2017

Elise Landais, Ben Murrell, Bryan Briney, Sasha Murrell, Kimmo Rantalainen, Zachary T. Berndsen, Alejandra Ramos, Lalinda Wickramasinghe, Melissa Laird Smith, Kemal Eren, Natalia de Val, Mengyu Wu, Audrey Cappelletti, Jeffrey Umotoy, Yolanda Lie, Terri Wrin, Paul Algate, Po-Ying Chan-Hui, Etienne Karita, The IAVI Protocol C Investigators, The IAVI African HIV Research Network, Andrew B. Ward, Ian A. Wilson, Dennis R. Burton, Davey Smith, Sergei L. Kosakovsky Pond, and Pascal Poignard. HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage. Immunity (In Press).

Neeru Bhardwaj, Manon Ragonnet-Cronin, Ben Murrell, Krishna Chodavarapu, Ross Martin, Silvia Chang, Michael D. Miller, Jordan J. Feld, Mark Sulkowski, Alessandra Mangia, Joel O. Wertheim, Anu Osinusi, John McNally, Diana Brainard, Hongmei Mo, and Evguenia S. Svarovskaia. Intrapatient viral diversity and treatment outcome in patients with genotype 3a hepatitis C virus infection on sofosbuvir-containing regimens. Journal of Viral Hepatitis (2017).

Marina Caskey, Till Schoofs, Henning Gruell, Allison Settler, Theodora Karagounis, Edward F. Kreider, Ben Murrell, Nico Pfeifer, Lilian Nogueira, Thiago Y. Oliveira, Gerald H. Learn, Yehuda Z. Cohen, Clara Lehmann, Daniel Gillor, Irina Shimeliovich, Cecilia Unson-O?Brien, Daniela Weiland, Alexander Robles, Tim Kummerle, Christoph Wyen, Rebeka Levin, Maggi Witmer-Pack, Kemal Eren, Caroline Ignacio, Szilard Kiss, Anthony P. West, Jr, Hugo Mouquet, Barry S. Zingman, Roy M. Gulick, Tibor Keler, Pamela J. Bjorkman, Michael S. Seaman, Beatrice H. Hahn, Gerd Fatkenheuer, Sarah J. Schlesinger, Michel C. Nussenzweig, Florian Klein. Antibody 10-1074 suppresses viremia in HIV-1- infected individuals. Nature Medicine (2017).

Joel O Wertheim, Sergei L Kosakovsky Pond, Lisa A Forgione, Sanjay R Mehta, Ben Murrell, Sharmila Shah, Davey M Smith, Konrad Scheffler, Lucia V Torian. Social and Genetic Networks of HIV-1 Transmission in New York City. PLoS Pathogens (2017).

Ramy El-Diwany, Valerie J Cohen; Madeleine M Mankowski, Lisa N Wasilewski, Jillian K Brady, Anna E Snider, William O Osburn, Ben Murrell, Stuart C Ray, Justin R Bailey. Extra-epitopic hepatitis C virus polymorphisms confer resistance to broadly neutralizing antibodies by modulating binding to scavenger receptor B1. PLoS Pathogens (2017).

2016

Ben Murrell, Thomas Vollbrecht, John Guatelli, Joel Wertheim. Antiretroviral proteins SERINC3 and SERINC5 evolutionary histories do not support an evolutionary arms race in primates. Journal of Virology (2016).

Melissa Laird Smith, Ben Murrell*, Kemal Eren, Caroline Ignacio, Elise Landais, Steven Weaver, Pham Phung, Colleen Ludka, Lance Hepler, Gemma Caballero, Tristan Pollner, Yan Guo, Douglas Richman, The IAVI Protocol C Investigators \& The IAVI African HIV Research Network, Pascal Poignard, Ellen E. Paxinos, Sergei Kosakovsky Pond, Davey Smith. Rapid sequencing of complete env genes from primary HIV-1 samples. Virus Evolution (2016).

Daniel T. MacLeod, Nancy M. Choi, Bryan Briney, Fernando Garces, Lorena Ver, Elise Landais, Ben Murrell, Terri Wrin, Chi-Hui Liang, Alejandra Ramos, Chaoran B. Bian, Lalinda Wickramasinghe, Leopold Kong, Kemal Eren, Chung-Yi Wu, Chi-Huey Wong, The IAVI Protocol C Investigators \& The IAVI African HIV Research Network, Sergei L. Kosakovsky Pond, Ian A. Wilson, Dennis R. Burton, Pascal Poignard. Early parallel development of a multi-limb broadly neutralizing HIV antibody lineage targeting the high mannose patch. Immunity (2016).

