Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 2

Results: 63

Correction to: USNAP: fast unique dense region detection and its application to lung cancer.

Published in:: Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btad736
Publication type:: Article

Correction to: GTExVisualizer: a web platform for supporting ageing studies.

Published in:: 2024
Publication type:: Correction Notice

scSemiGCN: boosting cell-type annotation from noise-resistant graph neural networks with extremely limited supervision.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae091

By:

Yang, Jue;
Wang, Weiwen;
Zhang, Xiwen

Publication type:

Article

Bioframe: operations on genomic intervals in Pandas dataframes.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae088

By:

Abdennur, Nezar;
Fudenberg, Geoffrey;
Flyamer, Ilya M;
Galitsyna, Aleksandra A;
Goloborodko, Anton;
Imakaev, Maxim;
Venev, Sergey

Publication type:

Article

Geometry-complete perceptron networks for 3D molecular graphs.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. N.PAG, doi. 10.1093/bioinformatics/btae087

By:

Morehead, Alex;
Cheng, Jianlin

Publication type:

Article

T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae083

By:

Guan, Xiaoyu;
Shao, Wei;
Zhang, Daoqiang

Publication type:

Article

Estimation of inbreeding and kinship coefficients via latent identity-by-descent states.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae082

By:

Guan, Yongtao;
Levy, Daniel

Publication type:

Article

NFTest: automated testing of Nextflow pipelines.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae081

By:

Patel, Yash;
Zhu, Chenghao;
Yamaguchi, Takafumi N;
Bugh, Yuan Zhe;
Tian, Mao;
Holmes, Aaron;
Fitz-Gibbon, Sorel T;
Boutros, Paul C

Publication type:

Article

RNA threading with secondary structure and sequence profile.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae080

By:

Du, Zongyang;
Peng, Zhenling;
Yang, Jianyi

Publication type:

Article

PipeVal: light-weight extensible tool for file validation.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae079

By:

Patel, Yash;
Beshlikyan, Arpi;
Jordan, Madison;
Kim, Gina;
Holmes, Aaron;
Yamaguchi, Takafumi N;
Boutros, Paul C

Publication type:

Article

mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae078

By:

Sintsova, Anna;
Ruscheweyh, Hans-Joachim;
Field, Christopher M;
Feer, Lilith;
Nguyen, Bidong D;
Daniel, Benjamin;
Hardt, Wolf-Dietrich;
Vorholt, Julia A;
Sunagawa, Shinichi

Publication type:

Article

Dynamic correlations: exact and approximate methods for mutual information.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae076

By:

Demirtaş, Kemal;
Erman, Burak;
Haliloğlu, Türkan

Publication type:

Article

GeneGPT: augmenting large language models with domain tools for improved access to biomedical information.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae075

By:

Jin, Qiao;
Yang, Yifan;
Chen, Qingyu;
Lu, Zhiyong

Publication type:

Article

pycofitness—Evaluating the fitness landscape of RNA and protein sequences.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae074

By:

Pucci, Fabrizio;
Zerihun, Mehari B;
Rooman, Marianne;
Schug, Alexander

Publication type:

Article

PanEffect: a pan-genome visualization tool for variant effects in maize.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae073

By:

Andorf, Carson M;
Haley, Olivia C;
Hayford, Rita K;
Portwood, John L;
Harding, Stephen;
Sen, Shatabdi;
Cannon, Ethalinda K;
Gardiner, Jack M;
Kim, Hye-Seon;
Woodhouse, Margaret R

Publication type:

Article

SpatialDDLS: an R package to deconvolute spatial transcriptomics data using neural networks.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae072

By:

Mañanes, Diego;
Rivero-García, Inés;
Relaño, Carlos;
Torres, Miguel;
Sancho, David;
Jimenez-Carretero, Daniel;
Torroja, Carlos;
Sánchez-Cabo, Fátima

Publication type:

Article

Zero is not absence: censoring-based differential abundance analysis for microbiome data.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae071

By:

Chan, Lap Sum;
Li, Gen

Publication type:

Article

Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae070

By:

Guo, Juanru;
Zhang, Wenjin;
Chen, Xuhua;
Yen, Allen;
Chen, Lucy;
Shively, Christian A;
Li, Daofeng;
Wang, Ting;
Dougherty, Joseph D;
Mitra, Robi D

Publication type:

Article

PMIpred: a physics-informed web server for quantitative protein–membrane interaction prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae069

By:

Hilten, Niek van;
Verwei, Nino;
Methorst, Jeroen;
Nase, Carsten;
Bernatavicius, Andrius;
Risselada, Herre Jelger

Publication type:

Article

AGImpute: imputation of scRNA-seq data based on a hybrid GAN with dropouts identification.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae068

By:

Zhu, Xiaoshu;
Meng, Shuang;
Li, Gaoshi;
Wang, Jianxin;
Peng, Xiaoqing

Publication type:

Article

Phenotype prediction from single-cell RNA-seq data using attention-based neural networks.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae067

By:

Mao, Yuzhen;
Lin, Yen-Yi;
Wong, Nelson K Y;
Volik, Stanislav;
Sar, Funda;
Collins, Colin;
Ester, Martin

Publication type:

Article

VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae066

By:

Charron, Philippe;
Kang, Mingsong

Publication type:

Article

DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae065

By:

Wang, Jun;
Horlacher, Marc;
Cheng, Lixin;
Winther, Ole

Publication type:

Article

CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae063

By:

Wang, Xiao;
Chai, Ziyi;
Li, Shaohua;
Liu, Yan;
Li, Chen;
Jiang, Yu;
Liu, Quanzhong

Publication type:

Article

Expanding the coverage of spatial proteomics: a machine learning approach.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae062

By:

Sun, Huangqingbo;
Li, Jiayi;
Murphy, Robert F

Publication type:

Article

Protein language models meet reduced amino acid alphabets.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae061

By:

Ieremie, Ioan;
Ewing, Rob M;
Niranjan, Mahesan

Publication type:

Article

PERSEUS: an interactive and intuitive web-based tool for pedigree visualization.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae060

By:

Pradas, Nicole;
Jurado-Ruiz, Federico;
Onielfa, Carles;
Arús, Pere;
Aranzana, Maria José

Publication type:

Article

Highly efficient clustering of long-read transcriptomic data with GeLuster.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae059

By:

Ma, Junchi;
Zhao, Xiaoyu;
Qi, Enfeng;
Han, Renmin;
Yu, Ting;
Li, Guojun

Publication type:

Article

PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae058

By:

Shi, Kexin;
Xiong, Yuanpeng;
Wang, Yu;
Deng, Yifan;
Wang, Wenjia;
Jing, Bingyi;
Gao, Xin

Publication type:

Article

StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae057

By:

Wang, Ding;
Jin, Junru;
Li, Zhongshen;
Wang, Yu;
Fan, Mushuang;
Liang, Sirui;
Su, Ran;
Wei, Leyi

Publication type:

Article

PERFUMES: pipeline to extract RNA functional motifs and exposed structures.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae056

By:

Chol, Arnaud;
Sarrazin-Gendron, Roman;
Lécuyer, Éric;
Blanchette, Mathieu;
Waldispühl, Jérôme

Publication type:

Article

High-dimensional quantile mediation analysis with application to a birth cohort study of mother–newborn pairs.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae055

By:

Zhang, Haixiang;
Hong, Xiumei;
Zheng, Yinan;
Hou, Lifang;
Zheng, Cheng;
Wang, Xiaobin;
Liu, Lei

Publication type:

Article

Scbean: a python library for single-cell multi-omics data analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae053

By:

Zhang, Haohui;
Wang, Yuwei;
Lian, Bin;
Wang, Yiran;
Li, Xingyi;
Wang, Tao;
Shang, Xuequn;
Yang, Hui;
Aziz, Ahmad;
Hu, Jialu

Publication type:

Article

BINGO: a blind unmixing algorithm for ultra-multiplexing fluorescence images.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae052

By:

Huang, Xinyuan;
Gao, Xiujuan;
Fu, Ling

Publication type:

Article

TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae051

By:

Karaoğlanoğlu, Fatih;
Orabi, Baraa;
Flannigan, Ryan;
Chauve, Cedric;
Hach, Faraz

Publication type:

Article

Interpreting protein abundance in Saccharomyces cerevisiae through relational learning.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae050

By:

Brunnsåker, Daniel;
Kronström, Filip;
Tiukova, Ievgeniia A;
King, Ross D

Publication type:

Article

vcfpp: a C++ API for rapid processing of the variant call format.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae049

By:

Li, Zilong

Publication type:

Article

DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae048

By:

Hamano, Momoko;
Nakamura, Toru;
Ito, Ryoku;
Shimada, Yuki;
Iwata, Michio;
Takeshita, Jun-ichi;
Eguchi, Ryohei;
Yamanishi, Yoshihiro

Publication type:

Article

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae047

By:

Koslicki, David;
White, Stephen;
Ma, Chunyu;
Novikov, Alexei

Publication type:

Article

NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae046

By:

Yin, Chenglin;
Wang, Ruheng;
Qiao, Jianbo;
Shi, Hua;
Duan, Hongliang;
Jiang, Xinbo;
Teng, Saisai;
Wei, Leyi

Publication type:

Article

A simple refined DNA minimizer operator enables 2-fold faster computation.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae045

By:

Pan, Chenxu;
Reinert, Knut

Publication type:

Article

MAGE: metafounders-assisted genomic estimation of breeding value, a novel additive-dominance single-step model in crossbreeding systems.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae044

By:

Zhuo, Yue;
Du, Heng;
Diao, ChenGuang;
Li, WeiNing;
Zhou, Lei;
Jiang, Li;
Jiang, JiCai;
Liu, JianFeng

Publication type:

Article

Statistical framework to determine indel-length distribution.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae043

By:

Wygoda, Elya;
Loewenthal, Gil;
Moshe, Asher;
Alburquerque, Michael;
Mayrose, Itay;
Pupko, Tal

Publication type:

Article

HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae042

By:

Holt, James M;
Saunders, Christopher T;
Rowell, William J;
Kronenberg, Zev;
Wenger, Aaron M;
Eberle, Michael

Publication type:

Article

3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae041

By:

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

Publication type:

Article

Deep centroid: a general deep cascade classifier for biomedical omics data classification.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae039

By:

Xie, Kuan;
Hou, Yuying;
Zhou, Xionghui

Publication type:

Article

BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae038

By:

Genovese, Giulio;
Rockweiler, Nicole B;
Gorman, Bryan R;
Bigdeli, Tim B;
Pato, Michelle T;
Pato, Carlos N;
Ichihara, Kiku;
McCarroll, Steven A

Publication type:

Article

Multi-indicator comparative evaluation for deep learning-based protein sequence design methods.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae037

By:

Yu, Jinyu;
Mu, Junxi;
Wei, Ting;
Chen, Hai-Feng

Publication type:

Article

The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae036

By:

Levi, Hagai;
Elkon, Ran;
Shamir, Ron

Publication type:

Article

2dGBH: Two-dimensional group Benjamini–Hochberg procedure for false discovery rate control in two-way multiple testing of genomic data.

Published in:

Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae035

By:

Yang, Lu;
Wang, Pei;
Chen, Jun

Publication type:

Article