Longitudinal dynamics of clonal hematopoiesis identifies gene-specific fitness effects

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

60 Years of clonal hematopoiesis research: From X-chromosome inactivation studies to the identification of driver mutations

(2020) Sami Ayachi et al.   EXPERIMENTAL HEMATOLOGY

Clonal hematopoiesis in cancer

(2020) Soo J. Park et al.   EXPERIMENTAL HEMATOLOGY

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

The evolutionary dynamics and fitness landscape of clonal hematopoiesis

(2020) Caroline J. Watson et al.   SCIENCE

Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios

(2020) Marc J Williams et al.   eLife

Clonality in haematopoietic stem cell ageing

(2020) Maria Terradas-Terradas et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations

(2020) Benjamin J Livesey et al.   Molecular Systems Biology

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Somatic mutation and clonal expansions in human tissues

(2019) Inigo Martincorena   Genome Medicine

Age-related clonal haemopoiesis is associated with increased epigenetic age

(2019) Neil A. Robertson et al.   CURRENT BIOLOGY

The landscape of somatic mutation in normal colorectal epithelial cells

(2019) Henry Lee-Six et al.   NATURE

Clonal hematopoiesis in human aging and disease

(2019) Siddhartha Jaiswal et al.   SCIENCE

Cohort Profile Update: The Lothian Birth Cohorts of 1921 and 1936

(2018) Adele M Taylor et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Prediction of acute myeloid leukaemia risk in healthy individuals

(2018) Sagi Abelson et al.   NATURE

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

COSMIC: the Catalogue Of Somatic Mutations In Cancer

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

DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins

(2017) Daniele Raimondi et al.   NUCLEIC ACIDS RESEARCH

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

(2016) Nilah M. Ioannidis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Extensive sequencing of seven human genomes to characterize benchmark reference materials

(2016) Justin M. Zook et al.   Scientific Data

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

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

(2015) I. Martincorena et al.   SCIENCE

Leukemia-Associated Somatic Mutations Drive Distinct Patterns of Age-Related Clonal Hemopoiesis

(2015) Thomas McKerrell et al.   Cell Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence

(2014) Giulio Genovese et al.   NEW ENGLAND JOURNAL OF MEDICINE

Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes

(2014) Siddhartha Jaiswal et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

DNMT3AMutations in Acute Myeloid Leukemia

(2010) Timothy J. Ley et al.   NEW ENGLAND JOURNAL OF MEDICINE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY