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Monk, B., Rajkovic, A., Petrus, S., Gaasterland, T., & Malinow, R. (2021). A machine learning method to identify genetic variants potentially associated with Alzheimer’s Disease. Frontiers in Genetics, 12. https://doi.org/10.3389/fgene.2021.647436

Gumber, D., Do, M., Kumar, N. S., Sonavane, P. R., Wu, C. C. N., Cruz, L. S., Grainger, S., Carson, D., Gaasterland, T., & Willert, K. (2020). Selective activation of FZD7 promotes mesendodermal differentiation of human pluripotent stem cells. Elife, 9. https://doi.org/10.7554/eLife.63060

Mascuch, S. J., Boudreau, P. D., Carland, T. M., Pierce, N. T., Olson, J., Hensler, M. E., Choi, H., Campanale, J., Hamdoun, A., Nizet, V., Gerwick, W. H., Gaasterland, T., & Gerwick, L. (2018). Marine natural product honaucin A attenuates inflammation by activating the Nrf2-ARE pathway. Journal of Natural Products, 81(3), 506–514. https://doi.org/10.1021/acs.jnatprod.7b00734

Bailey, J. N. C., Gharahkhani, P., Kang, J. H., Butkiewicz, M., Sullivan, D. A., Weinreb, R. N., Aschard, H., Allingham, R. R., Ashley-Koch, A., Lee, R. K., Moroi, S. E., Brilliant, M. H., Wollstein, G., Schuman, J. S., Fingert, J. H., Budenz, D. L., Realini, T., Gaasterland, T., Scott, W. K., … Pasquale, L. R. (2018). Testosterone Pathway Genetic Polymorphisms in Relation to Primary Open-Angle Glaucoma: An Analysis in Two Large Datasets. Investigative Ophthalmology & Visual Science, 59(2), 629–636. https://doi.org/10.1167/iovs.17-22708

Aschard, H., Kang, J. H., Iglesias, A. I., Hysi, P., Bailey, J. N. C., Khawaja, A. P., Allingham, R. R., Ashley-Koch, A., Lee, R. K., Moroi, S. E., Brilliant, M. H., Wollstein, G., Schuman, J. S., Fingert, J. H., Budenz, D. L., Realini, T., Gaasterland, T., Scott, W. K., Singh, K., … Int Glaucoma Genetics Consortium. (2017). Genetic correlations between intraocular pressure, blood pressure and primary open-angle glaucoma: a multi-cohort analysis. European Journal of Human Genetics, 25(11), 1261–1267. https://doi.org/10.1038/ejhg.2017.136

Huggins, I. J., Bos, T., Gaylord, O., Jessen, C., Lonquich, B., Puranen, A., Richter, J., Rossdam, C., Brafman, D., Gaasterland, T., & Willert, K. (2017). The WNT target SP5 negatively regulates WNT transcriptional programs in human pluripotent stem cells. Nature Communications, 8. https://doi.org/10.1038/s41467-017-01203-1

Hsu, C. C., Baker, M. W., Gaasterland, T., Meehan, M. J., Macagno, E. R., & Dorrestein, P. C. (2017). Top-Down Atmospheric Ionization Mass Spectrometry Microscopy Combined With Proteogenomics. Analytical Chemistry, 89(16), 8251–8258. https://doi.org/10.1021/acs.analchem.7b01096

Jamieson, C., Muldong, M., Gallegos, A., Wu, C., Mendoza, T., Park, J. S., Daejeon, S. G., Zhu, W., Raheem, O., Park, S. C., Liss, M., Burner, D., Edsall, L., Miakicheva, O., Cacalano, N., Jamieson, C., Kane, C., Kulidjian, A., & Gaasterland, T. (2017). Genomic analysis of a longitudinal series of surgical prostate cancer bone metastases and xenografts from the same patient revealed selection of a progressively therapy resistant metastatic clone. Journal of Urology, 197(4), E1169–E1169. https://doi.org/10.1016/j.juro.2017.02.2714

Pierce, N. T., Navarro, M. O., Gaasterland, T., & Burton, R. S. (2017). Effect of low pH and low oxygen conditions on developmental gene expression and hatching of Doryteuthis opalescens embryos. Integrative and Comparative Biology, 57, E132–E132.

Pasquale, L. R., Aschard, H., Kang, J. H., Bailey, J. N. C., Lindstrom, S., Chasman, D. I., Christen, W. G., Allingham, R. R., Ashley-Koch, A., Lee, R. K., Moroi, S. E., Brilliant, M. H., Wollstein, G., Schuman, J. S., Fingert, J., Budenz, D. L., Realini, T., Gaasterland, T., Gaasterland, D., … Wiggs, J. L. (2017). Age at natural menopause genetic risk score in relation to age at natural menopause and primary open-angle glaucoma in a US-based sample. Menopause-the Journal of the North American Menopause Society, 24(2), 150–156. https://doi.org/10.1097/Gme.0000000000000741

Khawaja, A. P., Bailey, J. N. C., Kang, J. H., Allingham, R. R., Hauser, M. A., Brilliant, M., Budenz, D. L., Christen, W. G., Fingert, J., Gaasterland, D., Gaasterland, T., Kraft, P., Lee, R. K., Lichter, P. R., Liu, Y. T., Medeiros, F., Moroi, S. E., Richards, J. E., Realini, T., … Wiggs, J. L. (2016). Assessing the Association of Mitochondrial Genetic Variation With Primary Open-Angle Glaucoma Using GeneSet Analyses. Investigative Ophthalmology & Visual Science, 57(11), 5046–5052. https://doi.org/10.1167/iovs.16-20017

Liu, Y. T., Bailey, J. C., Helwa, I., Dismuke, W. M., Cai, J. W., Drewry, M., Brilliant, M. H., Budenz, D. L., Christen, W. G., Chasman, D. I., Fingert, J. H., Gaasterland, D., Gaasterland, T., Gordon, M. O., Igo, R. P., Kang, J. H., Kass, M. A., Kraft, P., Lee, R. K., … Wiggs, J. L. (2016). A Common Variant in MIR182 Is Associated With Primary Open-Angle Glaucoma in the NEIGHBORHOOD Consortium. Investigative Ophthalmology & Visual Science, 57(10), 3974–3981. https://doi.org/10.1167/iovs.16-19688

Bailey, J. N. C., Loomis, S. J., Kang, J. H., Allingham, R. R., Gharahkhani, P., Khor, C. C., Burdon, K. P., Aschard, H., Chasman, D. I., Igo, R. P., Hysi, P. G., Glastonbury, C. A., Ashley-Koch, A., Brilliant, M., Brown, A. A., Budenz, D. L., Buil, A., Cheng, C. Y., Choi, H., … ANZRAG Consortium. (2016). Genome-wide association analysis identifies TXNRD2, ATXN2 and FOXC1 as susceptibility loci for primary open-angle glaucoma. Nature Genetics, 48(2), 189–194. https://doi.org/10.1038/ng.3482

Dickey, A. S., Pineda, V. V., Tsunemi, T., Liu, P. P., Miranda, H. C., Gilmore-Hall, S. K., Lomas, N., Sampat, K. R., Buttgereit, A., Torres, M. J. M., Flores, A. L., Arreola, M., Arbez, N., Akimov, S. S., Gaasterland, T., Lazarowski, E. R., Ross, C. A., Yeo, G. W., Sopher, B. L., … La Spada, A. R. (2016). PPAR-delta is repressed in Huntington’s disease, is required for normal neuronal function and can be targeted therapeutically. Nature Medicine, 22(1), 37-+. https://doi.org/10.1038/nm.4003

Kumar, N., Richter, J., Cutts, J., Bush, K. T., Trujillo, C., Nigam, S. K., Gaasterland, T., Brafman, D., & Willert, K. (2015). Generation of an expandable intermediate mesoderm restricted progenitor cell line from human pluripotent stem cells. Elife, 4. https://doi.org/10.7554/eLife.08413

Gerwick, L., Mascuch, S. J., Navarro, G., Boudreau, P., Carland, T. M., Gaasterland, T., & Gerwick, W. H. (2015). Honaucin A, mechanism of action and role as a potential cancer prevention agent. Planta Medica, 81(11), 927–927.

Gaasterland, T., Dubinsky, A., Gaasterland, D. E., & Willert, K. (2015). Study of diseased and normal optic nerve and retina to identify microRNAs involved in glaucomatous optic neuropathy. Investigative Ophthalmology & Visual Science, 56(7).

Moya, N., Cutts, J., Gaasterland, T., Willert, K., & Brafman, D. A. (2014). Endogenous WNT signaling regulates hPSC-derived neural progenitor cell heterogeneity and specifies their regional identity. Stem Cell Reports, 3(6), 1015–1028. https://doi.org/10.1016/j.stemcr.2014.10.004

Dubinsky, A. N., Dastidar, S. G., Hsu, C. L., Zahra, R., Djakovic, S. N., Duarte, S., Esau, C. C., Spencer, B., Ashe, T. D., Fischer, K. M., MacKenna, D. A., Sopher, B. L., Masliah, E., Gaasterland, T., Chau, B. N., de Almeida, L. P., Morrison, B. E., & La Spada, A. R. (2014). Let-7 coordinately suppresses components of the amino acid sensing pathway to repress mTORC1 and induce autophagy. Cell Metabolism, 20(4), 626–638. https://doi.org/10.1016/j.cmet.2014.09.001

Allison, K. A., Kaikkonen, M. U., Gaasterland, T., & Glass, C. K. (2014). Vespucci: a system for building annotated databases of nascent transcripts. Nucleic Acids Research, 42(4), 2433–2447. https://doi.org/10.1093/nar/gkt1237

Fernandez, A., Huggins, I. J., Perna, L., Brafman, D., Lu, D. S., Yao, S. Y., Gaasterland, T., Carson, D. A., & Willert, K. (2014). The WNT receptor FZD7 is required for maintenance of the pluripotent state in human embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America, 111(4), 1409–1414. https://doi.org/10.1073/pnas.1323697111

Mantovani, S. M., & Moore, B. S. (2013). Flavin-linked oxidase catalyzes pyrrolizine formation of dichloropyrrole-containing polyketide extender unit in chlorizidine a. Journal of the American Chemical Society, 135(48), 18032–18035. https://doi.org/10.1021/ja409520v

Brafman, D. A., Moya, N., Allen-Soltero, S., Fellner, T., Robinson, M., McMillen, Z. L., Gaasterland, T., & Willert, K. (2013). Analysis of SOX2-expressing cell populations derived from human pluripotent stem cells. Stem Cell Reports, 1(5), 464–478. https://doi.org/10.1016/j.stemcr.2013.09.005

Bauer, M., Benard, J., Gaasterland, T., Willert, K., & Cappellen, D. (2013). WNT5A encodes two isoforms with distinct functions in cancers. PLOS ONE, 8(11). https://doi.org/10.1371/journal.pone.0080526

Wiggs, J. L., Hauser, M. A., Abdrabou, W., Allingham, R. R., Budenz, D. L., DelBono, E., Friedman, D. S., Kang, J. H., Gaasterland, D., Gaasterland, T., Lee, R. K., Lichter, P. R., Loomis, S., Liu, Y. T., McCarty, C., Medeiros, F. A., Moroi, S. E., Olson, L. M., Realini, A., … Haines, J. L. (2013). The NEIGHBOR Consortium primary open-angle glaucoma genome-wide association study: Rationale, study design, and clinical variables. Journal of Glaucoma, 22(7), 517–525. https://doi.org/10.1097/Ijg.0b013e31824d4fd8

Pasquale, L. R., Loomis, S. J., Kang, J. H., Yaspan, B. L., Abdrabou, W., Budenz, D. L., Chen, T. C., DelBono, E., Friedman, D. S., Gaasterland, D., Gaasterland, T., Grosskreutz, C. L., Lee, R. K., Lichter, P. R., Liu, Y., McCarty, C. A., Moroi, S. E., Olson, L. M., Realini, T., … Wiggs, J. L. (2013). CDKN2B-AS1 genotype–glaucoma feature correlations in primary open-angle glaucoma patients from the United States. American Journal of Ophthalmology, 155(2), 342-353.e5. https://doi.org/10.1016/j.ajo.2012.07.023

