Dr Anna Cuomo

Anna is a Postdoctoral researcher at the Garvan Institute of Medical Research in Joseph Powell’s and Daniel MacArthur’s labs. Previously, she completed postdoctoral training at the Wellcome Trust Sanger Institute in Nicole Soranzo’s group, and obtained her PhD in Statistical Genetics at the Universi

Research Level

Postdoctoral Fellow

Biography

Anna is a Postdoctoral researcher at the Garvan Institute of Medical Research in Joseph Powell’s and Daniel MacArthur’s labs. Previously, she completed postdoctoral training at the Wellcome Trust Sanger Institute in Nicole Soranzo’s group, and obtained her PhD in Statistical Genetics at the University of Cambridge and the European Bioinformatics Institute, under the joint supervision of Oliver Stegle and John Marioni. Her PhD and postdoc work is concerned with the development of integrative statistical models to link DNA variants to single cell expression profiles, to uncover molecular mechanisms that might help unravelling the genotype-phenotype map. As part of this effort, she has contributed to the analysis of datasets from the HipSci (Human Induced Pluripotent Stem Cells Initiative) project, the HCA (Human Cell Atlas) and the sc-eQTL Gen (single-cell eQTL Gen) consortia. She is currently contributing to the analysis of data from the OneK1K project, where she studies the effect of rare and structural variants on blood single-cell expression profiles from nearly 2,000 Australian individuals.

Anna is a Postdoctoral researcher at the Garvan Institute of Medical Research in Joseph Powell’s and Daniel MacArthur’s labs. Previously, she completed postdoctoral training at the Wellcome Trust Sanger Institute in Nicole Soranzo’s group, and obtained her PhD in Statistical Genetics at the University of Cambridge and the European Bioinformatics Institute, under the joint supervision of Oliver Stegle and John Marioni. Her PhD and postdoc work is concerned with the development of integrative statistical models to link DNA variants to single cell expression profiles, to uncover molecular mechanisms that might help unravelling the genotype-phenotype map. As part of this effort, she has contributed to the analysis of datasets from the HipSci (Human Induced Pluripotent Stem Cells Initiative) project, the HCA (Human Cell Atlas) and the sc-eQTL Gen (single-cell eQTL Gen) consortia. She is currently contributing to the analysis of data from the OneK1K project, where she studies the effect of rare and structural variants on blood single-cell expression profiles from nearly 2,000 Australian individuals.

Education

2020 – PhD (Statistical Genetics), University of Cambridge – United Kingdom
2016 – MSc (Bioinformatics), Delft University of Technology – Netherlands
2014 – BSc (Mathematical Engineering), Milan Polytechnic – Italy

Selected Publications

Preprints

Anna SE Cuomo, Tobias Heinen, Danai Vagiaki, Danilo Horta, John C Marioni, Oliver Stegle. CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq. bioRxiv (2021, doi: https://doi.org/10.1101/2021.09.01.458524). link.

 

2021

Anna SE Cuomo, Giordano Alvari, Christina B Azodi, single-cell eQTLGen consortium, Davis J McCarthy & Marc Jan Bonder. Optimizing expression quantitative trait locus mapping workflows for single-cell studies. Genome Biology 22, 188 (2021). link.

 

Ricard Argelaguet, Anna SE Cuomo, Oliver Stegle & John C Marioni. Computational principles and challenges in single-cell data integration. Nature Biotechnology 39, 1202-1215 (2021). link.

 

Julie Jerber, Daniel D Seaton, Anna SE Cuomo, Natsuhiko Kumasaka, James Haldane, Juliette Steer, Minal Patel, Daniel Pearce, Malin Andersson, Marc Jan Bonder, Ed Mountjoy, Maya Ghoussaini, Madeline A Lancaster, John C Marioni, Florian T Merkle, Daniel J Gaffney, Oliver Stegle. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Nature Genetics 53, 304-312 (2021). link.

 

Christoph Muus, Malte D Luecken, Gökcen Eraslan, Lisa Sikkema, Avinash Waghray, Graham Heimberg,  Yoshihiko Kobayashi, Eeshit Dhaval Vaishnav, Ayshwarya Subramanian, Christopher Smillie, Karthik A Jagadeesh, Elizabeth Thu Duong, Evgenij Fiskin, Elena Torlai Triglia, Meshal Ansari, Peiwen Cai, Brian Lin, Justin Buchanan, Sijia Chen, Jian Shu, Adam L. Haber, Hattie Chung, Daniel T Montoro, Taylor Adams, Hananeh Aliee, Samuel J Allon, Zaneta Andrusivova, Ilias Angelidis, Orr Ashenberg, Kevin Bassler, Christophe Bécavin, Inbal Benhar, Joseph Bergenstråhle, Ludvig Bergenstråhle, Liam Bolt, Emelie Braun, Linh T Bui, Steven Callori, Mark Chaffin, Evgeny Chichelnitskiy, Joshua Chiou, Thomas M Conlon,  Michael S Cuoco, Anna SE Cuomo, Marie Deprez, Grant Duclos, Denise Fine, David S Fischer, Shila Ghazanfar, Astrid Gillich, Bruno Giotti, Joshua Gould, Minzhe Guo, Austin J Gutierrez, Arun C Habermann, Tyler Harvey, Peng He, Xiaomeng Hou, Lijuan Hu, Yan Hu, Alok Jaiswal, Lu Ji, Peiyong Jiang, Theodoros S Kapellos, Christin S Kuo, Ludvig Larsson, Michael A Leney-Greene, Kyungtae Lim, Monika Litviňuková, Leif S Ludwig, Soeren Lukassen, Wendy Luo, Henrike Maatz, Elo Madissoon, Lira Mamanova, Kasidet Manakongtreecheep, Sylvie Leroy, Christoph H Mayr, Ian M Mbano, Alexi M McAdams, Ahmad N Nabhan, Sarah K Nyquist, Lolita Penland, Olivier B Poirion, Sergio Poli, CanCan Qi, Rachel Queen, Daniel Reichart, Ivan Rosas, Jonas C Schupp, Conor V Shea, Xingyi Shi, Rahul Sinha, Rene V Sit, Kamil Slowikowski, Michal Slyper, Neal P Smith, Alex Sountoulidis, Maximilian Strunz, Travis B Sullivan, Dawei Sun, Carlos Talavera-López, Peng Tan, Jessica Tantivit, Kyle J Travaglini, Nathan R Tucker, Katherine A Vernon, Marc H Wadsworth, Julia Waldman, Xiuting Wang, Ke Xu, Wenjun Yan,  William Zhao, Carly GK Ziegler, The NHLBI LungMap Consortium & The Human Cell Atlas Lung Biological Network. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine 27, 546-559 (2021). link.

 

2020

Anna SE Cuomo, Daniel D Seaton, Davis J McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner, Andrew Knights, Kedar Nath Natarajan, HipSci Consortium, Ludovic Vallier, John C Marioni, Mariya Chhatriwala & Oliver Stegle. Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression. Nature Communications 11, 810 (2020). link.