RECOMB 2014 Talks

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

Slides, Paper

? 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

download code here

Here is what the community likes (according to Springer) -

Capture

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



Written by M. //