Flow Cytometry Bioinformatics

My group is focused on applying bioinformatics techniques to flow cytometry data. Flow cytometry is a technique that is widely used within the biomedical community. New high throughput methods can generate up to a thousand flow cytometry data files per day and each data file can consist of millions of multiparametric descriptions of individual cells. Consequently, there are a variety of challenges to archiving, analyzing and reporting the results of high throughput flow cytometry experiments. My group is developing big data analysis algorithms, including machine learning approaches, to allow users to implement analyses in a high throughput fashion, as well as exchange these analyses in more meaningful ways then are currently available. We are also testing our high throughput analysis methods to analyze flow cytometry data on datasets from the BC Cancer and the British Children's Hospital including developing methods for the high throughput analysis of lymphoma, Graft versus Host Disease and innate immunity. We are also developing user-friendly software that implements some of the new data analysis and visualization methods we and others have developed. We also collaborate with big pharma to analyze (primarily immunotherapy) clinical trial data. 

My research is supported by the NIH, CIHR, Genome Canada, Genome BC, The Michael Smith Foundation for Health Research and BC Cancer.

Members

Faculty/Leaders

Staff

Students/Trainees

Open Positions

Big Data Genome Studies

A graduate student position is available for students interested in pursuing MSc or Phd studies in Bioinformatics at the University of British Columbia. The project is aimed at characterizing the function of every mammalian gene through thorough analysis of every known and predicted gene in the mouse genome via “Big Data” analysis. To address this critical gap in biomedical research, the International Mouse Phenotyping Consortium was created to generate a null mutation for every gene in the mouse genome, to collect phenotypic data for each mutation, and to disseminate the data to the broader scientific community. Immunophenotyping by flow cytometry (FCM), is one of the 30 core phenotyping assays of this global effort. However, the full quantitative potential of the IMPC FCM effort can only be realized with mechanisms to effectively share, analyze and interpret the data.


The selected candidate will develop and use state-of-the-art computational methodologies for supervised and unsupervised clustering and classification to systematically analyze tens of thousands of high-dimensional samples to help understand the function of each gene. The candidate will also be supported to attend bioinformatics workshops and conferences to advance and disseminate their research.


Qualifications: The ideal candidate will have a strong background in Computational Biology, Bioinformatics, or equivalent with strong experience in handling high-throughput data sets as well as statistics and programming skills (we love R here). The individual will have strong verbal and written skills and the ability to work efficiently in a team environment.
In addition to the outstanding research opportunities available in this setting, students also enjoy the many cultural and sporting amenities provided in Vancouver.


Please contact Dr. Brinkman directly at rbrinkman@bccrc.ca and provide the following information:


– Short cover letter explaining your interest in the lab
– Resume
– Scanned copy of transcript or listing of course grades
– Names and contact information for two individuals who will be willing to provide letters of reference
 

Selected Publications

Single Cell Phenotypic Profiling of 27 DLBCL Cases Reveals Marked Intertumoral and Intratumoral Heterogeneity.

Cytometry. Part A : the journal of the International Society for Analytical Cytology, 2019
Nissen, Michael D, Kusakabe, Manabu, Wang, Xuehai, Simkin, Guillermo, Gracias, Deanne, Tyshchenko, Kateryna, Hill, Ainsleigh, Meskas, Justin, Hung, Stacy, Chavez, Elizabeth A, Ennishi, Daisuke, Aoki, Tomohiro, Sarkozy, Clementine, Connors, Joseph M, Farinha, Pedro, Slack, Graham W, Gascoyne, Randy D, Brinkman, Ryan R, Scott, David W, Steidl, Christian, Weng, Andrew P

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition).

European journal of immunology, 2019
Cossarizza, Andrea, Chang, Hyun-Dong, Radbruch, Andreas, Acs, Andreas, Adam, Dieter, Adam-Klages, Sabine, Agace, William W, Aghaeepour, Nima, Akdis, Mübeccel, Allez, Matthieu, Almeida, Larissa Nogueira, Alvisi, Giorgia, Anderson, Graham, Andrä, Immanuel, Annunziato, Francesco, Anselmo, Achille, Bacher, Petra, Baldari, Cosima T, Bari, Sudipto, Barnaba, Vincenzo, Barros-Martins, Joana, Battistini, Luca, Bauer, Wolfgang, Baumgart, Sabine, Baumgarth, Nicole, Baumjohann, Dirk, Baying, Bianka, Bebawy, Mary, Becher, Burkhard, Beisker, Wolfgang, Benes, Vladimir, Beyaert, Rudi, Blanco, Alfonso, Boardman, Dominic A, Bogdan, Christian, Borger, Jessica G, Borsellino, Giovanna, Boulais, Philip E, Bradford, Jolene A, Brenner, Dirk, Brinkman, Ryan R, Brooks, Anna E S, Busch, Dirk H, Büscher, Martin, Bushnell, Timothy P, Calzetti, Federica, Cameron, Garth, Cammarata, Ilenia, Cao, Xuetao, Cardell, Susanna L, Casola, Stefano, Cassatella, Marco A, Cavani, Andrea, Celada, Antonio, Chatenoud, Lucienne, Chattopadhyay, Pratip K, Chow, Sue, Christakou, Eleni, Čičin-Šain, Luka, Clerici, Mario, Colombo, Federico S, Cook, Laura, Cooke, Anne, Cooper, Andrea M, Corbett, Alexandra J, Cosma, Antonio, Cosmi, Lorenzo, Coulie, Pierre G, Cumano, Ana, Cvetkovic, Ljiljana, Dang, Van Duc, Dang-Heine, Chantip, Davey, Martin S, Davies, Derek, De Biasi, Sara, Del Zotto, Genny, Dela Cruz, Gelo Victoriano, Delacher, Michael, Della Bella, Silvia, Dellabona, Paolo, Deniz, Günnur, Dessing, Mark, Di Santo, James P, Diefenbach, Andreas, Dieli, Francesco, Dolf, Andreas, Dörner, Thomas, Dress, Regine J, Dudziak, Diana, Dustin, Michael, Dutertre, Charles-Antoine, Ebner, Friederike, Eckle, Sidonia B G, Edinger, Matthias, Eede, Pascale, Ehrhardt, Götz R A, Eich, Marcus, Engel, Pablo, Engelhardt, Britta, Erdei, Anna, Esser, Charlotte, Everts, Bart, Evrard, Maximilien, Falk, Christine S, Fehniger, Todd A, Felipo-Benavent, Mar, Ferry, Helen, Feuerer, Markus, Filby, Andrew, Filkor, Kata, Fillatreau, Simon, Follo, Marie, Förster, Irmgard, Foster, John, Foulds, Gemma A, Frehse, Britta, Frenette, Paul S, Frischbutter, Stefan, Fritzsche, Wolfgang, Galbraith, David W, Gangaev, Anastasia, Garbi, Natalio, Gaudilliere, Brice, Gazzinelli, Ricardo T, Geginat, Jens, Gerner, Wilhelm, Gherardin, Nicholas A, Ghoreschi, Kamran, Gibellini, Lara, Ginhoux, Florent, Goda, Keisuke, Godfrey, Dale I, Goettlinger, Christoph, González-Navajas, Jose M, Goodyear, Carl S, Gori, Andrea, Grogan, Jane L, Grummitt, Daryl, Grützkau, Andreas, Haftmann, Claudia, Hahn, Jonas, Hammad, Hamida, Hämmerling, Günter, Hansmann, Leo, Hansson, Goran, Harpur, Christopher M, Hartmann, Susanne, Hauser, Andrea, Hauser, Anja E, Haviland, David L, Hedley, David, Hernández, Daniela C, Herrera, Guadalupe, Herrmann, Martin, Hess, Christoph, Höfer, Thomas, Hoffmann, Petra, Hogquist, Kristin, Holland, Tristan, Höllt, Thomas, Holmdahl, Rikard, Hombrink, Pleun, Houston, Jessica P, Hoyer, Bimba F, Huang, Bo, Huang, Fang-Ping, Huber, Johanna E, Huehn, Jochen, Hundemer, Michael, Hunter, Christopher A, Hwang, William Y K, Iannone, Anna, Ingelfinger, Florian, Ivison, Sabine M, Jäck, Hans-Martin, Jani, Peter K, Jávega, Beatriz, Jonjic, Stipan, Kaiser, Toralf, Kalina, Tomas, Kamradt, Thomas, Kaufmann, Stefan H E, Keller, Baerbel, Ketelaars, Steven L C, Khalilnezhad, Ahad, Khan, Srijit, Kisielow, Jan, Klenerman, Paul, Knopf, Jasmin, Koay, Hui-Fern, Kobow, Katja, Kolls, Jay K, Kong, Wan Ting, Kopf, Manfred, Korn, Thomas, Kriegsmann, Katharina, Kristyanto, Hendy, Kroneis, Thomas, Krueger, Andreas, Kühne, Jenny, Kukat, Christian, Kunkel, Désirée, Kunze-Schumacher, Heike, Kurosaki, Tomohiro, Kurts, Christian, Kvistborg, Pia, Kwok, Immanuel, Landry, Jonathan, Lantz, Olivier, Lanuti, Paola, LaRosa, Francesca, Lehuen, Agnès, LeibundGut-Landmann, Salomé, Leipold, Michael D, Leung, Leslie Y T, Levings, Megan K, Lino, Andreia C, Liotta, Francesco, Litwin, Virginia, Liu, Yanling, Ljunggren, Hans-Gustaf, Lohoff, Michael, Lombardi, Giovanna, Lopez, Lilly, López-Botet, Miguel, Lovett-Racke, Amy E, Lubberts, Erik, Luche, Herve, Ludewig, Burkhard, Lugli, Enrico, Lunemann, Sebastian, Maecker, Holden T, Maggi, Laura, Maguire, Orla, Mair, Florian, Mair, Kerstin H, Mantovani, Alberto, Manz, Rudolf A, Marshall, Aaron J, Martínez-Romero, Alicia, Martrus, Glòria, Marventano, Ivana, Maslinski, Wlodzimierz, Matarese, Giuseppe, Mattioli, Anna Vittoria, Maueröder, Christian, Mazzoni, Alessio, McCluskey, James, McGrath, Mairi, McGuire, Helen M, McInnes, Iain B, Mei, Henrik E, Melchers, Fritz, Melzer, Susanne, Mielenz, Dirk, Miller, Stephen D, Mills, Kingston H G, Minderman, Hans, Mjösberg, Jenny, Moore, Jonni, Moran, Barry, Moretta, Lorenzo, Mosmann, Tim R, Müller, Susann, Multhoff, Gabriele, Muñoz, Luis Enrique, Münz, Christian, Nakayama, Toshinori, Nasi, Milena, Neumann, Katrin, Ng, Lai Guan, Niedobitek, Antonia, Nourshargh, Sussan, Núñez, Gabriel, O'Connor, José-Enrique, Ochel, Aaron, Oja, Anna, Ordonez, Diana, Orfao, Alberto, Orlowski-Oliver, Eva, Ouyang, Wenjun, Oxenius, Annette, Palankar, Raghavendra, Panse, Isabel, Pattanapanyasat, Kovit, Paulsen, Malte, Pavlinic, Dinko, Penter, Livius, Peterson, Pärt, Peth, Christian, Petriz, Jordi, Piancone, Federica, Pickl, Winfried F, Piconese, Silvia, Pinti, Marcello, Pockley, A Graham, Podolska, Malgorzata Justyna, Poon, Zhiyong, Pracht, Katharina, Prinz, Immo, Pucillo, Carlo E M, Quataert, Sally A, Quatrini, Linda, Quinn, Kylie M, Radbruch, Helena, Radstake, Tim R D J, Rahmig, Susann, Rahn, Hans-Peter, Rajwa, Bartek, Ravichandran, Gevitha, Raz, Yotam, Rebhahn, Jonathan A, Recktenwald, Diether, Reimer, Dorothea, Reis E Sousa, Caetano, Remmerswaal, Ester B M, Richter, Lisa, Rico, Laura G, Riddell, Andy, Rieger, Aja M, Robinson, J Paul, Romagnani, Chiara, Rubartelli, Anna, Ruland, Jürgen, Saalmüller, Armin, Saeys, Yvan, Saito, Takashi, Sakaguchi, Shimon, Sala-de-Oyanguren, Francisco, Samstag, Yvonne, Sanderson, Sharon, Sandrock, Inga, Santoni, Angela, Sanz, Ramon Bellmàs, Saresella, Marina, Sautes-Fridman, Catherine, Sawitzki, Birgit, Schadt, Linda, Scheffold, Alexander, Scherer, Hans U, Schiemann, Matthias, Schildberg, Frank A, Schimisky, Esther, Schlitzer, Andreas, Schlosser, Josephine, Schmid, Stephan, Schmitt, Steffen, Schober, Kilian, Schraivogel, Daniel, Schuh, Wolfgang, Schüler, Thomas, Schulte, Reiner, Schulz, Axel Ronald, Schulz, Sebastian R, Scottá, Cristiano, Scott-Algara, Daniel, Sester, David P, Shankey, T Vincent, Silva-Santos, Bruno, Simon, Anna Katharina, Sitnik, Katarzyna M, Sozzani, Silvano, Speiser, Daniel E, Spidlen, Josef, Stahlberg, Anders, Stall, Alan M, Stanley, Natalie, Stark, Regina, Stehle, Christina, Steinmetz, Tobit, Stockinger, Hannes, Takahama, Yousuke, Takeda, Kiyoshi, Tan, Leonard, Tárnok, Attila, Tiegs, Gisa, Toldi, Gergely, Tornack, Julia, Traggiai, Elisabetta, Trebak, Mohamed, Tree, Timothy I M, Trotter, Joe, Trowsdale, John, Tsoumakidou, Maria, Ulrich, Henning, Urbanczyk, Sophia, van de Veen, Willem, van den Broek, Maries, van der Pol, Edwin, Van Gassen, Sofie, Van Isterdael, Gert, van Lier, René A W, Veldhoen, Marc, Vento-Asturias, Salvador, Vieira, Paulo, Voehringer, David, Volk, Hans-Dieter, von Borstel, Anouk, von Volkmann, Konrad, Waisman, Ari, Walker, Rachael V, Wallace, Paul K, Wang, Sa A, Wang, Xin M, Ward, Michael D, Ward-Hartstonge, Kirsten A, Warnatz, Klaus, Warnes, Gary, Warth, Sarah, Waskow, Claudia, Watson, James V, Watzl, Carsten, Wegener, Leonie, Weisenburger, Thomas, Wiedemann, Annika, Wienands, Jürgen, Wilharm, Anneke, Wilkinson, Robert John, Willimsky, Gerald, Wing, James B, Winkelmann, Rieke, Winkler, Thomas H, Wirz, Oliver F, Wong, Alicia, Wurst, Peter, Yang, Jennie H M, Yang, Juhao, Yazdanbakhsh, Maria, Yu, Liping, Yue, Alice, Zhang, Hanlin, Zhao, Yi, Ziegler, Susanne Maria, Zielinski, Christina, Zimmermann, Jakob, Zychlinsky, Arturo

