Wang L, Huang AT, Katzelnick LC, Lefrancq N, Escoto AC, Duret L, Chowdhury N, Jarman R, Conte MA, Berry IM, Fernandez S, Klungthong C, Thaisomboonsuk B, Suntarattiwong P, Vandepitte W, Whitehead SS, Cauchemez S, Cummings DAT, Salje H. (2024). Antigenic distance between primary and secondary dengue infections correlates with disease risk. Science translational medicine, 16(744)
Beaty S, Collins N, Karasavvas N, Kuschner R, Hang J, Adhikari A, Maljkovic Berry I, Fung C, Walls S, Betancourt E, Mendy J, Lock M, Gierman E, Bennett S, Shabram P, Warfield K. (2023). A Phase 1 Two-Arm, Randomized, Double-Blind, Active-Controlled Study of Live, Oral Plasmid-Derived Adenovirus Type 4 and Type 7 Vaccines in Seronegative Adults. Vaccines, 11(6)
Wang L, Huang AT, Katzelnick LC, Lefrancq N, Escoto AC, Duret L, Chowdhury N, Jarman R, Conte MA, Berry IM, Fernandez S, Klungthong C, Thaisomboonsuk B, Suntarattiwong P, Vandepitte W, Whitehead S, Cauchemez S, Cummings DAT, Salje H. (2023). Antigenic diversity and dengue disease risk. Research square
Thommana A, Shakya M, Gandhi J, Fung CK, Chain PSG, Maljkovic Berry I, Conte MA. (2022). Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns. Viruses, 14(10)
Maljkovic Berry I, Hang J, Fung C, Yang Y, Chibucos M, Pollio A, Gandhi J, Li T, Conte MA, Lidl GM, Johannigman JA, Friberg H. (2022). Genomic surveillance of SARS-CoV-2 in US military compounds in Afghanistan reveals multiple introductions and outbreaks of Alpha and Delta variants. BMC genomics, 23(1)
Huang AT, Salje H, Escoto AC, Chowdhury N, Chávez C, Garcia-Carreras B, Rutvisuttinunt W, Maljkovic Berry I, Gromowski GD, Wang L, Klungthong C, Thaisomboonsuk B, Nisalak A, Trimmer-Smith LM, Rodriguez-Barraquer I, Ellison DW, Jones AR, Fernandez S, Thomas SJ, Smith DJ, Jarman R, Whitehead SS, Cummings DAT, Katzelnick LC. (2022). Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand. PLoS pathogens, 18(5)
Morton L, Forshey B, Bishop-Lilly K, Cer R, Fries A, Bogue A, Undewood R, Bazaco S, Starr C, Gruner W, Malagon F, Myers C, Maljkovic Berry I, Kugelman J, Creppage K, Scheckelhoff M, Taylor K, Pimentel G. (2022). Establishment of SARS-CoV-2 genomic surveillance within the Military Health System during 1 March-31 December 2020. MSMR, 29(7)
Pollett S, Johansson MA, Reich NG, Brett-Major D, Del Valle SY, Venkatramanan S, Lowe R, Porco T, Berry IM, Deshpande A, Kraemer MUG, Blazes DL, Pan-Ngum W, Vespigiani A, Mate SE, Silal SP, Kandula S, Sippy R, Quandelacy TM, Morgan JJ, Ball J, Morton LC, Althouse BM, Pavlin J, van Panhuis W, Riley S, Biggerstaff M, Viboud C, Brady O, Rivers C. (2021). Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines. PLoS medicine, 18(10)
Salje H, Wesolowski A, Brown TS, Kiang MV, Berry IM, Lefrancq N, Fernandez S, Jarman RG, Ruchusatsawat K, Iamsirithaworn S, Vandepitte WP, Suntarattiwong P, Read JM, Klungthong C, Thaisomboonsuk B, Engø-Monsen K, Buckee C, Cauchemez S, Cummings DAT. (2021). Reconstructing unseen transmission events to infer dengue dynamics from viral sequences. Nature communications, 12(1)
Sanborn MA, McGuckin Wuertz K, Kim HC, Yang Y, Li T, Pollett SD, Jarman RG, Maljkovic Berry I, Klein TA, Hang J. (2021). Metagenomic analysis reveals Culex mosquito virome diversity and Japanese encephalitis genotype V in the Republic of Korea. Molecular ecology
Katzelnick LC, Coello Escoto A, Huang AT, Garcia-Carreras B, Chowdhury N, Maljkovic Berry I, Chavez C, Buchy P, Duong V, Dussart P, Gromowski G, Macareo L, Thaisomboonsuk B, Fernandez S, Smith DJ, Jarman R, Whitehead SS, Salje H, Cummings DAT. (2021). Antigenic evolution of dengue viruses over 20 years. Science (New York, N.Y.), 374(6570)
Sapoval N, Mahmoud M, Jochum M, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie H, Lee MD, Villapol S, Hernandez K, Maljkovic Berry I, Foox J, Beheshti A, Ternus K, Aagaard K, Posada D, Mason C, Sedlazeck FJ, Treangen TJ. (2021). Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission. Genome research
Fung CK, Li T, Pollett S, Alera MT, Yoon IK, Hang J, Macareo L, Srikiatkhachorn A, Ellison D, Rothman AL, Fernandez S, Jarman RG, Maljkovic Berry I. (2021). Effect of low-passage number on dengue consensus genomes and intra-host variant frequencies. The Journal of general virology
Li T, Chung HK, Pireku PK, Beitzel BF, Sanborn MA, Tang CY, Hammer RD, Ritter D, Wan XF, Maljkovic Berry I, Hang J. (2021). Rapid High-Throughput Whole-Genome Sequencing of SARS-CoV-2 by Using One-Step Reverse Transcription-PCR Amplification with an Integrated Microfluidic System and Next-Generation Sequencing. Journal of clinical microbiology, 59(5)
Hughes JJ, Yang Y, Fries AC, Maljkovic Berry I, Pollio AR, Fung CK, Karasavvas N, Jarman RG, Kushner RA, Kajon AE, Collins ND, Macias E, Hang J. (2021). Complete Genome Sequences of Two Human Adenovirus Type 55 Isolates from South Korea and the United States. Microbiology resource announcements, 10(5)
Dussupt V, Sankhala RS, Gromowski GD, Donofrio G, De La Barrera RA, Larocca RA, Zaky W, Mendez-Rivera L, Choe M, Davidson E, McCracken MK, Brien JD, Abbink P, Bai H, Bryan AL, Bias CH, Berry IM, Botero N, Cook T, Doria-Rose NA, Escuer AGI, Frimpong JA, Geretz A, Hernandez M, Hollidge BS, Jian N, Kabra K, Leggat DJ, Liu J, Pinto AK, Rutvisuttinunt W, Setliff I, Tran U, Townsley S, Doranz BJ, Rolland M, McDermott AB, Georgiev IS, Thomas R, Robb ML, Eckels KH, Barranco E, Koren M, Smith DR, Jarman RG, George SL, Stephenson KE, Barouch DH, Modjarrad K, Michael NL, Joyce MG, Krebs SJ. (2020). Potent Zika and dengue cross-neutralizing antibodies induced by Zika vaccination in a dengue-experienced donor. Nature medicine, 26(2)
Maljkovic Berry I, Rutvisuttinunt W, Voegtly LJ, Prieto K, Pollett S, Cer RZ, Kugelman JR, Bishop-Lilly KA, Morton L, Waitumbi J, Jarman RG. (2020). A Department of Defense Laboratory Consortium Approach to Next Generation Sequencing and Bioinformatics Training for Infectious Disease Surveillance in Kenya. Frontiers in genetics, (11)
Maljkovic Berry I, Rutvisuttinunt W, Sippy R, Beltran-Ayala E, Figueroa K, Ryan S, Srikanth A, Stewart-Ibarra AM, Endy T, Jarman RG. (2020). The origins of dengue and chikungunya viruses in Ecuador following increased migration from Venezuela and Colombia. BMC evolutionary biology, 20(1)
Pollett S, Johansson M, Biggerstaff M, Morton LC, Bazaco SL, Brett Major DM, Stewart-Ibarra AM, Pavlin JA, Mate S, Sippy R, Hartman LJ, Reich NG, Maljkovic Berry I, Chretien JP, Althouse BM, Myer D, Viboud C, Rivers C. (2020). Identification and evaluation of epidemic prediction and forecasting reporting guidelines: A systematic review and a call for action. Epidemics, (33)
Sanborn MA, Li T, Victor K, Siegfried H, Fung C, Rothman AL, Srikiatkhachorn A, Fernandez S, Ellison D, Jarman RG, Friberg H, Maljkovic Berry I, Currier JR, Waickman AT. (2020). Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq. Scientific reports, 10(1)
Rivers C, Chretien JP, Riley S, Pavlin JA, Woodward A, Brett-Major D, Maljkovic Berry I, Morton L, Jarman RG, Biggerstaff M, Johansson MA, Reich NG, Meyer D, Snyder MR, Pollett S. (2019). Using "outbreak science" to strengthen the use of models during epidemics. Nature communications, 10(1)
Maljkovic Berry I, Eyase F, Pollett S, Konongoi SL, Joyce MG, Figueroa K, Ofula V, Koka H, Koskei E, Nyunja A, Mancuso JD, Jarman RG, Sang R. (2019). Global Outbreaks and Origins of a Chikungunya Virus Variant Carrying Mutations Which May Increase Fitness for Aedes aegypti: Revelations from the 2016 Mandera, Kenya Outbreak. The American journal of tropical medicine and hygiene, 100(5)
Salje H, Lessler J, Maljkovic Berry I, Melendrez MC, Endy T, Kalayanarooj S, A-Nuegoonpipat A, Chanama S, Sangkijporn S, Klungthong C, Thaisomboonsuk B, Nisalak A, Gibbons RV, Iamsirithaworn S, Macareo LR, Yoon IK, Sangarsang A, Jarman RG, Cummings DA. (2017). Dengue diversity across spatial and temporal scales: Local structure and the effect of host population size. Science (New York, N.Y.), 355(6331)
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