Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines

Nature Communications, Mar 2022

Leo, I.R., Aswad, L., Stahl, M., Kunold, E., Post, F., Erkers, T., Struyf, N., Mermelekas, G., Joshi, R.N., Gracia-Villacampa, E., Östling, P., Kallioniemi, O.P., Tamm, K.P., Siavelis, I., Lehtiö, J., Vesterlund, M., Jafari, R.

The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology

Nature Cancer, Feb 2022

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Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune-evasion mechanisms

Nature Cancer, Nov 2021

Lehtiö, J., Arslan, T., Siavelis, I., Pan, Y., Socciarelli, F., Berkovska, O., Umer, H.M., Mermelekas, G., Pirmoradian, M., Jönsson, M., Brunnström, H., Brustugun, O.T., Purohit, K.P., Cunningham, R., Asl, H.F., Isaksson, S., Arbajian, E., Aine, M., Karlsson, A., Kotevska, M., Hansen, C.G., Haakensen, V.D., Helland, Å., Tamborero, D., Johansson, H.J., Branca, R.M., Planck, M., Staaf, J., Orre, L.M.

Support systems to guide clinical decision-making in precision oncology: The Cancer Core Europe Molecular Tumor Board Portal.

Nature Medicine, Jul 2020

Tamborero, D., Dienstmann, R., Rachid, M.H., Boekel, J., Baird, R., Braña, I., De Petris, L., Yachnin, J., Massard, C., Opdam, F.L., Schlenk, R., Vernieri, C., Garralda, E., Masucci, M., Villalobos, X., Chavarria, E., Cancer Core Europe consortium, Calvo, F., Fröhling, S., Eggermont, A., Apolone, G., Voest, E.E., Caldas, C., Tabernero, J., Ernberg, I., Rodon, J., Lehtiö, J.

In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta.

eLife, Apr 2019

Pernemalm, M., Sandberg, A., Zhu, Y., Boekel, J., Tamburro, D., Schwenk, J.M., Bjork, A., Wahren-Herlenius, M., Amark, H., Ostenson, C.-G., Westgren, M., Lehtiö, J.

Breast cancer quantitative proteome and proteogenomic landscape.

Nature communications, Apr 2019

Johansson, H.J., Socciarelli, F., Vacanti, N.M., Haugen, M.H., Zhu, Y., Siavelis, I., Fernandez-Woodbridge, A., Aure, M.R., Sennblad, B., Vesterlund, M., Branca, R.M., Orre, L.M., Huss, M., Fredlund, E., Beraki, E., Garred, Ø., Boekel, J., Sauer, T., Zhao, W., Nord, S., Höglander, E.K., Jans, D.C., Brismar, H., Haukaas, T.H., Bathen, T.F., Schlichting, E., Naume, B., Geisler, J., Hofvind, S., Engebråten, O., Geitvik, G.A., Langerød, A., Kåresen, R., Mælandsmo, G.M., Sørlie, T., Skjerven, H.K., Park, D., Hartman-Johnsen, O.-J., Lüders, T., Borgen, E., Kristensen, V.N., Russnes, H.G., Lingjærde, O.C., Mills, G.B., Sahlberg, K.K., Børresen-Dale, A.-L., Lehtiö, J.

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia.

Nature communications, Apr 2019

Yang, M, Vesterlund, M, Siavelis, I, Moura-Castro, LH, Castor, A, Fioretos, T, Jafari, R, Lilljebjörn, H, Odom, DT, Olsson, L, Ravi, N, Woodward, EL, Harewood, L, Lehtiö, J, Paulsson, K.

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization.

Molecular Cell, Jan 2019

Orre LM, Vesterlund M, Pan Y, Arslan T, Zhu Y, Fernandez Woodbridge A, Frings O, Fredlund E, Lehtiö J.

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

Nature communications, Mar 2018

Zhu, Y, Orre, LM, Johansson, HJ, Huss, M, Boekel, J, Vesterlund, M, Fernandez-Woodbridge, A, Branca, RMM, Lehtiö, J

Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome.

Scientific reports, Jul 2017

Panizza, E, Branca, RMM, Oliviusson, P, Orre, LM, Lehtiö, J

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

Nucleic acids research, Mar 2017

Zhu, Y, Engström, PG, Tellgren-Roth, C, Baudo, CD, Kennell, JC, Sun, S, Billmyre, RB, Schröder, MS, Andersson, A, Holm, T, Sigurgeirsson, B, Wu, G, Sankaranarayanan, SR, Siddharthan, R, Sanyal, K, Lundeberg, J, Nystedt, B, Boekhout, T, Dawson, TL, Heitman, J, Scheynius, A, Lehtiö, J

Multi-omic data analysis using Galaxy.

Nature biotechnology, Feb 2015

Boekel, J, Chilton, JM, Cooke, IR, Horvatovich, PL, Jagtap, PD, Käll, L, Lehtiö, J, Lukasse, P, Moerland, PD, Griffin, TJ

SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.

Molecular & cellular proteomics : MCP, Jun 2014

Zhu, Y, Hultin-Rosenberg, L, Forshed, J, Branca, RM, Orre, LM, Lehtiö, J

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

Nature methods, Jan 2014

Branca, RM, Orre, LM, Johansson, HJ, Granholm, V, Huss, M, Pérez-Bercoff, Å, Forshed, J, Käll, L, Lehtiö, J

Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer.

Nature communications, Jan 2013

Johansson, HJ, Sanchez, BC, Mundt, F, Forshed, J, Kovacs, A, Panizza, E, Hultin-Rosenberg, L, Lundgren, B, Martens, U, Máthé, G, Yakhini, Z, Helou, K, Krawiec, K, Kanter, L, Hjerpe, A, Stål, O, Linderholm, BK, Lehtiö, J

S100A4 interacts with p53 in the nucleus and promotes p53 degradation.

Oncogene, Dec 2013

Orre, LM, Panizza, E, Kaminskyy, VO, Vernet, E, Gräslund, T, Zhivotovsky, B, Lehtiö, J