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Journal Article

Kart: a divide-and-conquer algorithm for NGS read alignment

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Hsin-Nan Lin, Wen-Lian Hsu
Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2281–2287, https://doi.org/10.1093/bioinformatics/btx189
Published: 04 April 2017
Journal Article

BEESEM: estimation of binding energy models using HT-SELEX data

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Shuxiang Ruan, S. Joshua Swamidass, Gary D. Stormo
Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2288–2295, https://doi.org/10.1093/bioinformatics/btx191
Published: 04 April 2017
Journal Article

Discriminating the reaction types of plant type III polyketide synthases

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Yugo Shimizu, Hiroyuki Ogata, Susumu Goto
Bioinformatics, Volume 33, Issue 13, 1 July 2017, Pages 1937–1943, https://doi.org/10.1093/bioinformatics/btx112
Published: 06 March 2017
Journal Article

Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning

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Zhen Gao, Jianhua Ruan
Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2097–2105, https://doi.org/10.1093/bioinformatics/btx115
Published: 01 March 2017
Journal Article

RNAscClust : clustering RNA sequences using structure conservation and graph based motifs

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Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E. Seemann, Jakob Hull Havgaard ...
Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2089–2096, https://doi.org/10.1093/bioinformatics/btx114
Published: 27 February 2017
Journal Article

Pseudoalignment for metagenomic read assignment

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L. Schaeffer, H. Pimentel, N. Bray, P. Melsted, L. Pachter
Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2082–2088, https://doi.org/10.1093/bioinformatics/btx106
Published: 21 February 2017
Journal Article

BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone

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Bite Yang, Feng Liu, Chao Ren, Zhangyi Ouyang, Ziwei Xie ...
Bioinformatics, Volume 33, Issue 13, 1 July 2017, Pages 1930–1936, https://doi.org/10.1093/bioinformatics/btx105
Published: 17 February 2017
Journal Article

Empirical comparison of web-based antimicrobial peptide prediction tools

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Musa Nur Gabere, William Stafford Noble
Bioinformatics, Volume 33, Issue 13, 1 July 2017, Pages 1921–1929, https://doi.org/10.1093/bioinformatics/btx081
Published: 15 February 2017
Journal Article

iRSpot-EL: identify recombination spots with an ensemble learning approach

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Bin Liu, Shanyi Wang, Ren Long, Kuo-Chen Chou
Bioinformatics, Volume 33, Issue 1, 1 January 2017, Pages 35–41, https://doi.org/10.1093/bioinformatics/btw539
Published: 17 December 2016
Journal Article

SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments

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Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Bioinformatics, Volume 33, Issue 3, 1 February 2017, Pages 347–353, https://doi.org/10.1093/bioinformatics/btw656
Published: 22 October 2016
Journal Article

iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals

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Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou
Bioinformatics, Volume 33, Issue 3, 1 February 2017, Pages 341–346, https://doi.org/10.1093/bioinformatics/btw644
Published: 14 October 2016
Journal Article

bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli

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Ilham Ayub Shahmuradov, Rozaimi Mohamad Razali, Salim Bougouffa, Aleksandar Radovanovic, Vladimir B. Bajic
Bioinformatics, Volume 33, Issue 3, 1 February 2017, Pages 334–340, https://doi.org/10.1093/bioinformatics/btw629
Published: 30 September 2016
Journal Article

LAMSA: fast split read alignment with long approximate matches

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Bo Liu, Yan Gao, Yadong Wang
Bioinformatics, Volume 33, Issue 2, 15 January 2017, Pages 192–201, https://doi.org/10.1093/bioinformatics/btw594
Published: 25 September 2016
Journal Article

An accessibility-incorporated method for accurate prediction of RNA–RNA interactions from sequence data

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Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa ...
Bioinformatics, Volume 33, Issue 2, 15 January 2017, Pages 202–209, https://doi.org/10.1093/bioinformatics/btw603
Published: 23 September 2016
Journal Article

FBB: a fast Bayesian-bound tool to calibrate RNA-seq aligners

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Irene Rodriguez-Lujan, Jeff Hasty, Ramón Huerta
Bioinformatics, Volume 33, Issue 2, 15 January 2017, Pages 210–218, https://doi.org/10.1093/bioinformatics/btw608
Published: 23 September 2016
Journal Article

Evolutionary conservation of Ebola virus proteins predicts important functions at residue level

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Ahmed Arslan, Vera van Noort
Bioinformatics, Volume 33, Issue 2, 15 January 2017, Pages 151–154, https://doi.org/10.1093/bioinformatics/btw610
Published: 21 September 2016
Journal Article

Seeksv: an accurate tool for somatic structural variation and virus integration detection

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Ying Liang, Kunlong Qiu, Bo Liao, Wen Zhu, Xuanlin Huang ...
Bioinformatics, Volume 33, Issue 2, 15 January 2017, Pages 184–191, https://doi.org/10.1093/bioinformatics/btw591
Published: 14 September 2016
Journal Article

Nanocall: an open source basecaller for Oxford Nanopore sequencing data

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Matei David, L. J. Dursi, Delia Yao, Paul C. Boutros, Jared T. Simpson
Bioinformatics, Volume 33, Issue 1, 1 January 2017, Pages 49–55, https://doi.org/10.1093/bioinformatics/btw569
Published: 10 September 2016
Journal Article

Imbalanced multi-label learning for identifying antimicrobial peptides and their functional types

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Weizhong Lin, Dong Xu
Bioinformatics, Volume 32, Issue 24, 15 December 2016, Pages 3745–3752, https://doi.org/10.1093/bioinformatics/btw560
Published: 26 August 2016
Journal Article

Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition

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Akinori Awazu
Bioinformatics, Volume 33, Issue 1, 1 January 2017, Pages 42–48, https://doi.org/10.1093/bioinformatics/btw562
Published: 25 August 2016