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

• 
  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

• 
  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

• 
  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
• 
  Sen Yao, Robert M. Flight, Hunter N. B. Moseley:
  Coordination characterization of zinc metalloproteins. P31
• 
  Charles A. Phillips, Erich J. Baker, Elissa J. Chesler, Michael A. Langston:
  Algorithmic tools for tripartite data analysis. P32
• 
  Hui Yu, Zhongming Zhao:
  Evaluating four major algorithms for identifying differential regulators in condition-specific transcriptional responses. P33
• 
  Guolian Kang, Wei Liu, Cheng Cheng, Carmen L. Wilson, Geoffrey Neale, Jun J. Yang, Kirsten K. Ness, Leslie L. Robison, Melissa M. Hudson, Kumar Srivastava:
  Evaluation of two-step iterative resampling procedure for internal validation of genome-wide association studies. P34
• 
  Georgina Iyamu, Pamela D. Thompson, Victor Paramov, Siddharth Pratap, Amos Sakwe, Josiah Ochieng, Dana Marshall:
  Shotgun proteomic analysis of human head and neck squamous cell carcinoma cell line SQ20B with diminished AHSG expression. P35
• 
  Joshua M. Mitchell, Teresa W.-M. Fan, Andrew N. Lane, Hunter N. B. Moseley:
  Development of large-scale metabolite identification methods for metabolomics. P36

Volume 15, Number S-11, October 2014

Proceedings of the 11th Annual MCBIOS Conference

• 
  Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Andy D. Perkins, Chaoyang Zhang, Peter Hoyt, Rakesh Kaundal:
  Proceedings of the 2014 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. I1
• 
  Zongliang Yue, Ping Wan, Hui Huang, Zhan Xie, Jake Yue Chen:
  SLDR: a computational technique to identify novel genetic regulatory relationships. S1
• 
  Nam S. Vo, Vinhthuy Phan:
  Exploiting dependencies of pairwise comparison outcomes to predict patterns of gene response. S2
• 
  Michael A. Bauer, Shweta S. Chavan, Erich A. Peterson, Christoph J. Heuck, Donald J. Johann:
  Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing. S3
• 
  Hui Wen Ng, Wenqian Zhang, Mao Shu, Heng Luo, Weigong Ge, Roger Perkins, Weida Tong, Huixiao Hong:
  Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists. S4
• 
  Wenchao Zhang, Patrick Xuechun Zhao:
  Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data. S5
• 
  Wenqian Zhang, Joe Meehan, Zhenqiang Su, Hui Wen Ng, Mao Shu, Heng Luo, Weigong Ge, Roger Perkins, Weida Tong, Huixiao Hong:
  Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population. S6
• 
  Jason Hennessey, Constantin Georgescu, Jonathan D. Wren:
  Trends in the production of scientific data analysis resources. S7
• 
  Inimary T. Toby, Jonah Widmer, David W. Dyer:
  Divergence of protein-coding capacity and regulation in the Bacillus cereus sensu lato group. S8
• 
  Erich A. Peterson, Shweta S. Chavan, Michael A. Bauer, Christoph J. Heuck, Donald J. Johann:
  Revealing the inherent heterogeneity of human malignancies by variant consensus strategies coupled with cancer clonal analysis. S9
• 
  Yan Peng, Andrew S. Maxwell, Natalie D. Barker, Jennifer G. Laird, Alan J. Kennedy, Nan Wang, Chaoyang Zhang, Ping Gong:
  SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data. S10
• 
  Weizhong Zhao, Wen Zou, James J. Chen:
  Topic modeling for cluster analysis of large biological and medical datasets. S11
• 
  Stephen C. Grace, Stephen Embry, Heng Luo:
  Haystack, a web-based tool for metabolomics research. S12
• 
  Sitanshu S. Sahu, Tyler Weirick, Rakesh Kaundal:
  Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches. S13
• 
  Taeho Jo, Jianlin Cheng:
  Improving protein fold recognition by random forest. S14
• 
  Tyler Weirick, Sitanshu S. Sahu, Ramamurthy Mahalingam, Rakesh Kaundal:
  LacSubPred: predicting subtypes of Laccases, an important lignin metabolism-related enzyme class, using in silico approaches. S15
• 
  Mihir Jaiswal, Nathaniel Crabtree, Michael A. Bauer, Roger A. Hall, Kevin D. Raney, Boris L. Zybailov:
  XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry. S16

Volume 15, Number S-12, November 2014

Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013): Bioinformatics

• 
  James Zijun Wang, Yuanyuan Zhang, Liang Dong, Lin Li, Pradip K. Srimani, Philip S. Yu:
  G-Bean: an ontology-graph based web tool for biomedical literature retrieval. S1
• 
  En-Shiun Annie Lee, Sanderz Fung, Ho-Yin Sze-To, Andrew K. C. Wong:
  Discovering co-occurring patterns and their biological significance in protein families. S2
• 
  Qianqian Wu, Kate Smith-Miles, Tianhai Tian:
  Approximate Bayesian computation schemes for parameter inference of discrete stochastic models using simulated likelihood density. S3
• 
  Wei Wang, Juan Liu, Xionghui Zhou:
  Identification of single-stranded and double-stranded dna binding proteins based on protein structure. S4
• 
  Lijun Quan, Qiang Lü, Haiou Li, Xiaoyan Xia, Hongjie Wu:
  Improved packing of protein side chains with parallel ant colonies. S5
• 
  Zijing Mao, Chifeng Ma, Tim Hui-Ming Huang, Yidong Chen, Yufei Huang:
  BIMMER: a novel algorithm for detecting differential DNA methylation regions from MBDCap-seq data. S6
• 
  Xianjun Shen, Yanli Zhao, Yanan Li, Tingting He, Jincai Yang, Xiaohua Hu:
  An efficient protein complex mining algorithm based on Multistage Kernel Extension. S7
• 
  Lizhi Cui, Josiah Poon, Simon K. Poon, Hao Chen, Junbin Gao, Paul Wing Hing Kwan, Kei Fan, Zhihao Ling:
  An improved independent component analysis model for 3D chromatogram separation and its solution by multi-areas genetic algorithm. S8
• 
  Liangxi Cheng, Hongfei Lin, Feng Zhou, Zhihao Yang, Jian Wang:
  Enhancing the accuracy of knowledge discovery: a supervised learning method. S9
• 
  Yue Shang, Huihui Hao, Jiajin Wu, Hongfei Lin:
  Learning to rank-based gene summary extraction. S10

Volume 15, Number S-13, November 2014

Selected articles from the 9th International Symposium on Bioinformatics Research and Applications (ISBRA-13): Bioinformatics

• 
  Cynthia Gibas, Zhipeng Cai, Oliver Eulenstein:
  Guest editors' introduction to the Proceedings of the 9^th International Symposium on Biomedical Research and Applications. S1
• 
  Alex R. Gawronski, Marcel Turcotte:
  RiboFSM: Frequent subgraph mining for the discovery of RNA structures and interactions. S2
• 
  Pawel Górecki, Oliver Eulenstein:
  Refining discordant gene trees. S3
• 
  Edward Hemphill, James Lindsay, Chih Lee, Ion I. Mandoiu, Craig E. Nelson:
  Feature selection and classifier performance on diverse bio- logical datasets. S4
• 
  Ke Liu, Xiangmiao Zeng, Lei Qiao, Xisheng Li, Yubo Yang, Cuihong Dai, Aiju Hou, Dechang Xu:
  The sensitivity and significance analysis of parameters in the model of pH regulation on lactic acid production by Lactobacillus bulgaricus. S5
• 
  Tianwei Yu, Yun Bai:
  Network-based modular latent structure analysis. S6

Volume 15, Number S-14, November 2014

Semantic, social, mobile applications for bioinformatics and biomedical laboratories: selected works from the 13th International Workshop on Network Tools and Applications in Biology (NETTAB 2013)

• 
  Paolo Romano, Nicola Cannata:
  NETTAB 2013: Semantic, social, and mobile applications for bioinformatics and biomedical laboratories. S1
• 
  Maciej Rybinski, José Francisco Aldana Montes:
  Calculating semantic relatedness for biomedical use in a knowledge-poor environment. S2
• 
  Francesco Venco, Yuriy Vaskin, Arnaud Céol, Heiko Müller:
  SMITH: a LIMS for handling next-generation sequencing workflows. S3
• 
  Alejandra N. González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra:
  linkedISA: semantic representation of ISA-Tab experimental metadata. S4
• 
  Larisa N. Soldatova, Daniel Nadis, Ross D. King, Piyali S. Basu, Emma Haddi, Véronique Baumlé, Nigel J. Saunders, Wolfgang Marwan, Brian B. Rudkin:
  EXACT2: the semantics of biomedical protocols. S5
• 
  Fabio Rinaldi, Simon Clematide, Hernani Marques, Tilia Ellendorff, Martin Romacker, Raul Rodriguez-Esteban:
  OntoGene web services for biomedical text mining. S6
• 
  Steffen Möller, Enis Afgan, Michael Banck, Raoul Jean Pierre Bonnal, Timothy Booth, John Chilton, Peter J. A. Cock, Markus Gumbel, Nomi L. Harris, Richard C. G. Holland, Matús Kalas, László Kaján, Eri Kibukawa, David R. Powell, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Clare Sloggett, Stian Soiland-Reyes, William Spooner, Sascha Steinbiss, Andreas Tille, Anthony J. Travis, Roman Guimera, Toshiaki Katayama, Brad A. Chapman:
  Community-driven development for computational biology at Sprints, Hackathons and Codefests. S7

Volume 15, Number S-15, December 2014

Proceedings of the 2013 International Conference on Intelligent Computing (ICIC 2013)

• 
  Xiaoli Lin, Xiaolong Zhang, Fengli Zhou:
  Protein structure prediction with local adjust tabu search algorithm. S1
• 
  Shu-Lin Wang, Liuchao Sun, Jianwen Fang:
  Molecular cancer classification using a meta-sample-based regularized robust coding method. S2
• 
  Chun-Hou Zheng, Lin Yuan, Wen Sha, Zhan-Li Sun:
  Gene differential coexpression analysis based on biweight correlation and maximum clique. S3
• 
  Peng Chen, Jianhua Z. Huang, Xin Gao:
  LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone. S4
• 
  Byungkyu Brian Park, Hyungchan Kim, Kyungsook Han:
  DBBP: database of binding pairs in protein-nucleic acid interactions. S5
• 
  Sheng-Lung Peng, Yu-Wei Tsay:
  Adjusting protein graphs based on graph entropy. S6
• 
  Vitoantonio Bevilacqua, Nicola Pietroleonardo, Ely Ignazio Giannino, Fabio Stroppa, Domenico Simone, Graziano Pesole, Ernesto Picardi:
  EasyCluster2: an improved tool for clustering and assembling long transcriptome reads. S7
• 
  Yu-Ting Hsiao, Wei-Po Lee:
  Reverse engineering gene regulatory networks: Coupling an optimization algorithm with a parameter identification technique. S8
• 
  Zhu-Hong You, Lin Zhu, Chun-Hou Zheng, Hongjie Yu, Suping Deng, Zhen Ji:
  Prediction of protein-protein interactions from amino acid sequences using a novel multi-scale continuous and discontinuous feature set. S9
• 
  Jiarui Zhou, Zhen Ji, Zexuan Zhu, Shan He:
  Compression of next-generation sequencing quality scores using memetic algorithm. S10

Volume 15, Number S-16, December 2014

Thirteenth International Conference on Bioinformatics (InCoB2014): Bioinformatics

