Search

Your search keyword '"Hide, Winston"' showing total 383 results
Start Over Author "Hide, Winston" Search Limiters Available in Library Collection
383 results on '"Hide, Winston"'

1. Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies

Author

Huang, Yu-Ning, Love, Michael I., Ronkowski, Cynthia Flaire, Deshpande, Dhrithi, Schriml, Lynn M., Wong-Beringer, Annie, Mons, Barend, Corbett-Detig, Russell, Hunter, Christopher I, Moore, Jason H., Garmire, Lana X., Reddy, T. B. K., Hide, Winston A., Butte, Atul J., Robinson, Mark D., and Mangul, Serghei

Subjects
Computer Science - Digital Libraries
Abstract

Metadata, often termed "data about data," is crucial for organizing, understanding, and managing vast omics datasets. It aids in efficient data discovery, integration, and interpretation, enabling users to access, comprehend, and utilize data effectively. Its significance spans the domains of scientific research, facilitating data reproducibility, reusability, and secondary analysis. However, numerous perceptual and technical barriers hinder the sharing of metadata among researchers. These barriers compromise the reliability of research results and hinder integrative meta-analyses of omics studies . This study highlights the key barriers to metadata sharing, including the lack of uniform standards, privacy and legal concerns, limitations in study design, limited incentives, inadequate infrastructure, and the dearth of well-trained personnel for metadata management and reuse. Proposed solutions include emphasizing the promotion of standardization, educational efforts, the role of journals and funding agencies, incentives and rewards, and the improvement of infrastructure. More accurate, reliable, and impactful research outcomes are achievable if the scientific community addresses these barriers, facilitating more accurate, reliable, and impactful research outcomes.

Published
2023

2. Region-based analysis of rare genomic variants in whole-genome sequencing datasets reveal two novel Alzheimer’s disease-associated genes: DTNB and DLG2

Author

Prokopenko, Dmitry, Lee, Sanghun, Hecker, Julian, Mullin, Kristina, Morgan, Sarah, Katsumata, Yuriko, Weiner, Michael W, Fardo, David W, Laird, Nan, Bertram, Lars, Hide, Winston, Lange, Christoph, and Tanzi, Rudolph E

Subjects
Aging, Genetics, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Biotechnology, Acquired Cognitive Impairment, Human Genome, Neurodegenerative, Alzheimer's Disease, Dementia, Brain Disorders, 2.1 Biological and endogenous factors, Aetiology, Neurological, Good Health and Well Being, Alzheimer Disease, Dithionitrobenzoic Acid, Dystrophin-Associated Proteins, Genetic Predisposition to Disease, Genome-Wide Association Study, Genomics, Guanylate Kinases, Humans, Neuropeptides, Polymorphism, Single Nucleotide, Tumor Suppressor Proteins, Whole Genome Sequencing, Alzheimer’s Disease Neuroimaging Initiative, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry
Abstract

Alzheimer's disease (AD) is a genetically complex disease for which nearly 40 loci have now been identified via genome-wide association studies (GWAS). We attempted to identify groups of rare variants (alternate allele frequency

Published
2022

5. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

Author

Delorey, Toni M., Ziegler, Carly G. K., Heimberg, Graham, Normand, Rachelly, Yang, Yiming, Segerstolpe, Åsa, Abbondanza, Domenic, Fleming, Stephen J., Subramanian, Ayshwarya, Montoro, Daniel T., Jagadeesh, Karthik A., Dey, Kushal K., Sen, Pritha, Slyper, Michal, Pita-Juárez, Yered H., Phillips, Devan, Biermann, Jana, Bloom-Ackermann, Zohar, Barkas, Nikolaos, Ganna, Andrea, Gomez, James, Melms, Johannes C., Katsyv, Igor, Normandin, Erica, Naderi, Pourya, Popov, Yury V., Raju, Siddharth S., Niezen, Sebastian, Tsai, Linus T.-Y., Siddle, Katherine J., Sud, Malika, Tran, Victoria M., Vellarikkal, Shamsudheen K., Wang, Yiping, Amir-Zilberstein, Liat, Atri, Deepak S., Beechem, Joseph, Brook, Olga R., Chen, Jonathan, Divakar, Prajan, Dorceus, Phylicia, Engreitz, Jesse M., Essene, Adam, Fitzgerald, Donna M., Fropf, Robin, Gazal, Steven, Gould, Joshua, Grzyb, John, Harvey, Tyler, Hecht, Jonathan, Hether, Tyler, Jané-Valbuena, Judit, Leney-Greene, Michael, Ma, Hui, McCabe, Cristin, McLoughlin, Daniel E., Miller, Eric M., Muus, Christoph, Niemi, Mari, Padera, Robert, Pan, Liuliu, Pant, Deepti, Pe’er, Carmel, Pfiffner-Borges, Jenna, Pinto, Christopher J., Plaisted, Jacob, Reeves, Jason, Ross, Marty, Rudy, Melissa, Rueckert, Erroll H., Siciliano, Michelle, Sturm, Alexander, Todres, Ellen, Waghray, Avinash, Warren, Sarah, Zhang, Shuting, Zollinger, Daniel R., Cosimi, Lisa, Gupta, Rajat M., Hacohen, Nir, Hibshoosh, Hanina, Hide, Winston, Price, Alkes L., Rajagopal, Jayaraj, Tata, Purushothama Rao, Riedel, Stefan, Szabo, Gyongyi, Tickle, Timothy L., Ellinor, Patrick T., Hung, Deborah, Sabeti, Pardis C., Novak, Richard, Rogers, Robert, Ingber, Donald E., Jiang, Z. Gordon, Juric, Dejan, Babadi, Mehrtash, Farhi, Samouil L., Izar, Benjamin, Stone, James R., Vlachos, Ioannis S., Solomon, Isaac H., Ashenberg, Orr, Porter, Caroline B. M., Li, Bo, Shalek, Alex K., Villani, Alexandra-Chloé, Rozenblatt-Rosen, Orit, and Regev, Aviv

Published
2021
Full Text
View/download PDF

6. Integrating sequencing datasets to form highly confident SNP and indel genotype calls for a whole human genome

Author

Zook, Justin M., Chapman, Brad, Wang, Jason, Mittelman, David, Hofmann, Oliver, Hide, Winston, and Salit, Marc

Subjects
Quantitative Biology - Genomics
Abstract

Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made clear the need for a highly accurate set of genotypes across a whole genome that could be used as a benchmark. We present methods to make highly confident SNP, indel, and homozygous reference genotype calls for NA12878, the pilot genome for the Genome in a Bottle Consortium. We minimize bias towards any method by integrating and arbitrating between 14 datasets from 5 sequencing technologies, 7 mappers, and 3 variant callers. Regions for which no confident genotype call could be made are identified as uncertain, and classified into different reasons for uncertainty. Our highly confident genotype calls are publicly available on the Genome Comparison and Analytic Testing (GCAT) website to enable real-time benchmarking of any method.

Published
2013
Full Text
View/download PDF

7. Enabling the genomic revolution in Africa

Author

Rotimi, Charles, Abayomi, Akin, Abimiku, Alash'le, Adabayeri, Victoria May, Adebamowo, Clement, Adebiyi, Ezekiel, Ademola, Adebowale D, Adeyemo, Adebowale, Adu, Dwomoa, Affolabi, Dissou, Agongo, Godfred, Ajayi, Samuel, Akarolo-Anthony, Sally, Akinyemi, Rufus, Akpalu, Albert, Alberts, Marianne, Alonso Betancourt, Orlando, Alzohairy, Ahmed Mansour, Ameni, Gobena, Amodu, Olukemi, Anabwani, Gabriel, Andersen, Kristian, Arogundade, Fatiu, Arulogun, Oyedunni, Asogun, Danny, Bakare, Rasheed, Balde, Naby, Baniecki, Mary Lynn, Beiswanger, Christine, Benkahla, Alia, Bethke, Lara, Boehnke, Micheal, Boima, Vincent, Brandful, James, Brooks, Andrew I, Brosius, Frank C, Brown, Chester, Bucheton, Bruno, Burke, David T, Burnett, Barrington G, Carrington-Lawrence, Stacy, Carstens, Nadia, Chisi, John, Christoffels, Alan, Cooper, Richard, Cordell, Heather, Crowther, Nigel, Croxton, Talishiea, de Vries, Jantina, Derr, Leslie, Donkor, Peter, Doumbia, Seydou, Duncanson, Audrey, Ekem, Ivy, El Sayed, Ahmed, Engel, Mark E, Enyaru, John CK, Everett, Dean, Fadlelmola, Faisal M, Fakunle, Eyitayo, Fischbeck, Kenneth H, Fischer, Anne, Folarin, Onikepe, Gamieldien, Junaid, Garry, Robert F, Gaseitsiwe, Simani, Gbadegesin, Rasheed, Ghansah, Anita, Giovanni, Maria, Goesbeck, Parham, Gomez-Olive, F Xavier, Grant, Donald S, Grewal, Ravnit, Guyer, Mark, Hanchard, Neil A, Happi, Christian T, Hazelhurst, Scott, Hennig, Branwen J, Hertz-, Christiane, Fowler, Hide, Winston, Hilderbrandt, Friedhelm, Hugo-Hamman, Christopher, Ibrahim, Muntaser E, James, Regina, Jaufeerally-Fakim, Yasmina, Jenkins, Carolyn, Jentsch, Ute, Jiang, Pan-Pan, Joloba, Moses, Jongeneel, Victor, Joubert, Fourie, Kader, Mukthar, Kahn, Kathleen, Kaleebu, Pontiano, Kapiga, Saidi H, Kassim, Samar Kamal, Kasvosve, Ishmael, Kayondo, Jonathan, and Keavney, Bernard

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Clinical Sciences, Medical Microbiology, Human Genome, Cancer, Infectious Diseases, HIV/AIDS, Clinical Research, Biotechnology, Rare Diseases, 2.6 Resources and infrastructure (aetiology), Aetiology, Infection, Good Health and Well Being, Africa, Disease, England, Genetics, Medical, Genome-Wide Association Study, Genomics, Health, Humans, National Institutes of Health (U.S.), United States, H3Africa Consortium, General Science & Technology
Abstract

H3Africa is developing capacity for health-related genomics research in Africa

Published
2014

8. Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis

Author

Initiative, International Glossina Genome, Attardo, Geoffrey M, Abila, Patrick P, Auma, Joanna E, Baumann, Aaron A, Benoit, Joshua B, Brelsfoard, Corey L, Ribeiro, José MC, Cotton, James A, Pham, Daphne QD, Darby, Alistair C, Van Den Abbeele, Jan, Denlinger, David L, Field, Linda M, Nyanjom, Steven RG, Gaunt, Michael W, Geiser, Dawn L, Gomulski, Ludvik M, Haines, Lee R, Hansen, Immo A, Jones, Jeffery W, Kibet, Caleb K, Kinyua, Johnson K, Larkin, Denis M, Lehane, Michael J, Rio, Rita VM, Macdonald, Sandy J, Macharia, Rosaline W, Malacrida, Anna R, Marco, Heather G, Marucha, Kevin K, Masiga, Daniel K, Meuti, Megan E, Mireji, Paul O, Obiero, George FO, Koekemoer, Jacobus JO, Okoro, Chinyere K, Omedo, Irene A, Osamor, Victor C, Balyeidhusa, Apollo SP, Peyton, Justin T, Price, David P, Quail, Michael A, Ramphul, Urvashi N, Rawlings, Neil D, Riehle, Michael A, Robertson, Hugh M, Sanders, Mandy J, Scott, Maxwell J, Dashti, Zahra Jalali Sefid, Snyder, Anna K, Srivastava, Tulika P, Stanley, Eleanor J, Swain, Martin T, Hughes, Daniel ST, Tarone, Aaron M, Taylor, Todd D, Telleria, Erich L, Thomas, Gavin H, Walshe, Deirdre P, Wilson, Richard K, Winzerling, Joy J, Acosta-Serrano, Alvaro, Aksoy, Serap, Arensburger, Peter, Aslett, Martin, Bateta, Rosemary, Benkahla, Alia, Berriman, Matthew, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christoffels, Alan, Falchetto, Marco, Friedrich, Markus, Fu, Shuhua, Gäde, Gerd, Githinji, George, Gregory, Richard, Hall, Neil, Harkins, Gordon, Hattori, Masahira, Hertz-Fowler, Christiane, Hide, Winston, Hu, Wanqi, Imanishi, Tadashi, Inoue, Noboru, Jonas, Mario, Kawahara, Yoshihiro, Koffi, Mathurin, Kruger, Adele, Lawson, Daniel, Lehane, Stella, Lehväslaiho, Heikki, Luiz, Thiago, Makgamathe, Mmule, Malele, Imna, Manangwa, Oliver, Manga, Lucien, and Megy, Karyn

Subjects
Vector-Borne Diseases, Genetics, Prevention, Infectious Diseases, Biotechnology, 2.2 Factors relating to the physical environment, Aetiology, Infection, Good Health and Well Being, Animals, Blood, Feeding Behavior, Female, Genes, Insect, Genome, Insect, Insect Proteins, Insect Vectors, Microbiota, Molecular Sequence Annotation, Molecular Sequence Data, Reproduction, Salivary Glands, Sensation, Sequence Analysis, DNA, Symbiosis, Trypanosoma, Trypanosomiasis, African, Tsetse Flies, Wolbachia, International Glossina Genome Initiative, General Science & Technology
Abstract

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.

Published
2014

10. Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

Author

Logullo, Francesco O., Simone, Isabella, Logroscino, Giancarlo, Salvi, Fabrizio, Bartolomei, Ilaria, Borghero, Giuseppe, Murru, Maria Rita, Costantino, Emanuela, Pani, Carla, Puddu, Roberta, Caredda, Carla, Piras, Valeria, Tranquilli, Stefania, Cuccu, Stefania, Corongiu, Daniela, Melis, Maurizio, Milia, Antonio, Marrosu, Francesco, Marrosu, Maria Giovanna, Floris, Gianluca, Cannas, Antonino, Capasso, Margherita, Caponnetto, Claudia, Mancardi, Gianluigi, Origone, Paola, Mandich, Paola, Conforti, Francesca L., Cavallaro, Sebastiano, Mora, Gabriele, Marinou, Kalliopi, Sideri, Riccardo, Penco, Silvana, Mosca, Lorena, Lunetta, Christian, Pinter, Giuseppe Lauria, Corbo, Massimo, Riva, Nilo, Carrera, Paola, Volanti, Paolo, Mandrioli, Jessica, Fini, Nicola, Fasano, Antonio, Tremolizzo, Lucio, Arosio, Alessandro, Ferrarese, Carlo, Trojsi, Francesca, Tedeschi, Gioacchino, Monsurrò, Maria Rosaria, Piccirillo, Giovanni, Femiano, Cinzia, Ticca, Anna, Ortu, Enzo, La Bella, Vincenzo, Spataro, Rossella, Colletti, Tiziana, Sabatelli, Mario, Zollino, Marcella, Conte, Amelia, Luigetti, Marco, Lattante, Serena, Marangi, Giuseppe, Santarelli, Marialuisa, Petrucci, Antonio, Pugliatti, Maura, Pirisi, Angelo, Parish, Leslie D., Occhineri, Patrizia, Giannini, Fabio, Battistini, Stefania, Ricci, Claudia, Benigni, Michele, Cau, Tea B., Loi, Daniela, Calvo, Andrea, Moglia, Cristina, Brunetti, Maura, Barberis, Marco, Restagno, Gabriella, Casale, Federico, Marrali, Giuseppe, Fuda, Giuseppe, Ossola, Irene, Cammarosano, Stefania, Canosa, Antonio, Ilardi, Antonio, Manera, Umberto, Grassano, Maurizio, Tanel, Raffaella, Pisano, Fabrizio, Harms, Matthew B., Goldstein, David B., Shneider, Neil A., Goutman, Stephen, Simmons, Zachary, Miller, Timothy M., Chandran, Siddharthan, Pal, Suvankar, Manousakis, Georgios, Appel, Stanley H., Simpson, Ericka, Wang, Leo, Baloh, Robert H., Gibson, Summer, Bedlack, Richard, Lacomis, David, Sareen, Dhruv, Sherman, Alexander, Bruijn, Lucie, Penny, Michelle, Allen, Andrew S., Appel, Stanley, Bedlack, Richard S., Boone, Braden E., Brown, Robert, Carulli, John P., Chesi, Alessandra, Chung, Wendy K., Cirulli, Elizabeth T., Cooper, Gregory M., Couthouis, Julien, Day-Williams, Aaron G., Dion, Patrick A., Gitler, Aaron D., Glass, Jonathan D., Han, Yujun, Harris, Tim, Hayes, Sebastian D., Jones, Angela L., Keebler, Jonathan, Krueger, Brian J., Lasseigne, Brittany N., Levy, Shawn E., Lu, Yi-Fan, Maniatis, Tom, McKenna-Yasek, Diane, Myers, Richard M., Petrovski, Slavé, Pulst, Stefan M., Raphael, Alya R., Ravits, John M., Ren, Zhong, Rouleau, Guy A., Sapp, Peter C., Sims, Katherine B., Staropoli, John F., Waite, Lindsay L., Wang, Quanli, Wimbish, Jack R., Xin, Winnie W., Phatnani, Hemali, Kwan, Justin, Broach, James R., Arcila-Londono, Ximena, Lee, Edward B., Van Deerlin, Vivianna M., Fraenkel, Ernest, Ostrow, Lyle W., Baas, Frank, Zaitlen, Noah, Berry, James D., Malaspina, Andrea, Fratta, Pietro, Cox, Gregory A., Thompson, Leslie M., Finkbeiner, Steve, Dardiotis, Efthimios, Hornstein, Eran, MacGowan, Daniel J., Heiman-Patterson, Terry, Hammell, Molly G., Patsopoulos, Nikolaos A., Dubnau, Joshua, Nath, Avindra, Kaye, Julia, Finkbeiner, Steven, Wyman, Stacia, LeNail, Alexander, Lima, Leandro, Rothstein, Jeffrey D., Svendsen, Clive N., Van Eyk, Jenny, Maragakis, Nicholas J., Kolb, Stephen J., Cudkowicz, Merit, Baxi, Emily, Benatar, Michael, Taylor, J. Paul, Wu, Gang, Rampersaud, Evadnie, Wuu, Joanne, Rademakers, Rosa, Züchner, Stephan, Schule, Rebecca, McCauley, Jacob, Hussain, Sumaira, Cooley, Anne, Wallace, Marielle, Clayman, Christine, Barohn, Richard, Statland, Jeffrey, Ravits, John, Swenson, Andrea, Jackson, Carlayne, Trivedi, Jaya, Khan, Shaida, Katz, Jonathan, Jenkins, Liberty, Burns, Ted, Gwathmey, Kelly, Caress, James, McMillan, Corey, Elman, Lauren, Pioro, Erik, Heckmann, Jeannine, So, Yuen, Walk, David, Maiser, Samuel, Zhang, Jinghui, Silani, Vincenzo, Ticozzi, Nicola, Gellera, Cinzia, Ratti, Antonia, Taroni, Franco, Lauria, Giuseppe, Verde, Federico, Fogh, Isabella, Tiloca, Cinzia, Comi, Giacomo P., Sorarù, Gianni, Cereda, Cristina, D’Alfonso, Sandra, Corrado, Lucia, De Marchi, Fabiola, Corti, Stefania, Ceroni, Mauro, Mazzini, Letizia, Siciliano, Gabriele, Filosto, Massimiliano, Inghilleri, Maurizio, Peverelli, Silvia, Colombrita, Claudia, Poletti, Barbara, Maderna, Luca, Del Bo, Roberto, Gagliardi, Stella, Querin, Giorgia, Bertolin, Cinzia, Pensato, Viviana, Castellotti, Barbara, Camu, William, Mouzat, Kevin, Lumbroso, Serge, Corcia, Philippe, Meininger, Vincent, Besson, Gérard, Lagrange, Emmeline, Clavelou, Pierre, Guy, Nathalie, Couratier, Philippe, Vourch, Patrick, Danel, Véronique, Bernard, Emilien, Lemasson, Gwendal, Al Kheifat, Ahmad, Al-Chalabi, Ammar, Andersen, Peter, Basak, A. Nazli, Blair, Ian P., Chio, Adriano, Cooper-Knock, Jonathan, de Carvalho, Mamede, Dekker, Annelot, Drory, Vivian, Redondo, Alberto Garcia, Gotkine, Marc, Hardiman, Orla, Hide, Winston, Iacoangeli, Alfredo, Glass, Jonathan, Kenna, Kevin, Kiernan, Matthew, Kooyman, Maarten, Landers, John, McLaughlin, Russell, Middelkoop, Bas, Mill, Jonathan, Neto, Miguel Mitne, Moisse, Mattieu, Pardina, Jesus Mora, Morrison, Karen, Newhouse, Stephen, Pinto, Susana, Pulit, Sara, Robberecht, Wim, Shatunov, Aleksey, Shaw, Pamela, Shaw, Chris, Sproviero, William, Tazelaar, Gijs, van Damme, Philip, van den Berg, Leonard, van der Spek, Rick, van Eijk, Kristel, van Es, Michael, van Rheenen, Wouter, van Vugt, Joke, Veldink, Jan, Weber, Markus, Williams, Kelly L., Zatz, Mayana, Bauer, Denis C., Twine, Natalie A., Nicolas, Aude, Kenna, Kevin P., Renton, Alan E., Faghri, Faraz, Chia, Ruth, Dominov, Janice A., Kenna, Brendan J., Nalls, Mike A., Keagle, Pamela, Rivera, Alberto M., Murphy, Natalie A., van Vugt, Joke J.F.A., Geiger, Joshua T., Van der Spek, Rick A., Pliner, Hannah A., Shankaracharya, Smith, Bradley N., Topp, Simon D., Abramzon, Yevgeniya, Gkazi, Athina Soragia, Eicher, John D., Kenna, Aoife, Messina, Sonia, Simone, Isabella L., Ferrucci, Luigi, Moreno, Cristiane de Araujo Martins, Kamalakaran, Sitharthan, Musunuri, Rajeeva Lochan, Evani, Uday Shankar, Abhyankar, Avinash, Zody, Michael C., Wyman, Stacia K., LeNail, Alex, Van Eyk, Jennifer E., Laaksovirta, Hannu, Myllykangas, Liisa, Jansson, Lilja, Valori, Miko, Ealing, John, Hamdalla, Hisham, Rollinson, Sara, Pickering-Brown, Stuart, Orrell, Richard W., Sidle, Katie C., Hardy, John, Singleton, Andrew B., Johnson, Janel O., Arepalli, Sampath, Polak, Meraida, Asress, Seneshaw, Al-Sarraj, Safa, King, Andrew, Troakes, Claire, Vance, Caroline, de Belleroche, Jacqueline, ten Asbroek, Anneloor L.M.A., Muñoz-Blanco, José Luis, Hernandez, Dena G., Ding, Jinhui, Gibbs, J. Raphael, Scholz, Sonja W., Floeter, Mary Kay, Campbell, Roy H., Landi, Francesco, Bowser, Robert, MacGowan, Daniel J.L., Kirby, Janine, Pioro, Erik P., Pamphlett, Roger, Broach, James, Gerhard, Glenn, Dunckley, Travis L., Brady, Christopher B., Kowall, Neil W., Troncoso, Juan C., Le Ber, Isabelle, Heiman-Patterson, Terry D., Kamel, Freya, Van Den Bosch, Ludo, Strom, Tim M., Meitinger, Thomas, Van Eijk, Kristel R., Moisse, Matthieu, McLaughlin, Russell L., Van Es, Michael A., Boylan, Kevin B., Van Blitterswijk, Marka, Morrison, Karen E., Mora, Jesús S., Drory, Vivian E., Shaw, Pamela J., Turner, Martin R., Talbot, Kevin, Fifita, Jennifer A., Nicholson, Garth A., Esteban-Pérez, Jesús, García-Redondo, Alberto, Rogaeva, Ekaterina, Zinman, Lorne, Cooper-Knock, Johnathan, Brice, Alexis, Goutman, Stephen A., Feldman, Eva L., Gibson, Summer B., Van Damme, Philip, Ludolph, Albert C., Andersen, Peter M., Weishaupt, Jochen H., Trojanowski, John Q., Brown, Robert H., Jr., van den Berg, Leonard H., Veldink, Jan H., Stone, David J., Tienari, Pentti, Chiò, Adriano, Shaw, Christopher E., Traynor, Bryan J., and Landers, John E.

Published
2018
Full Text
View/download PDF

11. The Generation and Utilization of a Cancer-Oriented Representation of the Human Transcriptome by Using Expressed Sequence Tags

Author

Brentani, Helena, Caballero, Otávia L., Camargo, Anamaria A., da Silva, Aline M., da Silva,, Wilson Araújo, Neto, Emmanuel Dias, Grivet, Marco, Gruber, Arthur, Hide, Winston, Iseli, Christian, Jongeneel, C. Victor, Kelso, Janet, Nagai, Maria Aparecida, Osorio, Elisson C., Riggins, Gregory J., de Souza, Sandro, Stevenson, Brian J., Strausberg, Robert L., Tajara, Eloiza H., and Verjovski-Almeida, Sergio

Published
2003

13. PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs.

Author

Yeganeh, Pourya Naderi, Teo, Yue Y, Karagkouni, Dimitra, Pita-Juárez, Yered, Morgan, Sarah L, Slack, Frank J, Vlachos, Ioannis S, and Hide, Winston A

Subjects
SYSTEMS biology, MICRORNA, GENE expression, COMPUTATIONAL biology, SYNTHETIC biology, RNA regulation, FUNCTIONAL groups
Abstract

Charting microRNA (miRNA) regulation across pathways is key to characterizing their function. Yet, no method currently exists that can quantify how miRNAs regulate multiple interconnected pathways or prioritize them for their ability to regulate coordinate transcriptional programs. Existing methods primarily infer one-to-one relationships between miRNAs and pathways using differentially expressed genes. We introduce PanomiR, an in silico framework for studying the interplay of miRNAs and disease functions. PanomiR integrates gene expression, mRNA–miRNA interactions and known biological pathways to reveal coordinated multi-pathway targeting by miRNAs. PanomiR utilizes pathway-activity profiling approaches, a pathway co-expression network and network clustering algorithms to prioritize miRNAs that target broad-scale transcriptional disease phenotypes. It directly resolves differential regulation of pathways, irrespective of their differential gene expression, and captures co-activity to establish functional pathway groupings and the miRNAs that may regulate them. PanomiR uses a systems biology approach to provide broad but precise insights into miRNA-regulated functional programs. It is available at https://bioconductor.org/packages/PanomiR. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

14. Exome sequencing reveals recurrent germ line variants in patients with familial Waldenström macroglobulinemia

Author

Roccaro, Aldo M., Sacco, Antonio, Shi, Jiantao, Chiarini, Marco, Perilla-Glen, Adriana, Manier, Salomon, Glavey, Siobhan, Aljawai, Yosra, Mishima, Yuji, Kawano, Yawara, Moschetta, Michele, Correll, Mick, Improgo, Ma. Reina, Brown, Jennifer R., Imberti, Luisa, Rossi, Giuseppe, Castillo, Jorge J., Treon, Steven P., Freedman, Matthew L., Van Allen, Eliezer M., Hide, Winston, Hiller, Elaine, Rainville, Irene, and Ghobrial, Irene M.

Published
2016
Full Text
View/download PDF

17. A comparison between similarity matrices for principal component analysis to assess population stratification in sequenced genetic data sets.

Author

Lee, Sanghun, Hahn, Georg, Hecker, Julian, Lutz, Sharon M, Mullin, Kristina, (ADNI), Alzheimer's Disease Neuroimaging Initiative, Hide, Winston, Bertram, Lars, DeMeo, Dawn L, Tanzi, Rudolph E, Lange, Christoph, and Prokopenko, Dmitry

Subjects
PRINCIPAL components analysis, EAST Asians, ALZHEIMER'S disease, NUCLEOTIDE sequencing, GENE frequency
Abstract

Genetic similarity matrices are commonly used to assess population substructure (PS) in genetic studies. Through simulation studies and by the application to whole-genome sequencing (WGS) data, we evaluate the performance of three genetic similarity matrices: the unweighted and weighted Jaccard similarity matrices and the genetic relationship matrix. We describe different scenarios that can create numerical pitfalls and lead to incorrect conclusions in some instances. We consider scenarios in which PS is assessed based on loci that are located across the genome ('globally') and based on loci from a specific genomic region ('locally'). We also compare scenarios in which PS is evaluated based on loci from different minor allele frequency bins: common (>5%), low-frequency (5–0.5%) and rare (<0.5%) single-nucleotide variations (SNVs). Overall, we observe that all approaches provide the best clustering performance when computed based on rare SNVs. The performance of the similarity matrices is very similar for common and low-frequency variants, but for rare variants, the unweighted Jaccard matrix provides preferable clustering features. Based on visual inspection and in terms of standard clustering metrics, its clusters are the densest and the best separated in the principal component analysis of variants with rare SNVs compared with the other methods and different allele frequency cutoffs. In an application, we assessed the role of rare variants on local and global PS, using WGS data from multiethnic Alzheimer's disease data sets and European or East Asian populations from the 1000 Genome Project. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

20. Most Pathways Can Be Related to the Pathogenesis of Alzheimer's Disease

Author

Morgan, Sarah L., Naderi, Pourya, Koler, Katjuša, Pita-Juarez, Yered, Prokopenko, Dmitry, Vlachos, Ioannis S., Tanzi, Rudolph E., Bertram, Lars, and Hide, Winston A.

Subjects
Aging, Cognitive Neuroscience
Abstract

Alzheimer’s disease (AD) is a complex neurodegenerative disorder. The relative contribution of the numerous underlying functional mechanisms is poorly understood. To comprehensively understand the context and distribution of pathways that contribute to AD, we performed text-mining to generate an exhaustive, systematic assessment of the breadth and diversity of biological pathways within a corpus of 206,324 dementia publication abstracts. A total of 91% (325/335) of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways have publications containing an association via at least 5 studies, while 63% of pathway terms have at least 50 studies providing a clear association with AD. Despite major technological advances, the same set of top-ranked pathways have been consistently related to AD for 30 years, including AD, immune system, metabolic pathways, cholinergic synapse, long-term depression, proteasome, diabetes, cancer, and chemokine signaling. AD pathways studied appear biased: animal model and human subject studies prioritize different AD pathways. Surprisingly, human genetic discoveries and drug targeting are not enriched in the most frequently studied pathways. Our findings suggest that not only is this disorder incredibly complex, but that its functional reach is also nearly global. As a consequence of our study, research results can now be assessed in the context of the wider AD literature, supporting the design of drug therapies that target a broader range of mechanisms. The results of this study can be explored at www.adpathways.org.

Published
2021

21. Genome-Wide Analysis of Cancer/Testis Gene Expression

Author

Hofmann, Oliver, Caballero, Otavia L., Stevenson, Brian J., Chen, Yao-Tseng, Cohen, Tzeela, Chua, Ramon, Maher, Christopher A., Panji, Sumir, Schaefer, Ulf, Kruger, Adele, Lehvaslaiho, Minna, Carninci, Piero, Hayashizaki, Yoshihide, Jongeneel, C. Victor, Simpson, Andrew J. G., Old, Lloyd J., and Hide, Winston

Published
2008
Full Text
View/download PDF

23. GCH1 Deficiency Activates Brain Innate Immune Response and Impairs Tyrosine Hydroxylase Homeostasis

Author

Larbalestier, Hannah, primary, Keatinge, Marcus, additional, Watson, Lisa, additional, White, Emma, additional, Gowda, Siri, additional, Wei, Wenbin, additional, Koler, Katjusa, additional, Semenova, Svetlana A., additional, Elkin, Adam M., additional, Rimmer, Neal, additional, Sweeney, Sean T., additional, Mazzolini, Julie, additional, Sieger, Dirk, additional, Hide, Winston, additional, McDearmid, Jonathan, additional, Panula, Pertti, additional, MacDonald, Ryan B., additional, and Bandmann, Oliver, additional

Published
2021
Full Text
View/download PDF

24. Cell-specifc translational profling in acute kidney injury

Author

Liu, Jing, Krautzberger, A. Michaela, Sui, Shannan H., Hofmann, Oliver M., Chen, Ying, Baetscher, Manfred, Grgic, Ivica, Kumar, Sanjeev, Humphreys, Benjamin, Hide, Winston A., and McMahon, Andrew P.

Subjects
Medical research, Medicine, Experimental, Kidney diseases -- Physiological aspects, Medical case management -- Methods, Health care industry
Abstract

Acute kidney injury (AKI) promotes an abrupt loss of kidney function that results in substantial morbidity and mortality. Considerable effort has gone toward identification of diagnostic biomarkers and analysis of AKI-associated molecular events; however, most studies have adopted organ-wide approaches and have not elucidated the interplay among different cell types involved in AKI pathophysiology. To better characterize AKI-associated molecular and cellular events, we developed a mouse line that enables the identification of translational profiles in specific cell types. This strategy relies on CRE recombinase--dependent activation of an EGFP-tagged L10a ribosomal protein subunit, which allows translating ribosome affinity purification (TRAP) of mRNA populations in CRE-expressing cells. Combining this mouse line with cell type--specific CRE-driver lines, we identified distinct cellular responses in an ischemia reperfusion injury (IRI) model of AKI. Twenty-four hours following IRI, distinct translational signatures were identified in the nephron, kidney interstitial cell populations, vascular endothelium, and macrophages/monocytes. Furthermore, TRAP captured known IRI-associated markers, validating this approach. Biological function annotation, canonical pathway analysis, and in situ analysis of identified response genes provided insight into cell-specific injury signatures. Our study provides a deep, cell-based view of early injury-associated molecular events in AKI and documents a versatile, genetic tool to monitor cell-specific and temporal-specific biological processes in disease modeling., Introduction Acute kidney injury (AKI) is characterized by a sudden deterioration in renal function associated with high morbidity and mortality (1). From 5% to 7% of hospitalized patients are reported [...]

Published
2014
Full Text
View/download PDF

26. Prenatal lead levels, plasma amyloid [beta] levels, and gene expression in young adulthood

Author

Mazumdar, Maitreyi, Xia, Weiming, Hofmann, Oliver, Gregas, Matthew, Ho Sui, Shannan, Hide, Winston, Yang, Ting, Needleman, Herbert L., and Bellinger, David C.

Subjects
Gene expression -- Research, Lead -- Health aspects -- Research, Amyloid beta-protein -- Physiological aspects -- Research, Alzheimer's disease -- Risk factors -- Research, Environmental issues, Health
Abstract

BACKGROUND; Animal studies suggest that early-life lead exposure influences gene expression and production of proteins associated with Alzheimer's disease (AD). OBJECTIVES: We attempted to assess the relationship between early-life lead [...]

Published
2012

27. Aberrant lipid metabolism disrupts calcium homeostasis causing liver endoplasmic reticulum stress in obesity

Author

Fu, Suneng, Yang, Ling, Li, Ping, Hofmann, Oliver, Dicker, Lee, Hide, Winston, Lin, Xihong, Watkins, Steven M., Ivanov, Alexander R., and Hotamisligil, Gokhan S.

Subjects
Obesity -- Complications and side effects -- Causes of, Endoplasmic reticulum -- Physiological aspects, Calcium, Dietary -- Physiological aspects, Lipid metabolism -- Abnormalities -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The endoplasmic reticulum (ER) is the main site of protein and lipid synthesis, membrane biogenesis, xenobiotic detoxification and cellular calcium storage, and perturbation of ER homeostasis leads to stress and the activation of the unfolded protein response (1). Chronic activation of ER stress has been shown to have an important role in the development of insulin resistance and diabetes in obesity (2). However, the mechanisms that lead to chronic ER stress in a metabolic context in general, and in obesity in particular, are not understood. Here we comparatively examined the proteomic and lipidomic landscape of hepatic ER purified from lean and obese mice to explore the mechanisms of chronic ER stress in obesity. We found suppression of protein but stimulation of lipid synthesis in the obese ER without significant alterations in chaperone content. Alterations in ER fatty acid and lipid composition result in the inhibition of sarco/endoplasmic reticulum calcium ATPase (SERCA) activity and ER stress. Correcting the obesity-induced alteration of ER phospholipid composition or hepatic Serca over-expression in vivo both reduced chronic ER stress and improved glucose homeostasis. Hence, we established that abnormal lipid and calcium metabolism are important contributors to hepatic ER stress in obesity., It has been generally accepted that a surplus of nutrients and energy stimulates synthetic pathways and may lead to client overloading in the ER. However, it has not been demonstrated [...]

Published
2011
Full Text
View/download PDF

30. A promoter-level mammalian expression atlas

Author

Forrest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., ’t Hoen, Peter A. C., Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero, and Hayashizaki, Yoshihide

Published
2014
Full Text
View/download PDF

31. The future of biocuration: to thrive, the field that links biologists and their data urgently needs structure, recognition and support

Author

Howe, Doug, Costanzo, Maria, Fey, Petra, Gojobori, Takashi, Hannick, Linda, Hide, Winston, Hill, David P., Kania, Renate, Schaeffer, Mary, Pierre, Susan St., Twigger, Simon, White, Owen, and Rhee, Seung Yon

Subjects
Medical research -- Information management -- Methods, Medicine, Experimental -- Information management -- Methods, Biologists -- Information management -- Methods, Information management -- Methods, Environmental issues, Science and technology, Zoology and wildlife conservation, Company systems management, Information accessibility, Information management, Methods
Abstract

The exponential growth in the amount of biological data means that revolutionary measures are needed for data management, analysis and accessibility. Online databases have become important avenues for publishing biological [...]

Published
2008

32. Protein kinase C [delta] is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes

Author

Schwegmann, Anita, Guler, Reto, Cutler, Antony J., Arendse, Berenice, Horsnell, William G.C., Flemming, Alexandra, Kottmann, Andreas H., Ryan, Gregory, Hide, Winston, Leitges, Michael, Seoighe, Cathal, and Brombacher, Frank

Subjects
Protein kinases -- Influence, Phagocytosis -- Methods, Listeria monocytogenes -- Control, Protein microarrays -- Properties, Science and technology
Abstract

Activation of macrophages and subsequent 'killing' effector functions against infectious pathogens are essential for the establishment of protective immunity. NF-IL6 is a transcription factor downstream of IFN-[gamma] and TNF in the macrophage activation pathway required for bacterial killing. Comparison of microarray expression profiles of Listeria monocytogenes (LM)-infected macrophages from WT and NF-IL6-deficient mice enabled us to identify candidate genes downstream of NF-IL6 involved in the unknown pathways of LM killing independent of reactive oxygen intermediates and reactive nitrogen intermediates. One differentially expressed gene, PKC[delta], had higher mRNA levels in the LM-infected NF-IL6-deficient macrophages as compared with WT. To define the role of PKC[delta] during listeriosis, we infected PKC[delta]-deficient mice with LM. PKC[delta]-deficient mice were highly susceptible to LM infection with increased bacterial burden and enhanced histopathology despite enhanced NF-IL6 mRNA expression. Subsequent studies in PKC[delta]-deficient macrophages demonstrated that, despite elevated levels of proinflammatory cytokines and NO production, increased escape of LM from the phagosome into the cytoplasm and uncontrolled bacterial growth occurred. Taken together these data identified PKC[delta] as a critical factor for confinement of LM within macrophage phagosomes. microarray | phagosomal escape | bacterial killing

Published
2007

35. The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons

Author

Ho Sui, Shannan J., Begley, Kimberly, Reilly, Dorothy, Chapman, Brad, McGovern, Ray, Rocca-Sera, Philippe, Maguire, Eamonn, Altschuler, Gabriel M., Hansen, Terah A. A., Sompallae, Ramakrishna, Krivtsov, Andrei, Shivdasani, Ramesh A., Armstrong, Scott A., Culhane, Aedín C., Correll, Mick, Sansone, Susanna-Assunta, Hofmann, Oliver, and Hide, Winston

Published
2012
Full Text
View/download PDF

36. Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models

Author

Wan, Ying-Wooi, primary, Al-Ouran, Rami, additional, Mangleburg, Carl G., additional, Perumal, Thanneer M., additional, Lee, Tom V., additional, Allison, Katherine, additional, Swarup, Vivek, additional, Funk, Cory C., additional, Gaiteri, Chris, additional, Allen, Mariet, additional, Wang, Minghui, additional, Neuner, Sarah M., additional, Kaczorowski, Catherine C., additional, Philip, Vivek M., additional, Howell, Gareth R., additional, Martini-Stoica, Heidi, additional, Zheng, Hui, additional, Mei, Hongkang, additional, Zhong, Xiaoyan, additional, Kim, Jungwoo Wren, additional, Dawson, Valina L., additional, Dawson, Ted M., additional, Pao, Ping-Chieh, additional, Tsai, Li-Huei, additional, Haure-Mirande, Jean-Vianney, additional, Ehrlich, Michelle E., additional, Chakrabarty, Paramita, additional, Levites, Yona, additional, Wang, Xue, additional, Dammer, Eric B., additional, Srivastava, Gyan, additional, Mukherjee, Sumit, additional, Sieberts, Solveig K., additional, Omberg, Larsson, additional, Dang, Kristen D., additional, Eddy, James A., additional, Snyder, Phil, additional, Chae, Yooree, additional, Amberkar, Sandeep, additional, Wei, Wenbin, additional, Hide, Winston, additional, Preuss, Christoph, additional, Ergun, Ayla, additional, Ebert, Phillip J., additional, Airey, David C., additional, Mostafavi, Sara, additional, Yu, Lei, additional, Klein, Hans-Ulrich, additional, Carter, Gregory W., additional, Collier, David A., additional, Golde, Todd E., additional, Levey, Allan I., additional, Bennett, David A., additional, Estrada, Karol, additional, Townsend, T. Matthew, additional, Zhang, Bin, additional, Schadt, Eric, additional, De Jager, Philip L., additional, Price, Nathan D., additional, Ertekin-Taner, Nilüfer, additional, Liu, Zhandong, additional, Shulman, Joshua M., additional, Mangravite, Lara M., additional, and Logsdon, Benjamin A., additional

Published
2020
Full Text
View/download PDF

38. Parental origin of sequence variants associated with complex diseases

Author

Kong, Augustine, Steinthorsdottir, Valgerdur, Masson, Gisli, Thorleifsson, Gudmar, Sulem, Patrick, Besenbacher, Soren, Jonasdottir, Aslaug, Sigurdsson, Asgeir, Th. Kristinsson, Kari, Jonasdottir, Adalbjorg, Frigge, Michael L., Gylfason, Arnaldur, Olason, Pall I., Gudjonsson, Sigurjon A., Sverrisson, Sverrir, Stacey, Simon N., Sigurgeirsson, Bardur, Benediktsdottir, Kristrun R., Sigurdsson, Helgi, Jonsson, Thorvaldur, Benediktsson, Rafn, Olafsson, Jon H., Th. Johannsson, Oskar, Hreidarsson, Astradur B., Sigurdsson, Gunnar, Voight, Benjamin F., Scott, Laura J., Dina, Christian, Zeggini, Eleftheria, Huth, Cornelia, Aulchenko, Yurii S., Welch, Ryan P., McCulloch, Laura J., Ferreira, Teresa, Grallert, Harald, Amin, Najaf, Wu, Guanming, Willer, Cristen J., Raychaudhuri, Soumya, Purcell, Shaun, McCarroll, Steve A., Langenberg, Claudia, Hoffmann, Oliver M., Dupuis, Josée, Qi, Lu, Segrè, Ayellet V., van Hoek, Mandy, Navarro, Pau, Ardlie, Kristin, Balkau, Beverley, Bennett, Amanda J., Blagieva, Roza, Boerwinkle, Eric, Bonnycastle, Lori L., Boström, Kristina Bengtsson, Bravenboer, Bert, Bumpstead, Suzannah, Burtt, Noël P., Charpentier, Guillaume, Chines, Peter S., Cornelis, Marilyn, Couper, David J., Crawford, Gabe, Doney, Alex S. F., Elliott, Katherine S., Elliott, Amanda L., Erdos, Michael R., Fox, Caroline S., Franklin, Christopher S., Ganser, Martha, Gieger, Christian, Grarup, Niels, Green, Todd, Griffin, Simon, Groves, Christopher J., Guiducci, Candace, Hadjadj, Samy, Hassanali, Neelam, Herder, Christian, Isomaa, Bo, Jackson, Anne U., Johnson, Paul R. V., Jørgensen, Torben, Kao, Wen H. L., Klopp, Norman, Kraft, Peter, Kuusisto, Johanna, Lauritzen, Torsten, Li, Man, Lieverse, Alouisius, Lindgren, Cecilia M., Lyssenko, Valeriya, Marre, Michel, Meitinger, Thomas, Midthjell, Kristian, Morken, Mario A, Narisu, Narisu, Nilsson, Peter, Owen, Katharine R., Payne, Felicity, Perry, John R. B., Petersen, Ann-Kristin, Platou, Carl, Proença, Christine, Prokopenko, Inga, Rathmann, Wolfgang, William Rayner, N., Robertson, Neil R., Rocheleau, Ghislain, Roden, Michael, Sampson, Michael J., Saxena, Richa, Shields, Beverley M., Shrader, Peter, Smith, Nicholas, Sparsø, Thomas, Strassburger, Klaus, Stringham, Heather M., Sun, Qi, Swift, Amy J., Thorand, Barbara, Tichet, Jean, Tuomi, Tiinamaija, van Dam, Rob, van Herpt, Thijs, Walters, Bragi G., Weedon, Michael N., Witteman, Jacqueline, Bergman, Richard N., Cauchi, Stephane, Collins, Francis S., Gloyn, Anna L., Gyllensten, Ulf, Hansen, Torben, Hide, Winston A., Hitman, Graham A., Hofman, Albert, Hunter, David, Hveem, Kristian, Laakso, Markku, Mohlke, Karen L., Morris, Andrew D., Palmer, Colin N. A., Pramstaller, Peter P., Rudan, Igor, Sijbrands, Eric, Stein, Lincoln D., Tuomilehto, Jaakko, Uitterlinden, Andre, Walker, Mark, Wareham, Nicholas J., Watanabe, Richard M., Abecasis, Goncalo R., Barroso, Inês, Boehm, Bernhard O., Campbell, Harry, Daly, Mark J., Florez, Jose C., Frayling, Timothy M., Groop, Leif, Hattersley, Andrew T., Hu, Frank B., Meigs, James B., Morris, Andrew P., Pankow, James S., Pedersen, Oluf, Sladek, Rob, Thorsteinsdottir, Unnur, Wichmann, H.-Erich, Wilson, James F., Illig, Thomas, Froguel, Philippe, van Duijn, Cornelia M., Stefansson, Kari, Altshuler, David, Boehnke, Michael, McCarthy, Mark I., Ferguson-Smith, Anne C., and Gudbjartsson, Daniel F.

Published
2009
Full Text
View/download PDF

40. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts*

Author

Yamasaki, Chisato, Murakami, Katsuhiko, Fujii, Yasuyuki, Sato, Yoshiharu, Harada, Erimi, Takeda, Jun-ichi, Taniya, Takayuki, Sakate, Ryuichi, Kikugawa, Shingo, Shimada, Makoto, Tanino, Motohiko, Koyanagi, Kanako O., Barrero, Roberto A., Gough, Craig, Chun, Hong-Woo, Habara, Takuya, Hanaoka, Hideki, Hayakawa, Yosuke, Hilton, Phillip B., Kaneko, Yayoi, Kanno, Masako, Kawahara, Yoshihiro, Kawamura, Toshiyuki, Matsuya, Akihiro, Nagata, Naoki, Nishikata, Kensaku, Noda, Akiko Ogura, Nurimoto, Shin, Saichi, Naomi, Sakai, Hiroaki, Sanbonmatsu, Ryoko, Shiba, Rie, Suzuki, Mami, Takabayashi, Kazuhiko, Takahashi, Aiko, Tamura, Takuro, Tanaka, Masayuki, Tanaka, Susumu, Todokoro, Fusano, Yamaguchi, Kaori, Yamamoto, Naoyuki, Okido, Toshihisa, Mashima, Jun, Hashizume, Aki, Jin, Lihua, Lee, Kyung-Bum, Lin, Yi-Chueh, Nozaki, Asami, Sakai, Katsunaga, Tada, Masahito, Miyazaki, Satoru, Makino, Takashi, Ohyanagi, Hajime, Osato, Naoki, Tanaka, Nobuhiko, Suzuki, Yoshiyuki, Ikeo, Kazuho, Saitou, Naruya, Sugawara, Hideaki, OʼDonovan, Claire, Kulikova, Tamara, Whitfield, Eleanor, Halligan, Brian, Shimoyama, Mary, Twigger, Simon, Yura, Kei, Kimura, Kouichi, Yasuda, Tomohiro, Nishikawa, Tetsuo, Akiyama, Yutaka, Motono, Chie, Mukai, Yuri, Nagasaki, Hideki, Suwa, Makiko, Horton, Paul, Kikuno, Reiko, Ohara, Osamu, Lancet, Doron, Eveno, Eric, Graudens, Esther, Imbeaud, Sandrine, Anne Debily, Marie, Hayashizaki, Yoshihide, Amid, Clara, Han, Michael, Osanger, Andreas, Endo, Toshinori, Thomas, Michael A., Hirakawa, Mika, Makalowski, Wojciech, Nakao, Mitsuteru, Kim, Nam-Soon, Yoo, Hyang-Sook, De Souza, Sandro J., de Fatima Bonaldo, Maria, Niimura, Yoshihito, Kuryshev, Vladimir, Schupp, Ingo, Wiemann, Stefan, Bellgard, Matthew, Shionyu, Masafumi, Jia, Libin, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Wagner, Lukas, Zhang, Qinghua, Go, Mitiko, Minoshima, Shinsei, Ohtsubo, Masafumi, Hanada, Kousuke, Tonellato, Peter, Isogai, Takao, Zhang, Ji, Lenhard, Boris, Kim, Sangsoo, Chen, Zhu, Hinz, Ursula, Estreicher, Anne, Nakai, Kenta, Makalowska, Izabela, Hide, Winston, Tiffin, Nicola, Wilming, Laurens, Chakraborty, Ranajit, Soares, Marcelo Bento, Chiusano, Maria Luisa, Suzuki, Yutaka, Auffray, Charles, Yamaguchi-Kabata, Yumi, Itoh, Takeshi, Hishiki, Teruyoshi, Fukuchi, Satoshi, Nishikawa, Ken, Sugano, Sumio, Nomura, Nobuo, Tateno, Yoshio, Imanishi, Tadashi, and Gojobori, Takashi

