The Applied Genomic Epidemiology Handbook
Black A, Dudas G, 2024. "The Applied Genomic Epidemiology Handbook: A Practical Guide to Leveraging Pathogen Genomic Data in Public Health". Chapman and Hall/CRC 1st ed., ISBN-13: 978-1032530260
CV
PDF version of my CV available here.
Postgraduate career
- 2024- : Principal Investigator / Research Professor, Life Sciences Centre at Vilnius University
- 2021-2024: 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 Center
- Mentor: Trevor Bedford.
Education
- 2011-2016: PhD, University of Edinburgh, Edinburgh, UK.
- Supervisor: Prof. Andrew Rambaut, secondary supervisor: Prof. Andrew Leigh-Brown; Thesis title: “Inference of Evolutionary and Ecological Processes from Reticulate Evolution in RNA Viruses”; 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
Accumulated metagenomic studies reveal recent migration, whole genome evolution, and undiscovered diversity of orthomyxoviruses
Dudas G and Batson J, 2023. "Accumulated metagenomic studies reveal recent migration, whole genome evolution, and undiscovered diversity of orthomyxoviruses". Journal of Virology 97(10): e01056-23
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.
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
On the importance of assessing topological convergence in Bayesian phylogenetic inference
Brusselmans M, Carvalho LM, Hong SL, Gao J, Matsen IV FA, Rambaut A, Lemey P, Suchard MA, Dudas G, Baele G, 2024. "On the importance of assessing topological convergence in Bayesian phylogenetic inference". Virus Evolution: veae081.
Emergence of the B.1.214.2 SARS-CoV-2 Lineage with an Omicron-Like Spike Insertion and a Unique Upper Airway Immune Signature
Holtz A, Van Weyenbergh J, Hong SL, Cuypers L, O'Toole Á, Dudas G, Gerdol M, Potter BI, Ntoumi F, Mapanguy CCM, Vanmechelen B, Wawina-Bokalanga T, Van Holm B, Menezes SM, Soubotko K, Van Pottelbergh G, Wollants E, Vermeersch P, Jacob AS, Maes B, Obbels D, Matheeussen V, Martens G, Gras J, Verhasselt B, Laffut W, Vael C, Goegebuer T, van der Kant R, Rousseau F, Schymkowitz J, Serrano L, Delgado J, Wenseleers T, Bours V, André E, Suchard MA, Rambaut A, Dellicour S, Maes P, Durkin K, Baele G, 2023. "Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature". BMC Infectious Diseases 24(1): 1139.
The global H5N1 influenza panzootic in mammals
Peacock T, Moncla L, Dudas G, VanInsberghe D, Sukhova K, Lloyd-Smith JO, Worobey M, Lowen AC, Nelson MI, 2023. "The global H5N1 influenza panzootic in mammals". Nature https://doi.org/10.1038/s41586-024-08054-z.
PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes
Glascock AL, Waltari E, Dudas G, Wong J, Ahyong V, 2024. "PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes". BMC Bioinformatics 25, 49.
Evolutionary genomics identifies host-directed therapeutics to treat intracellular bacterial infections
Medicielo J, Waltari E, Glascock AL, Dudas G, DeFelice B, Gray I, Tato CM, Wong J, Ahyong V, 2023. "Evolutionary genomics identifies host-directed therapeutics to treat intracellular bacterial infections". bioRxiv 2023.08.01.551011.
Phylogeographic analysis of dengue virus serotype 1 and Cosmopolitan serotype 2 in Africa
Selhorst P, Lequime S, Dudas G, Proesmans S, Lutumbah P, Katshongo F, Ramadan K, Micalessi I, Ahuka-Mundeke S, Vanlerberghe V, Van Esbroeck M, Arien KK, 2023. "Phylogeographic analysis of dengue virus serotype 1 and Cosmopolitan serotype 2 in Africa". International Journal of Infectious Diseases 133: 46-52.
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, 2022. "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.
