Works matching IS 14712105 AND DT 2023

Results: 494

IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05624-2

By:

Dorey-Robinson, Daniel;
Maccari, Giuseppe;
Hammond, John A.

Publication type:

Article

ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05599-0

By:

Paklao, Thummarat;
Suratanee, Apichat;
Plaimas, Kitiporn

Publication type:

Article

PWSC: a novel clustering method based on polynomial weight-adjusted sparse clustering for sparse biomedical data and its application in cancer subtyping.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05595-4

By:

Zhang, Xiaomeng;
Zhang, Hongtao;
Wang, Zhihao;
Ma, Xiaofei;
Luo, Jiancheng;
Zhu, Yingying

Publication type:

Article

Predicting potential microbe-disease associations based on auto-encoder and graph convolution network.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05611-7

By:

Lu, Shanghui;
Liang, Yong;
Li, Le;
Miao, Rui;
Liao, Shuilin;
Zou, Yongfu;
Yang, Chengjun;
Ouyang, Dong

Publication type:

Article

Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC/LC-MS-based sample preparation.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05598-1

By:

Lu, Miaoshan;
Jiang, Hengxuan;
Wang, Ruimin;
An, Shaowei;
Wang, Jiawei;
Yu, Changbin

Publication type:

Article

PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05613-5

By:

Faltejsková, Kateřina;
Vondrášek, Jiří

Publication type:

Article

Performance analysis of conventional and AI-based variant callers using short and long reads.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05596-3

By:

Abdelwahab, Omar;
Belzile, François;
Torkamaneh, Davoud

Publication type:

Article

PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05606-4

By:

Marrama, Daniel;
Chronister, William D.;
Westernberg, Luise;
Vita, Randi;
Koşaloğlu-Yalçın, Zeynep;
Sette, Alessandro;
Nielsen, Morten;
Greenbaum, Jason A.;
Peters, Bjoern

Publication type:

Article

Advancing drug–target interaction prediction: a comprehensive graph-based approach integrating knowledge graph embedding and ProtBert pretraining.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05593-6

By:

Djeddi, Warith Eddine;
Hermi, Khalil;
Ben Yahia, Sadok;
Diallo, Gayo

Publication type:

Article

BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05601-9

By:

Zheng, Xiangwen;
Wang, Xuanze;
Luo, Xiaowei;
Tong, Fan;
Zhao, Dongsheng

Publication type:

Article

Machine learning-based donor permission extraction from informed consent documents.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05568-7

By:

Zhang, Meng;
Sankaranarayanapillai, Madhuri;
Du, Jingcheng;
Xiang, Yang;
Manion, Frank J.;
Harris, Marcelline R.;
Stansbury, Cooper;
Pham, Huy Anh;
Tao, Cui

Publication type:

Article

Subtyping irritable bowel syndrome using cluster analysis: a systematic review.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05567-8

By:

Zarei, Diana;
Saghazadeh, Amene;
Rezaei, Nima

Publication type:

Article

GPDRP: a multimodal framework for drug response prediction with graph transformer.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05618-0

By:

Yang, Yingke;
Li, Peiluan

Publication type:

Article

TCGAplot: an R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05615-3

By:

Liao, Chenqi;
Wang, Xiong

Publication type:

Article

A compressed large language model embedding dataset of ICD 10 CM descriptions.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05597-2

By:

Kane, Michael J.;
King, Casey;
Esserman, Denise;
Latham, Nancy K.;
Greene, Erich J.;
Ganz, David A.

Publication type:

Article

scInterpreter: a knowledge-regularized generative model for interpretably integrating scRNA-seq data.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05579-4

By:

Guo, Zhen-Hao;
Wu, Yan;
Wang, Siguo;
Zhang, Qinhu;
Shi, Jin-Ming;
Wang, Yan-Bin;
Chen, Zhan-Heng

Publication type:

Article

A novel and innovative cancer classification framework through a consecutive utilization of hybrid feature selection.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05605-5

By:

Mahto, Rajul;
Ahmed, Saboor Uddin;
Rahman, Rizwan ur;
Aziz, Rabia Musheer;
Roy, Priyanka;
Mallik, Saurav;
Li, Aimin;
Shah, Mohd Asif

Publication type:

Article

Cellstitch: 3D cellular anisotropic image segmentation via optimal transport.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05608-2

By:

Liu, Yining;
Jin, Yinuo;
Azizi, Elham;
Blumberg, Andrew J.

Publication type:

Article

DL-PPI: a method on prediction of sequenced protein–protein interaction based on deep learning.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05594-5

By:

Wu, Jiahui;
Liu, Bo;
Zhang, Jidong;
Wang, Zhihan;
Li, Jianqiang

Publication type:

Article

Twnbiome: a public database of the healthy Taiwanese gut microbiome.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05585-6

By:

Chattopadhyay, Amrita;
Lee, Chien-Yueh;
Lee, Ya-Chin;
Liu, Chiang-Lin;
Chen, Hsin-Kuang;
Li, Yung-Hua;
Lai, Liang-Chuan;
Tsai, Mong-Hsun;
Ni, Yen-Hsuan;
Chiu, Han-Mo;
Lu, Tzu-Pin;
Chuang, Eric Y.

Publication type:

Article

primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05609-1

By:

Limberis, Jason D.;
Metcalfe, John Z.

Publication type:

Article

PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science, and its application on natural product (NP) occurrence database processing.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05588-3

By:

Cho, Min Hyung;
Cho, Kwang-Hwi;
No, Kyoung Tai

Publication type:

Article

Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05529-0

By:

Yang, Youpeng;
Zeng, Qiuhong;
Liu, Gaotong;
Zheng, Shiyao;
Luo, Tianyang;
Guo, Yibin;
Tang, Jia;
Huang, Yi

Publication type:

Article

PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05589-2

By:

Hu, Xiaojun;
Hurtado-Gonzales, Oscar P.;
Adhikari, Bishwo N.;
French-Monar, Ronald D.;
Malapi, Martha;
Foster, Joseph A.;
McFarland, Clint D.

Publication type:

Article

ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05602-8

By:

Richardson, Mary O.;
Eddy, Sean R.

Publication type:

Article

A score-based method of immune status evaluation for healthy individuals with complete blood cell counts.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05603-7

By:

Zhang, Min;
Zhao, Chengkui;
Cheng, Qi;
Xu, Jiayu;
Xu, Nan;
Yu, Lei;
Feng, Weixing

Publication type:

Article

An oscillating reaction network with an exact closed form solution in the time domain.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05600-w

By:

Hellerstein, Joseph

Publication type:

Article

Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05604-6

By:

Li, Ying;
Zhang, Xiao-Ou;
Liu, Yan;
Lu, Aiping

Publication type:

Article

Rendering protein mutation movies with MutAmore.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05610-8

By:

Weissenow, Konstantin;
Rost, Burkhard

Publication type:

Article

CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05477-9

By:

Ma, Lina;
Zhang, Sitao;
Liang, Qi;
Huang, Wenting;
Wang, Hui;
Pan, Emily;
Xu, Ping;
Zhang, Shuguang;
Tao, Fei;
Tang, Jin;
Qing, Rui

Publication type:

Article

AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05577-6

By:

Shin, Incheol;
Kang, Keumseok;
Kim, Juseong;
Sel, Sanghun;
Choi, Jeonghoon;
Lee, Jae-Wook;
Kang, Ho Young;
Song, Giltae

Publication type:

Article

Detection for melanoma skin cancer through ACCF, BPPF, and CLF techniques with machine learning approach.

Published in:

BMC Bioinformatics, 2023, p. 1, doi. 10.1186/s12859-023-05584-7

By:

Kavitha, P.;
Ayyappan, G.;
Jayagopal, Prabhu;
Mathivanan, Sandeep Kumar;
Mallik, Saurav;
Al-Rasheed, Amal;
Alqahtani, Mohammed S.;
Soufiene, Ben Othman

Publication type:

Article

PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05566-9

By:

Sun, Hui;
Zheng, Yingfeng;
Xie, Haonan;
Ma, Huidong;
Liu, Xiaoguang;
Wang, Gang

Publication type:

Article

Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05574-9

By:

Li, Dong-Xu;
Zhou, Peng;
Zhao, Bo-Wei;
Su, Xiao-Rui;
Li, Guo-Dong;
Zhang, Jun;
Hu, Peng-Wei;
Hu, Lun

Publication type:

Article

pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05578-5

By:

Behdenna, Abdelkader;
Colange, Maximilien;
Haziza, Julien;
Gema, Aryo;
Appé, Guillaume;
Azencott, Chloé-Agathe;
Nordor, Akpéli

Publication type:

Article

Machine learning-based approaches for ubiquitination site prediction in human proteins.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05581-w

By:

Pourmirzaei, Mahdi;
Ramazi, Shahin;
Esmaili, Farzaneh;
Shojaeilangari, Seyedehsamaneh;
Allahvardi, Abdollah

Publication type:

Article

G-bic: generating synthetic benchmarks for biclustering.

