Works matching IS 14675463 AND DT 2021 AND VI 22 AND IP 3

Results: 149

Challenges in gene-oriented approaches for pangenome content discovery.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa198

By:

Bonnici, Vincenzo;
Maresi, Emiliano;
Giugno, Rosalba

Publication type:

Article

Analysis, identification and visualization of subgroups in genomics.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa217

By:

Völkel, Gunnar;
Laban, Simon;
Fürstberger, Axel;
Kühlwein, Silke D;
Ikonomi, Nensi;
Hoffmann, Thomas K;
Brunner, Cornelia;
Neuberg, Donna S;
Gaidzik, Verena;
Döhner, Hartmut;
Kraus, Johann M;
Kestler, Hans A

Publication type:

Article

Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa210

By:

Jiang, Shuai;
Li, Hao;
Hong, Hao;
Du, Guifang;
Huang, Xin;
Sun, Yu;
Wang, Junting;
Tao, Huan;
Xu, Kang;
Li, Cheng;
Chen, Yang;
Chen, Hebing;
Bo, Xiaochen

Publication type:

Article

In silico prediction of host–pathogen protein interactions in melioidosis pathogen Burkholderia pseudomallei and human reveals novel virulence factors and their targets.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbz162

By:

Loaiza, Cristian D;
Duhan, Naveen;
Lister, Matthew;
Kaundal, Rakesh

Publication type:

Article

In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa223

By:

Chen, Jieming;
Madireddi, Shravan;
Nagarkar, Deepti;
Migdal, Maciej;
Heiden, Jason Vander;
Chang, Diana;
Mukhyala, Kiran;
Selvaraj, Suresh;
Kadel, Edward E;
Brauer, Matthew J;
Mariathasan, Sanjeev;
Hunkapiller, Julie;
Jhunjhunwala, Suchit;
Albert, Matthew L;
Hammer, Christian

Publication type:

Article

Letter to the Editor: Methods for mapping quantitative trait loci in autotetraploid species.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbz148

By:

Chen, Jing;
Leach, Lindsey J;
Luo, Zewei

Publication type:

Article

TEnGExA: an R package based tool for tissue enrichment and gene expression analysis.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa221

By:

Rawal, Hukam C;
Angadi, Ulavappa;
Mondal, Tapan Kumar

Publication type:

Article

AlzRiskMR database: an online database for the impact of exposure factors on Alzheimer's disease.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa213

By:

Wang, Zhe;
Meng, Lei;
Liu, Hong;
Shen, Liang;
Ji, Hong-Fang

Publication type:

Article

Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa203

By:

Torcivia, J P;
Mazumder, R

Publication type:

Article

NAMS webserver: coding potential assessment and functional annotation of plant transcripts.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa200

By:

Sun, Kun;
Wang, Huating;
Sun, Hao

Publication type:

Article

Modular arrangements of sequence motifs determine the functional diversity of KDM proteins.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa215

By:

Wang, Zerong;
Liu, Dongyang;
Xu, Baofang;
Tian, Ruixia;
Zuo, Yongchun

Publication type:

Article

Depiction of tumor stemlike features and underlying relationships with hazard immune infiltrations based on large prostate cancer cohorts.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa211

By:

Zhang, Chuanjie;
Chen, Tianhe;
Li, Zongtai;
Liu, Ao;
Xu, Yang;
Gao, Yi;
Xu, Danfeng

Publication type:

Article

Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa206

By:

Deutekom, Eva S;
Snel, Berend;
Dam, Teunis J P van

Publication type:

Article

DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa205

By:

Chu, Yanyi;
Shan, Xiaoqi;
Chen, Tianhang;
Jiang, Mingming;
Wang, Yanjing;
Wang, Qiankun;
Salahub, Dennis Russell;
Xiong, Yi;
Wei, Dong-Qing

Publication type:

Article

ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa192

By:

Shao, Jiangyi;
Liu, Bin

Publication type:

Article

Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa149

By:

Kaushik, Aman Chandra;
Wang, Yan-Jing;
Wang, Xiangeng;
Wei, Dong-Qing

Publication type:

Article

Topoly: Python package to analyze topology of polymers.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa196

By:

Dabrowski-Tumanski, Pawel;
Rubach, Pawel;
Niemyska, Wanda;
Gren, Bartosz Ambrozy;
Sulkowska, Joanna Ida

Publication type:

Article

Meta-i6mA: an interspecies predictor for identifying DNA N<sup>6</sup>-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa202

By:

Hasan, Md Mehedi;
Basith, Shaherin;
Khatun, Mst Shamima;
Lee, Gwang;
Manavalan, Balachandran;
Kurata, Hiroyuki

Publication type:

Article

How bioinformatics resources work with G4 RNAs.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa201

By:

Miskiewicz, Joanna;
Sarzynska, Joanna;
Szachniuk, Marta

Publication type:

Article

The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa191

By:

Kim, Soyeon;
Bai, YuLong;
Fan, Zhenjiang;
Diergaarde, Brenda;
Tseng, George C;
Park, Hyun Jung

Publication type:

Article

Extended application of genomic selection to screen multiomics data for prognostic signatures of prostate cancer.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa197

By:

Li, Ruidong;
Wang, Shibo;
Cui, Yanru;
Qu, Han;
Chater, John M;
Zhang, Le;
Wei, Julong;
Wang, Meiyue;
Xu, Yang;
Yu, Lei;
Lu, Jianming;
Feng, Yuanfa;
Zhou, Rui;
Huang, Yuhan;
Ma, Renyuan;
Zhu, Jianguo;
Zhong, Weide;
Jia, Zhenyu

Publication type:

Article

Benchmarking variant callers in next-generation and third-generation sequencing analysis.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa148

By:

Pei, Surui;
Liu, Tao;
Ren, Xue;
Li, Weizhong;
Chen, Chongjian;
Xie, Zhi

Publication type:

Article

Distance-based phylogenetic inference from typing data: a unifying view.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa147

By:

Vaz, Cátia;
Nascimento, Marta;
Carriço, João A;
Rocher, Tatiana;
Francisco, Alexandre P

Publication type:

Article

Discerning novel drug targets for treating Mycobacterium avium ss. paratuberculosis-associated autoimmune disorders: an in silico approach.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa195

By:

Garg, Anjali;
Singhal, Neelja;
Kumar, Manish

Publication type:

Article

Scopy: an integrated negative design python library for desirable HTS/VS database design.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa194

By:

Yang, Zi-Yi;
Yang, Zhi-Jiang;
Lu, Ai-Ping;
Hou, Ting-Jun;
Cao, Dong-Sheng

Publication type:

Article

Predicting human microbe–disease associations via graph attention networks with inductive matrix completion.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa146

By:

Long, Yahui;
Luo, Jiawei;
Zhang, Yu;
Xia, Yan

Publication type:

Article

FS–GBDT: identification multicancer-risk module via a feature selection algorithm by integrating Fisher score and GBDT.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa189

By:

Zhang, Jialin;
Xu, Da;
Hao, Kaijing;
Zhang, Yusen;
Chen, Wei;
Liu, Jiaguo;
Gao, Rui;
Wu, Chuanyan;
Marinis, Yang De

Publication type:

Article

A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa190

By:

Nguyen, Hung;
Tran, Duc;
Tran, Bang;
Pehlivan, Bahadir;
Nguyen, Tin

Publication type:

Article

Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa188

By:

Lee, Dohoon;
Park, Youngjune;
Kim, Sun

Publication type:

Article

Proteome-scale analysis of phase-separated proteins in immunofluorescence images.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa187

By:

Yu, Chunyu;
Shen, Boyan;
You, Kaiqiang;
Huang, Qi;
Shi, Minglei;
Wu, Congying;
Chen, Yang;
Zhang, Chaolin;
Li, Tingting

Publication type:

Article

Deep-belief network for predicting potential miRNA-disease associations.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa186

By:

Chen, Xing;
Li, Tian-Hao;
Zhao, Yan;
Wang, Chun-Chun;
Zhu, Chi-Chi

Publication type:

Article

TERL: classification of transposable elements by convolutional neural networks.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa185

By:

Cruz, Murilo Horacio Pereira da;
Domingues, Douglas Silva;
Saito, Priscila Tiemi Maeda;
Paschoal, Alexandre Rossi;
Bugatti, Pedro Henrique

Publication type:

Article

Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa184

By:

Bugnon, Leandro A;
Yones, Cristian;
Milone, Diego H;
Stegmayer, Georgina

Publication type:

Article

DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa183

By:

Wang, Jike;
Cao, Dongsheng;
Tang, Cunchen;
Xu, Lei;
He, Qiaojun;
Yang, Bo;
Chen, Xi;
Sun, Huiyong;
Hou, Tingjun

Publication type:

Article

Ori-Finder 3: a web server for genome-wide prediction of replication origins in Saccharomyces cerevisiae.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa182

By:

Wang, Dan;
Lai, Fei-Liao;
Gao, Feng

Publication type:

Article

The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa181

By:

Pham, Vu V H;
Li, Xiaomei;
Truong, Buu;
Nguyen, Thin;
Liu, Lin;
Li, Jiuyong;
Le, Thuc D

Publication type:

Article

Microsatellite instability status differentially associates with intratumoral immune microenvironment in human cancers.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa180

By:

Zhang, Peng;
Liu, Mingyue;
Cui, Ya;
Zheng, Pan;
Liu, Yang

Publication type:

Article

LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa179

By:

Deng, Yulan;
Luo, Hao;
Yang, Zhenyu;
Liu, Lunxu

Publication type:

Article

LncR2metasta: a manually curated database for experimentally supported lncRNAs during various cancer metastatic events.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa178

By:

Zhang, Shihua;
He, Xiaolong;
Zhang, Rui;
Deng, Wensheng

Publication type:

Article

Interpretation of deep learning in genomics and epigenomics.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa177

By:

Talukder, Amlan;
Barham, Clayton;
Li, Xiaoman;
Hu, Haiyan

Publication type:

Article

Expression profile of immune checkpoint genes and their roles in predicting immunotherapy response.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa176

By:

Hu, Fei-Fei;
Liu, Chun-Jie;
Liu, Lan-Lan;
Zhang, Qiong;
Guo, An-Yuan

Publication type:

Article

RNA-binding protein recognition based on multi-view deep feature and multi-label learning.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa174

By:

Yang, Haitao;
Deng, Zhaohong;
Pan, Xiaoyong;
Shen, Hong-Bin;
Choi, Kup-Sze;
Wang, Lei;
Wang, Shitong;
Wu, Jing

Publication type:

Article

Heritability jointly explained by host genotype and microbiome: will improve traits prediction?

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa175

By:

Awany, Denis;
Chimusa, Emile R

Publication type:

Article

The functional determinants in the organization of bacterial genomes.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa172

By:

Liu, Zhaoqian;
Feng, Jingtong;
Yu, Bin;
Ma, Qin;
Liu, Bingqiang

Publication type:

Article

An in silico approach to identification, categorization and prediction of nucleic acid binding proteins.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa171

By:

Xu, Lei;
Jiang, Shanshan;
Wu, Jin;
Zou, Quan

Publication type:

Article

Large-scale benchmark study of survival prediction methods using multi-omics data.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa167

By:

Herrmann, Moritz;
Probst, Philipp;
Hornung, Roman;
Jurinovic, Vindi;
Boulesteix, Anne-Laure

Publication type:

Article

Vertical integration methods for gene expression data analysis.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa169

By:

Wu, Mengyun;
Yi, Huangdi;
Ma, Shuangge

Publication type:

Article

Integrated omics analysis reveals the alteration of gut microbe–metabolites in obese adults.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa165

By:

Li, Rong;
Huang, Xue;
Liang, Xiao;
Su, Min;
Lai, Keng Po;
Chen, Jian

Publication type:

Article

A powerful framework for an integrative study with heterogeneous omics data: from univariate statistics to multi-block analysis.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa166

By:

Duruflé, Harold;
Selmani, Merwann;
Ranocha, Philippe;
Jamet, Elisabeth;
Dunand, Christophe;
Déjean, Sébastien

Publication type:

Article

An approach for normalization and quality control for NanoString RNA expression data.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa163

By:

Bhattacharya, Arjun;
Hamilton, Alina M;
Furberg, Helena;
Pietzak, Eugene;
Purdue, Mark P;
Troester, Melissa A;
Hoadley, Katherine A;
Love, Michael I

Publication type:

Article