Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 6

Results: 50

DDN3.0: determining significant rewiring of biological network structure with differential dependency networks.

Published in:

2024

By:

Fu, Yi;
Lu, Yingzhou;
Wang, Yizhi;
Zhang, Bai;
Zhang, Zhen;
Yu, Guoqiang;
Liu, Chunyu;
Clarke, Robert;
Herrington, David M;
Wang, Yue

Publication type:

Case Study

snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae377

By:

Vertacnik, Kim L;
Vernygora, Oksana V;
Dupuis, Julian R

Publication type:

Article

Correction to: For antibody sequence generative modeling, mixture models may be all you need.

Published in:: 2024
Publication type:: Correction Notice

Ragas: integration and enhanced visualization for single cell subcluster analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae366

By:

Balaji, Uthra;
Rodríguez-Alcázar, Juan;
Balasubramanian, Preetha;
Smitherman, Cynthia;
Baisch, Jeanine;
Pascual, Virginia;
Gu, Jinghua

Publication type:

Article

Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae379

By:

Gualdi, Francesco;
Oliva, Baldomero;
Piñero, Janet

Publication type:

Article

Interpretable deep learning in single-cell omics.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae374

By:

Wagle, Manoj M;
Long, Siqu;
Chen, Carissa;
Liu, Chunlei;
Yang, Pengyi

Publication type:

Article

MetaboReport: from metabolomics data analysis to comprehensive reporting.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae373

By:

Dong, Yonghui;
Malitsky, Sergey

Publication type:

Article

GenoFig: a user-friendly application for the visualization and comparison of genomic regions.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae372

By:

Branger, Maxime;
Leclercq, Sébastien O

Publication type:

Article

scCross: efficient search for rare subpopulations across multiple single-cell samples.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae371

By:

Gerniers, Alexander;
Nijssen, Siegfried;
Dupont, Pierre

Publication type:

Article

RNA m6A detection using raw current signals and basecalling errors from Nanopore direct RNA sequencing reads.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae375

By:

Ni, Peng;
Xu, Jinrui;
Zhong, Zeyu;
Luo, Feng;
Wang, Jianxin

Publication type:

Article

RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae369

By:

Chacko, Jonathan;
Ozadam, Hakan;
Cenik, Can

Publication type:

Article

Supervised learning of enhancer–promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae367

By:

Barth, Dylan;
Van, Richard;
Cardwell, Jonathan;
Han, Mira V

Publication type:

Article

biotextgraph: graphical summarization of functional similarities from textual information.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae357

By:

Sato, Noriaki;
Zhang, Yao-zhong;
Gu, Zuguang;
Imoto, Seiya

Publication type:

Article

GammaGateR: semi-automated marker gating for single-cell multiplexed imaging.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae356

By:

Xiong, Jiangmei;
Kaur, Harsimran;
Heiser, Cody N;
McKinley, Eliot T;
Roland, Joseph T;
Coffey, Robert J;
Shrubsole, Martha J;
Wrobel, Julia;
Ma, Siyuan;
Lau, Ken S;
Vandekar, Simon

Publication type:

Article

RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae370

By:

Bittrich, Sebastian;
Segura, Joan;
Duarte, Jose M;
Burley, Stephen K;
Rose, Yana

Publication type:

Article

MCDHGN: heterogeneous network-based cancer driver gene prediction and interpretability analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae362

By:

Wang, Lexiang;
Zhou, Jingli;
Wang, Xuan;
Wang, Yadong;
Li, Junyi

Publication type:

Article

Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae361

By:

Jiang, Yueyu;
McDonald, Daniel;
Perry, Daniela;
Knight, Rob;
Mirarab, Siavash

Publication type:

Article

Subtype-MGTP: a cancer subtype identification framework based on multi-omics translation.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae360

By:

Xie, Minzhu;
Kuang, Yabin;
Song, Mengyun;
Bao, Ergude

Publication type:

Article

OLB-AC: toward optimizing ligand bioactivities through deep graph learning and activity cliffs.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae365

By:

Yin, Yueming;
Hu, Haifeng;
Yang, Jitao;
Ye, Chun;
Goh, Wilson Wen Bin;
Kong, Adams Wai-Kin;
Wu, Jiansheng

Publication type:

Article

HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae364

By:

Xu, Xiaopeng;
Xu, Chencheng;
He, Wenjia;
Wei, Lesong;
Li, Haoyang;
Zhou, Juexiao;
Zhang, Ruochi;
Wang, Yu;
Xiong, Yuanpeng;
Gao, Xin

Publication type:

Article

Figeno: multi-region genomic figures with long-read support.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae354

By:

Sollier, Etienne;
Heilmann, Jessica;
Gerhauser, Clarissa;
Scherer, Michael;
Plass, Christoph;
Lutsik, Pavlo

Publication type:

Article

KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae353

By:

Matsumoto, Nicholas;
Moran, Jay;
Choi, Hyunjun;
Hernandez, Miguel E;
Venkatesan, Mythreye;
Wang, Paul;
Moore, Jason H

Publication type:

Article

Mariner: explore the Hi-Cs.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae352

By:

Davis, Eric S;
Parker, Sarah M;
Kramer, Nicole E;
Flores, J P;
Kiran, Manjari;
Phanstiel, Douglas H

Publication type:

Article

bnglViz: online visualization of rule-based models.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae351

By:

Liguori-Bills, Noah;
Blinov, Michael L

Publication type:

Article

Bigtools: a high-performance BigWig and BigBed library in Rust.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae350

By:

Huey, Jack D;
Abdennur, Nezar

Publication type:

Article

tstrait: a quantitative trait simulator for ancestral recombination graphs.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae334

By:

Tagami, Daiki;
Bisschop, Gertjan;
Kelleher, Jerome

Publication type:

Article

FMCA-DTI: a fragment-oriented method based on a multihead cross attention mechanism to improve drug–target interaction prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae347

By:

Zhang, Qi;
Zuo, Le;
Ren, Ying;
Wang, Siyuan;
Wang, Wenfa;
Ma, Lerong;
Zhang, Jing;
Xia, Bisheng

Publication type:

Article

CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae345

By:

Lin, Teng-Yu;
Chung, Szu-Chi

Publication type:

Article

SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae344

By:

Ju, Nianqiao;
Liu, Jiawei;
He, Qixin

Publication type:

Article

HE2Gene: image-to-RNA translation via multi-task learning for spatial transcriptomics data.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae343

By:

Chen, Xingjian;
Lin, Jiecong;
Wang, Yuchen;
Zhang, Weitong;
Xie, Weidun;
Zheng, Zetian;
Wong, Ka-Chun

Publication type:

Article

Drug–target interaction predictions with multi-view similarity network fusion strategy and deep interactive attention mechanism.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae346

By:

Song, Wei;
Xu, Lewen;
Han, Chenguang;
Tian, Zhen;
Zou, Quan

Publication type:

Article

Improving the performance and interpretability on medical datasets using graphical ensemble feature selection.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae341

By:

Battistella, Enzo;
Ghiassian, Dina;
Barabási, Albert-László

Publication type:

Article

SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae340

By:

Gjoni, Ketrin;
Pollard, Katherine S

Publication type:

Article

Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae339

By:

Duan, Ziheng;
Riffle, Dylan;
Li, Ren;
Liu, Junhao;
Min, Martin Renqiang;
Zhang, Jing

Publication type:

Article

SWGTS—a platform for stream-based host DNA depletion.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae332

By:

Spohr, Philipp;
Ried, Max;
Kühle, Laura;
Dilthey, Alexander

Publication type:

Article

ReactomeGSA: new features to simplify public data reuse.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae338

By:

