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ORCIDBMC Bioinformatics, Volume 16 - Supplements
Volume 16, Number S-1, January 2015
- Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, Tzu-Hao Chang, Neil Arvin Bretaña, K. Robert Lai, Julia Weng, Tzong-Yi Lee:
Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. S1 - Yun-Lung Li, Jui-Cheng Weng, Chiung-Chih Hsiao, Min-Te Chou, Chin-Wen Tseng, Jui-Hung Hung
:
PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm. S2 - Hong Sun, Shuang Yang, Liangliang Tun, Yixue Li:
IAOseq: inferring abundance of overlapping genes using RNA-seq data. S3 - Takahiro Mimori, Naoki Nariai, Kaname Kojima, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki:
Estimating copy numbers of alleles from population-scale high-throughput sequencing data. S4 - Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, Julia Weng:
An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients. S5 - Wenhui Wang, Xianghong Jasmine Zhou, Zhenqiu Liu, Fengzhu Sun:
Network tuned multiple rank aggregation and applications to gene ranking. S6 - Jau-Ji Lin, Zih-Lin Lin, Jenn-Kang Hwang, Tsun-Tsao Huang:
On the packing density of the unbound protein-protein interaction interface and its implications in dynamics. S7 - Tamara Vasylenko, Yi-Fan Liou, Hong-An Chen, Phasit Charoenkwan, Hui-Ling Huang, Shinn-Ying Ho:
SCMPSP: Prediction and characterization of photosynthetic proteins based on a scoring card method. S8 - Kai-Yao Huang, Tzong-Yi Lee, Yu-Chuan Teng, Tzu-Hao Chang:
ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors. S9
Volume 16, Number S-2, January 2015
- Farzana Rahman, Katie Wilkins, Annika Jacobsen, Alexander Junge, Esmeralda Vicedo, Dan F. DeBlasio, Anupama Jigisha, Tomás Di Domenico:
Highlights from the tenth ISCB Student Council Symposium 2014. A1 - Yassine Souilmi, Jae-Yoon Jung, Alex Lancaster, Erik Gafni, Saaid Amzazi, Hassan Ghazal, Dennis P. Wall, Peter J. Tonellato:
COSMOS: cloud enabled NGS analysis. A2 - Dan F. DeBlasio, John D. Kececioglu:
Parameter advising for multiple sequence alignment. A3 - Lin-Yang Cheng, Yansheng Liu, Ching-Yun Chang, Hannes L. Röst, Ruedi Aebersold, Olga Vitek:
Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition. A4 - Harriet Dashnow, Susan Tan, Debjani Das, Simon Easteal, Alicia Oshlack:
Genotyping microsatellites in next-generation sequencing data. A5 - Yi Zhong, Philipp Drewe, Andrew L. Wolfe, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch:
Protein translational control and its contribution to oncogenesis revealed by computational methods. A6 - Benjamin Siranosian, Emma Herold, Edward Williams, Chen Ye, Christopher de Graffenried:
Tetranucleotide usage in mycobacteriophage genomes: alignment-free methods to cluster phage and infer evolutionary relationships. A7 - Alex Salazar, Ashlee Earl, Christopher Desjardins, Thomas Abeel:
Normalizing alternate representations of large sequence variants across multiple bacterial genomes. A8 - Sarah L. Keasey, Mohan Natesan, Christine Pugh, Teddy Kamata, Stefan Wuchty, Robert G. Ulrich:
The road to linking genomics and proteomics of pathogenic bacteria: from binary protein complexes to interaction pathways. A9 - Amin Ardeshirdavani, Erika L. Souche, Luc Dehaspe, Jeroen K. J. Van Houdt, Joris Robert Vermeesch, Yves Moreau:
NGS-Logistics: data infrastructure for efficient analysis of NGS sequence variants across multiple centers. A10
Volume 16, Number S-3, February 2015
- Margherita Francescatto, Susanne M. A. Hermans, Sepideh Babaei, Esmeralda Vicedo, Alexandre Borrel, Pieter Meysman:
Highlights from the Third European International Society for Computational Biology (ISCB) Student Council Symposium 2014. A1 - Darius Kazlauskas, Ceslovas Venclovas:
Viral DNA replication: new insights and discoveries from large scale computational analysis. A2 - Aya Narunsky, Haim Ashkenazy, Rachel Kolodny, Nir Ben-Tal:
Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations. A3 - Isidro Cortes-Ciriano, Gerard J. P. van Westen, Daniel S. Murrell, Eelke B. Lenselink, Andreas Bender, Therese E. Malliavin:
Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling. A4 - Mélaine A. Kuenemann, Laura M. L. Bourbon, Céline M. Labbé, Bruno O. Villoutreix, Olivier Sperandio:
An exploration of the 3D chemical space has highlighted a specific shape profile for the compounds intended to inhibit protein-protein interactions. A5 - Stefan Naulaerts, Pieter Meysman, Wim Vanden Berghe, Kris Laukens:
Mining the human proteome for conserved mechanisms. A6 - Matthias Döring, Gilles Gasparoni, Jasmin Gries, Karl Nordström, Pavlo Lutsik, Jörn Walter, Nico Pfeifer:
Identification and analysis of methylation call differences between bisulfite microarray and bisulfite sequencing data with statistical learning techniques. A7 - Dagoberto Armenta-Medina, Ernesto Pérez-Rueda:
Hybrid approaches for the detection of networks of critical residues involved in functional motions in protein families. A8 - Amélie Peres, Hugues Roest Crollius:
Improving duplicated nodes position in vertebrate gene trees. A9
Volume 16, Number S-4, February 2015
- Abdollah Dehzangi, Sohrab Sohrabi, Rhys Heffernan, Alok Sharma, James G. Lyons, Kuldip K. Paliwal, Abdul Sattar:
Gram-positive and gram-negative subcellular localization using rotation forest and physicochemical-based features. S1 - Dusan Popovic, Alejandro Sifrim, Jesse Davis, Yves Moreau, Bart De Moor:
Problems with the nested granularity of feature domains in bioinformatics: the eXtasy case. S2 - Zina M. Ibrahim, Alioune Ngom:
The relative vertex clustering value - a new criterion for the fast discovery of functional modules in protein interaction networks. S3 - Erdogan Taskesen, Frank J. T. Staal, Marcel J. T. Reinders:
An integrated approach of gene expression and DNA-methylation profiles of WNT signaling genes uncovers novel prognostic markers in Acute Myeloid Leukemia. S4 - Erdogan Taskesen, Sepideh Babaei, Marcel J. T. Reinders, Jeroen de Ridder:
Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia. S5 - Jose Nunes, Martín Piquerez, Leonardo Pujadas, Eileen Armstrong, Alicia Fernández, Federico Lecumberry:
Beef quality parameters estimation using ultrasound and color images. S6 - Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Riccardo Rizzo, Alfonso Urso:
Analysis of miRNA expression profiles in breast cancer using biclustering. S7 - Hossam M. Ashtawy, Nihar R. Mahapatra:
BgN-Score and BsN-Score: Bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexes. S8
Volume 16, Number S-5, March 2015
- Jingchun Sun, Kevin W. Zhu, W. Jim Zheng, Hua Xu:
A comparative study of disease genes and drug targets in the human protein interactome. S1 - Ruichang Zhang, Zhanzhan Cheng, Jihong Guan, Shuigeng Zhou:
Exploiting topic modeling to boost metagenomic reads binning. S2 - Hao Wu, Lin Gao, Feng Li, Fei Song, Xiaofei Yang, Nikola K. Kasabov:
Identifying overlapping mutated driver pathways by constructing gene networks in cancer. S3 - Qing Zhan, Yongtao Ye, Tak Wah Lam, Siu-Ming Yiu, Yadong Wang, Hing-Fung Ting:
Improving multiple sequence alignment by using better guide trees. S4 - Andrew Quitadamo, Lu Tian, Benika Hall, Xinghua Shi:
An integrated network of microRNA and gene expression in ovarian cancer. S5 - Rong Xu, QuanQiu Wang:
Comparing a knowledge-driven approach to a supervised machine learning approach in large-scale extraction of drug-side effect relationships from free-text biomedical literature. S6 - Haitao Jiang, Guohui Lin, Weitian Tong, Daming Zhu, Binhai Zhu:
Isomorphism and similarity for 2-generation pedigrees. S7 - Xiaoqing Peng, Jianxin Wang, Zhen Zhang, Qianghua Xiao, Min Li, Yi Pan:
Re-alignment of the unmapped reads with base quality score. S8 - Danny S. Park, Yael Baran, Farhad Hormozdiari, Celeste Eng, Dara G. Torgerson, Esteban Gonzàlez Burchard, Noah Zaitlen:
PIGS: improved estimates of identity-by-descent probabilities by probabilistic IBD graph sampling. S9 - Jeffery Li, Travers Ching, Sijia Huang, Lana X. Garmire:
Using epigenomics data to predict gene expression in lung cancer. S10 - Mai A. Hamdalla, Reda A. Ammar, Sanguthevar Rajasekaran:
A molecular structure matching approach to efficient identification of endogenous mammalian biochemical structures. S11
Volume 16, Number S-6, April 2015
- Marta Avalos, Hélène Pouyes, Yves Grandvalet, Ludivine Orriols, Emmanuel Lagarde:
Sparse conditional logistic regression for analyzing large-scale matched data from epidemiological studies: a simple algorithm. S1 - Massimo La Rosa, Antonino Fiannaca, Riccardo Rizzo, Alfonso Urso:
Probabilistic topic modeling for the analysis and classification of genomic sequences. S2 - Hossam M. Ashtawy, Nihar R. Mahapatra:
Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins. S3 - Pietro Pinoli, Davide Chicco, Marco Masseroli:
Computational algorithms to predict Gene Ontology annotations. S4 - Ernst C. Wit, Antonino Abbruzzo:
Inferring slowly-changing dynamic gene-regulatory networks. S5
Volume 16, Number S-7, April 2015
- Robert Smith, John T. Prince, Dan Ventura:
A coherent mathematical characterization of isotope trace extraction, isotopic envelope extraction, and LC-MS correspondence. S1 - Robert Smith, Ryan M. Taylor, John T. Prince:
Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal. S2 - Gaurav Kaushik, Michael A. Thomas, Ken A. Aho:
Psychoactive pharmaceuticals as environmental contaminants may disrupt highly inter-connected nodes in an Autism-associated protein-protein interaction network. S3 - Azusa Ito, Takenao Ohkawa:
A method of searching for related literature on protein structure analysis by considering a user's intention. S4 - Paul M. Bodily, M. Stanley Fujimoto, Cameron Ortega, Nozomu Okuda, Jared C. Price, Mark J. Clement, Quinn Snell:
Heterozygous genome assembly via binary classification of homologous sequence. S5 - Tsendsuren Munkhdalai, Oyun-Erdene Namsrai, Keun Ho Ryu:
Self-training in significance space of support vectors for imbalanced biomedical event data. S6 - Haijun Gong, Jakob Klinger, Kevin Damazyn, Xiangrui Li, Shiyang Huang:
A novel procedure for statistical inference and verification of gene regulatory subnetwork. S7 - Saman Sargolzaei, Arman Sargolzaei, Mercedes Cabrerizo, Gang Chen, Mohammed Goryawala, Shirin Noei, Qi Zhou, Ranjan Duara, Warren Barker, Malek Adjouadi:
A practical guideline for intracranial volume estimation in patients with Alzheimer's disease. S8 - Saman Sargolzaei, Mercedes Cabrerizo, Arman Sargolzaei, Shirin Noei, Anas Salah Eddin, Hoda Rajaei, Alberto Pinzon-Ardila, Sergio M. Gonzalez-Arias, Prasanna Jayakar, Malek Adjouadi:
A probabilistic approach for pediatric epilepsy diagnosis using brain functional connectivity networks. S9 - Ruibang Luo, Jeanno Cheung, Edward Wu, Heng Wang, Sze-Hang Chan, Wai-Chun Law, Guangzhu He, Chang Yu, Chi-Man Liu, Dazong Zhou, Yingrui Li, Ruiqiang Li, Jun Wang, Xiaoqian Zhu, Shaoliang Peng, Tak Wah Lam:
MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC). S10
Volume 16, Number S-8, April 2015
- R. Parra, Franco L. Simonetti, Marcia A. Hasenahuer, Gabriel J. Olguin-Orellana, Avinash K. Shanmugam:
Highlights from the 1st ISCB Latin American Student Council Symposium 2014. A1 - Raony Guimarães Corrêa Do Carmo Lisboa Cardenas, Natália Duarte Linhares, Sérgio D. Junho Pena:
Mendel, MD: a user-friendly online program for clinical exome analysis. A2 - Julliane D. Medeiros, Laura R. Leite, Sara Cuadros-Orellana, Guilherme C. Oliveira:
Taxonomic and functional diversity of microbial community from a mining environment. A3 - Danillo C. Almeida-E.-Silva, Ricardo Z. N. Vêncio:
Sifter-T: A scalable framework for phylogenomic probabilistic protein domain functional annotation. A4 - Yerko Escalona, José Antonio Garate, Tomas Pérez-Acle:
Exploring the membrane potential of a simple dual membrane system by using a constant electric field. A5 - Franco L. Simonetti, Martin Banchero, Ariel J. Berenstein, Ariel Chernomoretz, Cristina Marino Buslje:
Using coevolution to improve protein subfamily classification. A6 - Jan Engelhardt, Peter F. Stadler:
Evolution of 3'UTR-associated RNAs. A7 - Javier Cáceres, Romina Sepúlveda, Camila Navas, Ramón Latorre, Fernando D. González Nilo:
Rational discovery of new capsaicin analogues as TRPV1 activators. A8
Volume 16, Number S-9, June 2015
- Angelo M. Facchiano, Claudia Angelini, Roberta Bosotti, Alessandro Guffanti, Anna Marabotti, Roberto Marangoni, Stefano Pascarella, Paolo Romano, Andreas Zanzoni, Manuela Helmer-Citterich:
Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. S1 - Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele A. Calogero, Francesca Zolezzi:
Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. S2 - Stefano Parodi, Rosa Filiberti, Paola Marroni, Roberta Libener, Giovanni Ivaldi, Michele Mussap, Enrico Ferrari, Chiara Manneschi, Erika Montani, Marco Muselli:
Differential diagnosis of pleural mesothelioma using Logic Learning Machine. S3 - Alberto Policriti, Nicola Prezza:
Fast randomized approximate string matching with succinct hash data structures. S4 - Andrea Calabria, Giulio Spinozzi, Fabrizio Benedicenti, Erika Tenderini, Eugenio Montini:
adLIMS: a customized open source software that allows bridging clinical and basic molecular research studies. S5 - Francesco Di Palma, Sandro Bottaro, Giovanni Bussi:
Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations. S6 - Gianvito Pio, Michelangelo Ceci, Donato Malerba, Domenica D'Elia:
ComiRNet: a web-based system for the analysis of miRNA-gene regulatory networks. S7 - Giulio Caravagna, Luca De Sano, Marco Antoniotti:
Automatising the analysis of stochastic biochemical time-series. S8
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