Comprehensive benchmarking of CITE-seq versus DOGMA-seq single cell multimodal omics

por Xu, Zhongli, Heidrich-O’Hare, Elisa, Chen, Wei, Duerr, Richard H.
Publicado 2022

BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data

por Wang, Xinjun, Sun, Zhe, Zhang, Yanfu, Xu, Zhongli, Xin, Hongyi, Huang, Heng, Duerr, Richard H, Chen, Kong, Ding, Ying, Chen, Wei
Publicado 2020

SECANT: a biology-guided semi-supervised method for clustering, classification, and annotation of single-cell multi-omics

por Wang, Xinjun, Xu, Zhongli, Hu, Haoran, Zhou, Xueping, Zhang, Yanfu, Lafyatis, Robert, Chen, Kong, Huang, Heng, Ding, Ying, Duerr, Richard H, Chen, Wei
Publicado 2022

GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing

por Xin, Hongyi, Lian, Qiuyu, Jiang, Yale, Luo, Jiadi, Wang, Xinjun, Erb, Carla, Xu, Zhongli, Zhang, Xiaoyi, Heidrich-O’Hare, Elisa, Yan, Qi, Duerr, Richard H., Chen, Kong, Chen, Wei
Publicado 2020

PTGER4 Expression-Modulating Polymorphisms in the 5p13.1 Region Predispose to Crohn's Disease and Affect NF-κB and XBP1 Binding Sites

por Glas, Jürgen, Seiderer, Julia, Czamara, Darina, Pasciuto, Giulia, Diegelmann, Julia, Wetzke, Martin, Olszak, Torsten, Wolf, Christiane, Müller-Myhsok, Bertram, Balschun, Tobias, Achkar, Jean-Paul, Kamboh, M. Ilyas, Franke, Andre, Duerr, Richard H., Brand, Stephan
Publicado 2012

Amino Acid Position 11 of HLA-DRβ1 is a Major Determinant of Chromosome 6p Association with Ulcerative Colitis

por Achkar, Jean-Paul, Klei, Lambertus, de Bakker, Paul I.W., Bellone, Gaia, Rebert, Nancy, Scott, Regan, Lu, Ying, Regueiro, Miguel, Brzezinski, Aaron, Kamboh, M. Ilyas, Fiocchi, Claudio, Devlin, Bernie, Trucco, Massimo, Ringquist, Steven, Roeder, Kathryn, Duerr, Richard H
Publicado 2011

Genomic architecture of inflammatory bowel disease in five families with multiple affected individuals

por Stittrich, Anna B, Ashworth, Justin, Shi, Mude, Robinson, Max, Mauldin, Denise, Brunkow, Mary E, Biswas, Shameek, Kim, Jin-Man, Kwon, Ki-Sun, Jung, Jae U, Galas, David, Serikawa, Kyle, Duerr, Richard H, Guthery, Stephen L, Peschon, Jacques, Hood, Leroy, Roach, Jared C, Glusman, Gustavo
Publicado 2016

High density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis

por Goyette, Philippe, Boucher, Gabrielle, Mallon, Dermot, Ellinghaus, Eva, Jostins, Luke, Huang, Hailiang, Ripke, Stephan, Gusareva, Elena S, Annese, Vito, Hauser, Stephen L, Oksenberg, Jorge R, Thomsen, Ingo, Leslie, Stephen, Daly, Mark J, Van Steen, Kristel, Duerr, Richard H, Barrett, Jeffrey C, McGovern, Dermot PB, Schumm, L Philip, Traherne, James A, Carrington, Mary N, Kosmoliaptsis, Vasilis, Karlsen, Tom H, Franke, Andre, Rioux, John D
Publicado 2015

Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients

por Wu, Yiming, Gettler, Kyle, Kars, Meltem Ece, Giri, Mamta, Li, Dalin, Bayrak, Cigdem Sevim, Zhang, Peng, Jain, Aayushee, Maffucci, Patrick, Sabic, Ksenija, Van Vleck, Tielman, Nadkarni, Girish, Denson, Lee A., Ostrer, Harry, Levine, Adam P., Schiff, Elena R., Segal, Anthony W., Kugathasan, Subra, Stenson, Peter D., Cooper, David N., Philip Schumm, L., Snapper, Scott, Daly, Mark J., Haritunians, Talin, Duerr, Richard H., Silverberg, Mark S., Rioux, John D., Brant, Steven R., McGovern, Dermot P. B., Cho, Judy H., Itan, Yuval
Publicado 2023

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 2013

Ulcerative colitis loci on chromosomes 1p36 and 12q15 identified by genome-wide association study

por Silverberg, Mark S., Cho, Judy H., Rioux, John D., McGovern, Dermot P.B., Wu, Jing, Annese, Vito, Achkar, Jean-Paul, Goyette, Philippe, Scott, Regan, Xu, Wei, Barmada, M. Michael, Klei, Lambertus, Daly, Mark J., Abraham, Clara, Bayless, Theodore M., Bossa, Fabrizio, Griffiths, Anne M., Ippoliti, Andrew F., Lahaie, Raymond G., Latiano, Anna, Paré, Pierre, Proctor, Deborah D., Regueiro, Miguel D., Steinhart, A. Hillary, Targan, Stephan R., Schumm, L. Philip, Kistner, Emily O., Lee, Annette T., Gregersen, Peter K., Rotter, Jerome I., Brant, Steven R., Taylor, Kent D., Roeder, Kathryn, Duerr, Richard H.
Publicado 2009

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 2011

A Genome-Wide Scan of Ashkenazi Jewish Crohn's Disease Suggests Novel Susceptibility Loci

por Kenny, Eimear E., Pe'er, Itsik, Karban, Amir, Ozelius, Laurie, Mitchell, Adele A., Ng, Sok Meng, Erazo, Monica, Ostrer, Harry, Abraham, Clara, Abreu, Maria T., Atzmon, Gil, Barzilai, Nir, Brant, Steven R., Bressman, Susan, Burns, Edward R., Chowers, Yehuda, Clark, Lorraine N., Darvasi, Ariel, Doheny, Dana, Duerr, Richard H., Eliakim, Rami, Giladi, Nir, Gregersen, Peter K., Hakonarson, Hakon, Jones, Michelle R., Marder, Karen, McGovern, Dermot P. B., Mulle, Jennifer, Orr-Urtreger, Avi, Proctor, Deborah D., Pulver, Ann, Rotter, Jerome I., Silverberg, Mark S., Ullman, Thomas, Warren, Stephen T., Waterman, Matti, Zhang, Wei, Bergman, Aviv, Mayer, Lloyd, Katz, Seymour, Desnick, Robert J., Cho, Judy H., Peter, Inga
Publicado 2012

Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study

por Cleynen, Isabelle, Boucher, Gabrielle, Jostins, Luke, Schumm, L Philip, Zeissig, Sebastian, Ahmad, Tariq, Andersen, Vibeke, Andrews, Jane M, Annese, Vito, Brand, Stephan, Brant, Steven R, Cho, Judy H, Daly, Mark J, Dubinsky, Marla, Duerr, Richard H, Ferguson, Lynnette R, Franke, Andre, Gearry, Richard B, Goyette, Philippe, Hakonarson, Hakon, Halfvarson, Jonas, Hov, Johannes R, Huang, Hailang, Kennedy, Nicholas A, Kupcinskas, Limas, Lawrance, Ian C, Lee, James C, Satsangi, Jack, Schreiber, Stephan, Théâtre, Emilie, van der Meulen-de Jong, Andrea E, Weersma, Rinse K, Wilson, David C, Parkes, Miles, Vermeire, Severine, Rioux, John D, Mansfield, John, Silverberg, Mark S, Radford-Smith, Graham, McGovern, Dermot P B, Barrett, Jeffrey C, Lees, Charlie W
Publicado 2016

Fine-mapping inflammatory bowel disease loci to single variant resolution

por Huang, Hailiang, Fang, Ming, Jostins, Luke, Mirkov, Maša Umićević, Boucher, Gabrielle, Anderson, Carl A, Andersen, Vibeke, Cleynen, Isabelle, Cortes, Adrian, Crins, François, D'Amato, Mauro, Deffontaine, Valérie, Dimitrieva, Julia, Docampo, Elisa, Elansary, Mahmoud, Farh, Kyle Kai-How, Franke, Andre, Gori, Ann-Stephan, Goyette, Philippe, Halfvarson, Jonas, Haritunians, Talin, Knight, Jo, Lawrance, Ian C, Lees, Charlie W, Louis, Edouard, Mariman, Rob, Meuwissen, Theo, Mni, Myriam, Momozawa, Yukihide, Parkes, Miles, Spain, Sarah L, Théâtre, Emilie, Trynka, Gosia, Satsangi, Jack, van Sommeren, Suzanne, Vermeire, Severine, Xavier, Ramnik J, Weersma, Rinse K, Duerr, Richard H, Mathew, Christopher G, Rioux, John D, McGovern, Dermot PB, Cho, Judy H, Georges, Michel, Daly, Mark J, Barrett, Jeffrey C
Publicado 2017

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 2016

Genetic architecture distinguishes systemic juvenile idiopathic arthritis from other forms of juvenile idiopathic arthritis: clinical and therapeutic implications

por Ombrello, Michael J, Arthur, Victoria L, Remmers, Elaine F, Hinks, Anne, Tachmazidou, Ioanna, Grom, Alexei A, Foell, Dirk, Martini, Alberto, Gattorno, Marco, Özen, Seza, Prahalad, Sampath, Zeft, Andrew S, Bohnsack, John F, Ilowite, Norman T, Mellins, Elizabeth D, Russo, Ricardo, Len, Claudio, Hilario, Maria Odete E, Oliveira, Sheila, Yeung, Rae S M, Rosenberg, Alan M, Wedderburn, Lucy R, Anton, Jordi, Haas, Johannes-Peter, Rosen-Wolff, Angela, Minden, Kirsten, Tenbrock, Klaus, Demirkaya, Erkan, Cobb, Joanna, Baskin, Elizabeth, Signa, Sara, Shuldiner, Emily, Duerr, Richard H, Achkar, Jean-Paul, Kamboh, M Ilyas, Kaufman, Kenneth M, Kottyan, Leah C, Pinto, Dalila, Scherer, Stephen W, Alarcón-Riquelme, Marta E, Docampo, Elisa, Estivill, Xavier, Gül, Ahmet, Langefeld, Carl D, Thompson, Susan, Zeggini, Eleftheria, Kastner, Daniel L, Woo, Patricia, Thomson, Wendy
Publicado 2017

Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population

por Rivas, Manuel A., Avila, Brandon E., Koskela, Jukka, Huang, Hailiang, Stevens, Christine, Pirinen, Matti, Haritunians, Talin, Neale, Benjamin M., Kurki, Mitja, Ganna, Andrea, Graham, Daniel, Glaser, Benjamin, Peter, Inga, Atzmon, Gil, Barzilai, Nir, Levine, Adam P., Schiff, Elena, Pontikos, Nikolas, Weisburd, Ben, Lek, Monkol, Karczewski, Konrad J., Bloom, Jonathan, Minikel, Eric V., Petersen, Britt-Sabina, Beaugerie, Laurent, Seksik, Philippe, Cosnes, Jacques, Schreiber, Stefan, Bokemeyer, Bernd, Bethge, Johannes, Heap, Graham, Ahmad, Tariq, Plagnol, Vincent, Segal, Anthony W., Targan, Stephan, Turner, Dan, Saavalainen, Paivi, Farkkila, Martti, Kontula, Kimmo, Palotie, Aarno, Brant, Steven R., Duerr, Richard H., Silverberg, Mark S., Rioux, John D., Weersma, Rinse K., Franke, Andre, Jostins, Luke, Anderson, Carl A., Barrett, Jeffrey C., MacArthur, Daniel G., Jalas, Chaim, Sokol, Harry, Xavier, Ramnik J., Pulver, Ann, Cho, Judy H., McGovern, Dermot P. B., Daly, Mark J.
Publicado 2018

Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population

por Rivas, Manuel A., Avila, Brandon E., Koskela, Jukka, Huang, Hailiang, Stevens, Christine, Pirinen, Matti, Haritunians, Talin, Neale, Benjamin M., Kurki, Mitja, Ganna, Andrea, Graham, Daniel, Glaser, Benjamin, Peter, Inga, Atzmon, Gil, Barzilai, Nir, Levine, Adam P., Schiff, Elena, Pontikos, Nikolas, Weisburd, Ben, Lek, Monkol, Karczewski, Konrad J., Bloom, Jonathan, Minikel, Eric V., Petersen, Britt-Sabina, Beaugerie, Laurent, Seksik, Philippe, Cosnes, Jacques, Schreiber, Stefan, Bokemeyer, Bernd, Bethge, Johannes, Heap, Graham, Ahmad, Tariq, Plagnol, Vincent, Segal, Anthony W., Targan, Stephan, Turner, Dan, Saavalainen, Paivi, Farkkila, Martti, Kontula, Kimmo, Palotie, Aarno, Brant, Steven R., Duerr, Richard H., Silverberg, Mark S., Rioux, John D., Weersma, Rinse K., Franke, Andre, Jostins, Luke, Anderson, Carl A., Barrett, Jeffrey C., MacArthur, Daniel G., Jalas, Chaim, Sokol, Harry, Xavier, Ramnik J., Pulver, Ann, Cho, Judy H., McGovern, Dermot P. B., Daly, Mark J.
Publicado 2019

Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease

por Somineni, Hari K., Nagpal, Sini, Venkateswaran, Suresh, Cutler, David J., Okou, David T., Haritunians, Talin, Simpson, Claire L., Begum, Ferdouse, Datta, Lisa W., Quiros, Antonio J., Seminerio, Jenifer, Mengesha, Emebet, Alexander, Jonathan S., Baldassano, Robert N., Dudley-Brown, Sharon, Cross, Raymond K., Dassopoulos, Themistocles, Denson, Lee A., Dhere, Tanvi A., Iskandar, Heba, Dryden, Gerald W., Hou, Jason K., Hussain, Sunny Z., Hyams, Jeffrey S., Isaacs, Kim L., Kader, Howard, Kappelman, Michael D., Katz, Jeffry, Kellermayer, Richard, Kuemmerle, John F., Lazarev, Mark, Li, Ellen, Mannon, Peter, Moulton, Dedrick E., Newberry, Rodney D., Patel, Ashish S., Pekow, Joel, Saeed, Shehzad A., Valentine, John F., Wang, Ming-Hsi, McCauley, Jacob L., Abreu, Maria T., Jester, Traci, Molle-Rios, Zarela, Palle, Sirish, Scherl, Ellen J., Kwon, John, Rioux, John D., Duerr, Richard H., Silverberg, Mark S., Zwick, Michael E., Stevens, Christine, Daly, Mark J., Cho, Judy H., Gibson, Greg, McGovern, Dermot P.B., Brant, Steven R., Kugathasan, Subra
Publicado 2021