RECOMB-Seq Accepted Papers Announced

RECOMB-Seq 2014, satellite workshop for sequence analysis methods to be held just before the main RECOMB conference at Pittsburgh has announced the list of accepted papers. The RECOMB-Seq accepted papers will be published in a special proceedings issue of BMC Bioinformatics. Here are the titles of the accepted papers.


  1. On the Complexity of Minimum Path Cover with Subpath Constraints for Multi-assembly by Romeo Rizzi, Alexandru I. Tomescu and Veli Mäkinen.
  2. SWAP-Assembler:  Scalable and Efficient Genome Assembly towards Thousands of Cores, Jintao Meng and Yanjie Wei.
  3. Near-optimal  Assembly for Shotgun Sequencing with Noisy Reads, Ka-Kit Lam, Asif Khalak and David Tse.
  4. ILP-based Maximum Likelihood Genome Scaffolding by  James Lindsay, Hamed Salooti, Alex Zelikovsky and Ion Mandoiu.

 RNA-Seq and Technology

  1. BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-seq data by Jingua Gu, Xiao Wang, Leena Hilakivi-Clarke, Robert Clarke and Jianhua Xuan.
  2. Adaptive Compressed Genome Sequencing Using Depth First Search Strategy by Zeinab Taghavi.
  3. Piecing the puzzle together: A revisit to transcription reconstruction problem RNA-seq by Yan Huang, Yin Hu and Jinze Liu

Emerging Trends

  1. Fast Lossless Compression via Cascading Bloom Filters, Roye Rozov, Ron Shamir and Eran Halperin.
  2. PuFFIN – A Parameter-free Method to Build Nucleosome Maps from Paired-end Reads by Anton Polishko, Evelien Bunnik, Karine Le Roch and Stefano Lonardi.


  1. Assembly-free Genome Comparison based on Next-Generation Sequencing Reads and Variable Length Patterns, by Matteo Comin and Michele Schimd.
  2. ARYANA: Aligning Reads by Yet Another Approach by Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi, Hamidreza Chitsaz and Mehdi Sadeghi.
  3. ProbeAlign: Incorporating high-throughput sequencing-based structure probing information into ncRNA homology search by Ping Ge, Cuncong Zhong and Shaojie Zhang.
  4. CASPER: Context-Aware Scheme for Paired-End Read from high-throughput amplicon sequencing by Sunyoung Kwon, Byunghan Lee and Sungroh Yoon.


  1. Detecting Epigenetic Motifs in Low Coverage and Metagenomics Settings by Noam D. Beckmann, Sashank Karri, Ali Bashir and Gang Fang.
  2.  A better sequence-read simulator program for metagenomics  by Stephen Johnson, Brett Trost, Jeffrey Long, Vanessa Pittet and Anthony Kusalik.
  3. Gene finding in metatransciptomic sequences by Wazim Mohammed Ismail, Yuzhen Ye and Haixu Tang.

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