The 21st Annual International Conference on Research in Computational Molecular Biology

Hong Kong, May 3-7, 2017

(May 3: Registration & Reception, May 4-7: Talks)

Jesper Jansson, Andrzej Lingas, Ramesh Rajaby and Wing-Kin Sung.
Determining the Consistency of Resolved Triplets and Fan Triplets

Benedict Paten, Adam Novak, Erik Garrison, Eric Dawson and Glenn Hickey.
Superbubbles, Ultrabubbles and Cacti

Yijie Wang, Dong-Yeon Cho, Hangnoh Lee, Brian Oliver and Teresa Przytycka.
NetREX: Network Rewiring using EXpression - Towards Context Specific Regulatory Networks [arXiv, biorXiv]

Uri Keich and William Stafford Noble.
Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy?

Guillaume Holley, Roland Wittler, Jens Stoye and Faraz Hach.
Dynamic Alignment-free and Reference-free Read Compression

David Haussler, Maciej Smuga-Otto, Benedict Paten, Adam Novak, Sergei Nikitin, Maria Zueva and Miagkov Dmitrii.
A flow procedure for the linearization of genome variation graphs

Yaron Orenstein, Ryan Kim, Polly Fordyce and Bonnie Berger.
Joker de Bruijn: sequence libraries to cover all k-mers using joker characters [Cell Systems]

Ewa Szczurek and Dariusz Matlak.
Epistasis in genomic and survival data of cancer patients [biorXiv]

Shubhanshu Shekhar, Sebastien Roch and Siavash Mirarab.
Species tree estimation using ASTRAL: how many genes are enough? [arXiv]

Zhen Li, Sheng Wang, Yizhou Yu and Jinbo Xu.
Predicting membrane protein contacts from non-membrane proteins by deep transfer learning [arXiv]

Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang and Jianyang Zeng.
ROSE: a deep learning based framework for predicting ribosome stalling [biorXiv]

Xiaoqian Wang, Li Shen and Heng Huang.
Longitudinal Genotype-Phenotype Association Study via Temporal Structure Auto-Learning Predictive Model

Christopher Pockrandt, Marcel Ehrhardt and Knut Reinert.
EPR-dictionaries: A practical and fast data structure for constant time searches in unidirectional and bidirectional FM-indices [arXiv]

Chen Sun, Robert Harris, Rayan Chikhi and Paul Medvedev.
Allsome Sequence Bloom Trees

Adegoke Ojewole, Jonathan Jou, Vance Fowler and Bruce Donald.
BBK* (Branch and Bound over K*): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces

Joshua Welch, Alexander Hartemink and Jan Prins.
E Pluribus Unum: United States of Single Cells [bioRxiv]

Linh Huynh and Fereydoun Hormozdiari.
Ultra-accurate complex disorder prediction: case study of neurodevelopmental disorders [bioRxiv]

Dan Deblasio and John Kececioglu.
Boosting alignment accuracy by adaptive local realignment

Phuong Dao, Yoo-Ah Kim, Damian Wojtowicz, Sanna Madan, Roded Sharan and Teresa Przytycka.
BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions [arXiv]

Elior Rahmani, Regev Schweiger, Liat Shenhav, Eleazar Eskin and Eran Halperin.
A Bayesian Framework for Estimating Cell Type Composition from DNA Methylation Without the Need for Methylation Reference

Robert Osazuwa Ness, Karen Sachs, Parag Mallick and Olga Vitek.
A Bayesian Active Learning Experimental Design for Inferring Signaling Networks

Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinling Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng, Ligong Chen and Jianyang Zeng.
A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information [bioRxiv]

Regev Schweiger, Eyal Fisher, Elior Rahmani, Liat Shenhav, Saharon Rosset and Eran Halperin.
Using stochastic approximation techniques to efficiently construct confidence intervals for heritability

Jingkang Zhao, Dongshunyi Li, Jungkyun Seo, Andrew Allen and Raluca Gordan.
Quantifying the impact of non-coding variants on transcription factor-DNA binding

Yue Wu, Farhad Hormozdiari, Jong Wha J Joo and Eleazar Eskin.
Improving imputation accuracy by inferring causal variants in genetic studies

Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze, Yana Safonova and Pavel Pevzner.
Reconstructing antibody repertoires from error-prone immunosequencing datasets [arXiv]

Ashok Rajaraman and Jian Ma.
Towards Recovering Allele-specific Cancer Genome Graphs

Chirag Jain, Alexander Dilthey, Sergey Koren, Srinivas Aluru and Adam Phillippy.
A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases

Brad Solomon and Carl Kingsford.
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees

Simone Zaccaria, Mohammed El-Kebir, Gunnar Klau and Ben Raphael.
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-Sample Bulk Sequencing Tumor Data

Borislav Hristov and Mona Singh.
Network-based coverage of mutational profiles reveals cancer genes [arXiv]

Ardalan Naseri, Xiaoming Liu, Shaojie Zhang and Degui Zhi.
Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows–Wheeler Transform [bioRxiv]

Soyeon Ahn and Haris Vikalo.
aBayesQR: A Bayesian method for reconstruction of viral populations characterized by low diversity

Michael Leung, Andrew Delong and Brendan Frey.
Inference of the Human Polyadenylation Code [bioRxiv]

Sudipto Mukherjee, Mark Chaisson, Sreeram Kannan and Evan Eichler.
Resolving multicopy duplications de novo using polyploid phasing

Wontack Han, Mingjie Wang and Yuzhen Ye.
A concurrent subtractive assembly approach for identification of disease associated sub-metagenomes

Yuchun Guo, Kevin Tian, Haoyang Zeng and David K. Gifford.
K-mer Set Memory (KSM) motif representation enables accurate prediction of the impact of regulatory variants [bioRxiv]

Victoria Popic, Volodymyr Kuleshov, Michael Snyder and Serafim Batzoglou.
GATTACA: Lightweight metagenomic binning using Kmer Counting [bioRxiv]

Michael Altenbuchinger, Thorsten Rehberg, Helena Zacharias, Frank Stämmler, Katja Dettmer, Daniela Weber, Andreas Hiergeist, André Gessner, Ernst Holler, Peter Oefner and Rainer Spang
Reference point insensitive molecular data analysis

Przemyslaw Szalaj, Zhonghui Tang, Paul Michalski, Michal Pietal, Michal Sadowski, Oskar Luo, Yijun Ruan and Dariusz Plewczynski
3D-GNOME: high-resolution model of chromatin looping architecture in human genome

Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang and Jinbo Xu
Folding Large Proteins by Ultra-Deep Learning

David Amar, Shai Izraeli and Ron Shamir
Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications

Vikram Alva Kullanja, Johannes Söding and Andrei Lupas
A vocabulary of ancient peptides at the origin of folded proteins

Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh, Esteban Burchard, Eleazar Eskin, James Zou and Eran Halperin
Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies

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