| HyPhy 2.5—a customizable platform for evolutionary hypothesis testing using phylogenies SL Kosakovsky Pond, AFY Poon, R Velazquez, S Weaver, NL Hepler, ... Molecular biology and evolution 37 (1), 295-299, 2020 | 386 | 2020 |
| The global transmission network of HIV-1 JO Wertheim, AJ Leigh Brown, NL Hepler, SR Mehta, DD Richman, ... The Journal of infectious diseases 209 (2), 304-313, 2014 | 247 | 2014 |
| Systems and methods for visualization of single-cell resolution characteristics J Mellen, KJ Wu, VKS Gopalan, NL Hepler, J Staab US Patent 11,574,706, 2023 | 58 | 2023 |
| Functional antibodies exhibit light chain coherence DB Jaffe, P Shahi, BA Adams, AM Chrisman, PM Finnegan, N Raman, ... Nature 611 (7935), 352-357, 2022 | 49 | 2022 |
| IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform NL Hepler, K Scheffler, S Weaver, B Murrell, DD Richman, DR Burton, ... PLoS computational biology 10 (9), e1003842, 2014 | 35 | 2014 |
| Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples M Laird Smith, B Murrell, K Eren, C Ignacio, E Landais, S Weaver, ... Virus Evolution 2 (2), vew018, 2016 | 32 | 2016 |
| Pacific Biosciences Sequencing and IMGT/HighV-QUEST Analysis of Full-Length Single Chain Fragment Variable from an In Vivo Selected Phage-Display … A Hemadou, V Giudicelli, ML Smith, MP Lefranc, P Duroux, S Kossida, ... Frontiers in immunology 8, 1796, 2017 | 30 | 2017 |
| Dynamics of viral evolution and neutralizing antibody response after HIV-1 superinfection A Chaillon, GA Wagner, NL Hepler, SJ Little, SL Kosakovsky Pond, ... Journal of virology 87 (23), 12737-12744, 2013 | 28 | 2013 |
| Joint single cell DNA-Seq and RNA-Seq of cancer reveals subclonal signatures of genomic instability and gene expression N Andor, BT Lau, C Catalanotti, V Kumar, A Sathe, K Belhocine, ... Biorxiv, 445932, 2018 | 20 | 2018 |
| Kosakovsky Pond SL, Caballero G, Pacold ME, Phung P, Wrin T, Richman DD, Wertheim JO, Smith DM. 2013. Dynamics of viral evolution and neutralizing antibody response after HIV-1 … A Chaillon, GA Wagner, NL Hepler, SJ Little J Virol 87, 12737-12744, 0 | 13 | |
| An improved circular consensus algorithm with an application to detect HIV-1 Drug-Resistance associated mutations (DRAMs) NL Hepler, N Delaney, M Brown, ML Smith, D Katzenstein, EE Paxinos, ... Conference on Advances in Genome Biology and Technology, 2016 | 6 | 2016 |
| OR57: Generation of 252 HLA class I genomic sequences in a single sequencing reaction using DNA barcodes and single molecule real-time (SMRT) DNA sequencing technology NP Mayor, J Robinson, S Ranade, K Eng, S Wallis-Jones, ... Human Immunology 75, 49, 2014 | 3 | 2014 |
| Kosakovsky Pond SL, Poon AFY, Velazquez R, Weaver S, Lance Hepler N, Murrell B, Shank SD, Magalis BR, Bouvier D, et al. 2020. HyPhy 2.5—a customizable platform for … SLK Pond Mol Biol Evol 37 (1), 295-299, 0 | 2 | |
| Systems and methods for visualization of single-cell resolution characteristics J Mellen, KJ Wu, VKS Gopalan, NL Hepler, J Staab US Patent App. 18/165,133, 2023 | | 2023 |
| Systems and methods for identifying cell-associated barcodes in mutli-genomic feature data from single-cell partitions AS Maheshwari, VKS Gopalan, B Olsen, NL Hepler US Patent App. 17/465,682, 2022 | | 2022 |
| Systems and methods for index hopping filtering NL Hepler, C Aluru, PJ Marks, N Srinivas, N Delaney US Patent App. 17/168,050, 2021 | | 2021 |
| HIV-1 Sequence Analysis: Approaches and Applications from Transmission Network Inference to Epitope Discovery NL Hepler UC San Diego, 2019 | | 2019 |
| MULTIPLEXING HUMAN HLA CLASS I AND II GENOTYPING WITH BARCODE ADAPTERS FOR HIGH-THROUGHPUT CLINICAL RESEARCH S Ranade, N Westerink, W Lee, J Harting, K Eng, L Hepler, B Bowman TISSUE ANTIGENS 85 (5), 325-325, 2015 | | 2015 |
| LONG AMPLICON ANALYSIS: A TOOL FOR GENERATING HIGHLY ACCURATE, FULL-LENGTH, PHASED, ALLELE-RESOLVED GENE SEQUENCES FROM MULTIPLEXED SMRT (R) SEQUENCING DATA BN Bowman, P Marks, L Hepler, K Eng, J Harting, T Shiina, S Ranade TISSUE ANTIGENS 84 (1), 124-124, 2014 | | 2014 |
| GENERATION OF MULTIPLE FULL LENGTH HLA CLASS I GENE SEQUENCES IN A SINGLE SEQUENCING REACTION USING SMRT DNA SEQUENCING TECHNOLOGY NP Mayor, J Robinson, AJM McWhinnie, S Ranade, K Eng, W Midwinter, ... TISSUE ANTIGENS 84 (1), 11-12, 2014 | | 2014 |
