Publications

Contributing to Over 180 Scientific Publications with Excellence in Genomics Research.

A total of more than 180 scientific papers have been published with XinLab's participation and co-authorship, among which more than 39 papers were published as major participants. Here is a list of our publications and you can visit our Google Scholar profile for more details.

Publications by Year

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Publications List

Year Title Journal Details
2026 Single-Nucleus Transcriptomic Sequencing Revealed Cellular and Molecular Changes in a Pilocarpine-Induced Epilepsy Rat Model Neuroscience Bulletin
2026 Integrated multi-omics decipher the complex nodule microbiota and distinct Frankiaceae symbiotic traits in wild actinorhizal plants New Phytologist
2025 Chromosome-level genomes of Arctic and Antarctic mosses: Aulacomnium turgidum and Polytrichastrum alpinum Scientific Data
2025 Chromatin dynamics and regulatory drivers of hypoplastic hepatic progenitor cells in partial hepatectomy model Communications Biology
2025 Brain-derived exosomal hemoglobin transfer contributes to neuronal mitochondrial homeostasis under hypoxia eLife
2025 Complete mitogenomes reveal high diversity and recent population dynamics in Antarctic krill BMC Genomics
2025 Single-cell transcriptome atlas of lamprey exploring Natterin- induced white adipose tissue browning Nat Commun
2025 Single-cell multiome reveals root hair-specific responses to salt stress New Phytol
2025 Human gastroids to model regional patterning in early stomach development Nature
2025 Single-cell spatial transcriptomics of tertiary lymphoid organ-like structures in human atherosclerotic plaques Nat Cardiovasc Res
2025 Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing Gigascience
2025 TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation Science Advances
2025 An Australian chickpea pan-genome provides insights into genome organization and offers opportunities for enhancing drought adaptation for crop improvement Plant Biotechnology Journal
2025 A large-scale integrated transcriptomic atlas for soybean organ development Mol Plant
2025 Unveiling the conserved nature of Heliconia chloroplast genomes: insights from the assembly and analysis of four complete chloroplast genomes Frontiers in Plant Science
2025 Transcriptional conservation and evolutionary divergence of cell types across mammalian hypothalamus development Developmental Cell
2025 Genomic and Cis-Regulatory Basis of a Plastic C3-C4 Photosynthesis in Eleocharis Baldwinii Advanced Science
2025 Spatial omics for accelerating plant research and crop improvement Trends in Biotechnology
2025 Single-nucleus and spatial transcriptomics reveal the cell populations of intercalary meristems in bamboo Proceedings of the National Academy of Sciences
2024 Chloroplast genome of Calamus tetradactylus revealed rattan phylogeny BMC Genom Data
2024 The Chromosome-Scale Genome of Chitala ornata Illuminates the Evolution of Early Teleosts Biology (Basel)
2024 Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea Plant Genome
2024 Single-cell mitochondrial sequencing reveals low-frequency mitochondrial mutations in naturally aging mice Aging Cell
2024 Multi-omics landscape and molecular basis of radiation tolerance in a tardigrade Science
2024 Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea Nature genetics
2024 Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies Plant Biotechnology Journal
2024 Celebrating Professor Rajeev K. Varshney's transformative research odyssey from genomics to the field on his induction as Fellow of the Royal Society Plant Biotechnology Journal
2024 Unveiling the conserved nature of Heliconia chloroplast genomes: insights from the assembly and analysis of four complete chloroplast genomes Front Plant Sci
2024 Global marine microbial diversity and its potential in bioprospecting Nature
2023 Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits DNA Res
2023 A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization Nat Commun
2023 Unravelling the genomic features, phylogeny and genetic basis of tooth ontogenesis in Characiformes through analysis of four genomes DNA Research
2023 Symbiont-screener: A reference-free tool to separate host sequences from symbionts for error-prone long reads Frontiers in Marine Science
2023 The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights Cell
2023 Chromosome-scale genomes of commercially important mahoganies, Swietenia macrophylla and Khaya senegalensis Sci Data
2023 Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis) Sci Data
2023 Cellular and molecular mechanisms of fibrosis and resolution in bleomycin-induced pulmonary fibrosis mouse model revealed by spatial transcriptome analysis Heliyon
2023 Inbreeding depression explains killer whale population dynamics Nat Ecol Evol
2023 Whole-genome resequencing deciphers new insight into genetic diversity and signatures of resistance in cultivated cotton Gossypium hirsutum Molecular Biotechnology
