/14/2010 Nirmalya Analyzing Metabolite Measurements for Automated Prediction of Underlying Biological Mechanisms.
Ali Cakmak, Arun Dsouza, Richard W. Hanson, Meral Ozsoyoglu.
ACM-BCB 2010, Niagara Falls, NY, USA.
03/16/2010 Nirmalya Modeling stochasticity and robustness in gene regulatory networks.
Garg A, Mohanram K, Di Cara A, De Micheli G, Xenarios I.
Bioinformatics. 2009 Jun 15;25(12):i101-9. (PDF)
03/02/2010 Ferhat A new constraint-based description of the steady-state flux cone of metabolic networks
Abdelhalim Larhlimi and Alexander Bockmayr
Discrete Applied Mathematics Volume 157, Issue 10, 28 May 2009, Pages 2257-2266. (PDF)

Tamer Kahveci
Last modified: Thu Oct 17 11:23:04 EDT 2013