Shiping Liu
A5017549166- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Irrigation Practices and Water Management
- Genomics and Phylogenetic Studies
- Cell Image Analysis Techniques
- Pancreatic and Hepatic Oncology Research
- Bone health and osteoporosis research
- Bone Metabolism and Diseases
- Immune cells in cancer
- Hepatitis B Virus Studies
- Genetic diversity and population structure
- Cancer Immunotherapy and Biomarkers
- Immune Cell Function and Interaction
- Neuroinflammation and Neurodegeneration Mechanisms
- Cancer-related molecular mechanisms research
- Chromosomal and Genetic Variations
- Silk-based biomaterials and applications
- Bone health and treatments
- Soil erosion and sediment transport
- RNA Research and Splicing
- RNA modifications and cancer
- Robot Manipulation and Learning
- Insect Resistance and Genetics
- Silkworms and Sericulture Research
- Photonic and Optical Devices
BGI Research
2023-2025
BGI Group (China)
2016-2025
Second Xiangya Hospital of Central South University
2004-2025
Central South University
2010-2025
Chongqing University of Science and Technology
2024
Affiliated Hospital of North Sichuan Medical College
2016-2024
North Sichuan Medical University
2024
Renmin Hospital of Wuhan University
2022-2024
Huazhong University of Science and Technology
2016-2024
Chinese Academy of Sciences
2006-2024
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis 48 species representing all orders Neoaves using phylogenomic methods created to handle data. We recovered highly resolved tree that confirms previously controversial sister or close relationships. identified first divergence in Neoaves, two groups named Passerea and Columbea, independent lineages diverse convergently evolved land water bird species. Among Passerea, infer common ancestor core...
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The genome is principally characterized by its constrained size, which predominantly arose because lineage-specific erosion repetitive elements, large segmental deletions, gene loss. Avian furthermore show a remarkably high degree evolutionary stasis at levels...
Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view current methodologies precludes their systematic application analyze relatively large three-dimensional mid- late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays in situ RNA capture create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied...
Robin Gasser and his colleagues report the whole-genome sequence of Schistosoma haematobium. They include comparisons to genome sequences S. mansoni japonicum, two other species that cause schistosomiasis in humans. Schistosomiasis is a neglected tropical disease caused by blood flukes (genus Schistosoma; schistosomes) affecting 200 million people worldwide1. No vaccines are available, treatment relies on one drug, praziquantel2. haematobium has come into spotlight as major urogenital...
The Taming of the Silkworm Silkworms, Bombyx mori , represent one few domesticated insects, having been over 10,000 years ago. Xia et al. (p. 433 published online 27 August) sequenced 29 domestic and 11 wild silkworm lines identified genes that were most likely to be selected during domestication. These those enhance silk production, reproduction, growth. Furthermore, silkworms probably only once from a large progenitor population, rather than on multiple occasions, as has observed for other animals.
Abstract Hepatitis B virus (HBV) can integrate into the human genome, contributing to genomic instability and hepatocarcinogenesis. Here by conducting high-throughput viral integration detection RNA sequencing, we identify 4,225 HBV events in tumour adjacent non-tumour samples from 426 patients with HCC. We show that is prone rare fragile sites functional regions including CpG islands. observe a distinct pattern preferential of between tissues. insertional are significantly enriched...
The genome of the common roundworm Ascaris suum, a major parasite in many parts world, has now been sequenced. Analyses reveal genes that encode peptidases linked to penetration and degradation host tissues, as well molecules likely modulate or evade immune responses. availability this sequence should contribute towards development new therapeutic interventions against ascariasis other nematode infections. Parasitic diseases have devastating, long-term impact on human health, welfare food...
Integrative analysis of multi-omics layers at single cell level is critical for accurate dissection cell-to-cell variation within certain populations. Here we report scCAT-seq, a technique simultaneously assaying chromatin accessibility and the transcriptome same cell. We show that combined signatures enable construction regulatory relationships between cis-regulatory elements target genes single-cell resolution, providing new dimension features helps direct discovery patterns specific to...
Patterns of genetic and genomic variance are informative in inferring population history for human, model species endangered populations. Here the genome sequence wild-born African cheetahs reveals extreme depletion SNV incidence, density, SNVs coding genes, MHC class I II mitochondrial DNA SNVs. Cheetah genomes on average 95 % homozygous compared to outbred domestic cat (24.08 homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian (62.63 Tasmanian devil, dog other mammalian...
Understanding the complex functions of plant leaves requires a thorough characterization discrete cell features. Although single-cell gene expression profiling technologies have been developed, their application in characterizing subtypes has not achieved yet. Here, we present scStereo-seq (single-cell spatial enhanced resolution omics sequencing) that enabled us to show bona fide transcriptome profiles Arabidopsis leaves. Subtle but significant transcriptomic differences between upper and...
Little is known about the transcriptomic plasticity and adaptive mechanisms of circulating tumor cells (CTCs) during hematogeneous dissemination. Here we interrogate transcriptome 113 single CTCs from 4 different vascular sites, including hepatic vein (HV), peripheral artery (PA), (PV) portal (PoV) using single-cell full-length RNA sequencing in hepatocellular carcinoma (HCC) patients. We reveal that transcriptional dynamics were associated with stress response, cell cycle immune-evasion...
Elucidating the cellular organization of cerebral cortex is critical for understanding brain structure and function. Using large-scale single-nucleus RNA sequencing spatial transcriptomic analysis 143 macaque cortical regions, we obtained a comprehensive atlas 264 transcriptome-defined cell types mapped their distribution across entire cortex. We characterized layer region preferences glutamatergic, GABAergic, non-neuronal types, as well regional differences in cell-type composition...
A major challenge in understanding vertebrate embryogenesis is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within hierarchy cell-fate decisions. Here, we employed Stereo-seq to profile 91 zebrafish embryo sections covering six critical time points during first 24 h development, obtaining a total 152,977 spots at resolution 10 × 15 μm3 (close cellular size) with spatial coordinates. Meanwhile, identified modules and co-varying genes for...
Abstract Dissecting and understanding the cancer ecosystem, especially that around tumor margins, which have strong implications for cell infiltration invasion, are essential exploring mechanisms of metastasis developing effective new treatments. Using a novel border scanning digitization model enabled by nanoscale resolution-SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq), we identified 500 µm-wide zone centered in patients with liver cancer, referred to as “the invasive zone”. We...
Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that leads to incongruent phenotypic variation. Here, performed phylogenomic analyses show the South American monito del monte is sister of all Australian marsupials, although over 31% its genome closer...
Five sediment cores from a north−south transect of Lake Michigan were collected using box deployed the RV Guardian and submersible (Johnson Sea Link II, Seward Johnson). The sediments, analyzed for PAHs (n = 28) 210Pb to obtain accumulation rates inventories PAHs, used determine role atmosphere in contaminant loading Michigan. sediments increased dramatically around 1900, reached plateau 1930−1975, decreased slightly recent time. Surface ∑PAHs 17 parent), corrected focusing with 210Pb,...
Significance We provide a de novo genome of the Tibetan frog, Nanorana parkeri , and conduct series comparisons with other vertebrates. Approximately one-half consists transposable elements (TEs). The frequencies distributional patterns TEs differ considerably between Xenopus only amphibian for which has been sequenced. genomes these two frogs exhibit substantial homologous synteny blocks rare interchromosomal intrachromosomal rearrangements. also identify 11 Mb amphibian-specific conserved...
Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach the common vampire bat (Desmodus rotundus), one of only three obligate blood-feeding (sanguivorous) mammals, study evolution its complex dietary adaptation. Specifically, we assembled high-quality reference genome (scaffold N50 = 26.9 Mb, contig 36.6 kb) gut metagenome, compared them against those insectivorous, frugivorous carnivorous bats. Our analyses...