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: 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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All other publications

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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