Kieran Campbell Lab Toronto


Partially scraped from pubmed
Date Title Journal Authors
February 2024 The impacts of active and self-supervised learning on efficient annotation of single-cell expression data Nature Communications MJ Geuenich, D Gong, KR Campbell
January 2024 Beyond benchmarking: towards predictive models of dataset-specific single-cell RNA-seq pipeline performance Preprint C Fang, A Selega, KR Campbell
March 2023 Multi-objective Bayesian Optimization with Heuristic Objectives for Biomedical and Molecular Data Analysis Workflows Transactions on Machine Learning Research Alina Selega and Kieran R Campbell
October 2022 The differential impacts of dataset imbalance in single-cell data integration Preprint Hassaan Maan, Lin Zhang, Chengxin Yu, Michael Geuenich, Kieran R Campbell, Bo Wang
September 2022 Loss of apelin blocks the emergence of sprouting angiogenesis in experimental tumors. FASEB journal : official publication of the Federation of American Societies for Experimental Biology Azad, Abul K; Campbell, Kieran R; Zhabyeyev, Pavel; Oudit, Gavin Y; Moore, Ronald B; Murray, Allan G
June 2022 Multi-objective Bayesian Optimization with Heuristic Objectives for Biomedical and Molecular Data Analysis Workflows Preprint Alina Selega; Kieran R Campbell
April 2022 The basics of machine learning NEJM Evidence Michael Fralick, Kieran R Campbell
November 2021 The Landscape of COVID-19 Research in the United States: a Cross-sectional Study of Randomized Trials Registered on ClinicalTrials.Gov. Journal of general internal medicine Sacks, Chana A; North, Crystal M; Wolf, Molly; Dougan, Michael; Campbell, Kieran R; Moggridge, Jason; Fralick, Michael
September 2021 Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data. Cell systems Geuenich, Michael J; Hou, Jinyu; Lee, Sunyun; Ayub, Shanza; Jackson, Hartland W; Campbell, Kieran R
June 2021 Clonal fitness inferred from time-series modelling of single-cell cancer genomes. Nature Salehi, Sohrab; Kabeer, Farhia; Ceglia, Nicholas; Andronescu, Mirela; Williams, Marc J; Campbell, Kieran R; Masud, Tehmina; Wang, Beixi; Biele, Justina; Brimhall, Jazmine; Gee, David; Lee, Hakwoo; Ting, Jerome; Zhang, Allen W; Tran, Hoa; O'Flanagan, Ciara; Dorri, Fatemeh; Rusk, Nicole; de Algara, Teresa Ruiz; Lee, So Ra; Cheng, Brian Yu Chieh; Eirew, Peter; Kono, Takako; Pham, Jenifer; Grewal, Diljot; Lai, Daniel; Moore, Richard; Mungall, Andrew J; Marra, Marco A; None, None; McPherson, Andrew; Bouchard-Côté, Alexandre; Aparicio, Samuel; Shah, Sohrab P
April 2021 Modelling hereditary diffuse gastric cancer initiation using transgenic mouse-derived gastric organoids and single-cell sequencing. The Journal of pathology Dixon, Katherine; Brew, Tom; Farnell, David; Godwin, Tanis D; Cheung, Simon; Chow, Christine; Ta, Monica; Ho, Germain; Bui, Minh; Douglas, J Maxwell; Campbell, Kieran R; El-Naggar, Amal; Kaurah, Pardeep; Kalloger, Steve E; Lim, Howard J; Schaeffer, David F; Cochrane, Dawn; Guilford, Parry; Huntsman, David G
November 2020 What went wrong and when? Instance-wise Feature Importance for Time-series Models. NeurIPS 2020 Sana Tonekaboni, Shalmali Joshi, Kieran Campbell, David Duvenaud, Anna Goldenberg
August 2020 Computational modelling in single-cell cancer genomics: methods and future directions. Physical biology Zhang, Allen W; Campbell, Kieran R
July 2020 Single cell transcriptomes of normal endometrial derived organoids uncover novel cell type markers and cryptic differentiation of primary tumours. The Journal of pathology Cochrane, Dawn R; Campbell, Kieran R; Greening, Kendall; Ho, Germain C; Hopkins, James; Bui, Minh; Douglas, J Maxwell; Sharlandjieva, Vassilena; Munzur, Aslı D; Lai, Daniel; DeGrood, Maya; Gibbard, Evan W; Leung, Samuel; Boyd, Niki; Cheng, Angela S; Chow, Christine; Lim, Jamie Lp; Farnell, David A; Kommoss, Stefan; Kommoss, Friedrich; Roth, Andrew; Hoang, Lien; McAlpine, Jessica N; Shah, Sohrab P; Huntsman, David G
February 2020 Eleven grand challenges in single-cell data science. Genome biology Lähnemann, David; Köster, Johannes; Szczurek, Ewa; McCarthy, Davis J; Hicks, Stephanie C; Robinson, Mark D; Vallejos, Catalina A; Campbell, Kieran R; Beerenwinkel, Niko; Mahfouz, Ahmed; Pinello, Luca; Skums, Pavel; Stamatakis, Alexandros; Attolini, Camille Stephan-Otto; Aparicio, Samuel; Baaijens, Jasmijn; Balvert, Marleen; Barbanson, Buys de; Cappuccio, Antonio; Corleone, Giacomo; Dutilh, Bas E; Florescu, Maria; Guryev, Victor; Holmer, Rens; Jahn, Katharina; Lobo, Thamar Jessurun; Keizer, Emma M; Khatri, Indu; Kielbasa, Szymon M; Korbel, Jan O; Kozlov, Alexey M; Kuo, Tzu-Hao; Lelieveldt, Boudewijn P F; Mandoiu, Ion I; Marioni, John C; Marschall, Tobias; Mölder, Felix; Niknejad, Amir; Raczkowski, Lukasz; Reinders, Marcel; Ridder, Jeroen de; Saliba, Antoine-Emmanuel; Somarakis, Antonios; Stegle, Oliver; Theis, Fabian J; Yang, Huan; Zelikovsky, Alex; McHardy, Alice C; Raphael, Benjamin J; Shah, Sohrab P; Schönhuth, Alexander
October 2019 Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses. Genome biology O'Flanagan, Ciara H; Campbell, Kieran R; Zhang, Allen W; Kabeer, Farhia; Lim, Jamie L P; Biele, Justina; Eirew, Peter; Lai, Daniel; McPherson, Andrew; Kong, Esther; Bates, Cherie; Borkowski, Kelly; Wiens, Matt; Hewitson, Brittany; Hopkins, James; Pham, Jenifer; Ceglia, Nicholas; Moore, Richard; Mungall, Andrew J; McAlpine, Jessica N; None, None; Shah, Sohrab P; Aparicio, Samuel
September 2019 Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling. Nature methods Zhang, Allen W; O'Flanagan, Ciara; Chavez, Elizabeth A; Lim, Jamie L P; Ceglia, Nicholas; McPherson, Andrew; Wiens, Matt; Walters, Pascale; Chan, Tim; Hewitson, Brittany; Lai, Daniel; Mottok, Anja; Sarkozy, Clementine; Chong, Lauren; Aoki, Tomohiro; Wang, Xuehai; Weng, Andrew P; McAlpine, Jessica N; Aparicio, Samuel; Steidl, Christian; Campbell, Kieran R; Shah, Sohrab P
June 2019 Decomposing feature-level variation with Covariate Gaussian Process Latent Variable Models. ICML 2019 (Proceedings of Machine Learning Research) Kaspar Märtens, Kieran Campbell, Christopher Yau
March 2019 clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers. Genome biology Campbell, Kieran R; Steif, Adi; Laks, Emma; Zahn, Hans; Lai, Daniel; McPherson, Andrew; Farahani, Hossein; Kabeer, Farhia; O'Flanagan, Ciara; Biele, Justina; Brimhall, Jazmine; Wang, Beixi; Walters, Pascale; None, None; Bouchard-Côté, Alexandre; Aparicio, Samuel; Shah, Sohrab P
December 2018 Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes. Cell stem cell Lang, Charmaine; Campbell, Kieran R; Ryan, Brent J; Carling, Phillippa; Attar, Moustafa; Vowles, Jane; Perestenko, Olga V; Bowden, Rory; Baig, Fahd; Kasten, Meike; Hu, Michele T; Cowley, Sally A; Webber, Caleb; Wade-Martins, Richard
June 2018 A descriptive marker gene approach to single-cell pseudotime inference. Bioinformatics (Oxford, England) Campbell, Kieran R; Yau, Christopher
June 2018 Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data. Nature communications Campbell, Kieran R; Yau, Christopher
May 2017 Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers. Wellcome open research Campbell, Kieran R; Yau, Christopher
January 2017 Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics (Oxford, England) McCarthy, Davis J; Campbell, Kieran R; Lun, Aaron T L; Wills, Quin F
December 2016 switchde: inference of switch-like differential expression along single-cell trajectories. Bioinformatics (Oxford, England) Campbell, Kieran R; Yau, Christopher
November 2016 Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference. PLoS computational biology Campbell, Kieran R; Yau, Christopher