Items where Community is "Dolan DNA Learning Center"

Paper

Williams, Jason, Nash, Bruce, Ghiban, Cornel, Khalfan, Mohammed, Hilgert, Uwe, Lauter, Susan, Yang, Chun-Hua, Micklos, David Andrew (April 2024) Analysis of DNA Barcodes Using DNA Subway. Methods in molecular biology (Clifton, N.J.), 2744. pp. 551-560. ISSN 1064-3745

Pepenella, Sharon, Hackett, Jennifer, Fernandez-Marco, Cristina, Petracca, Jeffry, Marizzi, Christine, Nash, Bruce, Micklos, David A (April 2024) A Rapid, Equipment-Free DNA Isolation Method for DNA Barcoding. Methods in molecular biology (Clifton, N.J.), 2744. pp. 517-523. ISSN 1064-3745

Hackett, Jennifer, Pepenella, Sharon, Marco, Cristina Fernandez, Bodt, Louise, Grajales, Lina Ruiz, Petracca, Jeffry, Burke, Justin, Mayle, Allison, Nash, Bruce, Micklos, David A (April 2024) Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification. Methods in molecular biology (Clifton, N.J.), 2744. pp. 119-127. ISSN 1064-3745

Senn, Savanah, Bhattacharyya, Sharmodeep, Presley, Gerald, Taylor, Anne E, Nash, Bruce, Enke, Ray A, Barnard-Kubow, Karen B, Ford, Jillian, Jasinski, Brandon, Badalova, Yekaterina (June 2022) The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National Forest. Microorganisms, 10 (6). p. 1218. ISSN 2076-2607

Harris, Nomi L, Hokamp, Karsten, Ménager, Hervé, Munoz-Torres, Monica, Unni, Deepak, Vasilevsky, Nicole, Williams, Jason (2022) BOSC 2022: the first hybrid and 23rd annual Bioinformatics Open Source Conference. F1000Research, 11. p. 1034. ISSN 2046-1402

Williams, Jason (2022) CyVerse for Reproducible Research: RNA-Seq Analysis. Methods in Molecular Biology, 2443. pp. 57-79. ISSN 1064-3745

Harris, Nomi L, Cock, Peter JA, Fields, Christopher J, Hokamp, Karsten, Maia, Jessica, Munoz-Torres, Monica, Sharan, Malvika, Williams, Jason (October 2021) BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference. F1000Research, 10. p. 1054. ISSN 2046-1402

Smith, T., Bock, H., Hewlett, J., Lazare, J., Madabushi, A., Mann, C., Micklos, D., Nash, B., Porter, S., Rao, P., Read, R., Tubon, T., Wolslegel, K., Fletcher, L. (August 2020) Introducing the NSF-ATE InnovATEBIO National Biotechnology Education Center. J Biomol Tech, 31 (Suppl). S29-S30. ISSN 1524-0215 (Print)1524-0215

Williams, J. J., Drew, J. C., Galindo-Gonzalez, S., Robic, S., Dinsdale, E., Morgan, W. R., Triplett, E. W., Burnette, J. M., Donovan, S. S., Fowlks, E. R., Goodman, A. L., Grandgenett, N. F., Goller, C. C., Hauser, C., Jungck, J. R., Newman, J. D., Pearson, W. R., Ryder, E. F., Sierk, M., Smith, T. M., Tosado-Acevedo, R., Tapprich, W., Tobin, T. C., Toro-Martinez, A., Welch, L. R., Wilson, M. A., Ebenbach, D., McWilliams, M., Rosenwald, A. G., Pauley, M. A. (November 2019) Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction. PLoS One, 14 (11). e0224288. ISSN 1932-6203

Tello-Ruiz, M. K., Marco, C. F., Hsu, F. M., Khangura, R. S., Qiao, P., Sapkota, S., Stitzer, M. C., Wasikowski, R., Wu, H., Zhan, J., Chougule, K., Barone, L. C., Ghiban, C., Muna, D., Olson, A. C., Wang, L., Ware, D., Micklos, D. A. (October 2019) Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS ONE, 14 (10). Article number e0224086. ISSN 19326203 (ISSN)

Clarke, Daniel JB, Wang, Lily, Jones, Alex, Wojciechowicz, Megan L, Torre, Denis, Jagodnik, Kathleen M, Jenkins, Sherry L, McQuilton, Peter, Flamholz, Zachary, Silverstein, Moshe C, Schilder, Brian M, Robasky, Kimberly, Castillo, Claris, Idaszak, Ray, Ahalt, Stanley C, Williams, Jason, Schurer, Stephan, Cooper, Daniel J, de Miranda Azevedo, Ricardo, Klenk, Juergen A, Haendel, Melissa A, Nedzel, Jared, Avillach, Paul, Shimoyama, Mary E, Harris, Rayna M, Gamble, Meredith, Poten, Rudy, Charbonneau, Amanda L, Larkin, Jennie, Brown, C Titus, Bonazzi, Vivien R, Dumontier, Michel J, Sansone, Susanna-Assunta, Ma’ayan, Avi (June 2019) FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources. BioRxiv. (Unpublished)

Gadermaier, G., Dörler, D., Heigl, F., Mayr, S., Rüdisser, J., Brodschneider, R., Marizzi, C. (September 2018) Peer-reviewed publishing of results from Citizen Science projects. Journal of Science Communication, 17 (3). Article no. L01. ISSN 18242049 (ISSN)

Jensen-Vargas, E., Marizzi, C. (June 2018) DNA Barcoding for Identification of Consumer-Relevant Fungi Sold in New York: A Powerful Tool for Citizen Scientists? Foods, 7 (6). ISSN 2304-8158 (Print)2304-8158

Wilson Sayres, M. A., Hauser, C., Sierk, M., Robic, S., Rosenwald, A. G., Smith, T. M., Triplett, E. W., Williams, J. J., Dinsdale, E., Morgan, W. R., Burnette, J. M., Donovan, S. S., Drew, J. C., Elgin, S. C. R., Fowlks, E. R., Galindo-Gonzalez, S., Goodman, A. L., Grandgenett, N. F., Goller, C. C., Jungck, J. R., Newman, J. D., Pearson, W., Ryder, E. F., Tosado-Acevedo, R., Tapprich, W., Tobin, T. C., Toro-Martinez, A., Welch, L. R., Wright, R., Barone, L., Ebenbach, D., McWilliams, M., Olney, K. C., Pauley, M. A. (June 2018) Bioinformatics core competencies for undergraduate life sciences education. PLoS One, 13 (6). e0196878. ISSN 1932-6203

Barone, L., Williams, J., Micklos, D. (October 2017) Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators. PLoS Comput Biol, 13 (10). e1005755. ISSN 1553-734x

Wilson Sayres, Melissa A, Hauser, Charles, Sierk, Michael, Robic, Srebrenka, Rosenwald, Anne G, Smith, Todd M, Triplett, Eric W, Williams, Jason J, Dinsdale, Elizabeth, Morgan, William, Burnette, James M, Donovan, Samuel S, Drew, Jennifer C, Elgin, Sarah CR, Fowlks, Edison R, Galindo-Gonzalez, Sebastian, Goodman, Anya L, Grandgenett, Neal F, Goller, Carlos C, Jungck, John, Newman, Jeffrey D, Pearson, William, Ryder, Elizabeth, Tosado-Acevedo, Rafael, Tapprich, William, Tobin, Tammy C, Toro-Martínez, Arlín, Welch, Lonnie R, Wright, Robin, Ebenbach, David, Olney, Kimberly C, McWilliams, Mindy, Pauley, Mark A (August 2017) Bioinformatics Core Competencies for Undergraduate Life Sciences Education. BioRxiv. (Unpublished)

Barone, Lindsay, Williams, Jason, Micklos, David (February 2017) Unmet Needs for Analyzing Biological Big Data: A Survey of 704 NSF Principal Investigators. BioRxiv. (Unpublished)

Williams, J. J., Teal, T. K. (January 2017) A vision for collaborative training infrastructure for bioinformatics. Ann N Y Acad Sci, 1387 (1). pp. 54-60. ISSN 1749-6632 (Electronic)0077-8923 (Linking)

Merchant, N., Lyons, E., Goff, S., Vaughn, M., Ware, D., Micklos, D., Antin, P. (January 2016) The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences. PLoS Biol, 14 (1). e1002342. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

Tello-Ruiz, M. K., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarasinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D. M., Kerhornou, A., Walts, B., Fonseca, N. A., Huerta, L., Keays, M., Tang, Y. A., Parkinson, H., Fabregat, A., McKay, S., Weiser, J., D'Eustachio, P., Stein, L., Petryszak, R., Kersey, P. J., Jaiswal, P., Ware, D. (January 2016) Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res, 44 (D1). D1133-40. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Zhao, Z., Chen, C. C., Rillahan, C. D., Shen, R., Kitzing, T., McNerney, M. E., Diaz-Flores, E., Zuber, J., Shannon, K., Le Beau, M. M., Spector, M. S., Kogan, S. C., Lowe, S. W. (March 2015) Cooperative loss of RAS feedback regulation drives myeloid leukemogenesis. Nature Genetics, 47. pp. 539-543. ISSN 1061-4036

Martin, L., Cook, C., Matasci, N., Williams, J., Bastow, R. (2015) Data mining with iPlant: A meeting report from the 2013 GARNet workshop, Data mining with iPlant. Journal of Experimental Botany, 66 (1). pp. 1-6. ISSN 0022-0957

Verster, A. J., Ramani, A. K., McKay, S. J., Fraser, A. G. (February 2014) Comparative RNAi Screens in C. elegans and C. briggsae Reveal the Impact of Developmental System Drift on Gene Function. Plos Genetics, 10 (2). e1004077. ISSN 1553-7390

McKay, S. J., Skidmore, E. J., LaRose, C. J., Mercer, A. W., Noutsos, C. (October 2013) Cloud Computing with iPlant Atmosphere. Curr Protoc Bioinformatics, 43. 9 15 1-20. ISSN 1934-340X (Electronic)1934-3396 (Linking)

Deck, Courtney A., McKay, Sheldon J., Fiedler, Tristan J., LeMoine, Christophe M. R., Kajimura, Makiko, Nawata, C. Michele, Wood, Chris M., Walsh, Patrick J. (October 2013) Transcriptome responses in the rectal gland of fed and fasted spiny dogfish shark (Squalus acanthias) determined by suppression subtractive hybridization. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. ISSN 1744-117X

Matasci, N., McKay, S. (June 2013) Phylogenetic analysis with the iPlant discovery environment. Current protocols in bioinformatics (SUPPL.). 6.13.1-6.13.13. ISSN 19343396 (ISSN)

Oliver, S. L., Lenards, A. J., Barthelson, R. A., Merchant, N., McKay, S. J. (June 2013) Using the iplant collaborative discovery environment. Current protocols in bioinformatics (SUPPL.). 1.22. ISSN 19343396 (ISSN)

Boyle, B., Hopkins, N., Lu, Z. Y., Garay, J. A. R., Mozzherin, D., Rees, T., Matasci, N., Narro, M. L., Piel, W. H., McKay, S. J., Lowry, S., Freeland, C., Peet, R. K., Enquist, B. J. (January 2013) The taxonomic name resolution service: an online tool for automated standardization of plant names. BMC Bioinformatics, 14. ISSN 1471-2105

Wolthuizen, M., Nisselle, A., Halliday, J., Metcalfe, S. A., Aitken, M., Allen, K. J., Delatycki, M. B. (January 2013) Why do people choose not to have screening for hemochromatosis? Genetic Testing and Molecular Biomarkers, 17 (1). pp. 21-24. ISSN 19450265

Vetere, F., Green, J., Nisselle, A., Dang, X. T., Zazryn, T., Deng, P. P. (May 2012) Inclusion during school absence: Using ambient technology to create a classroom presence for hospitalised children. Telecommunication Journal of Australia, 62 (5). Article no. 67. ISSN 00402486

Nisselle, A., Hanns, S., Green, J., Jones, T. (March 2012) Accessing Flexible Learning Opportunities: Children's and Young People's use of Laptops in a Paediatric Hospital. Technology, Pedagogy and Education, 21 (1). pp. 3-20. ISSN 1475939X (ISSN)

Micklos, D., Lauter, S., Nisselle, A. (2011) Essays on science and society. Lessons from a science education portal. Science, 334 (6063). pp. 1657-1658. ISSN 00368075 (ISSN)

Goff, S. A, Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E, Gessler, D. , Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M, Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W. H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S. J., Kvilekval, K., Manjunath, B.S., Tannen, V., Stamatakis, A., Sanderson, M. J., Welch, S. M., Cranston, K. , Soltis, P. , Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D. J., White, J. W., Leebens-Mack, J., Donoghue, M. J., Spalding, E. P., Vision, T. J., Myers, C. R., Lowenthal, D., Enquist, B. J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., Stanzione, D. (2011) The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science, 2. ISSN 1664-462X

Gerstein, M. B., Lu, Z. J., Van Nostrand, E. L., Cheng, C., Arshinoff, B. I., Liu, T., Yip, K. Y., Robilotto, R., Rechtsteiner, A., Ikegami, K., Alves, P., Chateigner, A., Perry, M., Morris, M., Auerbach, R. K., Feng, X., Leng, J., Vielle, A., Niu, W., Rhrissorrakrai, K., Agarwal, A., Alexander, R. P., Barber, G., Brdlik, C. M., Brennan, J., Brouillet, J. J., Carr, A., Cheung, M. S., Clawson, H., Contrino, S., Dannenberg, L. O., Dernburg, A. F., Desai, A., Dick, L., Dose, A. C., Du, J. A., Egelhofer, T., Ercan, S., Euskirchen, G., Ewing, B., Feingold, E. A., Gassmann, R., Good, P. J., Green, P., Gullier, F., Gutwein, M., Guyer, M. S., Habegger, L., Han, T., Henikoff, J. G., Henz, S. R., Hinrichs, A., Holster, H., Hyman, T., Iniguez, A. L., Janette, J., Jensen, M., Kato, M., Kent, W. J., Kephart, E., Khivansara, V., Khurana, E., Kim, J. K., Kolasinska-Zwierz, P., Lai, E. C., Latorre, I., Leahey, A., Lewis, S., Lloyd, P., Lochovsky, L., Lowdon, R. F., Lubling, Y., Lyne, R., MacCoss, M., Mackowiak, S. D., Mangone, M., McKay, S. J., Mecenas, D., Merrihew, G., Miller, D. M., Muroyama, A., Murray, J. I., Ooi, S. L., Pham, H., Phippen, T., Preston, E. A., Rajewsky, N., Ratsch, G., Rosenbaum, H., Rozowsky, J., Rutherford, K., Ruzanov, P., Sarov, M., Sasidharan, R., Sboner, A., Scheid, P., Segal, E., Shin, H. J., Shou, C., Slack, F. J., Stein, L. D. (December 2010) Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science, 330 (6012). pp. 1775-1787. ISSN 0036-8075

Fiedler, T. J., Hudder, A., McKay, S. J., Shivkumar, S., Capo, T. R., Schmale, M. C., Walsh, P. J. (June 2010) The transcriptome of the early life history stages of the California Sea Hare Aplysia californica. Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, 5 (2). pp. 165-170.

Robinson, S., Tang, L., Mooney, B., McKay, S. J., Clarke, W., Links, M., Karcz, S., Regan, S., Wu, Y.-Y., Gruber, M., Cui, D., Yu, M., Parkin, I. (July 2009) An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches. BMC Plant Biology, 9 (1). p. 101. ISSN 1471-2229

Meissner, B., Warner, A., Wong, K., Dube, N., Lorch, A., McKay, S. J., Khattra, J., Rogalski, T., Somasiri, A., Chaudhry, I., Fox, R. M., Miller Iii, D. M., Baillie, D. L., Holt, R. A., Jones, S. J. M., Marra, M. A., Moerman, D. G. (June 2009) An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genet, 5 (6). e1000537.

Hacisalihoglu, G., Hilgert, U., Nash, E. B., Micklos, D. A. (2008) An innovative plant genomics and gene annotation program for high school, community college, and university faculty. CBE Life Sci Educ, 7 (3). pp. 310-6.

Micklos, D. (August 2007) Coming into the gene age: The challenge to biology educators. Chromosome Research, 15 (S2). p. 70. ISSN 0967-3849

Tomov, B. W., Bernal, J. S., Vinson, S. B. (August 2003) Impacts of transgenic sugarcane expressing GNA lectin on parasitism of Mexican rice borer by Parallorhogas pyralophagus (Marsh) (Hymenoptera : Braconidae). Environmental Entomology, 32 (4). pp. 866-872. ISSN 0046-225X

Tomov, B. W., Bernal, J. S. (June 2003) Effects of GNA transgenic sugarcane on life history parameters of Parallorhogas pyralophagus (Marsh) (Hymenoptera : Braconidae), a parasitoid of Mexican rice borer. Journal of Economic Entomology, 96 (3). pp. 570-576. ISSN 0022-0493

Stein, L. D., Mungall, C., Shu, S. Q., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., Lewis, S. (October 2002) The Generic Genome Browser: A building block for a model organism system database. Genome Research, 12 (10). pp. 1599-1610. ISSN 1088-9051

Drier, E. A., Tello, M. K., Cowan, M., Wu, P., Blace, N., Sacktor, T. C., Yin, J. C. P. (April 2002) Memory enhancement and formation by atypical PKM activity in Drosophila melanogaster. Nature Neuroscience, 5 (4). pp. 316-324. ISSN 1097-6256

Micklos, D., Carlson, E. (November 2000) Engineering American society: the lesson of eugenics. Nature Reviews Genetics, 1 (2). pp. 153-158. ISSN 1471-0056

Silva, A. J., Elgersma, Y., Friedman, E., Stern, J., Kogan, J. (November 1998) A mouse model for learning and memory defects associated with neurofibromatosis type I. Pathol Biol (Paris), 46 (9). pp. 697-8. ISSN 0369-8114 (Print)

Hinkley, C. S., Blasco, M. A., Funk, W. D., Feng, J., Villeponteau, B., Greider, C. W., Herr, W. (January 1998) The mouse telomerase RNA 5"-end lies just upstream of the telomerase template sequence. Nucleic Acids Research, 26 (2). pp. 532-6. ISSN 0305-1048

Greenberg, M. E., Bronson, S., Lock, M., Neumann, M., Pavlakis, G. N., Skowronski, J. (December 1997) Co-localization of HIV-1 Nef with the AP-2 adaptor protein complex correlates with Nef-induced CD4 down-regulation. Embo Journal, 16 (23). pp. 6964-76. ISSN 0261-4189

Book

Hilgert, U., McKay, S., Ghiban, C., Khalfan, M., Micklos, D., Williams, J. (July 2014) DNA Subway: Making genome analysis egalitarian. ACM International Conference Proceeding Series . Association for Computing Machinery, Article number 70. ISBN 978-145032893-7

Micklos, D. A., Freyer, G. A. (1990) DNA science : a first course in recombinant DNA technology. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. ISBN 0892784113