Featured
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| Open AccessA village in a dish model system for population-scale hiPSC studies
Village cultures, where multiple stem cell lines are cultured in a single dish, provide an elegant solution for population-scale studies. Here, authors show the utility of village models – showing that expression heterogeneity is largely a result of line-specific effects and not village cultures.
- Drew R. Neavin
- , Angela M. Steinmann
- & Joseph E. Powell
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Article
| Open AccessPIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing
Tracking protein-RNA interaction across cell types is challenging. Here, Ruan et al develop a dual-deaminase method called PIE-Seq, where protein targets are marked by both C-to-U and A-to-I RNA base editors, and apply it to 25 human RNA-binding proteins.
- Xiangbin Ruan
- , Kaining Hu
- & Xiaochang Zhang
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Article
| Open AccessMoS2 nanopore identifies single amino acids with sub-1 Dalton resolution
Protein sequencing is one of the key aims of the nanopore field. Working toward this goal, here the authors report the direct identification of single amino acids in MoS2 nanopores with sub-1 Dalton resolution, as well as the discrimination of the amino acid isomers and amino acid phosphorylation.
- Fushi Wang
- , Chunxiao Zhao
- & Jiandong Feng
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Article
| Open AccessSingle cell transcriptomics clarifies the basophil differentiation trajectory and identifies pre-basophils upstream of mature basophils
Single cell sequencing can be used to better characterize immune cell progenitors. Here the authors characterize CLEC12Ahi pre-basophils downstream of pre-basophil and mast cell progenitors (pre-BMPs) but upstream of mature basophils and this population includes basophil progenitors (BaPs).
- Kensuke Miyake
- , Junya Ito
- & Hajime Karasuyama
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Article
| Open AccessCellular population dynamics shape the route to human pluripotency
The contribution of cell-extrinsic factors during cellular reprogramming to human induced pluripotent stem cells has long been overlooked. Here, the authors show functional protein communication between reprogramming intermediates and the re-shaping of a permissive extracellular environment.
- Francesco Panariello
- , Onelia Gagliano
- & Nicola Elvassore
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| Open AccessHigh-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq
Formalin-fixed paraffin-embedded (FFPE) tissues constitute a vast and valuable patient material bank, but single nucleus RNAseq using such tissues is challenging. Here the authors develop a droplet-based method called snRandom-seq for high-throughput and sensitive single nucleus RNA-seq of FFPE samples.
- Ziye Xu
- , Tianyu Zhang
- & Yongcheng Wang
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Article
| Open AccessHigh-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing
Long-read single-cell RNA isoform sequencing can elucidate the intricate landscape of alternative RNA splicing in individual cells, but it suffers from a low read throughput. Here, the authors develop circular consensus sequencing methods to allow high-throughput and high-accuracy single-cell RNA isoform sequencing.
- Zhuo-Xing Shi
- , Zhi-Chao Chen
- & Yi-Zhi Liu
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| Open AccessSingle-cell analysis reveals inflammatory interactions driving macular degeneration
Single-nucleus RNA-seq was used to profile 11 retinas with varying stages of age-related macular degeneration and 6 control retinas. The authors identified shared glial states across neurodegeneration, indicating that the retina provides a human system for investigating therapeutic approaches in neurodegeneration.
- Manik Kuchroo
- , Marcello DiStasio
- & Brian P. Hafler
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Article
| Open AccessReconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace
Methods to reanalyze scRNA-seq data in a spatial perspective are vital but lacking. Here, the authors develop scSpace, an integrative method that uses ST data as spatial reference to reconstruct the pseudo-space of scRNA-seq data and identify spatially variable cell subpopulations, providing insights into spatial heterogeneity from scRNA-seq data.
- Jingyang Qian
- , Jie Liao
- & Xiaohui Fan
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Article
| Open AccessA massively parallel screening platform for converting aptamers into molecular switches
Efforts to convert aptamers into molecular switches using rational design are often unsuccessful. Here the authors describe a massively parallel screening-based strategy whereby millions of potential aptamer switches are synthesised, sequenced and screened directly on a flow-cell.
- Alex M. Yoshikawa
- , Alexandra E. Rangel
- & H. Tom Soh
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Article
| Open AccessThe small and large intestine contain related mesenchymal subsets that derive from embryonic Gli1+ precursors
Stromal cells are essential for intestinal homeostasis. Here the authors describe the phenotype, transcriptional profile and location of stromal cell subsets in the adult murine small intestine and colon lamina propria and demonstrate that these cells derive from Gli1+ precursors present in embryonic day 12.5 intestine.
