Ph.D. Thesis

• One and Two Locus Likelihoods Under Complex Demography.
  Statistics, UC Berkeley, December 2015. {pdf}

Papers

• Viral Detection by Reverse Transcriptase Polymerase Chain Reaction in Upper Respiratory Tract and Metagenomic RNA Sequencing in Lower Respiratory Tract in Critically Ill Children With Suspected Lower Respiratory Tract Infection. Osborne, C. et al. Pediatric Critical Care Medicine (2023). {Journal}

• Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children. Mick, E.*, Tsitsiklis, A.*, Kamm, J.*, …, Mourani, P., Langelier, C. Journal of Clinical Investigation (2023). {Journal} {Preprint} {Code}

• A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants. Albright, J. et al. mSystems (2023). {Journal} {Preprint}

• Prolonged silent carriage, genomic virulence potential and transmission between staff and patients characterize a neonatal intensive care unit outbreak of methicillin-resistant Staphylococcus aureus. Madera et al. Infection Control & Hospital Epidemiology (2022). {Journal} {Preprint}

• Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy. Parikh, V. et al. Nature Communications (2022). {Journal} {Preprint}

• Functional transcriptomic studies of immune responses and endotoxin tolerance in early human sepsis. Leligdowicz, A. et al. Shock: Injury, Inflammation, and Sepsis: Laboratory and Clinical Approaches (2022). {Journal}

• Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics. Tsitsiklis, A. et al. The Lancet Microbe (2022). {Journal}

• Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. Stoddard, G., et al. BMC Public Health (2022). {Journal} {Preprint}

• SARS-CoV-2 infection of rhesus macaques treated early with human COVID-19 convalescent plasma. Deere, J. et al. Microbiology Spectrum (2021). {Journal}

• Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco. Chamie, G., et al. Clinical Infectious Diseases (2021). {Journal} {Preprint}

• Temporal Airway Microbiome Changes Related to Ventilator Associated Pneumonia in Children. Mourani, P., et al. European Respiratory Journal (2021). {Journal}

• Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by RT-PCR. Vanaerschot, M., et al. Journal of Clinical Microbiology (2020). {Journal} {Preprint}

• Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2. Mick, E.*, Kamm, J.*, Pisco, A., …, Kistler, A., Langelier, C. Nature Communications (2020). {Journal} {Code} {Preprint}

• High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs. Gorzynski, J., et al (2020). {Preprint}

• Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19. Shah, S., et al. EClinicalMedicine (2020). {Journal} {Preprint}

• Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh. Saha, S., et al. Microbiology Resource Announcements (2020). {Journal}

• Sepsis from an apheresis platelet contaminated with Acinetobacter calcoaceticus/baumannii complex bacteria and Staphylococcus saprophyticus after pathogen reduction. Fridey, J., et al. Transfusion (2020). {Journal}

• Insights into human genetic variation and population history from 929 diverse genomes. Bergström, A., et al. Science (2020). {Journal} {Preprint}

• Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing. Crawford, E.*, Kamm, J.*, Miller S., Li L., Caldera S., …, Langelier, C. Clinical Infectious Diseases (2019). {Journal} {Preprint}

• Inference of complex population histories using whole-genome sequences from multiple populations. Steinrücken, M., Kamm, J., Spence, J.P., and Song, Y.S. PNAS (2019). {Journal} {Preprint} {Software: diCal2}

• Sepsis Attributed to Bacterial Contamination of Platelets Associated with a Potential Common Source — Multiple States, 2018. Jones, S., et al. Morbidity and Mortality Weekly Report (2019). {Journal}

• Efficiently inferring the demographic history of many populations with allele count data. Kamm, J., Terhorst, J., Durbin, R., and Song, Y.S. Journal of the American Statistical Association (2019). {Journal} {Preprint} {Software: momi2}

• The first horse herders and the impact of early Bronze Age steppe expansions into Asia. de Barros Damgaard, P.*, Martiniano, R.*, Kamm, J.*, Moreno-Mayar, J. V.*, … Durbin, R., and Willerslev, E. Science (2018). {Journal}

• Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans. Steinrücken, M., Spence, J.P., Kamm, J.A., Wieczorek, E., and Song, Y.S. Molecular Ecology (2018). {Journal} {Preprint}

• Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Moreno-Mayar, J.V., Potter, B.A., Vinner, L, Steinrücken, M. Rasmussen, S., Terhorst, J., Kamm, J.A., Albrechtsen, A., Malaspinas, A.-S., Sikora, M., Reuther, J.D., Irish, J.D., Malhi, R.S., Orlando, L., Song, Y.S., Nielsen, R., Meltzer, D.J., and Willerslev, E. Nature, Vol. 553 (2018) 203-207. {Journal}

• Robust and scalable inference of population history from hundreds of unphased whole genomes. Terhorst, J., Kamm, J.A., and Song, Y.S. Nature Genetics, Vol. 49 (2017) 303-309. {Journal} {Software: SMC++}

• Efficient computation of the joint sample frequency spectra for multiple populations. Kamm, J.A., Terhorst, J., and Song, Y.S. Journal of Computational and Graphical Statistics, Vol. 26, No. 1 (2017) 182-194. {Journal} {Preprint} {Software: momi}

• Two-Locus Likelihoods under Variable Population Size and Fine-Scale Recombination Rate Estimation. Kamm, J.A.*, Spence, J.P.*, Chan, J., and Song, Y.S. Genetics, Vol. 203 No. 3 (2016) 1381-1399 2016. {Journal} {Preprint} {Software: LDpop}

• The site frequency spectrum for general coalescents. Spence, J.*, Kamm, J.A.*, and Song, Y.S.
  Genetics, Vol. 202 No. 4 (2016) 1549-1561. {Journal} {Preprint}

• Decoding coalescent hidden Markov models in linear time. Harris, K., Sheehan, S., Kamm, J.A., Song, Y.S. Proc. 18th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB), LNBI Vol. 8394, (2014), pp 100-114. {Journal} {Preprint}

• Approximate sampling formulae for general finite-alleles models of mutation. Bhaskar, A., Kamm, J.A., and Song, Y.S. Advances in Applied Probability, 44 (2012) 408-428. {Journal} {Preprint}

Posters

• Learning history from the SFS of low- and high-coverage ancient DNA.
  PopGroup @ University of Bristol, 2018. {pdf}
• LDpop: 2-locus likelihoods for recombination map estimation under variable population size.
  Probabilistic Modeling in Genomics @ Oxford, 2016. {pdf}
• momi: a new method for computing the multipopulation sample frequency spectrum.
  Probabilistic Modeling in Genomics @ Cold Spring Harbor, 2015. {pdf}