Proceedings of RECOMB-Seq

Full Proceedings Papers

2014

• Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns. Matteo Comin and Michele Schimd. BMC Bioinformatics 15 (Suppl 9) S1 (2014)
• SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores. Jintao Meng, Bingqiang Wang, Yanjie Wei, Shengzhong Feng and Pavan Balaji. BMC Bioinformatics 15 (Suppl 9) S2 (2014)
• Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq. Yan Huang, Yin Hu and Jinze Liu. BMC Bioinformatics 15 (Suppl 9) S3 (2014)
• Near-optimal assembly for shotgun sequencing with noisy reads. Ka-Kit Lam, Asif Khalak and David Tse. BMC Bioinformatics 15 (Suppl 9) S4 (2014)
• On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly. Romeo Rizzi, Alexandru I Tomescu and Veli Mäkinen. BMC Bioinformatics 15 (Suppl 9) S5 (2014)
• BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data. Jinghua Gu, Xiao Wang, Leena Halakivi-Clarke, Robert Clarke and Jianhua Xuan. BMC Bioinformatics 15 (Suppl 9) S6 (2014)
• Fast lossless compression via cascading Bloom filters. Roye Rozov, Ron Shamir and Eran Halperin. BMC Bioinformatics 15 (Suppl 9) S7 (2014)
• Gene finding in metatranscriptomic sequences. Wazim Mohammed Ismail, Yuzhen Ye and Haixu Tang. BMC Bioinformatics 15 (Suppl 9) S8 (2014)
• ILP-based maximum likelihood genome scaffolding. James Lindsay, Hamed Salooti, Ion Măndoiu and Alex Zelikovsky. BMC Bioinformatics 15 (Suppl 9) S9 (2014)
• CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing. Sunyoung Kwon, Byunghan Lee and Sungroh Yoon. BMC Bioinformatics 15 (Suppl 9) S10 (2014)
• PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads. Anton Polishko, Evelien M Bunnik, Karine G Le Roch and Stefano Lonardi. BMC Bioinformatics 15 (Suppl 9) S11 (2014)
• ARYANA: Aligning Reads by Yet Another Approach. Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi, Hamidreza Chitsaz and Mehdi Sadeghi. BMC Bioinformatics 15 (Suppl 9) S12 (2014)
• Ensemble analysis of adaptive compressed genome sequencing strategies. Zeinab Taghavi. BMC Bioinformatics 15 (Suppl 9) S13 (2014)
• A better sequence-read simulator program for metagenomics. Stephen Johnson, Brett Trost, Jeffrey R Long, Vanessa Pittet and Anthony Kusalik. BMC Bioinformatics 15 (Suppl 9) S14 (2014)
• ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search. Ping Ge, Cuncong Zhong and Shaojie Zhang. BMC Bioinformatics 15 (Suppl 9) S15 (2014)
• Detecting epigenetic motifs in low coverage and metagenomics settings. Noam D Beckmann, Sashank Karri, Gang Fang and Ali Bashir. BMC Bioinformatics 15 (Suppl 9) S16 (2014)