Published in:

BMC Bioinformatics, 2023, p. 1, doi. 10.1186/s12859-023-05587-4

By:

Castanho, Eduardo N.;
Lobo, João P.;
Henriques, Rui;
Madeira, Sara C.

Publication type:

Article

Detection of continuous hierarchical heterogeneity by single-cell surface antigen analysis in the prognosis evaluation of acute myeloid leukaemia.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05561-0

By:

Shao, Nan;
Ren, Chenshuo;
Hu, Tianyuan;
Wang, Dianbing;
Zhu, Xiaofan;
Li, Min;
Cheng, Tao;
Zhang, Yingchi;
Zhang, Xian-En

Publication type:

Article

Protein–protein interaction site prediction by model ensembling with hybrid feature and self-attention.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05592-7

By:

Cong, Hanhan;
Liu, Hong;
Cao, Yi;
Liang, Cheng;
Chen, Yuehui

Publication type:

Article

HostNet: improved sequence representation in deep neural networks for virus-host prediction.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05582-9

By:

Ming, Zhaoyan;
Chen, Xiangjun;
Wang, Shunlong;
Liu, Hong;
Yuan, Zhiming;
Wu, Minghui;
Xia, Han

Publication type:

Article

A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05583-8

By:

Zhao, He;
Liu, Guixia;
Cao, Xintian

Publication type:

Article

Completing a genomic characterisation of microscopic tumour samples with copy number.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05576-7

By:

Nulsen, Joel;
Hussain, Nosheen;
Al-Deka, Aws;
Yap, Jason;
Uddin, Khalil;
Yau, Christopher;
Ahmed, Ahmed Ashour

Publication type:

Article

Transformer-based tool recommendation system in Galaxy.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05573-w

By:

Kumar, Anup;
Grüning, Björn;
Backofen, Rolf

Publication type:

Article

scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05563-y

By:

Nale, Valentina;
Chiodi, Alice;
Di Nanni, Noemi;
Cifola, Ingrid;
Moscatelli, Marco;
Cocola, Cinzia;
Gnocchi, Matteo;
Piscitelli, Eleonora;
Sula, Ada;
Zucchi, Ileana;
Reinbold, Rolland;
Milanesi, Luciano;
Mezzelani, Alessandra;
Pelucchi, Paride;
Mosca, Ettore

Publication type:

Article

Predicting anticancer synergistic drug combinations based on multi-task learning.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05524-5

By:

Chen, Danyi;
Wang, Xiaowen;
Zhu, Hongming;
Jiang, Yizhi;
Li, Yulong;
Liu, Qi;
Liu, Qin

Publication type:

Article

Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05506-7

By:

Pettersen, Jakob P.;
Castillo, Sandra;
Jouhten, Paula;
Almaas, Eivind

Publication type:

Article

A cell abundance analysis based on efficient PAM clustering for a better understanding of the dynamics of endometrial remodelling.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05569-6

By:

Domingo, Juan;
Kutsyr-Kolesnyk, Oleksandra;
Leon, Teresa;
Perez-Moraga, Raul;
Ayala, Guillermo;
Roson, Beatriz

Publication type:

Article

Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05553-0

By:

Roth, Cullen;
Venu, Vrinda;
Job, Vanessa;
Lubbers, Nicholas;
Sanbonmatsu, Karissa Y.;
Steadman, Christina R.;
Starkenburg, Shawn R.

Publication type:

Article

Relating mutational signature exposures to clinical data in cancers via signeR 2.0.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05550-3

By:

Drummond, Rodrigo D.;
Defelicibus, Alexandre;
Meyenberg, Mathilde;
Valieris, Renan;
Dias-Neto, Emmanuel;
Rosales, Rafael A.;
da Silva, Israel Tojal

Publication type:

Article

Image-centric compression of protein structures improves space savings.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05570-z

By:

Staniscia, Luke;
Yu, Yun William

Publication type:

Article