Mehta SR, Ben Murrell, Anderson CZ, Kosakovsky Pond SL, Wertheim JO, Young JA, Freitas L, Richman DD, Mathews WC, Scheffler K, Little SJ, Smith DM. Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-Referral Testing for Acute HIV on Incident Diagnoses in San Diego, California. Clinical Infectious Diseases (2016).

Ben Murrell, Daniel Murrell, and Hugh Murrell. Discovering General Multidimensional Associations. PLoS One (2016).

2015

Elise Landais, Xiayu Huang, Colin Havenar-Daughton, Ben Murrell, Matt A. Price, Lalinda Wickramasinghe, Alejandra Ramos, Charoan B. Bian, Melissa Simek, Susan Allen, Etienne Karita, William Kilembe, Shabir Lakhi, Mubiana Inambao, Anatoli Kamali, Eduard J. Sanders, Omu Anzala, Vinodh Edward, Linda-Gail Bekker, Jianming Tang, Jill Gilmour, Sergei L. Kosakovsky-Pond, Pham Phung, Terri Wrin, Shane Crotty, Adam Godzik, and Pascal Poignard. Broadly neutralizing antibody responses in a large longitudinal Sub-Saharan HIV primary infection cohort. PLoS Pathogens, 12(1):e1005369+ (2016).

Ben Murrell, Steven Weaver, Martin D. Smith, Joel O. Wertheim, Sasha Murrell, Anthony Aylward, Kemal Eren, Tristan Pollner, Darren P. Martin, Davey M. Smith, Konrad Scheffler, and Sergei L. Kosakovsky Pond. Gene-wide identification of episodic selection. Molecular Biology and Evolution (2015).

Michelli Faria de, Ben Murrell, Josué Pérez-Santiago, Milenka Vargas, Ronald J. Ellis, Scott Letendre, Igor Grant, Davey M. Smith, Steven Paul, and Sara Gianella. Circulating HIV DNA correlates with neurocognitive impairment in older HIV-infected adults on suppressive ART. Scientific reports, 5 (2015).

Josué Pérez-Santiago, Rachel D Schrier, Michelli F de Oliveira, Sara Gianella, Susanna R Var, Tyler R Day, Miguel Ramirez-Gaona, Jesse D Suben, Ben Murrell, Marta Massanella, Mariana Cherner, Davey M Smith, Ronald J Ellis, Scott L Letendre, and Sanjay R Mehta. Cell-free mitochondrial DNA in CSF is associated with early viral rebound, inflammation, and severity of neurocognitive deficits in HIV infection. Journal of Neurovirolgy, pages 1–10 (2015).

Alistair M. McInnes, Arjun Khoosal, Ben Murrell, Dagmar Merkle, Miguel Lacerda, Reason Nyengera, Janet C. Coetzee, Loyd C. Edwards, Peter G. Ryan, Johan Rademan, Jan J. van der Westhuizen, and Lorien Pichegru. Recreational Fish-Finders—an inexpensive alternative to scientific Echo-Sounders for unravelling the links between marine top predators and their prey. PLoS ONE, 10(11):e0140936+ (2015).

Simon D.W. Frost, Ben Murrell, A. S. Md. Mukarram Hossain, Gregg J. Silverman, and Sergei L. Kosakovsky Pond. Assigning and visualising germline genes in antibody repertoires. Philosophical Transactions of the Royal Society, B (2015).

Sanjay R Mehta, Joel O Wertheim, Kimberly C Brouwer, Karla D Wagner, Antoine Chaillon, Steffanie Strathdee, Thomas L Patterson, Maria G Rangel, Mlenka Vargas, Ben Murrell, Richard Garfein, Susan J Little, and Davey M Smith. HIV Transmission Networks in the San Diego-Tijuana Border Region. EBioMedicine (2015).

Darren P Martin, Ben Murrell, Michael Golden, Arjun Khoosal, Brejnev Muhire. RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution (2015).

Denis Filloux, Sasha Murrell, Maneerat Koohapitagtam, Michael Golden, Charlotte Julian, Serge Galzi, Marilyne Uzest, Marguerite Rodier-Goud, Angelique D’Hont, Marie Vernerey, Paul Wilkin, Michel Peterschmitt, Stephan Winter, Ben Murrell, Darren Martin, Philippe Roumagnac. Evidence of functional protein expression from endogenous geminiviral sequences that have been integrated for millions of years within yam (Dioscorea L. spp.) genomes. Virus Evolution (2015).

Martin D. Smith, Joel O. Wertheim, Steven Weaver, Ben Murrell, Konrad Scheffler, and Sergei L. Kosakovsky Pond. Less is More: an Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection. Molecular Biology and Evolution (2015)

Joel O. Wertheim, Ben Murrell, Martin D. Smith, Sergei L. Kosakovsky Pond, Konrad Scheffler. RELAX: Detecting Relaxed Selection in a Phylogenetic Framework. Molecular Biology and Evolution (2015).

