Publications by authors named "Alexandre Bouchard-Cote"

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PhyClone: accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing.
Emilia Hurtado, Alexandre Bouchard-Côté, Andrew Roth

Bioinformatics· July 2025

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Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix.
Semih Kurt, Alexandre Bouchard-Côté, Jens Lagergren

Bioinformatics· November 2024

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SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data.
Eric Lee, Kevin Chern, Michael Nissen, Xuehai Wang,

Bioinformatics· June 2023

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Accurate determination of CRISPR-mediated gene fitness in transplantable tumours.
Peter Eirew, Ciara O'Flanagan, Jerome Ting, Sohrab Salehi, Jazmine Brimhall

Nat Commun· August 2022

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Clonal fitness inferred from time-series modelling of single-cell cancer genomes.
Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J Williams

Nature· July 2021

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Somatic mutation detection and classification through probabilistic integration of clonal population information.
Fatemeh Dorri, Sean Jewell, Alexandre Bouchard-Côté, Sohrab P Shah

Commun Biol· April 2020

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An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics.
Liangliang Wang, Shijia Wang, Alexandre Bouchard-Côté

Syst Biol· January 2020

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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

Genome Biol· March 2019

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Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.
Allen W Zhang, Andrew McPherson, Katy Milne, David R Kroeger, Phineas T Hamilton

Cell· June 2018

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Correction to: ReMixT: clone-specific genomic structure estimation in cancer.
Andrew W McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif

Genome Biol· October 2017

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A Poissonian Model of Indel Rate Variation for Phylogenetic Tree Inference.
Yongliang Zhai, Bouchard-Côté Alexandre

Syst Biol· September 2017

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ReMixT: clone-specific genomic structure estimation in cancer.
Andrew W McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif

Genome Biol· July 2017

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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

Genome Biol· March 2017

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Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.
Andrew McPherson, Andrew Roth, Emma Laks, Tehmina Masud, Ali Bashashati

Nat Genet· July 2016

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Clonal genotype and population structure inference from single-cell tumor sequencing.
Andrew Roth, Andrew McPherson, Emma Laks, Justina Biele, Damian Yap

Nat Methods· July 2016

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PyClone: statistical inference of clonal population structure in cancer.
Andrew Roth, Jaswinder Khattra, Damian Yap, Adrian Wan, Emma Laks

Nat Methods· April 2014

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A note on probabilistic models over strings: the linear algebra approach.
Alexandre Bouchard-Côté

Bull Math Biol· December 2013

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Automated reconstruction of ancient languages using probabilistic models of sound change.
Alexandre Bouchard-Côté, David Hall, Thomas L Griffiths, Dan Klein

Proc Natl Acad Sci U S A· March 2013

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Evolutionary inference via the Poisson Indel Process.
Alexandre Bouchard-Côté, Michael I Jordan

Proc Natl Acad Sci U S A· January 2013

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Phylogenetic inference via sequential Monte Carlo.
Alexandre Bouchard-Côté, Sriram Sankararaman, Michael I Jordan

Syst Biol· July 2012

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