CV

PDF version of my CV available here.

Postgraduate career

2021- Principal Investigator / Senior Researcher, Life Sciences Centre at Vilnius University
2020- Consultant, Ring Therapeutics
2018- Consultant, The Scripps Research Institute
2018- Consultant, Chan Zuckerberg BioHub
2016-2018 Mahan Postdoctoral Fellowship, Fred Hutchinson Cancer Research Center
Mentor: Trevor Bedford.

Education

2011-2016 PhD, University of Edinburgh, Edinburgh, UK.
Supervisor: Prof. Andrew Rambaut, secondary supervisor: Prof. Andrew Leigh-Brown; Thesis examiners: Prof. Oliver G Pybus, Prof. Paul Sharp.
2007-2011 BSc, Biological Sciences with Honours in Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
First Class, Ashworth Prize and Class Medal

Publications

Global disparities in SARS-CoV-2 genomic surveillance

Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Bulgarian SARS-CoV-2 sequencing group, Communicable Diseases Genomics Network (Australia and New Zealand), COVID-19 Impact Project, Danish Covid-19 Genome Consortium, Fiocruz COVID-19 Genomic Surveillance Network, GISAID core curation team, Network for Genomic Surveillance in South Africa (NGS-SA), Swiss SARS-CoV-2 Sequencing Consortium, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR, 2021. "Global disparities in SARS-CoV-2 genomic surveillance". Nature Communications 13: 7003.

Accumulated metagenomic studies reveal recent migration, whole genome evolution, and taxonomic incompleteness of orthomyxoviruses

Dudas G and Batson J, 2022. "Accumulated metagenomic studies reveal recent migration, whole genome evolution, and taxonomic incompleteness of orthomyxoviruses". bioRxiv 2022.08.31.505987

Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

Dudas G, Hong SL, Potter B, Calvignac-Spencer S, Niatou-Singa FS, Tombolomako TB, Fuh-Neba T, Vickos U, Ulrich M, Leendertz FH, Khan K, Huber C, Watts A, Olendraitė I, Snijder J, Wijnant KN, Bonvin AMJJ, Martres P, Behillil S, Ayouba A, Maidadi FM, Meta Djomsi D, Godwe C, Butel C, Šimaitis A, Gabrielaitė M, Katėnaitė M, Norvilas R, Raugaitė L, Koyaweda G, Kaleb Kandou J, Jonikas R, Nasvytienė I, Žemeckienė Ž, Gečys D, Tamušauskaitė K, Norkienė M, Vasiliūnaitė E, Žiogienė D, Timinskas A, Šukys M, Šarauskas M, Alzbutas G, Amuri A, Lusamaki E, Makangara J, Muyembe F, Lofiko E, Mbala P, Tamfum J, Darnycka Belizaire M, Essomba R, Assoumou M, Mboringong A, Dieng A, Juozapaitė D, Hosch S, Obama J, Ondo'o Ayekaba M, Naumovas D, Pautienius A, Rafaï C, Vitkauskienė A, Ugenskienė R, Gedvilaitė A, Čereškevičius D, Lesauskaitė V, Žemaitis L, Griškevičius L, Baele G, 2021. "Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions". Nature Communications 12: 5769.

Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome

Arze CA, Springer S, Dudas G, P Sneha, Bhattacharyya A, Swaminathan H, Brugnara C, Delagrave S, Ong T, Kahvejian A, Echelard Y, Weinstein EG, Hajjar RJ, Andersen KG, Yozwiak NL, 2021. "Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome". Cell Host & Microbe 29(8):1305-1315.e6.

Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay

Batson J, Kistler A, Dudas G, Li L, Ratnasari K, Haas-Stapleton E, Logan P, Retallack H, 2021. "Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay". eLife 10:e68353

Polymorphism of Genetic Ambigrams

Dudas G, Huber G, Wilkinson M, Yllanes D, 2021. "Polymorphism of Genetic Ambigrams". Virus Evolution 7(1): veab038.

The ability of single genes vs full genomes to resolve time and space in outbreak analysis

Dudas G, Bedford T, 2019. "The ability of single genes vs full genomes to resolve time and space in outbreak analysis". BMC Evolutionary Biology 19: 232.

MERS-CoV spillover at the camel-human interface

Dudas G, de Carvalho LM, Rambaut A, Bedford T, 2017. "MERS-CoV spillover at the camel-human interface". eLife 7: e31257.

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Mary Baniecki L, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC Jr, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Edgar W. Kopp IV, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG, 2017. "Genomic epidemiology reveals multiple introductions of Zika virus into the United States". Nature 546(7658): 401:405.

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Dudas G, de Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D’Ambrozio J, Dellicour S, di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A, 2017. "Virus genomes reveal factors that spread and sustained the Ebola epidemic". Nature 544(7650): 309:315.

Comment on “Mutation rate and genotype variation of Ebola virus from Mali case sequences”

Rambaut A, Dudas G, de Carvalho LM, Park DJ, Yozwiak NL, Holmes EC, Andersen KG, 2016. "Comment on “Mutation rate and genotype variation of Ebola virus from Mali case sequences”". Science 353(6300): 658.

MERS-CoV recombination: implications about the reservoir and potential for adaptation

Dudas G, Rambaut A, 2016. "MERS-CoV recombination: implications about the reservoir and potential for adaptation". Virus Evolution 2(1): vev023.

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

Park DJ, Dudas G, Wohl S, Goba A, Whitmer, SLM and 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, P, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally, James LB and 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 and Rambaut A, Garry RF, Sabeti PC, 2015. "Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone". Cell 161(7):1516-1526.

Reassortment between Influenza B Lineages and the Emergence of a Coadapted PB1–PB2–HA Gene Complex

Dudas G, Bedford T, Lycett S, Rambaut A, 2014. "Reassortment between Influenza B Lineages and the Emergence of a Coadapted PB1–PB2–HA Gene Complex", Molecular Biology and Evolution 32(1):162-172.

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

Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang P, Nekoui M, Colubri A, Moinya Coomber R, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Abdul Jalloh A, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, James L. B. Massally, 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, 2014. "Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak". Science 345(6202): 1369-1372.

Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak

Dudas G, Rambaut A, 2014. "Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak". PLOS Currents Outbreaks Edition 1.

Research contributions

Fitting stochastic epidemic models to gene genealogies using linear noise approximation

Tang M, Dudas G, Bedford T, Minin VN., 2023. "Fitting stochastic epidemic models to gene genealogies using linear noise approximation". Annals of Applied Statistics 17(1): 1-22.

Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades

Klitting R, Kafetzopoulou LE, Thiery W, Dudas G, Gryseels S, Kotamarthi A, Vrancken B, Gangavarapu K, Momoh M, Sandi JD, Goba A, Alhasan F, Grant DS, Okogbenin S, Ogbaini-Emovo E, Garry RF, Smither AR, Zeller M, Pauthner MG, McGraw M, Hughes LD, Duraffour S, Günther S, Suchard MA, Lemey P, Andersen KG, Dellicour S, 2021. "Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades". Nature Communications 13: 5596.

Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics

Tsitsiklis A, Osborne CM, Kamm J, Williamson K, Kalantar K, Dudas G, Caldera S, Lyden A, Tan M, Neff N, Soesanto V, Harris JK, Ambroggio L, Maddux AB, Carpenter TC, Reeder RW, Locandro C, Simões EAF, Leroue MK, Hall MW, Zuppa AF, Carcillo J, Meert KL, Sapru A, Pollack MM, McQuillen PS, Notterman DA, Dean JM, Zinter MS, Wagner BD, DeRisi JL, Mourani PM, Langelier CR, 2022. "Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics". The Lancet Microbe 3(4): e284-e293.

Antibody escape and global spread of SARS-CoV-2 lineage A.27

Kaleta T, Kern L, Hong S, Hölzer M, Kochs G, Beer J, Schnepf D, Schwemmle M, Bollen N, Kolb P, Huber M, Ulferts S, Weigang S, Dudas G, Wittig A, Jaki L, Padane A, Lagare A, Salou M, Ozer E, Nnaemeka N, Odoom J, Rutayisire R, Benkahla A, Akoua-Koffi C, Ouedraogo AS, Simon-Loriere E, Enouf V, Kröger S, Calvignac-Spencer S, Baele G, Panning M, Fuchs J, 2022. "Antibody escape and global spread of SARS-CoV-2 lineage A.27". Nature Communications 13: 1152.

Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies

Chazot N, Condamine FL, Dudas G, Peña C, Kodandaramaiah U, Matos-Maraví P, Aduse-Poku K, Elias M, Warren A, Lohman DJ, Penz CM, DeVries P, Fric ZF, Nylin S, Müller C, Kawahara AY, Silva-Brandão KL, Lamas G, Kleckova I, Zubek A, Ortiz-Acevedo E, Vila R, Vane-Wright RI, Mullen SP, Jiggins CD, Wheat C, Freitas AVL, Wahlberg N, 2021. "Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies". Nature Communications 12: 5717.

Bulk Milk Tank Samples Are Suitable to Assess Circulation of Tick-Borne Encephalitis Virus in High Endemic Areas

Pautienius A, Dudas G, Simkute E, Grigas J, Zakiene I, Paulauskas A, Armonaite A, Zienius D, Slyzius E, Stankevicius A., 2021. "Bulk Milk Tank Samples Are Suitable to Assess Circulation of Tick-Borne Encephalitis Virus in High Endemic Areas". Viruses 13(9): 1772.

Emergence of an early SARS-CoV-2 epidemic in the United States

Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos Jr G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh N, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG, 2021. "Emergence of an early SARS-CoV-2 epidemic in the United States". Cell 184, 4939–4952.

Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and Operations

Pirnay JP, Selhorst P, Hong SL, Cochez C, Potter B, Maes P, Petrillo M, Dudas G, Claes V, Van der Beken Y, Verbeken G, Degueldre J, Dellicour S, Cuypers L, T'Sas F, Van den Eede G, Verhasselt B, Weuts W, Smets C, Mertens J, Geeraerts P, Ariën KK, André E, Neirinckx P, Soentjens P, Baele G, 2021. "Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and Operations". Viruses 13(7): 1359.

Estimating effective population size changes from preferentially sampled genetic sequences

Karcher MD, Carvalho MC, Suchard MA, Dudas G, Minin VN., 2020. "Estimating effective population size changes from preferentially sampled genetic sequences". PLoS Comput Biol16(10): e1007774.

Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

Müller NF, Stolz U, Dudas G, Stadler T, Vaughan TG, 2019. "Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses". PNAS: 117 (29) 17104-17111.

Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations

Müller NF, Dudas G, Stadler T, 2019. "Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations". Virus Evolution 5(2): vez030.

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Rambaut A, Lemey P, 2018. "Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak". Nature Communications 9: 2222.

MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity

Chu DKW, Hui Kenrie PY, Perera RAPM, Miguel E, Niemeyer D, Zhao J, Channappanavar R, Dudas G, Oladipo JO, Traoré A, Fassi-Fihri O, Ali A, Demissie GF, Muth D, Chan MCW, Nicholls JM, Meyerholz DK, Kuranga SA, Mamo G, Zhou Z, So RTY, Hemida MG, Webby RJ, Roger F, Rambaut A, Poon LLM, Perlman S, Drosten C, Chevalier V, Peiris M, 2018. "MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity". PNAS 115(12): 3144-3149.

Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors

Whitmer SLM, Ladner JT, Wiley MR, Patel K, Dudas G, Rambaut A, Sahr F, Prieto K, Shepard SS, Carmody E, Knust B, Naidoo D, Deen G, Formenty P, Nichol ST, Palacios G, Ströher U, 2018. "Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors". Cell Reports 22(5): 1159-1168.

Preliminary Evaluation of the Effect of Investigational Ebola Virus Disease Treatments on Viral Genome Sequences

Whitmer SLM, Albariño C, Shepard SS, Dudas G, Sheth M, Brown SC, Cannon D, Erickson BR, Gibbons A, Schuh A, Sealy T, Ervin E, Frace M, Uyeki TM, Nichol ST, Ströher U, 2016. "Preliminary Evaluation of the Effect of Investigational Ebola Virus Disease Treatments on Viral Genome Sequences". Journal of Infectious Diseases: jiw177.

The global antigenic diversity of swine influenza A viruses

Lewis NS, Russell CA, Langat P, Anderson TK, Berger K, Bielejec F, Burke DF, Dudas G, Fonville JM, Fouchier RAM, Kellam P, Koel BF, Lemey P, Nguyen T, Nuansrichy B, Peiris MJS, Saito T, Simon G, Skepner E, Takemae N, Webby RJ, Van Reeth K, Brookes SM, Larsen L, Watson SJ, Brown IH, Vincent AL, 2016. "The global antigenic diversity of swine influenza A viruses". eLife 5: e12217.

