RECOMB 2013 Beijing, China

Accepted papers

The conference proceedings (Lecture Notes in Computer Science, Volume 7821, 2013) is now online. You can find information about it at http://www.springeronline.com/978-3-642-37194-3 or access the online version at http://www.springerlink.com/content/978-3-642-37194-3/. A subscription to Springer products is required in order for you to download full text.

ID	Authors and Title
2	Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty and Peter Clote
	Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches
5	Dong Xu, Hua Li and Yang Zhang
	Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform
17	Mohammad Javad Sadeh, Giusi Moffa and Rainer Spang
	Considering Unknown Unknowns - Reconstruction of Non-confoundable Causal Relations in Biological Networks
24	Yufeng Wu
	An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees
30	Dong-Yeon Cho and Teresa Przytycka
	Dissecting cancer heterogeneity with a probabilistic genotype-phenotype model
31	Mingxun Wang and Nuno Bandeira
	Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance
32	Zhizhuo Zhang, Guoliang Li, Kim-Chuan Toh and Wing-Kin Sung
	Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data
35	Roy Ronen, Nitin Udpa, Eran Halperin and Vineet Bafna
	Learning Natural Selection from the Site Frequency Spectrum
42	Jesper Jansson, Chuanqi Shen and Wing-Kin Sung
	An Optimal Algorithm for Building the Majority Rule Consensus Tree
43	Itamar Eskin, Farhad Hormozdiari, Lucia Conde, Chris Skibola, Jacques Riby, Eleazar Eskin and Eran Halperin
	eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data
49	Kriti Puniyani and Eric Xing
	NP-MuScL: Unsupervised global prediction of interaction networks from multiple data sources
53	Emrah Kostem and Eleazar Eskin
	Efficiently Identifying Significant Associations in Genome-wide Association Studies
56	Dan He, Zhanyong Wang, Laxmi Parida and Eleazar Eskin
	IPED: Inheritance Path based Pedigree Reconstruction Algorithm using Genotype Data
62	Ting Wang, Michael Stevens, Jeffrey Cheng, Mingchao Xie and Joseph Costello
	MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods
72	Alina Munteanu and Raluca Gordan
	Distinguishing between genomic regions bound by paralogous transcription factors
74	Xiaowen Liu, Shawna Hengel, Si Wu, Nikola Tolic, Ljiljana Pasa-Tolic and Pavel Pevzner
	Identification of proteins with multiple post-translational modifications using top-down tandem mass spectra
75	Shijian Chen, Anqi Wang and Lei Li
	SEME: A fast mapper of Illumina sequencing reads with statistical evaluation
80	Ngoc Hieu Tran, Kwok Pui Choi and Louxin Zhang
	Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data
92	Ali A Faruqi, William A Bryant and John W Pinney
	Analysis of metabolic evolution in bacteria using whole-genome metabolic models
96	Kyowon Jeong, Sangtae Kim and Pavel Pevzner
	UniNovo : a universal tool for de novo peptide sequencing
105	Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Mohl and Rolf Backofen
	SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs Without Sequence-Based Heuristics
110	Fei Guo, Shuai Cheng Li, Wenji Ma and Lusheng Wang
	Detecting Protein Conformational Changes in Interactions via Scaling Known Structures
112	Vladimir Reinharz, Yann Ponty and Jerume Waldispuhl
	A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequences W
115	Mukul S. Bansal, Eric J Alm and Manolis Kellis
	Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss
120	Jesse Rodriguez, Serafim Batzoglou and Sivan Bercovici
	An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test
121	Fabio Vandin, Alexandra Papoutsaki, Ben Raphael and Eli Upfal
	Genome-Wide Survival Analysis of Somatic Mutations in Cancer
127	Raheleh Salari, Syed Shayon Saleh, Dorna Kashef-Haghighi, David Khavari, Daniel E Newburger, Robert E West, Arend Sidow and Serafim Batzoglou
	Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery
133	Christopher Reeder and David Gifford
	High Resolution Modeling of Chromatin Interactions
146	Layla Oesper, Ahmad Mahmoody and Ben Raphael
	Estimating Tumor Purity and Cancer Subpopulations from High-Throughput DNA Sequencing Data
147	Chittaranjan Tripathy, Anthony Yan, Pei Zhou and Bruce Donald
	Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure
160	Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken, Glenn Tesler, Max Alekseyev and Pavel Pevzner
	Assembling Genomes and Multigenomes from Highly Chimeric Reads
178	Shuigeng Zhou
	Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties