Search Results - "Umer, HM"

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides by Umer, Husen M, Audain, Enrique, Zhu, Yafeng, Pfeuffer, Julianus, Sachsenberg, Timo, Lehtiö, Janne, Branca, Rui M, Perez-Riverol, Yasset

“…Abstract Summary We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow…”
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Proteogenomics refines the molecular classification of chronic lymphocytic leukemia by Herbst, Sophie A., Vesterlund, Mattias, Helmboldt, Alexander J., Jafari, Rozbeh, Siavelis, Ioannis, Stahl, Matthias, Schitter, Eva C., Liebers, Nora, Brinkmann, Berit J., Czernilofsky, Felix, Roider, Tobias, Bruch, Peter-Martin, Iskar, Murat, Kittai, Adam, Huang, Ying, Lu, Junyan, Richter, Sarah, Mermelekas, Georgios, Umer, Husen Muhammad, Knoll, Mareike, Kolb, Carolin, Lenze, Angela, Cao, Xiaofang, Österholm, Cecilia, Wahnschaffe, Linus, Herling, Carmen, Scheinost, Sebastian, Ganzinger, Matthias, Mansouri, Larry, Kriegsmann, Katharina, Kriegsmann, Mark, Anders, Simon, Zapatka, Marc, Del Poeta, Giovanni, Zucchetto, Antonella, Bomben, Riccardo, Gattei, Valter, Dreger, Peter, Woyach, Jennifer, Herling, Marco, Müller-Tidow, Carsten, Rosenquist, Richard, Stilgenbauer, Stephan, Zenz, Thorsten, Huber, Wolfgang, Tausch, Eugen, Lehtiö, Janne, Dietrich, Sascha

“…Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and…”
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Proteogenomic analysis of acute myeloid leukemia associates relapsed disease with reprogrammed energy metabolism both in adults and children by Stratmann, Svea, Vesterlund, Mattias, Umer, Husen M., Eshtad, Saeed, Skaftason, Aron, Herlin, Morten Krogh, Sundström, Christer, Eriksson, Anna, Höglund, Martin, Palle, Josefine, Abrahamsson, Jonas, Jahnukainen, Kirsi, Munthe-Kaas, Monica Cheng, Zeller, Bernward, Tamm, Katja Pokrovskaja, Lindskog, Cecilia, Cavelier, Lucia, Lehtiö, Janne, Holmfeldt, Linda

“…Despite improvement of current treatment strategies and novel targeted drugs, relapse and treatment resistance largely determine the outcome for acute myeloid…”
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Therapeutic Cancer Vaccination with Immunopeptidomics-Discovered Antigens Confers Protective Antitumor Efficacy by Peltonen, Karita, Feola, Sara, Umer, Husen M., Chiaro, Jacopo, Mermelekas, Georgios, Ylösmäki, Erkko, Pesonen, Sari, Branca, Rui M. M., Lehtiö, Janne, Cerullo, Vincenzo

“…Knowledge of clinically targetable tumor antigens is becoming vital for broader design and utility of therapeutic cancer vaccines. This information is obtained…”
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (vol 578, pg 102, 2020) by Rheinbay, E, Nielsen, MM, Abascal, F, Wala, JA, Shapira, O, Tiao, G, Hornshoj, H, Hess, JM, Juul, RI, Lin, Z, Feuerbach, L, Sabarinathan, R, Madsen, T, Kim, J, Mularoni, L, Shuai, S, Lanzos, A, Herrmann, C, Maruvka, YE, Shen, CY, Amin, SB, Bandopadhayay, P, Bertl, J, Boroevich, KA, Busanovich, J, Carlevaro-Fita, J, Chakravarty, D, Chan, CWY, Craft, D, Dhingra, P, Diamanti, K, Fonseca, NA, Gonzalez-Perez, A, Guo, QY, Hamilton, MP, Haradhvala, NJ, Hong, C, Isaev, K, Johnson, TA, Juul, M, Kahles, A, Kahraman, A, Kim, Y, Komorowski, J, Kumar, K, Kumar, S, Lee, D, Lehmann, KV, Li, YL, Liu, EM, Lochovsky, L, Park, K, Pich, O, Roberts, ND, Saksena, G, Schumacher, SE, Sidiropoulos, N, Sieverling, L, Sinnott-Armstrong, N, Stewart, C, Tamborero, D, Tubio, JMC, Umer, HM, Uuskula-Reimand, L, Wadelius, C, Wadi, L, Yao, XT, Zhang, CZ, Zhang, J, Haber, JE, Hobolth, A, Imielinski, M, Kellis, M, Lawrence, MS, von Mering, C, Nakagawa, H, Raphael, BJ, Rubin, MA, Sander, C, Stein, LD, Stuart, JM, Tsunoda, T, Wheeler, DA, Johnson, R, Reimand, J, Gerstein, M, Khurana, E, Campbell, PJ, Lopez-Bigas, N, Weischenfeldt, J, Beroukhim, R, Martincorena, I, Pedersen, JS

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Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes by Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A., Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M., Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E., Shen, Ciyue, Amin, Samirkumar B., Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A., Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A., Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P., Haradhvala, Nicholas J., Hong, Chen, Isaev, Keren, Johnson, Todd A., Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D., Saksena, Gordon, Schumacher, Steven E., Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose M. C., Umer, Husen M., Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E., Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S., von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J., Rubin, Mark A., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Tsunoda, Tatsuhiko, Wheeler, David A., Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J., López-Bigas, Núria, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, Getz, Gad

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Glioblastoma stem cells express non‐canonical proteins and exclusive mesenchymal‐like or non‐mesenchymal‐like protein signatures by Babačić, Haris, Galardi, Silvia, Umer, Husen M., Hellström, Mats, Uhrbom, Lene, Maturi, Nagaprathyusha, Cardinali, Deborah, Pellegatta, Serena, Michienzi, Alessandro, Trevisi, Gianluca, Mangiola, Annunziato, Lehtiö, Janne, Ciafrè, Silvia Anna, Pernemalm, Maria

“…Glioblastoma (GBM) cancer stem cells (GSCs) contribute to GBM's origin, recurrence, and resistance to treatment. However, the understanding of how mRNA…”
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Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms by Lehtiö, Janne, Arslan, Taner, Siavelis, Ioannis, Pan, Yanbo, Socciarelli, Fabio, Berkovska, Olena, Umer, Husen M, Mermelekas, Georgios, Pirmoradian, Mohammad, Jönsson, Mats, Brunnström, Hans, Brustugun, Odd Terje, Purohit, Krishna Pinganksha, Cunningham, Richard, Foroughi Asl, Hassan, Isaksson, Sofi, Arbajian, Elsa, Aine, Mattias, Karlsson, Anna, Kotevska, Marija, Gram Hansen, Carsten, Drageset Haakensen, Vilde, Helland, Åslaug, Tamborero, David, Johansson, Henrik J, Branca, Rui M, Planck, Maria, Staaf, Johan, Orre, Lukas M

“…Despite major advancements in lung cancer treatment, long-term survival is still rare, and a deeper understanding of molecular phenotypes would allow the…”
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Functional annotation of noncoding mutations in cancer by Umer, Husen M, Smolinska, Karolina, Komorowski, Jan, Wadelius, Claes

“…In a cancer genome, the noncoding sequence contains the vast majority of somatic mutations. While very few are expected to be cancer drivers, those affecting…”
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Production and Generation of Proteogenomics Databases using PyPGATK by Umer, HM, Zhu, YF, Audain, E, Lehtio, J, Branca, R, Perez-Riverol, Y

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