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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
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7. 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
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8. 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

9. 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

11. 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
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12. 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

14. 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
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17. 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
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18. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

Author

Pita-Juarez, Yered, primary, Karagkouni, Dimitra, additional, Kalavros, Nikolaos, additional, Melms, Johannes C., additional, Niezen, Sebastian, additional, Delorey, Toni M., additional, Essene, Adam L, additional, Brook, Olga R., additional, Pant, Deepti, additional, Skelton-Badlani, Disha, additional, Naderi, Pourya, additional, Huang, Pinzhu, additional, Pan, Liuliu, additional, Hether, Tyler, additional, Andrews, Tallulah S., additional, Ziegler, Carly G.K., additional, Reeves, Jason, additional, Myloserdnyy, Andriy, additional, Chen, Rachel, additional, Nam, Andy, additional, Phelan, Stefan, additional, Liang, Yan, additional, Amin, Amit Dipak, additional, Biermann, Jana, additional, Hibshoosh, Hanina, additional, Veregge, Molly, additional, Kramer, Zachary, additional, Jacobs, Christopher, additional, Yalcin, Yusuf, additional, Phillips, Devan, additional, Slyper, Michal, additional, Subramanian, Ayshwarya, additional, Ashenberg, Orr, additional, Bloom-Ackermann, Zohar, additional, Tran, Victoria M., additional, Gomez, James, additional, Sturm, Alexander, additional, Zhang, Shuting, additional, Fleming, Stephen J., additional, Warren, Sarah, additional, Beechem, Joseph, additional, Hung, Deborah, additional, Babadi, Mehrtash, additional, Padera, Robert F., additional, MacParland, Sonya A., additional, Bader, Gary D., additional, Imad, Nasser, additional, Solomon, Isaac H., additional, Miller, Eric, additional, Riedel, Stefan, additional, Porter, Caroline B.M., additional, Villani, Alexandra-Chloé, additional, Tsai, Linus T.-Y., additional, Hide, Winston, additional, Szabo, Gyongyi, additional, Hecht, Jonathan, additional, Rozenblatt-Rosen, Orit, additional, Shalek, Alex K., additional, Izar, Benjamin, additional, Regev, Aviv, additional, Popov, Yury, additional, Jiang, Z. Gordon, additional, and Vlachos, Ioannis S., additional

Published
2022
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25. 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

26. 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
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29. The S-Star Trial Bioinformatics Course: An On-line Learning Success

Author

Lim, Yun Ping, Hoog, Jan-Olov, Gardner, Phyllis, Ranganathan, Shoba, Andersson, Siv, Subbiah, Subramanian, Tan, Tin Wee, Hide, Winston, and Weiss, Anthony S.

Abstract

The S-Star Trial Bioinformatics on-line course (www.s-star.org) is a global experiment in bioinformatics distance education. Six universities from five continents have participated in this project. One hundred and fifty students participated in the first trial course of which 96 followed through the entire course and 70 fulfilled the overall course requirements. The course was built up of 12 lectures covering different basic and advanced topics within bioinformatics. The lectures consist of streaming video and synchronized slides with follow-up discussion forums and a final assessment. It draws on experts from diverse institutions to share their teaching expertise and resources via distance learning. A major goal of S-Star is to provide free introductory web-based education. Here we present the outline of the course, experiences from a global collaboration, and feedback from the first trial of the on-line S-Star course. (Contains 2 tables, 1 figure and 1 footnote.)

Published
2003
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30. 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
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32. 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
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34. 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
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37. 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

38. 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
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41. 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
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42. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Author

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

Published
2021
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43. 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

44. 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

45. Whole-genome sequencing reveals new Alzheimer’s disease-associated rare variants in loci related to synaptic function and neuronal development

Author

Prokopenko, Dmitry, primary, Morgan, Sarah L., additional, Mullin, Kristina, additional, Hofmann, Oliver, additional, Chapman, Brad, additional, Kirchner, Rory, additional, Amberkar, Sandeep, additional, Wohlers, Inken, additional, Lange, Christoph, additional, Hide, Winston, additional, Bertram, Lars, additional, and Tanzi, Rudolph E., additional

Published
2020
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46. Aβ-accelerated neurodegeneration caused by Alzheimer’s-associated ACE variant R1279Q is rescued by angiotensin system inhibition in mice

Author

Cuddy, Leah K., primary, Prokopenko, Dmitry, additional, Cunningham, Eric P., additional, Brimberry, Ross, additional, Song, Peter, additional, Kirchner, Rory, additional, Chapman, Brad A., additional, Hofmann, Oliver, additional, Hide, Winston, additional, Procissi, Daniele, additional, Hanania, Taleen, additional, Leiser, Steven C., additional, Tanzi, Rudolph E, additional, and Vassar, Robert, additional

Published
2020
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