Improving the Quality and Reproducibility of Flow Cytometry in the Lung. An Official American Thoracic Society Workshop Report.

American journal of respiratory cell and molecular biology, 2019
Tighe, Robert M, Redente, Elizabeth F, Yu, Yen-Rei, Herold, Susanne, Sperling, Anne I, Curtis, Jeffrey L, Duggan, Ryan, Swaminathan, Suchitra, Nakano, Hideki, Zacharias, William J, Janssen, William J, Freeman, Christine M, Brinkman, Ryan R, Singer, Benjamin D, Jakubzick, Claudia V, Misharin, Alexander V

Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops.

Cytometry. Part A : the journal of the International Society for Analytical Cytology, 2019
Czechowska, Kamila, Lannigan, Joanne, Wang, Lili, Arcidiacono, Judith, Ashhurst, Thomas M, Barnard, Ruth M, Bauer, Steven, Bispo, Cláudia, Bonilla, Diana L, Brinkman, Ryan R, Cabanski, Maciej, Chang, Hyun-Dong, Chakrabarti, Lina, Chojnowski, Grace, Cotleur, Bunny, Degheidy, Heba, Dela Cruz, Gelo V, Eck, Steven, Elliott, John, Errington, Rachel, Filby, Andy, Gagnon, Dominic, Gardner, Rui, Green, Cherie, Gregory, Michael, Groves, Christopher J, Hall, Christopher, Hammes, Frederik, Hedrick, Michael, Hoffman, Robert, Icha, Jaroslav, Ivaska, Johanna, Jenner, Dominic C, Jones, Derek, Kerckhof, Frederiek-Maarten, Kukat, Christian, Lanham, David, Leavesley, Silas, Lee, Michael, Lin-Gibson, Sheng, Litwin, Virginia, Liu, Yanli, Molloy, Jenny, Moore, Jonni S, Müller, Susann, Nedbal, Jakub, Niesner, Raluca, Nitta, Nao, Ohlsson-Wilhelm, Betsy, Paul, Nicole E, Perfetto, Stephen, Portat, Ziv, Props, Ruben, Radtke, Stefan, Rayanki, Radhika, Rieger, Aja, Rogers, Samson, Rubbens, Peter, Salomon, Robert, Schiemann, Matthias, Sharpe, John, Sonder, Soren Ulrik, Stewart, Jennifer J, Sun, Yongliang, Ulrich, Henning, Van Isterdael, Gert, Vitaliti, Alessandra, van Vreden, Caryn, Weber, Michael, Zimmermann, Jacob, Vacca, Giacomo, Wallace, Paul, Tárnok, Attila

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