Randall G. Fisher, Davey M. Smith, Ben Murrell, Ruhan Slabbert, Bronwyn M. Kirby, Clair Edson, Mark F. Cotton, Richard H. Haubrich, Sergei L. Kosakovsky Pond and Gert U. Van Zyl. Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure. Journal of Clinical Virology (2015).

2014

Ben Murrell, Daniel Murrell and Hugh Murrell. R² equitability is satisfiable. Proceedings of the National Academy of Sciences of the United States of America (2014).

N Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D Richman, Dennis R Burton, Pascal Poignard, Mojgan Haddad, Davey M Smith, Sergei L Kosakovsky Pond. IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. PLoS Computational Biology (2014).

Brejnev M. Muhire, Michael Golden, Ben Murrell, Pierre Lefeuvre, Jean-Michel Lett, Alistair Gray, Art Y. F. Poon, Nobubelo K. Ngandu, Yves Semegni, Emil P. Tanov, Aderito L. Monjane, Gordon W. Harkins, Arvind Varsani, Dionne N. Shepherd, and Darren P. Martin. Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic Single-Stranded DNA viruses. Journal of Virology (2014).

Konrad Scheffler, Ben Murrell, and Sergei L. Kosakovsky Pond. On the validity of evolutionary models with Site-Specific parameters. PLoS ONE, 9(4):e94534+ (2014).

2013

Ben Murrell, Sasha Moola, Amandla Mabona, Thomas Weighill, Daniel Sheward, Sergei L. Kosakovsky Pond and Konrad Scheffler. FUBAR: A Fast, Unconstrained Bayesian AppRoximation for inferring selection. Molecular Biology and Evolution (2013).

Miguel Lacerda, Penny Moore, Nobubelo Ngandu, Michael Seaman, Elin Gray, Ben Murrell, Mohan Krishnamoorthy, Molati Nonyane, Maphuti Madiga, Constantinos Wibmer, Daniel Sheward, Robert Bailer, Hongmei Gao, Kelli Greene, Salim S. Karim, John Mascola, Bette Korber, David Montefiori, Lynn Morris, Carolyn Williamson, Cathal Seoighe, and the CAVD NSDP Consortium. Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models. Virology Journal (2013).

2012

Ben Murrell, Joel O Wertheim, Sasha Moola, Thomas Weighill, Konrad Scheffler, and Sergei L. Kosakovsky Pond. Detecting individual sites subject to episodic diversifying selection. PLoS Genetics (2012).

Ben Murrell, Tulio de Oliveira, Chris Seebregts, Sergei L Kosakovsky Pond and Konrad Scheffler. Modeling HIV-1 drug resistance as episodic directional selection. PLoS Computational Biology (2012).

Daniel J. Sheward, Ben Murrell, and Carolyn Williamson. Degenerate primer IDs and the birthday problem. Proceedings of the National Academy of Sciences of the United States of America (2012).

Randall Fisher, Gert U. van Zyl, Simon A.A. Travers, Sergei L. Kosakovsky Pond, Susan Engelbrech, Ben Murrell, Konrad Scheffler, Davey Smith. Deep sequencing reveals minor protease resistance mutants in patients failing a protease inhibitor regimen. Journal of Virology (2012).

2011

Sergei L. Kosakovsky Pond, Ben Murrell, Mathieu Fourment, Simon D. W. Frost, Wayne Delport, and Konrad Scheffler. A random effects branch-site model for detecting episodic diversifying selection. Molecular Biology and Evolution (2011).

Ben Murrell, Weighill T, Buys J, Ketteringham R, Moola S, et al. Non-Negative Matrix Factorization for Learning Alignment-Specific Models of Protein Evolution. PLoS ONE (2011).

Book Chapters

Darren P Martin, Ben Murrell, Arjun Khoosal and Brejnev Muhire. Detecting and Analyzing Genetic Recombination Using RDP4, in Keith, Jonathan M. (ed) Bioinformatics: Volume I: Data, Sequence Analysis, and Evolution. Series: Methods in molecular biology (Springer, Clifton, N.J.), 433-460 (2017).

Sergei Kosakovsky L. Pond, Ben Murrell, and Art F. Poon. Evolution of viral genomes: interplay between selection, recombination, and other forces, in Maria Anisimova (ed) Evolutionary Genomics : Statistical and Computational Methods, Volume 2. Series: Methods in molecular biology (Springer, Clifton, N.J.), 856:239–272 (2012).

David Spurrett. and Ben Murrell. Measuring Dispositions to Bundle Choices, in D. Ross, P. Collins, H. Kincaid and D. Spurrett (eds), What is Addiction?, Cambridge, Mass. MIT Press (2010).