RECOMB 2014 Talks
We earlier covered two of the RECOMB talks.
a) The paper by Rayan Chikhi (Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared Simpson and Paul Medvedev. On the representation of de Bruijn graphs)
De Novo Assembly of Human Genome with Only 1.5 GB RAM
b) The paper by SPAdes group (Yana Safonova, Anton Bankevich and Pavel Pevzner. DipSPAdes: Assembler for Highly Polymorphic Diploid Genomes)
dipSpades Beats Haplomerger Hands Down in Diploid Assembly
The following talks also appear interesting -
c) Siavash Mirarab, Nam-Phuong Nguyen and Tandy Warnow. PASTA: ultra-large multiple sequence alignment
? Divide-and-conquer approach to alignment
? Decomposes the taxa set into small subsets
? Aligns the subsets using a base alignment
method
? Merges the subset alignments into a full MSA
? Co-estimates a phylogenetic tree
d) Ngan Nguyen, Glenn Hickey, Daniel Zerbino, Brian Raney, Dent Earl, Joel Armstrong, David Haussler and Benedict Paten. Building a Pangenome Reference for a Population
e) Henry C.M. Leung, S.M. Yiu and Francis Chin. IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information
Code can be downloaded from here
f) Derek Aguiar, Eric Morrow and Sorin Istrail. Tractatus: an exact and subquadratic algorithm for inferring identity-by-descent multi-shared haplotype tracts
Here is what the community likes (according to Springer) -
We looked for the last paper, but found this one instead (same authors, different title, different year). How different is their approach compared to Sailfish by Petro?
An Alignment-free Regression Approach to Estimating Allele-Speci c Expression in F1 Animals
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The remaining ones are given below.
Accepted Papers for RECOMB 2014
Jianzhu Ma, Sheng Wang and Jinbo Xu. MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
Siavash Mirarab, Nam-Phuong Nguyen and Tandy Warnow. PASTA: ultra-large multiple sequence alignment
Wen-Yun Yang, Farhad Hormozdiari, Eleazar Eskin and Bogdan Pasaniuc. A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation
Emily Berger, Deniz Yorukoglu and Bonnie Berger. HapTree: A novel Bayesian framework for single individual polyplotyping using NGS data
Ngan Nguyen, Glenn Hickey, Daniel Zerbino, Brian Raney, Dent Earl, Joel Armstrong, David Haussler and Benedict Paten. Building a Pangenome Reference for a Population
Zhanyong Wang, Jae-Hoon Sul, Sagi Snir, Jose A. Lozano and Eleazar Eskin. Gene-Gene Interactions Detection Using A Two-stage Model
Arne Mller, Frank Bruggeman, Brett Olivier and Leen Stougie. Fast Flux Module Detection using Matroid Theory
Shaun Mahony, Matthew Edwards, Esteban Mazzoni, Richard Sherwood, Akshay Kakumanu, Carolyn Morrison, Hynek Wichterle and David Gifford. An integrated model of multiple-condition ChIP-seq data reveals predeterminants of Cdx2 binding
Rui Wang and Scott Schmidler. Bayesian Multiple Protein Structure Alignment
Jianling Zhong, Todd Wasson and Alexander Hartemink. Learning protein-DNA interaction landscapes by integrating experimental data through computational models
Ewa Szczurek and Niko Beerenwinkel. Modeling mutual exclusivity of cancer mutations
Marinka Zitnik and Blaz Zupan. Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion
Hamidreza Chitsaz and Mohammad Aminisharifabad. Exact Learning of RNA Energy Parameters From Structure
Shutan Xu, Shuxue Zou and Lincong Wang. A geometric clustering algorithm and its applications to structural data
Armin Tpfer, Tobias Marschall, Rowena A Bull, Fabio Luciani, Alexander Schnhuth and Niko Beerenwinkel. Viral quasispecies assembly via maximal clique enumeration
Yana Safonova, Anton Bankevich and Pavel Pevzner. DipSPAdes: Assembler for Highly Polymorphic Diploid Genomes
Jan Hoinka, Alexey Berezhnoy, Zuben E. Sauna, Eli Gilboa and Teresa Przytycka. AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application
Mingfu Shao, Yu Lin and Bernard Moret. An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes
Kelley Harris, Sara Sheehan, John Kamm and Yun S. Song. Decoding Coalescent Hidden Markov Models in Linear Time
Chen-Ping Fu, Vladimir Jojic and Leonard Mcmillan. An Alignment-Free Regression Approach for Estimating Allele-Specific Expression using RNA-Seq Data
Henry C.M. Leung, S.M. Yiu and Francis Chin. IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information
Arun Konagurthu, Parthan Kasarapu, Lloyd Allison, James Collier and Arthur Lesk. On sufficient statistics of least-squares superposition of vector sets
Yu Zheng and Louxin Zhang. Reconciliation with Non-binary Gene Trees Revisited
Keith Noto, Carla Brodley, Saeed Majidi, Diana Bianchi and Donna Slonim. CSAX: Characterizing Systematic Anomalies in eXpression Data
Adrian Guthals, Christina Boucher and Nuno Bandeira. The generating function approach for peptide identification in spectral networks
Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin, Colin Collins, Gholamreza Haffari and S. Cenk Sahinalp. HIT.nDRIVE: Multi-Driver Gene Prioritization based on Hitting Time
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau and Alexander Schoenhuth. WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared Simpson and Paul Medvedev. On the representation of de Bruijn graphs
Adam Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael Jordan, David Patterson, Bin Yu and Yun Song. Changepoint Analysis for Efficient Variant Calling
Y. William Yu, Deniz Yorukoglu and Bonnie Berger. Traversing the k-mer landscape of NGS read datasets for quality score sparsification
Hetu Kamisetty, Bornika Ghosh, Christopher James Langmead and Chris Bailey- Kellogg. Learning Sequence Determinants of Protein:protein Interaction Specificity with Sparse Graphical Models
Ben Raphael and Fabio Vandin. Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data
Shay Zakov and Vineet Bafna. Reconstructing Breakage Fusion Bridge architectures using noisy copy numbers
Derek Aguiar, Eric Morrow and Sorin Istrail. Tractatus: an exact and subquadratic algorithm for inferring identity-by-descent multi-shared haplotype tracts
Hua Wang, Heng Huang and Chris Ding. Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency
