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Bioinformatics, Volume 34
Volume 34, Number 1, January 2018
Genome Analysis
- Karolina Elzbieta Kaczor-Urbanowicz
, Yong Kim, Feng Li
, Timur Galeev, Robert R. Kitchen, Mark Gerstein, Kikuye Koyano, Sung-Hee Jeong, Xiaoyan Wang, David Elashoff, So Young Kang, Su Mi Kim, Kyoung Kim, Sung Kim, David Chia, Xinshu Xiao
, Joel S. Rozowsky, David T. W. Wong:
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development. 1-8 - Sha Joe Zhu
, Jacob Almagro-Garcia, Gil McVean:
Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data. 9-15 - Brian J. Mendoza, Cong T. Trinh
:
Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms. 16-23
- Ergude Bao, Chang-Jin Song, Lingxiao Lan:
ReMILO: reference assisted misassembly detection algorithm using short and long reads. 24-32 - Bin Liu, Fan Yang, De-Shuang Huang, Kuo-Chen Chou:
iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC. 33-40
- Konrad Krawczyk
, Samuel Demharter
, Bernhard Knapp, Charlotte M. Deane
, Peter Minary:
In silico structural modeling of multiple epigenetic marks on DNA. 41-48 - Brian Jiménez-García
, Jorge Roel-Touris, Miguel Romero-Durana
, Miquel Vidal
, Daniel Jiménez-González
, Juan Fernández-Recio
:
LightDock: a new multi-scale approach to protein-protein docking. 49-55
- Xu Shi
, Xiao Wang, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke
, Jianhua Xuan
:
SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data. 56-63
- Andrew Elliott
, Elizabeth Leicht, Alan Whitmore, Gesine Reinert
, Felix Reed-Tsochas
:
A nonparametric significance test for sampled networks. 64-71
- Lewis H. Mervin
, Krishna C. Bulusu
, Leen Kalash, Avid M. Afzal, Fredrik Svensson, Mike A. Firth, Ian P. Barrett, Ola Engkvist
, Andreas Bender
:
Orthologue chemical space and its influence on target prediction. 72-79 - Chih-Hsuan Wei
, Lon Phan, Juliana Feltz, Rama Maiti, Tim Hefferon, Zhiyong Lu:
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine. 80-87
- Elco Bakker, Peter S. Swain
, Matthew M. Crane
:
Morphologically constrained and data informed cell segmentation of budding yeast. 88-96 - Carlo Biffi
, Antonio de Marvao
, Mark I Attard, Timothy J. W. Dawes
, Nicola Whiffin, Wenjia Bai, Wenzhe Shi, Catherine Francis
, Hannah Meyer
, Rachel J. Buchan
, Stuart A. Cook, Daniel Rueckert, Declan P. O'Regan
:
Three-dimensional cardiovascular imaging-genetics: a mass univariate framework. 97-103
Genome Analysis
- Laura Seaman
, Indika Rajapakse:
4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities. 104-106 - Jochen Singer, Hans-Joachim Ruscheweyh, Ariane L. Hofmann, Thomas Thurnherr, Franziska Singer
, Nora C. Toussaint
, Charlotte K. Y. Ng
, Salvatore Piscuoglio
, Christian Beisel
, Gerhard Christofori, Reinhard Dummer, Michael N. Hall
, Wilhelm Krek, Mitchell P. Levesque, Markus G. Manz
, Holger Moch, Andreas Papassotiropoulos
, Daniel J. Stekhoven
, Peter Wild, Thomas Wüst, Bernd Rinn, Niko Beerenwinkel:
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis. 107-108 - Kun-Tze Chen, Chia-Liang Liu, Shang-Hao Huang, Hsin-Ting Shen, Yi-Kung Shieh, Hsien-Tai Chiu, Chin Lung Lu:
CSAR: a contig scaffolding tool using algebraic rearrangements. 109-111 - Nils Ternès, Federico Rotolo
, Stefan Michiels
:
biospear: an R package for biomarker selection in penalized Cox regression. 112-113
- Christopher Wilks, Phani Gaddipati
, Abhinav Nellore
, Ben Langmead
:
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples. 114-116 - Houxiang Zhu, Emily Richmond, Chun Liang:
CRISPR-RT: a web application for designing CRISPR-C2c2 crRNA with improved target specificity. 117-119
- Yuri Binev, Daniela Peixoto
, Florbela Pereira
, Ian Rodrigues, Sofia Cavaco
, Ana M. Lobo
, João Aires-de-Sousa
:
NavMol 3.0: enabling the representation of metabolic reactions by blind users. 120-121 - Damiano Piovesan
, Silvio C. E. Tosatto
:
Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures. 122-123
- Carl D. Christensen, Jan-Hendrik S. Hofmeyr, Johann M. Rohwer
:
PySCeSToolbox: a collection of metabolic pathway analysis tools. 124-125 - Sara Brin Rosenthal
, Julia Len, Mikayla Webster, Aaron Gary, Amanda Birmingham, Kathleen M. Fisch
:
Interactive network visualization in Jupyter notebooks: visJS2jupyter. 126-128
- Oded Rimon
, Dana Reichmann
:
Kfits: a software framework for fitting and cleaning outliers in kinetic measurements. 129-130
- Oriol López-Massaguer
, Ferran Sanz
, Manuel Pastor
:
An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies. 131-133
- Rani Arielly
, Yuval Ebenstein:
Irys Extract. 134-136 - Kristoffer Bernhem, Hjalmar Brismar
:
SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy. 137-138
Gene expression
- Zhe Sun, Ting Wang
, Ke Deng, Xiao-Feng Wang, Robert Lafyatis, Ying Ding, Ming Hu, Wei Chen:
DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. 139-146
- Roye Rozov, Gil Goldshlager
, Eran Halperin, Ron Shamir:
Faucet: streaming de novo assembly graph construction. 147-154
- Vikas Bansal:
An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments. 155-162 - Pavel Skums, Alex Zelikovsky
, Rahul Singh, Walker Gussler, Zoya Dimitrova, Sergey Knyazev
, Igor Mandric, Sumathi Ramachandran
, David S. Campo
, Deeptanshu Jha, Leonid Bunimovich, Elizabeth Costenbader, Connie Sexton, Siobhán O'Connor, Guo-liang Xia, Yury Khudyakov:
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. 163-170 - Xinan Liu, Ye Yu
, Jinpeng Liu, Corrine F. Elliott
, Chen Qian, Jinze Liu:
A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures. 171-178
Sequence Analysis
- Greg Malysa, Mikel Hernaez
, Idoia Ochoa, Milind Rao, Karthik Ganesan
, Tsachy Weissman:
QVZ: lossy compression of quality values. 179
Sequence Analysis
- Zhi-Kai Yang
, Feng Gao:
The systematic analysis of ultraconserved genomic regions in the budding yeast. 180
Volume 34, Number 2, January 2018
Genome Analysis
- Gulce Kale, Erman Ayday, Öznur Tastan
:
A utility maximizing and privacy preserving approach for protecting kinship in genomic databases. 181-189
- Hsin-Nan Lin
, Wen-Lian Hsu:
DART: a fast and accurate RNA-seq mapper with a partitioning strategy. 190-197 - Jun Ding
, Xiaoman Li, Haiyan Hu
:
CCmiR: a computational approach for competitive and cooperative microRNA binding prediction. 198-206
- Matteo Tiberti
, Alessandro Pandini
, Franca Fraternali
, Arianna Fornili:
In silico identification of rescue sites by double force scanning. 207-214 - Dmytro Guzenko
, Sergei V. Strelkov:
CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments. 215-222 - Thomas C. Northey, Anja Baresic, Andrew C. R. Martin
:
IntPred: a structure-based predictor of protein-protein interaction sites. 223-229 - Jing Yang, Hong-Bin Shen:
MemBrain-contact 2.0: a new two-stage machine learning model for the prediction enhancement of transmembrane protein residue contacts in the full chain. 230-238
- Qiu Xiao
, Jiawei Luo, Cheng Liang, Jie Cai, Pingjian Ding
:
A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations. 239-248 - Yiming Kang
, Hien-Haw Liow, Ezekiel J. Maier
, Michael R. Brent
:
NetProphet 2.0: mapping transcription factor networks by exploiting scalable data resources. 249-257 - Nan Papili Gao, S. M. Minhaz Ud-Dean, Olivier Gandrillon, Rudiyanto Gunawan
:
SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. 258-266
- Yingli Zhong, Ping Xuan
, Xiao Wang, Tiangang Zhang, Jianzhong Li, Yong Liu, Weixiong Zhang
:
A non-negative matrix factorization based method for predicting disease-associated miRNAs in miRNA-disease bilayer network. 267-277
- Lei Du, Kefei Liu, Tuo Zhang, Xiaohui Yao, Jingwen Yan, Shannon L. Risacher
, Junwei Han, Lei Guo, Andrew J. Saykin, Li Shen
:
A novel SCCA approach via truncated ℓ1-norm and truncated group lasso for brain imaging genetics. 278-285
Genome Analysis
- Chris Chatzinakos, Donghyung Lee
, Bradley Todd Webb
, Vladimir I. Vladimirov, Kenneth S. Kendler, Silviu-Alin Bacanu
:
JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts. 286-288 - Roberto Vera Alvarez
, Shan Li, David Landsman, Ivan Ovcharenko:
SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome. 289-291
- James Hadfield, Nicholas J. Croucher
, Richard J. Goater, Khalil AbuDahab, David M. Aanensen, Simon R. Harris:
Phandango: an interactive viewer for bacterial population genomics. 292-293
- Guillaume Brysbaert
, Kevin Lorgouilloux, Wim F. Vranken
, Marc F. Lensink
:
RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction. 294-296 - Anastasia A. Anashkina
, Yuri Kravatsky
, Eugene N. Kuznetsov
, Alexander A. Makarov, Alexei A. Adzhubei
:
Meta-server for automatic analysis, scoring and ranking of docking models. 297-299
- Christopher J. Green, Matthew R. Gazzara
, Yoseph Barash
:
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data. 300-302
- Daniel Boloc
, Natalia Rodríguez
, Patricia Gassó
, Josep F. Abril, Miquel Bernardo
, Amalia Lafuente, Sergi Mas
:
SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling. 303-305 - Lisa A. Ouellette
, Robert W. Reid
, Steven G. Blanchard, Cory R. Brouwer:
LinkageMapView - rendering high-resolution linkage and QTL maps. 306-307
- Michael Seifert, Andreas Beyer
:
regNet: an R package for network-based propagation of gene expression alterations. 308-311 - Maxime Chazalviel
, Clément Frainay
, Nathalie Poupin
, Florence Vinson, Benjamin Merlet, Yoann Gloaguen
, Ludovic Cottret
, Fabien Jourdan
:
MetExploreViz: web component for interactive metabolic network visualization. 312-313 - Huey-Eng Chua, Sourav S. Bhowmick
, Jie Zheng:
TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks. 314-316
- Joe Wandy
, Yunfeng Zhu, Justin J. J. van der Hooft
, Rónán Daly, Michael P. Barrett, Simon Rogers:
Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. 317-318
- Kun-Hsing Yu
, Michael R. Fitzpatrick, Luke Pappas, Warren Chan, Jessica Kung, Michael Snyder:
Omics AnalySIs System for PRecision Oncology (OASISPRO): a web-based omics analysis tool for clinical phenotype prediction. 319-320 - Jonathan Lo, Deric Zhang, Emily Speranza
, Jose A. Negron, John H. Connor
:
HoTResDB: host transcriptional response database for viral hemorrhagic fevers. 321-322
Genome Analysis
- Kristoffer Forslund
, Cécile Pereira
, Salvador Capella-Gutiérrez
, Alan W. Sousa da Silva
, Adrian M. Altenhoff
, Jaime Huerta-Cepas
, Matthieu Muffato
, Mateus Patricio
, Klaas Vandepoele
, Ingo Ebersberger, Judith A. Blake, Jesualdo Tomás Fernández-Breis
, The Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz
, Suzanna Lewis:
Gearing up to handle the mosaic nature of life in the quest for orthologs. 323-329
Genome Analysis
- Xiaoqing Huang, Damian Wójtowicz
, Teresa M. Przytycka
:
Detecting presence of mutational signatures in cancer with confidence. 330-337 - Abhijit Chakraborty, Ferhat Ay
:
Identification of copy number variations and translocations in cancer cells from Hi-C data. 338-345
- Layla Oesper, Simone Dantas, Benjamin J. Raphael
:
Identifying simultaneous rearrangements in cancer genomes. 346-352 - Rebecca Elyanow
, Hsin-Ta Wu, Benjamin J. Raphael
:
Identifying structural variants using linked-read sequencing data. 353-360
Volume 34, Number 3, February 2018
Genome Analysis
- Zhi-Kai Yang, Feng Gao
:
The systematic analysis of ultraconserved genomic regions in the budding yeast. 361-366
- Zeljko Tomljanovic
, Mitesh Patel
, William Shin, Andrea Califano
, Andrew F. Teich
:
ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease. 367-371
Genome Analysis
- Tarmo Äijö
, Christian L. Müller, Richard Bonneau:
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. 372-380 - Weilong Guo
, Ping Zhu
, Matteo Pellegrini
, Michael Q. Zhang, Xiangfeng Wang
, Zhongfu Ni:
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. 381-387 - Sun-Ah Kim, Chang-Sung Cho, Suh-Ryung Kim, Shelley B. Bull, Yun Joo Yoo:
A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs. 388-397 - Wei Tang, Shixiang Wan, Zhen Yang, Andrew E. Teschendorff, Quan Zou
:
Tumor origin detection with tissue-specific miRNA and DNA methylation markers. 398-406
- Paul D. Blischak
, Laura Salter Kubatko, Andrea D. Wolfe:
SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data. 407-415 - Haoyu Cheng
, Ming Wu, Yun Xu:
FMtree: a fast locating algorithm of FM-indexes for genomic data. 416-424 - Tom Paridaens
, Glenn Van Wallendael
, Wesley De Neve, Peter Lambert:
AQUa: an adaptive framework for compression of sequencing quality scores with random access functionality. 425-433 - Evgenii I Olekhnovich
, Artem T. Vasilyev
, Vladimir Ulyantsev
, Elena S. Kostryukova, Alexander V. Tyakht:
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota. 434-444
- Marco Necci
, Damiano Piovesan
, Zsuzsanna Dosztányi
, Peter Tompa, Silvio C. E. Tosatto
:
A comprehensive assessment of long intrinsic protein disorder from the DisProt database. 445-452 - Yumeng Yan, Sheng-You Huang:
RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring. 453-458 - Francesca Nadalin
, Alessandra Carbone
:
Protein-protein interaction specificity is captured by contact preferences and interface composition. 459-468 - Hyun-Ho Kyeong, Yoonjoo Choi
, Hak-Sung Kim:
GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking. 469-476 - Ghazaleh Taherzadeh, Yaoqi Zhou
, Alan Wee-Chung Liew
, Yuedong Yang
:
Structure-based prediction of protein- peptide binding regions using Random Forest. 477-484
- Ghislain Durif
, Laurent Modolo
, Jakob Michaelsson, Jeff E. Mold, Sophie Lambert-Lacroix, Franck Picard
:
High dimensional classification with combined adaptive sparse PLS and logistic regression. 485-493
- Claudio Angione
:
Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism. 494-501 - Zhengwei Xie
, Tianyu Zhang, Qi Ouyang:
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm. 502-510
Genome Analysis
- Mark F. Rogers, Hashem A. Shihab, Matthew E. Mort
, David N. Cooper, Tom R. Gaunt
, Colin Campbell:
FATHMM-XF: accurate prediction of pathogenic point mutations via extended features. 511-513 - Fabiano B. Menegidio
, Daniela L. Jabes
, Regina Costa de Oliveira
, Luiz R. Nunes
:
Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses. 514-515 - Sergii Ivakhno, Eric Roller, Camilla Colombo, Philip Tedder, Anthony J. Cox:
Canvas SPW: calling de novo copy number variants in pedigrees. 516-518 - Ho Jang, Hyunju Lee
:
Identification of cancer driver genes in focal genomic aberrations from whole-exome sequencing data. 519-521 - Javier Palarea-Albaladejo
, Kevin McLean, Frank Wright, David G. E. Smith:
MALDIrppa: quality control and robust analysis for mass spectrometry data. 522-523
- María José Nueda
, Jordi Martorell-Marugan
, Cristina Martí
, Sonia Tarazona, Ana Conesa
:
Identification and visualization of differential isoform expression in RNA-seq time series. 524-526
- Anna Okula Basile
, Marta Byrska-Bishop, John R. Wallace, Alex Thomas Frase, Marylyn D. Ritchie:
Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants. 527-529
- Mahito Sugiyama
, M. Elisabetta Ghisu, Felipe Llinares-López, Karsten M. Borgwardt
:
graphkernels: R and Python packages for graph comparison. 530-532
- Sergio Picart-Armada
, Wesley K. Thompson, Alfonso Buil, Alexandre Perera-Lluna
:
diffuStats: an R package to compute diffusion-based scores on biological networks. 533-534
- Éva Schád, Erzsébet Fichó
, Rita Pancsa, István Simon
, Zsuzsanna Dosztányi
, Bálint Mészáros
:
DIBS: a repository of disordered binding sites mediating interactions with ordered proteins. 535-537
- Virginie Uhlmann
, Carsten Haubold, Fred A. Hamprecht, Michael Unser
:
DiversePathsJ: diverse shortest paths for bioimage analysis. 538-540
Volume 34, Number 4, February 2018
Genome Analysis
- Cristian A. Yones
, Georgina Stegmayer
, Diego H. Milone
:
Genome-wide pre-miRNA discovery from few labeled examples. 541-549 - Hequan Sun, Jia Ding, Mathieu Piednoël, Korbinian Schneeberger:
findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. 550-557 - Shubham Chandak
, Kedar Tatwawadi, Tsachy Weissman:
Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis. 558-567
- Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro:
Squeakr: an exact and approximate k-mer counting system. 568-575 - Taikai Takeda, Michiaki Hamada
:
Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm. 576-584 - Pierre Pericard
, Yoann Dufresne
, Loïc Couderc, Samuel Blanquart, Hélène Touzet
:
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes. 585-591
- Manuel Alejandro Marín-López
, Joan Planas-Iglesias
, Joaquim Aguirre-Plans
, Jaume Bonet
, Javier García-García, Narcis Fernandez-Fuentes
, Baldo Oliva:
On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. 592-598 - Stanislav A. Bondarev, Olga V. Bondareva, Galina A. Zhouravleva, Andrey V. Kajava
:
BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures. 599-608 - Jasmin Cevost, Cédric Vaillant, Sam Meyer
:
ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes. 609-616
- Y. X. Rachel Wang
, Ke Liu, Elizabeth Theusch
, Jerome I. Rotter, Marisa W. Medina, Michael S. Waterman, Haiyan Huang:
Generalized correlation measure using count statistics for gene expression data with ordered samples. 617-624 - Angela Serra
, Pietro Coretto, Michele Fratello, Roberto Tagliaferri
:
Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data. 625-634
- Xiayuan Huang
, Robert C. Elston, Guilherme J. M. Rosa
, John Mayer, Zhan Ye, Terrie E. Kitchner, Murray H. Brilliant, David Page, Scott J. Hebbring
:
Applying family analyses to electronic health records to facilitate genetic research. 635-642 - Jun Chen, Emily King
, Rebecca Deek
, Zhi Wei
, Yue Yu, Diane E. Grill, Karla V. Ballman:
An omnibus test for differential distribution analysis of microbiome sequencing data. 643-651
- Jake Lever
, Sitanshu Gakkhar, Michael Gottlieb, Tahereh Rashnavadi, Santina Lin, Celia Siu, Maia Smith, Martin R. Jones, Martin Krzywinski, Steven J. M. Jones
:
A collaborative filtering-based approach to biomedical knowledge discovery. 652-659
- Maxat Kulmanov
, Mohammad Asif Khan, Robert Hoehndorf
:
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. 660-668
Genome Analysis
- Rachel C. W. Chan
, Maxwell W. Libbrecht, Eric G. Roberts, Jeffrey A. Bilmes, William Stafford Noble, Michael M. Hoffman
:
Segway 2.0: Gaussian mixture models and minibatch training. 669-671 - Caleb A. Lareau
, Martin J. Aryee:
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data. 672-674 - Anandashankar Anil, Rapolas Spalinskas
, Örjan Åkerborg
, Pelin Sahlén:
HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications. 675-677 - Michael Molnar, Ehsan Haghshenas, Lucian Ilie
:
SAGE2: parallel human genome assembly. 678-680 - Lianming Du, Chi Zhang, Qin Liu, Xiuyue Zhang, Bisong Yue:
Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. 681-683
- Jiangning Song
, Fuyi Li
, André Leier
, Tatiana T. Marquez-Lago, Tatsuya Akutsu
, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb
, Robert N. Pike:
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. 684-687 - Marie-Elisa Pinson, Romain Pogorelcnik, Franck Court
, Philippe Arnaud
, Catherine Vaurs-Barrière
:
CLIFinder: identification of LINE-1 chimeric transcripts in RNA-seq data. 688-690
- Charlotte Soneson, Mark D. Robinson
:
Towards unified quality verification of synthetic count data with countsimQC. 691-692
- Sohrab Saraei, Tomi Suomi
, Otto Kauko, Laura L. Elo
:
Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics. 693-694
- Erin M. Shockley
, Jasper A. Vrugt
, Carlos F. Lopez
:
PyDREAM: high-dimensional parameter inference for biological models in python. 695-697 - Nozomu Sakurai
, Takafumi Narise, Joon-Soo Sim, Chang-Muk Lee, Chiaki Ikeda, Nayumi Akimoto, Shigehiko Kanaya:
UC2 search: using unique connectivity of uncharged compounds for metabolite annotation by database searching in mass spectrometry-based metabolomics. 698-700 - Karan Uppal
, Chunyu Ma, Young-Mi Go, Dean P. Jones:
xMWAS: a data-driven integration and differential network analysis tool. 701-702 - Charles Tapley Hoyt
, Andrej Konotopez, Christian Ebeling
:
PyBEL: a computational framework for Biological Expression Language. 703-704 - Paul Stapor
, Daniel Weindl
, Benjamin Ballnus, Sabine Hug, Carolin Loos
, Anna Fiedler, Sabrina Krause, Sabrina Hross, Fabian Fröhlich
, Jan Hasenauer
:
PESTO: Parameter EStimation TOolbox. 705-707
- Xiaosan Huang, Shaoling Zhang
, Kongqing Li, Jyothi Thimmapuram, Shaojun Xie:
ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data. 708-709 - Alexey Lagunin
, Anastasia V. Rudik
, Dmitry S. Druzhilovskiy
, Dmitry Filimonov
, Vladimir Poroikov:
ROSC-Pred: web-service for rodent organ-specific carcinogenicity prediction. 710-712
- Nathan W. Wong
, Yuhao Chen, Shuai Chen
, Xiaowei Wang:
OncomiR: an online resource for exploring pan-cancer microRNA dysregulation. 713-715 - Florian Auer
, Zaynab Hammoud
, Alexandr Ishkin, Dexter Pratt
, Trey Ideker
, Frank Kramer
:
ndexr - an R package to interface with the network data exchange. 716-717
- Michaël Barbier, Astrid Bottelbergs, Rony Nuydens, Andreas Ebneth, Winnok De Vos
:
SliceMap: an algorithm for automated brain region annotation. 718-720
Volume 34, Number 5, March 2018
Sequence Analysis
- Luis Sánchez-Pulido
, Chris P. Ponting
:
TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules. 721-724
Genome Analysis
- Sarah Yeo, Lauren Coombe
, René L. Warren
, Justin Chu, Inanç Birol
:
ARCS: scaffolding genome drafts with linked reads. 725-731 - Qiao Liu, Fei Xia
, Qijin Yin, Rui Jiang:
Chromatin accessibility prediction via a hybrid deep convolutional neural network. 732-738
- Lu Zhao, Zhimin Liu
, Sasha F. Levy
, Song Wu:
Bartender: a fast and accurate clustering algorithm to count barcode reads. 739-747 - Kresimir Krizanovic, Amina Echchiki, Julien Roux
, Mile Sikic:
Evaluation of tools for long read RNA-seq splice-aware alignment. 748-754 - Alejandro A. Schäffer, Eric P. Nawrocki, Yoon Choi, Paul A. Kitts, Ilene Karsch-Mizrachi
, Richard McVeigh:
VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening. 755-759 - Yu Li
, Sheng Wang
, Ramzan Umarov, Bingqing Xie, Ming Fan, Lihua Li, Xin Gao
:
DEEPre: sequence-based enzyme EC number prediction by deep learning. 760-769
- Kei Terayama
, Hiroaki Iwata
, Mitsugu Araki, Yasushi Okuno, Koji Tsuda:
Machine learning accelerates MD-based binding pose prediction between ligands and proteins. 770-778 - Yunhui Peng, Lexuan Sun, Zhe Jia, Lin Li, Emil Alexov:
Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver. 779-786
- Cynthia A. Kalita
, Gregory A. Moyerbrailean, Christopher Brown, Xiaoquan Wen, Francesca Luca, Roger Pique-Regi:
QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays. 787-794
- Xuan Guo
, Zhou Li, Qiuming Yao, Ryan S. Mueller, Jimmy K. Eng
, David L. Tabb
, IV William Judson Hervey, Chongle Pan
:
Sipros Ensemble improves database searching and filtering for complex metaproteomics. 795-802 - Bram Thijssen
, Tjeerd Dijkstra, Tom Heskes
, Lodewyk F. A. Wessels:
Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates. 803-811 - Yu-An Huang
, Keith C. C. Chan, Zhu-Hong You
:
Constructing prediction models from expression profiles for large scale lncRNA-miRNA interaction profiling. 812-819
- Jinglong Niu, Yan Shi, Maolin Cai, Zhixin Cao, Dandan Wang, Zhaozhi Zhang, Xiaohua Douglas Zhang
:
Detection of sputum by interpreting the time-frequency distribution of respiratory sound signal using image processing techniques. 820-827 - Yijia Zhang, Wei Zheng, Hongfei Lin, Jian Wang, Zhihao Yang, Michel Dumontier
:
Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths. 828-835 - Ramón Díaz-Uriarte
:
Cancer progression models and fitness landscapes: a many-to-many relationship. 836-844
- Blazej Ruszczycki
, Tytus Bernas:
Quality of biological images, reconstructed using localization microscopy data. 845-852 - Renmin Han
, Fa Zhang, Xin Gao
:
A fast fiducial marker tracking model for fully automatic alignment in electron tomography. 853-863
Genome Analysis
- Markus Hollander
, Mohamed Hamed, Volkhard Helms
, Kerstin Neininger:
MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks. 864-866 - Brent S. Pedersen, Aaron R. Quinlan
:
Mosdepth: quick coverage calculation for genomes and exomes. 867-868
- Sergio Díaz Del Pino
, Juan Falgueras Cano, Esteban Pérez-Wohlfeil
, Oswaldo Trelles:
mORCA: sailing bioinformatics world with mobile devices. 869-870 - Marco Beccuti
, Francesca Cordero
, Maddalena Arigoni
, Riccardo Panero, Elvio Gilberto Amparore, Susanna Donatelli, Raffaele A. Calogero
:
SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer. 871-872 - Minh Duc Cao, Devika Ganesamoorthy, Chenxi Zhou
, Lachlan J. M. Coin
:
Simulating the dynamics of targeted capture sequencing with CapSim. 873-874
- Soundhararajan Gopi
, Devanshu Devanshu, Praveen Krishna, Athi N. Naganathan
:
pStab: prediction of stable mutants, unfolding curves, stability maps and protein electrostatic frustration. 875-877 - Daniele Toti
, Le Viet Hung, Valentina Tortosa
, Valentina Brandi, Fabio Polticelli
:
LIBRA-WA: a web application for ligand binding site detection and protein function recognition. 878-880
- Jinting Guan
, Moliang Chen, Congting Ye
, James J. Cai
, Guoli Ji:
AEGS: identifying aberrantly expressed gene sets for differential variability analysis. 881-883 - Krzysztof Polanski
, Bo Gao
, Sam A. Mason, Paul Brown, Sascha Ott, Katherine J. Denby
, David L. Wild:
Bringing numerous methods for expression and promoter analysis to a public cloud computing service. 884-886
- Mitchell J. Machiela
, Stephen J. Chanock:
LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation. 887-889
- Andrea Rodriguez-Martinez, Joram M. Posma
, Rafael Ayala
, Ana Luísa Neves
, Maryam Anwar, Enrico Petretto
, Costanza Emanueli
, Dominique Gauguier
, Jeremy K. Nicholson
, Marc-Emmanuel Dumas
:
MWASTools: an R/bioconductor package for metabolome-wide association studies. 890-892 - Manuel Pájaro
, Irene Otero-Muras, Carlos Vázquez
, Antonio A. Alonso
:
SELANSI: a toolbox for simulation of stochastic gene regulatory networks. 893-895
- Simon Dirmeier, Christiane Fuchs
, Nikola S. Müller, Fabian J. Theis:
netReg: network-regularized linear models for biological association studies. 896-898
- Kyle I. S. Harrington
, Curtis T. Rueden
, Kevin W. Eliceiri:
FunImageJ: a Lisp framework for scientific image processing. 899-900
Volume 34, Number 6, March 2018
Genome Analysis
- Zaixiang Tang, Yueping Shen, Yan Li, Xinyan Zhang
, Jia Wen, Chen'ao Qian, Wenzhuo Zhuang, Xinghua Shi, Nengjun Yi:
Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information. 901-910 - Vida Ravanmehr, Minji Kim
, Zhiying Wang
, Olgica Milenkovic:
ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data. 911-919 - Bethany Signal, Brian S. Gloss
, Marcel E. Dinger
, Tim R. Mercer:
Machine learning annotation of human branchpoints. 920-927 - Altti Ilari Maarala
, Zurab Bzhalava, Joakim Dillner, Keijo Heljanko
, Davit Bzhalava:
ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads. 928-935 - Clinton L. Cario, John S. Witte:
Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations. 936-942
- Akshay Kumar Avvaru
, Divya Tej Sowpati
, Rakesh Kumar Mishra:
PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences. 943-948
- Claire Marks, Jiye Shi, Charlotte M. Deane
:
Predicting loop conformational ensembles. 949-956 - Roman R. Kapaev
, Philip V. Toukach
:
GRASS: semi-automated NMR-based structure elucidation of saccharides. 957-963
- Manuel Sanchez-Castillo, David Blanco, Isabel M. Tienda-Luna, Maria Carmen Carrion Perez, Yufei Huang:
A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data. 964-970 - Matthew M. Parks
:
An exact test for comparing a fixed quantitative property between gene sets. 971-977
- Weiqi Tang, Likun Huang, Suhong Bu, Xuzhang Zhang, Weiren Wu:
Estimation of QTL heritability based on pooled sequencing data. 978-984
- Lichy Han
, Mateusz Maciejewski, Christoph Brockel, William Gordon, Scott B. Snapper, Joshua R. Korzenik, Lovisa Afzelius, Russ B. Altman
:
A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease. 985-993 - Malte Lücken
, M. J. T. Page, A. J. Crosby, S. Mason, Gesine Reinert, Charlotte M. Deane
:
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias. 994-1000
- Somrudee Deepaisarn
, Paul D. Tar, Neil A. Thacker, A. Seepujak, A. W. McMahon:
Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra. 1001-1008 - Jérôme Mariette, Nathalie Villa-Vialaneix:
Unsupervised multiple kernel learning for heterogeneous data integration. 1009-1015
- Sergio Castillo-Lara
, Josep F. Abril:
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes. 1016-1023
- Jun Cheng, Xiaokui Mo, Xusheng Wang, Anil Parwani
, Qianjin Feng, Kun Huang:
Identification of topological features in renal tumor microenvironment associated with patient survival. 1024-1030
Genome Analysis
- Lucas Lochovsky
, Jing Zhang, Mark Gerstein:
MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool. 1031-1033 - Dorota H. Sendorek, Emilie Lalonde
, Cindy Q. Yao, Veronica Y. Sabelnykova, Robert G. Bristow
, Paul C. Boutros
:
NanoStringNormCNV: pre-processing of NanoString CNV data. 1034-1036 - Yasuhiro Tanizawa, Takatomo Fujisawa, Yasukazu Nakamura
:
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. 1037-1039 - Lauro Ângelo Gonçalves de Moraes, Érica Barbosa Felestrino, Renata de Almeida Barbosa Assis, Diogo Matos, Joubert de Castro Lima, Leandro de Araújo Lima, Nalvo F. de Almeida Jr.
, João Carlos Setubal
, Camila Carrião Machado Garcia
, Leandro Márcio Moreira:
TabPath: interactive tables for metabolic pathway analysis. 1040-1042 - Antonio Carvajal-Rodríguez
:
Myriads: P-value-based multiple testing correction. 1043-1045 - Tong Liu, Zheng Wang:
scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data. 1046-1047
- Antonio Solano-Román, Verónica Alfaro-Arias, Carlos Cruz-Castillo
, Allan Orozco-Solano:
Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains. 1048-1049
- Brian D. Piccolo
, Umesh D. Wankhade, Sree V. Chintapalli, Sudeepa Bhattacharyya, Luo Chunqiao, Kartik Shankar
:
Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data. 1050-1052 - Stilianos Louca
, Michael Doebeli:
Efficient comparative phylogenetics on large trees. 1053-1055 - Sarah Bastkowski
, Daniel Mapleson, Andreas Spillner, Taoyang Wu
, Monika Balvociute, Vincent Moulton
:
SPECTRE: a suite of phylogenetic tools for reticulate evolution. 1056-1057
- Marco Pietrosanto
, Marta Adinolfi
, Riccardo Casula, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich
:
BEAM web server: a tool for structural RNA motif discovery. 1058-1060 - Andrei L. Lomize
, Jacob M. Hage, Irina D. Pogozheva
:
Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers. 1061-1062 - Lim Heo, Michael Feig
:
PREFMD: a web server for protein structure refinement via molecular dynamics simulations. 1063-1065
- Gero Doose, Stephan H. Bernhart
, Rabea Wagener, Steve Hoffmann:
DIEGO: detection of differential alternative splicing using Aitchison's geometry. 1066-1068
- Tim Carver, Alex P. Cunningham, Chantal Babb de Villiers
, Andrew Lee, Simon Hartley
, Marc Tischkowitz, Fiona M. Walter
, Douglas F. Easton, Antonis C. Antoniou:
pedigreejs: a web-based graphical pedigree editor. 1069-1071 - Richard H. Adams, Drew R. Schield, Daren C. Card, Andrew Corbin, Todd A. Castoe:
ThetaMater: Bayesian estimation of population size parameter θ from genomic data. 1072-1073
- Sandy S. Pineda, Pierre-Alain Chaumeil, Anne Kunert, Quentin Kaas
, Mike W. C. Thang, Lien Le, Michael Nuhn
, Volker Herzig
, Natalie J. Saez
, Ben Cristofori-Armstrong
, Raveendra Anangi, Sebastian Senff
, Dominique Gorse
, Glenn F. King
:
ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins. 1074-1076 - Jeongbin Park
, Sangsu Bae
:
Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1. 1077-1079
Volume 34, Number 7, April 2018
Genome Analysis
- Jana Cechová, Jirí Lýsek, Martin Bartas
, Václav Brázda
:
Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability. 1081-1085
Genome Analysis
- Minjeong Kim, Jai-Hoon Kim, Kangseok Kim, Sunshin Kim:
Cost-effective and accurate method of measuring fetal fraction using SNP imputation. 1086-1091
- Reda Rawi, Raghvendra Mall
, Khalid Kunji, Chen-Hsiang Shen, Peter D. Kwong, Gwo-Yu Chuang:
PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine. 1092-1098 - Rui Guo
, Yan-Ran Li, Shan He, Le Ou-Yang, Yiwen Sun, Zexuan Zhu:
RepLong: de novo repeat identification using long read sequencing data. 1099-1107 - Kuan-Chieh Tseng, Yi-Fan Chiang-Hsieh, Hsuan Pai, Chi-Nga Chow, Shu-Chuan Lee
, Han-Qin Zheng, Po-Li Kuo, Guan-Zhen Li, Yu-Cheng Hung, Na-Sheng Lin, Wen-Chi Chang
:
microRPM: a microRNA prediction model based only on plant small RNA sequencing data. 1108-1115 - Anne Hoffmann
, Jörg Fallmann
, Elisa Vilardo
, Mario Mörl
, Peter F. Stadler
, Fabian Amman
:
Accurate mapping of tRNA reads. 1116-1124 - Samarth Rangavittal
, Robert S. Harris, Monika Cechova
, Marta Tomaszkiewicz
, Rayan Chikhi, Kateryna D. Makova, Paul Medvedev:
RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly. 1125-1131
- Saulo Henrique Pires de Oliveira, Eleanor C. Law
, Jiye Shi, Charlotte M. Deane
:
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction. 1132-1140
- Haidong Yi, Ayush T. Raman
, Han Zhang
, Genevera I. Allen, Zhandong Liu
:
Detecting hidden batch factors through data-adaptive adjustment for biological effects. 1141-1147 - Phan Nguyen
, Rosemary Braun
:
Semi-supervised network inference using simulated gene expression dynamics. 1148-1156
- Peizhou Liao, Glen A. Satten, Yi-Juan Hu:
Robust inference of population structure from next-generation sequencing data with systematic differences in sequencing. 1157-1163
- Rawan S. Olayan
, Haitham Ashoor
, Vladimir B. Bajic
:
DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches. 1164-1173 - Carlos Ramírez, Luis Mendoza
:
Phenotypic stability and plasticity in GMP-derived cells as determined by their underlying regulatory network. 1174-1182 - Andrei A. Ivanov
, Brian Revennaugh, Lauren Rusnak, Valentina Gonzalez-Pecchi
, Xiulei Mo, Margaret A. Johns
, Yuhong Du, Lee A. D. Cooper, Carlos Sanchez Moreno
, Fadlo R. Khuri
, Haian Fu:
The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. 1183-1191
- Pengyuan Li
, Xiangying Jiang, Chandra Kambhamettu, Hagit Shatkay:
Compound image segmentation of published biomedical figures. 1192-1199
- Fritz Lekschas
, Nils Gehlenborg:
SATORI: a system for ontology-guided visual exploration of biomedical data repositories. 1200-1207 - Antonio Fabregat
, Konstantinos Sidiropoulos
, Guilherme Viteri, Pablo Marín-García
, Peipei Ping, Lincoln Stein, Peter D'Eustachio
, Henning Hermjakob
:
Reactome diagram viewer: data structures and strategies to boost performance. 1208-1214
- Jens Behrmann, Christian Etmann, Tobias Boskamp
, Rita Casadonte
, Jörg Kriegsmann, Peter Maaß
:
Deep learning for tumor classification in imaging mass spectrometry. 1215-1223
Genome Analysis
- Pierre Lindenbaum
, Richard Redon
:
bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files. 1224-1225 - Thomas Cokelaer, Elisabeth Chen, Francesco Iorio
, Michael P. Menden
, Howard Lightfoot
, Julio Saez-Rodriguez
, Mathew Garnett:
GDSCTools for mining pharmacogenomic interactions in cancer. 1226-1228 - Yiming Yu
, Yidan Ouyang
, Wen Yao
:
shinyCircos: an R/Shiny application for interactive creation of Circos plot. 1229-1231
- Sunguk Shin, Hanna Lee, Hyeonju Son, Soonmyung Paik
, Sangwoo Kim
:
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing. 1232-1234 - Lauren J. McIver, Galeb Abu-Ali, Eric A. Franzosa
, Randall Schwager, Xochitl C. Morgan, Levi Waldron
, Nicola Segata
, Curtis Huttenhower:
bioBakery: a meta'omic analysis environment. 1235-1237
- Yangyu Huang, Haotian Li, Yi Xiao:
3dRPC: a web server for 3D RNA-protein structure prediction. 1238-1240 - Hai Nguyen, David A. Case, Alexander S. Rose
:
NGLview-interactive molecular graphics for Jupyter notebooks. 1241-1242
- Caleb A. Class
, Min Jin Ha
, Veerabhadran Baladandayuthapani, Kim-Anh Do:
iDINGO - integrative differential network analysis in genomics with Shiny application. 1243-1245 - Caleb Weinreb, Samuel L. Wolock
, Allon M. Klein:
SPRING: a kinetic interface for visualizing high dimensional single-cell expression data. 1246-1248
- Leander Dony
, Jonas Mackerodt, Scott Ward
, Sarah Filippi
, Michael P. H. Stumpf, Juliane Liepe
:
PEITH(Θ): perfecting experiments with information theory in Python with GPU support. 1249-1250
- Justin Nelson, Scott W. Simpkins, Hamid Safizadeh, Sheena C. Li
, Jeff S. Piotrowski, Hiroyuki Hirano
, Yoko Yashiroda, Hiroyuki Osada, Minoru Yoshida
, Charles Boone, Chad L. Myers:
MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action. 1251-1252
Systems Biology
- Mariano Rubiolo, Diego H. Milone
, Georgina Stegmayer
:
Extreme learning machines for reverse engineering of gene regulatory networks from expression time series. 1253-1260
Volume 34, Number 8, April 2018
Sequence Analysis
- Ziga Avsec, Mohammadamin Barekatain
, Jun Cheng
, Julien Gagneur
:
Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks. 1261-1269 - Brittney N. Keel, Bo Deng, Etsuko N. Moriyama
:
MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks. 1270-1277 - Nelson Gil
, András Fiser:
Identifying functionally informative evolutionary sequence profiles. 1278-1286 - Frédéric Escudié, Lucas Auer, Maria Bernard
, Mahendra Mariadassou, Laurent Cauquil, Katia Vidal, Sarah Maman
, Guillermina Hernandez-Raquet, Sylvie Combes
, Géraldine Pascal
:
FROGS: Find, Rapidly, OTUs with Galaxy Solution. 1287-1294
- Jie Hou, Badri Adhikari, Jianlin Cheng
:
DeepSF: deep convolutional neural network for mapping protein sequences to folds. 1295-1303 - Maciej Antczak
, Mariusz Popenda
, Tomasz Zok
, Michal Zurkowski
, Ryszard W. Adamiak
, Marta Szachniuk
:
New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation. 1304-1312
- Zong Miao
, Marcus Alvarez, Päivi Pajukanta, Arthur Ko:
ASElux: an ultra-fast and accurate allelic reads counter. 1313-1320 - Sunghwan Kim, Dongwan D. Kang, Zhiguang Huo, Yongseok Park, George C. Tseng:
Meta-analytic principal component analysis in integrative omics application. 1321-1328 - Yan Zhou, Xiang Wan, Baoxue Zhang, Tiejun Tong
:
Classifying next-generation sequencing data using a zero-inflated Poisson model. 1329-1335 - Joshua Mayer, Raziur Rahman, Souparno Ghosh, Ranadip Pal
:
Sequential feature selection and inference using multi-variate random forests. 1336-1344
- Wayne B. Hayes
, Nil Mamano:
SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments. 1345-1352 - Mehreen Ali
, Suleiman A. Khan, Krister Wennerberg
, Tero Aittokallio
:
Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach. 1353-1362 - Shyam Srinivasan, William R. Cluett, Radhakrishnan Mahadevan
:
Model-based design of bistable cell factories for metabolic engineering. 1363-1371
- Ine Melckenbeeck
, Pieter Audenaert, Didier Colle, Mario Pickavet
:
Efficiently counting all orbits of graphlets of any order in a graph using autogenerated equations. 1372-1380 - Ling Luo
, Zhihao Yang, Pei Yang, Yin Zhang, Lei Wang, Hongfei Lin, Jian Wang:
An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition. 1381-1388 - Axel J. Soto
, Chrysoula Zerva
, Riza Batista-Navarro
, Sophia Ananiadou:
LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models. 1389-1397
Genome Analysis
- Gabriel Renaud
:
glactools: a command-line toolset for the management of genotype likelihoods and allele counts. 1398-1400 - Jasper J. Koehorst
, Jesse C. J. van Dam
, Edoardo Saccenti
, Vítor A. P. Martins dos Santos
, María Suárez-Diez
, Peter J. Schaap
:
SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles. 1401-1403 - Askarbek N. Orakov, Nazgul Sakenova
, Anatoly A. Sorokin
, Igor Goryanin
:
ASAR: visual analysis of metagenomes in R. 1404-1405 - Katherine J. Harrison, Valérie de Crécy-Lagard
, Rémi Zallot
:
Gene Graphics: a genomic neighborhood data visualization web application. 1406-1408 - Bixia Tang, Feifei Li, Jing Li, Wenming Zhao, Zhihua Zhang:
Delta: a new web-based 3D genome visualization and analysis platform. 1409-1410
- Nick Weber
, David Liou, Jennifer Dommer, Philip MacMenamin, Mariam Quiñones
, Ian Misner, Andrew J. Oler, Joe Wan
, Lewis Kim, Meghan Coakley McCarthy
, Samuel Ezeji, Karlynn Noble
, Darrell E. Hurt:
Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis. 1411-1413 - Osvaldo Graña
, Hugo López-Fernández
, Florentino Fdez-Riverola
, David G. Pisano, Daniel Glez-Peña
:
Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data. 1414-1415
- Mattia Chiesa, Gualtiero I. Colombo
, Luca Piacentini
:
DaMiRseq - an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification. 1416-1418
- Robert Kofler:
SimulaTE: simulating complex landscapes of transposable elements of populations. 1419-1420
- Thomas S. Ligon
, Fabian Fröhlich
, Oana Chis, Julio R. Banga
, Eva Balsa-Canto
, Jan Hasenauer
:
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models. 1421-1423 - Tom Warnke
, Tobias Helms, Adelinde M. Uhrmacher:
Reproducible and flexible simulation experiments with ML-Rules and SESSL. 1424-1427 - Lin Wu, Min Li, Jianxin Wang, Fang-Xiang Wu
:
CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis. 1428-1430
- Alba Gutiérrez-Sacristán
, Romain Guedj, Gabor Korodi, Jason Stedman, Laura Inés Furlong
, Chirag J. Patel, Isaac S. Kohane, Paul Avillach:
Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API. 1431-1432
- Daniel Probst
, Jean-Louis Reymond
:
FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web. 1433-1435 - Andrew Palmer
, Prasad Phapale
, Dominik Fay
, Theodore Alexandrov:
Curatr: a web application for creating, curating and sharing a mass spectral library. 1436-1438
Databases and Ontologies
- Robert Kofler:
SimulaTE: simulating complex landscapes of transposable elements of populations. 1439
Databases and Ontologies
- Xing Chen, Yu-An Huang
, Zhu-Hong You, Guiying Yan, Xuesong Wang:
A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases. 1440
Volume 34, Number 9, May 2018
Genome Analysis
- Cristina Mitrea, Priyanga Wijesinghe, Gregory Dyson, Adéle Kruger, Douglas M. Ruden
, Sorin Draghici, Aliccia Bollig-Fischer
:
Integrating 5hmC and gene expression data to infer regulatory mechanisms. 1441-1447
- Xiang Cheng, Xuan Xiao, Kuo-Chen Chou:
pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information. 1448-1456 - Liren Huang, Jan Krüger, Alexander Sczyrba
:
Analyzing large scale genomic data on the cloud with Sparkhit. 1457-1465
- Badri Adhikari, Jie Hou, Jianlin Cheng
:
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks. 1466-1472 - Yuliang Pan
, Zixiang Wang, Weihua Zhan, Lei Deng:
Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach. 1473-1480 - S. M. Ashiqul Islam
, Benjamin J. Heil
, Christopher Michel Kearney, Erich J. Baker
:
Protein classification using modified n-grams and skip-grams. 1481-1487
- Scott S. Norton, Jorge Vaquero-Garcia, Nicholas F. Lahens, Gregory R. Grant, Yoseph Barash
:
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates. 1488-1497 - Francesco Napolitano, Diego Carrella, Barbara Mandriani
, Sandra Pisonero-Vaquero, Francesco Sirci, Diego L. Medina
, Nicola Brunetti-Pierri
, Diego di Bernardo
:
gene2drug: a computational tool for pathway-based rational drug repositioning. 1498-1505
- Andriy Derkach
, Haoyu Zhang, Nilanjan Chatterjee:
Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies. 1506-1513
- Mitra Ansariola
, Molly Megraw
, David Koslicki:
IndeCut evaluates performance of network motif discovery algorithms. 1514-1521 - Massimo Andreatta
, Thomas Trolle
, Zhen Yan, Jason A. Greenbaum, Bjoern Peters
, Morten Nielsen
:
An automated benchmarking platform for MHC class II binding prediction methods. 1522-1528
- Guangyuan Fu, Jun Wang
, Carlotta Domeniconi, Guoxian Yu
:
Matrix factorization-based data fusion for the prediction of lncRNA-disease associations. 1529-1537 - Kristina Preuer, Richard P. I. Lewis, Sepp Hochreiter
, Andreas Bender
, Krishna C. Bulusu
, Günter Klambauer:
DeepSynergy: predicting anti-cancer drug synergy with Deep Learning. 1538-1546 - Qile Zhu, Xiaolin Li, Ana Conesa
, Cécile Pereira
:
GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text. 1547-1554 - Zhuxuan Jin, Jian Kang
, Tianwei Yu
:
Missing value imputation for LC-MS metabolomics data by incorporating metabolic network and adduct ion relations. 1555-1561
Genome Analysis
- Alan M. Cleary
, Andrew D. Farmer:
Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny. 1562-1564 - Jacob M. Luber
, Braden T. Tierney, Evan M. Cofer, Chirag J. Patel, Aleksandar D. Kostic
:
Aether: leveraging linear programming for optimal cloud computing in genomics. 1565-1567 - Xiaobin Zheng, Yixian Zheng:
CscoreTool: fast Hi-C compartment analysis at high resolution. 1568-1570 - Xiao-Fei Zhang, Le Ou-Yang, Shuo Yang, Xiaohua Hu, Hong Yan:
DiffGraph: an R package for identifying gene network rewiring using differential graphical models. 1571-1573
- Xuan Ma
, Chunyan Liu, Lian-Feng Gu, Beixin Mo, Xiaofeng Cao, Xuemei Chen:
TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants. 1574-1576 - Duong Vu
, Sonja Georgievska, Szaniszlo Szoke, Arnold Kuzniar
, Vincent Robert:
fMLC: fast multi-level clustering and visualization of large molecular datasets. 1577-1579 - Yubang Gao, Huiyuan Wang, Hangxiao Zhang, Yongsheng Wang, Jinfeng Chen, Lian-Feng Gu:
PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq. 1580-1582 - Dmitry A. Suplatov
, Kirill E. Kopylov
, Nina N. Popova, Vladimir V. Voevodin
, Vytas K. Svedas
:
Mustguseal: a server for multiple structure-guided sequence alignment of protein families. 1583-1585
- Woonghee Lee
, John L. Markley
:
PINE-SPARKY.2 for automated NMR-based protein structure research. 1586-1588
- Hajk-Georg Drost
, Alexander Gabel, Jialin Liu
, Marcel Quint
, Ivo Grosse:
myTAI: evolutionary transcriptomics with R. 1589-1590
