Latest posts
Single Cell News
22 Sept, 05:21
Concentrating cell-type-specific transcriptional signatures in bone marrow from interspecies comparisonsLea Wölbert ... Duncan Odom generated a comprehensive scRNA-seq dataset spanning bone marrow hematopoietic progenitor and niche compartments from young and old females of four mouse species: Mus musculus strain C57BL/6J, Mus musculus castaneus, Mus spretus, and Mus caroli.Highlights ⚡️Bone marrow single-cell RNA sequencing atlas across four mouse species ⚡️Defining signature genes with conserved cell-type specificity and expression levels ⚡️Signatures resolve cell types across species, tissues, ages, and technologies ⚡️Bone marrow hematopoietic and niche signatures capture canonical and novel markers.#singlecellnews
Single Cell News
21 Sept, 07:33
iPscDB: a comprehensive platform for plant single-cell transcriptomic data integration and analysisPeng Lu ... Peijian Cao presented integrated Plant single-cell Database (iPscDB), an integrated and multifunctional platform that facilitates the integration and analysis of plant single-cell data.Key points ✔️4 688 428 cells, 288 139 curated cell markers, 946 experiments, and 38 plant species ✔️A Marker Confidence Level scheme ✔️A user-friendly online analysis pipeline ✔️Cross-species gene expression, electronic Single-Cell Pictograph, and developmental trajectory ✔️Accessible here#singlecellnews
Single Cell News
21 Sept, 03:28
⚡5 days to create solutions for precision medicine We invite you to take part in the Hackatomics 2026! 📍Goal: to bring together researchers, bioinformaticians, and AI specialists to develop innovative approaches in precision medicine based on single-cellSingle Cell News
18 Sept, 07:26
Tahoe-100M: Mapping drug-induced molecular phenotypes at single-cell resolutionJesse Zhang ... Johnny Yu presented Tahoe-100M, a giga-scale single-cell perturbation atlas comprising 100 million transcriptomes from 50 diverse cancer cell lines treated with 1,100 drug-dose conditionsHighlights ⚡️Tahoe-100M: 100 million single-cell transcriptomes from 50 cancer cell lines ⚡️“Mosaic” pooling profiles ∼1,100 drug-dose conditions at low batch effect ⚡️Single-cell phenotypes classify mechanisms and reveal off-target drug activity ⚡️Open release enables predictive AI modeling of drug-induced cell state.#singlecellnews
Single Cell News
17 Sept, 07:27
A single-cell multi-omic atlas of the human pancreas reveals potential for cellular plasticity across development, health, and diseaseElisabetta Mereu ... Roland Eils presented a single-cell multiomics atlas of the human pancreas, profiling over four million cells and nuclei from donors across fetal development, adult homeostasis, and type 2 diabetes.Highlights 🔸Multi-omic atlas profiles >4 million human pancreas cells across 57 donors 🔸Rare plastic centroacinar-like cells (pCACs) share fetal multipotency programs 🔸Beta cells show HNF1A-high/low chromatin states altered in type 2 diabetes 🔸Spatial transcriptomics profiling reveals endocrine heterogeneity outside islets.#singlecellnews
Single Cell News
16 Sept, 07:36
Ten quick tips for spatial transcriptomics analysisNagomi Kurogi ... Koki Tsuyuzaki presented practical guidance for spatial transcriptomics (ST) from platform selection and data understanding to biological interpretation, multi-omics integration, and recognition of technical limitations.Key points 📍Whether ST suits a given biological question 📍How to select a platform aligned with study objectives 📍How to understand and process ST data 📍Which software tools to employ for analysis and visualization 📍How to interpret spatial patterns in biological context 📍How to integrate complementary modalities such as scRNA seq and spatial proteomics.#singlecellnews
Single Cell News
15 Sept, 06:35
Spatial mapping of pediatric brain tumors across diagnoses and relapsesJavier Escudero Morlanes ... Linda Kvastad presented a spatial transcriptomic atlas of 19 pediatric brain tumor patients spanning nine major and rare diagnoses, including seven relapses, revealing their spatial cellular and molecular organization.Key points ✔️ 2-4 recurrent spatial archetypes across 11 biological themes ✔️ Developmental lineage patterns ✔️ Relapse-associated putative clones ✔️ An interactive viewer on pediatric brain tumor ecosystems, relapse biology, and therapeutic strategies.#singlecellnews
Single Cell News
14 Sept, 14:33
Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnoverMaria Kastriti … Igor Adameyko generated single-cell and spatial transcriptomic atlases of adult human and mouse adrenal glands, leveraging single-cell-resolution spatial data and a rare clonal mosaic case for lineage inference.Key points 🔹Identifying age-associated zona glomerulosa (ZG) cell states with direct cortisol synthesis capacity and sex-specific differences in inferred cholesterol balance in humans 🔹Conserved aldosterone-producing ZG but notable divergence in zona fasciculata markers, absence of zona reticularis homologs in mice and differential SHH–WNT4 signaling in proliferating cells 🔹Uncovering human WT1− capsule-to-ZG transition and vascular smooth muscle cell-to-steroidogenic transitions supported by mosaic lineage evidence 🔹 Revealing dispersed
Single Cell News
11 Sept, 11:11edited
📍The TOP 10 papers came out during ASCA vacation:🔹León-Periñán et al. Ultrafast and reference-free sequence discovery in single-cell data🔹Birk et al. Multi-scale modeling of human tissues from spatial transcriptomics with TERRA🔹Cohen et al. Whole-transcriptome-scale isoform-resolved spatial imaging of single cells in tissues🔹Sedlazeck et al. Integrated map of somatic mosaicism across human tissues in 25 individuals🔹Lian et al. Spatially resolved single-cell atlas reveals the macroevolutionary trajectory of animal hearts🔹Perik-Zavodskaia et al. CoexpressDeconvolve enables reference-free single-cell-resolution deconvolution from spot-based spatial transcriptomics🔹Zhou et al. Human body single-cell atlas of three-dimensional genome organization and DNA methylation🔹Quake et al. Tabula Sapiens 2.0: A comprehensive transcriptomic atlas of human cell types🔹Qiu et al.Single Cell News
10 Sept, 05:00
⚡5 days to create solutions for precision medicineWe invite you to take part in the Hackatomics 2026!📍Goal: to bring together researchers, bioinformaticians, and AI specialists to develop innovative approaches in precision medicine based on single-cell data.📍Dates: October 10–14, 2026 📍Registration deadline: September 22, 2026📍Venue: Research Institute of Molecular and Cellular Medicine + Faculty of Artificial Intelligence, RUDN University (Moscow, Podolskoye Sh., 8)✨The prize fund is 450,000 RUB➡Learn more: https://hackatomics.rudn.ru/
Single Cell News
8 Sept, 14:31
⚡️We’re back from break and ready to go — #singlecellnews is on! ⚡And we have good news: 🔸The ASCA CONGRESS 2026 program with talks selected from abstracts is already available here🔸Registration for the ASCA CONGRESS 2026 is extended for non‑speaking attendees.#ASCAinfo
Single Cell News pinned «Dear colleagues! ⚡️ We’re taking a short summer breather to recharge. Hope your summer is filled with sunshine, adventure, and plenty of fun. We’ll be back in September - can’t wait to catch up then! 🏖️ All the best, ASCA Team #ASCAinfo»
13 Jul, 12:53
Single Cell News
13 Jul, 12:53
Dear colleagues! ⚡️We’re taking a short summer breather to recharge.Hope your summer is filled with sunshine, adventure, and plenty of fun. We’ll be back in September - can’t wait to catch up then! 🏖️All the best, ASCA Team#ASCAinfoSingle Cell News
10 Jul, 13:16
A comprehensive epidermal map from a poplar single-cell shoot atlas reveals new trichome-specific genesAnita Giabardo ... C. Robin Buell presented a single-cell RNA-seq atlas of the poplar 717 shoot, including apical meristem, primary and secondary stems, and three stages of leaf development.Key points 🔹159,000 cells, 40 transcriptionally distinct clusters, and 7 major cell types 🔹Focus on the epidermis which constitutes >15% of cells in the shoot atlas 🔹Epidermal cell subclusters corresponding to developmental stages, spatial location, and specialized cell types 🔹Novel trichome markers 🔹A tool to support cell type-targeted-metabolic engineering ➡️ Available here#singlecellnews
Single Cell News
8 Jul, 04:20
