KaryoCreate: A CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres

Complete genomic and epigenetic maps of human centromeres

(2022) Nicolas Altemose et al.   SCIENCE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Proteogenomic analysis of cancer aneuploidy and normal tissues reveals divergent modes of gene regulation across cellular pathways

(2022) Pan Cheng et al.   eLife

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

(2021) Ruli Gao et al.   NATURE BIOTECHNOLOGY

CENP-A chromatin prevents replication stress at centromeres to avoid structural aneuploidy

(2021) Simona Giunta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immune evasion in HPV− head and neck precancer–cancer transition is driven by an aneuploid switch involving chromosome 9p loss

(2021) William N. William et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Clonal selection of stable aneuploidies in progenitor cells drives high-prevalence tumorigenesis

(2021) Marianna Trakala et al.   GENES & DEVELOPMENT

The Aurora B gradient sustains kinetochore stability in anaphase

(2021) Diana Papini et al.   Cell Reports

Genomic and functional variation of human centromeres

(2020) Lori L. Sullivan et al.   EXPERIMENTAL CELL RESEARCH

Pervasive chromosomal instability and karyotype order in tumour evolution

(2020) Thomas B. K. Watkins et al.   NATURE

Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements

(2019) Peter Ly et al.   NATURE GENETICS

Human chromosome‐specific aneuploidy is influenced by DNA ‐dependent centromeric features

(2019) Marie Dumont et al.   EMBO JOURNAL

Nuclease dead Cas9 is a programmable roadblock for DNA replication

(2019) Kelsey S. Whinn et al.   Scientific Reports

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

KNL1 Binding to PP1 and Microtubules Is Mutually Exclusive

(2018) Rakhi Bajaj et al.   STRUCTURE

The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA

(2018) V. Barra et al.   Nature Communications

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

A mitosis-specific and R loop–driven ATR pathway promotes faithful chromosome segregation

(2017) Lilian Kabeche et al.   SCIENCE

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Selective Y centromere inactivation triggers chromosome shattering in micronuclei and repair by non-homologous end joining

(2016) Peter Ly et al.   NATURE CELL BIOLOGY

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Chromothripsis and Kataegis Induced by Telomere Crisis

(2015) John Maciejowski et al.   CELL

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

(2015) Marc van de Wetering et al.   CELL

The Molecular Biology of Spindle Assembly Checkpoint Signaling Dynamics

(2015) Andrea Musacchio   CURRENT BIOLOGY

Sequential cancer mutations in cultured human intestinal stem cells

(2015) Jarno Drost et al.   NATURE

CopywriteR: DNA copy number detection from off-target sequence data

(2015) Thomas Kuilman et al.   GENOME BIOLOGY

Characterization of Aneuploid Populations with Trisomy 7 and 20 Derived from Diploid Human Colonic Epithelial Cells

(2015) Peter Ly et al.   NEOPLASIA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genetic and Clonal Dissection of Murine Small Cell Lung Carcinoma Progression by Genome Sequencing

(2014) David G. McFadden et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Single cell sequencing reveals low levels of aneuploidy across mammalian tissues

(2014) Kristin A. Knouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) A. P. Patel et al.   SCIENCE

The Kinetochore

(2014) I. M. Cheeseman   Cold Spring Harbor Perspectives in Biology

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei

(2013) Emily M. Hatch et al.   CELL

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Human centromere genomics: now it's personal

(2012) Karen E. Hayden   CHROMOSOME RESEARCH

Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

(2012) Silvia Stingele et al.   Molecular Systems Biology

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Active transcription and essential role of RNA polymerase II at the centromere during mitosis

(2012) F. L. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions

(2012) W. Xue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo

(2011) Kristen L. Meerbrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Merotelic kinetochore attachment: causes and effects

(2011) Juraj Gregan et al.   TRENDS IN CELL BIOLOGY

Regulated targeting of protein phosphatase 1 to the outer kinetochore by KNL1 opposes Aurora B kinase

(2010) Dan Liu et al.   JOURNAL OF CELL BIOLOGY

Dissecting the role of MPS1 in chromosome biorientation and the spindle checkpoint through the small molecule inhibitor reversine

(2010) Stefano Santaguida et al.   JOURNAL OF CELL BIOLOGY

Sustained Mps1 activity is required in mitosis to recruit O-Mad2 to the Mad1–C-Mad2 core complex

(2010) Laura Hewitt et al.   JOURNAL OF CELL BIOLOGY

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Regulation of kinetochore–microtubule attachments by Aurora B kinase

(2009) Dan Liu et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS