Works matching IS 13674803 AND DT 2022 AND VI 38 AND IP 6

Results: 49

Towards a reproducible interactome: semantic-based detection of redundancies to unify protein–protein interaction databases.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1685, doi. 10.1093/bioinformatics/btac013

By:

Melkonian, Marc;
Juigné, Camille;
Dameron, Olivier;
Rabut, Gwenaël;
Becker, Emmanuelle

Publication type:

Article

scNAME: neighborhood contrastive clustering with ancillary mask estimation for scRNA-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1575, doi. 10.1093/bioinformatics/btac011

By:

Wan, Hui;
Chen, Liang;
Deng, Minghua

Publication type:

Article

CRAM 3.1: advances in the CRAM file format.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1497, doi. 10.1093/bioinformatics/btac010

By:

Bonfield, James K

Publication type:

Article

Cross-species prediction of essential genes in insects.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1504, doi. 10.1093/bioinformatics/btac009

By:

Castro, Giovanni Marques de;
Hastenreiter, Zandora;
Monteiro, Thiago Augusto Silva;
Silva, Thieres Tayroni Martins da;
Lobo, Francisco Pereira

Publication type:

Article

Characterization of biofilm structure and properties via processing of 2D optical coherence tomography images in BISCAP.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1708, doi. 10.1093/bioinformatics/btac002

By:

Narciso, Diogo A C;
Pereira, Ana;
Dias, Nuno O;
Melo, Luis F;
Martins, F G

Publication type:

Article

differential activity of biological processes in tissues and cell subsets can illuminate disease-related processes and cell-type identities.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1584, doi. 10.1093/bioinformatics/btab883

By:

Sharon, Moran;
Vinogradov, Ekaterina;
Argov, Chanan M;
Lazarescu, Or;
Zoabi, Yazeed;
Hekselman, Idan;
Yeger-Lotem, Esti

Publication type:

Article

scPretrain: multi-task self-supervised learning for cell-type classification.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1607, doi. 10.1093/bioinformatics/btac007

By:

Zhang, Ruiyi;
Luo, Yunan;
Ma, Jianzhu;
Zhang, Ming;
Wang, Sheng

Publication type:

Article

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1770, doi. 10.1093/bioinformatics/btac004

By:

Neumann, Jacob;
Lin, Yen Ting;
Mallela, Abhishek;
Miller, Ely F;
Colvin, Joshua;
Duprat, Abell T;
Chen, Ye;
Hlavacek, William S;
Posner, Richard G

Publication type:

Article

MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome‐metabolome data.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1615, doi. 10.1093/bioinformatics/btac003

By:

Noecker, Cecilia;
Eng, Alexander;
Muller, Efrat;
Borenstein, Elhanan

Publication type:

Article

Inferring gene regulatory network via fusing gene expression image and RNA-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1716, doi. 10.1093/bioinformatics/btac008

By:

Li, Xuejian;
Ma, Shiqiang;
Liu, Jin;
Tang, Jijun;
Guo, Fei

Publication type:

Article

STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1648, doi. 10.1093/bioinformatics/btac001

By:

Balabin, Helena;
Hoyt, Charles Tapley;
Birkenbihl, Colin;
Gyori, Benjamin M;
Bachman, John;
Kodamullil, Alpha Tom;
Plöger, Paul G;
Hofmann-Apitius, Martin;
Domingo-Fernández, Daniel

Publication type:

Article

ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1514, doi. 10.1093/bioinformatics/btac006

By:

Wei, Lesong;
Ye, Xiucai;
Sakurai, Tetsuya;
Mu, Zengchao;
Wei, Leyi

Publication type:

Article

SPEQ: quality assessment of peptide tandem mass spectra with deep learning.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1568, doi. 10.1093/bioinformatics/btab874

By:

Gholamizoj, Soroosh;
Ma, Bin

Publication type:

Article

MedTator: a serverless annotation tool for corpus development.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1776, doi. 10.1093/bioinformatics/btab880

By:

He, Huan;
Fu, Sunyang;
Wang, Liwei;
Liu, Sijia;
Wen, Andrew;
Liu, Hongfang

Publication type:

Article

Alpha-Tri: a deep neural network for scoring the similarity between predicted and measured spectra improves peptide identification of DIA data.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1525, doi. 10.1093/bioinformatics/btab878

By:

Song, Jian;
Yu, Changbin

Publication type:

Article

Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1700, doi. 10.1093/bioinformatics/btab877

By:

Harris, Coleman R;
McKinley, Eliot T;
Roland, Joseph T;
Liu, Qi;
Shrubsole, Martha J;
Lau, Ken S;
Coffey, Robert J;
Wrobel, Julia;
Vandekar, Simon N

Publication type:

Article

Robust disease module mining via enumeration of diverse prize-collecting Steiner trees.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1600, doi. 10.1093/bioinformatics/btab876

By:

Bernett, Judith;
Krupke, Dominik;
Sadegh, Sepideh;
Baumbach, Jan;
Fekete, Sándor P;
Kacprowski, Tim;
List, Markus;
Blumenthal, David B

