Blanco Mendana, J., Donovan, M., Gengelbach, L., Auch, B., Garbe, J., Gohl, D.M. 2025. Deterministic Genetic Barcoding for Multiplexed Behavioral and Single-Cell Transcriptomic Studies. eLife. doi: https://doi.org/10.7554/eLife.88334.3
McCartney, M.A., Mallez, S., Anderson, S., Garbe, J., Hernández-Elizárraga, V.H., Gohl, D.M. 2025. Population genomics traces zebra mussel invasions along the expanding western North American front in Minnesota, USA to their source waters. Scientific Reports. 15, 43137. doi:https://doi.org/10.1038/s41598-025-27300-6
Heisel, T., Gonia, S., Dillon, A., Hoops, S.L., Al-Ghalith, G.A., Gohl, D., Mukhopadhyay, S., Puopolo, K., Kennedy, P., Sadowsky, M.J., Knights, D., Johnson A.J., Gerber, J.S., Gale, C.A. 2025. Gut mycobiome maturation and its determinants during early childhood: a comparison of ITS2 amplicon and shotgun metagenomic sequencing approaches. Frontiers in Microbiology. doi:https://doi.org/10.3389/fmicb.2025.1539750.
Alegria, A.D.*, Joshi, A.S.*, Blanco Mendana, J., Khosla, K., Smith, K.T., Auch, B., Donovan, M., Bischof, J., Gohl, D.M., Kodandaramaiah, S.B. 2024. High-throughput genetic manipulation of multicellular organisms using a machine-vision guided embryonic microinjection robot. Genetics. doi: https://doi.org/10.1093/genetics/iyae025
Forry, S.P., Servetas, S.L., Kralj, J.G., Soh, K., Hadjithomas, M., Carlin, M., de Amorim, M.G., Auch, B., Bakker, M.G., Bartelli, T.F., Bustamante, J.P., Cassol, I., Chalita, M., Dias-Neto, E., Gohl, D.M., Haruna, M.T., Kazantseva, J., Menzel, P., Moda, B.S., Neuberger-Castillo, L., Nunes, D., Patel, I.R., Peralta, R.D., Saliou, A., Schwarzer, R., Sevilla, S., Takenaka, I.K.T.M., Wang, J., Knight, R., Gevers, D., Jackson, S.A. 2024. Variability and Bias in Microbiome Metagenomic Sequencing: an Interlaboratory Study Comparing Experimental Protocols. Scientific Reports. 14:9785. doi: https://doi.org/10.1038/s41598-024-57981-4
Tan, A.*, Murugapiran, S.*, Mikalauskas, A.*, Koble, J., Kennedy, D., Hyde, F., Ruotti, V., Law, E., Jensen J., Schroth, G.P., Macklaim, J.M., Kuersten, S., Le François, B., Gohl, D.M. 2023. Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes. BMC Microbiology. 21:299. doi: https://doi.org/10.1186/s12866-023-03037-y
Hernández Elizárraga, V.H., Ballantyne, S., O'Brien, L.G., Americo, J.A., Suhr, S.T., Senut, M-C., Minerich, B., Merkes, C.M., Edwards, T.M., Klymus, K., Richter, C.A., Waller, D.L., Passamaneck, Y.J., Rebelo, M.F., Gohl, D.M. 2023. Towards Invasive Mussel Genetic Biocontrol: Approaches, Challenges, and Perspectives. iScience. 108027. https://doi.org/10.1016/j.isci.2023.108027
Born, G., Bieli, D., Metzler, M., Gohl, D.M., Affolter, M, Müller, M. 2023. No apparent role for the Wari insulator in transcriptional regulation of the endogenous white gene of Drosophila melanogaster. microPublication Biology, doi: https://doi.org/10.17912/micropub.biology.000702
Hughes, R.L., Frankenfeld, C. L., Gohl, D.M., Huttenhower, C., Jackson, S.A., Vandeputte, D., Vogtmann, E., Comstock, S.S., Kable, M.E. 2023. Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Sattelite Session [13 October 2022]. Nutrients. 15, 2451. doi: https://doi.org/10.3390/nu15112451
McCartney, M.A., Auch, B., Kono, T., Mallez, S., Zhang, Y., Obille, A., Becker, A., Abrahante, J., Garbe, J., Badalamenti, J., Herman, A., Mangelson, H., Liachko, I., Sullivan, S., Sone, E.D., Koren, S., Silverstein, K., Beckman, K., Gohl, D.M. 2022. The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol. G3 (Genes, Genomes, Genetics). doi: https://doi.org/10.1093/g3journal/jkab423
Holm, I., Nardini, L., Pain, A., Bischoff, E., Anderson, C.E., Zongo, S., Guelbeogo, W.M., Sagnon, N., Gohl, D.M., Nowling, R.J., Vernick, K.D., Riehle, M.M. 2022. Comprehensive genomic discovery of non-coding transcriptional enhancers in the African malaria vector Anopheles coluzzii. Frontiers in Genetics. doi: https://doi.org/10.3389/fgene.2021.785934
Gohl, D.M., Auch, B., Certano, A., LeFrançois, B., Bouevitch, A., Doukhanine, E., Fragel, C., Macklaim, J., Hollister, E., Garbe, J., Beckman, K.B. 2021. Dissecting and Tuning Primer Editing by Proofreading Polymerases. Nucleic Acids Reseach. gkab471. doi: https://doi.org/10.1093/nar/gkab471
Joshi, A.S*., Alegria, A.D*., Auch, B., Khosla, K., Blanco Mendana, J., Liu, K., Bischof, J., Gohl, D.M., Kodandaramaiah, S.B. 2021. Multiscale, multi-perspective imaging assisted robotic microinjection of 3D biological structures. 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), doi: https://doi.org/10.1109/EMBC46164.2021.9630858
Johnson, A.J., Zhou, S., Hoops, S.L., Hillmann, B., Schomaker, M., Kincaid, R., Daniel, J., Beckman, K., Gohl, D.M., Yohe, S., Knights, D., Nelson, A.C. 2021. Saliva testing is accurate for early-stage and presymptomatic COVID-19. Microbiology Spectrum. doi: https://doi.org/10.1128/Spectrum.00086-21
Colonnetta, M.M., Abrahante, J.E., Schedl, P., Gohl, D.M., Deshpande, G. 2021. CLAMP regulates zygotic genome activation in Drosophila embryos. Genetics. iyab107. doi: https://doi.org/10.1093/genetics/iyab107
Gohl, D.M., Garbe, J., Grady, P., Daniel, J., Watson, R.H.B., Nelson, A., Yohe, S., Beckman, K.B. 2020. A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2. BMC Genomics. 21:863. doi: https://doi.org/10.1186/s12864-020-07283-6
Nelson, A.C., Auch, B., Schomaker, M., Gohl, D.M., Grady, P., Johnson, D., Kincaid, R., Karnuth, K.E., Daniel, J., Fiege, J.K., Fay, E.J., Bold, T., Langlois, R.A., Beckman, K.B., Yohe, S. 2020. Analytical Validation of a COVID-19 qRT-PCR Detection Assay Using a 384-well Format and Three Extraction Methods. bioRxiv. doi: https://doi.org/10.1101/2020.04.02.022186
Gohl, D.M., Magli, A., Garbe, J., Becker, A., Johnson, D., Anderson, S., Auch, B., Billstein, B., Froehling, E., McDevitt, S.L., Beckman, K.B. 2019. Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification. Genome Biology. 20(1):85.
Minato, Y., Gohl D.M., Thiede, J.M., Chacón, J.M., Harcombe, W.R., Maruyama, F., Baughn, A.D. 2019. Genome-wide assessment of Mycobacterium tuberculosis conditionally essential metabolic pathways. mSystems. 4:e00070-19.
Nardini, L., Holm, I., Pain, A., Bischoff, E., Gohl, D.M., Zongo, S., Guelbeogo, W.M., Sagnon, N., Vernick, K.D., Riehle, M.M. 2019. Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii. Scientific Reports. 9:15275. doi: https://doi.org/10.1038/s41598-019-51730-8
McCartney, M.A., Mallez, S., Gohl, D.M. 2019. Genome projects in invasion biology. Conservation Genetics. https://doi.org/10.1007/s10592-019-01224-x
Hillmann, B., Al-Ghalith, G.A., Shields-Cutler, R., Zhu, Q., Gohl, D.M., Beckman, K.B., Knight, R., Knights, D. 2018. Evaluating the Information Content of Shallow Shotgun Metagenomics. mSystems. 3(6): https://doi.org/doi:10.1128/mSystems.00069-18
Song, Z., Schlatter, D., Gohl, D.M., Kinkel, L.L. 2018. Run-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal Microbiomes. Phytobiomes. https://doi.org/10.1094/PBIOMES-09-17-0041-R
Castle, S.C., Song, Z., Gohl, D.M., Gutknecht, J.L.M., Rosen, C.J., Sadowsky, M.J., Samac, D.A., Kinkel, L.L. 2018. DNA Template Dilution Impacts Amplicon Sequencing-Based Estimates of Soil Fungal Diversity. Phytobiomes. 2(2):100-107. https://doi.org/10.1094/PBIOMES-09-17-0037-R
Dale, J.L., Beckman, K.B., Willett, J.L.E., Nilson, J.L., Palani, N.P., Baller, J.A., Hauge, A., Gohl, D.M., Erickson, R., Manias, D.A., Sadowsky, M.J., Dunny, G.M. 2018. Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF. mSystems. 3(5): e00062-18. http://doi.org/10.1128/mSystems.00062-18
Liou, N-F., Lin, S-H., Chen, Y-J., Tsai, K-T., Yang, C-J., Lin, T-Y., Wu, T-H., Lin, H-J., Chen, Y-T., Gohl, D., Silies, M., Chou, Y-H. 2018. Diverse populations of local interneurons integrate into the Drosophila adult olfactory circuit. Nature Communications. 9:2232.
Burgos, A., Honjo, K., Ohyama, T., Qian, C. S., Shin, G. J., Gohl, D. M., Silies, M., Tracey, D.W., Zlatic, M., Cardona, A., Grueber, W. B. 2018. Nociceptive interneurons control modular motor pathways to promote escape behavior in Drosophila. eLife. 7:e26016. http://doi.org/10.7554/eLife.26016
Fisher Y.E., Yang, H.H, Isaacman-Beck, J., Xie, M., Gohl, D.M., Clandinin, T.R. 2017. FlpStop, a tool for conditional gene control in Drosophila. eLife. 6:e22279.
Rawson, J.M.O., Gohl, D.M., Landman, S.R., Roth, M.E., Meissner, M.E., Peterson, T.S., Hodges, J.S., Beckman, K.B., Mansky, L.M. 2017. Single strand consensus sequencing reveals that HIV type but not subtype significantly impacts viral mutation frequencies and spectra. Journal of Molecular Biology. https://doi.org/10.1016/j.jmb.2017.05.010
Belda, E., Coulibaly, B., Fofana, A., Beavogui, A.H., Traore, S.F., Gohl, D.M., Vernick, K.D, Riehle, M.M. 2017. Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome. Scientific Reports. 7:3421.
Sickmann, M., Gohl, D. M., Affolter, M., Müller, M. 2017. The Drosophila melanogaster straw locus is allelic to laccase2. Drosophila Information Service. 100:171-174.
Gohl, D.M. 2017. The ecological landscape of microbiome science. Nature Biotechnology. 35:1047-1049.
Gohl, D.M., Morante, J., Venken, K.J.T. 2017. The Current State of the Neuroanatomy Toolkit in the Fruit Fly Drosophila melanogaster. In: Decoding Neural Circuit Structure and Function. Editors: Mathias Wernet and Arzu Celik. Springer International Publishing.
Gohl, D.M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T.J., Clayton, J.B., Johnson, T.J., Hunter, R., Knights, D., Beckman, K.B. 2016. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nature Biotechnology. 34(9):942-949.
Fisher, Y.E., Leong, J.C.S., Sporar, K., Ketkar, M.D., Gohl, D.M., Clandinin, T.R., Silies, M.A. 2015. A class of visual neurons with wide-field properties is required for local motion detection. Current Biology. 25(24):3178-3189.
