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BMC Bioinformatics, Volume 15 - Supplements
Volume 15, Number S-1, January 2014
- 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
- 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 3rd 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
- 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