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

1. Reconstructing Native American Migrations from Whole-genome and Whole-exome Data

Author

Gravel, Simon, Zakharia, Fouad, Moreno-Estrada, Andres, 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, Andres, Burchard, Esteban G, Martinez-Cruzado, Juan Carlos, Bustamante, Carlos D., and Project, The 1000 Genomes

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics, 92D25
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 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 Ta\'ino 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 and ancestry tract length, we show that post-contact populations differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe., Comment: 30 pages, inludes supplement. v2 contains clarifications, extra analyses, and a change in the language classification scheme used

Published
2013

2. Reconstructing the Population Genetic History of the Caribbean

Author

Moreno-Estrada, Andres, Gravel, Simon, Zakharia, Fouad, McCauley, Jacob L., Byrnes, Jake K., Gignoux, Christopher R., Ortiz-Tello, Patricia A., Martinez, Ricardo J., Hedges, Dale J., Morris, Richard W., Eng, Celeste, Sandoval, Karla, Acevedo-Acevedo, Suehelay, Martinez-Cruzado, Juan Carlos, Norman, Paul J., Layrisse, Zulay, Parham, Peter, Burchard, Esteban Gonzalez, Cuccaro, Michael L., Martin, Eden R., and Bustamante, Carlos D.

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics
Abstract

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean., Comment: 26 pages, 6 figures, and supporting information

Published
2013

3. 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

4. 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 E. J., 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 L. M., 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 C. R.

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. [Contains 82 pages of Supplemental Material, which can be found at: http://www.lifescied.org/content/suppl/2014/02/12/13.1.111.DC1.html.]

Published
2014
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5. Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles

Author

Kolchanova, Sofiia, primary, Komissarov, Alexey, additional, Kliver, Sergei, additional, Mazo-Vargas, Anyi, additional, Afanador, Yashira, additional, Velez-Valentín, Jafet, additional, de la Rosa, Ricardo Valentín, additional, Castro-Marquez, Stephanie, additional, Rivera-Colon, Israel, additional, Majeske, Audrey J., additional, Wolfsberger, Walter W., additional, Hains, Taylor, additional, Corvelo, André, additional, Martinez-Cruzado, Juan-Carlos, additional, Glenn, Travis C., additional, Robinson, Orlando, additional, Koepfli, Klaus-Peter, additional, and Oleksyk, Taras K., additional

Published
2021
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7. A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education

Author

Oleksyk Taras K, Pombert Jean-Francois, Siu Daniel, Mazo-Vargas Anyimilehidi, Ramos Brian, Guiblet Wilfried, Afanador Yashira, Ruiz-Rodriguez Christina T, Nickerson Michael L, Logue David M, Dean Michael, Figueroa Luis, Valentin Ricardo, and Martinez-Cruzado Juan-Carlos

Subjects
Amazona vittata, Puerto rican parrot, Genome sequence, Annotation, Assembly, Local funding, Education, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Abstract Background Amazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale. Findings In a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50 = 6,983 bp, longest = 75,003 bp), which was further scaffolded into 148,255 fragments (N50 = 19,470, longest = 206,462 bp). This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences. Conclusions The current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts.

Published
2012
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8. Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangeredSolenodon paradoxusfrom the island of Hispaniola

Author

Grigorev, Kirill, primary, Kliver, Sergey, additional, Dobrynin, Pavel, additional, Komissarov, Aleksey, additional, Wolfsberger, Walter, additional, Krasheninnikova, Ksenia, additional, Afanador-Hernández, Yashira M., additional, Paulino, Liz A., additional, Carreras, Rosanna, additional, Rodríguez, Luis E., additional, Núñez, Adrell, additional, Silva, Filipe, additional, Hernández-Martich, J. David, additional, Majeske, Audrey J., additional, Antunes, Agostinho, additional, Roca, Alfred L., additional, O’Brien, Stephen J., additional, Martinez-Cruzado, Juan Carlos, additional, and Oleksyk, Taras K., additional

Published
2017
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9. Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

Author

Leung, Wilson, primary, Shaffer, Christopher D, additional, Reed, Laura K, additional, Smith, Sheryl T, additional, Barshop, William, additional, Dirkes, William, additional, Dothager, Matthew, additional, Lee, Paul, additional, Wong, Jeannette, additional, Xiong, David, additional, Yuan, Han, additional, Bedard, James E J, additional, Machone, Joshua F, additional, Patterson, Seantay D, additional, Price, Amber L, additional, Turner, Bryce A, additional, Robic, Srebrenka, additional, Luippold, Erin K, additional, McCartha, Shannon R, additional, Walji, Tezin A, additional, Walker, Chelsea A, additional, Saville, Kenneth, additional, Abrams, Marita K, additional, Armstrong, Andrew R, additional, Armstrong, William, additional, Bailey, Robert J, additional, Barberi, Chelsea R, additional, Beck, Lauren R, additional, Blaker, Amanda L, additional, Blunden, Christopher E, additional, Brand, Jordan P, additional, Brock, Ethan J, additional, Brooks, Dana W, additional, Brown, Marie, additional, Butzler, Sarah C, additional, Clark, Eric M, additional, Clark, Nicole B, additional, Collins, Ashley A, additional, Cotteleer, Rebecca J, additional, Cullimore, Peterson R, additional, Dawson, Seth G, additional, Docking, Carter T, additional, Dorsett, Sasha L, additional, Dougherty, Grace A, additional, Downey, Kaitlyn A, additional, Drake, Andrew P, additional, Earl, Erica K, additional, Floyd, Trevor G, additional, Forsyth, Joshua D, additional, Foust, Jonathan D, additional, Franchi, Spencer L, additional, Geary, James F, additional, Hanson, Cynthia K, additional, Harding, Taylor S, additional, Harris, Cameron B, additional, Heckman, Jonathan M, additional, Holderness, Heather L, additional, Howey, Nicole A, additional, Jacobs, Dontae A, additional, Jewell, Elizabeth S, additional, Kaisler, Maria, additional, Karaska, Elizabeth A, additional, Kehoe, James L, additional, Koaches, Hannah C, additional, Koehler, Jessica, additional, Koenig, Dana, additional, Kujawski, Alexander J, additional, Kus, Jordan E, additional, Lammers, Jennifer A, additional, Leads, Rachel R, additional, Leatherman, Emily C, additional, Lippert, Rachel N, additional, Messenger, Gregory S, additional, Morrow, Adam T, additional, Newcomb, Victoria, additional, Plasman, Haley J, additional, Potocny, Stephanie J, additional, Powers, Michelle K, additional, Reem, Rachel M, additional, Rennhack, Jonathan P, additional, Reynolds, Katherine R, additional, Reynolds, Lyndsey A, additional, Rhee, Dong K, additional, Rivard, Allyson B, additional, Ronk, Adam J, additional, Rooney, Meghan B, additional, Rubin, Lainey S, additional, Salbert, Luke R, additional, Saluja, Rasleen K, additional, Schauder, Taylor, additional, Schneiter, Allison R, additional, Schulz, Robert W, additional, Smith, Karl E, additional, Spencer, Sarah, additional, Swanson, Bryant R, additional, Tache, Melissa A, additional, Tewilliager, Ashley A, additional, Tilot, Amanda K, additional, VanEck, Eve, additional, Villerot, Matthew M, additional, Vylonis, Megan B, additional, Watson, David T, additional, Wurzler, Juliana A, additional, Wysocki, Lauren M, additional, Yalamanchili, Monica, additional, Zaborowicz, Matthew A, additional, Emerson, Julia A, additional, Ortiz, Carlos, additional, Deuschle, Frederic J, additional, DiLorenzo, Lauren A, additional, Goeller, Katie L, additional, Macchi, Christopher R, additional, Muller, Sarah E, additional, Pasierb, Brittany D, additional, Sable, Joseph E, additional, Tucci, Jessica M, additional, Tynon, Marykathryn, additional, Dunbar, David A, additional, Beken, Levent H, additional, Conturso, Alaina C, additional, Danner, Benjamin L, additional, DeMichele, Gabriella A, additional, Gonzales, Justin A, additional, Hammond, Maureen S, additional, Kelley, Colleen V, additional, Kelly, Elisabeth A, additional, Kulich, Danielle, additional, Mageeney, Catherine M, additional, McCabe, Nikie L, additional, Newman, Alyssa M, additional, Spaeder, Lindsay A, additional, Tumminello, Richard A, additional, Revie, Dennis, additional, Benson, Jonathon M, additional, Cristostomo, Michael C, additional, DaSilva, Paolo A, additional, Harker, Katherine S, additional, Jarrell, Jenifer N, additional, Jimenez, Luis A, additional, Katz, Brandon M, additional, Kennedy, William R, additional, Kolibas, Kimberly S, additional, LeBlanc, Mark T, additional, Nguyen, Trung T, additional, Nicolas, Daniel S, additional, Patao, Melissa D, additional, Patao, Shane M, additional, Rupley, Bryan J, additional, Sessions, Bridget J, additional, Weaver, Jennifer A, additional, Goodman, Anya L, additional, Alvendia, Erica L, additional, Baldassari, Shana M, additional, Brown, Ashley S, additional, Chase, Ian O, additional, Chen, Maida, additional, Chiang, Scott, additional, Cromwell, Avery B, additional, Custer, Ashley F, additional, DiTommaso, Tia M, additional, El-Adaimi, Jad, additional, Goscinski, Nora C, additional, Grove, Ryan A, additional, Gutierrez, Nestor, additional, Harnoto, Raechel S, additional, Hedeen, Heather, additional, Hong, Emily L, additional, Hopkins, Barbara L, additional, Huerta, Vilma F, additional, Khoshabian, Colin, additional, LaForge, Kristin M, additional, Lee, Cassidy T, additional, Lewis, Benjamin M, additional, Lydon, Anniken M, additional, Maniaci, Brian J, additional, Mitchell, Ryan D, additional, Morlock, Elaine V, additional, Morris, William M, additional, Naik, Priyanka, additional, Olson, Nicole C, additional, Osterloh, Jeannette M, additional, Perez, Marcos A, additional, Presley, Jonathan D, additional, Randazzo, Matt J, additional, Regan, Melanie K, additional, Rossi, Franca G, additional, Smith, Melanie A, additional, Soliterman, Eugenia A, additional, Sparks, Ciani J, additional, Tran, Danny L, additional, Wan, Tiffany, additional, Welker, Anne A, additional, Wong, Jeremy N, additional, Sreenivasan, Aparna, additional, Youngblom, Jim, additional, Adams, Andrew, additional, Alldredge, Justin, additional, Bryant, Ashley, additional, Carranza, David, additional, Cifelli, Alyssa, additional, Coulson, Kevin, additional, Debow, Calise, additional, Delacruz, Noelle, additional, Emerson, Charlene, additional, Farrar, Cassandra, additional, Foret, Don, additional, Garibay, Edgar, additional, Gooch, John, additional, Heslop, Michelle, additional, Kaur, Sukhjit, additional, Khan, Ambreen, additional, Kim, Van, additional, Lamb, Travis, additional, Lindbeck, Peter, additional, Lucas, Gabi, additional, Macias, Elizabeth, additional, Martiniuc, Daniela, additional, Mayorga, Lissett, additional, Medina, Joseph, additional, Membreno, Nelson, additional, Messiah, Shady, additional, Neufeld, Lacey, additional, Nguyen, San Francisco, additional, Nichols, Zachary, additional, Odisho, George, additional, Peterson, Daymon, additional, Rodela, Laura, additional, Rodriguez, Priscilla, additional, Rodriguez, Vanessa, additional, Ruiz, Jorge, additional, Sherrill, Will, additional, Silva, Valeria, additional, Sparks, Jeri, additional, Statton, Geeta, additional, Townsend, Ashley, additional, Valdez, Isabel, additional, Waters, Mary, additional, Westphal, Kyle, additional, Winkler, Stacey, additional, Zumkehr, Joannee, additional, DeJong, Randall J, additional, Hoogewerf, Arlene J, additional, Ackerman, Cheri M, additional, Armistead, Isaac O, additional, Baatenburg, Lara, additional, Borr, Matthew J, additional, Brouwer, Lindsay K, additional, Burkhart, Brandon J, additional, Bushhouse, Kelsey T, additional, Cesko, Lejla, additional, Choi, Tiffany Y Y, additional, Cohen, Heather, additional, Damsteegt, Amanda M, additional, Darusz, Jess M, additional, Dauphin, Cory M, additional, Davis, Yelena P, additional, Diekema, Emily J, additional, Drewry, Melissa, additional, Eisen, Michelle E M, additional, Faber, Hayley M, additional, Faber, Katherine J, additional, Feenstra, Elizabeth, additional, Felzer-Kim, Isabella T, additional, Hammond, Brandy L, additional, Hendriksma, Jesse, additional, Herrold, Milton R, additional, Hilbrands, Julia A, additional, Howell, Emily J, additional, Jelgerhuis, Sarah A, additional, Jelsema, Timothy R, additional, Johnson, Benjamin K, additional, Jones, Kelly K, additional, Kim, Anna, additional, Kooienga, Ross D, additional, Menyes, Erika E, additional, Nollet, Eric A, additional, Plescher, Brittany E, additional, Rios, Lindsay, additional, Rose, Jenny L, additional, Schepers, Allison J, additional, Scott, Geoff, additional, Smith, Joshua R, additional, Sterling, Allison M, additional, Tenney, Jenna C, additional, Uitvlugt, Chris, additional, VanDyken, Rachel E, additional, VanderVennen, Marielle, additional, Vue, Samantha, additional, Kokan, Nighat P, additional, Agbley, Kwabea, additional, Boham, Sampson K, additional, Broomfield, Daniel, additional, Chapman, Kayla, additional, Dobbe, Ali, additional, Dobbe, Ian, additional, Harrington, William, additional, Ibrahem, Marwan, additional, Kennedy, Andre, additional, Koplinsky, Chad A, additional, Kubricky, Cassandra, additional, Ladzekpo, Danielle, additional, Pattison, Claire, additional, Ramirez, Roman E, additional, Wande, Lucia, additional, Woehlke, Sarah, additional, Wawersik, Matthew, additional, Kiernan, Elizabeth, additional, Thompson, Jeffrey S, additional, Banker, Roxanne, additional, Bartling, Justina R, additional, Bhatiya, Chinmoy I, additional, Boudoures, Anna L, additional, Christiansen, Lena, additional, Fosselman, Daniel S, additional, French, Kristin M, additional, Gill, Ishwar S, additional, Havill, Jessen T, additional, Johnson, Jaelyn L, additional, Keny, Lauren J, additional, Kerber, John M, additional, Klett, Bethany M, additional, Kufel, Christina N, additional, May, Francis J, additional, Mecoli, Jonathan P, additional, Merry, Callie R, additional, Meyer, Lauren R, additional, Miller, Emily G, additional, Mullen, Gregory J, additional, Palozola, Katherine C, additional, Pfeil, Jacob J, additional, Thomas, Jessica G, additional, Verbofsky, Evan M, additional, Spana, Eric P, additional, Agarwalla, Anant, additional, Chapman, Julia, additional, Chlebina, Ben, additional, Chong, Insun, additional, Falk, I N, additional, Fitzgibbons, John D, additional, Friedman, Harrison, additional, Ighile, Osagie, additional, Kim, Andrew J, additional, Knouse, Kristin A, additional, Kung, Faith, additional, Mammo, Danny, additional, Ng, Chun Leung, additional, Nikam, Vinayak S, additional, Norton, Diana, additional, Pham, Philip, additional, Polk, Jessica W, additional, Prasad, Shreya, additional, Rankin, Helen, additional, Ratliff, Camille D, additional, Scala, Victoria, additional, Schwartz, Nicholas U, additional, Shuen, Jessica A, additional, Xu, Amy, additional, Xu, Thomas Q, additional, Zhang, Yi, additional, Rosenwald, Anne G, additional, Burg, Martin G, additional, Adams, Stephanie J, additional, Baker, Morgan, additional, Botsford, Bobbi, additional, Brinkley, Briana, additional, Brown, Carter, additional, Emiah, Shadie, additional, Enoch, Erica, additional, Gier, Chad, additional, Greenwell, Alyson, additional, Hoogenboom, Lindsay, additional, Matthews, Jordan E, additional, McDonald, Mitchell, additional, Mercer, Amanda, additional, Monsma, Nicholaus, additional, Ostby, Kristine, additional, Ramic, Alen, additional, Shallman, Devon, additional, Simon, Matthew, additional, Spencer, Eric, additional, Tomkins, Trisha, additional, Wendland, Pete, additional, Wylie, Anna, additional, Wolyniak, Michael J, additional, Robertson, Gregory M, additional, Smith, Samuel I, additional, DiAngelo, Justin R, additional, Sassu, Eric D, additional, Bhalla, Satish C, additional, Sharif, Karim A, additional, Choeying, Tenzin, additional, Macias, Jason S, additional, Sanusi, Fareed, additional, Torchon, Karvyn, additional, Bednarski, April E, additional, Alvarez, Consuelo J, additional, Davis, Kristen C, additional, Dunham, Carrie A, additional, Grantham, Alaina J, additional, Hare, Amber N, additional, Schottler, Jennifer, additional, Scott, Zackary W, additional, Kuleck, Gary A, additional, Yu, Nicole S, additional, Kaehler, Marian M, additional, Jipp, Jacob, additional, Overvoorde, Paul J, additional, Shoop, Elizabeth, additional, Cyrankowski, Olivia, additional, Hoover, Betsy, additional, Kusner, Matt, additional, Lin, Devry, additional, Martinov, Tijana, additional, Misch, Jonathan, additional, Salzman, Garrett, additional, Schiedermayer, Holly, additional, Snavely, Michael, additional, Zarrasola, Stephanie, additional, Parrish, Susan, additional, Baker, Atlee, additional, Beckett, Alissa, additional, Belella, Carissa, additional, Bryant, Julie, additional, Conrad, Turner, additional, Fearnow, Adam, additional, Gomez, Carolina, additional, Herbstsomer, Robert A, additional, Hirsch, Sarah, additional, Johnson, Christen, additional, Jones, Melissa, additional, Kabaso, Rita, additional, Lemmon, Eric, additional, Vieira, Carolina Marques dos Santos, additional, McFarland, Darryl, additional, McLaughlin, Christopher, additional, Morgan, Abbie, additional, Musokotwane, Sepo, additional, Neutzling, William, additional, Nietmann, Jana, additional, Paluskievicz, Christina, additional, Penn, Jessica, additional, Peoples, Emily, additional, Pozmanter, Caitlin, additional, Reed, Emily, additional, Rigby, Nichole, additional, Schmidt, Lasse, additional, Shelton, Micah, additional, Shuford, Rebecca, additional, Tirasawasdichai, Tiara, additional, Undem, Blair, additional, Urick, Damian, additional, Vondy, Kayla, additional, Yarrington, Bryan, additional, Eckdahl, Todd T, additional, Poet, Jeffrey L, additional, Allen, Alica B, additional, Anderson, John E, additional, Barnett, Jason M, additional, Baumgardner, Jordan S, additional, Brown, Adam D, additional, Carney, Jordan E, additional, Chavez, Ramiro A, additional, Christgen, Shelbi L, additional, Christie, Jordan S, additional, Clary, Andrea N, additional, Conn, Michel A, additional, Cooper, Kristen M, additional, Crowley, Matt J, additional, Crowley, Samuel T, additional, Doty, Jennifer S, additional, Dow, Brian A, additional, Edwards, Curtis R, additional, Elder, Darcie D, additional, Fanning, John P, additional, Janssen, Bridget M, additional, Lambright, Anthony K, additional, Lane, Curtiss E, additional, Limle, Austin B, additional, Mazur, Tammy, additional, McCracken, Marly R, additional, McDonough, Alexa M, additional, Melton, Amy D, additional, Minnick, Phillip J, additional, Musick, Adam E, additional, Newhart, William H, additional, Noynaert, Joseph W, additional, Ogden, Bradley J, additional, Sandusky, Michael W, additional, Schmuecker, Samantha M, additional, Shipman, Anna L, additional, Smith, Anna L, additional, Thomsen, Kristen M, additional, Unzicker, Matthew R, additional, Vernon, William B, additional, Winn, Wesley W, additional, Woyski, Dustin S, additional, Zhu, Xiao, additional, Du, Chunguang, additional, Ament, Caitlin, additional, Aso, Soham, additional, Bisogno, Laura Simone, additional, Caronna, Jason, additional, Fefelova, Nadezhda, additional, Lopez, Lenin, additional, Malkowitz, Lorraine, additional, Marra, Jonathan, additional, Menillo, Daniella, additional, Obiorah, Ifeanyi, additional, Onsarigo, Eric Nyabeta, additional, Primus, Shekerah, additional, Soos, Mahdi, additional, Tare, Archana, additional, Zidan, Ameer, additional, Jones, Christopher J, additional, Aronhalt, Todd, additional, Bellush, James M, additional, Burke, Christa, additional, DeFazio, Steve, additional, Does, Benjamin R, additional, Johnson, Todd D, additional, Keysock, Nicholas, additional, Knudsen, Nelson H, additional, Messler, James, additional, Myirski, Kevin, additional, Rekai, Jade Lea, additional, Rempe, Ryan Michael, additional, Salgado, Michael S, additional, Stagaard, Erica, additional, Starcher, Justin R, additional, Waggoner, Andrew W, additional, Yemelyanova, Anastasia K, additional, Hark, Amy T, additional, Bertolet, Anne, additional, Kuschner, Cyrus E, additional, Parry, Kesley, additional, Quach, Michael, additional, Shantzer, Lindsey, additional, Shaw, Mary E, additional, Smith, Mary A, additional, Glenn, Omolara, additional, Mason, Portia, additional, Williams, Charlotte, additional, Key, S Catherine Silver, additional, Henry, Tyneshia C P, additional, Johnson, Ashlee G, additional, White, Jackie X, additional, Haberman, Adam, additional, Asinof, Sam, additional, Drumm, Kelly, additional, Freeburg, Trip, additional, Safa, Nadia, additional, Schultz, Darrin, additional, Shevin, Yakov, additional, Svoronos, Petros, additional, Vuong, Tam, additional, Wellinghoff, Jules, additional, Hoopes, Laura L M, additional, Chau, Kim M, additional, Ward, Alyssa, additional, Regisford, E Gloria C, additional, Augustine, LaJerald, additional, Davis-Reyes, Brionna, additional, Echendu, Vivienne, additional, Hales, Jasmine, additional, Ibarra, Sharon, additional, Johnson, Lauriaun, additional, Ovu, Steven, additional, Braverman, John M, additional, Bahr, Thomas J, additional, Caesar, Nicole M, additional, Campana, Christopher, additional, Cassidy, Daniel W, additional, Cognetti, Peter A, additional, English, Johnathan D, additional, Fadus, Matthew C, additional, Fick, Cameron N, additional, Freda, Philip J, additional, Hennessy, Bryan M, additional, Hockenberger, Kelsey, additional, Jones, Jennifer K, additional, King, Jessica E, additional, Knob, Christopher R, additional, Kraftmann, Karen J, additional, Li, Linghui, additional, Lupey, Lena N, additional, Minniti, Carl J, additional, Minton, Thomas F, additional, Moran, Joseph V, additional, Mudumbi, Krishna, additional, Nordman, Elizabeth C, additional, Puetz, William J, additional, Robinson, Lauren M, additional, Rose, Thomas J, additional, Sweeney, Edward P, additional, Timko, Ashley S, additional, Paetkau, Don W, additional, Eisler, Heather L, additional, Aldrup, Megan E, additional, Bodenberg, Jessica M, additional, Cole, Mara G, additional, Deranek, Kelly M, additional, DeShetler, Megan, additional, Dowd, Rose M, additional, Eckardt, Alexandra K, additional, Ehret, Sharon C, additional, Fese, Jessica, additional, Garrett, Amanda D, additional, Kammrath, Anna, additional, Kappes, Michelle L, additional, Light, Morgan R, additional, Meier, Anne C, additional, O’Rouke, Allison, additional, Perella, Mallory, additional, Ramsey, Kimberley, additional, Ramthun, Jennifer R, additional, Reilly, Mary T, additional, Robinett, Deirdre, additional, Rossi, Nadine L, additional, Schueler, Mary Grace, additional, Shoemaker, Emma, additional, Starkey, Kristin M, additional, Vetor, Ashley, additional, Vrable, Abby, additional, Chandrasekaran, Vidya, additional, Beck, Christopher, additional, Hatfield, Kristen R, additional, Herrick, Douglas A, additional, Khoury, Christopher B, additional, Lea, Charlotte, additional, Louie, Christopher A, additional, Lowell, Shannon M, additional, Reynolds, Thomas J, additional, Schibler, Jeanine, additional, Scoma, Alexandra H, additional, Smith-Gee, Maxwell T, additional, Tuberty, Sarah, additional, Smith, Christopher D, additional, Lopilato, Jane E, additional, Hauke, Jeanette, additional, Roecklein-Canfield, Jennifer A, additional, Corrielus, Maureen, additional, Gilman, Hannah, additional, Intriago, Stephanie, additional, Maffa, Amanda, additional, Rauf, Sabya A, additional, Thistle, Katrina, additional, Trieu, Melissa, additional, Winters, Jenifer, additional, Yang, Bib, additional, Hauser, Charles R, additional, Abusheikh, Tariq, additional, Ashrawi, Yara, additional, Benitez, Pedro, additional, Boudreaux, Lauren R, additional, Bourland, Megan, additional, Chavez, Miranda, additional, Cruz, Samantha, additional, Elliott, GiNell, additional, Farek, Jesse R, additional, Flohr, Sarah, additional, Flores, Amanda H, additional, Friedrichs, Chelsey, additional, Fusco, Zach, additional, Goodwin, Zane, additional, Helmreich, Eric, additional, Kiley, John, additional, Knepper, John Mark, additional, Langner, Christine, additional, Martinez, Megan, additional, Mendoza, Carlos, additional, Naik, Monal, additional, Ochoa, Andrea, additional, Ragland, Nicolas, additional, Raimey, England, additional, Rathore, Sunil, additional, Reza, Evangelina, additional, Sadovsky, Griffin, additional, Seydoux, Marie-Isabelle B, additional, Smith, Jonathan E, additional, Unruh, Anna K, additional, Velasquez, Vicente, additional, Wolski, Matthew W, additional, Gosser, Yuying, additional, Govind, Shubha, additional, Clarke-Medley, Nicole, additional, Guadron, Leslie, additional, Lau, Dawn, additional, Lu, Alvin, additional, Mazzeo, Cheryl, additional, Meghdari, Mariam, additional, Ng, Simon, additional, Pamnani, Brad, additional, Plante, Olivia, additional, Shum, Yuki Kwan Wa, additional, Song, Roy, additional, Johnson, Diana E, additional, Abdelnabi, Mai, additional, Archambault, Alexi, additional, Chamma, Norma, additional, Gaur, Shailly, additional, Hammett, Deborah, additional, Kandahari, Adrese, additional, Khayrullina, Guzal, additional, Kumar, Sonali, additional, Lawrence, Samantha, additional, Madden, Nigel, additional, Mandelbaum, Max, additional, Milnthorp, Heather, additional, Mohini, Shiv, additional, Patel, Roshni, additional, Peacock, Sarah J, additional, Perling, Emily, additional, Quintana, Amber, additional, Rahimi, Michael, additional, Ramirez, Kristen, additional, Singhal, Rishi, additional, Weeks, Corinne, additional, Wong, Tiffany, additional, Gillis, Aubree T, additional, Moore, Zachary D, additional, Savell, Christopher D, additional, Watson, Reece, additional, Mel, Stephanie F, additional, Anilkumar, Arjun A, additional, Bilinski, Paul, additional, Castillo, Rostislav, additional, Closser, Michael, additional, Cruz, Nathalia M, additional, Dai, Tiffany, additional, Garbagnati, Giancarlo F, additional, Horton, Lanor S, additional, Kim, Dongyeon, additional, Lau, Joyce H, additional, Liu, James Z, additional, Mach, Sandy D, additional, Phan, Thu A, additional, Ren, Yi, additional, Stapleton, Kenneth E, additional, Strelitz, Jean M, additional, Sunjed, Ray, additional, Stamm, Joyce, additional, Anderson, Morgan C, additional, Bonifield, Bethany Grace, additional, Coomes, Daniel, additional, Dillman, Adam, additional, Durchholz, Elaine J, additional, Fafara-Thompson, Antoinette E, additional, Gross, Meleah J, additional, Gygi, Amber M, additional, Jackson, Lesley E, additional, Johnson, Amy, additional, Kocsisova, Zuzana, additional, Manghelli, Joshua L, additional, McNeil, Kylie, additional, Murillo, Michael, additional, Naylor, Kierstin L, additional, Neely, Jessica, additional, Ogawa, Emmy E, additional, Rich, Ashley, additional, Rogers, Anna, additional, Spencer, J Devin, additional, Stemler, Kristina M, additional, Throm, Allison A, additional, Van Camp, Matt, additional, Weihbrecht, Katie, additional, Wiles, T Aaron, additional, Williams, Mallory A, additional, Williams, Matthew, additional, Zoll, Kyle, additional, Bailey, Cheryl, additional, Zhou, Leming, additional, Balthaser, Darla M, additional, Bashiri, Azita, additional, Bower, Mindy E, additional, Florian, Kayla A, additional, Ghavam, Nazanin, additional, Greiner-Sosanko, Elizabeth S, additional, Karim, Helmet, additional, Mullen, Victor W, additional, Pelchen, Carly E, additional, Yenerall, Paul M, additional, Zhang, Jiayu, additional, Rubin, Michael R, additional, Arias-Mejias, Suzette M, additional, Bermudez-Capo, Armando G, additional, Bernal-Vega, Gabriela V, additional, Colon-Vazquez, Mariela, additional, Flores-Vazquez, Arelys, additional, Gines-Rosario, Mariela, additional, Llavona-Cartagena, Ivan G, additional, Martinez-Rodriguez, Javier O, additional, Ortiz-Fuentes, Lionel, additional, Perez-Colomba, Eliezer O, additional, Perez-Otero, Joseph, additional, Rivera, Elisandra, additional, Rodriguez-Giron, Luke J, additional, Santiago-Sanabria, Arnaldo J, additional, Senquiz-Gonzalez, Andrea M, additional, delValle, Frank R Soto, additional, Vargas-Franco, Dorianmarie, additional, Velázquez-Soto, Karla I, additional, Zambrana-Burgos, Joan D, additional, Martinez-Cruzado, Juan Carlos, additional, Asencio-Zayas, Lillyann, additional, Babilonia-Figueroa, Kevin, additional, Beauchamp-Pérez, Francis D, additional, Belén-Rodríguez, Juliana, additional, Bracero-Quiñones, Luciann, additional, Burgos-Bula, Andrea P, additional, Collado-Méndez, Xavier A, additional, Colón-Cruz, Luis R, additional, Correa-Muller, Ana I, additional, Crooke-Rosado, Jonathan L, additional, Cruz-García, José M, additional, Defendini-Ávila, Marianna, additional, Delgado-Peraza, Francheska M, additional, Feliciano-Cancela, Alex J, additional, Gónzalez-Pérez, Valerie M, additional, Guiblet, Wilfried, additional, Heredia-Negrón, Aldo, additional, Hernández-Muñiz, Jennifer, additional, Irizarry-González, Lourdes N, additional, Laboy-Corales, Ángel L, additional, Llaurador-Caraballo, Gabriela A, additional, Marín-Maldonado, Frances, additional, Marrero-Llerena, Ulises, additional, Martell-Martínez, Héctor A, additional, Martínez-Traverso, Idaliz M, additional, Medina-Ortega, Kiara N, additional, Méndez-Castellanos, Sonya G, additional, Menéndez-Serrano, Krizia C, additional, Morales-Caraballo, Carol I, additional, Ortiz-DeChoudens, Saryleine, additional, Ortiz-Ortiz, Patricia, additional, Pagán-Torres, Hendrick, additional, Pérez-Afanador, Diana, additional, Quintana-Torres, Enid M, additional, Ramírez-Aponte, Edwin G, additional, Riascos-Cuero, Carolina, additional, Rivera-Llovet, Michelle S, additional, Rivera-Pagán, Ingrid T, additional, Rivera-Vicéns, Ramón E, additional, Robles-Juarbe, Fabiola, additional, Rodríguez-Bonilla, Lorraine, additional, Rodríguez-Echevarría, Brian O, additional, Rodríguez-García, Priscila M, additional, Rodríguez-Laboy, Abneris E, additional, Rodríguez-Santiago, Susana, additional, Rojas-Vargas, Michael L, additional, Rubio-Marrero, Eva N, additional, Santiago-Colón, Albeliz, additional, Santiago-Ortiz, Jorge L, additional, Santos-Ramos, Carlos E, additional, Serrano-González, Joseline, additional, Tamayo-Figueroa, Alina M, additional, Tascón-Peñaranda, Edna P, additional, Torres-Castillo, José L, additional, Valentín-Feliciano, Nelson A, additional, Valentín-Feliciano, Yashira M, additional, Vargas-Barreto, Nadyan M, additional, Vélez-Vázquez, Miguel, additional, Vilanova-Vélez, Luis