- Khalid Kunji, Ehsan Ullah, Alejandro Q. Nato
, Ellen M. Wijsman, Mohamad Saad
:
GIGI-Quick: a fast approach to impute missing genotypes in genome-wide association family data. 1591-1593
- Brendan King, Terry Farrah, Matthew A. Richards, Michael B. Mundy
, Evangelos Simeonidis, Nathan D. Price
:
ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions. 1594-1596 - Min Li, Jie Yang, Fang-Xiang Wu
, Yi Pan
, Jianxin Wang:
DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization. 1597-1599
- Tal Galili
, Alan O'Callaghan, Jonathan Sidi, Carson Sievert:
heatmaply: an R package for creating interactive cluster heatmaps for online publishing. 1600-1602 - Anbo Zhou, Yeting Zhang, Yazhou Sun, Jinchuan Xing:
PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool. 1603-1605 - Tasnia Tahsin, Davy Weissenbacher, Karen O'Connor, Arjun Magge, Matthew Scotch
, Graciela Gonzalez-Hernandez
:
GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records. 1606-1608 - Xiaohua Douglas Zhang, Zhaozhi Zhang, Dandan Wang:
CGManalyzer: an R package for analyzing continuous glucose monitoring studies. 1609-1611
- Aziz Khan
, Anthony Mathelier
:
JASPAR RESTful API: accessing JASPAR data from any programming language. 1612-1614 - Lin Wei
, Zhilin Jin
, Shengjie Yang, Yanxun Xu
, Yitan Zhu, Yuan Ji:
TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data. 1615-1617 - Yuhan Fei
, Rui Wang, Haoyuan Li, Shu Liu, Hongsheng Zhang
, Ji Huang:
DPMIND: degradome-based plant miRNA-target interaction and network database. 1618-1620
Volume 34, Number 10, May 2018
Genome Analysis
- Tobias Fehlmann, Christina Backes
, Julia Alles, Ulrike Fischer, Martin Hart, Fabian Kern
, Hilde Langseth, Trine Rounge
, Sinan Ugur Umu, Mustafa Kahraman, Thomas Laufer, Jan Haas, Cord Staehler, Nicole Ludwig
, Matthias Hübenthal
, Benjamin Meder, Andre Franke, Hans-Peter Lenhof, Eckart Meese, Andreas Keller
:
A high-resolution map of the human small non-coding transcriptome. 1621-1628 - Athanasios Gaitatzes, Sarah H. Johnson, James B. Smadbeck, George Vasmatzis:
Genome U-Plot: a whole genome visualization. 1629-1634 - Damien Drubay
, Daniel Gautheret
, Stefan Michiels
:
A benchmark study of scoring methods for non-coding mutations. 1635-1641 - Matteo Benelli
, Dario Romagnoli
, Francesca Demichelis:
Tumor purity quantification by clonal DNA methylation signatures. 1642-1649
- Jan Voges
, Jörn Ostermann
, Mikel Hernaez
:
CALQ: compression of quality values of aligned sequencing data. 1650-1658 - Peter Audano
, Shashidhar Ravishankar, Fredrik Vannberg:
Mapping-free variant calling using haplotype reconstruction from k-mer frequencies. 1659-1665 - Yang Yang, Katherine E. Niehaus, Timothy M. Walker
, Zamin Iqbal
, A. Sarah Walker
, Daniel J. Wilson
, Tim E. A. Peto, Derrick W. Crook, E. Grace Smith, Tingting Zhu
, David A. Clifton:
Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data. 1666-1671 - Yen-Yi Lin, Alexander Gawronski, Faraz Hach
, Sujun Li, Ibrahim Numanagic, Iman Sarrafi, Swati Mishra, Andrew W. McPherson, Colin C. Collins, Milan Radovich, Haixu Tang, Süleyman Cenk Sahinalp:
Computational identification of micro-structural variations and their proteogenomic consequences in cancer. 1672-1681 - Jie Lin, Donald A. Adjeroh, Bing-Hua Jiang
, Yue Jiang:
K2 and K 2 * : efficient alignment-free sequence similarity measurement based on Kendall statistics. 1682-1689 - Castrense Savojardo
, Pier Luigi Martelli
, Piero Fariselli, Rita Casadio
:
DeepSig: deep learning improves signal peptide detection in proteins. 1690-1696 - Hamza Khan, Hamid Mohamadi, Benjamin P. Vandervalk, René L. Warren
, Justin Chu, Inanç Birol
:
ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. 1697-1704 - Juhua Zhang
, Wenbo Peng, Lei Wang:
LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks. 1705-1712 - Brian K. Mannakee, Uthra Balaji, Agnieszka K. Witkiewicz, Ryan N. Gutenkunst, Erik S. Knudsen:
Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors. 1713-1718
- Runze Dong
, Zhenling Peng
, Yang Zhang
, Jianyi Yang
:
mTM-align: an algorithm for fast and accurate multiple protein structure alignment. 1719-1725
- Alyssa Imbert
, Armand Valsesia
, Caroline Le Gall, Claudia Armenise, Gregory Lefebvre
, Pierre-Antoine Gourraud
, Nathalie Viguerie
, Nathalie Villa-Vialaneix:
Multiple hot-deck imputation for network inference from RNA sequencing data. 1726-1732 - Xi Chen, Jinghua Gu, Xiao Wang, Jin-Gyoung Jung, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke
, Jianhua Xuan
:
CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data. 1733-1740
- Danny Kit-Sang Yip, Landon L. Chan
, Iris K. Pang, Wei Jiang
, Nelson L. S. Tang
, Weichuan Yu, Kevin Y. Yip
:
A network approach to exploring the functional basis of gene-gene epistatic interactions in disease susceptibility. 1741-1749
- Jingpu Zhang, Zuping Zhang, Zixiang Wang, Yuting Liu, Lei Deng:
Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification. 1750-1757
- Constantin Georgescu, Jonathan D. Wren
:
Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values. 1758-1766
- Ching-Wei Wang
, Yu-Ching Lee
, Evelyne Calista, Fan Zhou, Hongtu Zhu, Ryohei Suzuki, Daisuke Komura
, Shumpei Ishikawa, Shih-Ping Cheng
:
A benchmark for comparing precision medicine methods in thyroid cancer diagnosis using tissue microarrays. 1767-1773
Genome Analysis
- Danny Antaki
, William M. Brandler, Jonathan Sebat:
SV2: accurate structural variation genotyping and de novo mutation detection from whole genomes. 1774-1777 - Sigve Nakken
, Ghislain Fournous, Daniel Vodák
, Lars Birger Aasheim, Ola Myklebost, Eivind Hovig
:
Personal Cancer Genome Reporter: variant interpretation report for precision oncology. 1778-1780 - Yoann Pageaud
, Christoph Plass, Yassen Assenov
:
Enrichment analysis with EpiAnnotator. 1781-1783
- Jaime Rodríguez-Guerra Pedregal
, Jean-Didier Maréchal
:
PyChimera: use UCSF Chimera modules in any Python 2.7 project. 1784-1785
- Jhih-rong Lin, Daniel Jaroslawicz, Ying Cai, Quanwei Zhang, Zhen Wang, Zhengdong D. Zhang:
PGA: post-GWAS analysis for disease gene identification. 1786-1788
- Ryne C. Ramaker
, Emily R. Gordon, Sara J. Cooper
:
R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R. 1789-1791 - Mengci Li
, Shouli Wang, Guoxiang Xie
, Xiaohui Ma, Tianlu Chen, Wei Jia
:
polyPK: an R package for pharmacokinetic analysis of multi-component drugs using a metabolomics approach. 1792-1794 - Vipin Vijayan
, Tijana Milenkovic:
Aligning dynamic networks with DynaWAVE. 1795-1798
- Nilesh R. Tawari
, Justine Jia Wen Seow, Dharuman Perumal, Jack L. Ow, Shimin Ang, Arun George Devasia, Pauline C. Ng:
ChronQC: a quality control monitoring system for clinical next generation sequencing. 1799-1800
Volume 34, Number 11, June 2018
Genome Analysis
- Joong Chae Na, Jongchan Lee, Je-Keun Rhee
, Soo-Yong Shin:
PEATH: single-individual haplotyping by a probabilistic evolutionary algorithm with toggling. 1801-1807 - Paul Deveau, Leo Colmet Daage
, Derek Oldridge, Virginie Bernard
, Angela Bellini, Mathieu Chicard
, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre
, John M. Maris, Gudrun Schleiermacher, Valentina Boeva
:
QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. 1808-1816 - Chao Ning
, Dan Wang, Huimin Kang, Raphael Mrode
, Lei Zhou
, Shizhong Xu, Jianfeng Liu:
A rapid epistatic mixed-model association analysis by linear retransformations of genomic estimated values. 1817-1825 - Umberto Ferraro Petrillo, Gianluca Roscigno
, Giuseppe Cattaneo, Raffaele Giancarlo:
Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms. 1826-1833 - Agnieszka Danek
, Sebastian Deorowicz
:
GTC: how to maintain huge genotype collections in a compressed form. 1834-1840 - Congting Ye
, Yuqi Long, Guoli Ji, Qingshun Quinn Li, Xiaohui Wu
:
APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. 1841-1849
- Ronesh Sharma
, Gaurav Raicar, Tatsuhiko Tsunoda
, Ashwini Patil
, Alok Sharma
:
OPAL: prediction of MoRF regions in intrinsically disordered protein sequences. 1850-1858
- Bahman Afsari, Theresa Guo, Michael Considine, Liliana Florea, Luciane T. Kagohara, Genevieve L. Stein-O'Brien, Dylan Kelley, Emily Flam
, Kristina D. Zambo
, Patrick K. Ha, Donald Geman, Michael F. Ochs, Joseph A. Califano, Daria A. Gaykalova
, Alexander V. Favorov, Elana J. Fertig
:
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer. 1859-1867 - Jennifer M. Franks
, Guoshuai Cai, Michael L. Whitfield:
Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data. 1868-1874
- Jie Zhang
, Zhi Wei
, Jun Chen:
A distance-based approach for testing the mediation effect of the human microbiome. 1875-1883
- Irina M. Armean, Kathryn S. Lilley, Matthew W. B. Trotter
, Nicholas Charles Victor Pilkington, Sean B. Holden:
Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation. 1884-1892 - Weifeng Guo
, Shao-Wu Zhang, Li-Li Liu, Fei Liu, Qianqian Shi, Lei Zhang, Ying Tang, Tao Zeng
, Luonan Chen:
Discovering personalized driver mutation profiles of single samples in cancer by network control strategy. 1893-1903 - Huimin Luo, Min Li, Shaokai Wang, Quan Liu, Yaohang Li, Jianxin Wang:
Computational drug repositioning using low-rank matrix approximation and randomized algorithms. 1904-1912 - Clemens Kreutz
:
An easy and efficient approach for testing identifiability. 1913-1921
Genome Analysis
- Thorhildur Juliusdottir, Karina Banasik
, Neil R. Robertson, Richard Mott
, Mark I. McCarthy
:
Toppar: an interactive browser for viewing association study results. 1922-1924 - Chunpeng James Chen
, Zhiwu Zhang
:
iPat: intelligent prediction and association tool for genomic research. 1925-1927 - Marius Wöste, Martin Dugas
:
VIPER: a web application for rapid expert review of variant calls. 1928-1929 - Luca Pinello
, Rick Farouni
, Guo-Cheng Yuan:
Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. 1930-1933 - Dimitri Desvillechabrol, Rachel Legendre
, Claire Rioualen
, Christiane Bouchier, Jacques van Helden
, Sean Kennedy
, Thomas Cokelaer
:
Sequanix: a dynamic graphical interface for Snakemake workflows. 1934-1936
- Triinu Koressaar, Maarja Lepamets, Lauris Kaplinski, Kairi Raime, Reidar Andreson
, Maido Remm
:
Primer3_masker: integrating masking of template sequence with primer design software. 1937-1938 - Peter V. Troshin, James B. Procter
, Alexander Sherstnev, Daniel L. Barton, Fábio Madeira
, Geoffrey J. Barton
:
JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure. 1939-1940
- Bernhard Knapp
, Marta Alcalá, Hao Zhang, Clare E. West
, P. Anton van der Merwe, Charlotte M. Deane
:
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions. 1941-1943 - Alejandro Panjkovich
, Dmitri I. Svergun
:
CHROMIXS: automatic and interactive analysis of chromatography-coupled small-angle X-ray scattering data. 1944-1946 - Lucia Fusani
, Ian D. Wall, David Palmer
, Álvaro Cortés Cabrera:
Optimal water networks in protein cavities with GAsol and 3D-RISM. 1947-1948 - Juexin Wang, Robert Sheridan, Selçuk Onur Sümer, Nikolaus Schultz, Dong Xu, Jianjiong Gao
:
G2S: a web-service for annotating genomic variants on 3D protein structures. 1949-1950
- Corinne E. Sexton
, Hayden Z. Smith, Peter D. Newell, Angela E. Douglas, John M. Chaston:
MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs. 1951-1952
- Liang Cheng
, Yang Hu
, Jie Sun, Meng Zhou
, Qinghua Jiang:
DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function. 1953-1956 - Michael J. Dagley, Malcolm J. McConville:
DExSI: a new tool for the rapid quantitation of 13C-labelled metabolites detected by GC-MS. 1957-1958 - David Amar, Amir Vizel, Carmit Levy, Ron Shamir:
ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases. 1959-1961
- Andon Tchechmedjiev
, Amine Abdaoui, Vincent Emonet, Soumia Melzi, Jitendra Jonnagaddala
, Clément Jonquet:
Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+. 1962-1965
- Kim Wong, José Fernández Navarro, Ludvig Bergenstråhle, Patrik L. Ståhl, Joakim Lundeberg:
ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets. 1966-1968
Gene expression
- Francisco Avila Cobos
, Jo Vandesompele
, Pieter Mestdagh
, Katleen De Preter:
Computational deconvolution of transcriptomics data from mixed cell populations. 1969-1979
Gene expression
- Vipin Vijayan, Tijana Milenkovic:
Aligning dynamic networks with DynaWAVE. 1980
Volume 34, Number 12, June 2018
Structural Bioinformatics
- Gurmeet Kaur
, Srikrishna Subramanian
:
Evolutionary relationship between the cysteine and histidine rich domains (CHORDs) and Btk-type zinc fingers. 1981-1985
Genome Analysis
- Yuhan Hao, Liying Yang
, Antonio Galvao Neto, Milan R. Amin
, Dervla Kelly
, Stuart M. Brown
, Ryan C. Branski
, Zhiheng Pei
:
HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA. 1986-1995 - Chao Xu
, Jian Fang, Hui Shen, Yu-Ping Wang, Hong-Wen Deng:
EPS-LASSO: test for high-dimensional regression under extreme phenotype sampling of continuous traits. 1996-2003 - Zhihui Luo, Xinping Fan, Yao Su, Yu S. Huang
:
Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants. 2004-2011 - Fei Guo, Dan Wang, Lusheng Wang:
Progressive approach for SNP calling and haplotype assembly using single molecular sequencing data. 2012-2018
- Anqi Wang
, Zhanyu Wang
, Zheng Li, Lei M. Li:
BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach. 2019-2028 - Cangzhi Jia, Yun Zuo
, Quan Zou:
O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique. 2029-2036 - Mindaugas Margelevicius:
A low-complexity add-on score for protein remote homology search with COMER. 2037-2045 - Sung Yong Park, Tanzy M. T. Love, Shivankur Kapoor, Ha Youn Lee:
HIITE: HIV-1 incidence and infection time estimator. 2046-2052
- Kamil Tamiola
, Ruud M. Scheek, Pieter S. van der Meulen, Frans A. A. Mulder:
pepKalc: scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides. 2053-2060 - Liang Zhao, Shaogui Wu, Jiawen Jiang, Wencui Li, Jie Luo, Jinyan Li:
Novel overlapping subgraph clustering for the detection of antigen epitopes. 2061-2068
- Seyoung Park
, Hongyu Zhao
:
Spectral clustering based on learning similarity matrix. 2069-2076 - Suoqin Jin, Adam L. Maclean, Tao Peng, Qing Nie:
scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. 2077-2086
- Alex J. Cornish, Alessia David, Michael J. E. Sternberg
:
PhenoRank: reducing study bias in gene prioritization through simulation. 2087-2095 - Ivan Laponogov, Noureddin Sadawi
, Dieter Galea, Reza Mirnezami, Kirill A. Veselkov
:
ChemDistiller: an engine for metabolite annotation in mass spectrometry. 2096-2102
- Vishrawas Gopalakrishnan, Kishlay Jha
, Guangxu Xun
, Hung Q. Ngo, Aidong Zhang:
Towards self-learning based hypotheses generation in biomedical text domain. 2103-2115
- Thomas A. Darde
, Pierre Gaudriault
, Rémi Beranger
, Clément Lancien, Annaëlle Caillarec-Joly, Olivier Sallou, Nathalie Bonvallot, Cécile Chevrier, Séverine Mazaud-Guittot
, Bernard Jégou
, Olivier Collin
, Emmanuelle Becker
, Antoine D. Rolland
, Frédéric Chalmel
:
TOXsIgN: a cross-species repository for toxicogenomic signatures. 2116-2122
Genome Analysis
- Guoli Ji, Moliang Chen, Wenbin Ye
, Sheng Zhu, Congting Ye
, Yaru Su, Haonan Peng, Xiaohui Wu
:
TSAPA: identification of tissue-specific alternative polyadenylation sites in plants. 2123-2125 - Eugene Urrutia, Hao Chen, Zilu Zhou
, Nancy Ruonan Zhang, Yuchao Jiang
:
Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny. 2126-2128 - Dapeng Wang
:
GCevobase: an evolution-based database for GC content in eukaryotic genomes. 2129-2131
- Alberto Pessia
, Jukka Corander:
Kpax3: Bayesian bi-clustering of large sequence datasets. 2132-2133 - Clerk Nuo Xu
, Dongfang Fu, Shiang Li, Yuxuan Wang, Aloysius Wong
:
GCPred: a web tool for guanylyl cyclase functional centre prediction from amino acid sequence. 2134-2135
- Veer Singh Marwah
, Pia Anneli Sofia Kinaret
, Angela Serra
, Giovanni Scala
, Antti Lauerma
, Vittorio Fortino, Dario Greco
:
INfORM: Inference of NetwOrk Response Modules. 2136-2138
- Hang J. Kim
, Zhenning Yu, Andrew Lawson, Hongyu Zhao
, Dongjun Chung
:
Improving SNP prioritization and pleiotropic architecture estimation by incorporating prior knowledge using graph-GPA. 2139-2141 - Maarten van Iterson, Davy Cats, Paul Hop, BIOS Consortium, Bastiaan T. Heijmans:
omicsPrint: detection of data linkage errors in multiple omics studies. 2142-2143 - Qi Yan, Zhou Fang, Wei Chen:
KMgene: a unified R package for gene-based association analysis for complex traits. 2144-2146
- Thierry D. G. A. Mondeel
, Frédéric Crémazy
, Matteo Barberis
:
GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae. 2147-2149 - Zichen Wang
, Alexander Lachmann, Alexandra B. Keenan, Avi Ma'ayan
:
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. 2150-2152 - Pablo Carbonell
, Jerry Wong, Neil Swainston
, Eriko Takano, Nicholas J. Turner, Nigel S. Scrutton, Douglas B. Kell
, Rainer Breitling, Jean-Loup Faulon
:
Selenzyme: enzyme selection tool for pathway design. 2153-2154 - Nathan Mih
, Elizabeth Brunk, Ke Chen, Edward Catoiu, Anand Sastry
, Erol S. Kavvas, Jonathan M. Monk
, Zhen Zhang, Bernhard O. Palsson:
ssbio: a Python framework for structural systems biology. 2155-2157
- Thammakorn Saethang, Kenneth Hodge, Ingorn Kimkong, D. Michael Payne, Mark A. Knepper, Trairak Pisitkun:
AbDesigner3D: a structure-guided tool for peptide-based antibody production. 2158-2160
Volume 34, Number 13, July 2018
Ismb 2018 - Intelligent Systems for molecular Biology Proceedings
Ismb 2018 Proceedings Papers Committee
- ISMB 2018 PROCEEDINGS PAPERS COMMITTEE. i1
- Yana Bromberg
, Predrag Radivojac:
ISMB 2018 proceedings. i2-i3
- K. Anton Feenstra
, Sanne Abeln
, Johan A. Westerhuis, Filipe Brancos dos Santos
, Douwe Molenaar
, Bas Teusink
, Huub C. J. Hoefsloot, Jaap Heringa:
Training for translation between disciplines: a philosophy for life and data sciences curricula. i4-i12
- Guillaume Marçais, Dan F. DeBlasio, Carl Kingsford:
Asymptotically optimal minimizers schemes. i13-i22 - Soyeon Ahn, Ziqi Ke
, Haris Vikalo
:
Viral quasispecies reconstruction via tensor factorization with successive read removal. i23-i31 - Ehsaneddin Asgari, Kiavash Garakani
, Alice C. McHardy
, Mohammad R. K. Mofrad:
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples. i32-i42
- Weihua Pan, Steve Wanamaker, Audrey M. V. Ah-Fong, Howard S. Judelson, Stefano Lonardi
:
Novo&Stitch: accurate reconciliation of genome assemblies via optical maps. i43-i51 - Fatima Zohra Smaili
, Xin Gao, Robert Hoehndorf
:
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. i52-i60 - Siamak Zamani Dadaneh, Mingyuan Zhou, Xiaoning Qian:
Covariate-dependent negative binomial factor analysis of RNA sequencing data. i61-i69 - Jean-Pierre Séhi Glouzon, Aïda Ouangraoua:
aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences. i70-i78 - Maziyar Baran Pouyan, Dennis Kostka:
Random forest based similarity learning for single cell RNA sequencing data. i79-i88 - Hsuan-Lin Her
, Yu-Wei Wu
:
A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains. i89-i95 - Jie Liu, Dejun Lin, Galip Gürkan Yardimci, William Stafford Noble:
Unsupervised embedding of single-cell Hi-C data. i96-i104 - Shilpa Garg, Mikko Rautiainen, Adam M. Novak
, Erik Garrison, Richard Durbin
, Tobias Marschall:
A graph-based approach to diploid genome assembly. i105-i114 - Maryam Ghareghani, David Porubsky
, Ashley D. Sanders
, Sascha Meiers
, Evan E. Eichler, Jan O. Korbel, Tobias Marschall:
Strand-seq enables reliable separation of long reads by chromosome via expectation maximization. i115-i123 - Sumit Mukherjee, Yue Zhang
, Joshua Fan, Georg Seelig, Sreeram Kannan:
Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge. i124-i132 - Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang
, Jian Ma
:
Predicting CTCF-mediated chromatin loops using CTCF-MP. i133-i141 - Alla Mikheenko
, Andrey D. Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey A. Gurevich
:
Versatile genome assembly evaluation with QUAST-LG. i142-i150
- Paul Stapor
, Fabian Fröhlich
, Jan Hasenauer
:
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis. i151-i159
- Bristena Oprisanu, Emiliano De Cristofaro:
AnoniMME: bringing anonymity to the Matchmaker Exchange platform for rare disease gene discovery. i160-i168 - Fatemeh Almodaresi, Hirak Sarkar
, Avi Srivastava
, Rob Patro:
A space and time-efficient index for the compacted colored de Bruijn graph. i169-i177 - Benjamin J. Lengerich, Bryon Aragam, Eric P. Xing:
Personalized regression enables sample-specific pan-cancer analysis. i178-i186
- Yue Wu, Sriram Sankararaman:
A scalable estimator of SNP heritability for biobank-scale data. i187-i194 - Ruth Johnson, Huwenbo Shi, Bogdan Pasaniuc, Sriram Sankararaman:
A unifying framework for joint trait analysis under a non-infinitesimal model. i195-i201 - Kendell Clement, Rick Farouni
, Daniel E. Bauer, Luca Pinello:
AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. i202-i210 - Gryte Satas, Benjamin J. Raphael:
Haplotype phasing in single-cell DNA-sequencing data. i211-i217
- Christopher Jürges, Lars Dölken, Florian Erhard:
Dissecting newly transcribed and old RNA using GRAND-SLAM. i218-i226 - Yixiu Zhao, Xiangrui Zeng
, Qiang Guo, Min Xu:
An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification. i227-i236 - Genta Aoki, Yasubumi Sakakibara:
Convolutional neural networks for classification of alignments of non-coding RNA sequences. i237-i244 - Yoonjoo Choi
, Jacob M. Furlon, Ryan B. Amos, Karl E. Griswold, Chris Bailey-Kellogg:
DisruPPI: structure-based computational redesign algorithm for protein binding disruption. i245-i253 - Seokjun Seo, Minsik Oh, Youngjune Park
, Sun Kim:
DeepFam: deep learning based alignment-free method for protein family modeling and prediction. i254-i262 - Jianwei Zhu, Sheng Wang
, Dongbo Bu, Jinbo Xu:
Protein threading using residue co-variation and deep learning. i263-i273 - Emmi Jokinen
, Markus Heinonen, Harri Lähdesmäki:
mGPfusion: predicting protein stability changes with Gaussian process kernel learning and data fusion. i274-i283 - Yu Li
, Fan Xu
, Fa Zhang, Pingyong Xu, Mingshu Zhang, Ming Fan, Lihua Li, Xin Gao
, Renmin Han
:
DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy. i284-i294 - Hakime Öztürk
, Elif Özkirimli Ölmez, Arzucan Özgür:
A novel methodology on distributed representations of proteins using their interacting ligands. i295-i303 - Yannick Mahlich
, Martin Steinegger
, Burkhard Rost
, Yana Bromberg
:
HFSP: high speed homology-driven function annotation of proteins. i304-i312 - Yisu Peng, Yuxiang Jiang, Predrag Radivojac:
Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. i313-i322
- Dai Hai Nguyen
, Canh Hao Nguyen
, Hiroshi Mamitsuka
:
SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra. i323-i332 - Marcus Ludwig, Kai Dührkop
, Sebastian Böcker
:
Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. i333-i340
- Nima Nouri, Steven H. Kleinstein:
A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data. i341-i349 - Edward L. Braun
:
An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins. i350-i356 - Jesse Eaton, Jingyi Wang, Russell Schwartz:
Deconvolution and phylogeny inference of structural variations in tumor genomic samples. i357-i365 - Manuel Lafond, Mona Meghdari Miardan, David Sankoff:
Accurate prediction of orthologs in the presence of divergence after duplication. i366-i375 - Jiafan Zhu, Luay Nakhleh:
Inference of species phylogenies from bi-allelic markers using pseudo-likelihood. i376-i385
- Wenhui Xing, Junsheng Qi, Xiaohui Yuan, Lin Li, Xiaoyu Zhang, Yuhua Fu, Shengwu Xiong
, Lun Hu
, Jing Peng:
A gene-phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach. i386-i394 - Iiris Sundin
, Tomi Peltola, Luana Micallef, Homayun Afrabandpey, Marta Soare, Muntasir Mamun Majumder
, Pedram Daee, Chen He
, Baris Serim, Aki S. Havulinna, Caroline Heckman
, Giulio Jacucci, Pekka Marttinen
, Samuel Kaski:
Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge. i395-i403 - Wensheng Zhang, Erik K. Flemington, Kun Zhang:
Driver gene mutations based clustering of tumors: methods and applications. i404-i411 - Arezou Rahimi, Mehmet Gönen
:
Discriminating early- and late-stage cancers using multiple kernel learning on gene sets. i412-i421 - Matthew J. McCoy
, Alexander J. Paul, Matheus B. Victor
, Michelle Richner, Harrison W. Gabel, Haijun Gong
, Andrew S. Yoo
, Tae-Hyuk Ahn
:
LONGO: an R package for interactive gene length dependent analysis for neuronal identity. i422-i428 - Hannes Bretschneider
, Shreshth Gandhi
, Amit G. Deshwar, Khalid Zuberi, Brendan J. Frey:
COSSMO: predicting competitive alternative splice site selection using deep learning. i429-i437 - Christian Bock
, Thomas Gumbsch, Michael Moor
, Bastian Rieck
, Damian Roqueiro
, Karsten M. Borgwardt
:
Association mapping in biomedical time series via statistically significant shapelet mining. i438-i446 - Pooya Zakeri, Jaak Simm, Adam Arany, Sarah ElShal, Yves Moreau
:
Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information. i447-i456 - Marinka Zitnik, Monica Agrawal
, Jure Leskovec:
Modeling polypharmacy side effects with graph convolutional networks. i457-i466 - Lisa Gai, Eleazar Eskin:
Finding associated variants in genome-wide association studies on multiple traits. i467-i474 - Natalie Sauerwald, Carl Kingsford:
Quantifying the similarity of topological domains across normal and cancer human cell types. i475-i483
- Wei Zhang
, Jianzhu Ma, Trey Ideker
:
Classifying tumors by supervised network propagation. i484-i493 - Benjamin Ballnus, Steffen Schaper, Fabian J. Theis, Jan Hasenauer
:
Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering. i494-i501 - Sushant Patkar, Roded Sharan:
An optimization framework for network annotation. i502-i508 - Anna Cichonska
, Tapio Pahikkala
, Sándor Szedmák
, Heli Julkunen
, Antti Airola
, Markus Heinonen, Tero Aittokallio
, Juho Rousu:
Learning with multiple pairwise kernels for drug bioactivity prediction. i509-i518 - Sumana Srivatsa
, Jack Kuipers
, Fabian Schmich
, Simone Eicher, Mario Emmenlauer, Christoph Dehio
, Niko Beerenwinkel:
Improved pathway reconstruction from RNA interference screens by exploiting off-target effects. i519-i527 - Francesca Petralia, Li Wang, Jie Peng, Arthur Yan, Jun Zhu, Pei Wang
:
A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity. i528-i536 - Karel Kalecky
, Young-Rae Cho
:
PrimAlign: PageRank-inspired Markovian alignment for large biological networks. i537-i546 - Jinfeng Xiao, Charles Blatti, Saurabh Sinha:
SigMat: a classification scheme for gene signature matching. i547-i554 - Rani K. Powers
, Andrew Goodspeed, Harrison Pielke-Lombardo, Aik Choon Tan
, James C. Costello
:
GSEA-InContext: identifying novel and common patterns in expression experiments. i555-i564
- Arjun Magge, Davy Weissenbacher, Abeed Sarker
, Matthew Scotch
, Graciela Gonzalez-Hernandez
:
Deep neural networks and distant supervision for geographic location mention extraction. i565-i573
- Marwan Abdellah, Juan Hernando, Stefan Eilemann, Samuel Lapere, Nicolas Antille, Henry Markram, Felix Schürmann:
NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks. i574-i582 - Pierre Boutillier, Mutaamba Maasha, Xing Li, Héctor F. Medina-Abarca, Jean Krivine, Jérôme Feret, Ioana Cristescu, Angus G. Forbes
, Walter Fontana:
The Kappa platform for rule-based modeling. i583-i592
- Author Index. i593-i594
Genome Analysis
- Claire Bertelli
, Fiona S. L. Brinkman
:
Improved genomic island predictions with IslandPath-DIMOB. 2161-2167 - Shuhua Fu, Yingke Ma, Hui Yao, Zhichao Xu
, Shilin Chen
, Jingyuan Song, Kin Fai Au:
IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing. 2168-2176
- Narayanan Raghupathy, Kwangbom Choi
, Matthew J. Vincent, Glen L. Beane, Keith S. Sheppard, Steven C. Munger, Ron Korstanje
, Fernando Pardo-Manual de Villena, Gary A. Churchill:
Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression. 2177-2184 - Zhen Cao, Xiaoyong Pan, Yang Yang
, Yan Huang, Hong-Bin Shen
:
The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. 2185-2194
- Sejal Modha
, Anil S. Thanki
, Susan F. Cotmore, Andrew J. Davison, Joseph Hughes
:
ViCTree: an automated framework for taxonomic classification from protein sequences. 2195-2200
- Ricardo N. dos Santos
, Allan J. R. Ferrari
, Hugo C. R. de Jesus, Fábio C. Gozzo, Faruck Morcos, Leandro Martínez
:
Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals. 2201-2208 - Jun Hu, Zi Liu, Dong-Jun Yu, Yang Zhang
:
LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening. 2209-2218 - Saulo Henrique Pires de Oliveira, Charlotte M. Deane
:
Combining co-evolution and secondary structure prediction to improve fragment library generation. 2219-2227
- Cheng-Hong Yang, Li-Yeh Chuang, Yu-Da Lin
:
Multiobjective multifactor dimensionality reduction to detect SNP-SNP interactions. 2228-2236
- Aditya Pratapa
, Neil Adames, Pavel K. Brazhnik, Nicholas Franzese, John J. Tyson, Jean Peccoud
, T. M. Murali:
CrossPlan: systematic planning of genetic crosses to validate mathematical models. 2237-2244 - Markus Lux
, Ryan Remy Brinkman
, Cédric Chauve
, Adam Laing, Anna Lorenc
, Lucie Abeler-Dörner, Barbara Hammer
:
flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry. 2245-2253
- Ajay Anand Kumar, Lut Van Laer, Maaike Alaerts, Amin Ardeshirdavani
, Yves Moreau
, Kris Laukens
, Bart Loeys, Geert Vandeweyer:
pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion. 2254-2262
- Xiaole Yin
, Xiaotao Jiang
, Benli Chai, Liguan Li, Ying Yang, James R. Cole, James M. Tiedje, Tong Zhang:
ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes. 2263-2270 - Jiansheng Wu, Qiuming Zhang, Weijian Wu, Tao Pang, Haifeng Hu, Wallace K. B. Chan, Xiaoyan Ke, Yang Zhang
:
WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest. 2271-2282
Genome Analysis
- Andrey A. Shabalin
, Mohammad W. Hattab, Shaunna L. Clark, Robin F. Chan
, Gaurav Kumar, Karolina A. Åberg
, Edwin J. C. G. van den Oord:
RaMWAS: fast methylome-wide association study pipeline for enrichment platforms. 2283-2285 - Selin Jessa
, Claudia L. Kleinman:
chromswitch: a flexible method to detect chromatin state switches. 2286-2288 - Marzia A. Cremona
, Alessia Pini
, Fabio Cumbo
, Kateryna D. Makova, Francesca Chiaromonte, Simone Vantini
:
IWTomics: testing high-resolution sequence-based 'Omics' data at multiple locations and scales. 2289-2291
- Tomás Vetrovský, Petr Baldrian, Daniel C. Morais
:
SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses. 2292-2294 - Anna Gogleva
, Hajk-Georg Drost
, Sebastian Schornack:
SecretSanta: flexible pipelines for functional secretome prediction. 2295-2296
- Christopher Monit
, Richard A. Goldstein
:
SubRecon: ancestral reconstruction of amino acid substitutions along a branch in a phylogeny. 2297-2299 - David A. Duchêne
, Sebastián Duchêne
, Simon Y. W. Ho:
PhyloMAd: efficient assessment of phylogenomic model adequacy. 2300-2301
- Anssi Nurminen, Vesa P. Hytönen
:
StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data. 2302-2304
- Yoojoong Kim
, Yeong Seon Kang, Junhee Seok:
GAIT: Gene expression Analysis for Interval Time. 2305-2307
- Aleksi Sipola
, Pekka Marttinen
, Jukka Corander:
Bacmeta: simulator for genomic evolution in bacterial metapopulations. 2308-2310
- Nadir Sella, Louis Verny, Guido Uguzzoni, Séverine Affeldt
, Hervé Isambert:
MIIC online: a web server to reconstruct causal or non-causal networks from non-perturbative data. 2311-2313 - Joe Wandy
, Mu Niu, Diana Giurghita, Rónán Daly
, Simon Rogers, Dirk Husmeier
:
ShinyKGode: an interactive application for ODE parameter inference using gradient matching. 2314-2315 - Michaela Gündel, Charles Tapley Hoyt
, Martin Hofmann-Apitius:
BEL2ABM: agent-based simulation of static models in Biological Expression Language. 2316-2318 - João G. R. Cardoso
, Ahmad A. Zeidan
, Kristian Jensen
, Nikolaus Sonnenschein
, Ana Rute Neves
, Markus J. Herrgård:
MARSI: metabolite analogues for rational strain improvement. 2319-2321
- José G. Pérez-Silva
, Miguel Araujo-Voces
, Víctor Quesada
:
nVenn: generalized, quasi-proportional Venn and Euler diagrams. 2322-2324
- A. Kulandaisamy
, S. Binny Priya
, R. Sakthivel, Svetlana Tarnovskaya, Ilya Bizin
, Peter Hönigschmid, Dmitrij Frishman, M. Michael Gromiha:
MutHTP: mutations in human transmembrane proteins. 2325-2326 - Neil Swainston
, Mark Dunstan
, Adrian J. Jervis, Christopher J. Robinson
, Pablo Carbonell
, Alan R. Williams, Jean-Loup Faulon
, Nigel S. Scrutton, Douglas B. Kell
:
PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts. 2327-2329
Databases and Ontologies
- Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2018 ISCB Overton Prize awarded to Cole Trapnell. 2330-2331 - Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
Message from the ISCB: 2018 ISCB Accomplishments by a Senior Scientist Award. 2332-2333 - Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
Message from the ISCB: 2018 Outstanding Contributions to ISCB Award: Russ Altman. 2334-2335 - Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2018 ISCB Innovator Award recognizes M. Madan Babu. 2336-2337
Databases and Ontologies
- Vahid Jalili
, Matteo Matteucci, Marco Masseroli, Marco J. Morelli:
Using combined evidence from replicates to evaluate ChIP-seq peaks. 2338 - Anne Hoffmann, Jörg Fallmann, Elisa Vilardo, Mario Mörl
, Peter F. Stadler
, Fabian Amman
:
Accurate mapping of tRNA reads. 2339 - Xiaohua Douglas Zhang, Zhaozhi Zhang, Dandan Wang:
CGManalyzer: an R package for analyzing continuous glucose monitoring studies. 2340
Volume 34, Number 14, July 2018
Genome Analysis
- Shijia Zhu, Gang Fang:
MatrixEpistasis: ultrafast, exhaustive epistasis scan for quantitative traits with covariate adjustment. 2341-2348 - Zilu Zhou
, Weixin Wang
, Li-San Wang, Nancy Ruonan Zhang:
Integrative DNA copy number detection and genotyping from sequencing and array-based platforms. 2349-2355 - Ryuichiro Nakato
, Katsuhiko Shirahige
:
Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile. 2356-2363
- Nicholas K. Akers, Eric E. Schadt, Bojan Losic:
STAR Chimeric Post for rapid detection of circular RNA and fusion transcripts. 2364-2370 - Robert C. Edgar
:
Updating the 97% identity threshold for 16S ribosomal RNA OTUs. 2371-2375 - Tobias P. Loka
, Simon H. Tausch
, Piotr Wojtek Dabrowski
, Aleksandar Radonic
, Andreas Nitsche
, Bernhard Y. Renard
:
PriLive: privacy-preserving real-time filtering for next-generation sequencing. 2376-2383
- Yu Hu, Jennie Lin
, Jian Hu, Gang Hu
, Kui Wang, Hanrui Zhang
, Muredach P. Reilly, Mingyao Li:
PennDiff: detecting differential alternative splicing and transcription by RNA sequencing. 2384-2391 - Trung-Nghia Vu
, Quin F. Wills, Krishna R. Kalari, Nifang Niu, Liewei Wang, Yudi Pawitan, Mattias Rantalainen
:
Isoform-level gene expression patterns in single-cell RNA-sequencing data. 2392-2400 - Wanseon Lee
, Katharine Plant, Peter Humburg
, Julian C. Knight
:
AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes. 2401-2408
- Sahely Bhadra
, Peter Blomberg, Sandra Castillo
, Juho Rousu:
Principal metabolic flux mode analysis. 2409-2417 - Joshua N. Sampson
, Simina M. Boca
, Steven C. Moore, Ruth Heller:
FWER and FDR control when testing multiple mediators. 2418-2424 - Xiangxiang Zeng
, Li Liu, Linyuan Lü, Quan Zou:
Prediction of potential disease-associated microRNAs using structural perturbation method. 2425-2432 - Nikolaos Tsiantis
, Eva Balsa-Canto
, Julio R. Banga
:
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework. 2433-2440 - Christos Dimitrakopoulos, Sravanth Kumar Hindupur
, Luca Häfliger, Jonas Behr, Hesam Montazeri
, Michael N. Hall
, Niko Beerenwinkel:
Network-based integration of multi-omics data for prioritizing cancer genes. 2441-2448
- Fabio Fabris, Aoife Doherty, Daniel Palmer
, João Pedro de Magalhães, Alex Alves Freitas
:
A new approach for interpreting Random Forest models and its application to the biology of ageing. 2449-2456 - Willem van den Boom
, Callie Mao, Rebecca A. Schroeder, David B. Dunson:
Extrema-weighted feature extraction for functional data. 2457-2464 - Ronghui You, Zihan Zhang, Yi Xiong
, Fengzhu Sun, Hiroshi Mamitsuka
, Shanfeng Zhu
:
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank. 2465-2473 - Dieter Galea, Ivan Laponogov, Kirill A. Veselkov
:
Exploiting and assessing multi-source data for supervised biomedical named entity recognition. 2474-2482
Genome Analysis
- Giovanna Ambrosini
, Romain Groux
, Philipp Bucher:
PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix. 2483-2484 - Chantriolnt-Andreas Kapourani
, Guido Sanguinetti
:
BPRMeth: a flexible Bioconductor package for modelling methylation profiles. 2485-2486
- Balázs Szalkai, Vince Grolmusz:
SECLAF: a webserver and deep neural network design tool for hierarchical biological sequence classification. 2487-2489 - Tsukasa Nakamura
, Kazunori D. Yamada, Kentaro Tomii
, Kazutaka Katoh
:
Parallelization of MAFFT for large-scale multiple sequence alignments. 2490-2492 - Yan-Bo Sun:
FasParser2: a graphical platform for batch manipulation of tremendous amount of sequence data. 2493-2495 - Cedric Landerer, Alexander Cope
, Russell L. Zaretzki
, Michael A. Gilchrist
:
AnaCoDa: analyzing codon data with Bayesian mixture models. 2496-2498 - Zhen Chen
, Pei Zhao, Fuyi Li
, André Leier
, Tatiana T. Marquez-Lago, Yanan Wang, Geoffrey I. Webb
, Alexander Ian Smith
, Roger J. Daly
, Kuo-Chen Chou, Jiangning Song
:
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences. 2499-2502 - Michele Berselli
, Enrico Lavezzo
, Stefano Toppo
:
NeSSie: a tool for the identification of approximate DNA sequence symmetries. 2503-2505
- Merly Escalona
, Sara Rocha
, David Posada
:
NGSphy: phylogenomic simulation of next-generation sequencing data. 2506-2507
- Changge Ji, Fredrik Svensson, Azedine Zoufir, Andreas Bender
:
eMolTox: prediction of molecular toxicity with confidence. 2508-2509
- Diem-Trang T. Tran
, Tian Zhang, Ryan Stutsman, Matthew Might, Umesh R. Desai, Balagurunathan Kuberan
:
anexVis: visual analytics framework for analysis of RNA expression. 2510-2512
- M. Kösters, Johannes Leufken
, Stefan Schulze
, K. Sugimoto, Joshua Klein
, R. P. Zahedi, Michael Hippler
, S. A Leidel, Christian Fufezan
:
pymzML v2.0: introducing a highly compressed and seekable gzip format. 2513-2514 - Ruidong Li
, Han Qu, Shibo Wang, Julong Wei, Le Zhang
, Renyuan Ma, Jianming Lu, Jianguo Zhu, Wei-De Zhong, Zhenyu Jia:
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC. 2515-2517
- R. Shyama Prasad Rao
, Ning Zhang
, Dong Xu, Ian Max Møller:
CarbonylDB: a curated data-resource of protein carbonylation sites. 2518-2520
Volume 34, Number 15, August 2018
Genome Analysis
- Ashraful Arefeen
, Juntao Liu, Xinshu Xiao
, Tao Jiang
:
TAPAS: tool for alternative polyadenylation site analysis. 2521-2529 - Igor Mandric
, Sergey Knyazev
, Alex Zelikovsky
:
Repeat-aware evaluation of scaffolding tools. 2530-2537 - Claudia Giambartolomei
, Jimmy Zhenli Liu, Wen Zhang, Mads Hauberg
, Huwenbo Shi, James Boocock
, Joe Pickrell, Andrew E. Jaffe
, The CommonMind Consortium, Bogdan Pasaniuc
, Panos Roussos:
A Bayesian framework for multiple trait colocalization from summary association statistics. 2538-2545 - Jiawei Wang
, Bingjiao Yang, André Leier
, Tatiana T. Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Yanju Zhang, Tatsuya Akutsu
, Kuo-Chen Chou, Richard A. Strugnell
, Jiangning Song
, Trevor Lithgow
:
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. 2546-2555
- Isaac Turner
, Kiran V. Garimella
, Zamin Iqbal
, Gil McVean:
Integrating long-range connectivity information into de Bruijn graphs. 2556-2565 - Matteo Lo Monte
, Candida Manelfi, Marica Gemei, Daniela Corda
, Andrea Rosario Beccari:
ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors. 2566-2574 - Hannah F. Löchel
, Mona Riemenschneider, Dmitrij Frishman, Dominik Heider
:
SCOTCH: subtype A coreceptor tropism classification in HIV-1. 2575-2580
- Clément Viricel, Simon de Givry, Thomas Schiex, Sophie Barbe
:
Cost function network-based design of protein-protein interactions: predicting changes in binding affinity. 2581-2589 - Piotr Klukowski
, Michal Augoff, Maciej Zieba
, Maciej Drwal, Adam Gonczarek, Michal J. Walczak:
NMRNet: a deep learning approach to automated peak picking of protein NMR spectra. 2590-2597 - Qiaozhen Meng, Zhenling Peng
, Jianyi Yang
:
CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction. 2598-2604 - Sameer Khurana, Reda Rawi, Khalid Kunji, Gwo-Yu Chuang, Halima Bensmail, Raghvendra Mall
:
DeepSol: a deep learning framework for sequence-based protein solubility prediction. 2605-2613
- Bethany Percha, Russ B. Altman
:
A global network of biomedical relationships derived from text. 2614-2624 - Paul D. Tar, Neil A. Thacker, M. Babur, Yvonne Watson, Sue Cheung, R. A Little, R. G. Gieling, K. J. Williams, J. P. B. O'Connor:
A new method for the high-precision assessment of tumor changes in response to treatment. 2625-2633 - Teng Fei
, Tengjiao Zhang, Weiyang Shi, Tianwei Yu
:
Mitigating the adverse impact of batch effects in sample pattern detection. 2634-2641 - Kevin K. Yang
, Zachary Wu
, Claire N. Bedbrook
, Frances H. Arnold
:
Learned protein embeddings for machine learning. 2642-2648
Genome Analysis
- John T. Lawson, Eleni M. Tomazou
, Christoph Bock
, Nathan C. Sheffield
:
MIRA: an R package for DNA methylation-based inference of regulatory activity. 2649-2650 - Andrew D. L. Nelson, Asher Haug-Baltzell, Sean Davey, Brian D. Gregory, Eric Lyons:
EPIC-CoGe: managing and analyzing genomic data. 2651-2653 - Jianhao Peng, Olgica Milenkovic, Idoia Ochoa
:
METHCOMP: a special purpose compression platform for DNA methylation data. 2654-2656 - Jing Xu, Linna Zhao, Di Liu, Simeng Hu
, Xiuling Song, Jin Li, Hongchao Lv, Lian Duan, Mingming Zhang, Qinghua Jiang, Guiyou Liu, Shuilin Jin, Mingzhi Liao, Meng Zhang, Rennan Feng, Fanwu Kong, Liangde Xu, Yongshuai Jiang
:
EWAS: epigenome-wide association study software 2.0. 2657-2658 - David J. Winter
, Steven H. Wu
, Abigail A. Howell, Ricardo B. R. Azevedo, Rebecca A. Zufall, Reed A. Cartwright:
accuMUlate: a mutation caller designed for mutation accumulation experiments. 2659-2660 - Jaehee Jung, Jong Im Kim, Young-Sik Jeong, Gangman Yi:
AGORA: organellar genome annotation from the amino acid and nucleotide references. 2661-2663
- Zheng Wei, Wei Zhang, Huan Fang, Yanda Li, Xiaowo Wang
:
esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis. 2664-2665 - Wouter De Coster
, Svenn D'Hert
, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
:
NanoPack: visualizing and processing long-read sequencing data. 2666-2669 - Stephen J. Fletcher
, Mikael Bodén
, Neena Mitter
, Bernard J. Carroll
:
SCRAM: a pipeline for fast index-free small RNA read alignment and visualization. 2670-2672 - Richard Wilton
, Xin Li
, Andrew P. Feinberg, Alexander S. Szalay:
Arioc: GPU-accelerated alignment of short bisulfite-treated reads. 2673-2675
- Florian Eggenhofer
, Ivo L. Hofacker
, Rolf Backofen, Christian Höner zu Siederdissen
:
CMV: visualization for RNA and protein family models and their comparisons. 2676-2678 - Ivan Yu Chernyshov
, Philip V. Toukach
:
REStLESS: automated translation of glycan sequences from residue-based notation to SMILES and atomic coordinates. 2679-2681
- Andrew R. Ghazi, Edward S. Chen, David M. Henke, Namrata Madan, Leonard C. Edelstein
, Chad A. Shaw:
Design tools for MPRA experiments. 2682-2683
- Alberto Calderone
, Gianni Cesareni:
SPV: a JavaScript Signaling Pathway Visualizer. 2684-2686
- Benedikt G. Brink
, Justin Meskas, Ryan Remy Brinkman
:
ddPCRclust: an R package and Shiny app for automated analysis of multiplexed ddPCR data. 2687-2689 - Veronika Suni
, Tomi Suomi
, Tomoya Tsubosaka, Susumu Y. Imanishi
, Laura L. Elo
, Garry L. Corthals:
SimPhospho: a software tool enabling confident phosphosite assignment. 2690-2692
- Anargyros Megalios
, Rónán Daly
, Karl E. V. Burgess
:
MetaboCraft: building a Minecraft plugin for metabolomics. 2693-2694
- Piotr Baniukiewicz, Sharon Collier, Till Bretschneider
:
QuimP: analyzing transmembrane signalling in highly deformable cells. 2695-2697
Data and Text Mining
- Paul Monsarrat
, Jean-Noel Vergnes:
Data mining of effect sizes from PubMed abstracts: a cross-study conceptual replication. 2698-2700
Volume 34, Number 16, August 2018
Genome Analysis
- Oana Ursu
, Nathan Boley, Maryna Taranova, Y. X. Rachel Wang
, Galip Gürkan Yardimci, William Stafford Noble, Anshul Kundaje
:
GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs. 2701-2707 - Franklin Delehelle, Sylvain Cussat-Blanc, Jean-Marc Alliot, Hervé Luga, Patricia Balaresque
:
ASGART: fast and parallel genome scale segmental duplications mapping. 2708-2714 - Xiwei Sun, Yi Han
, Liyuan Zhou, Enguo Chen, Bingjian Lu, Yong Liu, Xiaoqing Pan, Allen W. Cowley Jr., Mingyu Liang, Qingbiao Wu, Yan Lu, Pengyuan Liu
:
A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data. 2715-2723 - Mariusz Butkiewicz, Elizabeth E. Blue
, Yuk Yee Leung
, Xueqiu Jian, Edoardo Marcora
, Alan E. Renton
, Amanda Kuzma, Li-San Wang, Daniel C. Koboldt, Jonathan L. Haines, William S. Bush
:
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease. 2724-2731
- R. W. W. Brouwer, M. C. G. N. van den Hout, C. E. M. Kockx, Erwin Brosens
, B. Eussen, A. de Klein, F. Sleutels, Wilfred F. J. van IJcken
:
Nimbus: a design-driven analyses suite for amplicon-based NGS data. 2732-2739 - Daniel Veltri
, Uday Kamath, Amarda Shehu:
Deep learning improves antimicrobial peptide recognition. 2740-2747 - Lukasz Roguski, Idoia Ochoa
, Mikel Hernaez
, Sebastian Deorowicz
:
FaStore: a space-saving solution for raw sequencing data. 2748-2756
- Émilie Neveu
, Petr Popov
, Alexandre Hoffmann, Angelo Migliosi, Xavier Besseron
, Grégoire Danoy
, Pascal Bouvry
, Sergei Grudinin
:
RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules. 2757-2765