Works matching IS 13674803 AND DT 2020 AND VI 36 AND IP 10

Results: 58

6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3257, doi. 10.1093/bioinformatics/btaa113

By:

Xu, Haodong;
Hu, Ruifeng;
Jia, Peilin;
Zhao, Zhongming

Publication type:

Article

Nubeam-dedup: a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3254, doi. 10.1093/bioinformatics/btaa112

By:

Dai, Hang;
Guan, Yongtao

Publication type:

Article

Protein–ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3018, doi. 10.1093/bioinformatics/btaa110

By:

Xia, Chun-Qiu;
Pan, Xiaoyong;
Shen, Hong-Bin

Publication type:

Article

PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3043, doi. 10.1093/bioinformatics/btaa136

By:

Peabody, Michael A;
Lau, Wing Yin Venus;
Hoad, Gemma R;
Jia, Baofeng;
Maguire, Finlay;
Gray, Kristen L;
Beiko, Robert G;
Brinkman, Fiona S L

Publication type:

Article

MUM&Co: accurate detection of all SV types through whole-genome alignment.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3242, doi. 10.1093/bioinformatics/btaa115

By:

O'Donnell, Samuel;
Fischer, Gilles

Publication type:

Article

scRMD: imputation for single cell RNA-seq data via robust matrix decomposition.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3156, doi. 10.1093/bioinformatics/btaa139

By:

Chen, Chong;
Wu, Changjing;
Wu, Linjie;
Wang, Xiaochen;
Deng, Minghua;
Xi, Ruibin

Publication type:

Article

A path recorder algorithm for Multiple Longest Common Subsequences (MLCS) problems.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3035, doi. 10.1093/bioinformatics/btaa134

By:

Wei, Shiwei;
Wang, Yuping;
Yang, Yuanchao;
Liu, Sen

Publication type:

Article

StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3028, doi. 10.1093/bioinformatics/btaa131

By:

Fu, Xiangzheng;
Cai, Lijun;
Zeng, Xiangxiang;
Zou, Quan

Publication type:

Article

Connecting mathematical models to genomes: joint estimation of model parameters and genome-wide marker effects on these parameters.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3169, doi. 10.1093/bioinformatics/btaa129

By:

Onogi, Akio

Publication type:

Article

Rhapsody: predicting the pathogenicity of human missense variants.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3084, doi. 10.1093/bioinformatics/btaa127

By:

Ponzoni, Luca;
Peñaherrera, Daniel A;
Oltvai, Zoltán N;
Bahar, Ivet

Publication type:

Article

Composite Kernel Association Test (CKAT) for SNP-set joint assessment of genotype and genotype-by-treatment interaction in Pharmacogenetics studies.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3162, doi. 10.1093/bioinformatics/btaa125

By:

Zhang, Hong;
Zhao, Ni;
Mehrotra, Devan V;
Shen, Judong

Publication type:

Article

DeepMAsED: evaluating the quality of metagenomic assemblies.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3011, doi. 10.1093/bioinformatics/btaa124

By:

Mineeva, Olga;
Rojas-Carulla, Mateo;
Ley, Ruth E;
Schölkopf, Bernhard;
Youngblut, Nicholas D

Publication type:

Article

Phage protein receptors have multiple interaction partners and high expressions.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 2975, doi. 10.1093/bioinformatics/btaa123

By:

Zhang, Zheng;
Yu, Fen;
Zou, Yuanqiang;
Qiu, Ye;
Wu, Aiping;
Jiang, Taijiao;
Peng, Yousong

Publication type:

Article

A probabilistic graphical model for system-wide analysis of gene regulatory networks.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3192, doi. 10.1093/bioinformatics/btaa122

By:

Kotiang, Stephen;
Eslami, Ali

Publication type:

Article

Tally-2.0: upgraded validator of tandem repeat detection in protein sequences.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3260, doi. 10.1093/bioinformatics/btaa121

By:

Perovic, Vladimir;
Leclercq, Jeremy Y;
Sumonja, Neven;
Richard, Francois D;
Veljkovic, Nevena;
Kajava, Andrey V

Publication type:

Article

High-throughput and efficient multilocus genome-wide association study on longitudinal outcomes.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3004, doi. 10.1093/bioinformatics/btaa120

By:

Xu, Huang;
Li, Xiang;
Yang, Yaning;
Li, Yi;
Pinheiro, Jose;
Sasser, Kate;
Hamadeh, Hisham;
Steven, Xu;
Yuan, Min;
Initiative, and for the Alzheimer's Disease Neuroimaging

Publication type:

Article

Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3185, doi. 10.1093/bioinformatics/btaa119

By:

Ong, Edison;
Wang, Haihe;
Wong, Mei U;
Seetharaman, Meenakshi;
Valdez, Ninotchka;
He, Yongqun

Publication type:

Article

Proline: an efficient and user-friendly software suite for large-scale proteomics.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3148, doi. 10.1093/bioinformatics/btaa118

By:

Bouyssié, David;
Hesse, Anne-Marie;
Mouton-Barbosa, Emmanuelle;
Rompais, Magali;
Macron, Charlotte;
Carapito, Christine;
Peredo, Anne Gonzalez de;
Couté, Yohann;
Dupierris, Véronique;
Burel, Alexandre;
Menetrey, Jean-Philippe;
Kalaitzakis, Andrea;
Poisat, Julie;
Romdhani, Aymen;
Burlet-Schiltz, Odile;
Cianférani, Sarah;
Garin, Jerome;
Bruley, Christophe

Publication type:

Article

DIMERBOW: exploring possible GPCR dimer interfaces.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3271, doi. 10.1093/bioinformatics/btaa117

By:

García-Recio, Adrián;
Navarro, Gemma;
Franco, Rafael;
Olivella, Mireia;
Guixà-González, Ramon;
Cordomí, Arnau

Publication type:

Article

CMF-Impute: an accurate imputation tool for single-cell RNA-seq data.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3139, doi. 10.1093/bioinformatics/btaa109

By:

Xu, Junlin;
Cai, Lijun;
Liao, Bo;
Zhu, Wen;
Yang, JiaLiang

Publication type:

Article

A unified ILP framework for core ancestral genome reconstruction problems.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 2993, doi. 10.1093/bioinformatics/btaa100

By:

Avdeyev, Pavel;
Alexeev, Nikita;
Rong, Yongwu;
Alekseyev, Max A

Publication type:

Article

GeneSwitches: ordering gene expression and functional events in single-cell experiments.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3273, doi. 10.1093/bioinformatics/btaa099

By:

Cao, Elaine Y;
Ouyang, John F;
Rackham, Owen J L

Publication type:

Article

scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3131, doi. 10.1093/bioinformatics/btaa108

By:

Jin, Ke;
Ou-Yang, Le;
Zhao, Xing-Ming;
Yan, Hong;
Zhang, Xiao-Fei

Publication type:

Article

Marker controlled superpixel nuclei segmentation and automatic counting on immunohistochemistry staining images.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3225, doi. 10.1093/bioinformatics/btaa107

By:

Shu, Jie;
Liu, Jingxin;
Zhang, Yongmei;
Fu, Hao;
Ilyas, Mohammad;
Faraci, Giuseppe;
Mea, Vincenzo Della;
Liu, Bozhi;
Qiu, Guoping

Publication type:

Article

MichelaNglo: sculpting protein views on web pages without coding.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3268, doi. 10.1093/bioinformatics/btaa104

By:

Ferla, Matteo P;
Pagnamenta, Alistair T;
Damerell, David;
Taylor, Jenny C;
Marsden, Brian D

Publication type:

Article

PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3239, doi. 10.1093/bioinformatics/btaa103

By:

Fang, Zhencheng;
Tan, Jie;
Wu, Shufang;
Li, Mo;
Wang, Chunhui;
Liu, Yongchu;
Zhu, Huaiqiu

Publication type:

Article

SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3207, doi. 10.1093/bioinformatics/btaa106

By:

Abeysinghe, Rashmie;
Hinderer, Eugene W;
Moseley, Hunter N B;
Cui, Licong

Publication type:

Article

SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3276, doi. 10.1093/bioinformatics/btaa105

By:

Assefa, Alemu Takele;
Vandesompele, Jo;
Thas, Olivier

Publication type:

Article

ZIAQ: a quantile regression method for differential expression analysis of single-cell RNA-seq data.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3124, doi. 10.1093/bioinformatics/btaa098

By:

Zhang, Wenfei;
Wei, Ying;
Zhang, Donghui;
Xu, Ethan Y

Publication type:

Article

scBatch: batch-effect correction of RNA-seq data through sample distance matrix adjustment.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3115, doi. 10.1093/bioinformatics/btaa097

By:

Fei, Teng;
Yu, Tianwei

Publication type:

Article

OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3292, doi. 10.1093/bioinformatics/btaa096

By:

Hasnain, Zaki;
Fraser, Andrew K;
Georgess, Dan;
Choi, Alex;
Macklin, Paul;
Bader, Joel S;
Peyton, Shelly R;
Ewald, Andrew J;
Newton, Paul K

Publication type:

Article

BionoiNet: ligand-binding site classification with off-the-shelf deep neural network.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3077, doi. 10.1093/bioinformatics/btaa094

By:

Shi, Wentao;
Lemoine, Jeffrey M;
Shawky, Abd-El-Monsif A;
Singha, Manali;
Pu, Limeng;
Yang, Shuangyan;
Ramanujam, J;
Brylinski, Michal

Publication type:

Article

Methplotlib: analysis of modified nucleotides from nanopore sequencing.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3236, doi. 10.1093/bioinformatics/btaa093

By:

Coster, Wouter De;
Stovner, Endre Bakken;
Strazisar, Mojca

Publication type:

Article

ShinySOM: graphical SOM-based analysis of single-cell cytometry data.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3288, doi. 10.1093/bioinformatics/btaa091

By:

Kratochvíl, Miroslav;
Bednárek, David;
Sieger, Tomáš;
Fišer, Karel;
Vondrášek, Jiří

Publication type:

Article

Occupancy spectrum distribution: application for coalescence simulation with generic mergers.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3279, doi. 10.1093/bioinformatics/btaa090

By:

Becheler, Arnaud;
Knowles, L Lacey

Publication type:

Article

InterLig: improved ligand-based virtual screening using topologically independent structural alignments.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3266, doi. 10.1093/bioinformatics/btaa089

By:

Mirabello, Claudio;
Wallner, Björn

Publication type:

Article

Polar labeling: silver standard algorithm for training disease classifiers.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3200, doi. 10.1093/bioinformatics/btaa088

By:

Wagholikar, Kavishwar B;
Estiri, Hossein;
Murphy, Marykate;
Murphy, Shawn N

Publication type:

Article

Statistical significance of cluster membership for unsupervised evaluation of cell identities.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3107, doi. 10.1093/bioinformatics/btaa087

By:

Chung, Neo Christopher

Publication type:

Article

ColocML: machine learning quantifies co-localization between mass spectrometry images.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3215, doi. 10.1093/bioinformatics/btaa085

By:

Ovchinnikova, Katja;
Stuart, Lachlan;
Rakhlin, Alexander;
Nikolenko, Sergey;
Alexandrov, Theodore

Publication type:

Article

Bayesian inference using qualitative observations of underlying continuous variables.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3177, doi. 10.1093/bioinformatics/btaa084

By:

Mitra, Eshan D;
Hlavacek, William S

Publication type:

Article

FluPhenotype—a one-stop platform for early warnings of the influenza A virus.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3251, doi. 10.1093/bioinformatics/btaa083

By:

Lu, Congyu;
Cai, Zena;
Zou, Yuanqiang;
Zhang, Zheng;
Chen, Wenjun;
Deng, Lizong;
Du, Xiangjun;
Wu, Aiping;
Yang, Lei;
Wang, Dayan;
Shu, Yuelong;
Jiang, Taijiao;
Peng, Yousong

Publication type:

Article

A cautionary tale on using imputation methods for inference in matched-pairs design.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3099, doi. 10.1093/bioinformatics/btaa082

By:

Ramosaj, Burim;
Amro, Lubna;
Pauly, Markus

Publication type:

Article

DeepHIT: a deep learning framework for prediction of hERG-induced cardiotoxicity.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3049, doi. 10.1093/bioinformatics/btaa075

By:

Ryu, Jae Yong;
Lee, Mi Young;
Lee, Jeong Hyun;
Lee, Byung Ho;
Oh, Kwang-Seok

Publication type:

Article

Coolpup.py: versatile pile-up analysis of Hi-C data.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 2980, doi. 10.1093/bioinformatics/btaa073

By:

Flyamer, Ilya M;
Illingworth, Robert S;
Bickmore, Wendy A

Publication type:

Article

Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3263, doi. 10.1093/bioinformatics/btaa070

By:

Czech, Lucas;
Barbera, Pierre;
Stamatakis, Alexandros

Publication type:

Article

Estimating the power of sequence covariation for detecting conserved RNA structure.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3072, doi. 10.1093/bioinformatics/btaa080

By:

Rivas, Elena;
Clements, Jody;
Eddy, Sean R

Publication type:

Article

FTIP: an accurate and efficient method for global protein surface comparison.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3056, doi. 10.1093/bioinformatics/btaa076

By:

Zhang, Yuan;
Sui, Xing;
Stagg, Scott;
Zhang, Jinfeng

Publication type:

Article

PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA–lncRNA interaction prediction.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 2986, doi. 10.1093/bioinformatics/btaa074

By:

Kang, Qiang;
Meng, Jun;
Cui, Jun;
Luan, Yushi;
Chen, Ming

Publication type:

Article

Census of halide-binding sites in protein structures.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3064, doi. 10.1093/bioinformatics/btaa079

By:

Skitchenko, Rostislav K;
Usoltsev, Dmitrii;
Uspenskaya, Mayya;
Kajava, Andrey V;
Guskov, Albert

Publication type:

Article

GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3286, doi. 10.1093/bioinformatics/btaa078

By:

Tankhilevich, Evgeny;
Ish-Horowicz, Jonathan;
Hameed, Tara;
Roesch, Elisabeth;
Kleijn, Istvan;
Stumpf, Michael P H;
He, Fei

Publication type:

Article