2023 Species and condition shape the mutational spectrum in experimentally evolved biofilms mSystems
2023 VT3D: a visualization toolbox for 3D transcriptomic data J Genet Genomics
2023 genomes display massively convergent evolution with other extreme holoparasites and provide novel insights into parasite-host interactions Nature Plants
2023 Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex Cell
2022 Microbiota–muscle/immune interactions in rhesus macaque under simulated microgravity revealed by integrated multi‐omics analysis JCSM Rapid Communications
2022 Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants Frontiers in Plant Science
2022 Genome of New Phytologist
2022 The microbial diversity in industrial effluents makes high-throughput sequencing-based source tracking of the effluents possible Environ Res
2022 GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet Nature Communications
2022 A chickpea genetic variation map based on the sequencing of 3,366 genomes (vol 599, pg 622, 2021) Nature
2022 A chromosome-level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating Mol Ecol Resour
2022 MetaTrass: A high-quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads Imeta
2022 Genomic insights into the genetic signatures of selection and seed trait loci in cultivated peanut Journal of Advanced Research
2022 The Cycas genome and the early evolution of seed plants Nat Plants
2022 The earth BioGenome project 2020: Starting the clock New Phytol
2022 Standards recommendations for the Earth BioGenome Project Proc Natl Acad Sci U S A
2022 Green plant genomes: What we know in an era of rapidly expanding opportunities Proceedings of the National Academy of Sciences of the United States of America
2022 Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars Nat Genet
2022 Evolution of coastal forests based on a full set of mangrove genomes Nat Ecol Evol
2022 Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda Protein Cell
2022 Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement Journal of Advanced Research
2022 Long-read sequencing and de novo assembly of the cynomolgus macaque genome J Genet Genomics
2021 Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution Molecular ecology resources
2021 Analysis of 427 genomes reveals moso bamboo population structure and genetic basis of property traits Nat Commun
2021 The complete chloroplast genome of a shrub species, Smilax glabra (Smilacaceae) from Guangdong, China Mitochondrial DNA B Resour
2021 The genome of the naturally evolved obesity-prone Ossabaw miniature pig iScience
2021 Comparative genomics provides insights into the aquatic adaptations of mammals Proceedings of the National Academy of Sciences of the United States of America
2021 Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios Bioinformatics
2021 Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning Nat Commun
2021 Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce Nat Genet
2021 Metagenomic Analysis Reveals Microbial Community Structure and Metabolic Potential for Nitrogen Acquisition in the Oligotrophic Surface Water of the Indian Ocean Front Microbiol
2021 African lungfish genome sheds light on the vertebrate water-to-land transition Cell
2021 Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos BMC Plant Biol
2021 Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing Scientific Data
2021 A Chromosome-Level Genome of the Agile Gracile Mouse Opossum (Gracilinanus agilis) Genome Biol Evol
2021 Draft Genomes and Comparative Analysis of Seven Mangrove Rhizosphere-Associated Fungi Isolated From Kandelia obovata and Acanthus ilicifolius Front Fungal Biol
2021 Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw, Oplegnathus punctatus Mol Biol Evol
2021 Dynamic cell transition and immune response landscapes of axolotl limb regeneration revealed by single-cell analysis Protein Cell
2021 genome provides insights into the early diversification of angiosperms Nature Communications
2021 SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme BMC Bioinformatics
2021 Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda Science Bulletin
2021 Genomic and Transcriptomic Insight of Giant Sclerotium Formation of Wood-Decay Fungi Front Microbiol
2021 Comparative analysis of clonal evolution among patients with right- and left-sided colon and rectal cancer Iscience
2020 Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity Cell Rep
2020 The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish iScience
2020 An Indo-Pacific Humpback Dolphin Genome Reveals Insights into Chromosome Evolution and the Demography of a Vulnerable Species Iscience
2020 Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments Gigascience
2020 Haplotyping by CRISPR-mediated DNA circularization (CRISPR-hapC) broadens allele-specific gene editing Nucleic Acids Research
2020 TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads Gigascience
2020 Genomes of early-diverging streptophyte algae shed light on plant terrestrialization Nat Plants
2020 The genome of Mekong tiger perch ( Scientific Reports
2020 An atlas of the protein-coding genes in the human, pig, and mouse brain Science
2020 Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea Plant Biotechnol J
2020 Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses Biomed Res Int
2020 Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms BMC Bioinformatics
2020 The draft genome assembly of the critically endangered Nyssa yunnanensis, a plant species with extremely small populations endemic to Yunnan Province, China GigaByte
2020 A Chromosome-Level Genome Assembly of the Anglerfish Lophius litulon Front Genet
2020 The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis Molecular Plant
2020 Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds Msystems
2020 The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Nature ecology & evolution
2020 African Arowana Genome Provides Insights on Ancient Teleost Evolution iScience
2020 Lineage-specific evolution of mangrove plastid genomes Plant Genome
2020 Dissecting the genome of star fruit (Averrhoa carambola L.) Hortic Res
2020 Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K) Gigascience
2020 The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng iScience
2020 Comparative Plastome Analysis of Root- and Stem-Feeding Parasites of Santalales Untangle the Footprints of Feeding Mode and Lifestyle Transitions Genome Biol Evol
2019 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses Nat Biotechnol
2019 Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil Nat Commun
2019 Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs) Sci Rep
2019 Chromosome level comparative analysis of Brassica genomes Plant Mol Biol
2019 Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits Nature Genetics
2019 Draft genome sequence of Gigascience
2019 Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis) Genes (Basel)
2019 A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection Genome Res
2019 Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1 J Fungi (Basel)
2019 The complete plastid genomes of four species from Brassicales Mitochondrial DNA Part B-Resources
2019 Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity Nat Commun
2019 Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden Gigascience
2019 Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida International Journal of Molecular Sciences
2019 A survey of the sperm whale (Physeter catodon) commensal microbiome PeerJ
2019 Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan PLoS One
2019 African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops Planta
2019 A chromosome‐level genome of black rockfish, Sebastes schlegelii, provides insights into the evolution of live birth Molecular ecology resources
2019 Sequencing of the MHC region defines Annals of the Rheumatic Diseases
2019 Chromosomal level reference genome of Molecular Ecology Resources
2019 Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea Plant Biotechnology Journal
2019 Deciphering the Composition and Functional Profile of the Microbial Communities in Chinese Moutai Liquor Starters Front Microbiol
2019 The first chromosome‐level genome for a marine mammal as a resource to study ecology and evolution Molecular ecology resources
2019 New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes BMC Genomics
2019 Natural selection and repeated patterns of molecular evolution following allopatric divergence Elife
2019 Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution Cell
2019 Enhancement of de novo sequencing, assembly and annotation of the Mongolian gerbil genome with transcriptome sequencing and assembly from several different tissues Bmc Genomics
2019 The draft genomes of five agriculturally important African orphan crops Gigascience
2019 A recombination bin-map identified a major QTL for resistance to Tomato Spotted Wilt Virus in peanut (Arachis hypogaea) Sci Rep
2018 The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana) Gigascience
2018 The genetic architecture of floral traits in the woody plant Prunus mume Nat Commun
2018 The structure and function of the global citrus rhizosphere microbiome Nat Commun
2018 Population genomic data reveal genes related to important traits of quail Gigascience
2018 Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus Gigascience
2018 CRISPR-C: circularization of genes and chromosome by CRISPR in human cells Nucleic Acids Res
2018 Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases Gigascience
2018 Fern genomes elucidate land plant evolution and cyanobacterial symbioses Nat Plants
2018 Bph6 encodes an exocyst-localized protein and confers broad resistance to planthoppers in rice Nat Genet
2018 Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis Science
2018 Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression Gigascience
2018 10KP: A phylodiverse genome sequencing plan Gigascience