- Simone Isling Pærregaard
- , Line Wulff
- & William W. Agace
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Article
| Open AccessTargeting CXCL16 and STAT1 augments immune checkpoint blockade therapy in triple-negative breast cancer
Chemotherapy priming sensitizes triple-negative breast cancers to immune checkpoint blockade. However, immune suppressive myeloid cells may impede its optimal effect. Here authors characterise the immune suppressive myeloid cells via single-cell analyses of immune cells from low dose chemotherapy treated breast tumours and identify STAT1 signalling as a regulator for immune suppressive state.
- Bhavana Palakurthi
- , Shaneann R. Fross
- & Siyuan Zhang
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Article
| Open AccessScreening of Drosophila microRNA-degradation sequences reveals Argonaute1 mRNA’s role in regulating miR-999
miRNAs typically bind to target mRNAs to induce their degradation but when base-pairing between miRNAs and the target RNAs are extended, miRNAs themselves can be degraded. Here, by employing AGO1-CLASH in Drosophila cells, the authors show that RNA sequence in AGO1 mRNA 3′UTR induces decay of miR-999.
- Peike Sheng
- , Lu Li
- & Mingyi Xie
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Article
| Open AccessPredicting response to enzalutamide and abiraterone in metastatic prostate cancer using whole-omics machine learning
Prostate cancer is known to have a variable response to androgen receptor signalling inhibitors. Here, the authors use machine learning to predict response to therapy from genomic, transcriptomic and clinical data.
- Anouk C. de Jong
- , Alexandra Danyi
- & Martijn P. Lolkema
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Article
| Open AccessSystematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing
Direct RNA sequencing using nanopore platform can be used to detect N6-methyladenosine (m6A) modifications on mRNAs. Here the authors systematically compare tools used for m6A detection from nanopore direct sequencing.
- Zhen-Dong Zhong
- , Ying-Yuan Xie
- & Guan-Zheng Luo
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Article
| Open AccessMAIT cell inhibition promotes liver fibrosis regression via macrophage phenotype reprogramming
Liver cirrhosis is characterised by extensive fibrosis of the liver, and understanding the underpinning immunological processes is important in designing intervention. Here authors show that Mucosal-Associated Invariant T cells are instrumental to controlling the balance between profibrogenic and restorative macrophages and inhibiting their activation might reverse liver fibrosis.
- Morgane Mabire
- , Pushpa Hegde
- & Sophie Lotersztajn
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Article
| Open AccessMuscle cell-type diversification is driven by bHLH transcription factor expansion and extensive effector gene duplications
Different muscle cell types account for specific abilities in animals, yet how their diversification arose remains unclear. Here, the authors show that gene duplications of bHLH transcription factors and effector genes contributed to the diversification of muscle cell types in the sea anemone Nematostella.
- Alison G. Cole
- , Stefan M. Jahnel
- & Ulrich Technau
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Article
| Open AccessIGFBP5 is an ROR1 ligand promoting glioblastoma invasion via ROR1/HER2-CREB signaling axis
Glioblastoma stem-like cells (GSCs) contribute to therapeutic resistance and recurrence of glioblastomas. Here the authors show that Insulin-like Growth Factor-Binding Protein 5 (IGFBP5) is a ligand for Receptor tyrosine kinase-like Orphan Receptor 1 (ROR1) promotes GSCs invasion.
- Weiwei Lin
- , Rui Niu
- & Jinlong Yin
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| Open AccessSpatial transcriptomics using multiplexed deterministic barcoding in tissue
Examining the spatially resolved transcriptome of tissue sections promises advances in biomedical research. Here, the authors present xDBiT, a versatile, microfluidics-based approach to cost-effectively measure the spatial transcriptome of multiple tissue sections in parallel.
- Johannes Wirth
- , Nina Huber
- & Matthias Meier
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| Open AccessImmune subset-committed proliferating cells populate the human foetal intestine throughout the second trimester of gestation
The intestine is an important immunological organ in embryonic life, preparing the infant for the microbial colonization following birth. Here authors show that between gestational weeks 14 and 22, the human foetal intestine is first populated by myeloid and innate lymphoid cells, followed by the development of lymphoid cells and a wider range of proliferation-capable immune cell types.
- Nannan Guo
- , Na Li
- & Frits Koning
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Article
| Open AccessLongitudinal single-cell profiling of chemotherapy response in acute myeloid leukemia
Relapse within acute myeloid leukaemia may be driven by the presence of leukaemia stem cells. Here, the authors use single cell RNA-seq seq to characterise leukemia stem cells, and show miR-126 as a potential marker of resistance.
- Matteo Maria Naldini
- , Gabriele Casirati
- & Bernhard Gentner
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| Open AccessWell-TEMP-seq as a microwell-based strategy for massively parallel profiling of single-cell temporal RNA dynamics
Gene expression of cells is a heterogeneous and dynamic program involved in various biological processes. Here, authors develop Well-TEMPseq, a high-throughput, cost-effective, and accurate method for massively parallel profiling of the temporal dynamics of single-cell gene expression.
- Shichao Lin
- , Kun Yin
- & Chaoyong Yang
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| Open AccessBdLT-Seq as a barcode decay-based method to unravel lineage-linked transcriptome plasticity
Cellular plasticity is a core biological process; however, observing diversity in non-genetic inheritance and the resulting phenotypic outputs, is challenging. Here the authors develop a non-genetically based tracing technology which can be used to reveal lineage-linked transcriptome plasticity.
- Yelyzaveta Shlyakhtina
- , Bianca Bloechl
- & Maximiliano M. Portal
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| Open AccessSingle-cell transcriptome profiling of the stepwise progression of head and neck cancer
Head and neck squamous cell carcinomas (HNSCCs) undergo a stepwise progression from normal tissues. In order to better understand the molecular mechanisms behind such progression, here the authors profile HNSCC tumors at different stages using single-cell RNA-seq, and observe the role of interactions with the tumor microenvironment.
- Ji-Hye Choi
- , Bok-Soon Lee
- & Chul-Ho Kim
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Article
| Open AccessApplication of high-throughput single-nucleus DNA sequencing in pancreatic cancer
Implementing high-throughput single-cell DNA sequencing for the study of solid tumours has been challenging. Here, the authors present an optimised approach for snap-frozen tissue single nuclei extraction and DNA sequencing, which can be applied to study pancreatic ductal adenocarcinoma evolution and heterogeneity.
- Haochen Zhang
- , Elias-Ramzey Karnoub
- & Christine A. Iacobuzio-Donahue
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| Open AccessDissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses
The immune suppressive tumour microenvironment drives recurrence and metastatic disease in prostate cancer. Here authors provide a detailed analysis of the microenvironment via single cell RNA sequencing and high-resolution spatial transcriptomics to identify tumour-dependent changes compared to healthy tissue.
- Taghreed Hirz
- , Shenglin Mei
- & David B. Sykes
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Article
| Open AccessSingle-exonuclease nanocircuits reveal the RNA degradation dynamics of PNPase and demonstrate potential for RNA sequencing
Observing the natural process of RNA degradation in real-time is a significant challenge. Here, the authors develop and use single-exonuclease nanocircuits to reveal the single-base degradation behaviour of PNPase, and demonstrate proof-of-principle RNA sequencing using this approach.
- Zhiheng Yang
- , Wenzhe Liu
- & Xuefeng Guo
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Article
| Open AccessSpatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
Spatial transcriptomics relies on RNA quality, which is variable and dependent on sample handling, storage, and/or intrinsic factors. Here, authors present a genome-wide spatial gene expression profiling method called RNA Rescue Spatial Transcriptomics (RRST), designed for the analysis of moderate to low quality fresh frozen tissue samples and demonstrate its robustness on 7 different tissue types.
- Reza Mirzazadeh
- , Zaneta Andrusivova
- & Joakim Lundeberg
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Article
| Open AccessEpigenetic control of cellular crosstalk defines gastrointestinal organ fate and function
Mesenchymal-epithelial crosstalk plays a key role in gut development and stem cell homeostasis, though underlying mechanisms are still unclear. Here, the authors demonstrate that mesenchymal Polycomb Repressive Complex 2 controls niche signals for gut epithelial fate and growth.
- Ryan J. Smith
- , Minggao Liang
- & Tae-Hee Kim
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Article
| Open AccessDecision level integration of unimodal and multimodal single cell data with scTriangulate
Single-cell genomics has expanded to measure diverse molecular modalities within the same cell. Here the authors provide a computational framework called scTriangulate to integrate cluster annotations from diverse independent sources, algorithms, and modalities to define statistically stable populations.