Genome-wide evolutionary dynamics of influenza B viruses on a global scale
Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels R, Russell C, Pybus OG, McCauley J, Kellam P, Watson SJ, 2017. "Genome-wide evolutionary dynamics of influenza B viruses on a global scale". PLoS Pathogens 13(12): e1006749.
Genetic characterization of the Zika virus epidemic in the US Virgin Islands
Black A, Potter B, Dudas G, Feldstein L, Grubaugh ND, Andersen KG, Ellis BR, Ellis EM, Bedford T, 2017. "Genetic characterization of the Zika virus epidemic in the US Virgin Islands". bioRxiv: 113100.
The evolution of Ebola virus: Insights from the 2013–2016 epidemic
Holmes EC, Dudas G, Rambaut A, Andersen KG, 2016. "The evolution of Ebola virus: Insights from the 2013–2016 epidemic". Nature 538(7624): 193:200.
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
Rapid global population dynamics and fast surface protein evolution imply a vertebrate host for a prevalent mosquito orthomyxovirus
Talk at Virus Genomics, Evolution and Bioinformatics 2024, Cambridge, UK
A brief overview of genomic epidemiology & what we’ll do over the next two years
Talk at EC Twinning Project GE 21 NDICI HE 01 23 kick-off meeting, Tbilisi, Georgia
Reticulate evolution, temporal resolution and custom data visualisations for BEAST analyses
Talk at Phylogenomics Workshop 2024, Český Krumlov, Czechia
Basically flu but in mosquitoes: Wuhan mosquito virus 6 as a promising new study system
Talk at Virus Club, Edinburgh, UK
Towards genomic epidemiology of arthropod viruses
Talk at EMBO computational microbiology meeting, Chęciny, Poland
The modern response to infectious disease outbreaks using genetic sequencing
Talk at Open Readings 2023, Vilnius, Lithuania
Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
Talk at Health Sciences: Inaugural Symposium of CNRS (France) and Lithuanian scientists, Vilnius, Lithuania
The RNA virus research revolution slumbering in accumulated metagenomic data
Talk at Fred Hutchinson Cancer Center, Seattle, Washington
The RNA virus research revolution slumbering in accumulated metagenomic data
Talk at CZ Biohub, San Francisco Bay Area, California
Small victories of the Lithuanian SARS-CoV-2 genomic surveillance programme
Talk at Life Sciences Center, Vilnius University, Vilnius, Lithuania
SARS-CoV-2 in Lithuania
Talk at Life Sciences Center, Vilnius University, Vilnius, Lithuania
Lietuvos SARS-CoV-2 sekoskaitos projekto pasiekimai [in Lithuanian]
Talk at Vilnius University Hospital Santaros Klinikos (remote), Vilnius, Lithuania
MERS-CoV spillover at the camel-human interface
Talk at University of Cambridge (remote), Cambridge, UK
Phylogenetic trees: a technically true data-vis disaster
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
Talk at Genome Sciences seminar, University of Washington, Seattle, Washington
Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
Talk at Imperial College London, London, UK
Beyond (two) button phylogenetics
Talk at ETH Zurich, Basel, Basel, Switzerland
Reconstructing the history and drivers of viral epidemics from genomes of emerging RNA viruses
Talk at Arizona State University, Phoenix, Phoenix, Arizona
MERS-CoV spillover at the camel-human interface
Talk at Northern Arizona University, Flagstaff, Flagstaff, Arizona
MERS-CoV spillover at the camel-human interface
Talk at University of Edinburgh, Edinburgh, UK
Reconstructing the history and drivers of viral epidemics from genomes of Zika, MERS-CoV, and Ebola viruses
Talk at University of California, San Diego, San Diego, California
Reconstructing the history and drivers of viral epidemics from virus genomes
Talk at CZ BioHub, San Francisco Bay Area, California
Genomic epidemiology and population genetics of emerging RNA viruses
Talk at 6th Annual Disease Modeling Symposium, Bellevue, Washington
MERS-CoV spillover at the camel-human interface
Talk at BIO5 Institute, Tucson, Arizona
Reconstructing the history and drivers of viral epidemics from virus genomes
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
Talk at Vancouver Bioinformatics Users Group, Vancouver, British Columbia
MERS-CoV spillover at the camel-human interface
Talk at Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington
Virus genomes reveal factors that spread and sustained the Ebola epidemic
Talk at IHV2017: 19th Annual International Meeting of the Institute of Human Virology, Baltimore, Maryland
Reproducible visualisation using Jupyter notebooks
Talk at ARTIC Network meeting, Edinburgh, UK
Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
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
Talk at Broad Institute, Cambridge, Massachusetts
Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
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
Talk at MIDAS Network Meeting, Atlanta, Georgia
Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
Talk at Combi seminar, University of Washington, Seattle, Washington
Pattern and determinants of the geographic dissemination of Ebola virus in West Africa 2013-2016
Talk at Virus Genomics and Evolution 2016, Cambridge, UK
Lessons about virus biology from molecular clocks
Talk at University of Zurich, Zurich, Switzerland
Population genetics of Ebola virus in West Africa
Talk at SMBE 2015, Vienna, Austria
Population genetics of Ebola virus in West Africa
Talk at Forecasting Evolution?, Lisbon, Portugal
Reticulate evolution: unlikely lessons about RNA viruses and their hosts
Talk at Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
Phylodynamics of co-circulating influenza virus lineages
Talk at Department of Zoology, University of Oxford, Oxford, UK
Phylodynamics of co-circulating influenza virus lineages
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
Talk at Epidemics4, Amsterdam, Netherlands
Antagonistic interactions between co-circulating subtypes of human influenza viruses
Talk at Population Genetics Group meeting 46, Glasgow, UK
Teaching
2024 Apr: Bioinformatika. Filogenetika. , Vilnius University
2023 Oct: Molekulinė evoliucija. Genomų evoliucija. , Vilnius University
2022 Oct: Molekulinė evoliucija. Genomų evoliucija. , Vilnius University
2018 Mar: Genomic sequence data on the frontlines during the West African Ebola virus epidemic , University of Arizona
2015 Nov: Temporal tree calibration in BEAST , University of Zurich
Professional service
- 2024-2026: Component Leader for a genomic epidemiology European Commission Twinning project in Georgia (GE 21 NDICI HE 01 23). Assisting staff of the Richard Lugar Center for Public Health Research in Tbilisi in designing and implementing sustainable genomic surveillance for infectious diseases of local and international significance.
- 2021-2022: Co-author and chief data analyst for Lithuania’s pandemic SARS-CoV-2 genomic surveillance project. The project generated >39 000 SARS-CoV-2 genomes February 2021 - May 2022 averaging ~2.0% (between 0.2% and 28% in a given month) of all COVID-19 cases in Lithuania.
- 2021-2022: Advisory council of independent experts to the Lithuanian government tasked with advising the government on COVID-19 prevention, diagnostics, treatment, and application of other means of epidemic control.
- 2016-2018: Social media manager for Virus Evolution.
- Ad hoc journal 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.
- Ad hoc grant referee for The Wellcome Trust Early-Career Award.
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.
- 2016: Mahan postdocotral fellowship, Fred Hutchinson Cancer Center.
- 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.
