BMC Bioinformatics, Volume 15 - Supplements

Volume 15, Number S-1, January 2014

Integrated Bio-Search: Selected Works from the 12th International Workshop on Network Tools and Applications in Biology (NETTAB 2012)

• 
  Paolo Romano, Frédérique Lisacek, Marco Masseroli:
  NETTAB 2012 on "Integrated Bio-Search". S1
• 
  Marco Masseroli, Barend Mons, Erik Bongcam-Rudloff, Stefano Ceri, Alexander E. Kel, François Rechenmann, Frédérique Lisacek, Paolo Romano:
  Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. S2
• 
  Marco Masseroli, Matteo Picozzi, Giorgio Ghisalberti, Stefano Ceri:
  Explorative search of distributed bio-data to answer complex biomedical questions. S3
• 
  Gianvito Pio, Donato Malerba, Domenica D'Elia, Michelangelo Ceci:
  Integrating microRNA target predictions for the discovery of gene regulatory networks: a semi-supervised ensemble learning approach. S4
• 
  Víctor Martínez, Carlos Cano, Armando Blanco:
  ProphNet: A generic prioritization method through propagation of information. S5
• 
  Paolo Cremaschi, Sergio Rovida, Lucia Sacchi, Antonella Lisa, Francesca Calvi, Alessandra Montecucco, Giuseppe Biamonti, Silvia Bione, Gianni Sacchi:
  CorrelaGenes: a new tool for the interpretation of the human transcriptome. S6
• 
  Francesca Finotello, Enrico Lavezzo, Luca Bianco, Luisa Barzon, Paolo Mazzon, Paolo Fontana, Stefano Toppo, Barbara Di Camillo:
  Reducing bias in RNA sequencing data: a novel approach to compute counts. S7
• 
  Luca Zammataro, Rita DeMolfetta, Gabriele Bucci, Arnaud Céol, Heiko Müller:
  AnnotateGenomicRegions: a web application. S8
• 
  Matthew P. Campbell, René Ranzinger, Thomas Lütteke, Julien Mariethoz, Catherine A. Hayes, Jingyu Zhang, Yukie Akune, Kiyoko F. Aoki-Kinoshita, David Damerell, Giorgio Carta, William S. York, Stuart M. Haslam, Hisashi Narimatsu, Pauline M. Rudd, Niclas G. Karlsson, Nicolle H. Packer, Frédérique Lisacek:
  Toolboxes for a standardised and systematic study of glycans. S9
• 
  Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi:
  A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units. S10
• 
  Alejandra N. González-Beltrán, Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra:
  The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. S11
• 
  Sarah Cohen Boulakia, Jiuqiang Chen, Paolo Missier, Carole A. Goble, Alan R. Williams, Christine Froidevaux:
  Distilling structure in Taverna scientific workflows: a refactoring approach. S12
• 
  Piergiorgio Palla, Gianfranco Frau, Laura Vargiu, Patricia Rodriguez-Tomé:
  QTREDS: a Ruby on Rails-based platform for omics laboratories. S13
• 
  Federica Viti, Silvia Scaglione, Alessandro Orro, Luciano Milanesi:
  Guidelines for managing data and processes in bone and cartilage tissue engineering. S14
• 
  Emilie Pasche, Julien Gobeill, Olivier Kreim, Fatma Oezdemir-Zaech, Thérèse Vachon, Christian Lovis, Patrick Ruch:
  Development and tuning of an original search engine for patent libraries in medicinal chemistry. S15

Volume 15, Number S-2, January 2014

Selected articles from the Twelfth Asia Pacific Bioinformatics Conference (APBC 2014): Bioinformatics

