Rui Branca

About me
Publications
Public outreach and news

About me

Degree in Biochemistry from the University of Porto, Portugal
PhD in Biophysics from the University of Szeged, Hungary

Research

Interested in protein and peptide biochemistry
in protein/peptide separation
techniques (e.g. liquid chromatography and isoelectric focusing)
in mass
spectrometry based proteomics.

Articles

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; Lehtiö 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; Räsänen J; Mäyränpää M; Partanen J; Koskela S; Honkanen J; Halonen J; Kuryk L; Rescigno M; Grönholm M; Branca RM; Lehtiö 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; Ylösmäki E; Bonini C; Ruggiero E; Hamdan F; Feodoroff M; Antignani G; Viitala T; Pesonen S; Grönholm M; Branca RMM; Lehtiö J; Cerullo V
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; Lehtiö J; Branca RM; 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; Österlund 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.

Lehtiö J; Arslan T; Siavelis I; Pan Y; Socciarelli F; Berkovska O; Umer HM; Mermelekas G; Pirmoradian M; Jönsson M; Brunnström H; Brustugun OT; Purohit KP; Cunningham R; Foroughi Asl H; Isaksson S; Arbajian E; Aine M; Karlsson A; Kotevska M; Gram Hansen C; Drageset Haakensen V; Helland Å; Tamborero D; Johansson HJ; Branca RM; Planck 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; Pietiäinen V; Chiaro J; Feodoroff M; Russo S; Rannikko A; Fusciello M; Koskela S; Partanen J; Hamdan F; Tähkä SM; Ylösmäki E; Greco D; Grönholm M; Kekarainen T; Eshaghi M; Gurvich OL; Ylä-Herttuala S; M Branca RM; Lehtiö 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; Ylösmäki E; Pesonen S; Branca RMM; Lehtiö 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.

Zhou Tran Y; 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; Högbom 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 CB; Sandhow L; Kutzner J; Hed Myrberg I; Bunten SS; Axelsson H; Zhang SM; Rasti A; Mäkelä P; Coggins SA; Tao S; Suman S; Branca RM; Mermelekas G; Wiita E; Lee S; Walfridsson J; Schinazi RF; Kim B; Lehtiö J; Rassidakis GZ; Pokrovskaja Tamm K; Warpman-Berglund U; Heyman M; Grandér D; Lehmann S; Lundbäck 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 Assembly.

Ivanova A; Gill-Hille M; Huang S; Branca RM; Kmiec B; Teixeira PF; Lehtiö 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; Lehtiö 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; Högbom 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; Byström S; Sanchez-Rivera L; Ioannou M; Tamburro D; Pontén F; Branca RM; Nilsson P; Lehtiö 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 Ø; Boekel J; Sauer T; Zhao W; Nord S; Höglander EK; Jans DC; Brismar H; Haukaas TH; Bathen TF; Schlichting E; Naume B; Consortia Oslo Breast Cancer Research Consortium (; Luders T; Borgen E; Kristensen VN; Russnes HG; Lingjærde OC; Mills GB; Sahlberg KK; Børresen-Dale A-L; Lehtiö 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; Lehtiö 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; Sjöberg B-M; Högbom 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; Högbom 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; Lehtiö 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; Lehtiö 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; Wärmländer SKTS; Berntsson RP-A; Ankarcrona M; Gräslund A; Lehtiö 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; Hortobágyi T; Winblad B; Ballard C; Lehtiö 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; Högbom 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; Mamede Branca RM; 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; Lehtiö 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; Lehtiö 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; Lehtiö 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; Magné J; Branca RMM; Du L; Hultenby K; Petrini J; Fuxe J; MIBAVA Leducq Consortium; Lehtiö J; Franco-Cereceda A; Eriksson P; Björck 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; Lehtiö J; Wheelock ÅM
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; Nordström A; Lehtiö J; Haumann M; Högbom M
Article: EXPERIMENTAL CELL RESEARCH. 2015;336(1):158-170

Secretome protein signature of human gastrointestinal stromal tumor cells.

Berglund E; Daré E; Branca RMM; Akcakaya P; Fröbom R; Berggren P-O; Lui W-O; Larsson C; Zedenius J; Orre L; Lehtiö J; Kim J; Bränström 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; Lehtiö 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; Lehtiö J; Forshed J
Article: NATURE METHODS. 2014;11(1):59-62

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

Branca RMM; Orre LM; Johansson HJ; Granholm V; Huss M; Pérez-Bercoff Å; Forshed J; Käll L; Lehtiö 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; Lehtiö J; Gräslund A; Lubitz W; Siegbahn PEM; Högbom 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; Lehtiö 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; Påhlman S; Lewensohn R; Lehtiö 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; Lehtiö 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; Lehtiö 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; Lehtiö 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; Lehtiö 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; Källström BN; Branca RM; Danielsson KG; Dahlberg M; Larson B; Forshed J; Lehtiö 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; Ariës I; Nilsson P; Den Boer ML; Pokrovskaja K; Grandér D; Xiao G; Rocha S; Lehtiö 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; Lehtiö 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; Lehtiö J; Gellman SH; Rasmussen SGF; Nordlund S; Norén 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.

Ståhl S; Branca RM; Efazat G; Ruzzene M; Zhivotovsky B; Lewensohn R; Viktorsson K; Lehtiö 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; Höög A; Hulchiy M; Zedenius J; Larsson C; Lehtiö J
Article: BIOPHYSICAL JOURNAL. 2009;96(12):4976-4983

Concentration-dependent front velocity of the autocatalytic hydrogenase reaction.

Bodó G; Branca RMM; Tóth A; Horváth 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 c(4) from the purple sulfur photosynthetic bacterium Thiocapsa roseopersicina.

Branca RMM; Bodó G; Várkonyi 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.

Tomcová I; Branca RMM; Bodó G; Bagyinka C; Smatanová 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

Publisher Correction: 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; Lehtiö 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; Mamede Branca RM; Baltar F; González JM; Lehtiö J; Pinhassi J
Published 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 ion-cyclotron resonance mass spectrometry.

Branca RMM; Bodó G; Bagyinka C; Prokai L

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