• 
  Shoba Ranganathan, Tin Wee Tan, Christian Schönbach:
  InCoB2014: bioinformatics to tackle the data to knowledge challenge. I1
• 
  Hsin-Yi Wu, Cheng-Tsung Lu, Hui-Ju Kao, Yi-Ju Chen, Yu-Ju Chen, Tzong-Yi Lee:
  Characterization and identification of protein O-GlcNAcylation sites with substrate specificity. S1
• 
  Jinwoo Kim, Miyoung Shin:
  An integrative model of multi-organ drug-induced toxicity prediction using gene-expression data. S2
• 
  Qian Liu, Zhenhua Li, Jinyan Li:
  Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts. S3
• 
  Yi-Fan Liou, Phasit Charoenkwan, Yerukala Sathipati Srinivasulu, Tamara Vasylenko, Shih-Chung Lai, Hua-Chin Lee, Yi-Hsiung Chen, Hui-Ling Huang, Shinn-Ying Ho:
  SCMHBP: prediction and analysis of heme binding proteins using propensity scores of dipeptides. S4
• 
  Lingxiao Zhou, Renate Griffith, Bruno Gaëta:
  Combining spatial and chemical information for clustering pharmacophores. S5
• 
  Yadav Kuleesha, Wee Choo Puah, Feng Lin, Martin Wasser:
  FMAj: a tool for high content analysis of muscle dynamics in Drosophila metamorphosis. S6
• 
  Bhyravabhotla Jayaram, Priyanka Dhingra, Avinash Mishra, Rahul Kaushik, Goutam Mukherjee, Ankita Singh, Shashank Shekhar:
  Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. S7
• 
  Maad Shatnawi, Nazar Zaki, Paul D. Yoo:
  Protein inter-domain linker prediction using Random Forest and amino acid physiochemical properties. S8
• 
  Chinh Tran To Su, Thuy-Diem Nguyen, Jie Zheng, Chee Keong Kwoh:
  IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking. S9
• 
  Tzu-Hsien Yang, Hong-Tsun Chang, Eric S. L. Hsiao, Juo-Ling Sun, Chung-Ching Wang, Hsin-Yi Wu, Pao-Chi Liao, Wei-Sheng Wu:
  iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation. S10
• 
  Piers Johnson, Luke Vandewater, William J. Wilson, Paul Maruff, Greg Savage, Petra Graham, Lance S. Macaulay, Kathryn A. Ellis, Cassandra Szoeke, Ralph N. Martins, Christopher Rowe, Colin L. Masters, David Ames, Ping Zhang:
  Genetic algorithm with logistic regression for prediction of progression to Alzheimer's disease. S11
• 
  Kuldip K. Paliwal, Alok Sharma, James G. Lyons, Abdollah Dehzangi:
  Improving protein fold recognition using the amalgamation of evolutionary-based and structural based information. S12
• 
  Sonam Grover, Jaspreet Kaur Dhanjal, Sukriti Goyal, Abhinav Grover, Durai Sundar:
  Computational identification of novel natural inhibitors of glucagon receptor for checking type II diabetes mellitus. S13
• 
  Benjamin Drinkwater, Michael A. Charleston:
  Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem. S14
• 
  Eleni Giannoulatou, Shin-Ho Park, David T. Humphreys, Joshua Wing Kei Ho:
  Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie. S15
• 
  Ran Su, Yao Li, Daniele Zink, Lit-Hsin Loo:
  Supervised prediction of drug-induced nephrotoxicity based on interleukin-6 and -8 expression levels. S16

Volume 15, Number S-17, December 2014

Selected articles from the 2014 International Conference on Bioinformatics and Computational Biology

• 
  Jack Y. Yang, A. Keith Dunker, Jun S. Liu, Xiang Qin, Hamid R. Arabnia, William Yang, Andrzej Niemierko, Zhongxue Chen, Zuojie Luo, Liangjiang Wang, Yunlong Liu, Dong Xu, Youping Deng, Weida Tong, Mary Qu Yang:
  Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. I1
• 
  Mary Qu Yang, Laura Elnitski:
  Orthology-driven mapping of bidirectional promoters in human and mouse genomes. S1
• 
  William Yang, Kenji Yoshigoe, Xiang Qin, Jun S. Liu, Jack Y. Yang, Andrzej Niemierko, Youping Deng, Yunlong Liu, A. Keith Dunker, Zhongxue Chen, Liangjiang Wang, Dong Xu, Hamid R. Arabnia, Weida Tong, Mary Qu Yang:
  Identification of genes and pathways involved in kidney renal clear cell carcinoma. S2
• 
  Zhongxue Chen, William Yang, Qingzhong Liu, Jack Y. Yang, Jing Li, Mary Yang:
  A new statistical approach to combining p-values using gamma distribution and its application to genome-wide association study. S3
• 
  Fei Huang, Christopher J. Oldfield, Bin Xue, Wei-Lun Hsu, Jingwei Meng, Xiaowen Liu, Li Shen, Pedro Romero, Vladimir N. Uversky, A. Keith Dunker:
  Improving protein order-disorder classification using charge-hydropathy plots. S4
• 
  Chang Liu, Lili Lu, Quan Kong, Yan Li, Haihua Wu, William Yang, Shandan Xu, Xinyu Yang, Xiaolei Song, Jack Y. Yang, Mary Qu Yang, Youping Deng:
  Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2. S5
• 
  Ke Yu, Jie Zhang, Minjun Chen, Xiaowei Xu, Ayako Suzuki, Katarina Ilic, Weida Tong:
  Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study. S6