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  Daniel Asarnow, Rahul Singh:
  Automatic classification of protein structures using low-dimensional structure space mappings. S1
• 
  Pablo A. Jaskowiak, Ricardo J. G. B. Campello, Ivan G. Costa:
  On the selection of appropriate distances for gene expression data clustering. S2
• 
  Bin Liu, Jinghao Xu, Quan Zou, Ruifeng Xu, Xiaolong Wang, Qingcai Chen:
  Using distances between Top-n-gram and residue pairs for protein remote homology detection. S3
• 
  Wenting Liu, Kui Miao, Guangxia Li, Kuiyu Chang, Jie Zheng, Jagath C. Rajapakse:
  Extracting rate changes in transcriptional regulation from MEDLINE abstracts. S4
• 
  Jiajie Peng, Yadong Wang, Jin Chen:
  Towards integrative gene functional similarity measurement. S5
• 
  Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu:
  Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels. S6
• 
  Dipan Lal Shaw, A. S. M. Shohidull Islam, M. Sohel Rahman, Masud Hasan:
  Protein folding in HP model on hexagonal lattices with diagonals. S7
• 
  Qingyao Wu, Yunming Ye, Michael K. Ng, Shen-Shyang Ho, Ruichao Shi:
  Collective prediction of protein functions from protein-protein interaction networks. S9
• 
  Denan Zhang, Guohua Wang, Yadong Wang:
  Transcriptional regulation prediction of antiestrogen resistance in breast cancer based on RNA polymerase II binding data. S10

Volume 15, Number S-3, February 2014

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  Tomás Di Domenico, Cynthia Prudence, Esmeralda Vicedo, Emre Guney, Anupama Jigisha, Avinash Kumar Shanmugam:
  Highlights from the ISCB Student Council Symposium 2013. A1
• 
  Han Lie:
  Towards breaking the curse of dimensionality in computational methods for the conformational analysis of molecules. A2
• 
  Achchuthan Shanmugasundram, Faviel F. Gonzalez-Galarza, Jonathan M. Wastling, Olga Vasieva, Andrew R. Jones:
  An integrated approach to understand apicomplexan metabolism from their genomes. A3
• 
  Séverine Affeldt, Param Priya Singh, Giulia Malaguti, Hervé Isambert:
  On the expansion of "dangerous" gene families in vertebrates. A4
• 
  Aya Narunsky, Nir Ben-Tal:
  ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure. A5
• 
  Nathan Medina-Rodríguez, Ángelo Santana, Ana M. Wägner, José M. Quinteiro:
  alleHap: an efficient algorithm to reconstruct zero-recombinant haplotypes from parent-offspring pedigrees. A6
• 
  Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch:
  Oqtans: a multifunctional workbench for RNA-seq data analysis. A7
• 
  Maribel Hernandez-Rosales, Nicolas Wieseke, Marc Hellmuth, Peter F. Stadler:
  Simulation of gene family histories. A8
• 
  Nadezda Kryuchkova, Marc Robinson-Rechavi:
  Determinants of protein evolutionary rates in light of ENCODE functional genomics. A9

Volume 15, Number S-4, March 2014

• 
  Anne S. De Groot, Phoebe De Groot, Yongqun He:
  ICoVax 2013: The 3^rd ISV Pre-conference Computational Vaccinology Workshop. I1
• 
  Lu He, Anne S. De Groot, Andres H. Gutiérrez, William D. Martin, Lenny Moise, Chris Bailey-Kellogg:
  Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage. S1
• 
  Rebecca Racz, Xinna Li, Mukti Patel, Zuoshuang Xiang, Yongqun He:
  DNAVaxDB: the first web-based DNA vaccine database and its data analysis. S2
• 
  Peng Fu, Linlin Yang, Yi Sun, Li Ye, Zhiwei Cao, Kailin Tang:
  Target network differences between western drugs and Chinese herbal ingredients in treating cardiovascular disease. S3

Volume 15, Number S-5, May 2014

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  Safwat Abdel-Azeim, Edrisse Chermak, Anna Vangone, Romina Oliva, Luigi Cavallo:
  MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories. S1
• 
  Gianni D'Angelo, Salvatore Rampone:
  Towards a HPC-oriented parallel implementation of a learning algorithm for bioinformatics applications. S2
• 
  Paolo G. V. Martini, Gabriele Sales, Enrica Calura, Stefano Cagnin, Monica Chiogna, Chiara Romualdi:
  timeClip: pathway analysis for time course data without replicates. S3
• 
  Davide Cangelosi, Marco Muselli, Stefano Parodi, Fabiola Blengio, Pamela Becherini, Rogier Versteeg, Massimo Conte, Luigi Varesio:
  Use of Attribute Driven Incremental Discretization and Logic Learning Machine to build a prognostic classifier for neuroblastoma patients. S4

Volume 15, Number S-6, May 2014

• 
  Andreas Holzinger, Matthias Dehmer, Igor Jurisica:
  Knowledge Discovery and interactive Data Mining in Bioinformatics - State-of-the-Art, future challenges and research directions. I1
• 
  Jun Sun, Vasile Palade, Yujie Cai, Wei Fang, Xiaojun Wu:
  Biochemical systems identification by a random drift particle swarm optimization approach. S1
• 
  Christopher C. Mayer, Martin Bachler, Matthias Hörtenhuber, Christof Stocker, Andreas Holzinger, Siegfried Wassertheurer:
  Selection of entropy-measure parameters for knowledge discovery in heart rate variability data. S2
• 
  Rachel D. Melamed, Hossein Khiabanian, Raul Rabadan:
  Data-driven discovery of seasonally linked diseases from an Electronic Health Records system. S3
• 
  Marc Streit, Samuel Gratzl, Michael Gillhofer, Andreas Mayr, Andreas Mitterecker, Sepp Hochreiter:
  Furby: fuzzy force-directed bicluster visualization. S4
• 
  Heimo Müller, Robert Reihs, Kurt Zatloukal, Andreas Holzinger:
  Analysis of biomedical data with multilevel glyphs. S5
• 
  Frank Emmert-Streib, Ricardo de Matos Simoes, Galina V. Glazko, Simon S. McDade, Benjamin Haibe-Kains, Andreas Holzinger, Matthias Dehmer, Frederick Campbell:
  Functional and genetic analysis of the colon cancer network. S6
• 
  Pinar Yildirim, Ljiljana Majnaric, Ilyas Ozgur Ekmekci, Andreas Holzinger:
  Knowledge discovery of drug data on the example of adverse reaction prediction. S7

Volume 15, Number S-7, May 2014

• 
  Nathan L. Clement, Lee Parnell Thompson, Daniel P. Miranker:
  ADaM: augmenting existing approximate fast matching algorithms with efficient and exact range queries. S1
• 
  Cristian Coarfa, Christina Pichot, Andrew R. Jackson, Arpit Tandon, Viren Amin, Sriram Raghuraman, Sameer Paithankar, Adrian V. Lee, Sean E. McGuire, Aleksandar Milosavljevic:
  Analysis of interactions between the epigenome and structural mutability of the genome using Genboree workbench tools. S2
• 
  M. Stanley Fujimoto, Paul M. Bodily, Nozomu Okuda, Mark J. Clement, Quinn Snell:
  Effects of error-correction of heterozygous next-generation sequencing data. S3
• 
  Wenlong Xu, F. Anthony San Lucas, Zixing Wang, Yin Liu:
  Identifying microRNA targets in different gene regions. S4
• 
  Jung Hun Oh, Joseph O. Deasy:
  Inference of radio-responsive gene regulatory networks using the graphical lasso algorithm. S5
• 
  Perry G. Ridge, Taylor J. Maxwell, Spencer J. Foutz, Matthew H. Bailey, Christopher D. Corcoran, JoAnn T. Tschanz, Maria C. Norton, Ronald G. Munger, Elizabeth O'Brien, Richard A. Kerber, Richard M. Cawthon, John S. K. Kauwe:
  Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging. S6
• 
  Ahmadreza Ghaffarizadeh, Nicholas S. Flann, Gregory J. Podgorski:
  Multistable switches and their role in cellular differentiation networks. S7
• 
  Aaron R. Sharp, Perry G. Ridge, Matthew H. Bailey, Kevin L. Boehme, Maria C. Norton, JoAnn T. Tschanz, Ronald G. Munger, Christopher D. Corcoran, John S. K. Kauwe:
  Population substructure in Cache County, Utah: the Cache County study. S8
• 
  Robert Smith, Andrew D. Mathis, Dan Ventura, John T. Prince:
  Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view. S9
• 
  Swarup Roy, Dhruba K. Bhattacharyya, Jugal K. Kalita:
  Reconstruction of gene co-expression network from microarray data using local expression patterns. S10
• 
  Jingran Wen, Daniel R. Scoles, Julio C. Facelli:
  Structure prediction of polyglutamine disease proteins: comparison of methods. S11
• 
  Mark T. W. Ebbert, Mark E. Wadsworth, Kevin L. Boehme, Kaitlyn L. Hoyt, Aaron R. Sharp, Brendan D. O'Fallon, John S. K. Kauwe, Perry G. Ridge:
  Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files. S12
• 
  Abhishek Majumdar, Stephen D. Scott, Jitender S. Deogun, Steven Harris:
  Yeast pheromone pathway modeling using Petri nets. S13

Volume 15, Number S-8, July 2014

• 
  Junjie Li, Sanjay Ranka, Sartaj Sahni:
  Multicore and GPU algorithms for Nussinov RNA folding. S1
• 
  Rittika Shamsuddin, Milka Doktorova, Sheila Jaswal, Audrey Lee-St. John, Kathryn McMenimen:
  Computational prediction of hinge axes in proteins. S2
• 
  Ashraf Yaseen, Yaohang Li:
  Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features. S3
• 
  Kevin Molloy, M. Jennifer Van, Daniel Barbará, Amarda Shehu:
  Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space. S4
• 
  James Lara, F. Xavier López-Labrador, Fernando González-Candelas, Marina Berenguer, Yuri Khudyakov:
  Computational models of liver fibrosis progression for hepatitis C virus chronic infection. S5

Volume 15, Number S-9, September 2014

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

Volume 15, Number S-10, September 2014

UT-KBRIN Bioinformatics Summit 2014: Abstracts

• 
  Eric C. Rouchka, Julia H. Chariker:
  Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014. I1
• 
  Xue Zhong, Qi Liu, Yu Shyr:
  CLIP-EZ: a computational tool for HITS-CLIP data analysis. P1
• 
  Neil Moore, Jerzy W. Jaromczyk, Christopher L. Schardl, Joedocei Hill, Devin Wright:
  Automating deployment of several GBrowse instances. P2
• 
  Yue Huang, Xiaodong Zhu, Lishi Wang, Xiaoyun Liu, Robert W. Williams, Lu Lu, Yan Jiao, Weikuan Gu:
  Genome wide analysis of sex difference in gene expression profiles of bone formations. P3
• 
  Meredith Ray, Xin Tong, Hongmei Zhang, Wilfried Karmaus:
  Screening genome-wide DNA methylation CpG sites via training and testing data utilizing surrogate variables. P4
• 
  Yan Zhang, Michelle Barati, Ignacio Munoz, Ming Li, Danny Wilkey, Eric C. Rouchka, Michael Merchant:
  Transcriptomic characterization of short duration endoplasmic reticulum stress on cultured human proximal tubule cells. P5
• 
  Hossein Taghizad, Mohammed Yeasin, Tara Cherry, Vida Abedi:
  Obnet: Network of semantic associations for obesity. P6
• 
  Xing Li, Almudena Martinez-Fernandez, Jeanne Theis, Jean-Pierre A. Kocher, Andre Terzic, Timothy Olson, Timothy J. Nelson:
  Prioritizing disease-related genes and pathways by integrating patient-specific iPSC-derived RNA-seq and whole genome sequencing in hypoplastic left heart syndrome. P7
• 
  Vida Abedi, Mohammed Yeasin, Ramin Zand:
  Context-sensitive use of bioinformatics tools with complementary functionalities for generation of relevant hypothesis. P8
• 
  Shuqiu Sun, Yan Jiao, Wei Wei, Arnold E. Postlethwaite, Weikuan Gu, Dianjun Sun:
  Comparing genetic pathways variation of immunoinhibitory receptor LAIR-1 in murine vs human internal organs. P9
• 
  Yan Jiao, Xiaoyun Liu, Yanhong Cao, Nan Deng, Yonghui Ma, Karen A. Hasty, John M. Stuart, Weikuan Gu:
  Analysis of effect of congenic mice on the gene expression under genomic background of BALB/c mice. P10
• 
  Benjamin J. Harrison, Robert M. Flight, Abdallah M. Eteleeb, Eric C. Rouchka, Jeffrey C. Petruska:
  UTR extension and alternate polyadenylation in neuroplasticity: an emerging paradigm? P11
• 
  Lishi Wang, Yan Jiao, Yue Huang, Beth Bennett, Robert W. Williams, Dawei Li, Hongyu Zhao, Joel Gelernter, Henry R. Kranzler, Lindsay A. Farrer, Weikuan Gu:
  Ttn as a likely causal gene for QTL of alcohol preference on mouse chromosome 2. P12
• 
  Shreyas Joshi, Bruce F. O'Hara:
  Identifying candidate genes for variation in sleep-related quantitative traits. P13
• 
  Behrouz Madahian, Lih-Yuan Deng, Ramin Homayouni:
  Development of sparse Bayesian multinomial generalized linear model for multi-class prediction. P14
• 
  Ferhan M. Atici, Mustafa Atici, Ngoc Nguyen:
  Parameter estimations of sigmoidal models of cancer. P15
• 
  Shilin Zhao, Yan Guo, Quanhu Sheng, Yu Shyr:
  Heatmap3: an improved heatmap package with more powerful and convenient features. P16
• 
  Naga Nagisetty, Eunice Y. Huang, Grady Wade, Teeradache Viangteeravat:
  Building a knowledge base to assist clinical decision-making using the Pediatric Research Database (PRD) and machine learning: a case study on pediatric asthma patients. P17
• 
  Nataliya I. Lenchik, Hao Chen, Dorothy N. Kakoola, Ivan Gerling:
  Differences in gene expression profiles between individual islets from case #6213. P18
• 
  Nam S. Vo, Vinhthuy Phan:
  Exploiting the bootstrap method to analyze patterns of gene expression. P19
• 
  Vinay Raj, Susan Kadlubar:
  Identification of gene expression profiles associated with prognostic groups of patients with Merkel cell carcinoma. P20
• 
  Shruti S. Sakhare, Gautam G. Rao, Sammed N. Mandape, Siddharth Pratap:
  Transcriptome profile of OVCAR3 cisplatin-resistant ovarian cancer cell line. P21
• 
  Shanshan Guo, Vinthuy Phan:
  A distributed framework for aligning short reads to genomes. P22
• 
  Quang Tran, Vinhthuy Phan:
  Alignment of short reads to multiple genomes using hashing. P23
• 
  Kevin L. O'kello, Vinhthuy Phan:
  Determining gene response patterns of time series gene expression data using R. P24
• 
  Mark L. Farman, Patrick Calie, Jerzy W. Jaromczyk, Jolanta Jaromczyk, Neil Moore, Daniel R. Harris, Christopher L. Schardl:
  An adaptive landscape for training in the essentials of next gen sequencing data acquisition and bioinformatic analysis. P25
• 
  Hao Chen:
  Evaluating statistical learning methods for cell type classification and feature selection using RNA-seq data. P26
• 
  Hao Chen, Burt M. Sharp:
  Establishing a protocol for single cell transcriptome sequencing of the rat brain. P27
• 
  Irit Hochberg, Quynh T. Tran, Ariel R. Barkan, Alan R. Saltiel, William F. Chandler, Dave Bridges:
  Gene expression signature in adipose tissue of acromegaly patients. P28
• 
  Wenjian Bi, Guolian Kang, Yuehua Cui, Yun Li, Christine Hartford, Wing Leung, Ji-Feng Zhang:
  A new set-valued system identification approach to identifying rare genetic variants for ordered categorical phenotype. P29
• 
  Nam S. Vo, Quang Tran, Vinhthuy Phan:
  An integrated approach for SNP calling based on population of genomes. P30
•