Grentner, Alexander;
Ragueneau, Eliot;
Gong, Chuqiao;
Prinz, Adrian;
Gansberger, Sabina;
Oyarzun, Inigo;
Hermjakob, Henning;
Griss, Johannes

Publication type:

Article

spillR: spillover compensation in mass cytometry data.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae337

By:

Guazzini, Marco;
Reisach, Alexander G;
Weichwald, Sebastian;
Seiler, Christof

Publication type:

Article

Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae336

By:

Chen, Siang;
Wang, Hao;
Zhang, Dongdong;
Chen, Runsheng;
Luo, Jianjun

Publication type:

Article

MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae335

By:

Faizi, Marjan;
Fellers, Ryan T;
Lu, Dan;
Drown, Bryon S;
Jambhekar, Ashwini;
Lahav, Galit;
Kelleher, Neil L;
Gunawardena, Jeremy

Publication type:

Article

Flexible parsing, interpretation, and editing of technical sequences with splitcode.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae331

By:

Sullivan, Delaney K;
Pachter, Lior

Publication type:

Article

MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae329

By:

Chim, Ho Yeung;
Elofsson, Arne

Publication type:

Article

SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae328

By:

Urhan, Aysun;
Cosma, Bianca-Maria;
Earl, Ashlee M;
Manson, Abigail L;
Abeel, Thomas

Publication type:

Article

Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy's outcome for HIV-1.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae327

By:

Teodoro, Giulia Di;
Pirkl, Martin;
Incardona, Francesca;
Vicenti, Ilaria;
Sönnerborg, Anders;
Kaiser, Rolf;
Palagi, Laura;
Zazzi, Maurizio;
Lengauer, Thomas

Publication type:

Article

Computing linkage disequilibrium aware genome embeddings using autoencoders.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae326

By:

Taş, Gizem;
Westerdijk, Timo;
Postma, Eric;
Consortium, Project MinE ALS GWAS;
Veldink, Jan H;
Schönhuth, Alexander;
Balvert, Marleen

Publication type:

Article

TARO: tree-aggregated factor regression for microbiome data integration.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae321

By:

Mishra, Aditya K;
Mahmud, Iqbal;
Lorenzi, Philip L;
Jenq, Robert R;
Wargo, Jennifer A;
Ajami, Nadim J;
Peterson, Christine B

Publication type:

Article

DEAttentionDTA: protein–ligand binding affinity prediction based on dynamic embedding and self-attention.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae319

By:

Chen, Xiying;
Huang, Jinsha;
Shen, Tianqiao;
Zhang, Houjin;
Xu, Li;
Yang, Min;
Xie, Xiaoman;
Yan, Yunjun;
Yan, Jinyong

Publication type:

Article

gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae318

By:

Rodriguez-Flores, Carlos J;
Barrena, Naroa;
Olaverri-Mendizabal, Danel;
Ochoa, Idoia;
Valcárcel, Luis V;
Planes, Francisco J

Publication type:

Article

MolDy: molecular dynamics simulation made easy.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae313

By:

Khan, Mohd Imran;
Pathania, Sheetal;
Al-Rabia, Mohammed W;
Ethayathulla, Abdul S;
Khan, Mohammad Imran;
Allemailem, Khaled S;
Azam, Mohd;
Hariprasad, Gururao;
Imran, Mohammad Azhar

Publication type:

Article

PathwayNexus: a tool for interactive metabolic data analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae310

By:

Eberhard, Philipp;
Kern, Martin;
Aichem, Michael;
Borlinghaus, Hanna;
Klein, Karsten;
Delp, Johannes;
Suciu, Ilinca;
Moser, Benjamin;
Dietrich, Daniel;
Leist, Marcel;
Schreiber, Falk

Publication type:

Article

AmplificationTimeR: an R package for timing sequential amplification events.

Published in:

Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae281

By:

Jakobsdottir, G Maria;
Dentro, Stefan C;
Bristow, Robert G;
Wedge, David C

Publication type:

Article