Publication type:

Article

Completing gene trees without species trees in sub-quadratic time.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1532, doi. 10.1093/bioinformatics/btab875

By:

Mai, Uyen;
Mirarab, Siavash

Publication type:

Article

CACONET: a novel classification framework for microbial correlation networks.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1639, doi. 10.1093/bioinformatics/btab879

By:

Xu, Yuanwei;
Nash, Katrina;
Acharjee, Animesh;
Gkoutos, Georgios V

Publication type:

Article

On the identifiability of the isoform deconvolution problem: application to select the proper fragment length in an RNA-seq library.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1491, doi. 10.1093/bioinformatics/btab873

By:

Ferrer-Bonsoms, Juan A;
Morales, Xabier;
Afshar, Pegah T;
Wong, Wing H;
Rubio, Angel

Publication type:

Article

TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1752, doi. 10.1093/bioinformatics/btab872

By:

Brezovsky, Jan;
Thirunavukarasu, Aravind Selvaram;
Surpeta, Bartlomiej;
Sequeiros-Borja, Carlos Eduardo;
Mandal, Nishita;
Sarkar, Dheeraj Kumar;
Foumthuim, Cedrix J Dongmo;
Agrawal, Nikhil

Publication type:

Article

GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1754, doi. 10.1093/bioinformatics/btab871

By:

MacCarthy, Elijah A;
Zhang, Chengxin;
Zhang, Yang;
KC, Dukka B

Publication type:

Article

Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1729, doi. 10.1093/bioinformatics/btab870

By:

Lee, Soohyun;
Bakker, Clara R;
Vitzthum, Carl;
Alver, Burak H;
Park, Peter J

Publication type:

Article

Efficient gradient boosting for prognostic biomarker discovery.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1631, doi. 10.1093/bioinformatics/btab869

By:

Li, Kaiqiao;
Yao, Sijie;
Zhang, Zhenyu;
Cao, Biwei;
Wilson, Christopher M;
Kalos, Denise;
Kuan, Pei Fen;
Zhu, Ruoqing;
Wang, Xuefeng

Publication type:

Article

LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1767, doi. 10.1093/bioinformatics/btab867

By:

Pellegrino, Roberto Maria;
Giulietti, Matteo;
Alabed, Husam B R;
Buratta, Sandra;
Urbanelli, Lorena;
Piva, Francesco;
Emiliani, Carla

Publication type:

Article

HOMELETTE: a unified interface to homology modelling software.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1749, doi. 10.1093/bioinformatics/btab866

By:

Junk, Philipp;
Kiel, Christina

Publication type:

Article

SIGNORApp: a Cytoscape 3 application to access SIGNOR data.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1764, doi. 10.1093/bioinformatics/btab865

By:

Marinis, Ilaria De;
Surdo, Prisca Lo;
Cesareni, Gianni;
Perfetto, Livia

Publication type:

Article

GC-Profile 2.0: an extended web server for the prediction and visualization of CpG islands.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1738, doi. 10.1093/bioinformatics/btab864

By:

Lai, Fei-Liao;
Gao, Feng

Publication type:

Article

RAxML Grove: an empirical phylogenetic tree database.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1741, doi. 10.1093/bioinformatics/btab863

By:

Höhler, Dimitri;
Pfeiffer, Wayne;
Ioannidis, Vassilios;
Stockinger, Heinz;
Stamatakis, Alexandros

Publication type:

Article

MAINE: a web tool for multi-omics feature selection and rule-based data exploration.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1773, doi. 10.1093/bioinformatics/btab862

By:

Gruca, Aleksandra;
Henzel, Joanna;
Kostorz, Iwona;
Stęclik, Tomasz;
Wróbel, Łukasz;
Sikora, Marek

Publication type:

Article

Chromosomal imbalances detected via RNA-sequencing in 28 cancers.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1483, doi. 10.1093/bioinformatics/btab861

By:

Ozcan, Zuhal;
Lucas, Francis A San;
Wong, Justin W;
Chang, Kyle;
Stopsack, Konrad H;
Fowler, Jerry;
Jakubek, Yasminka A;
Scheet, Paul

Publication type:

Article

Comparing transmembrane protein structures with ATOLL.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1743, doi. 10.1093/bioinformatics/btab860

By:

Jacquemard, Célien;
Bret, Guillaume;
Grutter, Thomas;
Kellenberger, Esther

Publication type:

Article

DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1677, doi. 10.1093/bioinformatics/btab859

By:

Althagafi, Azza;
Alsubaie, Lamia;
Kathiresan, Nagarajan;
Mineta, Katsuhiko;
Aloraini, Taghrid;
Mutairi, Fuad Al;
Alfadhel, Majid;
Gojobori, Takashi;
Alfares, Ahmad;
Hoehndorf, Robert

Publication type:

Article

CoDNaS-RNA: a database of conformational diversity in the native state of RNA.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1745, doi. 10.1093/bioinformatics/btab858

By:

