Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer

HTSlib: C library for reading/writing high-throughput sequencing data

(2021) James K Bonfield et al.   GigaScience

Single Cell Analysis Can Define Distinct Evolution of Tumor Sites in Follicular Lymphoma

(2021) Sarah Elena Haebe et al.   BLOOD

Targeted long-read sequencing identifies missing disease-causing variation

(2021) Danny E. Miller et al.   AMERICAN JOURNAL OF HUMAN GENETICS

High resolution copy number inference in cancer using short-molecule nanopore sequencing

(2021) Timour Baslan et al.   NUCLEIC ACIDS RESEARCH

Single cell genomic characterization reveals the cellular reprogramming of the gastric tumor microenvironment

(2020) Anuja Sathe et al.   CLINICAL CANCER RESEARCH

Clinical and Biological Prognostic Factors in Follicular Lymphoma

(2020) Anand A. Patel et al.   HEMATOLOGY-ONCOLOGY CLINICS OF NORTH AMERICA

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

(2020) Joseph M. Replogle et al.   NATURE BIOTECHNOLOGY

High throughput error corrected Nanopore single cell transcriptome sequencing

(2020) Kevin Lebrigand et al.   Nature Communications

Readfish enables targeted nanopore sequencing of gigabase-sized genomes

(2020) Alexander Payne et al.   NATURE BIOTECHNOLOGY

GENCODE 2021

(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

(2019) Mandeep Singh et al.   Nature Communications

ClinVar: improvements to accessing data

(2019) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

(2019) Peter Edge et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-cell RNA-Seq of lymphoma cancers reveals malignant B cell types and co-expression of T cell immune checkpoints

(2018) Noemi Andor et al.   BLOOD

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Real-time selective sequencing using nanopore technology

(2016) Matthew Loose et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Critical Role of Smad2 in Tumor Suppression and Transforming Growth Factor- -Induced Apoptosis of Prostate Epithelial Cells

(2009) J. Yang et al.   CANCER RESEARCH