Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita et al.   BIOINFORMATICS

Clonal Analysis via Barcoding Reveals Diverse Growth and Differentiation of Transplanted Mouse and Human Mammary Stem Cells

(2014) Long V. Nguyen et al.   Cell Stem Cell

Cellular barcoding: A technical appraisal

(2014) Shalin H. Naik et al.   EXPERIMENTAL HEMATOLOGY

Asymmetry in skeletal distribution of mouse hematopoietic stem cell clones and their equilibration by mobilizing cytokines

(2014) Evgenia Verovskaya et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

In vivo generation of DNA sequence diversity for cellular barcoding

(2014) Ian D. Peikon et al.   NUCLEIC ACIDS RESEARCH

Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

(2014) Claire T. Deakin et al.   NUCLEIC ACIDS RESEARCH

Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo

(2014) Shaina N Porter et al.   GENOME BIOLOGY

Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding

(2013) E. Verovskaya et al.   BLOOD

Analysis of the clonal growth and differentiation dynamics of primitive barcoded human cord blood cells in NSG mice

(2013) A. M. S. Cheung et al.   BLOOD

Massively parallel sequencing: the new frontier of hematologic genomics

(2013) J. M. Johnsen et al.   BLOOD

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

(2013) Tilo Buschmann et al.   BMC BIOINFORMATICS

Discovering motifs that induce sequencing errors

(2013) Manuel Allhoff et al.   BMC BIOINFORMATICS

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Impact of new sequencing technologies on studies of the human B cell repertoire

(2013) Jessica A Finn et al.   CURRENT OPINION IN IMMUNOLOGY

Immunosequencing: applications of immune repertoire deep sequencing

(2013) Harlan Robins   CURRENT OPINION IN IMMUNOLOGY

Diverse and heritable lineage imprinting of early haematopoietic progenitors

(2013) Shalin H. Naik et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

(2013) D. I. Lou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterogeneous Differentiation Patterns of Individual CD8+ T Cells

(2013) C. Gerlach et al.   SCIENCE

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

(2013) Sara El-Metwally et al.   PLoS Computational Biology

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

(2012) Vincent Plagnol et al.   BIOINFORMATICS

Accuracy of RNA-Seq and its dependence on sequencing depth

(2012) Guoshuai Cai et al.   BMC BIOINFORMATICS

Efficient error correction for next-generation sequencing of viral amplicons

(2012) Pavel Skums et al.   BMC BIOINFORMATICS

Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms

(2012) Dmitry A. Bolotin et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

High Efficiency Restriction Enzyme–Free Linear Amplification-Mediated Polymerase Chain Reaction Approach for Tracking Lentiviral Integration Sites Does Not Abrogate Retrieval Bias

(2012) Chuanfeng Wu et al.   HUMAN GENE THERAPY

Models and methods for analysis of lymphocyte repertoire generation, development, selection and evolution

(2012) Ramit Mehr et al.   IMMUNOLOGY LETTERS

Defining the mode of tumour growth by clonal analysis

(2012) Gregory Driessens et al.   NATURE

A restricted cell population propagates glioblastoma growth after chemotherapy

(2012) Jian Chen et al.   NATURE

Generalized DNA Barcode Design Based on Hamming Codes

(2012) Leonid V. Bystrykh   PLoS One

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Detection of ultra-rare mutations by next-generation sequencing

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

Lineage Tracing Reveals Lgr5+ Stem Cell Activity in Mouse Intestinal Adenomas

(2012) A. G. Schepers et al.   SCIENCE

Brief Report: Intravital Imaging of Cancer Stem Cell Plasticity in Mammary Tumors

(2012) Anoek Zomer et al.   STEM CELLS

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire

(2011) Phuong Nguyen et al.   BMC GENOMICS

Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

A method to sequence and quantify DNA integration for monitoring outcome in gene therapy

(2011) Troy Brady et al.   NUCLEIC ACIDS RESEARCH

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

(2010) Osvaldo Zagordi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

EDAR: An Efficient Error Detection and Removal Algorithm for Next Generation Sequencing Data

(2010) Xiaohong Zhao et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Comprehensive assessment of T-cell receptor  -chain diversity in    T cells

(2009) H. S. Robins et al.   BLOOD

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Recruitment of Antigen-Specific CD8+ T Cells in Response to Infection Is Markedly Efficient

(2009) J. W. J. van Heijst et al.   SCIENCE

Dissecting T cell lineage relationships by cellular barcoding

(2008) Koen Schepers et al.   JOURNAL OF EXPERIMENTAL MEDICINE