Buitrón, Martín González;
Cahui, Ronaldo Romario Tunque;
Ríos, Emilio García;
Hirsh, Layla;
Parisi, Gustavo;
Fornasari, María Silvina;
Palopoli, Nicolas

Publication type:

Article

Gene set analysis with graph-embedded kernel association test.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1560, doi. 10.1093/bioinformatics/btab851

By:

Qu, Jialin;
Cui, Yuehua

Publication type:

Article

CRPMKB: a knowledge base of cancer risk prediction models for systematic comparison and personalized applications.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1669, doi. 10.1093/bioinformatics/btab850

By:

Ren, Shumin;
Jin, Yanwen;
Chen, Yalan;
Shen, Bairong

Publication type:

Article

Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1542, doi. 10.1093/bioinformatics/btab848

By:

He, Huan;
Guo, Xinyun;
Yu, Jialin;
Ai, Chen;
Shi, Shaoping

Publication type:

Article

AMC: accurate mutation clustering from single-cell DNA sequencing data.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1732, doi. 10.1093/bioinformatics/btab857

By:

Yu, Zhenhua;
Du, Fang

Publication type:

Article

CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1735, doi. 10.1093/bioinformatics/btab856

By:

Chen, Chaoran;
Nadeau, Sarah;
Yared, Michael;
Voinov, Philippe;
Xie, Ning;
Roemer, Cornelius;
Stadler, Tanja

Publication type:

Article

GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1727, doi. 10.1093/bioinformatics/btab855

By:

Ebmeyer, Stefan;
Coertze, Roelof Dirk;
Berglund, Fanny;
Kristiansson, Erik;
Larsson, D G Joakim

Publication type:

Article

BATL: Bayesian annotations for targeted lipidomics.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1593, doi. 10.1093/bioinformatics/btab854

By:

Chitpin, Justin G;
Surendra, Anuradha;
Nguyen, Thao T;
Taylor, Graeme P;
Xu, Hongbin;
Alecu, Irina;
Ortega, Roberto;
Tomlinson, Julianna J;
Crawley, Angela M;
McGuinty, Michaeline;
Schlossmacher, Michael G;
Saunders-Pullman, Rachel;
Cuperlovic-Culf, Miroslava;
Bennett, Steffany A L;
Perkins, Theodore J

Publication type:

Article

BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1692, doi. 10.1093/bioinformatics/btab853

By:

Vulliard, Loan;
Hancock, Joel;
Kamnev, Anton;
Fell, Christopher W;
Silva, Joana Ferreira da;
Loizou, Joanna I;
Nagy, Vanja;
Dupré, Loïc;
Menche, Jörg

Publication type:

Article

geoCancerPrognosticDatasetsRetriever: a bioinformatics tool to easily identify cancer prognostic datasets on Gene Expression Omnibus (GEO).

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1761, doi. 10.1093/bioinformatics/btab852

By:

Alameer, Abbas;
Chicco, Davide

Publication type:

Article

Identifying cancer pathway dysregulations using differential causal effects.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1550, doi. 10.1093/bioinformatics/btab847

By:

Jablonski, Kim Philipp;
Pirkl, Martin;
Ćevid, Domagoj;
Bühlmann, Peter;
Beerenwinkel, Niko

Publication type:

Article

Benchmarking table recognition performance on biomedical literature on neurological disorders.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1624, doi. 10.1093/bioinformatics/btab843

By:

Adams, Tim;
Namysl, Marcin;
Kodamullil, Alpha Tom;
Behnke, Sven;
Jacobs, Marc

Publication type:

Article

MACA: marker-based automatic cell-type annotation for single-cell expression data.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1756, doi. 10.1093/bioinformatics/btab840

By:

Xu, Yang;
Baumgart, Simon J;
Stegmann, Christian M;
Hayat, Sikander

Publication type:

Article

TMBleR: a bioinformatic tool to optimize TMB estimation and predictive power.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1724, doi. 10.1093/bioinformatics/btab836

By:

Fancello, Laura;
Guida, Alessandro;
Frige, Gianmaria;
Ceol, Arnaud Gerard Michel;
Babini, Gabriele;
Scaglione, Giovanni Luca;
Zanfardino, Mario;
Mazza, Tommaso;
Ferrando, Lorenzo;
Pelicci, Pier Giuseppe;
Mazzarella, Luca

Publication type:

Article

Corrigendum to: NMF-RI: blind spectral unmixing of highly mixed multispectral flow and image cytometry data.

Published in:

2022

By:

Jiménez-Sánchez, Daniel;
Ariz, Mikel;
Morgado, José Mário;
Cortés-Domínguez, Iván;
Ortiz-de-Solórzano, Carlos

Publication type:

Correction Notice

Mainzelliste SecureEpiLinker (MainSEL): privacy-preserving record linkage using secure multi-party computation.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1657, doi. 10.1093/bioinformatics/btaa764

By:

Stammler, Sebastian;
Kussel, Tobias;
Schoppmann, Phillipp;
Stampe, Florian;
Tremper, Galina;
Katzenbeisser, Stefan;
Hamacher, Kay;
Lablans, Martin

Publication type:

Article