Published
2008

43. The LIFEdb database in 2006

Author

Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, del Val, Coral, Arlt, Dorit, Hahne, Florian, Bechtel, Stephanie, Simpson, Jeremy, Hofmann, Oliver, Hide, Winston, Glatting, Karl-Heinz, Huber, Wolfgang, Pepperkok, Rainer, Poustka, Annemarie, and Wiemann, Stefan

Published
2006

45. The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms

Author

Tanino, Motohiko, Debily, Marie-Anne, Tamura, Takuro, Hishiki, Teruyoshi, Ogasawara, Osamu, Murakawa, Katsuji, Kawamoto, Shoko, Itoh, Kouichi, Watanabe, Shinya, de Souza, Sandro José, Imbeaud, Sandrine, Graudens, Esther, Eveno, Eric, Hilton, Phillip, Sudo, Yukio, Kelso, Janet, Ikeo, Kazuho, Imanishi, Tadashi, Gojobori, Takashi, Auffray, Charles, Hide, Winston, and Okubo, Kousaku

Published
2005

46. Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set

Author

VanBuren, Vincent, Piao, Yulan, Dudekula, Dawood B., Qian, Yong, Carter, Mark G., Martin, Patrick R., Stagg, Carole A., Bassey, Uwem C., Aiba, Kazuhiro, Hamatani, Toshio, Kargul, George J., Luo, Amber G., Kelso, Janet, Hide, Winston, and Ko, Minoru S. H.

Subjects
Genomes -- Research, Cloning -- Genetic aspects, DNA -- Genetic aspects, Stem cells -- Genetic aspects, Health
Abstract

Research has been conducted on 7407 cDNA clone set from early mouse embryos derived from different stem cell lines. The development of this clone set which represents genes transcribed in stem cells and embryonic and newborn organ cell types is described.

Published
2002

47. Is the guinea-pig a rodent?

Author

Graur, Dan, Hide, Winston A., and Li, Wen-Hsiung

Subjects
Guinea pigs -- Physiological aspects, Rodents -- Physiological aspects, Zoology -- Identification and classification, Environmental issues, Science and technology, Zoology and wildlife conservation
Published
1991

49. Targeted genetic screen in amyotrophic lateral sclerosis reveals novel genetic variants with synergistic effect on clinical phenotype

Author

Cooper-Knock, Johnathan, Robins, Henry, Niedermoser, Isabell, Wyles, Matthew, Heath, Paul R., Higginbottom, Adrian, Walsh, Theresa, Kazoka, Mbombe, Al Kheifat, Ahmad, Al-Chalabi, Ammar, Basak, Nazli, Blair, Ian, Dekker, Annelot, Hardiman, Orla, Hide, Winston, Iacoangeli, Alfredo, Kenna, Kevin, Landers, John, McLaughlin, Russel, Mill, Jonathan, Middelkoop, Bas, Moisse, Mattieu, Pardina, Jesus Mora, Morrison, Karen, Newhouse, Stephen, Pulit, Sara, Shatunov, Aleksey, Shaw, Chris, Sproviero, William, Tazelaar, Gijs, van Damme, Philip, van den Berg, Leonard, van der Spek, Rick, Eijk, Kristelvan, van Es, Michael, van Rheenen, Wouter, van Vugt, Joke, Veldink, Jan, Kooyman, Maarten, Glass, Jonathan, Robberecht, Wim, Gotkine, Marc, Drory, Vivian, Kiernan, Matthew, Neto, Miguel Mitne, Ztaz, Mayana, Couratier, Philippe, Corcia, Philippe, Silani, Vincenzo, Chio, Adriano, and Project MinE ALS Sequencing Consortium

Subjects
Oligogenic inheritance, Cellular and Molecular Neuroscience, C9ORF72, DNA sequencing, RNA binding proteins, Amyotrophic lateral sclerosis, Molecular Biology
Abstract

Amyotrophic lateral sclerosis (ALS) is underpinned by an oligogenic rare variant architecture. Identified genetic variants of ALS include RNA-binding proteins containing prion-like domains (PrLDs). We hypothesized that screening genes encoding additional similar proteins will yield novel genetic causes of ALS. The most common genetic variant of ALS patients is a G4C2-repeat expansion within C9ORF72. We have shown that G4C2-repeat RNA sequesters RNA-binding proteins. A logical consequence of this is that loss-of-function mutations in G4C2-binding partners might contribute to ALS pathogenesis independently of and/or synergistically with C9ORF72 expansions. Targeted sequencing of genomic DNA encoding either RNA-binding proteins or known ALS genes (n = 274 genes) was performed in ALS patients to identify rare deleterious genetic variants and explore genotype-phenotype relationships. Genomic DNA was extracted from 103 ALS patients including 42 familial ALS patients and 61 young-onset (average age of onset 41 years) sporadic ALS patients; patients were chosen to maximize the probability of identifying genetic causes of ALS. Thirteen patients carried a G4C2-repeat expansion of C9ORF72. We identified 42 patients with rare deleterious variants; 6 patients carried more than one variant. Twelve mutations were discovered in known ALS genes which served as a validation of our strategy. Rare deleterious variants in RNA-binding proteins were significantly enriched in ALS patients compared to control frequencies (p = 5.31E-18). Nineteen patients featured at least one variant in a RNA-binding protein containing a PrLD. The number of variants per patient correlated with rate of disease progression (t-test, p = 0.033). We identified eighteen patients with a single variant in a G4C2-repeat binding protein. Patients with a G4C2-binding protein variant in combination with a C9ORF72 expansion had a significantly faster disease course (t-test, p = 0.025). Our data are consistent with an oligogenic model of ALS. We provide evidence for a number of entirely novel genetic variants of ALS caused by mutations in RNA-binding proteins. Moreover we show that these mutations act synergistically with each other and with C9ORF72 expansions to modify the clinical phenotype of ALS. A key finding is that this synergy is present only between functionally interacting variants. This work has significant implications for ALS therapy development.

Published
2017

50. Immunotherapy for breast cancer using EpCAM aptamer tumor-targeted gene knockdown.

Author

Ying Zhang, Xuemei Xie, Yeganeh, Pourya Naderi, Dian-Jang Lee, Valle-Garcia, David, Meza-Sosa, Karla F., Junqueira, Caroline, Jiayu Su, Hongbo R. Luo, Hide, Winston, and Lieberman, Judy

Subjects
GENES, CELL adhesion molecules, APTAMERS, BREAST cancer, ANTIGEN presentation, CURCUMIN
Abstract

New strategies for cancer immunotherapy are needed since most solid tumors do not respond to current approaches. Here we used epithelial cell adhesion molecule EpCAM (a tumor-associated antigen highly expressed on common epithelial cancers and their tumor-initiating cells) aptamer-linked small-interfering RNA chimeras (AsiCs) to knock down genes selectively in EpCAM+ tumors with the goal of making cancers more visible to the immune system. Knockdown of genes that function in multiple steps of cancer immunity was evaluated in aggressive triple-negative and HER2+ orthotopic, metastatic, and genetically engineered mouse breast cancer models. Gene targets were chosen whose knockdown was predicted to promote tumor neoantigen expression (Upf2, Parp1, Apex1), phagocytosis, and antigen presentation (Cd47), reduce checkpoint inhibition (Cd274), or cause tumor cell death (Mcl1). Four of the six AsiC (Upf2, Parp1, Cd47, and Mcl1) potently inhibited tumor growth and boosted tumor-infiltrating immune cell functions. AsiC mixtures were more effective than individual AsiC and could synergize with anti-PD-1 checkpoint inhibition. [ABSTRACT FROM AUTHOR]

Published
2021
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results