2018 A western Sahara centre of domestication inferred from pearl millet genomes Nat Ecol Evol
2018 Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia Nat Genet
2018 High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut Plant Biotechnol J
2017 Announcing the Genome Atlas of Bamboo and Rattan (GABR) project: promoting research in evolution and in economically and ecologically beneficial plants Gigascience
2017 Patient iPSC-Derived Neurons for Disease Modeling of Frontotemporal Dementia with Mutation in CHMP2B Stem Cell Reports
2017 Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences PLoS One
2017 A novel Enterovirus 96 circulating in China causes hand, foot, and mouth disease Virus Genes
2017 RED-ML: a novel, effective RNA editing detection method based on machine learning Gigascience
2017 Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments Nat Biotechnol
2017 The high‐quality genome of Brassica napus cultivar ‘ZS11’reveals the introgression history in semi‐winter morphotype The Plant Journal
2017 Comparative Genomics Reveals Two Major Bouts of Gene Retroposition Coinciding with Crucial Periods of Symbiodinium Evolution Genome Biol Evol
2017 Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat Sci Rep
2017 Improvement of peptide identification with considering the abundance of mRNA and peptide BMC Bioinformatics
2017 Deep whole-genome sequencing of 90 Han Chinese genomes Gigascience
2017 Taxonomic structure and functional association of foxtail millet root microbiome Gigascience
2017 The gut microbiome in atherosclerotic cardiovascular disease Nat Commun
2017 A reference human genome dataset of the BGISEQ-500 sequencer Gigascience
2017 Two distinct metacommunities characterize the gut microbiota in Crohn's disease patients Gigascience
2017 Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata Gigascience
2017 The pearl oyster Gigascience
2017 Retinoic acid combined with spermatogonial stem cell conditions facilitate the generation of mouse germ-like cells Biosci Rep
2016 A reference gene catalogue of the pig gut microbiome Nat Microbiol
2016 PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq BMC Bioinformatics
2016 Landscape of genomic diversity and trait discovery in soybean Sci Rep
2016 Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea ( Scientific Reports
2016 Complete Genome Sequence of a Salivirus in Respiratory Specimens from a Child with Adenovirus Infection Genome Announc
2016 The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing Elife
2016 Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax) Nat Genet
2016 Draft genome of the living fossil Ginkgo biloba Gigascience
2016 Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants Plant Journal
2016 First documented case of avian influenza (H5N1) virus infection in a lion Emerg Microbes Infect
2016 The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut Nat Genet
2015 A genome draft of the legless anguid lizard, Ophisaurus gracilis Gigascience
2015 The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis Science
2015 Genome sequence of cultivated Upland cotton ( Nature Biotechnology
2015 The genome sequence of the orchid Phalaenopsis equestris Nature genetics
2014 Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes Nature Communications
2014 Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing Nat Commun
2014 Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation Genome Biol
2014 The sheep genome illuminates biology of the rumen and lipid metabolism Science
2014 Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops Genome Biol
2013 Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations Nature Communications
2013 The sacred lotus genome provides insights into the evolution of flowering plants Plant Journal
2013 A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity Nature Genetics
2013 Analysis of elite variety tag SNPs reveals an important allele in upland rice Nat Commun
2013 Draft genome of the wheat A-genome progenitor Triticum urartu Nature
2013 Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Nature Biotechnology
2013 ReSeqTools: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis Genet Mol Res
2013 Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus) Nat Biotechnol
2013 The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers Plant Cell
2012 Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential Nat Biotechnol
2012 The tomato genome sequence provides insights into fleshy fruit evolution Nature
2012 Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean Plant Cell
2012 Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm Cell
2012 Maize HapMap2 identifies extant variation from a genome in flux Nat Genet
2011 The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line Nat Biotechnol
2011 Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes Nat Biotechnol
2010 Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection Nat Genet

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