{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T17:37:35Z","timestamp":1785951455047,"version":"3.56.0"},"reference-count":92,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2021,2,3]],"date-time":"2021-02-03T00:00:00Z","timestamp":1612310400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Nature Scientific Foundation of China","doi-asserted-by":"crossref","award":["62061034"],"award-info":[{"award-number":["62061034"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Nature Scientific Foundation of China","doi-asserted-by":"crossref","award":["61861036"],"award-info":[{"award-number":["61861036"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Nature Scientific Foundation of China","doi-asserted-by":"crossref","award":["61702290"],"award-info":[{"award-number":["61702290"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region","award":["NJYT-18-B01"],"award-info":[{"award-number":["NJYT-18-B01"]}]},{"name":"Fund for Excellent Young Scholars of Inner Mongolia","award":["2017JQ04"],"award-info":[{"award-number":["2017JQ04"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Hematopoietic stem cells (HSCs) give rise to all blood cells and play a vital role throughout the whole lifespan through their pluripotency and self-renewal properties. Accurately identifying the stages of early HSCs is extremely important, as it may open up new prospects for extracorporeal blood research. Existing experimental techniques for identifying the early stages of HSCs development are time-consuming and expensive. Machine learning has shown its excellence in massive single-cell data processing and it is desirable to develop related computational models as good complements to experimental techniques.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we presented a novel predictor called eHSCPr specifically for predicting the early stages of HSCs development. To reveal the distinct genes at each developmental stage of HSCs, we compared F-score with three state-of-art differential gene selection methods (limma, DESeq2, edgeR) and evaluated their performance. F-score captured the more critical surface markers of endothelial cells and hematopoietic cells, and the area under receiver operating characteristic curve (ROC) value was 0.987. Based on SVM, the 10-fold cross-validation accuracy of eHSCpr in the independent dataset and the training dataset reached 94.84% and 94.19%, respectively. Importantly, we performed transcription analysis on the F-score gene set, which indeed further enriched the signal markers of HSCs development stages. eHSCPr can be a powerful tool for predicting early stages of HSCs development, facilitating hypothesis-driven experimental design and providing crucial clues for the in vitro blood regeneration studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/bioinfor.imu.edu.cn\/ehscpr.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab071","type":"journal-article","created":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T18:40:40Z","timestamp":1611859240000},"page":"2157-2164","source":"Crossref","is-referenced-by-count":33,"title":["eHSCPr discriminating the cell identity involved in endothelial to hematopoietic transition"],"prefix":"10.1093","volume":"37","author":[{"given":"Hao","family":"Wang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengfei","family":"Liang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Zheng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"ChunShen","family":"Long","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"HanShuang","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6065-7835","authenticated-orcid":false,"given":"Yongchun","family":"Zuo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,2,3]]},"reference":[{"key":"2023061310431512400_btab071-B1","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1002\/1098-1004(200009)16:3<183::AID-HUMU1>3.0.CO;2-L","article-title":"Activating and inactivating mutations in the human GNAS1 gene","volume":"16","author":"Aldred","year":"2000","journal-title":"Hum. Mutat"},{"key":"2023061310431512400_btab071-B2","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1038\/nprot.2013.099","article-title":"Count-based differential expression analysis of RNA sequencing data using R and Bioconductor","volume":"8","author":"Anders","year":"2013","journal-title":"Nat. Protoc"},{"key":"2023061310431512400_btab071-B3","doi-asserted-by":"crossref","first-page":"4666","DOI":"10.1016\/j.ygeno.2020.08.016","article-title":"Prediction of antioxidant proteins using hybrid feature representation method and random forest","volume":"112","author":"Ao","year":"2020","journal-title":"Genomics"},{"key":"2023061310431512400_btab071-B4","doi-asserted-by":"crossref","first-page":"2517","DOI":"10.1038\/s41467-018-04893-3","article-title":"Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta","volume":"9","author":"Baron","year":"2018","journal-title":"Nat. Commun"},{"key":"2023061310431512400_btab071-B5","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1038\/nrc.2017.58","article-title":"Unravelling