Real-time, portable genome sequencing for Ebola surveillance

Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, Bore JA, Koundouno R, Dudas G, Mikhail A, Ouédraogo N, Afrough B, Bah A, Baum JHJ, Becker-Ziaja B, Boettcher JP, Cabeza-Cabrerizo M, Camino-Sánchez A, Carter LL, Doerrbecker J, Enkirch T, García-Dorival I, Hetzelt N, Hinzmann J, Holm T, Kafetzopoulou LE, Koropogui M, Kosgey A, Kuisma E, Logue CH, Mazzarelli A, Meisel S, Mertens M, Michel J, Ngabo D, Nitzsche K, Pallasch E, Patrono LV, Portmann J, Repits JG, Rickett NY, Sachse A, Singethan K, Vitoriano I, Yemanaberhan RL, Zekeng EG, Racine T, Bello A, Faye O, Faye O, Magassouba N, Williams CV, Amburgey V, Winona L, Davis E, Gerlach J, Washington F, Monteil V, Jourdain M, Bererd M, Camara A, Somlare H, Camara A, Gerard M, Bado G, Baillet B, Delaune D, Yacouba Nebie KY, Diarra A, Savane Y, Pallawo RB, Gutierrez GJ, Milhano N, Roger I, Williams CJ, Yattara F, Lewandowski K, Taylor J, Rachwal P, Turner DJ, Pollakis G, Hiscox JA, Matthews DA, O’Shea MK, Johnston AMcD, Wilson D, Hutley E, Smit E, Di Caro A, Wölfel R, Stoecker K, Fleischmann E, Gabriel M, Weller SA, Koivogui L, Diallo B, Keïta S, Rambaut A, Formenty P, Günther S, Carroll MW, 2016. "Real-time, portable genome sequencing for Ebola surveillance". Nature 530(7589), 228-232.

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases

Arias A, Watson SJ, Asogun D, Tobin EA, Lu J, Phan MVT, Jah U, Wadoum REG, Meredith L, Caddy LTS, Tarawalie A, Langat P, Dudas G, Faria NR, Dellicour S, Kamara A, Kargbo B, Kamara BO, Gevao S, Cooper D, Newport M, Horby P, Dunning J, Sahr F, Brooks T, Simpson AJH, Groppelli E, Liu G, Mulakken N, Rhodes K, Akpablie J, Yoti Z, Lamunu M, Vitto E, Otim P, Owilli C, Boateng I, Okoror L, Omomoh E, Oyakhilome J, Omiunu R, Yemisis I, Adomeh D, Ehikhiametalor S, Akhilomen P, Aire C, Kurth A, Cook N, Baumann J, Gabriel M, Wölfel R, Di Caro A, Carroll MW, Günther S, Redd J, Naidoo D, Pybus OG, Rambaut A, Kellam P, Goodfellow I, Cotten M, 2016. "Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases". Virus Evolution 2(1): vew016.

Evolution and Spread of Ebola Virus in Liberia, 2014–2015

Ladner JT, Wiley MR, Mate S, Dudas G, Prieto K, Lovett S, Nagle ER, Beitzel B, Gilbert ML, Fakoli L, Diclaro JW, Schoepp RJ, Fair J, Kuhn JH, Hensley LE, Park DJ, Sabeti PC, Rambaut A, Sanchez-Lockhart M, Bolay FK, Kugelman JR, Palacios G, 2015. "Evolution and Spread of Ebola Virus in Liberia, 2014–2015". Cell 18(6), 659-669.

Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa

Carroll MW, Matthews DA, Hiscox JA, Elmore MJ, Pollakis G, Rambaut A, Hewson R, García-Dorival I, Bore JA, Koundouno R, Abdellati S, Afrough B, Aiyepada J, Akhilomen P, Asogun D, Atkinson B, Badusche M, Bah A, Bate S, Baumann J, Becker D, Becker-Ziaja B, Bocquin A, Borremans B, Bosworth A, Boettcher JP, Cannas A, Carletti F, Castilletti C, Clark S, Colavita F, Diederich S, Donatus A, Duraffour S, Ehichioya D, Ellerbrok H, Fernandez-Garcia MD, Fizet A, Fleischmann E, Gryseels S, Hermelink A, Hinzmann J, Hopf-Guevara U, Ighodalo Y, Jameson L, Kelterbaum A, Kis Z, Kloth S, Kohl C, Korva M, Kraus A, Kuisma E, Kurth A, Liedigk B, Logue CH, Lüdtke A, Maes P, McCowen J, Mély S, Mertens M, Meschi S, Meyer B, Michel J, Molkenthin P, Muñoz-Fontela C, Muth D, Newman ENC, Ngabo D, Oestereich L, Okosun J, Olokor T, Omiunu R, Omomoh E, Pallasch E, Pályi B, Portmann J, Pottage T, Pratt C, Priesnitz S, Quartu S, Rappe J, Repits J, Richter M, Rudolf M, Sachse A, Schmidt KM, Schudt G, Strecker T, Thom R, Thomas S, Tobin E, Tolley H, Trautner J, Vermoesen T, Vitoriano I, Wagner M, Wolff S, Yue C, Rosaria Capobianchi M, Kretschmer B, Hall Y, Kenny JG, Rickett NY, Dudas G, Coltart CEM, Kerber R, Steer D, Wright C, Senyah F, Keita S, Drury P, Diallo B, de Clerck H, Herp MV, Sprecher A, Traore A, Diakite M, Konde MK, Koivogui L, Magassouba N, Avšič-Županc T, Nitsche A, Strasser M, Ippolito G, Becker S, Stoecker K, Gabriel M, Raoul H, Di Caro A, Wölfel R, Formenty P, Günther S, 2015. "Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa". Nature 524(7563), 97–101.

Phylogeny: Are arthropods at the heart of virus evolution?

Dudas G, Obbard DJ, 2014. "Phylogeny: Are arthropods at the heart of virus evolution?". eLife 4: e06837.

The genetics of host–virus coevolution in invertebrates

Obbard DJ, Dudas G, 2014. "The genetics of host–virus coevolution in invertebrates". Current Opinion in Virology 8: 73–78.

Integrating influenza antigenic dynamics with molecular evolution

Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, Hay AJ, McCauley JW, Russell CA, Smith DJ, Rambaut A, 2014. "Integrating influenza antigenic dynamics with molecular evolution". eLife 3: e01914.

Funding

2023- EMBO installation grant, 3 years, €150 000.

Talks

The RNA virus research revolution slumbering in accumulated metagenomic data

November 07, 2022

Talk at Fred Hutchinson Cancer Center, Seattle, Washington

The RNA virus research revolution slumbering in accumulated metagenomic data

October 14, 2022

Talk at CZ Biohub, San Francisco Bay Area, California

Small victories of the Lithuanian SARS-CoV-2 genomic surveillance programme

September 30, 2022

Talk at Life Sciences Center, Vilnius University, Vilnius, Lithuania

SARS-CoV-2 in Lithuania

January 26, 2022

Talk at Life Sciences Center, Vilnius University, Vilnius, Lithuania

Lietuvos SARS-CoV-2 sekoskaitos projekto pasiekimai [in Lithuanian]

August 31, 2021

Talk at Vilnius University Hospital Santaros Klinikos (remote), Vilnius, Lithuania

MERS-CoV spillover at the camel-human interface

April 29, 2021

Talk at University of Cambridge (remote), Cambridge, UK

Phylogenetic trees: a technically true data-vis disaster

October 26, 2020

Talk at BioVis Challenges Workshop at IEEE VIS 2020 (fully remote), Salt Lake City, Utah

Single mosquito metatranscriptomics in California: globe-trotting straws from the haystack that turned out to be needles

August 18, 2020

Talk at Genome Sciences seminar, University of Washington, Seattle, Washington

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

June 03, 2019

Talk at Imperial College London, London, UK

Beyond (two) button phylogenetics

April 02, 2019

Talk at ETH Zurich, Basel, Basel, Switzerland

Reconstructing the history and drivers of viral epidemics from genomes of emerging RNA viruses

March 11, 2019

Talk at Arizona State University, Phoenix, Phoenix, Arizona

MERS-CoV spillover at the camel-human interface

March 08, 2019

Talk at Northern Arizona University, Flagstaff, Flagstaff, Arizona

MERS-CoV spillover at the camel-human interface

October 17, 2018

Talk at University of Edinburgh, Edinburgh, UK

Reconstructing the history and drivers of viral epidemics from genomes of Zika, MERS-CoV, and Ebola viruses

May 11, 2018

Talk at University of California, San Diego, San Diego, California

Reconstructing the history and drivers of viral epidemics from virus genomes

May 08, 2018

Talk at CZ BioHub, San Francisco Bay Area, California

Genomic epidemiology and population genetics of emerging RNA viruses

April 17, 2018

Talk at 6th Annual Disease Modeling Symposium, Bellevue, Washington

MERS-CoV spillover at the camel-human interface

March 23, 2018

Talk at BIO5 Institute, Tucson, Arizona

Reconstructing the history and drivers of viral epidemics from virus genomes

March 20, 2018

Talk at School of Plant Sciences, University of Arizona, Tucson, Arizona

Virus genomes reveal factors that spread and sustained the West African Ebola virus epidemic

January 11, 2018

Talk at Vancouver Bioinformatics Users Group, Vancouver, British Columbia

MERS-CoV spillover at the camel-human interface

November 14, 2017

Talk at Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington

Virus genomes reveal factors that spread and sustained the Ebola epidemic

October 24, 2017

Talk at IHV2017: 19th Annual International Meeting of the Institute of Human Virology, Baltimore, Maryland

Reproducible visualisation using Jupyter notebooks

October 04, 2017

Talk at ARTIC Network meeting, Edinburgh, UK

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

July 17, 2017

Talk at Next Generation Informatics for Global Health: Disease Dynamics and Digital Epidemiology, Hong Kong

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

May 30, 2017

Talk at Broad Institute, Cambridge, Massachusetts

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

May 26, 2017

Talk at Harvard T.H. Chan School of Public Health, Boston, Massachusetts

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

May 23, 2017

Talk at MIDAS Network Meeting, Atlanta, Georgia

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

October 19, 2016

Talk at Combi seminar, University of Washington, Seattle, Washington

Pattern and determinants of the geographic dissemination of Ebola virus in West Africa 2013-2016

June 10, 2016

Talk at Virus Genomics and Evolution 2016, Cambridge, UK

Lessons about virus biology from molecular clocks

November 17, 2015

Talk at University of Zurich, Zurich, Switzerland

Population genetics of Ebola virus in West Africa

July 15, 2015

Talk at SMBE 2015, Vienna, Austria

Population genetics of Ebola virus in West Africa

July 10, 2015

Talk at Forecasting Evolution?, Lisbon, Portugal

Reticulate evolution: unlikely lessons about RNA viruses and their hosts

January 31, 2015

Talk at Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington

Phylodynamics of co-circulating influenza virus lineages

January 24, 2014

Talk at Department of Zoology, University of Oxford, Oxford, UK

Phylodynamics of co-circulating influenza virus lineages

January 19, 2014

Talk at School of Public Health, Imperial College London, London, UK

Inter-subtype reassortment patterns in influenza B reveal selective maintenance of co-reassorting segment complexes

November 21, 2013

Talk at Epidemics4, Amsterdam, Netherlands

Antagonistic interactions between co-circulating subtypes of human influenza viruses

March 01, 2012

Talk at Population Genetics Group meeting 46, Glasgow, UK

Teaching

Temporal tree calibration in BEAST

Genomic sequence data on the frontlines during the West African Ebola virus epidemic

Molekulinė evoliucija. Genomų evoliucija.

Professional service

Ad hoc referee for BMC Bioinformatics, Cell Reports, Nature Communications, Nature Medicine, Nature Microbiology, PLoS Currents Outbreaks, eLife, PLoS Neglected Tropical Diseases, BMC Genome Medicine, Molecular Biology and Evolution, Infection, Genetics and Evolution, The Journal of Infectious Diseases, PLoS Pathogens, PeerJ, Proceedings of the Royal Society B, Scientific Reports, Virology Journal, Virus Evolution.
Social media manager for Virus Evolution.

Awards

2018 SciPy John Hunter Excellence in Plotting Prize, 1st place, for “History of Ebola Virus Epidemic in West Africa 2013-2015”, a matplotlib-based phylogeographic visualisation.
2017 Young Investigator Award to attend “Next Generation Informatics for Global Health: Disease Dynamics and Digital Epidemiology” in Hong Kong.
2015 SMBE Young Investigator Travel Award to attend the SMBE 2015 meeting in Vienna.
2015 Wellcome Trust Travel Grant to attend the “Forecasting Evolution?” meeting in Lisbon.