Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 5

Results: 69

gExcite: a start-to-end framework for single-cell gene expression, hashing, and antibody analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad329

By:

Grob, Linda;
Bertolini, Anne;
Carrara, Matteo;
Lischetti, Ulrike;
Tastanova, Aizhan;
Beisel, Christian;
Levesque, Mitchell P;
Stekhoven, Daniel J;
Singer, Franziska

Publication type:

Article

ODNA: identification of organellar DNA by machine learning.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad326

By:

Martin, Roman;
Nguyen, Minh Kien;
Lowack, Nick;
Heider, Dominik

Publication type:

Article

NanoPack2: population-scale evaluation of long-read sequencing data.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad311

By:

Coster, Wouter De;
Rademakers, Rosa

Publication type:

Article

AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad310

By:

Luo, Ling;
Wei, Chih-Hsuan;
Lai, Po-Ting;
Leaman, Robert;
Chen, Qingyu;
Lu, Zhiyong

Publication type:

Article

Genome mining for anti-CRISPR operons using machine learning.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad309

By:

Yang, Bowen;
Khatri, Minal;
Zheng, Jinfang;
Deogun, Jitender;
Yin, Yanbin

Publication type:

Article

TRASH: Tandem Repeat Annotation and Structural Hierarchy.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad308

By:

Wlodzimierz, Piotr;
Hong, Michael;
Henderson, Ian R

Publication type:

Article

HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad299

By:

Wang, Zixuan;
Xiong, Shuwen;
Yu, Yun;
Zhou, Jiliu;
Zhang, Yongqing

Publication type:

Article

Correction to: Integrative analysis of individual-level data and high-dimensional summary statistics.

Published in:: 2023
Publication type:: Correction Notice

uORF4u: a tool for annotation of conserved upstream open reading frames.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad323

By:

Egorov, Artyom A;
Atkinson, Gemma C

Publication type:

Article

Correction to: Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data.

Published in:: 2023
Publication type:: Correction Notice

Efficient short read mapping to a pangenome that is represented by a graph of ED strings.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad320

By:

Büchler, Thomas;
Olbrich, Jannik;
Ohlebusch, Enno

Publication type:

Article

ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad317

By:

Moshiri, Niema

Publication type:

Article

High-quality, customizable heuristics for RNA 3D structure alignment.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad315

By:

Zurkowski, Michal;
Antczak, Maciej;
Szachniuk, Marta

Publication type:

Article

CscoreTool-M infers 3D sub-compartment probabilities within cell population.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad314

By:

Zheng, Xiaobin;
Tran, Joseph R;
Zheng, Yixian

Publication type:

Article

copMEM2: robust and scalable maximum exact match finding.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad313

By:

Grabowski, Szymon;
Bieniecki, Wojciech

Publication type:

Article

fimpera: drastic improvement of Approximate Membership Query data-structures with counts.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad305

By:

Robidou, Lucas;
Peterlongo, Pierre

Publication type:

Article

GTExVisualizer: a web platform for supporting ageing studies.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad303

By:

Guzz, Pietro Hiram;
Lomoio, Ugo;
Veltri, Pierangelo

Publication type:

Article

A co-adaptive duality-aware framework for biomedical relation extraction.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad301

By:

Zhang, Weiyan;
Chen, Chuang;
Wang, Jiacheng;
Liu, Jingping;
Ruan, Tong

Publication type:

Article

STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad302

By:

Zhou, Boyan;
Li, Huilin

Publication type:

Article

ppBAM: ProteinPaint BAM track for read alignment visualization and variant genotyping.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad300

By:

Paul, Robin;
Wang, Jian;
Reilly, Colleen;
Sioson, Edgar;
Patel, Jaimin;
Matt, Gavriel;
Acić, Aleksandar;
Zhou, Xin

Publication type:

Article

Correction to: wpLogicNet: logic gate and structure inference in gene regulatory networks.

Published in:: 2023
Publication type:: Correction Notice

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad298

By:

Wu, Tianqi;
Guo, Zhiye;
Cheng, Jianlin

Publication type:

Article

Metapaths: similarity search in heterogeneous knowledge graphs via meta-paths.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad297

By:

Noori, Ayush;
Li, Michelle M;
Tan, Amelia L M;
Zitnik, Marinka

Publication type:

Article

PascalX: a Python library for GWAS gene and pathway enrichment tests.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad296

By:

Krefl, Daniel;
Cammarata, Alessandro Brandulas;
Bergmann, Sven

Publication type:

Article

BUSZ: compressed BUS files.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad295

By:

Einarsson, Pétur Helgi;
Melsted, Páll

Publication type:

Article

pyGOMoDo: GPCRs modeling and docking with python.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad294

By:

Ribeiro, Rui P;
Giorgetti, A

Publication type:

Article

VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad293

By:

Kim, Kijin;
Park, Kyungmin;
Lee, Seonghyeon;
Baek, Seung-Hwan;
Lim, Tae-Hun;
Kim, Jongwoo;
Manavalan, Balachandran;
Song, Jin-Won;
Kim, Won-Keun

Publication type:

Article

ROptimus: a parallel general-purpose adaptive optimization engine.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad292

By:

Johnson, Nicholas A G;
Tamon, Liezel;
Liu, Xin;
Sahakyan, Aleksandr B

Publication type:

Article

A maximum kernel-based association test to detect the pleiotropic genetic effects on multiple phenotypes.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad291

By:

Wang, Jinjuan;
Long, Mingya;
Li, Qizhai

Publication type:

Article

CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad290

By:

Macnee, Marie;
Pérez-Palma, Eduardo;
Brünger, Tobias;
Klöckner, Chiara;
Platzer, Konrad;
Stefanski, Arthur;
Montanucci, Ludovica;
Bayat, Allan;
Radtke, Maximilian;
Collins, Ryan L;
Talkowski, Michael;
Blankenberg, Daniel;
Møller, Rikke S;
Lemke, Johannes R;
Nothnagel, Michael;
May, Patrick;
Lal, Dennis

Publication type:

Article

PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad289

By:

Holstein, Tanja;
Kistner, Franziska;
Martens, Lennart;
Muth, Thilo

Publication type:

Article

twas_sim, a Python-based tool for simulation and power analysis of transcriptome-wide association analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad288

By:

Wang, Xinran;
Lu, Zeyun;
Bhattacharya, Arjun;
Pasaniuc, Bogdan;
Mancuso, Nicholas

Publication type:

Article

DIGGER-Bac: prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad285

By:

Philipp, Niklas;
Brinkmann, Cedric K;
Georg, Jens;
Schindler, Daniel;
Berghoff, Bork A

Publication type:

Article

epiTCR: a highly sensitive predictor for TCR–peptide binding.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad284

By:

Pham, My-Diem Nguyen;
Nguyen, Thanh-Nhan;
Tran, Le Son;
Nguyen, Que-Tran Bui;
Nguyen, Thien-Phuc Hoang;
Pham, Thi Mong Quynh;
Nguyen, Hoai-Nghia;
Giang, Hoa;
Phan, Minh-Duy;
Nguyen, Vy

Publication type:

Article

HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad283

By:

Ji, Yongxin;
Shang, Jiayu;
Tang, Xubo;
Sun, Yanni

Publication type:

Article

DeepMicroGen: a generative adversarial network-based method for longitudinal microbiome data imputation.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad286

By:

Choi, Joung Min;
Ji, Ming;
Watson, Layne T;
Zhang, Liqing

Publication type:

Article

Digital PCR cluster predictor: a universal R-package and shiny app for the automated analysis of multiplex digital PCR data.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad282

By:

Falco, Alfonso De;
Olinger, Christophe M;
Klink, Barbara;
Mittelbronn, Michel;
Stieber, Daniel

Publication type:

Article

pyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad287

By:

Ferchen, Kyle;
Salomonis, Nathan;
Grimes, H Leighton

Publication type:

Article

A functional analysis of omic network embedding spaces reveals key altered functions in cancer.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad281

By:

Doria-Belenguer, Sergio;
Xenos, Alexandros;
Ceddia, Gaia;
Malod-Dognin, Noël;
Pržulj, Nataša

Publication type:

Article

Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad280

By:

Schmidt, Axel;
Röner, Sebastian;
Mai, Karola;
Klinkhammer, Hannah;
Kircher, Martin;
Ludwig, Kerstin U

Publication type:

Article

Kimma: flexible linear mixed effects modeling with kinship covariance for RNA-seq data.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad279

By:

Dill-McFarland, Kimberly A;
Mitchell, Kiana;
Batchu, Sashank;
Segnitz, Richard Max;
Benson, Basilin;
Janczyk, Tomasz;
Cox, Madison S;
Mayanja-Kizza, Harriet;
Boom, William Henry;
Benchek, Penelope;
Stein, Catherine M;
Hawn, Thomas R;
Altman, Matthew C

Publication type:

Article

ICAT: a novel algorithm to robustly identify cell states following perturbations in single-cell transcriptomes.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad278

By:

Hawkins, Dakota Y;
Zuch, Daniel T;
Huth, James;
Rodriguez-Sastre, Nahomie;
McCutcheon, Kelley R;
Glick, Abigail;
Lion, Alexandra T;
Thomas, Christopher F;
Descoteaux, Abigail E;
Johnson, William Evan;
Bradham, Cynthia A

Publication type:

Article

Effective design and inference for cell sorting and sequencing based massively parallel reporter assays.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad277

By:

Gilliot, Pierre-Aurélien;
Gorochowski, Thomas E

Publication type:

Article

spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad276

By:

Boniolo, Fabio;
Hoffmann, Markus;
Roggendorf, Norman;
Tercan, Bahar;
Baumbach, Jan;
Castro, Mauro A A;
Robertson, A Gordon;
Saur, Dieter;
List, Markus

Publication type:

Article

Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad200

By:

Li, Mengbo;
Smyth, Gordon K

Publication type:

Article

matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad197

By:

Davis, Eric S;
Mu, Wancen;
Lee, Stuart;
Dozmorov, Mikhail G;
Love, Michael I;
Phanstiel, Douglas H

Publication type:

Article

EBD: an eye biomarker database.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad194

By:

Zhang, Xueli;
Kong, Lingcong;
Liu, Shunming;
Zhang, Xiayin;
Shang, Xianwen;
Zhu, Zhuoting;
Huang, Yu;
Ma, Shuo;
Jason, Ha;
Kiburg, Katerina V;
Zheng, Chunwen;
Hu, Yunyan;
Li, Cong;
Wu, Guanrong;
Liang, Yingying;
He, Mengxia;
Wang, Yan;
Bai, Xiaohe;
Shi, Danli;
Wang, Wei

Publication type:

Article

Predicting allosteric pockets in protein biological assemblages.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad275

By:

Kumar, Ambuj;
Kaynak, Burak T;
Dorman, Karin S;
Doruker, Pemra;
Jernigan, Robert L

Publication type:

Article

Fixing molecular complexes in BioPAX standards to enrich interactions and detect redundancies using semantic web technologies.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad257

By:

Juigné, Camille;
Dameron, Olivier;
Moreews, François;
Gondret, Florence;
Becker, Emmanuelle

Publication type:

Article

FAS: assessing the similarity between proteins using multi-layered feature architectures.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad226

By:

Dosch, Julian;
Bergmann, Holger;
Tran, Vinh;
Ebersberger, Ingo

Publication type:

Article