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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
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Posts
Why are sundials not used on GPS satellites?
Published:
The animation that changed all
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Leaving Seattle and moving on
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Welcome to behind the scenes
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contributions
Integrating influenza antigenic dynamics with molecular evolution
Published in eLife, 2014 FebBedford 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.
The genetics of host–virus coevolution in invertebrates
Published in Current Opinion in Virology, 2014 JulObbard DJ, Dudas G, 2014. "The genetics of host–virus coevolution in invertebrates". Current Opinion in Virology 8: 73–78.
Phylogeny: Are arthropods at the heart of virus evolution?
Published in eLife, 2015 MarDudas G, Obbard DJ, 2014. "Phylogeny: Are arthropods at the heart of virus evolution?". eLife 4: e06837.
Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa
Published in Nature, 2015 JunCarroll 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.
Evolution and Spread of Ebola Virus in Liberia, 2014–2015
Published in Cell, 2015 DecLadner 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.
Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases
Published in Virus Evolution, 2016 FebArias 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.
Real-time, portable genome sequencing for Ebola surveillance
Published in Nature, 2016 FebQuick 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.
The global antigenic diversity of swine influenza A viruses
Published in eLife, 2016 AprLewis 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.
Preliminary Evaluation of the Effect of Investigational Ebola Virus Disease Treatments on Viral Genome Sequences
Published in Journal of Infectious Diseases, 2016 OctWhitmer 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 evolution of Ebola virus: Insights from the 2013–2016 epidemic
Published in Science, 2016 OctHolmes EC, Dudas G, Rambaut A, Andersen KG, 2016. "The evolution of Ebola virus: Insights from the 2013–2016 epidemic". Nature 538(7624): 193:200.
Genetic characterization of the Zika virus epidemic in the US Virgin Islands
Published in bioRxiv, 2017 MarBlack 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.
Genome-wide evolutionary dynamics of influenza B viruses on a global scale
Published in PLoS Pathogens, 2017 DecLangat 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.
Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors
Published in Cell Reports, 2018 JanWhitmer 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.
MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity
Published in PNAS, 2018 MarChu 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.
Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak
Published in Nature Communications, 2018 JunDellicour 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.
Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations
Published in Virus Evolution, 2019 AugMüller 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.
Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses
Published in PNAS, 2020 JulMüller 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.
Estimating effective population size changes from preferentially sampled genetic sequences
Published in PLoS Computation Biology, 2020 OctKarcher 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.
Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and Operations
Published in Viruses, 2021 JulPirnay 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.
Emergence of an early SARS-CoV-2 epidemic in the United States
Published in Cell, 2021 JulZeller 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.
Bulk Milk Tank Samples Are Suitable to Assess Circulation of Tick-Borne Encephalitis Virus in High Endemic Areas
Published in Viruses, 2021 SepPautienius 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.
Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies
Published in Nature Communications, 2021 SepChazot 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.
Antibody escape and global spread of SARS-CoV-2 lineage A.27
Published in Nature Communications, 2022 MarKaleta 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.
Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics
Published in The Lancet Microbe, 2022 MarTsitsiklis 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.
Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades
Published in Nature Communications, 2022 SepKlitting 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.
Fitting stochastic epidemic models to gene genealogies using linear noise approximation
Published in Annals of Applied Statistics, 2023 MarTang 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.
Phylogeographic analysis of dengue virus serotype 1 and Cosmopolitan serotype 2 in Africa
Published in International Journal of Infectious Diseases, 2023 AprSelhorst 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.
Evolutionary genomics identifies host-directed therapeutics to treat intracellular bacterial infections
Published in bioRxiv, 2023 AugMedicielo 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.
PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes
Published in BMC Bioinformatics, 2024 JanGlascock 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.
The global H5N1 influenza panzootic in mammals
Published in Nature, 2024 SepPeacock 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.
Emergence of the B.1.214.2 SARS-CoV-2 Lineage with an Omicron-Like Spike Insertion and a Unique Upper Airway Immune Signature
Published in BMC Infectious Diseases, 2024 OctHoltz 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.
On the importance of assessing topological convergence in Bayesian phylogenetic inference
Published in Virus Evolution, 2024 OctBrusselmans 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.