HLiCA: An integrated cell atlas of the healthy human liverRachel Edgar ... Gary Bader presented the Human Liver Cell Atlas (HLiCA), an integrated reference of non-disease liver cells assembled from eight datasets across six research centers, encompassing more than 525,000 cells from 110 donors.Key points 🔸 Expert-curated cell annotations 🔸 Classifying cells into six lineages and 47 distinct types 🔸 Evaluating the range of ancestral backgrounds represented in the atlas 🔸 Identification of previously unrecognized liver cell types, including NRXN1+ stromal cells localized to periportal regions 🔸 Differential expression of drug metabolism genes in hepatocytes between sexes and mucus-production genes in cholangiocytes, varied with age.#singlecellnews
Single Cell News
7 Jul, 11:05
Pubertal maturation and chemotherapy-associated disruption of the pediatric ovary revealed by multimodal single-cell profilingLoren Méar … Pauliina Damdimopoulou analyzed ovarian tissue from 16 patients undergoing fertility preservation (aged 1-16 years) and 11 adult controls (aged 22-32 years) using scRNA-seq, spatial transcriptomics, and multiplex immunostaining.Key points ✔️ Extensive stromal remodeling across puberty, accompanied by vascular and neural maturation and a shift in germline transcriptional programs ✔️ Distinct tissue organization and follicular niche composition between children and adults ✔️ Broader transcriptional alterations in chemotherapy than puberty, including ECM disruption and reduced intercellular communication ✔️ Challenging the direct extrapolation of adult ovarian tissue cryopreservation protocols to prepubertal patients#singlecellnews
Single Cell News
6 Jul, 12:24
⚡Dear Colleagues,📍 Don't miss the registration for the ASCA CONGRESS 2026, which is open until July 24.The program includes 11 sections with talks by key researchers and technology developers in the field of single-cell and spatial analysis.📍 Online access is also available.➡️ More details: https://ascanet.org/events/asca-congress-2026/Sincerely, Organizing Committee
Single Cell News
3 Jul, 04:40
Four-dimensional molecular mapping from a spatial snapshot reveals the dynamics of hair follicle organogenesisSoichiro Asami ... Reza Kalhor developed 3D DNase-Enhanced Expression Profiling (3DEEP), a tissue-clearing approach that removes genomic DNA to extend spatial transcriptomic profiling hundreds of microns into intact tissues.Highlights 🔸 Spatial pseudotiming reconstructs hair follicle organogenesis in space and time 🔸 Stratification of stem cell compartment along the hair axis precedes bulb formation 🔸 Two cavities emerge between three structures and merge to form the hair canal 🔸 Nude follicles show developmental delay and instability before hair shaft defects.#singlecellnews
Single Cell News
2 Jul, 11:23
SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell typesCarlos Anerillas ... Myriam Gorospe profiled the transcriptomes and proteomes in 14 different primary human cell types undergoing over 30 senescence paradigms to create a senescence catalog “SenCat”.Key points 🔷 Senescent cells lack universal markers but share metabolic and damage-response pathways implicated in tissue repair 🔷 Machine-learning-refined SenCat signatures enable senescence scoring and identification across multiple human and mouse datasets.#singlecellnews
Single Cell News
1 Jul, 04:15
scEPS integrates genetic and single-cell disease atlas data to provide granular mechanistic insights into complex human diseasesLuli Zou ... Huwenbo Shi developed scEPS, an integrative approach for identifying disease-associated cell neighborhoods, where the expression of disease GWAS genes explains more variance in the disease phenotype than randomly selected mean expression matched control genes.Key points ⚡️Capture of the genetic covariance between gene expression and diseases, mitigating the effect of reverse causation and prioritizing cell populations mediating the effects of GWAS genes ⚡️Recapitulation of known and uncovered novel disease-associated cell populations, identifying more significant associations than a CNA-based approach and scDRS ⚡️Detection of different cell populations, contrasting clinical diagnoses vs. their polygenic risk scores, revealing distinct biology
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