Matthew Bendall
Matthew Bendall
Ph.D.
Associate Research Professor
Full-time Faculty
School: Milken Institute School of Public Health
Department: Biostatistics and Bioinformatics
Contact:
Email:
Matthew Bendall
Mobile Phone:
202-994-3461
Science & Engineering Hall
800 22nd Street, NW
Washington DC 20052
I am a Computational Biologist with broad experience in genomics and next-generation sequencing (NGS) data analysis. My roles in the proposed research include 1) Develop computational workflows for analyzing TE expression at single cell level in humans and non-human primates, 2) Analyze TE expression patterns in the context of other genomic and biochemical features and integrate with spatial transcriptomics, and 3) Implement novel approaches for data analysis. I have the scientific and practical expertise necessary for successfully designing and implementing these analysis pipelines, as evidenced by my academic training and research experience.
My academic work spans several disciplines, including biology, biomedical science, computer science, and statistics. My experience includes over 21 years of computer programming experience, including 16 years of bioinformatics research and 14 years analyzing NGS data. After completing my master’s degree, I joined Berkeley National Laboratory at the Joint Genome Institute (JGI) as a Bioinformatics Software developer. At this position, I designed and successfully deployed NGS data analysis pipelines to support the JGI’s single-cell and synthetic biology research groups. I also have experience in developing novel approaches for analyzing single-molecule real-time sequencing data and terabyte-scale metagenomic data. At the Computational Biology Institute, I was involved in a range of projects that involve the analysis of NGS data. I am proficient in developing, testing, and deploying computational workflows in high-performance computing environments, and adhere to best practices of reproducible research. In addition, I possess extensive expertise in differential gene expression analysis through my work on endogenous retrovirus expression. On the respective SCORCH grant, I will serve as a Co-Investigator at GWU under the direction of the mPIs, leading the bioinformatics efforts in single cell analyses of transposable elements, especially in the context of HIV-1 infection, for which I can considered a world expert. Dr. Nixon and I have a ten year long history of successful collaborations as is demonstrated by our joint published work of 19 papers. I have worked with Dr. Ndhlovu and Dr. Corley for over 5 years while at Weill Cornell Medicine with a recently published study with Dr. Ndhlovu and Dr. Corley as first and senior authors, respectively. I have worked with Helena Reyes-Gopar who is a postdoctoral fellow in Dr. Nixon’s lab at FIMR/Northwell on the development of single cell TE analyses. I also have extensive experience developing tools for investigating TE-derived tumor-specific antigens, including published work in methodology development and in infectious diseases.
a. Reyes-Gopar H*, Marston JL*, Singh B, Greenig M, Lin J, Ostrowski MA, Randall KN Jr, Sandoval- Motta S, Dopkins N, Lawrence E, O'Mara MM, Fei T, Duarte RRR, Powell TR, Hernández-Lemus E, Iñiguez LP, Nixon DF, Bendall ML. A single-cell transposable element atlas of human cell identity. Cell Rep Methods. 2025 Jul 21;5(7):101086. doi: 10.1016/j.crmeth.2025.101086. Epub 2025 Jun 20. PubMed PMID: 40543500; PubMed Central PMCID: PMC12296447. *co-first authors.
b. Ndhlovu LC, Bendall ML, Dwaraka V, Pang APS, Dopkins N, Carreras N, Smith R, Nixon DF, Corley MJ. Retro-age: A unique epigenetic biomarker of aging captured by DNA methylation states of retroelements. Aging Cell. 2024 Oct;23(10):e14288. doi: 10.1111/acel.14288. Epub 2024 Aug 2. PubMed PMID: 39092674; PubMed Central PMCID: PMC11464121.
c. Duarte RRR, Pain O, Bendall ML, de Mulder Rougvie M, Marston JL, Selvackadunco S, Troakes C, Leung SK, Bamford RA, Mill J, O'Reilly PF, Srivastava DP, Nixon DF, Powell TR. Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions. Nat Commun. 2024 May 22;15(1):3803. doi: 10.1038/s41467-024-48153- z. PMID: 38778015; PMCID: PMC11111684.
d. Bendall ML, de Mulder M, Iñiguez LP, Lecanda-Sánchez A, Pérez-Losada M, Ostrowski MA, Jones RB, Mulder LCF, Reyes-Terán G, Crandall KA, Ormsby CE, Nixon DF. Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLoS Comput Biol. 2019 Sep;15(9):e1006453. PubMed Central PMCID: PMC6786656.
Ph.D. in Genomics and Bioinformatics George Washington University, Washington DC May 2019
M.S. in Biology Brigham Young University, Provo, UT Aug 2012
B.S. in Bioinformatics Brigham Young University, Provo, UT Aug 2009
A.A. in Computer Science Montgomery College, Rockville, MD May 2006
Doctoral Research Assistant – Nixon Lab Jan 2015 - Jul 2018
George Washington University School of Medicine, Washington DC
Advisor: Douglas Nixon, MD, PhD
o Developed Telescope – computational approach for quantifying transposable element expression using RNA-seq.
o Investigated HERV expression profiles in cancer, neurodevelopment, psychiatry, and embryonic development [ 14 , 15 , 17 , 18 ]
Doctoral Research Assistant – Computational Biology Institute Aug 2014 - Jul 2019
George Washington University Milken Institute of Public Health, Washington DC
Advisor: Keith Crandall, PhD
o Investigated microbiome community composition and host-pathogen interactions in schizophrenia, pediatric asthma, and cystic fibrosis [ 26 , 28 , 29 ]
o Performed statistical analysis for the WE-HEAL study and identified transcriptional patterns in hidradenitis suppurativa [ 22 ].
o Developed the software package HAPHPIPE for viral haplotype assembly and phylodynamics; characterized HIV phylodynamics in Washington DC [ 16 , 19 , 20 , 21 ]
Bioinformatics Software Developer – Joint Genome Institute Dec 2011- Aug 2014
Lawrence Berkeley National Laboratory, Walnut Creek, CA
Synthetic Biology (Samuel Deutsch, PhD)
Single Cell Genomics (Rex Malmstrom, PhD)
o Implemented analysis pipelines for the assembly, mapping, and annotation of metagenomic data using high-performance computing. Developed approaches for detecting selective sweeps using metagenomic time-series [ 27 ]
o Led a team of software developers in building laboratory information managements systems to support JGI’s Synthetic Biology and Single Cell Genomics programs [ 28 ]
o Developed novel methods for identifying epigenetic modifications using PacBio’s single- molecule real-time (SMRT) sequencing technology [ 32 ]
Graduate Research Assistant – Crandall Lab Aug 2009 - Dec 2011
Brigham Young University, Provo, UT
Advisor: Keith Crandall, PhD
o Developed the software package Pathoscope for strain level quantification of metagenomic NGS data [ 33 ]
o Evaluated phylogenetic node calibration methods using empirical phylogenetic and fossil history [ 31 ].
o Compared phylogenetic and structural approaches for identifying deleterious variants in ANGPTL4 [ 34 ]
o Evaluated the performance of methods for predicting sites under positive selection in drug-resistant HIV [thesis]
Undergraduate Research Assistant – Crandall Lab Oct 2007 – Aug 2009
Brigham Young University, Provo, UT
Mentor: Nicole Lewis Rogers, PhD
o Examined phylogenetic relationships among 300+ enterovirus isolates to test hypotheses of recombination and adaptation [ 35 ]
Publications
0000-0001-9816-5425 NCBI Bibliography 35204612500 h-index: 16
Asterisk indicates shared authorship Peer Reviewed Publications (Total: 38, First/Senior Author: 10)
1. Reyes-Gopar H, Marston JL, Singh B, Greenig M, Lin J, Ostrowski MA, Randall KN Jr, Sandoval-Motta S, Dopkins N, Lawrence E, O'Mara MM, Fei T, Duarte RRR, Powell TR, Hernández-Lemus E, Iñiguez LP, Nixon DF, Bendall ML. A single-cell transposable element atlas of human cell identity. Cell Rep Methods. 2025 Jul 21;5(7):101086. doi: 10.1016/j.crmeth.2025.101086. Epub 2025 Jun 20. PubMed PMID: 40543500.
2. Reyes-Gopar H, Pérez-Fuentes KA, Bendall ML, Hernández-Lemus E. Integration of chromosome conformation and gene expression networks reveals regulatory mechanisms in triple negative breast cancer. Front Cell Dev Biol. 2025;13:1597245. doi: 10.3389/fcell.2025.1597245. eCollection 2025. PubMed PMID: 40688355; PubMed Central PMCID: PMC12271745.
3. Singh B, Dopkins N, Fei T, Marston JL, Michael S, Reyes-Gopar H, Curty G, Heymann JJ, Chadburn A, Martin P, Leal FE, Cesarman E, Nixon DF, Bendall ML. Locus-specific human endogenous retroviruses reveal lymphoma subtypes. iScience. 2025 Jun 20;28(6):112541. doi:
10.1016/j.isci.2025.112541. eCollection 2025 Jun 20. PubMed PMID: 40487447; PubMed Central PMCID: PMC12141099.
4. Singh M, Leddy SM, Iñiguez LP, Bendall ML, Nixon DF, Feschotte C. Transposable elements may enhance antiviral resistance in HIV-1 elite controllers. Genome Biol. 2025 Feb 24;26(1):28. doi: 10.1186/s13059-025-03484-y. PubMed PMID: 39988678; PubMed Central PMCID: PMC11849351.
5. Michael S, Liotta N, Fei T, Bendall ML, Nixon DF, Dopkins N. Endogenous retroelement expression in modeled airway epithelial repair. Microbes Infect. 2024 Dec 15;:105465. doi: 10.1016/j.micinf.2024.105465. [Epub ahead of print] PubMed PMID: 39681187.
6. Ndhlovu LC, Bendall ML, Dwaraka V, Pang APS, Dopkins N, Carreras N, Smith R, Nixon DF, Corley MJ. Retro-age: A unique epigenetic biomarker of aging captured by DNA methylation states of retroelements. Aging Cell. 2024 Oct;23(10):e14288. doi: 10.1111/acel.14288. Epub 2024 Aug 2. PubMed PMID: 39092674; PubMed Central PMCID: PMC11464121.
7. Duarte RRR, Pain O, Bendall ML, de Mulder Rougvie M, Marston JL, Selvackadunco S, Troakes C, Leung SK, Bamford RA, Mill J, O'Reilly PF, Srivastava DP, Nixon DF, Powell TR. Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions. Nat Commun. 2024 May 22;15(1):3803. doi: 10.1038/s41467-024-48153-z. PubMed PMID:
38778015.
8. Dopkins N, Fei T, Michael S, Liotta N, Guo K, Mickens KL, Barrett BS, Bendall ML, Dillon SM, Wilson CC, Santiago ML, Nixon DF. Endogenous retroelement expression in the gut microenvironment of people living with HIV-1. EBioMedicine. 2024 May;103:105133. doi: 10.1016/j.ebiom.2024.105133. Epub 2024 Apr 26. PubMed PMID: 38677181; PubMed Central PMCID: PMC11061259.
9. Dopkins N, Singh B, Michael S, Zhang P, Marston JL, Fei T, Singh M, Feschotte C, Collins N, Bendall ML, Nixon DF. Ribosomal profiling of human endogenous retroviruses in healthy tissues. BMC Genomics. 2024 Jan 2;25(1):5. doi: 10.1186/s12864-023-09909-x. Review. PubMed PMID: 38166631; PubMed Central PMCID: PMC10759522.
10. Kanholm T, Rentia U, Hadley M, Karlow JA, Cox OL, Diab N, Bendall ML, Dawson T, McDonald JI, Xie W, Crandall KA, Burns KH, Baylin SB, Easwaran H, Chiappinelli KB. Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci. Cancer Res. 2023 Aug 1;83(15):2584-2599. doi: 10.1158/0008-5472.CAN-22-3485. PubMed PMID: 37249603; PubMed Central
PMCID: PMC10527578.
11. Dopkins N, Singh B, Michael S, O'Mara MM, Marston JL, Fei T, Bendall ML, Nixon DF. Endogenous Reverse Transcriptase Inhibition Attenuates TLR5-Mediated Inflammation. mBio. 2023 Feb 28;14(1):e0328022. doi: 10.1128/mbio.03280-22. Epub 2023 Jan 16. PubMed PMID: 36645307; PubMed Central PMCID: PMC9973353.
12. Viana MC, Curty G, Furtado C, Singh B, Bendall ML, Viola JPB, de Melo AC, Soares MA, Moreira MAM. Naso-oropharyngeal microbiome from breast cancer patients diagnosed with COVID-19. Front Microbiol. 2022;13:1074382. doi: 10.3389/fmicb.2022.1074382. eCollection 2022. PubMed PMID: 36713167; PubMed Central PMCID: PMC9874304.
13. Dopkins N, O'Mara MM, Lawrence E, Fei T, Sandoval-Motta S, Nixon DF, Bendall ML. A field guide to
endogenous retrovirus regulatory networks. Mol Cell. 2022 Oct 20;82(20):3763-3768. doi: 10.1016/j.molcel.2022.09.011. PubMed PMID: 36270247.
14. Dopkins N, O'Mara MM, Singh B, Marston JL, Bendall ML, Nixon DF. How human endogenous retroviruses interact with the microbiota in health and disease. Trends Microbiol. 2022 Sep;30(9):812-815. doi: 10.1016/j.tim.2022.05.011. Epub 2022 Jun 5. PubMed PMID: 35672223.
15. Bendall ML, Francis JH, Shoushtari AN, Nixon DF. Specific human endogenous retroviruses predict metastatic potential in uveal melanoma. JCI Insight. 2022 May 9;7(9). doi: 10.1172/jci.insight.147172. PubMed PMID: 35349481; PubMed Central PMCID: PMC9090245.
16. Marston JL, Greenig M, Singh M, Bendall ML, Duarte RR, Feschotte C, Iñiguez LP, Nixon DF. SARS-CoV-2 infection mediates differential expression of human endogenous retroviruses and long interspersed nuclear elements. JCI Insight. 2021 Nov 3;. doi: 10.1172/jci.insight.147170. [Epub ahead of print] PubMed PMID: 34731091.
17. Steiner MC, Marston JL, Iñiguez LP, Bendall ML, Chiappinelli KB, Nixon DF, Crandall KA. Locus-Specific Characterization of Human Endogenous Retrovirus Expression in Prostate, Breast, and Colon Cancers. Cancer Res. 2021 Jul 1;81(13):3449-3460. doi: 10.1158/0008-5472.CAN-20-3975. Epub 2021 May 3. PubMed PMID: 33941616; PubMed Central PMCID: PMC8260468.
18. Stearrett N, Dawson T, Rahnavard A, Bachali P, Bendall ML, Zeng C, Caricchio R, Pérez-Losada M, Grammer AC, Lipsky PE, Crandall KA. Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression. Front Immunol. 2021;12:661437. doi: 10.3389/fimmu.2021.661437. eCollection 2021. PubMed PMID: 33986751; PubMed Central PMCID:
PMC8112243.
19. Bendall ML*, Gibson KM*, Steiner MC, Rentia U, Pérez-Losada M, Crandall KA. HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations. Mol Biol Evol. 2021 Apr 13;38(4):1677-1690. doi: 10.1093/molbev/msaa315. PubMed PMID: 33367849; PubMed Central PMCID: PMC8042772.
20. Curty G*, Beckerle GA*, Iñiguez LP*, Furler RL, de Carvalho PS, Marston JL, Champiat S, Heymann JJ, Ormsby CE, Reyes-Terán G, Soares MA*, Nixon DF*, Bendall ML*, Leal FE*, de Mulder Rougvie M*. Human Endogenous Retrovirus Expression Is Upregulated in the Breast Cancer Microenvironment of HIV Infected Women: A Pilot Study. Front Oncol. 2020;10:553983. doi: 10.3389/fonc.2020.553983. eCollection 2020. PubMed PMID: 33194615; PubMed Central PMCID: PMC7649802.
21. Kolbe AR, Bendall ML, Pearson AT, Paul D, Nixon DF, Pérez-Losada M, Crandall KA. Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival. Viruses. 2020 Aug 28;12(9). doi: 10.3390/v12090956. PubMed PMID: 32872377; PubMed Central PMCID: PMC7552064.
22. Eliseev A, Gibson KM, Avdeyev P, Novik D, Bendall ML, Pérez-Losada M, Alexeev N, Crandall KA. Evaluation of haplotype callers for next-generation sequencing of viruses. Infect Genet Evol. 2020 Aug;82:104277. doi: 10.1016/j.meegid.2020.104277. Epub 2020 Mar 6. PubMed PMID: 32151775; PubMed Central PMCID: PMC7293574.
23. Gibson KM, Steiner MC, Rentia U, Bendall ML, Pérez-Losada M, Crandall KA. Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses. Viruses. 2020 Jul 14;12(7). doi: 10.3390/v12070758. PubMed PMID: 32674515; PubMed Central PMCID: PMC7412389.
24. Gibson KM, Jair K, Castel AD, Bendall ML, Wilbourn B, Jordan JA, Crandall KA, Pérez-Losada M. A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. Sci Rep. 2020 Feb 6;10(1):1989. doi: 10.1038/s41598-020-58410-y. PubMed PMID: 32029767; PubMed Central PMCID: PMC7004982.
25. Shanmugam VK, Jones D, McNish S, Bendall ML, Crandall KA. Transcriptome patterns in hidradenitis suppurativa: support for the role of antimicrobial peptides and interferon pathways in disease pathogenesis. Clin Exp Dermatol. 2019 Dec;44(8):882-892. doi: 10.1111/ced.13959. Epub 2019 Apr 24. PubMed PMID: 30828847.
26. Iñiguez LP, de Mulder Rougvie M, Stearrett N, Jones RB, Ormsby CE, Reyes-Terán G, Crandall KA, Nixon DF, Bendall ML. Transcriptomic analysis of human endogenous retroviruses in systemic lupus erythematosus. Proc Natl Acad Sci U S A. 2019 Oct 22;116(43):21350-21351. doi: 10.1073/pnas.1907705116. Epub 2019 Oct 8. PubMed PMID: 31594853; PubMed Central PMCID: PMC6815141.
27. Bendall ML, de Mulder M, Iñiguez LP, Lecanda-Sánchez A, Pérez-Losada M, Ostrowski MA, Jones RB, Mulder LCF, Reyes-Terán G, Crandall KA, Ormsby CE, Nixon DF. Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLoS Comput Biol. 2019 Sep;15(9):e1006453. doi: 10.1371/journal.pcbi.1006453. eCollection 2019 Sep. PubMed PMID: 31568525; PubMed Central PMCID: PMC6786656.
28. Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
29. Hahn A, Bendall ML, Gibson KM, Chaney H, Sami I, Perez GF, Koumbourlis AC, McCaffrey TA, Freishtat RJ, Crandall KA. Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity. Front Microbiol. 2018;9:1069. doi: 10.3389/fmicb.2018.01069. eCollection 2018. PubMed PMID: 29887843; PubMed Central PMCID: PMC5980964.
30. Bendall ML*, Stevens SL*, Chan LK, Malfatti S, Schwientek P, Tremblay J, Schackwitz W, Martin J, Pati A, Bushnell B, Froula J, Kang D, Tringe SG, Bertilsson S, Moran MA, Shade A, Newton RJ, McMahon KD, Malmstrom RR. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J. 2016 Jul;10(7):1589-601. doi: 10.1038/ismej.2015.241. Epub 2016 Jan 8. PubMed PMID: 26744812; PubMed Central PMCID: PMC4918448.
31. Castro-Nallar E, Bendall ML, Pérez-Losada M, Sabuncyan S, Severance EG, Dickerson FB, Schroeder JR, Yolken RH, Crandall KA. Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. PeerJ. 2015;3:e1140. doi: 10.7717/peerj.1140. eCollection 2015. PubMed PMID: 26336637; PubMed Central PMCID: PMC4556144.
32. Pérez-Losada M, Castro-Nallar E, Bendall ML, Freishtat RJ, Crandall KA. Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma. PLoS One. 2015;10(6):e0131819. doi: 10.1371/journal.pone.0131819. eCollection 2015. PubMed PMID: 26125632; PubMed Central PMCID: PMC4488395.
33. Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S. Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol. 2014 Sep 19;9(9):2082- 91. doi: 10.1021/cb500244v. Epub 2014 Jul 17. PubMed PMID: 24984213; PubMed Central PMCID: PMC4168791.
34. Bracken-Grissom HD, Ahyong ST, Wilkinson RD, Feldmann RM, Schweitzer CE, Breinholt JW, Bendall ML, Palero F, Chan TY, Felder DL, Robles R, Chu KH, Tsang LM, Kim D, Martin JW, Crandall KA. The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida). Syst Biol. 2014
Jul;63(4):457-79. doi: 10.1093/sysbio/syu008. Epub 2014 Feb 20. PubMed PMID: 24562813.
35. Bendall ML, Luong K, Wetmore KM, Blow M, Korlach J, Deutschbauer A, Malmstrom RR. Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. J Bacteriol. 2013 Nov;195(21):4966-74. doi: 10.1128/JB.00935-13. Epub 2013 Aug 30. PubMed PMID: 23995632; PubMed Central PMCID: PMC3807482.
36. Francis OE, Bendall ML, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE. Pathoscope: species identification and strain attribution with unassembled sequencing data. Genome Res. 2013 Oct;23(10):1721-9. doi: 10.1101/gr.150151.112. Epub 2013 Jul 10. PubMed PMID: 23843222; PubMed Central PMCID: PMC3787268.
37. Maxwell TJ, Bendall ML, Staples J, Jarvis T, Crandall KA. Phylogenetics applied to genotype/phenotype association and selection analyses with sequence data from angptl4 in humans. Int J Mol Sci. 2010 Jan 25;11(1):370-85. doi: 10.3390/ijms11010370. PubMed PMID: 20162021; PubMed Central PMCID: PMC2821009.
38. Lewis-Rogers N, Bendall ML, Crandall KA. Phylogenetic relationships and molecular adaptation dynamics of human rhinoviruses. Mol Biol Evol. 2009 May;26(5):969-81. doi: 10.1093/molbev/msp009. Epub 2009 Jan 30. PubMed PMID: 19182223.
In Progress (Total: 3)
39. Fei T, Singh B, Dopkins N, Marston JL, Francis JH, Nixon DF, Shoushtari AN, Bendall ML. Human endogenous retrovirus landscape of melanoma metastases in response to immune checkpoint inhibition. Submitted.
40. Marston JL*, Reyes-Gopar H*, Singh B, Greenig M, Dopkins N, Sandoval-Motta S, Lawrence E, O’Mara MM, Fei T, Lin J, Randall KN, Hernandez-Lemus E, Cesarman E, Iñiguez LP, Nixon DF, Bendall ML. Single-cell retrotranscriptomics of human germinal center B cells reveals trajectories of cell fate. In Progress.
41. Greenig M, Bendall ML*, Nixon DF*, Marston JL*. Human endogenous retrovirus-mediated transcriptional regulation in the MHC and beyond. Under review.
Lecturer – Thesis research exploration (CMPB 6001), Weill Cornell Graduate School 2020 - 2024
Teaching Assistant – Bioinformatics (BIO465), Brigham Young University 2009 - 2011
Teaching Assistant – Computational Biology (BIO365), Brigham Young University 2009 - 2011
Telescope Codeathon – Scientific Organizer Sep 2021
Telescope “Dark Matter” Codeathon 2021, New York, NY
Organized and led a four-day codeathon involving 12 biologists and computational scientists.
Developed Stellarscope software.
Telescope intensive course – Lead instructor Jul 2017
Endogenous Retroelements in Psychiatry Workshop, London, UK
Taught two-day workshop introducing RNA-seq and Telescope retrotranscriptome analysis
PathoScope and PathoStat Tutorial – Instructor Feb 2017
Global Biodiversity Genomics Conference, Washington DC
Taught four-hour workshop on microbiome analysis using PathoScope
PathoScope and PathoStat Tutorial – Instructor Nov 2016
Mid-Atlantic Microbiome Meetup, College Park, MD
Taught two-hour workshop on microbiome analysis using PathoScope