Katherine Siddle – Sabeti Lab

KATHERINE SIDDLE, Ph.D.

Katie Siddle is a postdoctoral fellow at Harvard University and the Broad Institute, where she is interested in the evolution of viral pathogens, host-pathogen interactions and the etiology of uncharacterized infections.

In her research Katie combines developing methods to improve the detection and assembly of viral genomes and active surveillance for emerging infections, with a particular focus on West Africa. Recently, Katie jointly developed and validated a novel tool to design optimized probe sets to enrich diverse viral sequences, improving the sensitivity of high-throughput sequencing. Katie also works closely with partners in Senegal and Nigeria to implement these technologies locally and study emerging infections in these regions. As part of this, Katie co-led a study of the genomic epidemiology of the 2018 Lassa virus outbreak in Nigeria. She is also studying other viral pathogens including Yellow fever virus and Dengue virus in West Africa to understand their diversity and detect biomarkers of infection.

Katie obtained her Ph.D. in human immunogenomics from the Institut Pasteur and the Université Pierre et Marie Curie in Paris, France, under Lluis Quintana-Murci. Her doctoral work focused on microRNA regulation in the human innate immune response to infection, where she performed the first study of the impact of external stimuli on the genetic regulation of microRNA expression and the first demonstration of consistent changes in microRNA isoform expression in response to infection. Katie was a fellow of the Pasteur-Paris University International Doctoral Program. Prior to this, Katie completed her BA and MPhil in Biological Anthropology at the University of Cambridge, UK, where she studied the genetic ancestry of indigenous populations in the Philippines.

Katie is the recipient of postdoctoral fellowships from Human Frontiers in Science Program (HFSP) and the Fondation pour la Recherche Médicale (FRM). Her work is currently supported by the American Society for Tropical Medicine and Hygiene (ASTMH) Centennial Award.

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.

KATHERINE SIDDLE, Ph.D.

FIRST AUTHOR PUBLICATIONS

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

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

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

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

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.

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

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

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

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

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

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

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

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

Nature Communications. 2014. Patin E, Siddle KJ, Laval G, Quach H, Harmant C, Becker N, Froment A.