Public outreach
2024 Nov: Kodas RNR. Nuo kovos su virusais iki tobulų genų (book) , Vilnius University Press
2024 Aug: COVID-19 banga, uodų platinamas virusas ir nerimas dėl paukščių gripo , Žinių Radijas
2024 Jun: Ask the scientist , iGEM Vilnius
2024 May: Tracking bird flu virus changes in cows is stymied by missing data, scientists say , STAT news
2024 Apr: Pavojingiausi kandidatai ant mokslininkų stalo: kas, jeigu mus vėl ištiktų pandemija? [Lithuanian] , LRT
2024 Mar: Mokslininkų tiriamas uodų pernešamo viruso modelis gali tapti nauju įrankiu ligų protrūkiams nuspėti [Lithuanian] , SPECTRUM
2024 Jan: VU ekspertai padeda suprasti. Dr. Gytis Dudas apie pandemijas , Vilnius University
2024 Jan: Ką žinome apie koronavirusą ir kitus RNR virusus? [Lithuanian] , LRT
2023 Dec: Mūsų treji su puse COVID metų. Pokalbis su virusų tyrėju Gyčiu Dudu [Lithuanian] , NARA interview
2023 Oct: It’s viruses all the way down , EMBO podcast
2023 Oct: Tada ir dabar iš užkrečiamųjų ligų perspektyvos [Lithuanian] , Longevity
2023 Sep: Genominė epidemiologija šiuolaikinių protrūkių fronto linijose [Lithuanian] , Library of the Lithuanian Academy of Sciences
2023 Aug: Moksleiviai - į vyriausybę [Lithuanian] , Government of the Republic of Lithuania
2023 May: Aštuonios ligos, kurioms mokslas nėra pasiruošęs [Lithuanian] , LOGIN
2023 Mar: Kas tie virusai ir kam jų reikia? [Lithuanian] , Mokonomika
2022 Aug: Mokslininkas prabilo apie didžiausią problemą dėl COVID-19: virusas gali kelti riziką net šimtmečiais [Lithuanian] , TV3
2022 Mar: Genominė epidemiologija: kaip atrodo protrūkiai iš virusų perspektyvos? [Lithuanian] , Vilnius University
2022 Feb: Kaip mutuoja virusai? [Lithuanian] , Mokslo Sriuba
2022 Jan: Mokslas be pamokslų. Koronaviruso evoliucija: ko laukti? [Lithuanian] , Lithuanian National Radio and Television / Vilnius University
2021 Sep: COVID-19 atmainos [Lithuanian] , Visuotinė lietuvių enciklopedija
2021 May: Scientists tracking coronavirus variants struggle with global blind spots , ScienceInsider
2021 May: How a worrisome coronavirus variant spread unnoticed , Nature News
2021 Feb: Lectures ‘Evoliucija populiacijos lygmeniu: kertinės idėjos’ and ‘Šiuolaikinis mokslo atsakas į epidemijas’ [Lithuanian] , National Student Academy
2021 Jan: Mokslininkas Gytis Dudas apie pačius˛įdomiausius ir pavojingiausius virusus: mirtiniausią galima sutikti ir Lietuvoje [Lithuanian] , Lithuanian National Radio and Television
2020 Jul: Koronavirusas: ką jau žinome, o ko dar ne [Lithuanian] , NYLA Talks podcast
2020 May: How countries are using genomics to help avoid a second coronavirus wave , Nature News
2020 Apr: Genetic Tracking Helped Us Fight Ebola. Why Can’t It Halt COVID-19? , FiveThirtyEight
2020 Mar: Dar neseniai pasaulis kovojo su mirtinu Ebolos virusu: kaip pavyko suvaldyti epidemiją neturint veikiančios vakcinos [Lithuanian] , Lithuanian National Radio and Television
2020 Mar: Gyventi su COVID-19. Kalba mokslininkai [Lithuanian] , NYLA Talks podcast
2019 Mar: Ebolos virusą perpratęs Gytis Dudas: „Lietuvoje vis dar jauti, kad gali kažką pakeisti“ [Lithuanian] , Moteris magazine
2018 Dec: Perpratęs ebolą: Gytis Dudas [Lithuanian] , NYLA Talks podcast
2018 Jan: MERS remains primarily a camel virus for now , Hutch News
2018 Jan: Virus genomes reveal factors that spread and sustained the West African Ebola virus epidemic , Vancouver Bioinformatics Users
2017 May: Reconstructing the history of the Ebola epidemic , Cascadia Users of Geospatial Open Source
2017 Apr: The March for Science could save lives , The Washington Post
2017 Apr: A big-picture look at the world’s worst Ebola epidemic , Hutch News
2017 Apr: Ebola Genomes Help Reconstruct Virus’ Spread During West African Outbreak , GenomeWeb
2014 Oct: Edinburgh plays a part in solving Ebola crisis , The Scotsman
2014 Sep: NERC-funded student helps analyse Ebola genome sequence , NERC News
2014 Jun: Ongoing Ebola outbreak highlights research shortcomings , SciDev.Net