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X
Published in bioRxiv, 2024 DecBaele G, Carvalho LM, Brusselmans M, Dudas G, Ji X, McCrone JT, Lemey P, Suchard M, Rambaut A, 2024. "HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X". bioRxiv 2024.12.08.627395.
outreach
2014 Jun 04, SciDev.Net, Ongoing Ebola outbreak highlights research shortcomings
2014 Sep 05, NERC News, NERC-funded student helps analyse Ebola genome sequence
2014 Oct 31, The Scotsman, Edinburgh plays a part in solving Ebola crisis
2017 Apr 12, GenomeWeb, Ebola Genomes Help Reconstruct Virus’ Spread During West African Outbreak
2017 Apr 12, Hutch News, A big-picture look at the world's worst Ebola epidemic
2017 Apr 19, The Washington Post, The March for Science could save lives
2017 May 20, Cascadia Users of Geospatial Open Source, Reconstructing the history of the Ebola epidemic
2018 Jan 11, Vancouver Bioinformatics Users, Virus genomes reveal factors that spread and sustained the West African Ebola virus epidemic
2018 Jan 16, Hutch News, MERS remains primarily a camel virus for now
2018 Dec 14, NYLA Talks podcast, Perpratęs ebolą: Gytis Dudas [Lithuanian]
2019 Mar 22, Moteris magazine, Ebolos virusą perpratęs Gytis Dudas: „Lietuvoje vis dar jauti, kad gali kažką pakeisti“ [Lithuanian]
2020 Mar 15, NYLA Talks podcast, Gyventi su COVID-19. Kalba mokslininkai [Lithuanian]
2020 Mar 25, Lithuanian National Radio and Television, Dar neseniai pasaulis kovojo su mirtinu Ebolos virusu: kaip pavyko suvaldyti epidemiją neturint veikiančios vakcinos [Lithuanian]
2020 Apr 15, FiveThirtyEight, Genetic Tracking Helped Us Fight Ebola. Why Can’t It Halt COVID-19?
2020 May 27, Nature News, How countries are using genomics to help avoid a second coronavirus wave
2020 Jul 23, NYLA Talks podcast, Koronavirusas: ką jau žinome, o ko dar ne [Lithuanian]
2021 Jan 24, Lithuanian National Radio and Television, Mokslininkas Gytis Dudas apie pačius˛įdomiausius ir pavojingiausius virusus: mirtiniausią galima sutikti ir Lietuvoje [Lithuanian]
2021 Feb 19, National Student Academy, Lectures 'Evoliucija populiacijos lygmeniu: kertinės idėjos' and 'Šiuolaikinis mokslo atsakas į epidemijas' [Lithuanian]
2021 May 13, Nature News, How a worrisome coronavirus variant spread unnoticed
2021 May 14, ScienceInsider, Scientists tracking coronavirus variants struggle with global blind spots
2021 Sep 21, Visuotinė lietuvių enciklopedija, COVID-19 atmainos [Lithuanian]
2022 Jan 06, Lithuanian National Radio and Television / Vilnius University, Mokslas be pamokslų. Koronaviruso evoliucija: ko laukti? [Lithuanian]
2022 Feb 28, Mokslo Sriuba, Kaip mutuoja virusai? [Lithuanian]
2022 Mar 18, Vilnius University, Genominė epidemiologija: kaip atrodo protrūkiai iš virusų perspektyvos? [Lithuanian]
2022 Aug 20, TV3, Mokslininkas prabilo apie didžiausią problemą dėl COVID-19: virusas gali kelti riziką net šimtmečiais [Lithuanian]
2023 Mar 09, Mokonomika, Kas tie virusai ir kam jų reikia? [Lithuanian]
2023 May 12, LOGIN, Aštuonios ligos, kurioms mokslas nėra pasiruošęs [Lithuanian]
2023 Aug 24, Government of the Republic of Lithuania, Moksleiviai - į vyriausybę [Lithuanian]
2023 Sep 04, Library of the Lithuanian Academy of Sciences, Genominė epidemiologija šiuolaikinių protrūkių fronto linijose [Lithuanian]
2023 Oct 16, Longevity, Tada ir dabar iš užkrečiamųjų ligų perspektyvos [Lithuanian]
2023 Oct 30, EMBO podcast, It’s viruses all the way down
2023 Dec 01, NARA interview, Mūsų treji su puse COVID metų. Pokalbis su virusų tyrėju Gyčiu Dudu [Lithuanian]
2024 Jan 03, LRT, Ką žinome apie koronavirusą ir kitus RNR virusus? [Lithuanian]
2024 Jan 17, Vilnius University, VU ekspertai padeda suprasti. Dr. Gytis Dudas apie pandemijas
2024 Mar 27, SPECTRUM, Mokslininkų tiriamas uodų pernešamo viruso modelis gali tapti nauju įrankiu ligų protrūkiams nuspėti [Lithuanian]
2024 Apr 23, LRT, Pavojingiausi kandidatai ant mokslininkų stalo: kas, jeigu mus vėl ištiktų pandemija? [Lithuanian]
2024 May 02, STAT news, Tracking bird flu virus changes in cows is stymied by missing data, scientists say
2024 Jun 05, iGEM Vilnius, Ask the scientist
2024 Aug 05, Žinių Radijas, COVID-19 banga, uodų platinamas virusas ir nerimas dėl paukščių gripo
2024 Nov 19, Vilnius University Press, Kodas RNR. Nuo kovos su virusais iki tobulų genų (book)
2024 Nov 21, LRT, DI išgelbės nuo pandemijų ar sukurs naujų?
2024 Nov 22, Utena regional STEAM open access center, Genomų detektyvai šuolaikinių protrūkių fronto linijose
publications
Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak
Published in PLOS Currents Outbreaks, 2014 MayDudas G, Rambaut A, 2014. "Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak". PLOS Currents Outbreaks Edition 1.
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Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
Published in Science, 2014 SepGire 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.
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Reassortment between Influenza B Lineages and the Emergence of a Coadapted PB1–PB2–HA Gene Complex
Published in Molecular Biology and Evolution, 2014 OctDudas 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.
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Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone
Published in Cell, 2015 JunPark 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.
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MERS-CoV recombination: implications about the reservoir and potential for adaptation
Published in Virus Evolution, 2016 JanDudas G, Rambaut A, 2016. "MERS-CoV recombination: implications about the reservoir and potential for adaptation". Virus Evolution 2(1): vev023.
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Comment on “Mutation rate and genotype variation of Ebola virus from Mali case sequences”
Published in Science, 2016 AugRambaut 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.
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Virus genomes reveal factors that spread and sustained the Ebola epidemic
Published in Nature, 2017 AprDudas 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.
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Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Published in Nature, 2017 MayGrubaugh 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.
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MERS-CoV spillover at the camel-human interface
Published in eLife, 2017 DecDudas G, de Carvalho LM, Rambaut A, Bedford T, 2017. "MERS-CoV spillover at the camel-human interface". eLife 7: e31257.
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The ability of single genes vs full genomes to resolve time and space in outbreak analysis
Published in BMC Evolutionary Biology, 2019 DecDudas 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.
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Polymorphism of Genetic Ambigrams
Published in Virus Evolution, 2021 AprDudas G, Huber G, Wilkinson M, Yllanes D, 2021. "Polymorphism of Genetic Ambigrams". Virus Evolution 7(1): veab038.
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Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay
Published in eLife, 2021 AprBatson 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
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Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome
Published in Cell Host & Microbe, 2021 JulArze 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.
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Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
Published in Nature Communications, 2021 OctDudas 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.
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Global disparities in SARS-CoV-2 genomic surveillance
Published in Nature Communications, 2022 NovBrito 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.
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Accumulated metagenomic studies reveal recent migration, whole genome evolution, and undiscovered diversity of orthomyxoviruses
Published in Journal of Virology, 2023 OctDudas 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
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The Applied Genomic Epidemiology Handbook
Published in CRC Press, LLC, 2024 MarBlack 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
talks
Pattern and determinants of the geographic dissemination of Ebola virus in West Africa 2013-2016
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Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
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Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
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Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
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Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
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Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
Published:
Virus genomes reveal factors that spread and sustained the West African Ebola virus epidemic
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Reconstructing the history and drivers of viral epidemics from genomes of emerging RNA viruses
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Beyond (two) button phylogenetics
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Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
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SARS-CoV-2 in Lithuania
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Reticulate evolution, temporal resolution and custom data visualisations for BEAST analyses
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teaching
Temporal tree calibration in BEAST
Workshop, University of Zurich, 2015
Genomic sequence data on the frontlines during the West African Ebola virus epidemic
Lecture, University of Arizona, 2018
Molekulinė evoliucija. Genomų evoliucija.
Lecture, Vilnius University, 2022
Molekulinė evoliucija. Genomų evoliucija.
Lecture, Vilnius University, 2023
Bioinformatika. Filogenetika.
Lecture, Vilnius University, 2024