biology and shifting paradigms in cancer with single-cell sequencing","volume":"17","author":"Baslan","year":"2017","journal-title":"Nat. Rev. Cancer"},{"key":"2023061310431512400_btab071-B6","doi-asserted-by":"crossref","first-page":"1427","DOI":"10.1182\/blood.V97.5.1427","article-title":"Vascular endothelial cell growth factor is an autocrine promoter of abnormal localized immature myeloid precursors and leukemia progenitor formation in myelodysplastic syndromes","volume":"97","author":"Bellamy","year":"2001","journal-title":"Blood"},{"key":"2023061310431512400_btab071-B7","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nature08738","article-title":"Haematopoietic stem cells derive directly from aortic endothelium during development","volume":"464","author":"Bertrand","year":"2010","journal-title":"Nature"},{"key":"2023061310431512400_btab071-B8","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. Biotechnol"},{"key":"2023061310431512400_btab071-B9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/1961189.1961199","article-title":"Libsvm","volume":"2","author":"Chang","year":"2011","journal-title":"ACM Trans. Intell. Syst. Techno"},{"key":"2023061310431512400_btab071-B10","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1038\/nature07619","article-title":"Runx1 is required for the endothelial to haematopoietic cell transition but not thereafter","volume":"457","author":"Chen","year":"2009","journal-title":"Nature"},{"key":"2023061310431512400_btab071-B11","doi-asserted-by":"crossref","first-page":"445","DOI":"10.2174\/1574893615666200106115421","article-title":"A sequence-segment neighbor encoding schema for protein hotspot residue prediction","volume":"15","author":"Chen","year":"2020","journal-title":"Curr. Bioinf"},{"key":"2023061310431512400_btab071-B12","first-page":"785","author":"Chen","year":"2016"},{"key":"2023061310431512400_btab071-B13","doi-asserted-by":"crossref","first-page":"3518","DOI":"10.1093\/bioinformatics\/btx479","article-title":"iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties","volume":"33","author":"Chen","year":"2017","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B14","first-page":"315","volume-title":"Combining SVMs with Various Feature Selection Strategies","author":"Chen","year":"2006"},{"key":"2023061310431512400_btab071-B15","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/sj.cdd.4401698","article-title":"Enforced expression of KDR receptor promotes proliferation, survival and megakaryocytic differentiation of TF1 progenitor cell line","volume":"13","author":"Coppola","year":"2006","journal-title":"Cell Death Differ"},{"key":"2023061310431512400_btab071-B16","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1093\/bioinformatics\/bty943","article-title":"Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique","volume":"35","author":"Dao","year":"2019","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B17","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.3390\/molecules22071057","article-title":"Recent advances in conotoxin classification by using machine learning methods","volume":"22","author":"Dao","year":"2017","journal-title":"Molecules"},{"key":"2023061310431512400_btab071-B18","first-page":"7697","article-title":"Machine learning classifies cancer","volume":"555","author":"Derek","year":"2018","journal-title":"Nature"},{"key":"2023061310431512400_btab071-B19","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/s41556-020-0512-1","article-title":"Differentiation of transplanted haematopoietic stem cells tracked by single-cell transcriptomic analysis","volume":"22","author":"Dong","year":"2020","journal-title":"Nature Cell Biol"},{"key":"2023061310431512400_btab071-B20","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1016\/j.stem.2018.04.015","article-title":"Blood development: hematopoietic stem cell dependence and independence","volume":"22","author":"Dzierzak","year":"2018","journal-title":"Cell Stem Cell"},{"key":"2023061310431512400_btab071-B21","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1016\/j.stem.2016.10.019","article-title":"DNA methylation dynamics of human hematopoietic stem cell differentiation","volume":"19","author":"Farlik","year":"2016","journal-title":"Cell Stem Cell"},{"key":"2023061310431512400_btab071-B22","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1093\/bioinformatics\/bty827","article-title":"iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators","volume":"35","author":"Feng","year":"2019","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B23","doi-asserted-by":"crossref","first-page":"3028","DOI":"10.1093\/bioinformatics\/btaa131","article-title":"StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency","volume":"36","author":"Fu","year":"2020","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B24","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1007\/s00109-002-0397-4","article-title":"The role of VEGF in normal and neoplastic hematopoiesis","volume":"81","author":"Gerber","year":"2003","journal-title":"J. Mol. Med"},{"key":"2023061310431512400_btab071-B25","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1016\/j.devcel.2016.01.024","article-title":"Dynamic gene regulatory networks drive hematopoietic specification and differentiation","volume":"36","author":"Goode","year":"2016","journal-title":"Dev. Cell"},{"key":"2023061310431512400_btab071-B26","doi-asserted-by":"crossref","first-page":"4415","DOI":"10.1093\/bioinformatics\/btaa293","article-title":"scVAE: variational auto-encoders for single-cell gene expression data","volume":"36","author":"Gronbech","year":"2020","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B27","doi-asserted-by":"crossref","first-page":"147","DOI":"10.2174\/1574893611666160727160757","article-title":"ExomeHMM: a hidden Markov model for detecting copy number variation using whole-exome sequencing data","volume":"12","author":"Guo","year":"2017","journal-title":"Curr. Bioinf"},{"key":"2023061310431512400_btab071-B28","doi-asserted-by":"crossref","first-page":"767","DOI":"10.2174\/1574893615666200120103050","article-title":"A deep convolutional neural network to improve the prediction of protein secondary structure","volume":"15","author":"Guo","year":"2020","journal-title":"Curr. Bioinf"},{"key":"2023061310431512400_btab071-B29","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.1093\/bioinformatics\/btu083","article-title":"iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition","volume":"30","author":"Guo","year":"2014","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B30","doi-asserted-by":"crossref","first-page":"359","DOI":"10.2174\/1574893614666191017094331","article-title":"Application of a deep matrix factorization model on integrated gene expression data","volume":"15","author":"Hao","year":"2020","journal-title":"Curr. Bioinf"},{"key":"2023061310431512400_btab071-B31","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/bty668","article-title":"4mCPred: machine learning methods for DNA N-4-methylcytosine sites prediction","volume":"35","author":"He","year":"2019","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B32","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/s41422-020-0300-2","article-title":"Embryonic endothelial evolution towards first hematopoietic stem cells revealed by single-cell transcriptomic and functional analyses","volume":"30","author":"Hou","year":"2020","journal-title":"Cell Res"},{"key":"2023061310431512400_btab071-B33","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.neucom.2018.07.068","article-title":"F-score feature selection based Bayesian reconstruction of visual image from human brain activity","volume":"316","author":"Huang","year":"2018","journal-title":"Neurocomputing"},{"key":"2023061310431512400_btab071-B34","doi-asserted-by":"crossref","first-page":"2323","DOI":"10.1242\/dev.134866","article-title":"Human haematopoietic stem cell development: from the embryo to the dish","volume":"144","author":"Ivanovs","year":"2017","journal-title":"Development"},{"key":"2023061310431512400_btab071-B35","doi-asserted-by":"crossref","first-page":"864","DOI":"10.1093\/bioinformatics\/btu746","article-title":"GASS: identifying enzyme active sites with genetic algorithms","volume":"31","author":"Izidoro","year":"2015","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B36","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1161\/CIRCULATIONAHA.114.013395","article-title":"Molecular and genetic analyses of collagen type IV mutant mouse models of spontaneous intracerebral hemorrhage identify mechanisms for stroke prevention","volume":"131","author":"Jeanne","year":"2015","journal-title":"Circulation"},{"key":"2023061310431512400_btab071-B37","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.ajhg.2011.11.022","article-title":"COL4A2 mutations impair COL4A1 and COL4A2 secretion and cause hemorrhagic stroke","volume":"90","author":"Jeanne","year":"2012","journal-title":"Am. J. Hum. Genet"},{"key":"2023061310431512400_btab071-B38","doi-asserted-by":"crossref","first-page":"725","DOI":"10.2174\/1574893614666191114123453","article-title":"Prediction of Neddylation sites using the composition of k-spaced amino acid pairs and fuzzy SVM","volume":"15","author":"Ju","year":"2020","journal-title":"Curr. Bioinf"},{"key":"2023061310431512400_btab071-B39","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.stem.2018.04.014","article-title":"Single-cell transcriptomics meets lineage tracing","volume":"23","author":"Kester","year":"2018","journal-title":"Cell Stem Cell"},{"key":"2023061310431512400_btab071-B40","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nmeth.4236","article-title":"SC3: consensus clustering of single-cell RNA-seq data","volume":"14","author":"Kiselev","year":"2017","journal-title":"Nat. Methods"},{"key":"2023061310431512400_btab071-B41","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1186\/gb-2014-15-2-r29","article-title":"voom: precision weights unlock linear model analysis tools for RNA-seq read counts","volume":"15","author":"Law","year":"2014","journal-title":"Genome Biol"},{"key":"2023061310431512400_btab071-B42","doi-asserted-by":"crossref","first-page":"246","DOI":"10.3389\/fgene.2018.00246","article-title":"Identification and analysis of blood gene expression signature for osteoarthritis with advanced feature selection methods","volume":"9","author":"Li","year":"2018","journal-title":"Front. Genet"},{"key":"2023061310431512400_btab071-B43","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.stem.2012.07.004","article-title":"Mouse embryonic head as a site for hematopoietic stem cell development","volume":"11","author":"Li","year":"2012","journal-title":"Cell Stem Cell"},{"key":"2023061310431512400_btab071-B44","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1016\/j.jgg.2013.09.001","article-title":"Generation of hematopoietic stem cells from purified embryonic endothelial cells by a simple and efficient strategy","volume":"40","author":"Li","year":"2013","journal-title":"J. Genet. Genomics"},{"key":"2023061310431512400_btab071-B45","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.omtn.2020.02.004","article-title":"Machine learning of single-cell transcriptome highly identifies mRNA signature by comparing F-score selection with DGE analysis","volume":"20","author":"Liang","year":"2020","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2023061310431512400_btab071-B46","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.omtn.2020.02.004","article-title":"Machine learning of single-cell transcriptome highly identifies mRNA signature by comparing F-score selection with DGE analysis","volume":"20","author":"Liang","year":"2020","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2023061310431512400_btab071-B47","doi-asserted-by":"crossref","first-page":"57","DOI":"10.2174\/1574893611666160609081155","article-title":"Cancer diagnosis through IsomiR expression with machine learning method","volume":"13","author":"Liao","year":"2018","journal-title":"Curr. Bioinf"},{"key":"2023061310431512400_btab071-B48","doi-asserted-by":"crossref","first-page":"4318","DOI":"10.1038\/emboj.2012.275","article-title":"RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis","volume":"31","author":"Lichtinger","year":"2012","journal-title":"EMBO J"},{"key":"2023061310431512400_btab071-B49","doi-asserted-by":"crossref","first-page":"dev149419","DOI":"10.1242\/dev.149419","article-title":"Regulation of RUNX1 dosage is crucial for efficient blood formation from hemogenic endothelium","volume":"145","author":"Lie-A-Ling","year":"2018","journal-title":"Development"},{"key":"2023061310431512400_btab071-B50","doi-asserted-by":"crossref","first-page":"7739","DOI":"10.1038\/ncomms8739","article-title":"Repression of arterial genes in hemogenic endothelium is sufficient for haematopoietic fate acquisition","volume":"6","author":"Lizama","year":"2015","journal-title":"Nat. Commun"},{"key":"2023061310431512400_btab071-B51","doi-asserted-by":"crossref","first-page":"300","DOI":"10.2174\/1574893614666190902154332","article-title":"Predicting protein phosphorylation sites based on deep learning","volume":"15","author":"Long","year":"2020","journal-title":"Curr. Bioinf"},{"key":"2023061310431512400_btab071-B52","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023061310431512400_btab071-B53","doi-asserted-by":"crossref","first-page":"100991","DOI":"10.1016\/j.isci.2020.100991","article-title":"iDNA-MS: an integrated computational tool for detecting DNA modification sites in multiple genomes","volume":"23","author":"Lv","year":"2020","journal-title":"iScience"},{"key":"2023061310431512400_btab071-B54","doi-asserted-by":"crossref","first-page":"164","DOI":"10.3389\/fgene.2016.00164","article-title":"In Papyro comparison of TMM (edgeR), RLE (DESeq2), and MRN normalization methods for a simple two-conditions-without-replicates RNA-Seq experimental design","volume":"7","author":"Maza","year":"2016","journal-title":"Front. Genet"},{"key":"2023061310431512400_btab071-B55","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/978-1-4939-0512-6_3","article-title":"edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology","volume":"1150","author":"Nikolayeva","year":"2014","journal-title":"Methods Mol. Biol"},{"key":"2023061310431512400_btab071-B56","author":"Paszke","year":"2019"},{"key":"2023061310431512400_btab071-B57","doi-asserted-by":"crossref","first-page":"10367","DOI":"10.1016\/j.eswa.2009.01.041","article-title":"A new feature selection method on classification of medical datasets: kernel F-score feature selection","volume":"36","author":"Polat","year":"2009","journal-title":"Expert Syst. Appl"},{"key":"2023061310431512400_btab071-B58","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1038\/s41581-018-0021-7","article-title":"Single-cell RNA sequencing for the study of development, physiology and disease","volume":"14","author":"Potter","year":"2018","journal-title":"Nat. Rev. Nephrol"},{"key":"2023061310431512400_btab071-B59","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023061310431512400_btab071-B60","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B61","doi-asserted-by":"crossref","first-page":"2881","DOI":"10.1093\/bioinformatics\/btm453","article-title":"Moderated statistical tests for assessing differences in tag abundance","volume":"23","author":"Robinson","year":"2007","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B62","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1093\/biostatistics\/kxm030","article-title":"Small-sample estimation of negative binomial dispersion, with applications to SAGE data","volume":"9","author":"Robinson","year":"2007","journal-title":"Biostatistics"},{"key":"2023061310431512400_btab071-B63","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1084\/jem.20102419","article-title":"Hierarchical organization and early hematopoietic specification of the developing HSC lineage in the AGM region","volume":"208","author":"Rybtsov","year":"2011","journal-title":"J. Exp. Med"},{"key":"2023061310431512400_btab071-B64","doi-asserted-by":"crossref","first-page":"3883","DOI":"10.1182\/blood-2003-05-1634","article-title":"Internal and external autocrine VEGF\/KDR loops regulate survival of subsets of acute leukemia through distinct signaling pathways","volume":"103","author":"Santos","year":"2004","journal-title":"Blood"},{"key":"2023061310431512400_btab071-B65","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1016\/S0092-8674(00)80283-4","article-title":"A requirement for Flk1 in primitive and definitive hematopoiesis and vasculogenesis","volume":"89","author":"Shalaby","year":"1997","journal-title":"Cell"},{"key":"2023061310431512400_btab071-B66","first-page":"431","author":"Smyth","year":"2005"},{"key":"2023061310431512400_btab071-B68","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Swami","year":"2013","journal-title":"J. Mach. Learn. Res"},{"key":"2023061310431512400_btab071-B69","doi-asserted-by":"crossref","first-page":"2924","DOI":"10.1038\/ncomms3924","article-title":"Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level","volume":"4","author":"Swiers","year":"2013","journal-title":"Nat. Commun"},{"key":"2023061310431512400_btab071-B70","doi-asserted-by":"crossref","first-page":"204","DOI":"10.2174\/1574893614666190723120716","article-title":"MD-LBP: an efficient computational model for protein subcellular localization from HeLa cell lines using SVM","volume":"15","author":"Tahir","year":"2020","journal-title":"Curr. Bioinf"},{"key":"2023061310431512400_btab071-B71","doi-asserted-by":"crossref","first-page":"3327","DOI":"10.1093\/bioinformatics\/btaa143","article-title":"DNA4mC-LIP: a linear integration method to identify N4-methylcytosine site in multiple species","volume":"36","author":"Tang","year":"2020","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B72","doi-asserted-by":"crossref","first-page":"S63","DOI":"10.1016\/j.exphem.2014.07.242","article-title":"In vitro human embryonic stem cell hematopoiesis mimics MYB independent yolk sac hematopoiesis","volume":"42","author":"Vanhee","year":"2014","journal-title":"Exp. Hematol"},{"key":"2023061310431512400_btab071-B73","doi-asserted-by":"crossref","first-page":"5501","DOI":"10.1111\/jcmm.15205","article-title":"Characterization of the relationship between FLI1 and immune infiltrate level in tumour immune microenvironment for breast cancer","volume":"24","author":"Wang","year":"2020","journal-title":"J. Cell Mol. Med"},{"key":"2023061310431512400_btab071-B74","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1002\/ana.22682","article-title":"COL4A1 mutations in patients with sporadic late-onset intracerebral hemorrhage","volume":"71","author":"Weng","year":"2012","journal-title":"Ann. Neurol"},{"key":"2023061310431512400_btab071-B75","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"2023061310431512400_btab071-B76","article-title":"idenPC-MIIP: identify protein complexes from weighted PPI networks using mutual important interacting partner relation","author":"Wu","year":"2020","journal-title":"Brief. Bioinf"},{"key":"2023061310431512400_btab071-B77","doi-asserted-by":"crossref","first-page":"1472","DOI":"10.1038\/nm.3733","article-title":"Age-related mutations associated with clonal hematopoietic expansion and malignancies","volume":"20","author":"Xie","year":"2014","journal-title":"Nat. Med"},{"key":"2023061310431512400_btab071-B78","article-title":"Single-cell transcriptomic landscape of human blood