RECOMB 2010 Proceedings

Lisbon, Portugal, August 12 - 15, 2010

PC Chair: Bonnie Berger
Organization Committee: Arlindo Oliveira (co-chair), Ana Teresa Freitas (co-chair), João Carriço, Alexandre Francisco, Paulo Fonseca, José Pereira Leal, Sara Madeira, Luís Rocha, Sara Silva, Susana Vinga
Keynote Speakers: Cecilia Arraiano, David Bartel, Isaac Kohane, Phil Kapranov, Norbert Perrimon, Mona Singh
Website: https://recomb.org/recomb2010
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List of Publications

• An Algorithmic Framework for Predicting Side-Effects of Drugs. Nir Atias and Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 1-14, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_1
  • Journal: An Algorithmic Framework for Predicting Side Effects of Drugs. Nir Atias, Roded Sharan. Journal of Computational Biology, 18(3): 207-218, 2011.
    • DOI: 10.1089/cmb.2010.0255
• SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. Ferhat Ay and Tamer Kahveci.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 15-30, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_2
  • Journal: SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings. Ferhat Ay, Manolis Kellis, Tamer Kahveci. Journal of Computational Biology, 18(3): 219-235, 2011.
    • DOI: 10.1089/cmb.2010.0280
• Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA. Sivan Bercovici and Dan Geiger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 31-49, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_3
  • Journal: Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA. Sivan Bercovici, Dan Geiger. Journal of Computational Biology, 18(3): 237-249, 2011.
    • DOI: 10.1089/cmb.2010.0250
• Pathway-Based Functional Analysis of Metagenomes. Sivan Bercovici, Itai Sharon, Ron Y. Pinter, Tomer Shlomi.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 50-64, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_4
  • Journal: Pathway-Based Functional Analysis of Metagenomes. Itai Sharon, Sivan Bercovici, Ron Y. Pinter, Tomer Shlomi. Journal of Computational Biology, 18(3): 495-505, 2011.
    • DOI: 10.1089/cmb.2010.0260
• Hierarchical Generative Biclustering for MicroRNA Expression Analysis. José Caldas and Samuel Kaski.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 65-79, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_5
  • Journal: Hierarchical Generative Biclustering for MicroRNA Expression Analysis. José Caldas, Samuel Kaski. Journal of Computational Biology, 18(3): 251-261, 2011.
    • DOI: 10.1089/cmb.2010.0256
• Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutürk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 80-95, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_6
  • Journal: Subnetwork State Functions Define Dysregulated Subnetworks in Cancer. Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutürk. Journal of Computational Biology, 18(3): 263-281, 2011.
    • DOI: 10.1089/cmb.2010.0269
• Proteome Coverage Prediction for Integrated Proteomics Datasets. Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 96-109, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_7
  • Journal: Proteome Coverage Prediction for Integrated Proteomics Datasets. Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann. Journal of Computational Biology, 18(3): 283-293, 2011.
    • DOI: 10.1089/cmb.2010.0261
• Discovering Regulatory Overlapping RNA Transcripts. Timothy Danford, Robin Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David Gifford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 110-122, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_8
  • Journal: Discovering Regulatory Overlapping RNA Transcripts. Timothy Danford, Robin D. Dowell, Sudeep D. Agarwala, Paula Grisafi, Gerald R. Fink, David K. Gifford. Journal of Computational Biology, 18(3): 295-303, 2011.
    • DOI: 10.1089/cmb.2010.0267
• Alignment-Free Phylogenetic Reconstruction. Constantinos Daskalakis and Sebastien Roch.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 123-137, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_9
  • Preprint: arXiv:1109.5002
  • Journal: Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis. Constantinos Daskalakis, Sebastien Roch. The Annals of Applied Probability, 23(2): 693-721, 2013.
    • DOI: 10.1214/12-aap852
• Inference of Isoforms from Short Sequence Reads. Jianxing Feng, Wei Li, Tao Jiang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 138-157, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_10
  • Journal: Inference of Isoforms from Short Sequence Reads. Jianxing Feng, Wei Li, Tao Jiang. Journal of Computational Biology, 18(3): 305-321, 2011.
    • DOI: 10.1089/cmb.2010.0243
• The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS. Bjarni V. Halldórsson, Derek Aguiar, Ryan Tarpine, Sorin Istrail.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 158-173, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_11
  • Journal: The Clark Phaseable Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS. Bjarni V. Halldórsson, Derek Aguiar, Ryan Tarpine, Sorin Istrail. Journal of Computational Biology, 18(3): 323-333, 2011.
    • DOI: 10.1089/cmb.2010.0288
• A New Algorithm for Improving the Resolution of Cryo-EM Density Maps. Michael Hirsch, Bernhard Schölkopf, Michael Habeck.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 174-188, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_12
  • Journal: A Blind Deconvolution Approach for Improving the Resolution of Cryo-EM Density Maps. Michael Hirsch, Bernhard Schölkopf, Michael Habeck. Journal of Computational Biology, 18(3): 335-346, 2011.
    • DOI: 10.1089/cmb.2010.0264
• Towards Automated Structure-Based NMR Resonance Assignment. Richard Jang, Xin Gao, Ming Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 189-207, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_13
  • Journal: Towards Fully Automated Structure-Based NMR Resonance Assignment of 15 N-Labeled Proteins From Automatically Picked Peaks. Richard Jang, Xin Gao, Ming Li. Journal of Computational Biology, 18(3): 347-363, 2011.
    • DOI: 10.1089/cmb.2010.0251
• Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra. Kyowon Jeong, Sangtae Kim, Nuno Bandeira, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 208-232, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_14
  • Journal: Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra. Kyowon Jeong, Sangtae Kim, Nuno Bandeira, Pavel A. Pevzner. Molecular & Cellular Proteomics, 10(6): M110.002220, 2011.
    • DOI: 10.1074/mcp.m110.002220
• naive BayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. Wei-Chun Kao and Yun S. Song.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 233-247, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_15
  • Journal: naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. Wei‐Chun Kao, Yun S. Song. Journal of Computational Biology, 18(3): 365-377, 2011.
    • DOI: 10.1089/cmb.2010.0247
• Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. David R. Kelley and Carl Kingsford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 248-262, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_16
  • Journal: Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression. David R. Kelley, Carl Kingsford. Journal of Computational Biology, 18(3): 379-390, 2011.
    • DOI: 10.1089/cmb.2010.0268
• Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases. Yoo-Ah Kim, Stefan Wuchty, Teresa M. Przytycka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 263-280, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_17
• Incremental Signaling Pathway Modeling by Data Integration. Geoffrey Koh, David Hsu, P.S. Thiagarajan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 281-296, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_18
• The Poisson Margin Test for Normalisation Free Significance Analysis of NGS Data. Adam Kowalczyk, Justin Bedo, Thomas Conway, Bryan Beresford-Smith.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 297-309, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_19
  • Journal: The Poisson Margin Test for Normalization-Free Significance Analysis of NGS Data. Adam Kowalczyk, Justin Bedő, Thomas Conway, Bryan Beresford‐Smith. Journal of Computational Biology, 18(3): 391-400, 2011.
    • DOI: 10.1089/cmb.2010.0272
• Compressing Genomic Sequence Fragments Using SlimGene. Christos Kozanitis, Chris Saunders, Semyon Kruglyak, Vineet Bafna, George Varghese.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 310-324, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_20
  • Journal: Compressing Genomic Sequence Fragments Using SlimG ene. Christos Kozanitis, Christopher T. Saunders, Semyon Kruglyak, Vineet Bafna, Varghese George. Journal of Computational Biology, 18(3): 401-413, 2011.
    • DOI: 10.1089/cmb.2010.0253
• On the Genealogy of Asexual Diploids. Fumei Lam, Charles H. Langley, Yun S. Song.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 325-340, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_21
  • Journal: On the Genealogy of Asexual Diploids. Fumei Lam, Charles H. Langley, Yun S. Song. Journal of Computational Biology, 18(3): 415-428, 2011.
    • DOI: 10.1089/cmb.2010.0270
• Genovo: De Novo Assembly for Metagenomes. Jonathan Laserson, Vladimir Jojic, Daphne Koller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 341-356, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_22
  • Journal: Genovo: De Novo Assembly for Metagenomes. Jonathan Laserson, Vladimir Jojic, Daphne Koller. Journal of Computational Biology, 18(3): 429-443, 2011.
    • DOI: 10.1089/cmb.2010.0244
• MOGUL: Detecting Common Insertions and Deletions in a Population. Seunghak Lee, Eric Xing, Michael Brudno.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 357-368, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_23
• Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny. Navodit Misra, Guy Blelloch, R. Ravi, Russell Schwartz.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 369-383, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_24
  • Journal: Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-State Phylogeny. Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz. Journal of Computational Biology, 18(3): 445-457, 2011.
    • DOI: 10.1089/cmb.2010.0254
• Seed Design Framework for Mapping SOLID Reads. Laurent Noé, Marta Gîrdea, Gregory Kucherov.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 384-396, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_25
• Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments. Bogdan Pasaniuc, Noah Zaitlen, Eran Halperin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 397-409, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_26
  • Journal: Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments. Bogdan Pasaniuc, Noah Zaitlen, Eran Halperin. Journal of Computational Biology, 18(3): 459-468, 2011.
    • DOI: 10.1089/cmb.2010.0259
• Cactus Graphs for Genome Comparisons. Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard Suh, David Haussler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 410-425, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_27
  • Journal: Cactus Graphs for Genome Comparisons. Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard Suh, David Haussler. Journal of Computational Biology, 18(3): 469-481, 2011.
    • DOI: 10.1089/cmb.2010.0252
• IDBA A Practical Iterative de Bruijn Graph De Novo Assembler. Yu Peng, Henry C.M. Leung, S.M. Yiu, Francis Y.L. Chin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 426-440, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_28
• Predicting Nucleosome Positioning Using Multiple Evidence Tracks. Sheila M. Reynolds, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 441-455, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_29
• Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs. Barna Saha, Allison Hoch, Samir Khuller, Louiga Raschid, Xiao-Ning Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 456-472, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_30
• Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. Raheleh Salari, Mathias Möhl, Sebastian Will, S. Cenk Sahinalp, Rolf Backofen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 473-490, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_31
• HLA Type Inference via Haplotypes Identical by Descent. Manu N. Setty, Alexander Gusev, Itsik Pe’er.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 491-505, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_32
  • Journal: HLA Type Inference via Haplotypes Identical by Descent. Manu Setty, Alexander Gusev, Itsik Pe’er. Journal of Computational Biology, 18(3): 483-493, 2011.
    • DOI: 10.1089/cmb.2010.0258
• Algorithms for Detecting Significantly Mutated Pathways in Cancer. Fabio Vandin, Eli Upfal, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 506-521, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_33
  • Journal: Algorithms for Detecting Significantly Mutated Pathways in Cancer. Fabio Vandin, Eli Upfal, Benjamin J. Raphael. Journal of Computational Biology, 18(3): 507-522, 2011.
    • DOI: 10.1089/cmb.2010.0265
• Leveraging Sequence Classification by Taxonomy-Based Multitask Learning. Christian Widmer, Jose Leiva, Yasemin Altun, Gunnar Rätsch.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 522-534, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_34
• A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using ℓ-Tuples. Yu-Wei Wu and Yuzhen Ye.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 535-549, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_35
  • Journal: A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using ℓ-tuples. Yu‐Wei Wu, Yuzhen Ye. Journal of Computational Biology, 18(3): 523-534, 2011.
    • DOI: 10.1089/cmb.2010.0245
• A Markov Random Field Framework for Protein Side-Chain Resonance Assignment. Jianyang Zeng, Pei Zhou, Bruce Randall Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 550-570, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_36
• Genomic DNA k-mer Spectra: Models and Modalities. Benny Chor, David Horn, Nick Goldman, Yaron Levy, Tim Massingham.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 571-571, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_37
  • Journal: Genomic DNA k-mer spectra: models and modalities. Benny Chor, D. Horn, Nick Goldman, Yaron Y. Levy, Tim Massingham. Genome Biology, 10(10): R108, 2009.
    • DOI: 10.1186/gb-2009-10-10-r108
• Deciphering the Swine-Flu Pandemics of 1918 and 2009. Richard Goldstein, Mario dos Reis, Asif Tamuri, Alan Hay.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 572-573, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_38
• Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions. Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 574-574, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_39
  • Journal: Distinguishing direct versus indirect transcription factor–DNA interactions. Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk. Genome Research, 19(11): 2090-2100, 2009.
    • DOI: 10.1101/gr.094144.109
• A Self-regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning. Jean-Denis Benazet, Mirko Bischofberger, Eva Tiecke, Alexandre Gonalves, James F. Martin, Aime Zuniga, Felix Naef, Rolf Zeller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 575-576, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_40
  • Journal: A Self-Regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning. Jean-Denis Bénazet, Mirko Bischofberger, Eva Tiecke, Alexandre Gonçalves, James F. Martin, Aimée Zúñiga, Félix Naef, Rolf Zeller. Science, 323(5917): 1050-1053, 2009.
    • DOI: 10.1126/science.1168755
• Automated High-Dimensional Flow Cytometric Data Analysis. Saumyadipta Pyne, Xinli Hu, Kui Wang, Elizabeth Rossin, Tsung-I Lin, Lisa Maier, Clare Baecher-Allan, Geoffrey McLachlan, Pablo Tamayo, David Hafler, Philip De Jager, Jill Mesirov.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 577-577, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_41
  • Journal: Automated high-dimensional flow cytometric data analysis.. Saumyadipta Pyne, Xinli Hu, Kui Wang, Elizabeth J. Rossin, Tsung‐I Lin, Lisa M. Maier, Clare Baecher‐Allan, Geoffrey J. McLachlan, Pablo Tamayo, David A. Hafler, Philip L. De Jager, Jill P. Mesirov. Proceedings of the National Academy of Sciences, 106(21): 8519-24, 2009.
    • DOI: 10.1073/pnas.0903028106
• Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences. Yonit Halperin, Chaim Linhart, Igor Ulitsky, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044, pp 578-580, Springer, Cham.
    • DOI: 10.1007/978-3-642-12683-3_42