Abstract is missing.
- Ancient angiosperm hexaploidy meets ancestral eudicot gene orderChunfang Zheng, Victor A. Albert, Eric Lyons, David Sankoff. 1-6 [doi]
- Invited: Using novel small RNAs to understand genome structure and functionRachel J. O'Neill, Mark Longo, Chu Zhang, Sarah Trusiak, Laura Hall, Judy Brown, Craig Obergfell. 1 [doi]
- Effects of rooting via outgroups on ingroup topology in phylogenyMargareta Ackerman, Dan Brown, David Loker. 1-7 [doi]
- Finding consensus stable local optimal structures for aligned RNA sequencesYuan Li, Shaojie Zhang. 1-6 [doi]
- Periodic rigidity of protein crystal structuresPamela Clark, Jessica Grant, Samantha Monastra, Filip Jagodzinski, Ileana Streinu. 1-6 [doi]
- Demarcation of bacterial ecotypes from DNA sequence data: A comparative analysis of four algorithmsJuan Carlos Francisco, Frederick Cohan, Danny Krizanc. 1-6 [doi]
- Workshop: Transcriptome assembly and isoform expression level estimation from biased RNA-Seq readsWei Li 0035, Tao Jiang. 1 [doi]
- Hierarchical factor modeling of proteomics dataRicardo Henao, J. Will Thompson, M. Arthur Moseley, Geoffrey S. Ginsburg, Lawrence Carin, Joseph E. Lucas. 1-6 [doi]
- Poster: In silico microarray algorithm: Accurate and fast taxonomic profiling from short read sequencesTomoya Tagami, Tsuyoshi Hachiya, Yasubumi Sakakibara. 1 [doi]
- Workshop: Taxonomic clustering of large-scale metagnomic dataSrinivas Aluru. 1 [doi]
- Workshop: Comparative assembly of metagenomic sequencesBo Liu, Mihai Pop. 1 [doi]
- Pairwise sequence alignment for very long sequences on GPUsJunjie Li, Sanjay Ranka, Sartaj Sahni. 1-6 [doi]
- Shifting the bioinformatics computing paradigm: A case study in parallelizing genome annotation using MAKER and Work QueueAndrew Thrasher, Douglas Thain, Scott J. Emrich, Zachary Musgrave. 1-6 [doi]
- Discovering non-coding RNA elements in drosophila 3′ untranslated regionsCuncong Zhong, Justen Andrews, Shaojie Zhang. 1-6 [doi]
- A gene signature based method for identifying subtypes and subtype-specific drivers in cancer with an application to medulloblastomaPeikai Chen, Y. S. Hung, Tsz-Kwong Man, Ching C. Lau, Yubo Fan, Stephen T. C. Wong. 1-6 [doi]
- Volume matching with application in medical treatment planningYam Ki Cheung, Ovidiu Daescu, J. Steven Kirtzic, Lech Papiez. 1-6 [doi]
- Workshop: An efficient data structure for exact-match overlap graphs and next generation sequence assemblyHieu Dinh, Sanguthevar Rajasekaran. 1 [doi]
- Invited: Reverse engineering whole-genome networksSrinivas Aluru. 1 [doi]
- Towards accurate modeling for protein rigidity analysisNaomi Fox, Ileana Streinu. 1-6 [doi]
- Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distributionSerghei Mangul, Adrian Caciula, Ion I. Mandoiu, Alexander Zelikovsky. 1 [doi]
- Poster: Accurate scaffolding of large genomes using integer programming and Non-Serial Dynamic ProgrammingJames Lindsay, Ion I. Mandoiu, Hamed Salooti, Alexander Zelikovsky. 1 [doi]
- Workshop: Inference of allele specific expression levels from RNA-Seq dataSahar Al Seesi, Ion I. Mandoiu. 1 [doi]
- Invited: A protein domain-centric approach to translational bioinformaticsMaricel G. Kann. 1 [doi]
- Poster evaluation of the level set method by using similarity criterion (KCC) for clustering and analysis of functional MRI dataMaryam Rahimi, Mohamadali Oghabiyan. 1 [doi]
- Decision procedure based discovery of rare behaviors in Stochastic Differential Equation models of biological systemsArup K. Ghosh, Faraz Hussain, Sumit Kumar Jha, Christopher James Langmead, Susmit Jha. 1-6 [doi]
- A Bayesian network for early diagnosis of sepsis patients: a basis for a clinical decision support systemEren Gultepe, Hien Nguyen, Timothy E. Albertson, Ilias Tagkopoulos. 1-5 [doi]
- Poster: Characterization of distinguishing regions for Renal Cell Carcinoma discriminationItalo Zoppis, Massimiliano Borsani, Erica Gianazza, Clizia Chinello, Giancarlo Albo, Francesco Rocco, André M. Deelder, Yuri E. M. van der Burgt, Marco Antoniotti, Fulvio Magni, Giancarlo Mauri. 1 [doi]
- Workshop: Error correction, noise filtering, and phylogenetic analysis of HIV sequences using the 454 platformKonrad Scheffler, N. Lance Hepler, Martin D. Smith, Wayne Delport, Art F. Y. Poon, Douglas D. Richman, Sergei L. Kosakovsky Pond. 1 [doi]
- Poster: Public health applications of metagenomic data using publicly available computing frameworkMarissa Smith, Jesse Port, Jame C. Wallace, Elaine Faustman. 1 [doi]
- Poster title (mass spectrometric protein profiling analyses of pathological and physiological hypertrophy cardiac muscle tissues)Hyekyeong Kwon, Jang-Soo Chun, Zee-Yong Park, Dong-Yu Kim. 1 [doi]
- Keynote: De novo sequencing of novel peptide antibiotics by tandem mass spectrometryPavel A. Pevzner. 1 [doi]
