CD8+ cell somatic mutations in multiple sclerosis patients and controls—Enrichment of mutations in STAT3 and other genes implicated in hematological malignancies

Somatic mutation landscapes at single-molecule resolution

(2021) Federico Abascal et al.   NATURE

Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population

(2021) Jeffrey B S Gaither et al.   GigaScience

Complete Epstein-Barr virus seropositivity in a large cohort of patients with early multiple sclerosis

(2020) Sargis Abrahamyan et al.   JOURNAL OF NEUROLOGY NEUROSURGERY AND PSYCHIATRY

MBIP (MAP3K12 binding inhibitory protein) drives NSCLC metastasis by JNK-dependent activation of MMPs

(2020) Joshua Kapere Ochieng et al.   ONCOGENE

SOCS, Intrinsic Virulence Factors, and Treatment of COVID-19

(2020) Howard M. Johnson et al.   Frontiers in Immunology

Somatic Mutations in UBA1 and Severe Adult-Onset Autoinflammatory Disease

(2020) David B. Beck et al.   NEW ENGLAND JOURNAL OF MEDICINE

BRM transcriptionally regulates miR-302a-3p to target SOCS5/STAT3 signaling axis to potentiate pancreatic cancer metastasis

(2019) Zhengkui Zhang et al.   CANCER LETTERS

Clonal hematopoiesis in human aging and disease

(2019) Siddhartha Jaiswal et al.   SCIENCE

Somatic mutations and T-cell clonality in patients with immunodeficiency

(2019) Paula Savola et al.   HAEMATOLOGICA

Somatic Variants: New Kids on the Block in Human Immunogenetics

(2019) L. Van Horebeek et al.   TRENDS IN GENETICS

Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations

(2018) Jesse J. Salk et al.   NATURE REVIEWS GENETICS

Multiple Sclerosis: Mechanisms and Immunotherapy

(2018) Clare Baecher-Allan et al.   NEURON

Somatic Activating KRAS Mutations in Arteriovenous Malformations of the Brain

(2018) Sergey I. Nikolaev et al.   NEW ENGLAND JOURNAL OF MEDICINE

High expression of SMARCA4 or SMARCA2 is frequently associated with an opposite prognosis in cancer

(2018) Jose A. Guerrero-Martínez et al.   Scientific Reports

Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates

(2018) Benjamin Werner et al.   PLoS Computational Biology

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

Somatic STAT3 mutations in Felty syndrome: an implication for a common pathogenesis with large granular lymphocyte leukemia

(2017) Paula Savola et al.   HAEMATOLOGICA

Effector CD8 T cells dedifferentiate into long-lived memory cells

(2017) Ben Youngblood et al.   NATURE

Aging and neurodegeneration are associated with increased mutations in single human neurons

(2017) Michael A. Lodato et al.   SCIENCE

Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis

(2017) P. Savola et al.   Nature Communications

Annotating pathogenic non-coding variants in genic regions

(2017) Sahar Gelfman et al.   Nature Communications

Somatic STAT3 mutations in Felty syndrome: an implication for a common pathogenesis with large granular lymphocyte leukemia

(2017) Paula Savola et al.   HAEMATOLOGICA

Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile

(2017) Theres Oakes et al.   Frontiers in Immunology

Examining Sources of Error in PCR by Single-Molecule Sequencing

(2017) Vladimir Potapov et al.   PLoS One

Interleukin-15-Dependent T-Cell-like Innate Intraepithelial Lymphocytes Develop in the Intestine and Transform into Lymphomas in Celiac Disease

(2016) Julien Ettersperger et al.   IMMUNITY

Activating somatic mutations outside the SH2-domain of STAT3 in LGL leukemia

(2015) E Andersson et al.   LEUKEMIA

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

(2015) I. Martincorena et al.   SCIENCE

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Exome sequencing in single cells from the cerebrospinal fluid in multiple sclerosis

(2014) AK Kemppinen et al.   Multiple Sclerosis Journal

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

Assessing T Cell Clonal Size Distribution: A Non-Parametric Approach

(2014) Olesya V. Bolkhovskaya et al.   PLoS One

The DLK signalling pathway—a double-edged sword in neural development and regeneration

(2013) Andrea Tedeschi et al.   EMBO REPORTS

The mutational landscape of adenoid cystic carcinoma

(2013) Allen S Ho et al.   NATURE GENETICS

SomaticSTAT3Mutations in Large Granular Lymphocytic Leukemia

(2012) Hanna L.M. Koskela et al.   NEW ENGLAND JOURNAL OF MEDICINE

New Mutations in Chronic Lymphocytic Leukemia Identified by Target Enrichment and Deep Sequencing

(2012) Elena Doménech et al.   PLoS One

Integrative genomic profiling reveals conserved genetic mechanisms for tumorigenesis in common entities of non-Hodgkin's lymphoma

(2011) Michael R. Green et al.   GENES CHROMOSOMES & CANCER

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

(2011) Stephen Sawcer et al.   NATURE

Somatic KRAS mutations associated with a human nonmalignant syndrome of autoimmunity and abnormal leukocyte homeostasis

(2010) J. E. Niemela et al.   BLOOD

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS