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

Jordan Cran, MSc, PMP

Research Projects Manager

Post-Docs

Students/Trainees

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, 2020
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

High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation.

Nature immunology, 2020
Abeler-Dörner, Lucie, Laing, Adam G, Lorenc, Anna, Ushakov, Dmitry S, Clare, Simon, Speak, Anneliese O, Duque-Correa, Maria A, White, Jacqueline K, Ramirez-Solis, Ramiro, Saran, Namita, Bull, Katherine R, Morón, Belén, Iwasaki, Jua, Barton, Philippa R, Caetano, Susana, Hng, Keng I, Cambridge, Emma, Forman, Simon, Crockford, Tanya L, Griffiths, Mark, Kane, Leanne, Harcourt, Katherine, Brandt, Cordelia, Notley, George, Babalola, Kolawole O, Warren, Jonathan, Mason, Jeremy C, Meeniga, Amrutha, Karp, Natasha A, Melvin, David, Cawthorne, Eleanor, Weinrick, Brian, Rahim, Albina, Drissler, Sibyl, Meskas, Justin, Yue, Alice, Lux, Markus, Song-Zhao, George X, Chan, Anna, Ballesteros Reviriego, Carmen, Abeler, Johannes, Wilson, Heather, Przemska-Kosicka, Agnieszka, Edmans, Matthew, Strevens, Natasha, Pasztorek, Markus, Meehan, Terrence F, Powrie, Fiona, Brinkman, Ryan, Dougan, Gordon, Jacobs, William, Lloyd, Clare M, Cornall, Richard J, Maloy, Kevin J, Grencis, Richard K, Griffiths, Gillian M, Adams, David J, Hayday, Adrian C

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

Dynamic molecular changes during the first week of human life follow a robust developmental trajectory.

Nature communications, 2019
Lee, Amy H, Shannon, Casey P, Amenyogbe, Nelly, Bennike, Tue B, Diray-Arce, Joann, Idoko, Olubukola T, Gill, Erin E, Ben-Othman, Rym, Pomat, William S, van Haren, Simon D, Cao, Kim-Anh Lê, Cox, Momoudou, Darboe, Alansana, Falsafi, Reza, Ferrari, Davide, Harbeson, Daniel J, He, Daniel, Bing, Cai, Hinshaw, Samuel J, Ndure, Jorjoh, Njie-Jobe, Jainaba, Pettengill, Matthew A, Richmond, Peter C, Ford, Rebecca, Saleu, Gerard, Masiria, Geraldine, Matlam, John Paul, Kirarock, Wendy, Roberts, Elishia, Malek, Mehrnoush, Sanchez-Schmitz, Guzmán, Singh, Amrit, Angelidou, Asimenia, Smolen, Kinga K, , , Brinkman, Ryan R, Ozonoff, Al, Hancock, Robert E W, van den Biggelaar, Anita H J, Steen, Hanno, Tebbutt, Scott J, Kampmann, Beate, Levy, Ofer, Kollmann, Tobias R

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