Spatially resolved clonal copy number alterations in benign and malignant tissue

Spatially resolved transcriptomics adds a new dimension to genomics

(2021) Ludvig Larsson et al.   NATURE METHODS

Development, maturation, and maintenance of human prostate inferred from somatic mutations

(2021) Sebastian Grossmann et al.   Cell Stem Cell

Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse

(2021) S. Taavitsainen et al.   Nature Communications

Spatial genomics enables multi-modal study of clonal heterogeneity in tissues

(2021) Tongtong Zhao et al.   NATURE

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

(2020) Joseph Bergenstråhle et al.   BMC GENOMICS

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

(2020) Andrew L. Ji et al.   CELL

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

(2019) Keren Yizhak et al.   SCIENCE

A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing

(2019) Allegra A. Petti et al.   Nature Communications

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

(2018) Emelie Berglund et al.   Nature Communications

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

(2018) Freddie Bray et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections

(2018) Fredrik Salmén et al.   Nature Protocols

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells

(2017) Kyung Yeon Han et al.   GENOME RESEARCH

Differences between germline and somatic mutation rates in humans and mice

(2017) Brandon Milholland et al.   Nature Communications

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries

(2016) Anders Jemt et al.   Scientific Reports

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

The evolutionary history of lethal metastatic prostate cancer

(2015) Gunes Gundem et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

(2015) Colin S Cooper et al.   NATURE GENETICS

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

(2015) Tyler Garvin et al.   NATURE METHODS

Epigenetic determinism in science and society

(2015) Miranda R. Waggoner et al.   NEW GENETICS AND SOCIETY

High burden and pervasive positive selection of somatic mutations in normal human skin

(2015) I. Martincorena et al.   SCIENCE

Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer

(2015) Matthew K.H. Hong et al.   Nature Communications

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

(2015) H. Ross-Adams et al.   EBioMedicine

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing

(2013) Paul Igor Costea et al.   PLoS One

Do Adenocarcinomas of the Prostate With Gleason Score (GS)≤6 Have the Potential to Metastasize to Lymph Nodes?

(2012) Hillary M. Ross et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Standardization of Gleason grading among 337 European pathologists

(2012) Lars Egevad et al.   HISTOPATHOLOGY

The mutational landscape of lethal castration-resistant prostate cancer

(2012) Catherine S. Grasso et al.   NATURE

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Integrative Genomic Profiling of Human Prostate Cancer

(2010) Barry S. Taylor et al.   CANCER CELL

The potential value of microseminoprotein-β as a prostate cancer biomarker and therapeutic target

(2009) Hayley C. Whitaker et al.   PROSTATE