- The use of graph matching algorithms to identify biochemical substructures in synthetic chemical compounds: Application to metabolomicsMai Hamdalla, David F. Grant, Ion I. Mandoiu, Dennis W. Hill, Sanguthevar Rajasekaran, Reda A. Ammar. 1-6 [doi]
- Keynote: Aspects of fractionationDavid Sankoff. 1 [doi]
- Invited: Discovering combinatorial biomarkersGowtham Atluri, Sanjoy Dey, Gang Fang, Sean Landman, Vanja Paunic, Wen Wang, Michael Steinbach, Vipin Kumar. 1-2 [doi]
- Workshop: Calling Structural Variation with low-coverage sequencing data by mapping to focal regionJin Zhang, Yufeng Wu. 1 [doi]
- Workshop: Bioinformatics methods for reconstruction of Infectious Bronchitis Virus quasispecies from next generation sequencing dataRachel J. O'Neill, Ion I. Mandoiu, Mazhar I. Khan, Craig Obergfell, Hongjun Wang, Andrew Bligh, Bassam Tork, Nicholas Mancuso, Alexander Zelikovsky. 1 [doi]
- Poster: De novo expression fragment assembly from Spanning Trees (EAST)Yuan Zhang, Dhananjai Rao, Mufit Ozden, Jens Mueller, Praveen Raj Kumar, Chun Liang, John E. Karro. 1 [doi]
- Workshop: Graph compression approaches in assemblyJason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown. 1-2 [doi]
- A machine learning framework for trait based genomicsWei Zhang, Erliang Zeng, Dan Liu, Stuart Jones, Scott J. Emrich. 1-6 [doi]
- Poster: Applying data mining algorithms to early detection of liver cancerFabiola M. R. Pinheiro, Mu-Hsing Kuo. 1 [doi]
- Poster: Randomized algorithms for planted Motif SearchJerlin C. Merlin, Hieu Dinh. 1 [doi]
- Workshop: Opportunities and challenges of non-model ecoinformaticsScott J. Emrich. 1 [doi]
- Poster: Sequence classification of homopolymer emissions (SCOPE)James T. Morton, Patricia Abrudan, Chun Liang, John E. Karro. 1 [doi]
- Poster: Image registration and visualization tool for in-situ gene expression imagesErnur Saka, Eric C. Rouchka. 1 [doi]
- PMS6: A fast algorithm for motif discoveryShibdas Bandyopadhyay, Sartaj Sahni, Sanguthevar Rajasekaran. 1-6 [doi]
- A robust, library-based, optimization-driven method for automatic gene circuit designLinh Hunyh, Ilias Tagkopoulos. 1-6 [doi]
- Workshop: A maximum likelihood method for quasispecies spectrum assemblyNicholas Mancuso, Bassam Tork, Pavel Skums, Lilia Ganova-Raeva, Ion I. Mandoiu, Alexander Zelikovsky. 1 [doi]
- The ruzzo-tompa algorithm can find the maximal paths in weighted, directed graphs on a one-dimensional latticeJohn L. Spouge, Leonardo Mariño-Ramírez, Sergey Sheetlin. 1-6 [doi]
- Invited: From protein networks to disease mechanismsRoded Sharan. 1 [doi]
- Invited: Algorithmic challenges in DNA sequencing and disease associationBjarni V. Halldórsson. 1 [doi]
- Invited: Computational behavioral ecologyTanya Y. Berger-Wolf. 1 [doi]
- Workshop: Algorithms for discovery of mutated pathways in cancerFabio Vandin, Eli Upfal, Benjamin J. Raphael. 1 [doi]
- Workshop: Robust algorithms for inferring haplotype phase and deletion polymorphism from high-throughput whole genome sequence dataDerek Aguiar, Sorin Istrail. 1 [doi]
- Parameter discovery for stochastic biological models against temporal behavioral specifications using an SPRT based Metric for simulated annealingFaraz Hussain, Raj Gautam Dutta, Sumit Kumar Jha, Christopher James Langmead, Susmit Jha. 1-6 [doi]
- A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete informationYuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni. 1-6 [doi]
- Poster: Parameter estimation for a reduced order spiking neuron model with relevance to in vitro embryonic rat motoneuronal dataLingfei Zhi, Zhao Wang, Aman Behal. 1 [doi]
- Signal extraction from movies of honeybee brain activity by convex analysisMartin Strauch, Julia Rein, C. Giovanni Galizia. 1-6 [doi]
- Poster: MIGL - a database for identifying the mechanisms of intron gain and lossPaul Yenerall, Yuanyuan Jiang, Leming Zhou. 1 [doi]
- Filtering of MS/MS data for peptide identificationJason Gallia, Katelyn Lavrich, Rachel McGough, Anna Tan-Wilson, Patrick H. Madden. 1-6 [doi]
- Automatic B cell lymphoma detection using flow cytometry dataMing-Chih Shih, Shou-Hsuan Stephen Huang, Youli Zu, Rachel Donohue, Chung-Che Jeff Chang. 1-6 [doi]
- Workshop: Gene fusion detection with short and medium length next generation sequencingOnur Sakarya, Heinz Breu. 1 [doi]
- Identifying cancer biomarkers by knowledge discovery from medical literatureKhaled Dawoud, Ala Qabaja, Shang Gao, Reda Alhajj, Jon G. Rokne. 1 [doi]
- Accelerating gene regulatory networks inference through GPU/CUDA programmingFabrizio F. Borelli, Raphael Y. de Camargo, David C. Martins, Beatriz Stransky, Luiz C. S. Rozante. 1-6 [doi]
- Invited: Identifying mutations from TILLING experimentsVladimir Filkov. 1 [doi]