A Flexible Approach for the Analysis of Rare Variants Allowing for a Mixture of Effects on Binary or Quantitative Traits

Por Clarke, Geraldine M., Rivas, Manuel A., Morris, Andrew P.
Publicado em 2013

Choice of transcripts and software has a large effect on variant annotation

Por McCarthy, Davis J, Humburg, Peter, Kanapin, Alexander, Rivas, Manuel A, Gaulton, Kyle, Cazier, Jean-Baptiste, Donnelly, Peter
Publicado em 2014

Assessing allele-specific expression across multiple tissues from RNA-seq read data

Por Pirinen, Matti, Lappalainen, Tuuli, Zaitlen, Noah A., Dermitzakis, Emmanouil T., Donnelly, Peter, McCarthy, Mark I., Rivas, Manuel A.
Publicado no Bioinformatics (2015)

A Protein Domain and Family Based Approach to Rare Variant Association Analysis

Por Richardson, Tom G., Shihab, Hashem A., Rivas, Manuel A., McCarthy, Mark I., Campbell, Colin, Timpson, Nicholas J., Gaunt, Tom R.
Publicado no PLoS One (2016)

Assessing association between protein truncating variants and quantitative traits

Por Rivas, Manuel A., Pirinen, Matti, Neville, Matthew J., Gaulton, Kyle J., Moutsianas, Loukas, Lindgren, Cecilia M., Karpe, Fredrik, McCarthy, Mark I., Donnelly, Peter
Publicado em 2013

Testing for an Unusual Distribution of Rare Variants

Por Neale, Benjamin M., Rivas, Manuel A., Voight, Benjamin F., Altshuler, David, Devlin, Bernie, Orho-Melander, Marju, Kathiresan, Sekar, Purcell, Shaun M., Roeder, Kathryn, Daly, Mark J.
Publicado em 2011

The Power of Gene-Based Rare Variant Methods to Detect Disease-Associated Variation and Test Hypotheses About Complex Disease

Por Moutsianas, Loukas, Agarwala, Vineeta, Fuchsberger, Christian, Flannick, Jason, Rivas, Manuel A., Gaulton, Kyle J., Albers, Patrick K., McVean, Gil, Boehnke, Michael, Altshuler, David, McCarthy, Mark I.
Publicado no PLoS Genet (2015)

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing

Por Ferreira, Pedro G., Oti, Martin, Barann, Matthias, Wieland, Thomas, Ezquina, Suzana, Friedländer, Marc R., Rivas, Manuel A., Esteve-Codina, Anna, Rosenstiel, Philip, Strom, Tim M, Lappalainen, Tuuli, Guigó, Roderic, Sammeth, Michael
Publicado no Sci Rep (2016)

A null mutation in ANGPTL8 does not associate with either plasma glucose or type 2 diabetes in humans

Por Clapham, Katharine R., Chu, Audrey Y., Wessel, Jennifer, Natarajan, Pradeep, Flannick, Jason, Rivas, Manuel A., Sartori, Samantha, Mehran, Roxana, Baber, Usman, Fuster, Valentin, Scott, Robert A., Rader, Daniel J., Boehnke, Michael, McCarthy, Mark I., Altshuler, David M., Kathiresan, Sekar, Peloso, Gina M.
Publicado no BMC Endocr Disord (2016)

Genetic Adaptation of Fatty-Acid Metabolism: A Human-Specific Haplotype Increasing the Biosynthesis of Long-Chain Omega-3 and Omega-6 Fatty Acids

Por Ameur, Adam, Enroth, Stefan, Johansson, Åsa, Zaboli, Ghazal, Igl, Wilmar, Johansson, Anna C.V., Rivas, Manuel A., Daly, Mark J., Schmitz, Gerd, Hicks, Andrew A., Meitinger, Thomas, Feuk, Lars, van Duijn, Cornelia, Oostra, Ben, Pramstaller, Peter P., Rudan, Igor, Wright, Alan F., Wilson, James F., Campbell, Harry, Gyllensten, Ulf
Publicado em 2012

High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency

Por Calvo, Sarah E, Tucker, Elena J, Compton, Alison G, Kirby, Denise M, Crawford, Gabriel, Burtt, Noel P, Rivas, Manuel A, Guiducci, Candace, Bruno, Damien L, Goldberger, Olga A, Redman, Michelle C, Wiltshire, Esko, Wilson, Callum J, Altshuler, David, Gabriel, Stacey B, Daly, Mark J, Thorburn, David R, Mootha, Vamsi K
Publicado em 2010

The landscape of genomic imprinting across diverse adult human tissues

Por Baran, Yael, Subramaniam, Meena, Biton, Anne, Tukiainen, Taru, Tsang, Emily K., Rivas, Manuel A., Pirinen, Matti, Gutierrez-Arcelus, Maria, Smith, Kevin S., Kukurba, Kim R., Zhang, Rui, Eng, Celeste, Torgerson, Dara G., Urbanek, Cydney, Li, Jin Billy, Rodriguez-Santana, Jose R., Burchard, Esteban G., Seibold, Max A., MacArthur, Daniel G., Montgomery, Stephen B., Zaitlen, Noah A., Lappalainen, Tuuli
Publicado no Genome Res (2015)

Pooled Resequencing of 122 Ulcerative Colitis Genes in a Large Dutch Cohort Suggests Population-Specific Associations of Rare Variants in MUC2

Por Visschedijk, Marijn C., Alberts, Rudi, Mucha, Soren, Deelen, Patrick, de Jong, Dirk J., Pierik, Marieke, Spekhorst, Lieke M., Imhann, Floris, van der Meulen-de Jong, Andrea E., van der Woude, C. Janneke, van Bodegraven, Adriaan A., Oldenburg, Bas, Löwenberg, Mark, Dijkstra, Gerard, Ellinghaus, David, Schreiber, Stefan, Wijmenga, Cisca, Rivas, Manuel A., Franke, Andre, van Diemen, Cleo C., Weersma, Rinse K.
Publicado no PLoS One (2016)

Rare, Low-Frequency, and Common Variants in the Protein-Coding Sequence of Biological Candidate Genes from GWASs Contribute to Risk of Rheumatoid Arthritis

Por Diogo, Dorothée, Kurreeman, Fina, Stahl, Eli A., Liao, Katherine P., Gupta, Namrata, Greenberg, Jeffrey D., Rivas, Manuel A., Hickey, Brendan, Flannick, Jason, Thomson, Brian, Guiducci, Candace, Ripke, Stephan, Adzhubey, Ivan, Barton, Anne, Kremer, Joel M., Alfredsson, Lars, Sunyaev, Shamil, Martin, Javier, Zhernakova, Alexandra, Bowes, John, Eyre, Steve, Siminovitch, Katherine A., Gregersen, Peter K., Worthington, Jane, Klareskog, Lars, Padyukov, Leonid, Raychaudhuri, Soumya, Plenge, Robert M.
Publicado em 2013

Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis

Por Beaudoin, Mélissa, Goyette, Philippe, Boucher, Gabrielle, Lo, Ken Sin, Rivas, Manuel A., Stevens, Christine, Alikashani, Azadeh, Ladouceur, Martin, Ellinghaus, David, Törkvist, Leif, Goel, Gautam, Lagacé, Caroline, Annese, Vito, Bitton, Alain, Begun, Jakob, Brant, Steve R., Bresso, Francesca, Cho, Judy H., Duerr, Richard H., Halfvarson, Jonas, McGovern, Dermot P. B., Radford-Smith, Graham, Schreiber, Stefan, Schumm, Philip L., Sharma, Yashoda, Silverberg, Mark S., Weersma, Rinse K., D'Amato, Mauro, Vermeire, Severine, Franke, Andre, Lettre, Guillaume, Xavier, Ramnik J., Daly, Mark J., Rioux, John D.
Publicado em 2013

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease

Por Rivas, Manuel A., Beaudoin, Melissa, Gardet, Agnes, Stevens, Christine, Sharma, Yashoda, Zhang, Clarence K., Boucher, Gabrielle, Ripke, Stephan, Ellinghaus, David, Burtt, Noel, Fennell, Tim, Kirby, Andrew, Latiano, Anna, Goyette, Philippe, Green, Todd, Halfvarson, Jonas, Haritunians, Talin, Korn, Joshua M., Kuruvilla, Finny, Lagacé, Caroline, Neale, Benjamin, Lo, Ken Sin, Schumm, Phil, Törkvist, Leif, Dubinsky, Marla, Brant, Steven R., Silverberg, Mark, Duerr, Richard H., Altshuler, David, Gabriel, Stacey, Lettre, Guillaume, Franke, Andre, D’Amato, Mauro, McGovern, Dermot P.B., Cho, Judy H., Rioux, John D., Xavier, Ramnik J., Daly, Mark J.
Publicado em 2011

Impact of predicted protein-truncating genetic variants on the human transcriptome

Por Rivas, Manuel A., Pirinen, Matti, Conrad, Donald F., Lek, Monkol, Tsang, Emily K., Karczewski, Konrad J., Maller, Julian B., Kukurba, Kimberly R., DeLuca, David, Fromer, Menachem, Ferreira, Pedro G., Smith, Kevin S., Zhang, Rui, Zhao, Fengmei, Banks, Eric, Poplin, Ryan, Ruderfer, Douglas, Purcell, Shaun M., Tukiainen, Taru, Minikel, Eric V., Stenson, Peter D., Cooper, David N., Huang, Katharine H., Sullivan, Timothy J., Nedzel, Jared, Bustamante, Carlos D., Li, Jin Billy, Daly, Mark J., Guigo, Roderic, Donnelly, Peter, Ardlie, Kristin, Sammeth, Michael, Dermitzakis, Emmanouil, McCarthy, Mark I., Montgomery, Stephen B., Lappalainen, Tuuli, MacArthur, Daniel G.
Publicado no Science (2015)

Erratum: A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis

Por Rivas, Manuel A., Graham, Daniel, Sulem, Patrick, Stevens, Christine, Desch, A. Nicole, Goyette, Philippe, Gudbjartsson, Daniel, Jonsdottir, Ingileif, Thorsteinsdottir, Unnur, Degenhardt, Frauke, Mucha, Sören, Kurki, Mitja I., Li, Dalin, D'Amato, Mauro, Annese, Vito, Vermeire, Severine, Weersma, Rinse K., Halfvarson, Jonas, Paavola-Sakki, Paulina, Lappalainen, Maarit, Lek, Monkol, Cummings, Beryl, Tukiainen, Taru, Haritunians, Talin, Halme, Leena, Koskinen, Lotta L. E., Ananthakrishnan, Ashwin N., Luo, Yang, Heap, Graham A., Visschedijk, Marijn C., MacArthur, Daniel G., Neale, Benjamin M., Ahmad, Tariq, Anderson, Carl A., Brant, Steven R., Duerr, Richard H., Silverberg, Mark S., Cho, Judy H., Palotie, Aarno, Saavalainen, Päivi, Kontula, Kimmo, Färkkilä, Martti, McGovern, Dermot P. B., Franke, Andre, Stefansson, Kari, Rioux, John D., Xavier, Ramnik J., Daly, Mark J.
Publicado no Nat Commun (2016)

Transcriptome and genome sequencing uncovers functional variation in humans

Por Lappalainen, Tuuli, Sammeth, Michael, Friedländer, Marc R, ‘t Hoen, Peter AC, Monlong, Jean, Rivas, Manuel A, Gonzàlez-Porta, Mar, Kurbatova, Natalja, Griebel, Thasso, Ferreira, Pedro G, Barann, Matthias, Wieland, Thomas, Greger, Liliana, van Iterson, Maarten, Almlöf, Jonas, Ribeca, Paolo, Pulyakhina, Irina, Esser, Daniela, Giger, Thomas, Tikhonov, Andrew, Sultan, Marc, Bertier, Gabrielle, MacArthur, Daniel G, Lek, Monkol, Lizano, Esther, Buermans, Henk PJ, Padioleau, Ismael, Schwarzmayr, Thomas, Karlberg, Olof, Ongen, Halit, Kilpinen, Helena, Beltran, Sergi, Gut, Marta, Kahlem, Katja, Amstislavskiy, Vyacheslav, Stegle, Oliver, Pirinen, Matti, Montgomery, Stephen B, Donnelly, Peter, McCarthy, Mark I, Flicek, Paul, Strom, Tim M, Lehrach, Hans, Schreiber, Stefan, Sudbrak, Ralf, Carracedo, Ángel, Antonarakis, Stylianos E, Häsler, Robert, Syvänen, Ann-Christine, van Ommen, Gert-Jan, Brazma, Alvis, Meitinger, Thomas, Rosenstiel, Philip, Guigó, Roderic, Gut, Ivo G, Estivill, Xavier, Dermitzakis, Emmanouil T
Publicado em 2013

Association Between Variants of PRDM1 and NDP52 and Crohn’s Disease, Based on Exome Sequencing and Functional Studies

Por Ellinghaus, David, Zhang, Hu, Zeissig, Sebastian, Lipinski, Simone, Till, Andreas, Jiang, Tao, Stade, Björn, Bromberg, Yana, Ellinghaus, Eva, Keller, Andreas, Rivas, Manuel A, Skieceviciene, Jurgita, Doncheva, Nadezhda T, Liu, Xiao, Liu, Qing, Jiang, Fuman, Forster, Michael, Mayr, Gabriele, Albrecht, Mario, Häsler, Robert, Boehm, Bernhard O, Goodall, Jane, Berzuini, Carlo R, Lee, James, Andersen, Vibeke, Vogel, Ulla, Kupcinskas, Limas, Kayser, Manfred, Krawczak, Michael, Nikolaus, Susanna, Weersma, Rinse K, Ponsioen, Cyriel Y, Sans, Miquel, Wijmenga, Cisca, Strachan, David P, McArdle, Wendy L, Vermeire, Séverine, Rutgeerts, Paul, Sanderson, Jeremy D, Mathew, Christopher G, Vatn, Morten H, Wang, Jun, Nöthen, Markus M, Duerr, Richard H, Büning, Carsten, Brand, Stephan, Glas, Jürgen, Winkelmann, Juliane, Illig, Thomas, Latiano, Anna, Annese, Vito, Halfvarson, Jonas, D’Amato, Mauro, Daly, Mark J, Nothnagel, Michael, Karlsen, Tom H, Subramani, Suresh, Rosenstiel, Philip, Schreiber, Stefan, Parkes, Miles, Franke, Andre
Publicado em 2013