Cukras, C., Gaasterland, T., Lee, P., Gudiseva, H. V., Chavali, V. R. M., Pullakhandam, R., Maranhao, B., Edsall, L., Soares, S., Reddy, G. B., Sieving, P. A., & Ayyagari, R. (2012). Exome analysis identified a novel mutation in the RBP4 gene in a consanguineous pedigree with retinal dystrophy and developmental abnormalities. PLOS ONE, 7(11). https://doi.org/10.1371/journal.pone.0050205

Rost, B., Gaasterland, T., Lengauer, T., Linial, M., Markel, S., Mckay, B. J. M., Schneider, R., Horton, P., & Kelso, J. (2012). Paving the future: finding suitable ISMB venues. Bioinformatics, 28(19), 2556–2559. https://doi.org/10.1093/Bioinformatics/Bts420

Wiggs, J. L., Yapan, B. L., Hauser, M. A., Kane, J. H., Allingham, R. R., Olson, L. M., Abdrabou, W., Fan, B. J., Wang, D. Y., Brodeur, W., Budenz, D. L., Caprioli, J., Crenshaw, A., Crooks, K., DelBono, E., Doheny, K. F., Friedman, D. S., Gaasterland, D., Gaasterland, T., … Haines, J. L. (2012). Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. Plos Genetics, 8(4), 413–424. https://doi.org/10.1371/Journal.Pgen.1002654

Kandarian, B., Sethi, J., Wu, A. A., Baker, M., Yazdani, N., Kym, E., Sanchez, A., Edsall, L., Gaasterland, T., & Macagno, E. (2012). The medicinal leech genome encodes 21 innexin genes: different combinations are expressed by identified central neurons. Development Genes and Evolution, 222(1), 29–44. https://doi.org/10.1007/s00427-011-0387-z

Taneri, B., Asilmaz, E., & Gaasterland, T. (2012). Biomedical Impact of Splicing Mutations Revealed through Exome Sequencing. Molecular Medicine, 18(2), 314–319. https://doi.org/10.2119/molmed.2011.00126

Van Nieuwerburgh, F., Thompson, R. C., Ledesma, J., Deforce, D., Gaasterland, T., Ordoukhanian, P., & Head, S. R. (2012). Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination. Nucleic Acids Research, 40(3). https://doi.org/10.1093/nar/gkr1000

Lee, P. L., Gaasterland, T., & Barton, J. C. (2012). Mild Iron Overload in an African American Man with SLC40A1 D270V. Acta Haematologica, 128(1), 28–32. https://doi.org/10.1159/000337034

Norden-Krichmar, T. M., Allen, A. E., Gaasterland, T., & Hildebrand, M. (2011). Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana. PLOS ONE, 6(8). https://doi.org/10.1371/journal.pone.0022870

Sopher, B. L., Ladd, P. D., Pineda, V. V., Libby, R. T., Sunkin, S. M., Hurley, J. B., Thienes, C. P., Gaasterland, T., Filippova, G. N., & La Spada, A. R. (2011). CTCF Regulates Ataxin-7 Expression through Promotion of a Convergently Transcribed, Antisense Noncoding RNA. Neuron, 70(6), 1071–1084. https://doi.org/10.1016/j.neuron.2011.05.027

Meriaux, C., Arafah, K., Tasiemski, A., Wisztorski, M., Bruand, J., Boidin-Wichlacz, C., Desmons, A., Debois, D., Laprevote, O., Brunelle, A., Gaasterland, T., Macagno, E., Fournier, I., & Salzet, M. (2011). Multiple Changes in Peptide and Lipid Expression Associated with Regeneration in the Nervous System of the Medicinal Leech. PLOS ONE, 6(4). https://doi.org/10.1371/journal.pone.0018359

Bruand, J., Sistla, S., Meriaux, C., Dorrestein, P. C., Gaasterland, T., Ghassemian, M., Wisztorski, M., Fournier, I., Salzet, M., Macagno, E., & Bafna, V. (2011). Automated Querying and Identification of Novel Peptides using MALDI Mass Spectrometric Imaging. Journal of Proteome Research, 10(4), 1915–1928. https://doi.org/10.1021/pr101159e

Junier, P., Junier, T., Podell, S., Sims, D. R., Detter, J. C., Lykidis, A., Han, C. S., Wigginton, N. S., Gaasterland, T., & Bernier-Latmani, R. (2010). The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1. Environmental Microbiology, 12(10), 2738–2754. https://doi.org/10.1111/j.1462-2920.2010.02242.x

Macagno, E. R., Gaasterland, T., Edsall, L., Bafna, V., Soares, M. B., Scheetz, T., Casavant, T., Da Silva, C., Wincker, P., Tasiemski, A., & Salzet, M. (2010). Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. Bmc Genomics, 11. https://doi.org/10.1186/1471-2164-11-407

Podell, S., Gaasterland, T., & Allen, E. E. (2008). A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics, 9. https://doi.org/10.1186/1471-2105-9-419

Dick, G. J., Podell, S., Johnson, H. A., Rivera-Espinoza, Y., Bernier-Latmani, R., McCarthy, J. K., Torpey, J. W., Clement, B. G., Gaasterland, T., & Tebo, B. M. (2008). Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp strain SI85-9A1. Applied and Environmental Microbiology, 74(9), 2646–2658. https://doi.org/10.1128/aem.01656-07

Robidart, J. C., Bench, S. R., Feldman, R. A., Novoradovsky, A., Podell, S. B., Gaasterland, T., Allen, E. E., & Felbeck, H. (2008). Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environmental Microbiology, 10(3), 727–737. https://doi.org/10.1111/j.1462-2920.2007.01496.x

Norden-Krichmar, T. M., Holtz, J., Pasquinelli, A. E., & Gaasterland, T. (2007). Computational prediction and experimental validation of Ciona intestinalis microRNA genes. Bmc Genomics, 8. https://doi.org/10.1186/1471-2164-8-445

Dorr, B. J., & Gaasterland, T. (2007). Exploiting aspectual features and connecting words for summarization-inspired temporal-relation extraction. Information Processing & Management, 43(6), 1681–1704. https://doi.org/10.1016/j.ipm.2007.01.008

Chang, E. J., Begum, R., Chait, B. T., & Gaasterland, T. (2007). Prediction of Cyclin-Dependent Kinase Phosphorylation Substrates. PLOS ONE, 2(8). https://doi.org/10.1371/journal.pone.0000656

Palenik, B., Grimwood, J., Aerts, A., Rouze, P., Salamov, A., Putnam, N., Dupont, C., Jorgensen, R., Derelle, E., Rombauts, S., Zhou, K., Otillar, R., Merchant, S. S., Podell, S., Gaasterland, T., Napoli, C., Gendler, K., Manuell, A., Tai, V., … Grigoriev, I. V. (2007). The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proceedings of the National Academy of Sciences of the United States of America, 104(18), 7705–7710. https://doi.org/10.1073/pnas.0611046104

Li, X. C., Wang, X. J., Tannenhauser, J., Podell, S., Mukherjee, P., Hertel, M., Biane, J., Masuda, S., Nottebohm, F., & Gaasterland, T. (2007). Genomic resources for songbird research and their use in characterizing gene expression during brain development. Proceedings of the National Academy of Sciences of the United States of America, 104(16), 6834–6839. https://doi.org/10.1073/pnas.0701619104

Zhang, H., Hou, Y. B., Miranda, L., Campbell, D. A., Sturm, N. R., Gaasterland, T., & Lin, S. J. (2007). Spliced leader RNA trans-splicing in dinoflagellates. Proceedings of the National Academy of Sciences of the United States of America, 104(11), 4618–4623. https://doi.org/10.1073/pnas.0700258104

Sobral, R. G., Jones, A. E., Des Etages, S. G., Dougherty, T. J., Peitzsch, R. M., Gaasterland, T., Ludovice, A. M., de Lencastre, H., & Tomasz, A. (2007). Extensive and genome-wide changes in the transcription profile of Staphylococcus aureus induced by modulating the transcription of the cell wall synthesis gene murF. Journal of Bacteriology, 189(6), 2376–2391. https://doi.org/10.1128/jb.01439-06