Emma Lundberg

Emma Lundberg is associate professor at KTH and head of the Cell Atlas project within the Human Protein Atlas with research focusing on spatial proteomics and cell biology.

Emma Lundberg is also Director of the Cell Profiling facility at SciLifeLab, enabling researchers to make use of the knowledge and resources of the Human Protein Atlas applied to their research projects.

She is presently a sabbatical visitor at the Chan-Zuckerberg Biohub, and a visiting associate professor at Stanford School of Medicine.

External homepage: https://cellprofiling.org/


Key publications:

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, Kato S, Royer LA, Thiagarajah JR, Eliceiri KW, Lundberg E, Mehta SB, Waller L. Pycro-Manager: open-source software for customized and reproducible microscope control. (2021) Nature methods

Mahdessian D, Cesnik AJ, Gnann C, Danielsson F, Stenström L, Arif M, Zhang C, Le T, Johansson F, Shutten 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. Spatiotemporal dissection of the cell cycle with single-cell proteogenomics. (2021) Nature

Rozenblatt-Rosen O, Shin JW, Rood JE, Hupalowska A, Regev A, Heyn H, Ardlie K, Clatworthy M, Carninci P, Enard W, Greenleaf W, Heyn H, Lein E, Levin JZ, Linnarsson S, Lundberg E, Meyer K, Navin N, Nolan G, Teichmann S, Voet T, Zhuang X. Building a high-quality Human Cell Atlas. (2021) Nature biotechnology

Gnann C, Cesnik AJ, Lundberg E. Illuminating Non-genetic Cellular Heterogeneity with Imaging-Based Spatial Proteomics. (2021) Trends in cancer

Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, 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 C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. (2020) Nature communications

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, Alberi L, Alexander S, Alexandrov T, Arenas E, Bagni C, Balderas R, Bandelli A, Becher B, Becker M, Beerenwinkel N, Benkirame M, Beyer M, Bickmore W, Biessen EEAL, Blomberg N, Blumcke I, Bodenmiller B, Borroni B, Boumpas DT, Bourgeron T, Bowers S, Braeken D, Brooksbank C, Brose N, Bruining H, Bury J, Caporale N, Cattoretti G, Chabane N, Chneiweiss H, Cook SA, Curatolo P, de Jonge MI, Deplancke B, De Strooper B, de Witte P, Dimmeler S, Draganski B, Drews A, Dumbrava C, Engelhardt S, Gasser T, Giamarellos-Bourboulis EJ, Graff C, Grün D, Gut I, Hansson O, Henshall DC, Herland A, Heutink P, Heymans SRB, Heyn H, Huch M, Huitinga I, Jackowiak P, Jongsma KR, Journot L, Junker JP, Katz S, Kehren J, Kempa S, Kirchhof P, Klein C, Koralewska N, Korbel JO, Kühnemund M, Lamond AI, Lauwers E, Le Ber I, Leinonen V, Tobon AL, Lundberg E, Lunkes A, Maatz H, Mann M, Marelli L, Matser V, Matthews PM, Mechta-Grigoriou F, Menon R, Nielsen AF, Pagani M, Pasterkamp RJ, Pitkänen A, Popescu V, Pottier C, Puisieux A, Rademakers R, Reiling D, Reiner O, Remondini D, Ritchie C, Rohrer JD, Saliba AE, Sanchez-Valle R, Santosuosso A, Sauter A, Scheltema RA, Scheltens P, Schiller HB, Schneider A, Seibler P, Sheehan-Rooney K, Shields D, Sleegers K, Smit AB, Smith KGC, Smolders I, Synofzik M, Tam WL, Teichmann S, Thom M, Turco MY, van Beusekom HMM, Vandenberghe R, Van den Hoecke S, Van de Poel I, van der Ven A, van der Zee J, van Lunzen J, van Minnebruggen G, van Oudenaarden A, Van Paesschen W, van Swieten J, van Vught R, Verhage M, Verstreken P, Villa CE, Vogel J, von Kalle C, Walter J, Weckhuysen S, Weichert W, Wood L, Ziegler AG, Zipp F. LifeTime and improving European healthcare through cell-based interceptive medicine. (2020) Nature

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. Author Correction: Analysis of the Human Protein Atlas Image Classification competition. (2020) Nature methods

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. Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition. (2020) Nature methods

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. Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition. (2019) Nature methods

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. Analysis of the Human Protein Atlas Image Classification competition. (2019) Nature methods

Ouyang W, Mueller F, Hjelmare M, Lundberg E, Zimmer C. ImJoy: an open-source computational platform for the deep learning era. (2019) Nature methods

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, 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. Voices in methods development. (2019) Nature methods

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. Deep learning is combined with massive-scale citizen science to improve large-scale image classification. (2018) Nature biotechnology

Sullivan DP, Lundberg E. Seeing More: A Future of Augmented Microscopy. (2018) Cell

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, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B. How many human proteoforms are there? (2018) Nature chemical biology

Carreras-Puigvert J, Zitnik M, Jemth AS, Carter M, Unterlass JE, Hallström B, Loseva O, Karem Z, Calderón-Montaño JM, Lindskog C, Edqvist PH, Matuszewski 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. A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family. (2017) Nature communications

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 P, Mattsson J, Schwenk JM, Brunnström H, Glimelius B, Sjöblom T, Edqvist PH, Djureinovic D, Micke P, Lindskog C, Mardinoglu A, Ponten F. A pathology atlas of the human cancer transcriptome. (2017) Science (New York, N.Y.)

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. A subcellular map of the human proteome. (2017) Science (New York, N.Y.)

Uhlen M, Bandrowski A, Carr S, Edwards A, Ellenberg J, Lundberg E, Rimm DL, Rodriguez H, Hiltke T, Snyder M, Yamamoto T. A proposal for validation of antibodies. (2016) Nature methods

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 H, June C, Kamb S, Khvorova A, Kim DH, Kim JS, Krishnan Y, Lakadamyali M, Lappalainen T, Lewin S, Liao J, Loman N, Lundberg E, Lynd L, Martin C, Mellman I, Miyawaki A, Mummery C, Nelson K, Paz J, Peralta-Yahya P, Picotti P, Polyak K, Prather K, Qin J, Quake S, Regev A, Rogers JA, Shetty R, Sommer M, Stevens M, Stolovitzky G, Takahashi M, Tang F, Teichmann S, Torres-Padilla ME, Tripathi L, Vemula P, Verdine G, Vollmer F, Wang J, Ying JY, Zhang F, Zhang T. Voices of biotech. (2016) Nature biotechnology

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. Proteomics. Tissue-based map of the human proteome. (2015) Science (New York, N.Y.)

Stadler C, Rexhepaj E, Singan VR, Murphy RF, Pepperkok R, Uhlén M, Simpson JC, Lundberg E. Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells. (2013) Nature methods

Akan P, Alexeyenko A, Costea PI, Hedberg L, Solnestam BW, Lundin S, Hällman J, Lundberg E, Uhlén M, Lundeberg J. Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines. (2012) Genome medicine

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. Towards a knowledge-based Human Protein Atlas. (2010) Nature biotechnology