R, additional, Zambrana-Echevarría, Cristina, additional, MacKinnon, Christy, additional, Chung, Hui-Min, additional, Kay, Chris, additional, Pinto, Anthony, additional, Kopp, Olga R, additional, Burkhardt, Joshua, additional, Harward, Chris, additional, Allen, Robert, additional, Bhat, Pavan, additional, Chang, Jimmy Hsiang-Chun, additional, Chen, York, additional, Chesley, Christopher, additional, Cohn, Dara, additional, DuPuis, David, additional, Fasano, Michael, additional, Fazzio, Nicholas, additional, Gavinski, Katherine, additional, Gebreyesus, Heran, additional, Giarla, Thomas, 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Nguyen, Hien, additional, Nylander, Andrew, additional, Pollack, Jason, additional, Rastogi, Suchita, additional, Reddy, Himabindu, additional, Regenold, Nathaniel, additional, Sarezky, Jon, additional, Schultz, Michael, additional, Shim, Jien, additional, Skorupa, Tara, additional, Smith, Kenneth, additional, Spencer, Sarah J, additional, Srikanth, Priya, additional, Stancu, Gabriel, additional, Stein, Andrew P, additional, Strother, Marshall, additional, Sudmeier, Lisa, additional, Sun, Mengyang, additional, Sundaram, Varun, additional, Tazudeen, Noor, additional, Tseng, Alan, additional, Tzeng, Albert, additional, Venkat, Rohit, additional, Venkataram, Sandeep, additional, Waldman, Leah, additional, Wang, Tracy, additional, Yang, Hao, additional, Yu, Jack Y, additional, Zheng, Yin, additional, Preuss, Mary L, additional, Garcia, Angelica, additional, Juergens, Matt, additional, Morris, Robert W, additional, Nagengast, Alexis A, additional, Azarewicz, Julie, additional, Carr, Thomas J, additional, Chichearo, Nicole, additional, Colgan, Mike, additional, Donegan, Megan, additional, Gardner, Bob, additional, Kolba, Nik, additional, Krumm, Janice L, additional, Lytle, Stacey, additional, MacMillian, Laurell, additional, Miller, Mary, additional, Montgomery, Andrew, additional, Moretti, Alysha, additional, Offenbacker, Brittney, additional, Polen, Mike, additional, Toth, John, additional, Woytanowski, John, additional, Kadlec, Lisa, additional, Crawford, Justin, additional, Spratt, Mary L, additional, Adams, Ashley L, additional, Barnard, Brianna K, additional, Cheramie, Martin N, additional, Eime, Anne M, additional, Golden, Kathryn L, additional, Hawkins, Allyson P, additional, Hill, Jessica E, additional, Kampmeier, Jessica A, additional, Kern, Cody D, additional, Magnuson, Emily E, additional, Miller, Ashley R, additional, Morrow, Cody M, additional, Peairs, Julia C, additional, Pickett, Gentry L, additional, Popelka, Sarah A, additional, Scott, Alexis J, additional, Teepe, Emily J, additional, TerMeer, Katie A, additional, Watchinski, Carmen A, additional, Watson, Lucas A, additional, Weber, Rachel E, additional, Woodard, Kate A, additional, Barnard, Daron C, additional, Appiah, Isaac, additional, Giddens, Michelle M, additional, McNeil, Gerard P, additional, Adebayo, Adeola, additional, Bagaeva, Kate, additional, Chinwong, Justina, additional, Dol, Chrystel, additional, George, Eunice, additional, Haltaufderhyde, Kirk, additional, Haye, Joanna, additional, Kaur, Manpreet, additional, Semon, Max, additional, Serjanov, Dmitri, additional, Toorie, Anika, additional, Wilson, Christopher, additional, Riddle, Nicole C, additional, Buhler, Jeremy, additional, Mardis, Elaine R, additional, and Elgin, Sarah C R, additional

Published
2015
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12. 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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13. Reconstructing Native American migrations from whole-genome and whole-exome data.

Author

Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, and Bustamante CD

Subjects
Black People genetics, Chromosome Mapping, Exome, Genome, Human, Hispanic or Latino genetics, Human Genome Project, Humans, Mexican Americans genetics, Mexico, Puerto Rico, Racial Groups genetics, White People genetics, Gene Frequency genetics, Genetics, Population, Human Migration, Indians, North American genetics
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 American 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., Competing Interests: The authors have declared that no competing interests exist.

Published
2013
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