Lydia Krasilnikova, Ph.D.

LYDIA KRASILNIKOVA, Ph.D.

Lydia Andreyevna Krasilnikova was an MEng student at MIT in Course 6-7 (Computer Science and Molecular Biology), a PhD candidate in Harvard’s department of Organismic and Evolutionary Biology, and then a postdoctoral associate in the lab. She worked on pathogen identification and characterization through metagenomic and amplicon sequencing, which she used to study disease outbreaks, especially among vulnerable and underserved populations. Her MEng thesis work focused on co-detected infections during the 2014-2016 Ebola outbreak in Sierra Leone. Her PhD thesis work focused on learning from SARS-CoV-2 outbreaks, especially the effect of vaccination on transmission, as well as cross-contamination detection and species identification from genomic sequencing data.

Outside of research, Lydia works on visual and written communication about math, science, and scientist culture. She has written for MIT Admissions and MIT Technology Review and has illustrated MIT outreach publications. You can follow her work at lakrasilnikova.home.blog.

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

Cell. 2015.
Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JL, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC

Discovery Of Novel Rhabdoviruses In The Blood Of Healthy Individuals From West Africa

PLoS Negl Trop Dis 17;9(3):e0003631
Stremlau MH, Andersen KG, Folarin OA, Grove JN, Odia I, Ehiane PE, Omoniwa O, Omoregie O, Jiang PP, Yozwiak NL, Matranga CB, Yang X, Gire SK, Winnicki SM, Tariyal R, Schaffner SF, Okokhere PO, Okogbenin S, Akpede GO, Asogun DA, Agbonlahor DE, Walker PJ, Tesh RB, Levin JZ, Garry RF, Sabeti PC, Happi CT

Enhanced Methods For Unbiased Deep Sequencing Of Lassa And Ebola RNA Viruses In Clinical And Biological Samples.

Genome Biol 15(11):519
Matranga CB, Andersen KG, Winnicki SM, Busby M, Gladden AD, Tewhey R, Stremlau M, Berlin A, Gire SK, England E, Moses LM, Mikkelsen TS, Odia I, Ehiane PE, Folarin O, Goba A, Kahn SH, Grant DS, Honko A, Hensley L, Happi C, Garry RF, Malboeuf CM, Birren BW, Gnirke A, Levin JZ, Sabeti PC

Clinical Illness And Outcomes In Patients With Ebola In Sierra Leone

N Engl J Med 371(22):2092-100
Schieffelin JS, Shaffer JG, Goba A, Gbakie M, Gire SK, Colubri A, Sealfon RSG, Kanneh L, Moigboi A, Momoh M, Fullah M, Moses LM, Brown BL, Andersen KG, Winnicki SM, Schaffner SF, Park DJ, Yozwiak NL, Jiang PP, Kargbo D, Jalloh S, Fonnie M, Sinnah V, French I, Kovoma A, Kamara FK, Tucker V, Konuwa E, Sellu J, Mustapha I, Foday M, Yillah M, Kanneh F, Saffa S, Massally JL, Boisen ML, Branco LM, Vandi MA, Grant DS, Happi C, Gevao SM, Fletcher TE, Fowler RA, Bausch DG, Sabeti PC, Khan SH, Garry RF for the KGH Lassa Fever Program, the Viral Hemorrhagic Fever Consortium and the WHO Clinical Response Team

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

Science 345(6202):1369-72
Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki SM, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC.

Research capacity. Enabling the genomic revolution in Africa.

Science 344(6190):1346-8
H3Africa Consortium

Identifying Recent Adaptations In Large-Scale Genomic Data

Cell 152(4):703-713
Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki SM, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, Cabili M, Adegbola RA, Bamezai RNK, Hill AVS, Vannberg FO, Rinn JL, 1000 Genomes Project, Lander ES, Schaffner SF, Sabeti PC

Early host-pathogen interactions in a marine bivalve: Crassostrea virginica pallial mucus modulates Perkinsus marinus growth and virulence.

Dis Aquat Organ. 104(3):237-47
Pales Espinosa E, Winnicki SM, Allam B.

Early host-pathogen interactions in marine bivalves: evidence that the alveolate parasite Perkinsus marinus infects through the oyster mantle during rejection of pseudofeces.