2013

• Discovering motifs that induce sequencing errors. Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G Costa, Sven Rahmann and Tobias Marschall. BMC Bioinformatics 14 (Suppl 5) S1 (2013)
• metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. Christina Ander, Ole B Schulz-Trieglaff, Jens Stoye and Anthony J Cox. BMC Bioinformatics 14 (Suppl 5) S2 (2013)
• Joint genotype inference with germline and somatic mutations. Eric Bareke, Virginie Saillour, Jean-François Spinella, Ramon Vidal, Jasmine Healy, Daniel Sinnett and Miklós Csűrös. BMC Bioinformatics 14 (Suppl 5) S3 (2013)
• Discovering and mapping chromatin states using a tree hidden Markov model. Jacob Biesinger, Yuanfeng Wang and Xiaohui Xie. BMC Bioinformatics 14 (Suppl 5) S4 (2013)
• Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles. Jie Zhu, Yufang Qin, Taigang Liu, Jun Wang and Xiaoqi Zheng. BMC Bioinformatics 14 (Suppl 5) S5 (2013)
• Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data. Matthew Hayes and Jing Li. BMC Bioinformatics 14 (Suppl 5) S6 (2013)
• De Bruijn superwalk with multiplicities problem is NP-hard. Evgeny Kapun and Fedor Tsarev. BMC Bioinformatics 14 (Suppl 5) S7 (2013)
• A random-permutations-based approach to fast read alignment. Roy Lederman. BMC Bioinformatics 14 (Suppl 5) S8 (2013)
• Assembling contigs in draft genomes using reversals and block-interchanges. Chi-Long Li, Kun-Tze Chen and Chin Lung Lu. BMC Bioinformatics 14 (Suppl 5) S9 (2013)
• An optimized algorithm for detecting and annotating regional differential methylation. Sheng Li, Francine E Garrett-Bakelman, Altuna Akalin, Paul Zumbo, Ross Levine, Bik L To, Ian D Lewis, Anna L Brown, Richard J D’Andrea, Ari Melnick and Christopher E Mason. BMC Bioinformatics 14 (Suppl 5) S10 (2013)
• A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues. Yi Li and Xiaohui Xie. BMC Bioinformatics 14 (Suppl 5) S11 (2013)
• Gene prediction in metagenomic fragments based on the SVM algorithm. Yongchu Liu, Jiangtao Guo, Gangqing Hu and Huaiqiu Zhu. BMC Bioinformatics 14 (Suppl 5) S12 (2013)
• Evaluating genome architecture of a complex region via generalized bipartite matching. Christine Lo, Sangwoo Kim, Shay Zakov and Vineet Bafna. BMC Bioinformatics 14 (Suppl 5) S13 (2013)
• CLASS: constrained transcript assembly of RNA-seq reads. Li Song and Liliana Florea. BMC Bioinformatics 14 (Suppl 5) S14 (2013)
• A novel min-cost flow method for estimating transcript expression with RNA-Seq. Alexandru I Tomescu, Anna Kuosmanen, Romeo Rizzi and Veli Mäkinen. BMC Bioinformatics 14 (Suppl 5) S15 (2013)
• Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing. Xi Wang and Murray J Cairns. BMC Bioinformatics 14 (Suppl 5) S16 (2013)
• De novo inference of stratification and local admixture in sequencing studies. Yu Zhang. BMC Bioinformatics 14 (Suppl 5) S17 (2013)
• Optimal assembly for high throughput shotgun sequencing. Guy Bresler, Ma’ayan Bresler and David Tse. BMC Bioinformatics 14 (Suppl 5) S18 (2013)

2012

• Exploiting sparseness in de novo genome assembly. Chengxi Ye, Zhanshan Sam Ma, Charles H Cannon, Mihai Pop and Douglas W Yu. BMC Bioinformatics 13 (Suppl 6), S1 (2012).
• MGMR: leveraging RNA-Seq population data to optimize expression estimation. Roye Rozov, Eran Halperin and Ron Shamir. BMC Bioinformatics 13 (Suppl 6), S2 (2012).
• Haplotype reconstruction using perfect phylogeny and sequence data. Anatoly Efros and Eran Halperin. BMC Bioinformatics 13 (Suppl 6), S3 (2012).
• Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. Ekaterina E Khrameeva and Mikhail S Gelfand. BMC Bioinformatics 13 (Suppl 6), S4 (2012).
• KIS SPLICE: de-novo calling alternative splicing events from RNA-seq data. Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix. BMC Bioinformatics 13 (Suppl 6), S5 (2012).
• An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data. Jin Zhang, Jiayin Wang and Yufeng Wu. BMC Bioinformatics 13 (Suppl 6), S6 (2012).
• PAIR: polymorphic Alu insertion recognition. Jón Ingi Sveinbjörnsson and Bjarni V Halldórsson. BMC Bioinformatics 13 (Suppl 6), S7 (2012).
• High-resolution genetic mapping with pooled sequencing. Matthew D Edwards and David K Gifford. BMC Bioinformatics 13 (Suppl 6), S8 (2012).
• A context-based approach to identify the most likely mapping for RNA-seq experiments. Thomas Bonfert, Gergely Csaba, Ralf Zimmer and Caroline C Friedel. BMC Bioinformatics 13 (Suppl 6), S9 (2012).
• Reconstructing cancer genomes from paired-end sequencing data. Layla Oesper, Anna Ritz, Sarah J Aerni, Ryan Drebin and Benjamin J Raphael. BMC Bioinformatics 13 (Suppl 6), S10 (2012).
• Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. Boyko Kakaradov, Hui Yuan Xiong, Leo J Lee, Nebojsa Jojic and Brendan J Frey. BMC Bioinformatics 13 (Suppl 6), S11 (2012).

