Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting.

Kleinendorst RWD, Barzaghi G, Smith ML, Zaugg JB, Krebs AR

Nature protocols, 2021

doi:10.1038/s41596-021-00630-1.

Genome-wide screens implicate loss of cullin ring ligase 3 in persistent proliferation and genome instability in TP53-deficient cells.

Drainas AP, Lambuta RA, Ivanova I, Serçin Ö, Sarropoulos I, Smith ML, Efthymiopoulos T, Raeder B, Stütz AM, Waszak SM, Mardin BR, Korbel JO

Cell reports, 2020

doi:10.1016/j.celrep.2020.03.029.

Publisher correction: orchestrating single-cell analysis with Bioconductor.

Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Hicks SC, Gottardo R

Nature methods, 2019

doi:10.1038/s41592-019-0700-8.

Orchestrating single-cell analysis with Bioconductor.

Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Martini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Hicks SC, Gottardo R

Nature methods, 2019

doi:10.1038/s41592-019-0654-x.

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Farmery JHR, Smith ML, Lynch AG

Scientific reports, 2018

doi:10.1038/s41598-018-31524-0.

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types.

Lun ATL, Pagès H, Smith ML

PLoS computational biology, 2018

doi:10.1371/journal.pcbi.1006135.

Authoring Bioconductor workflows with BiocWorkflowTools.

Smith ML, Oleś AK, Huber W

2018

doi:10.12688/f1000research.14399.1.

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Farmery JHR, Smith ML, Lynch AG

Scientific reports, 2018

doi:10.1038/s41598-017-14403-y.