List of Accepted Papers RECOMB 2012

Download the list in pdf here.

  • Matthew Francis and Elana Fertig. Quantifying the dynamics of coupled networks of switches and oscillators
  • Babak Alipanahi Ramandi, Nathan Krislock, Henry Wolkowicz, Ali Ghodsi, Logan Donaldson and Ming Li. Protein Structure by Semidefinite Facial Reduction
  • Marcus Kinsella and Vineet Bafna. Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics
  • Imran Rauf, Florian Rasche, Francois Nicolas and Sebastian Böcker. Finding Maximum Colorful Subtrees in practice
  • Zhizhuo Zhang, Cheng Wei Chang, Willy Hugo, Edwin Cheung and Wing-Kin Sung. Simultaneously Learning DNA Motif along with  Its Position and Sequence Rank Preferences through EM Algorithm
  • Yaw-Ling Lin, Charles Ward and Steven Skiena. Synthetic Sequence Design for Signal Location Search
  • Raheleh Salari, Chava Kimchi-Sarfaty, Michael Gottesman and Teresa Przytycka. Detecting SNP-induced structural changes in RNA: application to disease studies
  • Roded Sharan and Richard Karp. Reconstructing Boolean models of Signaling
  • Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng and Fengzhu Sun. Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads
  • Lu He, Fabio Vandin, Gopal Pandurangan and Chris Bailey-Kellogg. Ballast: A Ball-based Algorithm for Structural Motifs
  • Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon. RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks
  • Osvaldo Zagordi, Armin Toepfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin and Niko Beerenwinkel. Probabilistic inference of viral quasispecies subject to recombination
  • Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer Chayes, Christian Borgs, Riccardo Zecchina and Ernest Fraenkel. Simultaneous reconstruction of multiple signaling pathways via the prize-collecting Steiner forest problem
  • Andrew Parker, Karl Griswold and Chris Bailey-Kellogg. Structure-Guided Deimmunization of Therapeutic Proteins
  • Christina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will and Rolf Backofen. Exact Pattern Matchings for RNA Structure Ensembles
  • Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin and Eleazar Eskin. CNVeM: Copy Number Variation detection Using Uncertainty of Read Mapping
  • Patrick Holloway, Krister Swenson, David Ardell and Nadia El-Mabrouk. Evolution of Genome Organization by Duplication and Loss: a Linear Programming approach
  • Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner and Max Alekseyev. PATH-SETS: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly
  • Daniel Holtby, Shuai Cheng Li and Ming Li. LoopWeaver - Loop Modeling by the Weighted Scaling of Verified Proteins
  • Stefan Canzar, Mohammed El-Kebir, Rene Pool, Khaled Elbassioni, Alpesh Malde, Alan Mark, Daan Geerke, Leen Stougie and Gunnar W. Klau. Charge Group Partitioning in Biomolecular Simulation
  • Sebastian Will, Michael Yu and Bonnie Berger. Structure-based Whole Genome Realignment Reveals Many Novel Non-coding RNAs
  • Andrew Mcpherson, Chunxiao Wu, Alexander Wyatt, Sohrab Shah, Colin Collins and Cenk Sahinalp. Discovery of complex genomic rearrangements in cancer using high-throughput sequencing
  • Dan He, Buhm Han and Eleazar Eskin. Optimal Algorithm for Haplotype Phasing with Imputation using Sequencing Data
  • Hua Wang, Heng Huang and Chris Ding. Predicting Protein-Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Factorization
  • Sebastien Roch and Sagi Snir. Recovering a tree-like trend of evolution despite extensive lateral genetic transfer: A probabilistic analysis
  • Melissa Gymrek, David Golan, Saharon Rosset and Yaniv Erlich. lobSTR: A Novel Pipeline for Short Tandem Repeats Profiling in Personal Genomes
  • Yan Huang, Yin Hu and Jinze Liu. A Robust Method for Transcript Quantification with RNA-seq Data
  • Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene Robinson and Jian Ma. TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq
  • Hua Wang, Heng Huang and Chris Ding. Function-Function Correlated Multi-Label Protein Function Prediction over Interaction Networks
  • Sivan Bercovici, Jesse Rodriguez, Megan Elmore and Serafim Batzoglou. Ancestry inference in complex admixtures via variable-length Markov chain linkage models
  • Dan DeBlasio, Travis Wheeler and John Kececioglu. Estimating the Accuracy of Multiple Alignments and Its Use in Parameter Advising


The 16th International Conference on Research in Computational Molecular Biology (RECOMB 2012) will be held in Barcelona on April 21-24, 2012. RECOMB 2012 will provide a general forum for disseminating the latest research in bioinformatics and computational biology. As a multidisciplinary conference, it brings together academic and industrial scientists from molecular biology, medicine, computer science, mathematics, and statistics. Papers reporting on original research (both theoretical and experimental) in all areas of computational molecular biology are sought. Topics of interest include, but are not limited to:

  • Molecular sequence analysis
  • Recognition of genes and regulatory elements
  • Molecular evolution
  • Gene expression 
  • Biological networks
  • Sequencing and genotyping technologies
  • Genomics 
  • Metagenomics
  • Population, statistical genetics
  • Systems biology
  • Imaging
  • Computational proteomics
  • Molecular structural biology

Papers submitted for review should represent original, previously unpublished work.  The Program Committee will rigorously review submitted abstracts. Selected papers will be accepted for presentation at the conference. Accepted abstracts will be published as a proceedings volume in the Lecture Notes in Bioinformatics (LNBI) series from Springer-Verlag, which will be available at the conference. RECOMB is partnering with the Journal of Computational Biology. Select accepted papers will be invited, but not required, to submit an edited journal version for a special issue of JCB. Finally, RECOMB will also have a highlights.html track featuring presentations of exciting recent developments that have already appeared in journals within the past year. 


Parallel Submission:

Parallel submission to RECOMB and to a journal is allowed. Authors who wish to publish the edited manuscript elsewhere must clearly indicate this at the time of submission to RECOMB, and submit a complete manuscript for review. If accepted for oral presentation at RECOMB, they will submit a final two-page extended abstract for inclusion in the LNBI proceedings in lieu of the full paper.


Manuscript preparation:

The cover page should contain the title, author(s) names and affiliations, an abstract, the keywords, and the contact author e-mail. If this is or is going to be a parallel submission, the words "parallel submission" should appear at the bottom of the page.

The manuscript should start with a succinct statement of the problem, the results achieved, their significance, and a comparison with previous work. This material should be understandable to non-specialists. A technical exposition directed to the specialist should follow. The length, excluding cover page and bibliography, should not exceed 10 pages. The manuscript should be easy to read, using at least 11 point font size on U.S. standard 8 1/2 by 11 inch paper with no less than one inch margin all around. To assist in the refereeing process, a short list of one to three topics (preferably, but not limited to the list above) should appear at the bottom of the front page. If the authors believe that more details are absolutely necessary to substantiate the claims of the paper, they may include a clearly marked appendix, which might be read at the discretion of the reviewers.

Manuscripts that deviate significantly from these guidelines risk rejection without consideration of their merits. 

Manuscripts can be submitted through:

For submissions published in the RECOMB proceedings volume, detailed formatting instructions are at the Springer-Verlag site, under "Information for LNCS Authors," at:


Paper submission procedures and notification:

Submission of papers to RECOMB2012 will be through the EasyChair conference system, following the link from the conference web page. The submission system will be open starting September 13th, 2011 and ending October 28th, 2011. For full details, please see the submissions link at the conference website.

The Program Committee, chaired by Benny Chor (Tel-Aviv /university), will referee the conference submissions. Authors will be notified of acceptance or rejection by email on or before December 19th, 2011. We request that an author of each accepted paper provides LaTeX files or an MS Word file in the special format for Lecture Notes in Bioinformatics by January 20, 2012.

An author of each accepted paper is expected to attend the conference and present the paper; otherwise, alternative arrangements should be made to have the paper presented.