Guidelines for reporting single-cell RNA-Seq experiments

Authors: Füllgrabe, Anja, George, Nancy, Green, Matthew, Nejad, Parisa, Aronow, Bruce, Clarke, Laura, Fexova, Silvie Korena, Fischer, Clay, Freeberg, Mallory Ann, Huerta, Laura, Morrison, Norman, Scheuermann, Richard H., Taylor, Deanne, Vasilevsky, Nicole, Gehlenborg, Nils, Marioni, John, Teichmann, Sarah, Brazma, Alvis, Papatheodorou, Irene

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1910.14623

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Authors: Abbott, Kristin M., Banka, Siddharth, de Boer, Elke, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Denommé-Pichon, Anne-Sophie, Faivre, Laurence, Gilissen, Christian, Haack, Tobias B., Havlovicova, Marketa, Hoischen, Alexander, Jackson, Adam, Kerstjens, Mieke, Kleefstra, Tjitske, Martín, Estrella López, Macek, Milan, Jr., Matalonga, Leslie, Maystadt, Isabelle, Morleo, Manuela, Nigro, Vicenzo, Pinelli, Michele, Pizzi, Simone, Posada, Manuel, Radio, Francesca C., Renieri, Alessandra, Riess, Olaf, Rooryck, Caroline, Ryba, Lukas, Agathe, Jean-Madeleine de Sainte, Santen, Gijs W.E., Schwarz, Martin, Tartaglia, Marco, Thauvin, Christel, Torella, Annalaura, Trimouille, Aurélien, Verloes, Alain, Vissers, Lisenka, Vitobello, Antonio, Votypka, Pavel, Zguro, Kristina, Boer, Elke de, Cohen, Enzo, Danis, Daniel, Gao, Fei, Horvath, Rita, Johari, Mridul, Johanson, Lennart, Li, Shuang, Morsy, Heba, Nelson, Isabelle, Paramonov, Ida, te Paske, Iris B.A.W., Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, van der Velde, Joeri K., Vandrovcova, Jana, Graessner, Holm, Zurek, Birte, Ellwanger, Kornelia, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, ‘t Hoen, Peter A.C., Vissers, Lisenka E.L.M., Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, Paske, Iris te, Janssen, Erik, Steehouwer, Marloes, Yaldiz, Burcu, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Alexander, Elizabeth, Duffourd, Yannis, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Ben Yaou, Rabah, Metay, Corinne, Eymard, Bruno, Atalaia, Antonio, Stojkovic, Tanya, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Lišková, Petra, Doležalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Efthymiou, Stephanie, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Varavallo, Alessandra, Banfi, Sandro, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A., Johansson, Lennart, van der Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Kerstjens Frederikse, Wilhemina S., Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, Lacombe, Didier, Trimouille, Aurelien, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Hackman, Peter, Udd, Bjarne, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Osorio, Andrés Nascimento, Depienne, Christel, Roos, Andreas, Cordts, Isabell, Deschauer, Marcus, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Başak, Ayşe Nazlı, Claeys, Kristl, Boztug, Kaan, Haimel, Matthias, W.E, Gijs, Ruivenkamp, Claudia A.L., Natera de Benito, Daniel, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Radio, Francesca Clementina, Balicza, Peter, Molnar, Maria Judit, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Delgado, Beatriz Martínez, Alonso García de la Rosa, F. Javier, Schröck, Evelin, Rump, Andreas, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Chinnery, Patrick F., Ratnaike, Thiloka, Schon, Katherine, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, May, Patrick, Beeson, David, Cossins, Judith, Furini, Simone, Fallerini, Chiara, Benetti, Elisa, Afenjar, Alexandra, Goldenberg, Alice, Masurel, Alice, Phan, Alice, Dieux-Coeslier, Anne, Fargeot, Anne, Guerrot, Anne-Marie, Toutain, Annick, Molin, Arnaud, Sorlin, Arthur, Putoux, Audrey, Jouret, Béatrice, Laudier, Béatrice, Demeer, Bénédicte, Doray, Bérénice, Bonniaud, Bertille, Isidor, Bertrand, Gilbert-Dussardier, Brigitte, Leheup, Bruno, Reversade, Bruno, Paul, Carle, Vincent-Delorme, Catherine, Neiva, Cecilia, Poirsier, Céline, Quélin, Chloé, Chiaverini, Christine, Coubes, Christine, Francannet, Christine, Colson, Cindy, Desplantes, Claire, Wells, Constance, Goizet, Cyril, Sanlaville, Damien, Amram, Daniel, Lehalle, Daphné, Geneviève, David, Gaillard, Dominique, Zivi, Einat, Sarrazin, Elisabeth, Steichen, Elisabeth, Schaefer, Élise, Lacaze, Elodie, Jacquemin, Emmanuel, Bongers, Ernie, Kilic, Esra, Colin, Estelle, Giuliano, Fabienne, Prieur, Fabienne, Laffargue, Fanny, Morice-Picard, Fanny, Petit, Florence, Cartault, François, Feillet, François, Baujat, Geneviève, Morin, Gilles, Diene, Gwenaëlle, Journel, Hubert, Perthus, Isabelle, Lespinasse, James, Alessandri, Jean-Luc, Amiel, Jeanne, Martinovic, Jelena, Delanne, Julian, Albuisson, Juliette, Lambert, Laëtitia, Perrin, Laurence, Ousager, Lilian Bomme, Van Maldergem, Lionel, Pinson, Lucile, Ruaud, Lyse, Samimi, Mahtab, Bournez, Marie, Bonnet-Dupeyron, Marie Noëlle, Vincent, Marie, Jacquemont, Marie-Line, Cordier-Alex, Marie-Pierre, Gérard-Blanluet, Marion, Willems, Marjolaine, Spodenkiewicz, Marta, Doco-Fenzy, Martine, Rossi, Massimiliano, Renaud, Mathilde, Fradin, Mélanie, Mathieu, Michèle, Holder-Espinasse, Muriel H., Houcinat, Nada, Hanna, Nadine, Leperrier, Nathalie, Chassaing, Nicolas, Philip, Nicole, Boute, Odile, Van Kien, Philippe Khau, Parent, Philippe, Bitoun, Pierre, Sarda, Pierre, Vabres, Pierre, Jouk, Pierre-Simon, Touraine, Renaud, El Chehadeh, Salima, Whalen, Sandra, Marlin, Sandrine, Passemard, Sandrine, Grotto, Sarah, Bellanger, Séverine Audebert, Blesson, Sophie, Nambot, Sophie, Naudion, Sophie, Lyonnet, Stanislas, Odent, Sylvie, Attie-Bitach, Tania, Busa, Tiffany, Drouin-Garraud, Valérie, Layet, Valérie, Bizaoui, Varoona, Cusin, Véronica, Capri, Yline, Alembik, Yves, Jean-Marçais, Nolwenn, López-Martín, Estrella, Macek, Milan, Mencarelli, Maria Antonietta, Moutton, Sébastien, Pfundt, Rolph, Safraou, Hana, Thauvin-Robinet, Christel, Thevenon, Julien, Tran Mau-Them, Frédéric, de Vries, Bert B.A., Willemsen, Marjolein H., Philippe, Christophe

Source: In Genetics in Medicine April 2023 25(4)

Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases

Authors: Corvò, Alberto, Matalonga, Leslie, Spalding, Dylan, Senf, Alexander, Laurie, Steven, Picó-Amador, Daniel, Fernandez-Callejo, Marcos, Paramonov, Ida, Romero, Anna Foix, Garcia-Rios, Emilio, Ciges, Jorge Izquierdo, Mohan, Anand, Thomas, Coline, Silva Valencia, Andres Felipe, Halmagyi, Csaba, Freeberg, Mallory Ann, Töpf, Ana, Horvath, Rita, Saunders, Gary, Gut, Ivo, Keane, Thomas, Piscia, Davide, Beltran, Sergi

Source: In Cell Genomics 8 February 2023 3(2)

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024.

Authors: Thakur, Matthew, Brooksbank, Catherine, Finn, Robert D, Firth, Helen V, Foreman, Julia, Freeberg, Mallory, Gurwitz, Kim T, Harrison, Melissa, Hulcoop, David, Hunt, Sarah E, R. Leach, Andrew, Levchenko, Mariia, Marques, Diana, McDonagh, Ellen M, Mithani, Aziz, Parkinson, Helen, Perez-Riverol, Yasset, Perova, Zinaida, Sarkans, Ugis, Tirunagari, Santosh

Source: Nucleic Acids Research; 1/6/2025, Vol. 53 Issue D1, pD10-D19, 10p

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Authors: Rehm, Heidi L., Page, Angela J.H., Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J.S., Beck, Tim, Beckmann, Jacques S., Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K., Boughtwood, Tiffany F., Bourque, Guillaume, Bowers, Sarion R., Brookes, Anthony J., Brudno, Michael, Brush, Matthew H., Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, L. Jonathan, Dyke, Stephanie O.M., Eddy, James A., Eilbeck, Karen, Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M., Ho, Calvin W.L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jené, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J.M., Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M., Kekesi-Lafrance, Kristina, Kelleher, Jerome, Kerry, Giselle, Khor, Seik-Soon, Knoppers, Bartha M., Konopko, Melissa A., Kosaki, Kenjiro, Kuba, Martin, Lawson, Jonathan, Leinonen, Rasko, Li, Stephanie, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Liyanage, Isuru Udara, Lopez, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Metke-Jimenez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Munoz-Torres, Monica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Ota Wang, Vivian, Paglione, Laura A.D., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Rodriguez, Laura Lyman, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos, Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Guimera, Roman Valls, Vamathevan, Jessica, Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, North, Kathryn, Birney, Ewan

Source: In Cell Genomics 10 November 2021 1(2)

The Data Use Ontology to streamline responsible access to human biomedical datasets

Authors: Lawson, Jonathan, Cabili, Moran N., Kerry, Giselle, Boughtwood, Tiffany, Thorogood, Adrian, Alper, Pinar, Bowers, Sarion R., Boyles, Rebecca R., Brookes, Anthony J., Brush, Matthew, Burdett, Tony, Clissold, Hayley, Donnelly, Stacey, Dyke, Stephanie O.M., Freeberg, Mallory A., Haendel, Melissa A., Hata, Chihiro, Holub, Petr, Jeanson, Francis, Jene, Aina, Kawashima, Minae, Kawashima, Shuichi, Konopko, Melissa, Kyomugisha, Irene, Li, Haoyuan, Linden, Mikael, Rodriguez, Laura Lyman, Morita, Mizuki, Mulder, Nicola, Muller, Jean, Nagaie, Satoshi, Nasir, Jamal, Ogishima, Soichi, Ota Wang, Vivian, Paglione, Laura D., Pandya, Ravi N., Parkinson, Helen, Philippakis, Anthony A., Prasser, Fabian, Rambla, Jordi, Reinold, Kathy, Rushton, Gregory A., Saltzman, Andrea, Saunders, Gary, Sofia, Heidi J., Spalding, John D., Swertz, Morris A., Tulchinsky, Ilia, van Enckevort, Esther J., Varma, Susheel, Voisin, Craig, Yamamoto, Natsuko, Yamasaki, Chisato, Zass, Lyndon, Guidry Auvil, Jaime M., Nyrönen, Tommi H., Courtot, Mélanie

Source: In Cell Genomics 10 November 2021 1(2)

The Federated European Genome–Phenome Archive as a global network for sharing human genomics data

Authors: D’Altri, Teresa, Freeberg, Mallory Ann, Curwin, Amy J., Alonso, Ana, Freitas, Ana T., Capella-Gutierrez, Salvador, Gadelha, Luiz, Hagwall, Anna, Hovig, Eivind, Kerry, Giselle, Kirli, Koray, Kochel, Krzysztof, Kohlbacher, Oliver, Korbel, Jan O., Leinonen, Jaakko, Marciniak, Blazej, Oliveira, Jorge S., Petersen, Kjell, Silva, Mário J., Stegle, Oliver, Valencia, Alfonso, Viklund, Johan, Guigo, Roderic, Parkinson, Helen, Navarro, Arcadi, Rambla, Jordi, Keane, Thomas M.

