Steif Lab University of British Columbia

Publication

Our research is dedicated to develop computational tools for the analysis of genomic data, with a particular focus on advancing methodologies for both single cell sequencing and cancer development analysis. You can check out our publications listed below, or find them listed on Google Scholar.

Highlighted

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers
clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers
Kieran R. Campbell, Adi Steif, Emma Laks, Hans Zahn, Daniel Lai, …, Pascale Walters, IMAXT Consortium, Alexandre Bouchard-Côté, Samuel Aparicio, Sohrab P. Shah
Genome Biology  ·  12 Mar 2019  ·  doi:10.1186/s13059-019-1645-z
Code Availablility
Data Access
Tool
Scalable whole-genome single-cell library preparation without preamplification
Scalable whole-genome single-cell library preparation without preamplification
Hans Zahn, Adi Steif, Emma Laks, Peter Eirew, Michael VanInsberghe, Sohrab P Shah, Samuel Aparicio, Carl L Hansen
Nature Methods  ·  09 Jan 2017  ·  doi:10.1038/nmeth.4140
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution
Peter Eirew, Adi Steif, Jaswinder Khattra, Gavin Ha, Damian Yap, …, Carl Hansen, Marco A. Marra, Carlos Caldas, Sohrab P. Shah, Samuel Aparicio
Nature  ·  26 Nov 2014  ·  doi:10.1038/nature13952

All

2023

A Human Breast Cell Atlas Mapping the Homeostatic Cellular Shifts in the Adult Breast
Austin D. Reed, Sara Pensa, Adi Steif, Jack Stenning, Daniel J. Kunz, …, Iain Goulding, Jennifer J. Gomm, Louise Jones, John C. Marioni, Walid T. Khaled
Cold Spring Harbor Laboratory  ·  21 Apr 2023  ·  doi:10.1101/2023.04.21.537845

2020

Tumour evolution at single-cell resolution
Adi Steif
University of British Columbia  ·  01 Jan 2020  ·  doi:10.14288/1.0365645

2019

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing
Emma Laks, Andrew McPherson, Hans Zahn, Daniel Lai, Adi Steif, …, Jean Fan, Hsuan Lee, Leonardo Sepulveda Duran, Chenglong Xia, Pu Zheng
Cell  ·  01 Nov 2019  ·  doi:10.1016/j.cell.2019.10.026
clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers
Kieran R. Campbell, Adi Steif, Emma Laks, Hans Zahn, Daniel Lai, …, Pascale Walters, IMAXT Consortium, Alexandre Bouchard-Côté, Samuel Aparicio, Sohrab P. Shah
Genome Biology  ·  12 Mar 2019  ·  doi:10.1186/s13059-019-1645-z

2018

Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires
Emma Laks, Hans Zahn, Daniel Lai, Andrew McPherson, Adi Steif, …, Andy J. Mungall, Marco A. Marra, Carl Hansen, Sohrab P. Shah, Samuel Aparicio
Cold Spring Harbor Laboratory  ·  07 Sep 2018  ·  doi:10.1101/411058

2017

ReMixT: clone-specific genomic structure estimation in cancer
Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, …, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp, Sohrab P. Shah
Genome Biology  ·  27 Jul 2017  ·  doi:10.1186/s13059-017-1267-2
E-scape: interactive visualization of single-cell phylogenetics and cancer evolution
Maia A Smith, Cydney B Nielsen, Fong Chun Chan, Andrew McPherson, Andrew Roth, Hossein Farahani, Daniel Machev, Adi Steif, Sohrab P Shah
Nature Methods  ·  30 May 2017  ·  doi:10.1038/nmeth.4303
ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data
Sohrab Salehi, Adi Steif, Andrew Roth, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P. Shah
Genome Biology  ·  01 Mar 2017  ·  doi:10.1186/s13059-017-1169-3
Scalable whole-genome single-cell library preparation without preamplification
Hans Zahn, Adi Steif, Emma Laks, Peter Eirew, Michael VanInsberghe, Sohrab P Shah, Samuel Aparicio, Carl L Hansen
Nature Methods  ·  09 Jan 2017  ·  doi:10.1038/nmeth.4140

2016

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates
Kaston Leung, Anders Klaus, Bill K. Lin, Emma Laks, Justina Biele, …, Anne-Marie Mes-Masson, Martin Hirst, Sohrab P. Shah, Samuel Aparicio, Carl L. Hansen
Proceedings of the National Academy of Sciences  ·  13 Jul 2016  ·  doi:10.1073/pnas.1520964113

2014

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution
Peter Eirew, Adi Steif, Jaswinder Khattra, Gavin Ha, Damian Yap, …, Carl Hansen, Marco A. Marra, Carlos Caldas, Sohrab P. Shah, Samuel Aparicio
Nature  ·  26 Nov 2014  ·  doi:10.1038/nature13952

2013

Transient RNA structure features are evolutionarily conserved and can be computationally predicted
Jing Yun A. Zhu, Adi Steif, Jeff R. Proctor, Irmtraud M. Meyer
Nucleic Acids Research  ·  26 Apr 2013  ·  doi:10.1093/nar/gkt319

2012

ThehokmRNA family
Adi Steif, Irmtraud M. Meyer
RNA Biology  ·  01 Dec 2012  ·  doi:10.4161/rna.22746