Publications
Browse our published articles
2023
Single Cell Spatial Biology for Precision Cancer Medicine.
Gentles AJ, Nirmal AJ, Heiser LM, Lundberg E, Newman AM.
Pac Symp Biocomput. 2023;28:549-553. PMID: 36541010.
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.
Sountoulidis A, Marco Salas S, Braun E, Avenel C, Bergenstråhle J, Theelke J, Vicari M, Czarnewski P, Liontos A, Abalo X, Andrusivová Ž, Mirzazadeh R, Asp M, Li X, Hu L, Sariyar S, Martinez Casals A, Ayoglu B, Firsova A, Michaëlsson J, Lundberg E, Wählby C, Sundström E, Linnarsson S, Lundeberg J, Nilsson M, Samakovlis C.
Nat Cell Biol. 2023 Feb;25(2):351-365. doi: 10.1038/s41556-022-01064-x.
The emerging landscape of spatial profiling technologies.
Moffitt JR, Lundberg E, Heyn H.
Nat Rev Genet. 2022 Dec;23(12):741-759. doi:10.1038/s41576-022-00515-3.
Analysis of the Human Protein Atlas Weakly Supervised Single-Cell Classification competition.
Le T, Winsnes CF, Axelsson U, Xu H, Mohanakrishnan Kaimal J, Mahdessian D, Dai S, Makarov IS, Ostankovich V, Xu Y, Benhamou E, Henkel C, Solovyev RA, Banić N, Bošnjak V, Bošnjak A, Miličević A, Ouyang W, Lundberg E.
Nat Methods. 2022 Oct;19(10):1221-1229. doi: 10.1038/s41592-022-01606-z.
Deep Visual Proteomics defines single-cell identity and heterogeneity.
Mund A, Coscia F, Kriston A, Hollandi R, Kovács F, Brunner AD, Migh E, Schweizer L, Santos A, Bzorek M, Naimy S, Rahbek-Gjerdrum LM, Dyring-Andersen B, Bulkescher J, Lukas C, Eckert MA, Lengyel E, Gnann C, Lundberg E, Horvath P, Mann M.
Nat Biotechnol. 2022 Aug;40(8):1231-1240. doi: 10.1038/s41587-022-01302-5..
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.
Mahdessian D, Cesnik AJ, Gnann C, Danielsson F, Stenström L, Arif M, Zhang C, Le T, Johansson F, Schutten R, Bäckström A, Axelsson U, Thul P, Cho NH, Carja O, Uhlén M, Mardinoglu A, Stadler C, Lindskog C, Ayoglu B, Leonetti MD, Pontén F, Sullivan DP, Lundberg E.
Nature. 2022 Aug;608(7924):E32. doi:10.1038/s41586-022-05180-4.
Andrews B, Chang JB, Collinson L, Li D, Lundberg E, Mahamid J, Manley S, Mhlanga M, Nakano A, Schöneberg J, Van Valen D, Wu T', Zaritsky A.
Nat Cell Biol. 2022 Aug;24(8):1180-1185. doi:10.1038/s41556-022-00960-6.
Understudied proteins: opportunities and challenges for functional proteomics.
Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J.
Nat Methods. 2022 Jul;19(7):774-779. doi: 10.1038/s41592-022-01454-x.
New Views of Old Proteins: Clarifying the Enigmatic Proteome.
Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL.
Mol Cell Proteomics. 2022 Jul;21(7):100254. doi: 10.1016/j.mcpro.2022.100254.
An open invitation to the Understudied Proteins Initiative.
Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J.
Nat Biotechnol. 2022 Jun;40(6):815-817. doi:10.1038/s41587-022-01316-z.
Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK.
Nat Methods. 2022 Mar;19(3):284-295. doi: 10.1038/s41592-021-01316-y.
The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells.
Melani RD, Gerbasi VR, Anderson LC, Sikora JW, Toby TK, Hutton JE, Butcher DS, Negrão F, Seckler HS, Srzentić K, Fornelli L, Camarillo JM, LeDuc RD, Cesnik AJ, Lundberg E, Greer JB, Fellers RT, Robey MT, DeHart CJ, Forte E, Hendrickson CL, Abbatiello SE, Thomas PM, Kokaji AI, Levitsky J, Kelleher NL.
Science. 2022 Jan 28;375(6579):411-418. doi: 10.1126/science.aaz5284.
The new era of quantitative cell imaging-challenges and opportunities.
Bagheri N, Carpenter AE, Lundberg E, Plant AL, Horwitz R.
Mol Cell. 2022 Jan20;82(2):241-247. doi: 10.1016/j.molcel.2021.12.024.
A multi-scale map of cell structure fusing protein images and interactions.
Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T.
Nature. 2021 Dec;600(7889):536-542. doi: 10.1038/s41586-021-04115-9.
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ..
Haniffa M, Taylor D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Camp JG, Chédotal A, Copp A, Etchevers HC, Giacobini P, Göttgens B, Guo G, Hupalowska A, James KR, Kirby E, Kriegstein A, Lundeberg J, Marioni JC, Meyer KB, Niakan KK, Nilsson M, Olabi B, Pe'er D, Regev A, Rood J, Rozenblatt-Rosen O, Satija R, Teichmann SA, Treutlein B, Vento-Tormo R, Webb S, Human Cell Atlas Developmental Biological Network.
Nat Methods. 2021 Oct;18(10):1192-1195. doi:10.1038/s41592-021-01262-9.
A roadmap for the Human Developmental Cell Atlas.
Gómez-de-Mariscal E, García-López-de-Haro C, Ouyang W, Donati L, Lundberg E, Unser M, Muñoz-Barrutia A, Sage D.
Nature. 2021 Sep;597(7875):196-205. doi: 10.1038/s41586-021-03620-1.
Christopher JS, Stadler Ch, Martin CE, Morgenstern M, Pan Y, Betsinger CN, Rattray DG, Mahdessian D, Gingras AC, Warscheid B, Lehtiö J, Cristea IM, Foster LJ, Emili A, Lilley KS.
Nature Reviews Methods Primers volume 1, Article number: 32 (2021).
Lundberg E, Funke J, Uhlmann V, Gerlich D, Walter T, Carpenter A, Coehlo LP.
Cell Syst. 2021 May 19;12(5):384-387. doi:10.1016/j.cels.2021.04.012.
LifeTime and improving European healthcare through cell-based interceptive medicine.
Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T; LifeTime Community Working Groups.
Nature. 2021 Apr;592(7852):E8. doi:10.10341586-021-03287-8. 8/s
Illuminating Non-genetic Cellular Heterogeneity with Imaging-Based Spatial Proteomics.
Gnann C, Cesnik AJ, Lundberg E.
Trends Cancer. 2021 Apr;7(4):278-282.doi: 10.1016/j.trecan.2020.12.006. Epub 2021 Jan 10.
Pycro-Manager: open-source software for customized and reproducible microscope control.
Pinkard H, Stuurman N, Ivanov IE, Anthony NM, Ouyang W, Li B, Yang B, Tsuchida MA, Chhun B, Zhang G, Mei R, Anderson M, Shepherd DP, Hunt-Isaak I, Dunn RL, Jahr W, KatoS, Royer LA, Thiagarajah JR, Eliceiri KW, Lundberg E, Mehta SB, Waller L.
Nat Methods. 2021 Mar;18(3):226-228.doi: 10.1038/s41592-021-01087-6.
Interactive biomedical segmentation tool powered by deep learning and ImJoy.
Ouyang W, Le T, Xu H, Lundberg E.
This article is included in the NEUBIAS - the Bioimage Analysts Network gateway.
Building a high-quality Human Cell Atlas.
Rozenblatt-Rosen O, Shin JW, Rood JE, Hupalowska A; Human Cell Atlas, Standards and Technology Working Group; Regev A, Heyn H.
Nat Biotechnol. 2021 Feb;39(2):149-153. doi:10.1038/s41587-020-00812-4.
Danielsson F, Mahdessian D, Axelsson U, Sullivan D, Uhlén M, Andersen JS, Thul PJ, Lundberg E.
Proteomics. 2020 Dec;20(23):e1900361.doi: 10.1002/pmic.201900361. Epub 2020 Aug 26.
LifeTime and improving European healthcare through cell-based interceptive medicine.
Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock Ch, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, Strooper BD, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, Oudenaarden A, Vidal M, Voet T. et al.
Nature. 2020 Nov;587(7834):377-386.doi: 10.1038/s41586-020-2715-9. Epub 2020 Sep 7.
A high-stringency blueprint of the human proteome.
Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik IK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau Ch, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS.
Nat Commun. 2020 Oct 16;11(1):5301.doi: 10.1038/s41467-020-19045-9.
Stenström L, Mahdessian D, Gnann C, Cesnik AJ, Ouyang W, Leonetti MD, Uhlén M, Cuylen-Haering S, Thul PJ, Lundberg E.
Mol Syst Biol. 2020 Aug;16(8):e9469.doi: 10.15252/msb.20209469.
Bäckström A, Kugel L, Gnann C, Xu H, Aslan JE, Lundberg E, Stadler Ch.
BJ Histochem Cytochem. 2020 Jul;68(7):473-489.doi: 10.1369/0022155420935403. Epub 2020 Jun 20.
Uhlén M, Karlsson M. J, Hober A, Svensson A-S, Scheffei J, Kotol D, Zhong W, Tebani A, Strandberg L, Edfors F, Sjöstedt E, Mulder J, Mardinoglu A, Berling A, Ekblad S, Dannemeyer M, Kanje S, Rockberg J, Lundqvist M, Malm M, Volk A-L, Nilsson P, Månberg A, Dodig-Crnkovic T, Pin E, Zwahlen M, Oksvold P, Oksvold KV, Häussler R S, Hong M-G, Lindskog C, Ponten F, Katona B, Vuu J, Lindström E, Nielsen J, Robinson J, Ayoglu B, Mahdessian D, Sullivan D, Thul P, Danielsson F, Stadler C, Lundberg E, Bergström G, Gummesson A, Voldborg BG, Tegel H, Hober S, Forsström B, Schwenk J M., Fagerberg L, Sivertsson Å.
Science Signaling. 2019 Nov ;12(609). pii: eaaz0274. doi: 10.1126/scisignal.aaz0274.
Analysis of the Human Protein Atlas Image Classification competition.
Ouyang W, Winsnes CF, Hjelmare M, Cesnik AJ, Åkesson L, Xu H, Sullivan DP, Dai S, Lan J, Jinmo P, Galib SM, Henkel C, Hwang K, Poplavskiy D, Tunguz B, Wolfinger RD, Gu Y, Li C, Xie J, Buslov D, Fironov S, Kiselev A, Panchenko D, Cao X, Wei R, Wu Y, Zhu X, Tseng KL, Gao Z, Ju C, Yi X, Zheng H, Kappel C, Lundberg E.
Nat Methods. 2019 Dec;16(12):1199-1200. doi: 10.1038/s41592-019-0627-0.
ImJoy: an open-source computational platform for the deep learning era.
Ouyang W, Mueller F, Hjelmare M, Lundberg E, Zimmer Ch.
Nat Methods. 2019 Dec;16(12):1254-1261. doi: 10.1038/s41592-019-0658-6. Epub 2019 Nov 28.
Voices in methods development.
Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW Jr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X.
Nat Methods. 2019 Oct;16(10):945-951. doi: 10.1038/s41592-019-0585-6.
Spatial proteomics: a powerful discovery tool for cell biology.
Lundberg E, Borner GHH.
Nat Rev Mol Cell Biol. 2019 Jan 18. doi: 10.1038/s41580-018-0094-y.
Sullivan DP, Winsnes CF, Åkesson L, Hjelmare M, Wiking M, Schutten R, Campbell L, Leifsson H, Rhodes S, Nordgren A, Smith K, Revaz B, Finnbogason B, Szantner A, Lundberg E.
Nat Biotechnol. 2018 Oct;36(9):820-828. doi: 10.1038/nbt.4225. Epub 2018 Aug 20.
Danielsson F, Fasterius E, Sullivan D, Hases L, Sanli K, Zhang C, Mardinoglu A, Al-Khalili C, Huss M, Uhlén M, Williams C, Lundberg E.
Oncotarget. 2018 Apr 13;9(28):19730-19744. doi: 10.18632/oncotarget.24808. eCollection 2018 Apr 13.
Seeing More: A Future of Augmented Microscopy.
Sullivan DP, Lundberg E.
Cell. 2018 Apr 19;173(3):546-548. doi: 10.1016/j.cell.2018.04.003.
Experimental validation of predicted cancer genes using FRET.
Guala D, Bernhem K, Blal HA, Jans D, Lundberg E, Brismar H, Sonnhammer ELL.
Methods Appl Fluoresc. 2018 Apr 25;6(3):035007. doi: 10.1088/2050-6120/aab932.
Mönnich M, Borgeskov L, Breslin L, Jakobsen L, Rogowski M, Doganli C, Schrøder JM, Mogensen JB, Blinkenkjær L, Harder LM, Lundberg E, Geimer S, Christensen ST, Andersen JS, Larsen LA, Pedersen LB.
Cell Rep. 2018 Mar 6;22(10):2584-2592. doi: 10.1016/j.celrep.2018.02.043.
How many human proteoforms are there?.
Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, et al.
Nat Chem Biol. 2018 Feb 14;14(3):206-214. doi: 10.1038/nchembio.2576.
O'Hagan S, Wright Muelas M, Day PJ, Lundberg E, Kell DB.
Cell Syst. 2018 Feb 28;6(2):230-244.e1. doi: 10.1016/j.cels.2018.01.003. Epub 2018 Feb 7.
Boström J, Sramkova Z, Salašová A, Johard H, Mahdessian D, Fedr R, Marks C, Medalová J, Souček K, Lundberg E, Linnarsson S, Bryja V, Sekyrova P, Altun M, Andäng M.
PLoS One. 2017 Dec 11;12(12):e0188772. doi: 10.1371/journal.pone.0188772. eCollection 2017.
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M3, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.
Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.
Carreras-Puigvert J1, Zitnik M, Jemth AS, Carter M, Unterlass JE, Hallström B, Loseva O, Karem Z, Calderón-Montaño JM, Lindskog C, Edqvist PH, Matusewski DJ, Ait Blal H, Berntsson RPA, Häggblad M, Martens U, Studham M, Lundgren B, Wählby C, Sonnhammer ELL, Lundberg E, Stenmark P, Zupan B, Helleday T.
Nat Commun. 2017 Nov 16;8(1):1541. doi: 10.1038/s41467-017-01642-w.
Ly T, Whigham A, Clarke R, Brenes-Murillo AJ, Estes B, Madhessian D, Lundberg E, Wadsworth P, Lamond AI.
Elife. 2017 Oct 20;6. pii: e27574. doi: 10.7554/eLife.27574.
Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.
Omenn GS, Lane L, Lundberg EK, Overall CM, Deutsch EW.
J Proteome Res. 2017 Dec 1;16(12):4281-4287. doi: 10.1021/acs.jproteome.7b00375. Epub 2017 Oct 9.
A pathology atlas of the human cancer transcriptome.
Uhlen M, Zhang C, Lee S, Sjöstedt E, Fagerberg L, Bidkhori G, Benfeitas R, Arif M, Liu Z, Edfors F, Sanli K, von Feilitzen K, Oksvold P, Lundberg E, Hober S, Nilsson 4, Mattsson J, Schwenk JM, Brunnström H, Glimelius B, Sjöblom T, Edqvist PH, Djureinovic D, Micke P, Lindskog C, Mardinoglu A, Ponten F.
Science. 2017 Aug 18;357(6352). pii: eaan2507. doi: 10.1126/science.aan2507.
A subcellular map of the human proteome.
Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, Alm T, Asplund A, Björk L, Breckels LM, Bäckström A, Danielsson F, Fagerberg L, Fall J, Gatto L, Gnann C, Hober S, Hjelmare M, Johansson F, Lee S, Lindskog C, Mulder J, Mulvey CM, Nilsson P, Oksvold P, Rockberg J, Schutten R, Schwenk JM, Sivertsson Å, Sjöstedt E, Skogs M, Stadler C, Sullivan DP, Tegel H, Winsnes C, Zhang C, Zwahlen M, Mardinoglu A, Pontén F, von Feilitzen K, Lilley KS, Uhlén M, Lundberg E.
Science. 2017 May 26;356(6340). pii: eaal3321. doi: 10.1126/science.aal3321. Epub 2017 May 11.
RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.
Alkasalias T, Alexeyenko A, Hennig K, Danielsson F, Lebbink RJ, Fielden M, Turunen SP, Lehti K, Kashuba V, Madapura HS, Bozoky B, Lundberg E, Balland M, Guvén H, Klein G, Gad AK, Pavlova T.
Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1413-E1421. doi: 10.1073/pnas.1621161114. Epub 2017 Feb 7.
Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins.
Skogs M, Stadler C, Schutten R, Hjelmare M, Gnann C, Björk L, Poser I, Hyman A, Uhlén M, Lundberg E.
J Proteome Res. 2017 Jan 6;16(1):147-155. doi: 10.1021/acs.jproteome.6b00821. Epub 2016 Oct 26.
Gene-specific correlation of RNA and protein levels in human cells and tissues.
Edfors F, Danielsson F, Hallström BM, Käll L, Lundberg E, Pontén F, Forsström B, Uhlén M.
Mol Syst Biol. 2016 Oct 20;12(10):883. doi: 10.15252/msb.20167144.
The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.
Scharaw S, Iskar 2, Ori A, Boncompain G, Laketa V, Poser I, Lundberg E, Perez F, Beck M, Bork P, Pepperkok R.
J Cell Biol. 2016 Nov 21;215(4):543-558. Epub 2016 Nov 8.
Omenn GS, Lane L, Lundberg EK, Beavis RC, Overall CM, Deutsch EW.
J Proteome Res. 2016 Nov 4;15(11):3951-3960. Epub 2016 Sep 20.
A proposal for validation of antibodies.
Uhlen M, Bandrowski A, Carr S, Edwards A, Ellenberg J, Lundberg E, Rimm DL, Rodriguez H, Hiltke T, Snyder M, Yamamoto T.
Nat Methods. 2016 Oct;13(10):823-7. doi: 10.1038/nmeth.3995. Epub 2016 Sep 5.
Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca, June C, Kamb S, Khvorova A, Kim DH, Kim JS, Krishnan Y, Lakadamyali M, Lappalainen T, Lewin S, Liao J, Loman N, Lundberg et at al.
Nat Biotechnol. 2016 Mar;34(3):270-5. doi: 10.1038/nbt.3502.
Alm T, Lundberg E, Uhlén M.
EuPA Open Proteom. 2016 Jan 7;10:56-58. doi: 10.1016/j.euprot.2016.01.002. eCollection 2016 Mar.
Towards a functional definition of the mitochondrial human proteome.
Fasano M, Alberio T, Babu M, Lundberg E, Urbani A.
EuPA Open Proteom. 2016 Jan 7;10:24-27. doi: 10.1016/j.euprot.2016.01.004. eCollection 2016 Mar.
Systems Proteomics View of the Endogenous Human Claudin Protein Family.
Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS.
J Proteome Res. 2016 Feb 5;15(2):339-59. doi: 10.1021/acs.jproteome.5b00769. Epub 2016 Jan 12.
The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation.
Gustafsson Sheppard N, Jarl L, Mahadessian D, Strittmatter L, Schmidt A, Madhusudan N, Tegnér J, Lundberg EK, Asplund A, Jain M, Nilsson R.
Sci Rep. 2015 Oct 13;5:15029. doi: 10.1038/srep15029.
O'Hurley G, Busch C, Fagerberg L, Hallström BM, Stadler C, Tolf A, Lundberg E, Schwenk JM, Jirström K, Bjartell A, Gallagher WM, Uhlén M, Pontén F.
PLoS One. 2015 Aug 3;10(8):e0133449. doi: 10.1371/journal.pone.0133449. eCollection 2015.
Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW.
J Proteome Res. 2015 Sep 4;14(9):3452-60. doi: 10.1021/acs.jproteome.5b00499. Epub 2015 Jul 30.
Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.
Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC et al.
J Proteome Res. 2015 Sep 4;14(9):3415-31. doi: 10.1021/pr5013009. Epub 2015 Jul 23.
Proteomics. Tissue-based map of the human proteome.
Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F.
Science. 2015 Jan 23;347(6220):1260419. doi: 10.1126/science.1260419.
Edfors F, Boström T, Forsström B, Zeiler M, Johansson H, Lundberg E, Hober S, Lehtiö J, Mann M, Uhlen M.
Mol Cell Proteomics. 2014 Jun;13(6):1611-24. doi: 10.1074/mcp.M113.034140. Epub 2014 Apr 10.
The human liver-specific proteome defined by transcriptomics and antibody-based profiling.
Kampf C, Mardinoglu A, Fagerberg L, Hallström BM, Edlund K, Lundberg E, Pontén F, Nielsen J, Uhlen M.
FASEB J. 2014 Jul;28(7):2901-14. doi: 10.1096/fj.14-250555. Epub 2014 Mar 19.
Liem DA, Nsair A, Setty SP, Cadeiras M, Wang D, Maclellan R, Lotz C, Lin AJ, Tabaraki J, Li H, Ge J, Odeberg J, Ponten F, Larson E, Mulder J, Lundberg E, Weiss JN, Uhlen M, Ping P, Deng MC.
Circ Heart Fail. 2014 Mar 1;7(2):359-66. doi: 10.1161/CIRCHEARTFAILURE.113.000250.
RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.
Stadler C, Fagerberg L, Sivertsson Å, Oksvold P, Zwahlen M, Hallström BM, Lundberg E, Uhlén M.
J Proteome Res. 2014 Apr 4;13(4):2019-27. doi: 10.1021/pr401156g. Epub 2014 Mar 12.
A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia.
Alm T, von Feilitzen K, Lundberg E, Sivertsson Å, Uhlén M.
J Proteome Res. 2014 Mar 7;13(3):1669-76. doi: 10.1021/pr4011525. Epub 2014 Feb 17.
Antibody performance in western blot applications is context-dependent.
Algenäs C, Agaton C, Fagerberg L, Asplund A, Björling L, Björling E, Kampf C, Lundberg E, Nilsson P, Persson A, Wester K, Pontén F, Wernérus H, Uhlén M, Ottosson Takanen J, Hober S.
Biotechnol J. 2014 Mar;9(3):435-45. doi: 10.1002/biot.201300341. Epub 2014 Jan 29.
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins.
Lane L1, Bairoch A, Beavis RC, Deutsch EW, Gaudet P, Lundberg E, Omenn GS.
J Proteome Res. 2014 Jan 3;13(1):15-20. doi: 10.1021/pr401144x. Epub 2013 Dec 23.
Fagerberg L, Hallström BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S, Danielsson A, Edlund K, Asplund A, Sjöstedt E, Lundberg E, Szigyarto CA, Skogs M, Takanen JO, Berling H, Tegel H, Mulder J, Nilsson P, Schwenk JM, Lindskog C, Danielsson F, Mardinoglu A, Sivertsson A, von Feilitzen K, Forsberg M, Zwahlen M, Olsson I, Navani S, Huss M, Nielsen J, Ponten F, Uhlén M.
Mol Cell Proteomics. 2014 Feb;13(2):397-406. doi: 10.1074/mcp.M113.035600. Epub 2013 Dec 5.
Rexhepaj E, Agnarsdóttir M, Bergman J, Edqvist PH, Bergqvist M, Uhlén M, Gallagher WM, Lundberg E, Ponten F.
PLoS One. 2013 May 17;8(5):e62070. doi: 10.1371/journal.pone.0062070. Print 2013.
Danielsson F, Skogs M, Huss M, Rexhepaj E, O'Hurley G, Klevebring D, Pontén F, Gad AK, Uhlén M, Lundberg E.
Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6853-8. doi: 10.1073/pnas.1216436110. Epub 2013 Apr 8.
Centrosome isolation and analysis by mass spectrometry-based proteomics.
Jakobsen L, Schrøder JM, Larsen KM, Lundberg E, Andersen JS.
Methods Enzymol. 2013;525:371-93. doi: 10.1016/B978-0-12-397944-5.00018-3.
Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.
Geiger T, Velic A, Macek B, Lundberg E, Kampf C, Nagaraj N, Uhlen M, Cox J, Mann M.
Mol Cell Proteomics. 2013 Jun;12(6):1709-22. doi: 10.1074/mcp.M112.024919. Epub 2013 Feb 22.
Stadler C, Rexhepaj E, Singan VR, Murphy RF, Pepperkok R, Uhlén M, Simpson JC, Lundberg E.
Nat Methods. 2013 Apr;10(4):315-23. doi: 10.1038/nmeth.2377. Epub 2013 Feb 24.
Fagerberg L, Oksvold P, Skogs M, Algenäs C, Lundberg E, Pontén F, Sivertsson A, Odeberg J, Klevebring D, Kampf C, Asplund A, Sjöstedt E, Al-Khalili Szigyarto C, Edqvist PH, Olsson I, Rydberg U, Hudson P, Ottosson Takanen J, Berling H, Björling L, Tegel H, Rockberg J, Nilsson P, Navani S, Jirström K, Mulder J, Schwenk JM, Zwahlen M, Hober S, Forsberg M, von Feilitzen K, Uhlén M.
J Proteome Res. 2013 Jun 7;12(6):2439-48. doi: 10.1021/pr300924j. Epub 2012 Dec 31.
Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, Dalton S, Fenyo D, Fanayan S, Gates C, Gaudet P, Hincapie M, Hanash S, Kim H, Jeong SK, Lundberg E, Mias G, Menon R, Mu Z, Nice E, Paik YK, Uhlen M, Wells L, Wu SL, Yan F, Zhang F, Zhang Y, Snyder M, Omenn GS, Beavis RC, Hancock WS.
J Proteome Res. 2013 Jan 4;12(1):45-57. doi: 10.1021/pr300985j. Epub 2012 Dec 21.
Danielsson F, Wiking M, Mahdessian D, Skogs M, Ait Blal H, Hjelmare M, Stadler C, Uhlén M, Lundberg E.
J Proteome Res. 2013 Jan 4;12(1):299-307. doi: 10.1021/pr3009308. Epub 2012 Dec 20.
Li J, Shariff A, Wiking M, Lundberg E, Rohde GK, Murphy RF.
PLoS One. 2012;7(11):e50292. doi: 10.1371/journal.pone.0050292. Epub 2012 Nov 28.
Akan P, Alexeyenko A, Costea PI, Hedberg L, Solnestam BW, Lundin S, Hällman J, Lundberg E, Uhlén M, Lundeberg J.
Genome Med. 2012 Nov 18;4(11):86. doi: 10.1186/gm387. eCollection 2012.
Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.
Solnestam BW1, Stranneheim H, Hällman J, Käller M, Lundberg E, Lundeberg J, Akan P.
BMC Genomics. 2012 Oct 30;13:574. doi: 10.1186/1471-2164-13-574.
Kampf C, Bergman J, Oksvold P, Asplund A, Navani S, Wiking M, Lundberg E, Uhlén M, Ponten F.
BMC Med. 2012 Sep 12;10:103. doi: 10.1186/1741-7015-10-103.
Bock T, Moest H, Omasits U, Dolski S, Lundberg E, Frei A, Hofmann A, Bausch-Fluck D, Jacobs A, Krayenbuehl N, Uhlen M, Aebersold R, Frei K, Wollscheid B.
J Proteome Res. 2012 Oct 5;11(10):4885-93. doi: 10.1021/pr300360a. Epub 2012 Aug 31.
Stadler C, Hjelmare M, Neumann B, Jonasson K, Pepperkok R, Uhlén M, Lundberg E.
J Proteomics. 2012 Apr 3;75(7):2236-51. doi: 10.1016/j.jprot.2012.01.030. Epub 2012 Feb 15.
Dengjel J, Høyer-Hansen M, Nielsen MO, Eisenberg T, Harder LM, Schandorff S, Farkas T, Kirkegaard T, Becker AC, Schroeder S, Vanselow K, Lundberg E, Nielsen MM, Kristensen AR, Akimov V, Bunkenborg J, Madeo F, Jäättelä M, Andersen JS.
Mol Cell Proteomics. 2012 Mar;11(3):M111.014035. doi: 10.1074/mcp.M111.014035. Epub 2012 Feb 6.
Antibody-based protein profiling of the human chromosome 21.
Uhlén M, Oksvold P, Älgenäs C, Hamsten C, Fagerberg L, Klevebring D, Lundberg E, Odeberg J, Pontén F, Kondo T, Sivertsson Å.
Mol Cell Proteomics. 2012 Mar;11(3):M111.013458. doi: 10.1074/mcp.M111.013458. Epub 2011 Oct 31.
Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway.
Larance M, Kirkwood KJ, Xirodimas DP, Lundberg E, Uhlen M, Lamond AI.
Mol Cell Proteomics. 2012 Mar;11(3):M111.014407. doi: 10.1074/mcp.M111.014407. Epub 2011 Oct 29.
Ahmad Y, Boisvert FM, Lundberg E, Uhlen M, Lamond AI.
Mol Cell Proteomics. 2012 Mar;11(3):M111.013680. doi: 10.1074/mcp.M111.013680. Epub 2011 Oct 16.
Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M.
Mol Cell Proteomics. 2012 Mar;11(3):O111.009613. doi: 10.1074/mcp.O111.009613. Epub 2011 Sep 30.
Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.
Hjelm B, Forsström B, Igel U, Johannesson H, Stadler C, Lundberg E, Ponten F, Sjöberg A, Rockberg J, Schwenk JM, Nilsson P, Johansson C, Uhlén M.
Protein Sci. 2011 Nov;20(11):1824-35. doi: 10.1002/pro.716. Epub 2011 Oct 12.
SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas.
Magnusson K, de Wit M, Brennan DJ, Johnson LB, McGee SF, Lundberg E, Naicker K, Klinger R, Kampf C, Asplund A, Wester K, Gry M, Bjartell A, Gallagher WM, Rexhepaj E, Kilpinen S, Kallioniemi OP, Belt E, Goos J, Meijer G, Birgisson H, Glimelius B, Borrebaeck CA, Navani S, Uhlén M, O'Connor DP, Jirström K, Pontén F.
Am J Surg Pathol. 2011 Jul;35(7):937-48. doi: 10.1097/PAS.0b013e31821c3dae.
Mapping the subcellular protein distribution in three human cell lines.
Fagerberg L, Stadler C, Skogs M, Hjelmare M, Jonasson K, Wiking M, Abergh A, Uhlén M, Lundberg E.
J Proteome Res. 2011 Aug 5;10(8):3766-77. doi: 10.1021/pr200379a. Epub 2011 Jun 29.
Jakobsen L, Vanselow K, Skogs M, Toyoda Y, Lundberg E, Poser I, Falkenby LG, Bennetzen M, Westendorf J, Nigg EA, Uhlen M, Hyman AA, Andersen JS.
EMBO J. 2011 Apr 20;30(8):1520-35. doi: 10.1038/emboj.2011.63. Epub 2011 Mar 11.
Borsics T, Lundberg E, Geerts D, Koomoa DL, Koster J, Wester K, Bachmann AS.
Cancer Sci. 2010 Jul;101(7):1624-31. doi: 10.1111/j.1349-7006.2010.01570.x. Epub 2010 Mar 19.
What determines specific cell functions?
Lundberg E, Svahn HA.
Lab Chip. 2011 Jun 21;11(12):2039-41. doi: 10.1039/c1lc90018h. Epub 2011 Mar 8.
Defining the transcriptome and proteome in three functionally different human cell lines.
Lundberg E, Fagerberg L, Klevebring D, Matic I, Geiger T, Cox J, Algenäs C, Lundeberg J, Mann M, Uhlen M.
Mol Syst Biol. 2010 Dec 21;6:450. doi: 10.1038/msb.2010.106.
Towards a knowledge-based Human Protein Atlas.
Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Björling L, Ponten F.
Nat Biotechnol. 2010 Dec;28(12):1248-50. doi: 10.1038/nbt1210-1248.
Analysis of transcript and protein overlap in a human osteosarcoma cell line.
Klevebring D, Fagerberg L, Lundberg E, Emanuelsson O, Uhlén M, Lundeberg J.
BMC Genomics. 2010 Dec 2;11:684. doi: 10.1186/1471-2164-11-684.
Grimm S, Lundberg E, Yu F, Shibasaki S, Vernet E, Skogs M, Nygren PÅ, Gräslund T.
N Biotechnol. 2010 Dec 31;27(6):766-73. doi: 10.1016/j.nbt.2010.07.016. Epub 2010 Jul 30.
Creation of an antibody-based subcellular protein atlas.
Lundberg E, Uhlén M.
Proteomics. 2010 Nov;10(22):3984-96. doi: 10.1002/pmic.201000125.
Borsics T, Lundberg E, Geerts D, Koomoa DL, Koster J, Wester K, Bachmann AS.
Cancer Sci. 2010 Jul;101(7):1624-31. doi: 10.1111/j.1349-7006.2010.01570.x. Epub 2010 Mar 19.
Li J, Lundberg E, Vernet E, Larsson B, Höidén-Guthenberg I, Gräslund T.
Biotechnol Appl Biochem. 2010 Feb 25;55(2):99-109. doi: 10.1042/BA20090226.
Selective expression of Syntaxin-7 protein in benign melanocytes and malignant melanoma.
Strömberg S, Agnarsdóttir M, Magnusson K, Rexhepaj E, Bolander A, Lundberg E, Asplund A, Ryan D, Rafferty M, Gallagher WM, Uhlen M, Bergqvist M, Ponten F.
J Proteome Res. 2009 Apr;8(4):1639-46. doi: 10.1021/pr800745e.
Vernet E, Lundberg E, Friedman M, Rigamonti N, Klausing S, Nygren PA, Gräslund T.
N Biotechnol. 2009 Sep;25(6):417-23. doi: 10.1016/j.nbt.2009.02.001.
Automated Analysis of Human Protein Atlas Immunofluorescence Images.
Newberg JY, Li J, Rao A, Pontén F, Uhlén M, Lundberg E, Murphy RF.
Proc IEEE Int Symp Biomed Imaging. 2009;5193229:1023-1026.
Selection and characterization of Affibody ligands to the transcription factor c-Jun.
Lundberg E, Brismar H, Gräslund T.
Biotechnol Appl Biochem. 2009 Jan;52(Pt 1):17-27. doi: 10.1042/BA20070178.
Vernet E, Konrad A, Lundberg E, Nygren PA, Gräslund T.
J Immunol Methods. 2008 Sep 30;338(1-2):1-6. doi: 10.1016/j.jim.2008.06.005. Epub 2008 Jul 29.
A genecentric Human Protein Atlas for expression profiles based on antibodies.
Berglund L, Björling E, Oksvold P, Fagerberg L, Asplund A, Szigyarto CA, Persson A, Ottosson J, Wernérus H, Nilsson P, Lundberg E, Sivertsson A, Navani S, Wester K, Kampf C, Hober S, Pontén F, Uhlén M.
Mol Cell Proteomics. 2008 Oct;7(10):2019-27. doi: 10.1074/mcp.R800013-MCP200.
Lundberg E, Gry M, Oksvold P, Kononen J, Andersson-Svahn H, Pontén F, Uhlén M, Asplund A.
J Proteomics. 2008 Oct 7;71(4):448-60. doi: 10.1016/j.jprot.2008.06.014. Epub 2008 Jul 5.
Toward a confocal subcellular atlas of the human proteome.
Barbe L, Lundberg E, Oksvold P, Stenius A, Lewin E, Björling E, Asplund A, Pontén F, Brismar H, Uhlén M, Andersson-Svahn H.
Mol Cell Proteomics. 2008 Mar;7(3):499-508. Epub 2007 Nov 19.
A novel method for reproducible fluorescent labeling of small amounts of antibodies on solid phase.
Lundberg E, Sundberg M, Gräslund T, Uhlén M, Svahn HA.
J Immunol Methods. 2007 Apr 30;322(1-2):40-9. Epub 2007 Feb 28.
Lundberg E, Höidén-Guthenberg I, Larsson B, Uhlén M, Gräslund T.
J Immunol Methods. 2007 Jan 30;319(1-2):53-63. Epub 2006 Nov 21.