Polygenic risk scores: a biased prediction?

por De La Vega, Francisco M., Bustamante, Carlos D.
Publicado 2018

Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes

por Shringarpure, Suyash S., Carroll, Andrew, De La Vega, Francisco M., Bustamante, Carlos D.
Publicado 2015

A deep-learning-based RNA-seq germline variant caller

por Cook, Daniel E, Venkat, Aarti, Yelizarov, Dennis, Pouliot, Yannick, Chang, Pi-Chuan, Carroll, Andrew, De La Vega, Francisco M
Publicado 2023

Identifying Selected Regions from Heterozygosity and Divergence Using a Light-Coverage Genomic Dataset from Two Human Populations

por Oleksyk, Taras K., Zhao, Kai, De La Vega, Francisco M., Gilbert, Dennis A., O'Brien, Stephen J., Smith, Michael W.
Publicado 2008

Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples

por Kidd, Judith R, Friedlaender, Françoise R, Speed, William C, Pakstis, Andrew J, De La Vega, Francisco M, Kidd, Kenneth K
Publicado 2011

The Transcriptomes of Two Heritable Cell Types Illuminate the Circuit Governing Their Differentiation

por Tuch, Brian B., Mitrovich, Quinn M., Homann, Oliver R., Hernday, Aaron D., Monighetti, Cinna K., De La Vega, Francisco M., Johnson, Alexander D.
Publicado 2010

Clinical Pertinence Metric Enables Hypothesis-Independent Genome-Phenome Analysis for Neurologic Diagnosis

por Segal, Michael M., Abdellateef, Mostafa, El-Hattab, Ayman W., Hilbush, Brian S., De La Vega, Francisco M., Tromp, Gerard, Williams, Marc S., Betensky, Rebecca A., Gleeson, Joseph
Publicado 2015

Nucleosome regulatory dynamics in response to TGFβ

por Enroth, Stefan, Andersson, Robin, Bysani, Madhusudhan, Wallerman, Ola, Termén, Stefan, Tuch, Brian B., De La Vega, Francisco M., Heldin, Carl-Henrik, Moustakas, Aristidis, Komorowski, Jan, Wadelius, Claes
Publicado 2014

Genome sequencing and analysis of admixed genomes of African and Mexican ancestry: implications for personal ancestry reconstruction and multi-ethnic medical genomics

por De La Vega, Francisco M, Bryc, Katarzyna, Degehnardt, Jeremiah D, Musharoff, Shaila, Kidd, Jeffrey M, Seth, Vrunda, Stanley, Sarah, Brisbin, Abra, Keinan, Alon, Clark, Andrew, Bustamante, Carlos D
Publicado 2010

Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data

por Shringarpure, Suyash S, Mathias, Rasika A, Hernandez, Ryan D, O’Connor, Timothy D, Szpiech, Zachary A, Torres, Raul, De La Vega, Francisco M, Bustamante, Carlos D, Barnes, Kathleen C, Taub, Margaret A
Publicado 2017

A robust targeted sequencing approach for low input and variable quality DNA from clinical samples

por So, Austin P., Vilborg, Anna, Bouhlal, Yosr, Koehler, Ryan T., Grimes, Susan M., Pouliot, Yannick, Mendoza, Daniel, Ziegle, Janet, Stein, Jason, Goodsaid, Federico, Lucero, Michael Y., De La Vega, Francisco M., Ji, Hanlee P.
Publicado 2018

An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels

por Nassir, Rami, Kosoy, Roman, Tian, Chao, White, Phoebe A, Butler, Lesley M, Silva, Gabriel, Kittles, Rick, Alarcon-Riquelme, Marta E, Gregersen, Peter K, Belmont, John W, De La Vega, Francisco M, Seldin, Michael F
Publicado 2009

An open resource for accurately benchmarking small variant and reference calls

por Zook, Justin M., McDaniel, Jennifer, Olson, Nathan D., Wagner, Justin, Parikh, Hemang, Heaton, Haynes, Irvine, Sean A., Trigg, Len, Truty, Rebecca, McLean, Cory Y., De La Vega, Francisco M., Xiao, Chunlin, Sherry, Stephen, Salit, Marc
Publicado 2019

Molecular profiling of a real-world breast cancer cohort with genetically inferred ancestries reveals actionable tumor biology differences between European ancestry and African anc...

por Miyashita, Minoru, Bell, Joshua S. K., Wenric, Stephane, Karaesmen, Ezgi, Rhead, Brooke, Kase, Matthew, Kaneva, Kristiyana, De La Vega, Francisco M., Zheng, Yonglan, Yoshimatsu, Toshio F., Khramtsova, Galina, Liu, Fang, Zhao, Fangyuan, Howard, Frederick M., Nanda, Rita, Beaubier, Nike, White, Kevin P., Huo, Dezheng, Olopade, Olufunmilayo I.
Publicado 2023

The status of the human gene catalogue

por Amaral, Paulo, Carbonell-Sala, Silvia, De La Vega, Francisco M., Faial, Tiago, Frankish, Adam, Gingeras, Thomas, Guigo, Roderic, Harrow, Jennifer L, Hatzigeorgiou, Artemis G., Johnson, Rory, Murphy, Terence D., Pertea, Mihaela, Pruitt, Kim D., Pujar, Shashikant, Takahashi, Hazuki, Ulitsky, Igor, Varabyou, Ales, Wells, Christine A., Yandell, Mark, Carninci, Piero, Salzberg, Steven L.
Publicado 2023

Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations

por Tuch, Brian B., Laborde, Rebecca R., Xu, Xing, Gu, Jian, Chung, Christina B., Monighetti, Cinna K., Stanley, Sarah J., Olsen, Kerry D., Kasperbauer, Jan L., Moore, Eric J., Broomer, Adam J., Tan, Ruoying, Brzoska, Pius M., Muller, Matthew W., Siddiqui, Asim S., Asmann, Yan W., Sun, Yongming, Kuersten, Scott, Barker, Melissa A., De La Vega, Francisco M., Smith, David I.
Publicado 2010

Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

por De La Vega, Francisco M., Chowdhury, Shimul, Moore, Barry, Frise, Erwin, McCarthy, Jeanette, Hernandez, Edgar Javier, Wong, Terence, James, Kiely, Guidugli, Lucia, Agrawal, Pankaj B., Genetti, Casie A., Brownstein, Catherine A., Beggs, Alan H., Löscher, Britt-Sabina, Franke, Andre, Boone, Braden, Levy, Shawn E., Õunap, Katrin, Pajusalu, Sander, Huentelman, Matt, Ramsey, Keri, Naymik, Marcus, Narayanan, Vinodh, Veeraraghavan, Narayanan, Billings, Paul, Reese, Martin G., Yandell, Mark, Kingsmore, Stephen F.
Publicado 2021

An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases

por Owen, Mallory J., Lefebvre, Sebastien, Hansen, Christian, Kunard, Chris M., Dimmock, David P., Smith, Laurie D., Scharer, Gunter, Mardach, Rebecca, Willis, Mary J., Feigenbaum, Annette, Niemi, Anna-Kaisa, Ding, Yan, Van Der Kraan, Luca, Ellsworth, Katarzyna, Guidugli, Lucia, Lajoie, Bryan R., McPhail, Timothy K., Mehtalia, Shyamal S., Chau, Kevin K., Kwon, Yong H., Zhu, Zhanyang, Batalov, Sergey, Chowdhury, Shimul, Rego, Seema, Perry, James, Speziale, Mark, Nespeca, Mark, Wright, Meredith S., Reese, Martin G., De La Vega, Francisco M., Azure, Joe, Frise, Erwin, Rigby, Charlene Son, White, Sandy, Hobbs, Charlotte A., Gilmer, Sheldon, Knight, Gail, Oriol, Albert, Lenberg, Jerica, Nahas, Shareef A., Perofsky, Kate, Kim, Kyu, Carroll, Jeanne, Coufal, Nicole G., Sanford, Erica, Wigby, Kristen, Weir, Jacqueline, Thomson, Vicki S., Fraser, Louise, Lazare, Seka S., Shin, Yoon H., Grunenwald, Haiying, Lee, Richard, Jones, David, Tran, Duke, Gross, Andrew, Daigle, Patrick, Case, Anne, Lue, Marisa, Richardson, James A., Reynders, John, Defay, Thomas, Hall, Kevin P., Veeraraghavan, Narayanan, Kingsmore, Stephen F.
Publicado 2022

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort

por Waszak, Sebastian M, Northcott, Paul A, Buchhalter, Ivo, Robinson, Giles W, Sutter, Christian, Groebner, Susanne, Grund, Kerstin B, Brugières, Laurence, Jones, David T W, Pajtler, Kristian W, Morrissy, A Sorana, Kool, Marcel, Sturm, Dominik, Chavez, Lukas, Ernst, Aurelie, Brabetz, Sebastian, Hain, Michael, Zichner, Thomas, Segura-Wang, Maia, Weischenfeldt, Joachim, Rausch, Tobias, Mardin, Balca R, Zhou, Xin, Baciu, Cristina, Lawerenz, Christian, Chan, Jennifer A, Varlet, Pascale, Guerrini-Rousseau, Lea, Fults, Daniel W, Grajkowska, Wiesława, Hauser, Peter, Jabado, Nada, Ra, Young-Shin, Zitterbart, Karel, Shringarpure, Suyash S, De La Vega, Francisco M, Bustamante, Carlos D, Ng, Ho-Keung, Perry, Arie, MacDonald, Tobey J, Hernáiz Driever, Pablo, Bendel, Anne E, Bowers, Daniel C, McCowage, Geoffrey, Chintagumpala, Murali M, Cohn, Richard, Hassall, Timothy, Fleischhack, Gudrun, Eggen, Tone, Wesenberg, Finn, Feychting, Maria, Lannering, Birgitta, Schüz, Joachim, Johansen, Christoffer, Andersen, Tina V, Röösli, Martin, Kuehni, Claudia E, Grotzer, Michael, Kjaerheim, Kristina, Monoranu, Camelia M, Archer, Tenley C, Duke, Elizabeth, Pomeroy, Scott L, Shelagh, Redmond, Frank, Stephan, Sumerauer, David, Scheurlen, Wolfram, Ryzhova, Marina V, Milde, Till, Kratz, Christian P, Samuel, David, Zhang, Jinghui, Solomon, David A, Marra, Marco, Eils, Roland, Bartram, Claus R, von Hoff, Katja, Rutkowski, Stefan, Ramaswamy, Vijay, Gilbertson, Richard J, Korshunov, Andrey, Taylor, Michael D, Lichter, Peter, Malkin, David, Gajjar, Amar, Korbel, Jan O, Pfister, Stefan M
Publicado 2018

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

por Brownstein, Catherine A, Beggs, Alan H, Homer, Nils, Merriman, Barry, Yu, Timothy W, Flannery, Katherine C, DeChene, Elizabeth T, Towne, Meghan C, Savage, Sarah K, Price, Emily N, Holm, Ingrid A, Luquette, Lovelace J, Lyon, Elaine, Majzoub, Joseph, Neupert, Peter, McCallie Jr, David, Szolovits, Peter, Willard, Huntington F, Mendelsohn, Nancy J, Temme, Renee, Finkel, Richard S, Yum, Sabrina W, Medne, Livija, Sunyaev, Shamil R, Adzhubey, Ivan, Cassa, Christopher A, de Bakker, Paul IW, Duzkale, Hatice, Dworzyński, Piotr, Fairbrother, William, Francioli, Laurent, Funke, Birgit H, Giovanni, Monica A, Handsaker, Robert E, Lage, Kasper, Lebo, Matthew S, Lek, Monkol, Leshchiner, Ignaty, MacArthur, Daniel G, McLaughlin, Heather M, Murray, Michael F, Pers, Tune H, Polak, Paz P, Raychaudhuri, Soumya, Rehm, Heidi L, Soemedi, Rachel, Stitziel, Nathan O, Vestecka, Sara, Supper, Jochen, Gugenmus, Claudia, Klocke, Bernward, Hahn, Alexander, Schubach, Max, Menzel, Mortiz, Biskup, Saskia, Freisinger, Peter, Deng, Mario, Braun, Martin, Perner, Sven, Smith, Richard JH, Andorf, Janeen L, Huang, Jian, Ryckman, Kelli, Sheffield, Val C, Stone, Edwin M, Bair, Thomas, Black-Ziegelbein, E Ann, Braun, Terry A, Darbro, Benjamin, DeLuca, Adam P, Kolbe, Diana L, Scheetz, Todd E, Shearer, Aiden E, Sompallae, Rama, Wang, Kai, Bassuk, Alexander G, Edens, Erik, Mathews, Katherine, Moore, Steven A, Shchelochkov, Oleg A, Trapane, Pamela, Bossler, Aaron, Campbell, Colleen A, Heusel, Jonathan W, Kwitek, Anne, Maga, Tara, Panzer, Karin, Wassink, Thomas, Van Daele, Douglas, Azaiez, Hela, Booth, Kevin, Meyer, Nic, Segal, Michael M, Williams, Marc S, Tromp, Gerard, White, Peter, Corsmeier, Donald, Fitzgerald-Butt, Sara, Herman, Gail, Lamb-Thrush, Devon, McBride, Kim L, Newsom, David, Pierson, Christopher R, Rakowsky, Alexander T, Maver, Aleš, Lovrečić, Luca, Palandačić, Anja, Peterlin, Borut, Torkamani, Ali, Wedell, Anna, Huss, Mikael, Alexeyenko, Andrey, Lindvall, Jessica M, Magnusson, Måns, Nilsson, Daniel, Stranneheim, Henrik, Taylan, Fulya, Gilissen, Christian, Hoischen, Alexander, van Bon, Bregje, Yntema, Helger, Nelen, Marcel, Zhang, Weidong, Sager, Jason, Zhang, Lu, Blair, Kathryn, Kural, Deniz, Cariaso, Michael, Lennon, Greg G, Javed, Asif, Agrawal, Saloni, Ng, Pauline C, Sandhu, Komal S, Krishna, Shuba, Veeramachaneni, Vamsi, Isakov, Ofer, Halperin, Eran, Friedman, Eitan, Shomron, Noam, Glusman, Gustavo, Roach, Jared C, Caballero, Juan, Cox, Hannah C, Mauldin, Denise, Ament, Seth A, Rowen, Lee, Richards, Daniel R, Lucas, F Anthony San, Gonzalez-Garay, Manuel L, Caskey, C Thomas, Bai, Yu, Huang, Ying, Fang, Fang, Zhang, Yan, Wang, Zhengyuan, Barrera, Jorge, Garcia-Lobo, Juan M, González-Lamuño, Domingo, Llorca, Javier, Rodriguez, Maria C, Varela, Ignacio, Reese, Martin G, De La Vega, Francisco M, Kiruluta, Edward, Cargill, Michele, Hart, Reece K, Sorenson, Jon M, Lyon, Gholson J, Stevenson, David A, Bray, Bruce E, Moore, Barry M, Eilbeck, Karen, Yandell, Mark, Zhao, Hongyu, Hou, Lin, Chen, Xiaowei, Yan, Xiting, Chen, Mengjie, Li, Cong, Yang, Can, Gunel, Murat, Li, Peining, Kong, Yong, Alexander, Austin C, Albertyn, Zayed I, Boycott, Kym M, Bulman, Dennis E, Gordon, Paul MK, Innes, A Micheil, Knoppers, Bartha M, Majewski, Jacek, Marshall, Christian R, Parboosingh, Jillian S, Sawyer, Sarah L, Samuels, Mark E, Schwartzentruber, Jeremy, Kohane, Isaac S, Margulies, David M
Publicado 2014