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

    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 / Silver Key, S Catherine / 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 / Elgin, Sarah C R

    CBE life sciences education

    2013  Volume 13, Issue 1, Page(s) 111–130

    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 ... ...

    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.
    MeSH term(s) Attitude ; Biology/education ; Cooperative Behavior ; Curriculum ; Data Collection ; Faculty ; Genome ; Genomics/education ; Humans ; Knowledge ; Learning ; Molecular Sequence Annotation ; Program Evaluation ; Research/education ; Research Personnel ; Self Report ; Surveys and Questionnaires ; Time Factors
    Language English
    Publishing date 2013-09-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2465176-X
    ISSN 1931-7913 ; 1931-7913
    ISSN (online) 1931-7913
    ISSN 1931-7913
    DOI 10.1187/cbe-13-08-0152
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.

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

    G3 (Bethesda, Md.)

    2015  Volume 5, Issue 5, Page(s) 719–740

    Abstract: The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we ... ...

    Abstract The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
    MeSH term(s) Animals ; Codon ; Computational Biology ; DNA Transposable Elements ; Drosophila/genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Exons ; Gene Rearrangement ; Genome ; Genomics ; Heterochromatin ; Introns ; Molecular Sequence Annotation ; Polytene Chromosomes ; Repetitive Sequences, Nucleic Acid ; Selection, Genetic ; Species Specificity
    Chemical Substances Codon ; DNA Transposable Elements ; Drosophila Proteins ; Heterochromatin
    Language English
    Publishing date 2015-03-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.114.015966
    Database MEDical Literature Analysis and Retrieval System OnLINE

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