2011

• Inferring viral spectrum from 454 pyrosequencing reads. Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion Mandoiu, Peter Balfe and Alex Zelikovsky. BMC Bioinformatics 12 (Suppl 6), S1 (2011).
• Genotyping common and rare variation using overlapping pool sequencing. Dan He, Noah Zaitlen, Bogdan Pasaniuc, Eleazar Eskin and Eran Halperin. BMC Bioinformatics 12 (Suppl 6), S2 (2011).
• Assembly of non-unique insertion content using next-generation sequencing. Nathaniel Parrish, Farhad Hormozdiari and Eleazar Eskin. BMC Bioinformatics 12 (Suppl 6), S3 (2011).
• A Hidden Markov Model for copy number variant prediction from whole genome resequencing data. Yufeng Shen, Yiwei Gu and Itsik Pe’Er. BMC Bioinformatics 12 (Suppl 6), S4 (2011).

Short Talks Selected from Abstracts

2011

• A whole-genome probe design for massively parallel variant validation using selective circularization. Daniel Newburger, Georges Natsoulis, Hua Xu, Sue Grimes, John Bell and Hanlee Ji.
• Accurate estimation of gene expression levels from DGE sequencing data. Marius Nicolae and Ion Mandoiu.
• Constrained traversal of repeats with paired sequences. Sébastien Boisvert, Élénie Godzaridis, François Laviolette and Jacques Corbeil.
• Contig graph mining for duplication breakpoints. Jurgen F. Nijkamp, Jean-Marc Daran, Marcel J.T. Reinders and Dick De Ridder.
• Counting k-mers with a Bloom Filter. Pall Melsted and Jonathan Pritchard.
• Finding deletions with exact break points from noisy low coverage paired-end short sequence reads. Jin Zhang and Yufeng Wu.
• Improved variant discovery and allele frequency estimation from pooled dna resequencing with Bayesian latent class analysis and compositional bias models. Shom Paul and Aaron Mackey.
• Modeling and automation of sequencing-based determination of RNA structure. Sharon Aviran, Cole Trapnell, Julius Lucks, Stefanie Mortimer, Shujun Luo, Gary Schroth, Jennifer Doudna, Adam Arkin and Lior Pachter.
• mTiM: margin-based transcript mapping from RNA-seq. Georg Zeller, Nico Goernitz, Gunnar Raetsch, Jonas Behr, Andre Kahles, Soeren Sonnenburg and Pramod Mudrakarta.
• Separating metagenomic data into genomes via clustering. Olga Tanaseichuk and Tao Jiang.
• TavernaPBS: custom next-generation sequence analysis workflows using high-performance computing resources with Taverna and PBS. Mark Lawson, Paul Shuber and Aaron Mackey.

Posters

2011

• Epigenetics of atherosclerosis. Lauren Mills, Brian Wamhoff, Brett Blackman, Aaron Mackey and Jessica Connelly.
• Genome-scale analysis of promoter melting in eukaryotic gene transcription. Fedor Kouzine, Damian Wójtowicz, Arito Yamane, Wolfgang Resch, Teresa M. Przytycka, David Levens and Rafael Casellas.
• Haplotype discovery based on unassembled sequences estimation. Serghei Mangul and Alex Zelikovsky.
• RGASP evaluation of RNA-seq read alignment algorithms. Andre Kahles, Regina Bohnert, Paolo Ribeca, Jonas Behr and Gunnar Raetsch.
• Screening for transposable element-induced adaptations in Drosophila melanogaster using next-gen sequencing data. Anna-Sophie Fiston-Lavier, Dmitri Petrov and Josefa Gonzalez.
• SeqMDD: symbolic data structures for accurate mapping. Marco Beccuti, Francesca Cordero, Susanna Donatelli and Raffaele Calogero.
• SlideSort: A fast and exact tool for finding all similar pairs from next-generation sequencing data. Kana Shimizu and Koji Tsuda.
• Smarti - A fast short read alignment algorithm. Florian Schatz, Sascha Möller and Manfred Schimmler.
• Toward assessing the quality of de novo assembly. Rasiah Loganantharaj.