Katherine Siddle, Ph.D.

KATHERINE SIDDLE, Ph.D.

Katie was a postdoctoral fellow and research scientist in the Sabeti Lab where she investigated the evolution and epidemiology of viral pathogens, and the etiology of uncharacterized infections. Her research combined developing methods to improve the detection and assembly of viral genomes and applying these tools to surveil emerging infections, with a particular focus on viral hemorrhagic fevers and SARS-CoV-2.

Katie obtained her Ph.D. from the Institut Pasteur and the Université Pierre et Marie Curie in Paris, France, under Lluis Quintana-Murci, studying microRNA regulation in the human innate immune response to infection. Prior to this, Katie completed her BA and MPhil in Biological Anthropology at the University of Cambridge, UK.

Katie is currently an Assistant Professor in the department of Molecular Microbiology and Immunology at Brown University. She is also a core member of the Center for Computational Molecular Biology and an affiliate of the Brown Pandemic Center.

FIRST AUTHOR PUBLICATIONS

Capturing Sequence Diversity in Metagenomes with Comprehensive and Scalable Probe Design.

Nature Biotechnology. 2019.
Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, et al.

Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018.

The New England Journal of Medicine. 2018.
Siddle KJ, Eromon P, Barnes K, Mehta S, Oguzie J, Odia I, Schaffner SF, et al.

Bacterial Infection Drives the Expression Dynamics of microRNAs and Their isomiRs.

PLoS Genetics. 2015.
Siddle KJ , Tailleux L, Deschamps M, Loh YHE, Deluen C, Gicquel B, Antoniewski C, Barreiro LB, Farinelli L, Quintana-Murci L.

The Red Queen's long race: human adaptation to pathogen pressure.

Current Opinion in Genetics and Development. 2014.
Siddle KJ & Quintana-Murci L

A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection.

Genome Research. 2014.
Siddle KJ , Deschamps M, Tailleux L, Nédélec Y, Pothlichet J, Lugo-Villarino G, Libri V, Gicquel B, Neyrolles O, Laval G, Patin E, Barreiro LB, Quintana-Murci L.

Bases Adjacent to Mononucleotide Repeats Show an Increased Single Nucleotide Polymorphism Frequency in the Human Genome.

Bioinformatics. 2011.
Siddle KJ , Goodship JA, Keavney BD, Santibanez-Koref MF

Genetic diversity and evidence for population admixture in Batak Negritos from Palawan.

American Journal of Physical Anthropology. 2011.
Scholes C, Siddle KJ, Ducourneau A, Crivellaro F, Jarve M, Rootsi S, Bellatti M, Tabbada K, Mormina M, Reidla M, Villems R, Kivisild T, Lahr MM, Migliano AB
(* equal contributors)

SELECTED OTHER PUBLICATIONS

Negative Selection by Spiral Inertial Microfluidics Improves Viral Recovery and Sequencing from Blood.

Analytical Chemistry. 2018.
Choi K, Ryu H, Siddle K, Piantadosi A, Freimark L, Park DJ, Sabeti P, Han J.

miR-222 Isoforms Are Differentially Regulated by Type-I Interferon.

RNA. 2018.
Boisen ML, Hartnett JN, Shaffer JG, Goba A, Momoh M, Sandi JD, Fullah M.

miR-222 Isoforms Are Differentially Regulated by Type-I Interferon.

RNA. 2018.
Nejad C, Pillman KA, Siddle KJ, Pépin G, Änkö M, McCoy CE, Beilharz TH, et al.

Field Validation of Recombinant Antigen Immunoassays for Diagnosis of Lassa Fever.

Scientific Reports. 2018.
Boisen ML, Hartnett JN, Shaffer JG, Goba A, Momoh M, Sandi JD, Fullah M.

Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery.

Clinical Infectious Diseases. 2017.
Barnes KG, Kindrachuk J, Lin AE, Wohl S, Qu J, Tostenson SD, Dorman WR.

Widespread Shortening of 3’ Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection.

PLoS Genetics. 2016.
Pai, AA, Baharian G, Sabourin AP, Brinkworth JF, Nédélec Y, Foley JW, Grenier J.

The Impact of Agricultural Emergence on the Genetic History of African Rainforest Hunter-Gatherers and Agriculturalists.