cells","author":"Xie","year":"2020","journal-title":"Natl. Sci. Rev"},{"key":"2023061310431512400_btab071-B79","doi-asserted-by":"crossref","first-page":"4922","DOI":"10.1093\/bioinformatics\/btz358","article-title":"iRNAD: a computational tool for identifying D modification sites in RNA sequence","volume":"35","author":"Xu","year":"2019","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B80","doi-asserted-by":"crossref","first-page":"3651","DOI":"10.1242\/dev.051094","article-title":"Three-dimensional cartography of hematopoietic clusters in the vasculature of whole mouse embryos","volume":"137","author":"Yokomizo","year":"2010","journal-title":"Development"},{"key":"2023061310431512400_btab071-B81","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: An R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"key":"2023061310431512400_btab071-B82","doi-asserted-by":"crossref","first-page":"106227","DOI":"10.1016\/j.bpc.2019.106227","article-title":"Identifying DNase I hypersensitive sites using multi-features fusion and F-score features selection via Chou's 5-steps rule \u2013 ScienceDirect","volume":"253","author":"Yunyun","year":"2019","journal-title":"Biophys. Chem"},{"key":"2023061310431512400_btab071-B83","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/s41422-019-0228-6","article-title":"Tracing the first hematopoietic stem cell generation in human embryo by single-cell RNA sequencing","volume":"29","author":"Zeng","year":"2019","journal-title":"Cell Res"},{"key":"2023061310431512400_btab071-B84","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1093\/bioinformatics\/btz016","article-title":"MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters","volume":"35","author":"Zhang","year":"2019","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B85","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bib\/bbz177","article-title":"Design powerful predictor for mRNA subcellular location prediction in Homo sapiens","volume":"22","author":"Zhang","year":"2021","journal-title":"Brief. Bioinf"},{"key":"2023061310431512400_btab071-B86","article-title":"RaacLogo: a new sequence logo generator by using reduced amino acid clusters","author":"Zheng","year":"2020","journal-title":"Brief Bioinf"},{"key":"2023061310431512400_btab071-B87","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/nature17997","article-title":"Tracing haematopoietic stem cell formation at single-cell resolution","volume":"533","author":"Zhou","year":"2016","journal-title":"Nature"},{"key":"2023061310431512400_btab071-B88","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.stem.2018.11.023","article-title":"Combined single-cell profiling of lncRNAs and functional screening reveals that H19 is pivotal for embryonic hematopoietic stem cell development","volume":"24","author":"Zhou","year":"2019","journal-title":"Cell Stem Cell"},{"key":"2023061310431512400_btab071-B89","doi-asserted-by":"crossref","first-page":"368","DOI":"10.2174\/1574893614666191105155713","article-title":"ConvsPPIS: identifying protein\u2013protein interaction sites by an ensemble convolutional neural network with feature graph","volume":"15","author":"Zhu","year":"2020","journal-title":"Curr. Bioinf"},{"key":"2023061310431512400_btab071-B90","article-title":"Developmental trajectory of pre-hematopoietic stem cell formation from endothelium","author":"Zhu","year":"2019","journal-title":"Blood"},{"key":"2023061310431512400_btab071-B91","doi-asserted-by":"crossref","first-page":"314","DOI":"10.2174\/1574893614666181120095038","article-title":"Analysis of single-cell RNA-seq data by clustering approaches","volume":"14","author":"Zhu","year":"2019","journal-title":"Curr. Bioinform"},{"key":"2023061310431512400_btab071-B92","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1093\/bioinformatics\/btw564","article-title":"PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition","volume":"33","author":"Zuo","year":"2017","journal-title":"Bioinformatics"},{"key":"2023061310431512400_btab071-B93","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.ab.2014.04.032","article-title":"Predicting peroxidase subcellular location by hybridizing different descriptors of Chou' pseudo amino acid patterns","volume":"458","author":"Zuo","year":"2014","journal-title":"Anal. Biochem"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab071\/36297334\/btab071.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/15\/2157\/50579057\/btab071.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/15\/2157\/50579057\/btab071.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T10:44:42Z","timestamp":1686653082000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/15\/2157\/6126801"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,2,3]]},"references-count":92,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2021,8,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab071","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,8,1]]},"published":{"date-parts":[[2021,2,3]]}}}