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3 results on '"Martinez-Cruzado, Juan Carlos"'

1. A course-based research experience: how benefits change with increased investment in instructional time.

Author

Shaffer CD, Alvarez CJ, Bednarski AE, Dunbar D, Goodman AL, Reinke C, Rosenwald AG, Wolyniak MJ, Bailey C, Barnard D, Bazinet C, Beach DL, Bedard JE, Bhalla S, Braverman J, Burg M, Chandrasekaran V, Chung HM, Clase K, Dejong RJ, Diangelo JR, Du C, Eckdahl TT, Eisler H, Emerson JA, Frary A, Frohlich D, Gosser Y, Govind S, Haberman A, Hark AT, Hauser C, Hoogewerf A, Hoopes LL, Howell CE, Johnson D, Jones CJ, Kadlec L, Kaehler M, Silver Key SC, Kleinschmit A, Kokan NP, Kopp O, Kuleck G, Leatherman J, Lopilato J, Mackinnon C, Martinez-Cruzado JC, McNeil G, Mel S, Mistry H, Nagengast A, Overvoorde P, Paetkau DW, Parrish S, Peterson CN, Preuss M, Reed LK, Revie D, Robic S, Roecklein-Canfield J, Rubin MR, Saville K, Schroeder S, Sharif K, Shaw M, Skuse G, Smith CD, Smith MA, Smith ST, Spana E, Spratt M, Sreenivasan A, Stamm J, Szauter P, Thompson JS, Wawersik M, Youngblom J, Zhou L, Mardis ER, Buhler J, Leung W, Lopatto D, and Elgin SC

Subjects
Attitude, Cooperative Behavior, Data Collection, Faculty, Genome, Genomics education, Humans, Knowledge, Learning, Molecular Sequence Annotation, Program Evaluation, Research Personnel, Self Report, Surveys and Questionnaires, Time Factors, Biology education, Curriculum, Research education
Abstract

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

Published
2014
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2. A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

Author

Shaffer, Christopher D, Alvarez, Consuelo J, Bednarski, April E, Dunbar, David, Goodman, Anya L, Reinke, Catherine, Rosenwald, Anne G, Wolyniak, Michael J, Bailey, Cheryl, Barnard, Daron, Bazinet, Christopher, Beach, Dale L, Bedard, James EJ, Bhalla, Satish, Braverman, John, Burg, Martin, Chandrasekaran, Vidya, Chung, Hui-Min, Clase, Kari, DeJong, Randall J, DiAngelo, Justin R, Du, Chunguang, Eckdahl, Todd T, Eisler, Heather, Emerson, Julia A, Frary, Amy, Frohlich, Donald, Gosser, Yuying, Govind, Shubha, Haberman, Adam, Hark, Amy T, Hauser, Charles, Hoogewerf, Arlene, Hoopes, Laura LM, Howell, Carina E, Johnson, Diana, Jones, Christopher J, Kadlec, Lisa, Kaehler, Marian, Key, S Catherine Silver, Kleinschmit, Adam, Kokan, Nighat P, Kopp, Olga, Kuleck, Gary, Leatherman, Judith, Lopilato, Jane, MacKinnon, Christy, Martinez-Cruzado, Juan Carlos, McNeil, Gerard, Mel, Stephanie, Mistry, Hemlata, Nagengast, Alexis, Overvoorde, Paul, Paetkau, Don W, Parrish, Susan, Peterson, Celeste N, Preuss, Mary, Reed, Laura K, Revie, Dennis, Robic, Srebrenka, Roecklein-Canfield, Jennifer, Rubin, Michael R, Saville, Kenneth, Schroeder, Stephanie, Sharif, Karim, Shaw, Mary, Skuse, Gary, Smith, Christopher D, Smith, Mary A, Smith, Sheryl T, Spana, Eric, Spratt, Mary, Sreenivasan, Aparna, Stamm, Joyce, Szauter, Paul, Thompson, Jeffrey S, Wawersik, Matthew, Youngblom, James, Zhou, Leming, Mardis, Elaine R, Buhler, Jeremy, Leung, Wilson, Lopatto, David, and Elgin, Sarah CR

Subjects
Attitude, Biology, Cooperative Behavior, Curriculum, Data Collection, Faculty, Genome, Genomics, Humans, Knowledge, Learning, Molecular Sequence Annotation, Program Evaluation, Research, Research Personnel, Self Report, Surveys and Questionnaires, Time Factors, Curriculum and Pedagogy, Education
Abstract

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

Published
2014

3. Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

Author

Gravel, Simon, Zakharia, Fouad, Moreno Estrada, Andrés, Byrnes, Jake K., Muzzio, Marina, Rodriguez Flores, Juan L., Kenny, Eimear E., Gignoux, Christopher R., Maples, Brian K., Guiblet, Wilfried, Dutil, Julie, Via, Marc, Sandoval, Karla, Bedoya, Gabriel, Oleksyk, Taras K., Ruiz Linares, Andrés, Burchard, Esteban G., Martinez Cruzado, Juan Carlos, Bustamante, Carlos D., The 1000 Genomes Project, and Universitat de Barcelona

Subjects
Cancer Research, Population genetics, Amèrica, Genoma humà, 92D25, purl.org/becyt/ford/1 [https], Effective population size, Gene Frequency, Models, Human Genome Project, Mexican Americans, Sequencing, Exome, Aborígens, Genetics (clinical), Native American Migrations, Genetics, 0303 health sciences, education.field_of_study, Human migration, Population size, 030305 genetics & heredity, Chromosome Mapping, Hispanic or Latino, Bioquímica y Biología Molecular, Full Genomes, CIENCIAS NATURALES Y EXACTAS, Research Article, lcsh:QH426-470, Human Migration, Population, Black People, America, Biology, White People, Ciencias Biológicas, 03 medical and health sciences, Pobles indígenes, Migració de pobles, Humans, Ciencias Naturales, Quantitative Biology - Genomics, 1000 Genomes Project, purl.org/becyt/ford/1.6 [https], education, Quantitative Biology - Populations and Evolution, Molecular Biology, Genotyping, Allele frequency, Mexico, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genomics (q-bio.GN), Human genome, business.industry, Genome, Human, Puerto Rico, Racial Groups, Native American, Populations and Evolution (q-bio.PE), 15. Life on land, Migrations of nations, lcsh:Genetics, Genetics, Population, Evolutionary biology, FOS: Biological sciences, Indians, North American, Indigenous peoples, business
Abstract

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations., Facultad de Ciencias Naturales y Museo, Instituto Multidisciplinario de Biología Celular

Published
2013

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