scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors

Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress

(2022) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes

(2021) Ruli Gao et al.   NATURE BIOTECHNOLOGY

Effective ribosomal RNA depletion for single-cell total RNA-seq by scDASH

(2021) Danson S.C. Loi et al.   PeerJ

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Breast tumours maintain a reservoir of subclonal diversity during expansion

(2021) Darlan C. Minussi et al.   NATURE

Modular, efficient and constant-memory single-cell RNA-seq preprocessing

(2021) Páll Melsted et al.   NATURE BIOTECHNOLOGY

The 2021 WHO Classification of Tumors of the Central Nervous System: a summary

(2021) David N Louis et al.   NEURO-ONCOLOGY

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

(2020) Lei Zhang et al.   CELL

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

Single-Cell RNA Sequencing of Human, Macaque, and Mouse Testes Uncovers Conserved and Divergent Features of Mammalian Spermatogenesis

(2020) Adrienne Niederriter Shami et al.   DEVELOPMENTAL CELL

Synaptic input to brain tumors: clinical implications

(2020) Varun Venkataramani et al.   NEURO-ONCOLOGY

A Highly Scalable Method for Joint Whole-Genome Sequencing and Gene-Expression Profiling of Single Cells

(2020) Vasilios Zachariadis et al.   MOLECULAR CELL

Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL

(2020) Simone Zaccaria et al.   NATURE BIOTECHNOLOGY

Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics

(2020) Anna S. Nam et al.   NATURE REVIEWS GENETICS

Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans

(2020) Nicola Thrupp et al.   Cell Reports

Cancer Stem Cells: The Architects of the Tumor Ecosystem

(2019) Briana C. Prager et al.   Cell Stem Cell

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

(2019) Cyril Neftel et al.   CELL

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

(2019) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

High-Throughput Single-Cell Sequencing with Linear Amplification

(2019) Yi Yin et al.   MOLECULAR CELL

Electrical and synaptic integration of glioma into neural circuits

(2019) Humsa S. Venkatesh et al.   NATURE

Glutamatergic synaptic input to glioma cells drives brain tumour progression

(2019) Varun Venkataramani et al.   NATURE

Emerging intersections between neuroscience and glioma biology

(2019) Erik Jung et al.   NATURE NEUROSCIENCE

OUP accepted manuscript

(2018)   BIOINFORMATICS

Single-cell multi-omics sequencing of human early embryos

(2018) Lin Li et al.   NATURE CELL BIOLOGY

Genetic and transcriptional evolution alters cancer cell line drug response

(2018) Uri Ben-David et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Mutational Landscape of Secondary Glioblastoma Guides MET-Targeted Trial in Brain Tumor

(2018) Huimin Hu et al.   CELL

The AMPA Receptor Code of Synaptic Plasticity

(2018) Graham H. Diering et al.   NEURON

Establishment and characterization of new tumor xenografts and cancer cell lines from EBV-positive nasopharyngeal carcinoma

(2018) Weitao Lin et al.   Nature Communications

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

Effective detection of variation in single-cell transcriptomes using MATQ-seq

(2017) Kuanwei Sheng et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Scalable whole-genome single-cell library preparation without preamplification

(2017) Hans Zahn et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

(2017) Andrew S. Venteicher et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

(2016) Michele Ceccarelli et al.   CELL

Single-cell triple omics sequencing reveals genetic, epigenetic and transcriptomic heterogeneity in hepatocellular carcinomas

(2016) Yu Hou et al.   CELL RESEARCH

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer

(2016) Ruli Gao et al.   NATURE GENETICS

Clonal evolution of glioblastoma under therapy

(2016) Jiguang Wang et al.   NATURE GENETICS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Synaptic AMPA receptor composition in development, plasticity and disease

(2016) Jeremy M. Henley et al.   NATURE REVIEWS NEUROSCIENCE

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

Interactive analysis and assessment of single-cell copy-number variations

(2015) Tyler Garvin et al.   NATURE METHODS

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

(2015) Xiaoying Fan et al.   GENOME BIOLOGY

Evolution of the Cancer Stem Cell Model

(2014) Antonija Kreso et al.   Cell Stem Cell

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

(2013) Gro Nilsen et al.   BMC GENOMICS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma

(2013) B. E. Johnson et al.   SCIENCE

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

(2013) Layla Oesper et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

High-throughput injection with microfluidics using picoinjectors

(2010) A. R. Abate et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

(2008) William F. Marzluff et al.   NATURE REVIEWS GENETICS