Lee, S., Mendoza, T. R., Burner, D. N., Muldong, M. T., Wu, C. C. N., Arreola-Villanueva, C., Zuniga, A., Greenburg, O., Zhu, W. Y., Murtadha, J., Koutouan, E., Pineda, N., Pham, H., Kang, S. G., Kim, H. T., Pineda, G., Lennon, K. M., Cacalano, N. A., Jamieson, C. H. M., … Jamieson, C. A. M. (2022). Novel dormancy mechanism of castration resistance in bone metastatic prostate cancer organoids. International Journal of Molecular Sciences, 23(6), 27.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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-+.
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.
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.
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.
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.
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.
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.
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.
Bauer, M., Benard, J., Gaasterland, T., Willert, K., & Cappellen, D. (2013). WNT5A encodes two isoforms with distinct functions in cancers. PLOS ONE, 8(11).
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.
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.
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).
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.
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.
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.
Taneri, B., Asilmaz, E., & Gaasterland, T. (2012). Biomedical Impact of Splicing Mutations Revealed through Exome Sequencing. Molecular Medicine, 18(2), 314–319.
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).
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.
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).
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.
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).
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.
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.
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.
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.
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.
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.
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.
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.
Chang, E. J., Begum, R., Chait, B. T., & Gaasterland, T. (2007). Prediction of Cyclin-Dependent Kinase Phosphorylation Substrates. PLOS ONE, 2(8).
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.
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.
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.
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.