Source: Nature Genetics; March 2025, Vol. 57 Issue: 3 p481-485, 5p

Sharing sensitive data in life sciences: an overview of centralized and federated approaches.

Authors: Rujano, Maria A¹, Boiten, Jan-Willem², Ohmann, Christian¹, Canham, Steve¹, Contrino, Sergio¹, David, Romain³, Ewbank, Jonathan³, Filippone, Claudia³, Connellan, Claire³, Custers, Ilse², Nuland, Rick van², Mayrhofer, Michaela Th⁴, Holub, Petr⁴, Álvarez, Eva García⁴, Bacry, Emmanuel⁵, Hughes, Nigel⁶, Freeberg, Mallory A⁷, Schaffhauser, Birgit⁸, Wagener, Harald⁹, Sánchez-Pla, Alex¹⁰

Source: Briefings in Bioinformatics; Jul2024, Vol. 25 Issue 4, p1-16, 16p

Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress

Authors: Jin, Meiyan, Fuller, Gregory G., Han, Ting, Yao, Yao, Alessi, Amelia F., Freeberg, Mallory A., Roach, Nathan P., Moresco, James J., Karnovsky, Alla, Baba, Misuzu, Yates, John R., III, Gitler, Aaron D., Inoki, Ken, Klionsky, Daniel J., Kim, John K.

Source: In Cell Reports 25 July 2017 20(4):895-908

MORC-1 Integrates Nuclear RNAi and Transgenerational Chromatin Architecture to Promote Germline Immortality

Authors: Weiser, Natasha E., Yang, Danny X., Feng, Suhua, Kalinava, Natallia, Brown, Kristen C., Khanikar, Jayshree, Freeberg, Mallory A., Snyder, Martha J., Csankovszki, Györgyi, Chan, Raymond C., Gu, Sam G., Montgomery, Taiowa A., Jacobsen, Steven E., Kim, John K.

Source: In Developmental Cell 22 May 2017 41(4):408-423

An interconnected data infrastructure to support large-scale rare disease research.

Authors: Johansson, Lennart F, Laurie, Steve, Spalding, Dylan, Gibson, Spencer, Ruvolo, David, Thomas, Coline, Piscia, Davide, de Andrade, Fernanda, Been, Gerieke, Bijlsma, Marieke, Brunner, Han, Cimerman, Sandi, Dizjikan, Farid Yavari, Ellwanger, Kornelia, Fernandez, Marcos, Freeberg, Mallory, van de Geijn, Gert-Jan, Kanninga, Roan, Maddi, Vatsalya, Mehtarizadeh, Mehdi

Source: GigaScience; 2024, Vol. 13 Issue 1, p1-14, 14p

Subject Terms: COMPUTATIONAL biology, RARE diseases, NUCLEOTIDE sequencing, MULTIOMICS, GENETICS, METADATA

Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box RNA helicase CGH-1

Authors: Alessi, Amelia F., Khivansara, Vishal, Han, Ting, Freeberg, Mallory A., Moresco, James J., Tu, Patricia G., Montoye, Eric, Yates, John R., Karp, Xantha, Kim, John K.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2015 Dec . 112(52), E7213-E7222.

Access URL: https://www.jstor.org/stable/26466292

Transcriptional Regulation by Pho23 Modulates the Frequency of Autophagosome Formation

Authors: Jin, Meiyan, He, Ding, Backues, Steven K., Freeberg, Mallory A., Liu, Xu, Kim, John K., Klionsky, Daniel J.

Source: In Current Biology 16 June 2014 24(12):1314-1322

Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Bioinformatic Analysis

Authors: Freeberg, Mallory A., Kim, John K.

Source: Methods in molecular biology. 1361:91-104

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN603615177&indx=1&recIds=ETOCRN603615177

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.

Authors: Thakur, Matthew, Bateman, Alex, Brooksbank, Cath, Freeberg, Mallory, Harrison, Melissa, Hartley, Matthew, Keane, Thomas, Kleywegt, Gerard, Leach, Andrew, Levchenko, Mariia, Morgan, Sarah, McDonagh, Ellen M, Orchard, Sandra, Papatheodorou, Irene, Velankar, Sameer, Vizcaino, Juan Antonio, Witham, Rick, Zdrazil, Barbara, McEntyre, Johanna

Source: Nucleic Acids Research; 1/6/2023, Vol. 51 Issue D1, pD9-D17, 9p

Computational Analysis of the Post-Transcriptional Gene Regulatory Network

Authors: Freeberg, Mallory Ann., University of Michigan. Library. Deep Blue.

Access URL: http://hdl.handle.net/2027/mdp.39015089716164

European Genome-phenome Archive in 2021.

Authors: Freeberg, Mallory Ann, Fromont, Lauren A, D'Altri, Teresa, Romero, Anna Foix, Ciges, Jorge Izquierdo, Jene, Aina, Kerry, Giselle, Moldes, Mauricio, Ariosa, Roberto, Bahena, Silvia, Barrowdale, Daniel, Barbero, Marcos Casado, Fernandez-Orth, Dietmar, Garcia-Linares, Carles, Garcia-Rios, Emilio, Haziza, Frédéric, Juhasz, Bela, Llobet, Oscar Martinez, Milla, Gemma, Mohan, Anand

Source: Nucleic Acids Research; 1/7/2022, Vol. 50 Issue D1, pD980-D987, 8p

Community-Driven Data Analysis Training for Biology

Authors: Batut, Bérénice, Hiltemann, Saskia, Bagnacani, Andrea, Baker, Dannon, Bhardwaj, Vivek, Blank, Clemens, Bretaudeau, Anthony, Brillet-Guéguen, Loraine, Čech, Martin, Chilton, John, Clements, Dave, Doppelt-Azeroual, Olivia, Erxleben, Anika, Freeberg, Mallory Ann, Gladman, Simon, Hoogstrate, Youri, Hotz, Hans-Rudolf, Houwaart, Torsten, Jagtap, Pratik, Larivière, Delphine, Le Corguillé, Gildas, Manke, Thomas, Mareuil, Fabien, Ramírez, Fidel, Ryan, Devon, Sigloch, Florian Christoph, Soranzo, Nicola, Wolff, Joachim, Videm, Pavankumar, Wolfien, Markus, Wubuli, Aisanjiang, Yusuf, Dilmurat, Taylor, James, Backofen, Rolf, Nekrutenko, Anton, Grüning, Björn

Source: In Cell Systems 27 June 2018 6(6):752-758

Glycolysis enzymes coalesce in G bodies in hypoxia nucleated by RNA

Authors: Fuller, Gregory, Freeberg, Mallory, Han, Ting, Kim, John

Source: FASEB journal. 34(S1):1-1

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100140397421.0x000001&indx=1&recIds=ETOCvdc_100140397421.0x000001

A Conserved Upstream Motif Orchestrates Autonomous, Germline-Enriched Expression of Caenorhabditis elegans piRNAs.

Authors: Billi, Allison C.^1,2, Freeberg, Mallory A.^1,3, Day, Amanda M.^1,4, Sang Young Chun^1,2, Khivansara, Vishal¹, Kim, John K.^1,4 jnkim@umich.edu

Source: PLoS Genetics. Mar2013, Vol. 9 Issue 3, Special section p1-17. 17p. 2 Diagrams, 1 Chart, 4 Graphs.

Subject Terms: *CAENORHABDITIS elegans, *NUCLEOTIDES, *GERM cells, *NUCLEOTIDE sequence