- Guangyuan Li
- , Baobao Song
- & Nathan Salomonis
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| Open AccessTopological identification and interpretation for single-cell gene regulation elucidation across multiple platforms using scMGCA
A major challenge in analyzing scRNA-seq data arises from challenges related to dimensionality and the prevalence of dropout events. Here the authors develop a deep graph learning method called scMGCA based on a graph-embedding autoencoder that simultaneously learns cell-cell topology representation and cluster assignments, outperforming other state-of-the-art models across multiple platforms.
- Zhuohan Yu
- , Yanchi Su
- & Xiangtao Li
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Article
| Open Accessscm6A-seq reveals single-cell landscapes of the dynamic m6A during oocyte maturation and early embryonic development
Modification of RNA with N6-methyladenosine can regulate RNA metabolism. Here they developed scm6A-seq to profile the methylome and transcriptome in single cells, and reveal the functions of m6A modification during oocyte maturation and early embryo development.
- Huan Yao
- , Chun-Chun Gao
- & Yun-Gui Yang
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| Open AccessSemi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing
Pseudouridine (psi) is an RNA modification that can affect its physiology, including increased half-life. Here the authors identify sites of psi modification in the human transcriptome using direct RNA sequencing and provide a “ground truth” list of psi sites, sites of high psi occupancy, and transcripts that may be modified at multiple sites.
- Sepideh Tavakoli
- , Mohammad Nabizadeh
- & Sara H. Rouhanifard
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Article
| Open AccessIn vivo induction of activin A-producing alveolar macrophages supports the progression of lung cell carcinoma
Alveolar macrophages represent a cell type that is physiologic to the lung immune landscape, however, it is not known whether they play an active role to maintain the tumour immune microenvironment. Here authors show by single cell RNA sequencing and functional experiments, that intra-tumour alveolar macrophages are phenotypically and transcriptionally different from the healthy ones, and likely play an aetio-pathologic role in tumorigenesis.
- Seiji Taniguchi
- , Takahiro Matsui
- & Masaru Ishii
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Article
| Open AccessGermline TP53 mutations undergo copy number gain years prior to tumor diagnosis
Li-Fraumeni syndrome (LFS) is associated with pathogenic germline TP53 variants and predisposes patients to cancer; understanding the evolution and drivers of LFS-related tumours remains crucial. Here, the authors analyse 22 LFS tumours using whole-genome sequencing and reconstruct the evolution and timing of somatic driver alterations.
- Nicholas Light
- , Mehdi Layeghifard
- & Adam Shlien
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Article
| Open AccessTAPE-seq is a cell-based method for predicting genome-wide off-target effects of prime editor
Methods to predict genome-wide off-target activities of prime editors (PEs) are currently lacking. Here the authors report a cell-based assay, TAgmentation of Prime Editor sequencing (TAPE-seq), that provides genome-wide off-target candidates for PEs.
- Jeonghun Kwon
- , Minyoung Kim
- & Jungjoon K. Lee
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Article
| Open AccessSimultaneous profiling of histone modifications and DNA methylation via nanopore sequencing
The interplay between histone modifications and DNA methylation plays a crucial role in establishing and maintaining the epigenomic landscape. Here, the authors develop a nanopore sequencing based method for mapping histone modifications and DNA methylation from native, long, single DNA molecules.
- Xue Yue
- , Zhiyuan Xie
- & Yimeng Yin
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Article
| Open AccessDysfunctional Sars-CoV-2-M protein-specific cytotoxic T lymphocytes in patients recovering from severe COVID-19
Cytotoxic T lymphocytes play important roles in the anti-viral immune response in COVID-19, and it is important to know how they contribute to disease outcome. Authors here identify a dominant SARS-CoV-2 M protein epitope, M198–206, and show that M198–206-specific cytotoxic T cells from convalescent patients with severe disease harbour a gene expression pattern indicative of poor functionality.
- Hideki Ogura
- , Jin Gohda
- & Satoshi Ishido
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Article
| Open AccessHigh-throughput robust single-cell DNA methylation profiling with sciMETv2
Despite the importance of DNA methylation, accessible and high-throughput methods to profile methylation at the single-cell level are lacking. Here, the authors present sciMETv2, a high-throughput workflow that provides high-quality single-cell methylomes in a robust and simple workflow.