Bieli, D., Kanca, O., Requena, D., Hamaratoglu, F., Gohl, D., Schedl, P., Affolter, M., Slattery, M., Müller, M., Estella, C. 2015. Establishment of a developmental compartment requires interactions between three synergistic cis-regulatory modules. PLOS Genetics. 11(10):e1005376.
Bieli, D., Kanca, O., Gohl, D., Denes, A., Schedl, P., Affolter, M., Slattery, M., Müller, M. 2015. The Drosophila melanogaster Mutants apblot and apXasta Affect an Essential apterous Wing Enhancer. G3 (Genes, Genomes, Genetics). 5(6):1129–1143.
Baldwin, E.A., Walther-Antonio, M., MacLean, A.M., Gohl, D.M., Beckman, K.B., Chen, J., White, B., Creedon, D.J., Chia, N. 2015. Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery. PeerJ. 3:e1398.
Gohl, D.M.*, Freifeld, L.*, Silies, M., Horowitz, M., Clandinin, T.R. 2014 Large-scale mapping of transposable element insertion sites using digital encoding of DNA sample identity. Genetics. 196(3):615-623.
Velez, M.M. , Gohl, D. , Clandinin, T.R., Wernet, M.F. 2014. Differences in neural circuitry guiding behavioral responses to polarized light presented to either the dorsal or ventral retina in Drosophila. Journal of Neurogenetics. 28(3-4):348-360.
Silies, M.A., Gohl, D.M., Clandinin, T.R. 2014. Motion-Detecting Circuits in Flies: Coming into View. Annual Review of Neuroscience. 37:307-327.
Silies, M.*, Gohl, D.M.*, Fisher, Y.E., Freifeld, L., Clark D.A., Clandinin, T.R. 2013. Modular use of peripheral input channels tunes motion-detecting circuitry. Neuron. 79(1):111-117.
Clark, D.A.*, Fitzgerald, J.E.*, Ales, J.M.*, Gohl, D.M., Silies, M., Norcia, A.M., and Clandinin,T.R. 2013. Flies and humans use a shared computational strategy that exploits natural scene statistics to estimate motion. Nature Neuroscience. 17(2):296-303.
Gao, X.J., Potter, C.J., Gohl, D.M., Silies, M., Katsov, A.Y., Clandinin, T.R. and Luo, L. 2013. Specific Kinematics and Motor-Related Neurons for Aversive Chemotaxis in Drosophila. Current Biology. 23(13):1163-1172.
Burke, C.J., Huetteroth, W., Owald, D., Perisse, E., Krashes, M.J., Das, G., Gohl, D., Silies, M., Certel, S., and Waddell, S. 2012. Layered reward signaling through octopamine and dopamine in Drosophila. Nature. 492(7429):433-7.
Manzo, A., Silies, M., Gohl, D.M., Scott, K. 2012. Motor neurons controlling fluid injestion in Drosophila. Proceedings of the National Academy of Sciences. 109(16):6307-12.
Gohl, D.M., Silies, M.A., Clandinin, T.R. 2012. Drosophila as a genetic model to investigate motion vision. In: The Making and Unmaking of Neural Circuits in Drosophila. Editor: Bassem Hassen. Humana Press.
Gohl, D.M., Silies, M.A., Gao, X.J., Bhalerao, S., Luongo, F.J., Lin, C-C., Potter, C.J., Clandinin, T.R. 2011. A versatile in vivo system for directed dissection of gene expression patterns. Nature Methods. 8:231-237.
Gohl, D., Aoki, T., Blanton, J., Shanower, G., Kappes, G., Schedl, P. 2011. Mechanism of boundary action: roadblock, sink, or loop? Genetics. 187(3):731-748.
Gohl, D., Müller, M., Pirrotta, V., Affolter, M., Schedl, P. 2008. Enhancer blocking and transvection at the Drosophila apterous locus. Genetics. 178(1):127-143.
Schweinsberg, S., Hagstrom, K., Gohl, D., Schedl, P., Kumar, R.P., Mishra, R.., Karch F. 2004. The enhancer blocking activity of the Fab-7 boundary from the Drosophila bithorax complex requires GAGA-factor binding sites. Genetics. 168(3):1371-1384.