Rui Branca

Publikationer
Populärvetenskap och samverkan

Artiklar

Article: PROTEIN SCIENCE. 2024;33(8):e5115
A suicidal and extensively disordered luciferase with a bright luminescence
Dijkema FM; Escarpizo-Lorenzana MI; Nordentoft MK; Rabe HC; Sahin C; Landreh M; Branca RM; Sorensen ES; Christensen B; Prestel A; Teilum K; Winther JR
Article: SCIENCE ADVANCES. 2023;9(48):eadg8014
Harnessing T cell exhaustion and trogocytosis to isolate patient-derived tumor-specific TCR
Manfredi F; Stasi L; Buonanno S; Marzuttini F; Noviello M; Mastaglio S; Abbati D; Potenza A; Balestrieri C; Cianciotti BC; Tassi E; Feola S; Toffalori C; Punta M; Magnani Z; Camisa B; Tiziano E; Lupo-Stanghellini MT; Branca RM; Lehtioe J; Sikanen TM; Haapala MJ; Cerullo V; Casucci M; Vago L; Ciceri F; Bonini C; Ruggiero E
Article: NATURE COMMUNICATIONS. 2023;14(1):7056
Development of mesothelioma-specific oncolytic immunotherapy enabled by immunopeptidomics of murine and human mesothelioma tumors
Chiaro J; Antignani G; Feola S; Feodoroff M; Martins B; Cojoc H; Russo S; Fusciello M; Hamdan F; Ferrari V; Ciampi D; Ilonen I; Raesaenen J; Maeyraenpaeae M; Partanen J; Koskela S; Honkanen J; Halonen J; Kuryk L; Rescigno M; Groenholm M; Branca RM; Lehtioe J; Cerullo V
Article: ELIFE. 2022;11:e71156
A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines
Feola S; Chiaro J; Martins B; Russo S; Fusciello M; Yloesmaeki E; Bonini C; Ruggiero E; Hamdan F; Feodoroff M; Antignani G; Viitala T; Pesonen S; Groenholm M; Branca RMM; Lehtioe J; Cerullo V; Ho P-C
Article: BIOINFORMATICS. 2022;38(5):1470-1472
Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
Umer HM; Audain E; Zhu Y; Pfeuffer J; Sachsenberg T; Lehtio J; Branca R; Perez-Riverol Y
Article: JACS AU. 2021;1(12):2385-2393
Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry
Abramsson ML; Sahin C; Hopper JTS; Branca RMM; Danielsson J; Xu M; Chandler SA; Osterlund N; Ilag LL; Leppert A; Costeira-Paulo J; Lang L; Teilum K; Laganowsky A; Benesch JLP; Oliveberg M; Robinson CV; Marklund EG; Allison TM; Winther JR; Landreh M
Article: NATURE CANCER. 2021;2(11):1224-1242
Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune-evasion mechanisms
Lehtio J; Arslan T; Siavelis I; Pan Y; Socciarelli F; Berkovska O; Umer HM; Mermelekas G; Pirmoradian M; Jonsson M; Brunnstrom H; Brustugun OT; Purohit KP; Cunningham R; Asl HF; Isaksson S; Arbajian E; Aine M; Karlsson A; Kotevskaz M; Hansen CG; Haakensen VD; Helland A; Tamborero D; Johansson HJ; Branca RM; Planckz M; Staaf J; Orre LM
Article: ACS NANO. 2021;15(10):15992-16010
PeptiCHIP: A Microfluidic Platform for Tumor Antigen Landscape Identification
Feola S; Haapala M; Peltonen K; Capasso C; Martins B; Antignani G; Federico A; Pietiainen V; Chiaro J; Feodoroff M; Russo S; Rannikko A; Fusciello M; Koskela S; Partanen J; Hamdan F; Tahka SM; Ylosmaki E; Greco D; Gronholm M; Kekarainen T; Eshaghi M; Gurvich OL; Yla-Herttuala S; Branca RMM; Lehtio J; Sikanen TM; Cerullo V
Article: CANCERS. 2021;13(14):3408
Therapeutic Cancer Vaccination with Immunopeptidomics-Discovered Antigens Confers Protective Antitumor Efficacy
Peltonen K; Feola S; Umer HM; Chiaro J; Mermelekas G; Ylosmaki E; Pesonen S; Branca RMM; Lehtio J; Cerullo V
Article: ARTIFICIAL INTELLIGENCE IN MEDICINE. 2020;108:101928
Domain expertise-agnostic feature selection for the analysis of breast cancer data
Pozzoli S; Soliman A; Bahri L; Branca RM; Girdzijauskas S; Brambilla M
Article: MOLECULAR & CELLULAR PROTEOMICS. 2020;19(6):928-943
Immediate Adaptation Analysis Implicates BCL6 as an EGFR-TKI Combination Therapy Target in NSCLC
Tran YZ; Minozada R; Cao X; Johansson HJ; Branca RM; Seashore-Ludlow B; Orre LM
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2020;142(11):5338-5354
Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein
Kisgeropoulos EC; Griese JJ; Smith ZR; Branca RMM; Schneider CR; Hogbom M; Shafaat HS
Article: EMBO MOLECULAR MEDICINE. 2020;12(3):e10419
Ribonucleotide reductase inhibitors suppress SAMHD1 ara-CTPase activity enhancing cytarabine efficacy
Rudd SG; Tsesmetzis N; Sanjiv K; Paulin CBJ; Sandhow L; Kutzner J; Myrberg IH; Bunten SS; Axelsson H; Zhang SM; Rasti A; Makela P; Coggins SA; Tao S; Suman S; Branca RM; Mermelekas G; Wiita E; Lee S; Walfridsson J; Schinazi RF; Kim B; Lehtio J; Rassidakis GZ; Tamm KP; Warpman-Berglund U; Heyman M; Grander D; Lehmann S; Lundback T; Qian H; Henter J-I; Schaller T; Helleday T; Herold N
Article: PLANT PHYSIOLOGY. 2019;181(4):1632-1650
A Mitochondrial LYR Protein Is Required for Complex I Assembly¹^[OPEN]
Ivanova A; Gill-Hille M; Huang S; Branca RM; Kmiec B; Teixeira PF; Lehtio J; Whelan J; Murcha MW
Article: AGING CELL. 2019;18(6):e13029
Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice
Ross JM; Coppotelli G; Branca RM; Kim KM; Lehtio J; Sinclair DA; Olson L
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2019;294(48):18372-18386
Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins
Kutin Y; Kositzki R; Branca RMM; Srinivas V; Lundin D; Haumann M; Hogbom M; Cox N; Griese JJ
Article: JOURNAL OF CELL BIOLOGY. 2019;218(7):2425-2432
Phosphorylation of G3BP1-S149 does not influence stress granule assembly
Panas MD; Kedersha N; Schulte T; Branca RM; Ivanov P; Anderson P
Article: SCIENTIFIC REPORTS. 2019;9(1):8324
Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles
Fredolini C; Bystrom S; Sanchez-Rivera L; Ioannou M; Tamburro D; Ponten F; Branca RM; Nilsson P; Lehtio J; Schwenk JM
Article: NATURE COMMUNICATIONS. 2019;10(1):1600
Breast cancer quantitative proteome and proteogenomic landscape
Johansson HJ; Socciarelli F; Vacanti NM; Haugen MH; Zhu Y; Siavelis I; Fernandez-Woodbridge A; Aure MR; Sennblad B; Vesterlund M; Branca RM; Orre LM; Huss M; Fredlund E; Beraki E; Garred O; Boekel J; Sauer T; Zhao W; Nord S; Hoglander EK; Jans DC; Brismar H; Haukaas TH; Bathen TF; Schlichting E; Naume B; Geisler J; Hofvind S; Engebraten O; Geitvik GA; Langerod A; Karesen R; Maelandsmo GM; Sorlie T; Skjerven HK; Park D; Hartman-Johnsen O-J; Luders T; Borgen E; Kristensen VN; Russnes HG; Lingjaerde OC; Mills GB; Sahlberg KK; Borresen-Dale A-L; Lehtio J
Article: PLANT JOURNAL. 2018;96(4):705-715
Accumulation of endogenous peptides triggers a pathogen stress response in Arabidopsis thaliana
Kmiec B; Branca RMM; Berkowitz O; Li L; Wang Y; Murcha MW; Whelan J; Lehtioe J; Glaser E; Teixeira PF
Article: NATURE. 2018;563(7731):416-420
Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens
Srinivas V; Lebrette H; Lundin D; Kutin Y; Sahlin M; Lerche M; Eirich J; Branca RMM; Cox N; Sjoberg B-M; Hogbom M
Article: JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY. 2018;23(6):879-886
Ether cross-link formation in the R2-like ligand-binding oxidase
Griese JJ; Branca RMM; Srinivas V; Hogbom M
Article: NATURE COMMUNICATIONS. 2018;9(1):903
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow
Zhu Y; Orre LM; Johansson HJ; Huss M; Boekel J; Vesterlund M; Fernandez-Woodbridge A; Branca RMM; Lehtio J
Article: MOLECULAR PLANT. 2018;11(2):342-345
A Common Peptidolytic Mechanism for Targeting Peptide Degradation in Mitochondria and Chloroplasts
Kmiec B; Branca RMM; Murcha MW; Lehtio J; Glaser E; Teixeira PF
Article: JOURNAL OF MOLECULAR BIOLOGY. 2018;430(3):348-362
Mechanism of Peptide Binding and Cleavage by the Human Mitochondrial Peptidase Neurolysin
Teixeira PF; Masuyer G; Pinho CM; Branca RMM; Kmiec B; Wallin C; Warmlander SKTS; Berntsson RP-A; Ankarcrona M; Graslund A; Lehtio J; Stenmark P; Glaser E
Article: BRAIN. 2018;141(2):582-595
Synaptic markers of cognitive decline in neurodegenerative diseases: a proteomic approach
Bereczki E; Branca RM; Francis PT; Pereira JB; Baek J-H; Hortobagyi T; Winblad B; Ballard C; Lehtio J; Aarsland D
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2018;140(4):1471-1480
Driving Protein Conformational Changes with Light: Photoinduced Structural Rearrangement in a Heterobimetallic Oxidase
Maugeri PT; Griese JJ; Branca RM; Miller EK; Smith ZR; Eirich J; Hogbom M; Shafaat HS
Article: KIDNEY INTERNATIONAL REPORTS. 2017;2(6):1208-1218
Altered Protein Composition of Subcutaneous Adipose Tissue in Chronic Kidney Disease
Gertow J; Ng CZ; Branca RMM; Werngren O; Du L; Kjellqvist S; Hemmingsson P; Bruchfeld A; MacLaughlin H; Eriksson P; Axelsson J; Fisher RM
Article: BMC CANCER. 2017;17(1):650
Tartrate-resistant acid phosphatase (TRAP/ACP5) promotes metastasis-related properties via TGFβ2/TβR and CD44 in MDA-MB-231 breast cancer cells
Reithmeier A; Panizza E; Krumpel M; Orre LM; Branca RMM; Lehtio J; Ek-Rylander B; Andersson G
Article: SCIENTIFIC REPORTS. 2017;7(1):4513
Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome
Panizza E; Branca RMM; Oliviusson P; Orre LM; Lehtio J
Article: IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 2017;14(2):272-281
Optimizing Analytical Depth and Cost Efficiency of IEF-LC/MS Proteomics
Kifer I; Branca RM; Ben-Dor A; Zhai L; Xu P; Lehtio J; Yakhini Z
Article: ONCOGENE. 2017;36(6):731-745
microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network
Zhou Y; Frings O; Branca RM; Boekel J; le Sage C; Fredlund E; Agami R; Orre LM
Article: NATURE CHEMICAL BIOLOGY. 2017;13(1):15-17
A multi-step peptidolytic cascade for amino acid recovery in chloroplasts
Teixeira PF; Kmiec B; Branca RMM; Murcha MW; Byzia A; Ivanova A; Whelan J; Drag M; Lehtio J; Glaser E
Article: SCIENTIFIC REPORTS. 2016;6:35712
Mesenchymal state of intimal cells may explain higher propensity to ascending aortic aneurysm in bicuspid aortic valves
Maleki S; Kjellqvist S; Paloschi V; Magne J; Branca RMM; Du L; Hultenby K; Petrini J; Fuxe J; Lehtio J; Franco-Cereceda A; Eriksson P; Bjorck HM
Article: SARCOIDOSIS VASCULITIS AND DIFFUSE LUNG DISEASES. 2016;33(1):17-28
ALTERATIONS IN THE MEMBRANE-ASSOCIATED PROTEOME FRACTION OF ALVEOLAR MACROPHAGES IN SARCOIDOSIS
Kjellin H; Silva E; Branca RM; Eklund A; Jakobsson P-J; Grunewald J; Lehtio J; Wheelock AM
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2015;290(42):25254-25272
Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor
Griese JJ; Kositzki R; Schrapers P; Branca RMM; Nordstrom A; Lehtio J; Haumann M; Hogbom M
Article: EXPERIMENTAL CELL RESEARCH. 2015;336(1):158-170
Secretome protein signature of human gastrointestinal stromal tumor cells
Berglund E; Dare E; Branca RMM; Akcakaya P; Frobom R; Berggren P-O; Lui W-O; Larsson C; Zedenius J; Orre L; Lehtio J; Kim J; Branstrom R
Article: METHODS IN MOLECULAR BIOLOGY. 2015;1305:123-130
A flowchart to analyze protease activity in plant mitochondria.
Teixeira PF; Branca RM; Kmiec B; Glaser E
Article: MOLECULAR & CELLULAR PROTEOMICS. 2014;13(6):1552-1562
SpliceVista, a Tool for Splice Variant Identification and Visualization in Shotgun Proteomics Data
Zhu Y; Hultin-Rosenberg L; Forshed J; Branca RMM; Orre LM; Lehtio J
Article: JOURNAL OF PROTEOMICS. 2014;96:133-144
Quantitative accuracy in mass spectrometry based proteomics of complex samples: The impact of labeling and precursor interference
Sandberg A; Branca RMM; Lehtio J; Forshed J
Article: NATURE METHODS. 2014;11(1):59-62
HiRIEF LC-MSMS enables deep proteome coverage and unbiased proteogenomics
Branca RMM; Orre LM; Johansson HJ; Granholm V; Huss M; Perez-Bercoff A; Forshed J; Kall L; Lehtio J
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2013;110(43):17189-17194
Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein
Griese JJ; Roos K; Cox N; Shafaat HS; Branca RMM; Lehtio J; Graslund A; Lubitz W; Siegbahn PEM; Hogbom M
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2013;110(40):e3761-e3769
Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts
Kmiec B; Teixeira PF; Berntsson RP-A; Murcha MW; Branca RMM; Radomiljac JD; Regberg J; Svensson LM; Bakali A; Langel U; Lehtio J; Whelan J; Stenmark P; Glaser E
Article: JOURNAL OF PROTEOME RESEARCH. 2013;12(9):3934-3943
Quantitative Proteomics Profiling of Primary Lung Adenocarcinoma Tumors Reveals Functional Perturbations in Tumor Metabolism
Pernemalm M; De Petris L; Branca RM; Forshed J; Kanter L; Soria J-C; Girard P; Validire P; Pawitan Y; van den Oord J; Lazar V; Pahlman S; Lewensohn R; Lehtio J
Article: MOLECULAR & CELLULAR PROTEOMICS. 2013;12(7):2021-2031
Defining, Comparing, and Improving iTRAQ Quantification in Mass Spectrometry Proteomics Data
Hultin-Rosenberg L; Forshed J; Branca RMM; Lehtio J; Johansson HJ
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2013;288(22):15556-15570
Mammalian Target of Rapamycin (mTor) Mediates Tau Protein Dyshomeostasis IMPLICATION FOR ALZHEIMER DISEASE
Tang Z; Bereczki E; Zhang H; Wang S; Li C; Ji X; Branca RM; Lehtio J; Guan Z; Filipcik P; Xu S; Winblad B; Pei J-J
Article: MOLECULAR & CELLULAR PROTEOMICS. 2013;12(2):407-425
A Combined Proteomic and Transcriptomic Approach Shows Diverging Molecular Mechanisms in Thoracic Aortic Aneurysm Development in Patients with Tricuspid- And Bicuspid Aortic Valve
Kjellqvist S; Maleki S; Olsson T; Chwastyniak M; Branca RMM; Lehtio J; Pinet F; Franco-Cereceda A; Eriksson P
Article: FREE RADICAL BIOLOGY AND MEDICINE. 2012;53(11):2188-2195
In vitro oxidative inactivation of human presequence protease (hPreP)
Teixeira PF; Pinho CM; Branca RM; Lehtio J; Levine RL; Glaser E
Article: MOLECULAR & CELLULAR PROTEOMICS. 2012;11(7):M112.016998
Tumor Proteomics by Multivariate Analysis on Individual Pathway Data for Characterization of Vulvar Cancer Phenotypes
Sandberg A; Lindell G; Kallstrom BN; Branca RM; Danielsson KG; Dahlberg M; Larson B; Forshed J; Lehtio J
Article: NATURE COMMUNICATIONS. 2012;3:976
Proteomic screen reveals Fbw7 as a modulator of the NF-κB pathway
Arabi A; Ullah K; Branca RMM; Johansson J; Bandarra D; Haneklaus M; Fu J; Aries I; Nilsson P; Den Boer ML; Pokrovskaja K; Grander D; Xiao G; Rocha S; Lehtio J; Sangfelt O
Article: MOLECULAR & CELLULAR PROTEOMICS. 2011;10(10):m111.010264
Enhanced Information Output From Shotgun Proteomics Data by Protein Quantification and Peptide Quality Control (PQPQ)
Forshed J; Johansson HJ; Pernemalm M; Branca RMM; Sandberg A; Lehtio J
Article: JOURNAL OF PROTEOME RESEARCH. 2011;10(6):2703-2714
Identification of Chromatophore Membrane Protein Complexes Formed under Different Nitrogen Availability Conditions in Rhodospirillum rubrum
Selao TT; Branca R; Chae PS; Lehtio J; Gellman SH; Rasmussen SGF; Nordlund S; Noren A
Article: JOURNAL OF PROTEOME RESEARCH. 2011;10(5):2566-2578
Phosphoproteomic Profiling of NSCLC Cells Reveals that Ephrin B3 Regulates Pro-survival Signaling through Akt1-Mediated Phosphorylation of the EphA2 Receptor
Stahl S; Branca RM; Efazat G; Ruzzene M; Zhivotovsky B; Lewensohn R; Viktorsson K; Lehtio J
Article: THYROID. 2010;20(10):1067-1076
Proteomic Study of Thyroid Tumors Reveals Frequent Up-Regulation of the Ca²⁺-Binding Protein S100A6 in Papillary Thyroid Carcinoma
Sofiadis A; Dinets A; Orre LM; Branca RM; Juhlin CC; Foukakis T; Wallin G; Hoog A; Hulchiy M; Zedenius J; Larsson C; Lehtio J
Article: BIOPHYSICAL JOURNAL. 2009;96(12):4976-4983
Concentration-Dependent Front Velocity of the Autocatalytic Hydrogenase Reaction
Bodo G; Branca RMM; Toth A; Horvath D; Bagyinka C
Article: ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS. 2007;467(2):174-184
Oxygen and temperature-dependent structural and redox changes in a novel cytochrome c₄ from the purple sulfur photosynthetic bacterium Thiocapsa roseopersicina
Branca RMM; Bodo G; Varkonyi Z; Debreczeny M; Osz J; Bagyinka C
Article: ACTA CRYSTALLOGRAPHICA SECTION F: STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS. 2006;62(Pt 8):820-824
Cross-crystallization method used for the crystallization and preliminary diffraction analysis of a novel di-haem cytochrome c₄
Tomcova I; Branca RMM; Bodo G; Bagyinka C; Smatanova IK
Article: BIOPHYSICAL JOURNAL. 2005;89(3):1957-1964
Theoretical calculations on hydrogenase kinetics:: Explanation of the lag phase and the enzyme concentration dependence of the activity of hydrogenase uptake
Osz J; Bodó G; Branca RMM; Bagyinka C
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Corrigendum: NATURE COMMUNICATIONS. 2018;9(1):1852
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow (vol 9, 2018)
Zhu Y; Orre LM; Johansson HJ; Huss M; Boekel J; Vesterlund M; Fernandez-Woodbridge A; Branca RMM; Lehtio J
Review: ENVIRONMENTAL MICROBIOLOGY. 2017;19(6):2301-2319
Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria
Muthusamy S; Lundin D; Branca RMM; Baltar F; Gonzalez JM; Lehtio J; Pinhassi J
Published conference paper: JOURNAL OF MASS SPECTROMETRY. 2007;42(12):1569-1582
De novo sequencing of a 21-kDa cytochrome c₄ from Thiocapsa roseopersicina by nanoelectrospray ionization ion-trap and Fourier-transform icon-cyclotron resonance mass spectrometry
Branca RMM; Bodo G; Bagyinka C; Prokai L

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