- Ruth V. Nichols
- , Brendan L. O’Connell
- & Andrew C. Adey
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Article
| Open AccessWhole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program
Most genetic association studies have been done on single nucleotide polymorphisms and small indels, while other types of variants have been less studied. Here, the authors use whole genome sequencing in a diverse population to identify and provide experimental evidence for associations between structural variants and blood-cell traits.
- Marsha M. Wheeler
- , Adrienne M. Stilp
- & Alex P. Reiner
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Article
| Open AccessRetrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells
Retrotransposons are mobile genetic elements normally repressed by DNA methylation in differentiated cells. Here, the authors show that DNA hypomethylation in mouse induced pluripotent stem cells allows retrotransposons to jump, but this can be blocked with a reverse transcriptase inhibitor.
- Patricia Gerdes
- , Sue Mei Lim
- & Geoffrey J. Faulkner
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Article
| Open AccessA unified computational framework for single-cell data integration with optimal transport
Integrating heterogeneous single-cell multi-omics as well as spatially resolved transcriptomic data remains a major challenge. Here the authors report a unified single-cell data integration framework using an unbalanced optimal transport-based deep network.
- Kai Cao
- , Qiyu Gong
- & Lin Wan
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Article
| Open AccessLow-dose IL-2 reduces IL-21+ T cell frequency and induces anti-inflammatory gene expression in type 1 diabetes
Low-dose interleukin-2 is showing promise in the treatment of several autoimmune inflammatory diseases. Here authors map the trajectory of cellular and transcriptional changes in type 1 diabetes patients receiving an interval dosing interleukin-2 regimen, which shows an anti-inflammatory gene expression signature shared by all immune cell types analysed, persisting for at least a month after ending treatment.
- Jia-Yuan Zhang
- , Fiona Hamey
- & Ricardo C. Ferreira
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Article
| Open AccessLeveraging data-driven self-consistency for high-fidelity gene expression recovery
Recovering dropout-affected gene expression values is a challenging problem in bioinformatics. Here, the authors propose a data-driven framework, that first learns the underlying data distribution and then recovers the expression values by imposing a self-consistency on the expression matrix.
- Md Tauhidul Islam
- , Jen-Yeu Wang
- & Lei Xing
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Article
| Open AccessSystematic tissue annotations of genomics samples by modeling unstructured metadata
The 1+ million publicly-available human –omics samples currently remain acutely underused. Here the authors present an approach combining natural language processing and machine learning to infer the source tissue of public genomics samples based on their plain text descriptions, making these samples easy to discover and reuse.
- Nathaniel T. Hawkins
- , Marc Maldaver
- & Arjun Krishnan
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Article
| Open AccessDeep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis
Traditional bulk sequencing data lack information about cell-type-specific gene expression. Here, the authors develop a Tissue-AdaPtive autoEncoder (TAPE), a deep learning method connecting bulk RNA-seq and single-cell RNA-seq, and apply it to analyze the cell type fractions and cell-type-specific gene expression in clinical data.
- Yanshuo Chen
- , Yixuan Wang
- & Yu Li
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Article
| Open AccessAnalysis of matched primary and recurrent BRCA1/2 mutation-associated tumors identifies recurrence-specific drivers
Carriers of pathogenic BRCA1/2 variants have a higher risk of breast and ovarian cancers, which recur frequently. Here, the authors sequence primary and recurrent tumours of BRCA1/2 mutation carriers, finding PARP1 amplifications, differential BRCA2 isoform usage, and discordant loss of heterozygosity that are associated with recurrence.
- Jennifer B. Shah
- , Dana Pueschl
- & Katherine L. Nathanson
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Article
| Open AccessVeChat: correcting errors in long reads using variation graphs
Consensus sequence-based methods for self-correction of long-read sequencing data are affected by biases that can mask true variants characterizing little-covered or low-frequency haplotypes. Here, to address this issue, the authors develop a variation graph-based method for performing haplotype-aware self-correction of long reads.
- Xiao Luo
- , Xiongbin Kang
- & Alexander Schönhuth
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Article
| Open AccessUniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference
RNA velocity can detect the differentiation directionality by modelling sparse unspliced RNAs, but suffers from high estimation errors. Here, the authors develop a computational method called UniTVelo to reinforce the velocity estimation by introducing a unified time and a top-down model design.
- Mingze Gao
- , Chen Qiao
- & Yuanhua Huang