| June 2024 |
Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance |
Genome Biology |
C Fang, A Selega, KR Campbell |
| March 2024 |
Segmentation error aware clustering for highly multiplexed imaging |
Preprint |
Yuju Lee, Edward L. Y. Chen, Darren C. H. Chan, Anuroopa Dinesh, Somaieh Afiuni-Zadeh, Conor Klamann, Alina Selega, Miralem Mrkonjic, Hartland W Jackson, Kieran R Campbell |
| March 2024 |
Characterizing the impacts of dataset imbalance on single-cell data integration |
Nature Biotechnology |
Hassaan Maan, Lin Zhang, Chengxin Yu, Michael Geuenich, Kieran R. Campbell, and Bo Wang. |
| 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 |
| 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 |
