PUBLICATIONS
2023
Alexander JL, Mullish BH, Danckert NP, Liu Z, Olbei ML, Saifuddin A, Torkizadeh M, Ibraheim H, Blanco JM, Roberts LA, Bewshea CM, Nice R, Lin S, Prabhudev H, Sands C, Horneffer-van der Sluis V, Lewis M, Sebastian S, Lees CW, Teare JP, Hart A, Goodhand JR, Kennedy NA, Korcsmaros T, Marchesi JR, Ahmad T, Powell N.: The gut microbiota and metabolome are associated with diminished COVID-19 vaccine-induced antibody responses in immunosuppressed inflammatory bowel disease patients. [version 1; peer review: 2 approved with reservations]. EBioMedicine. 2023 Feb;88:104430. doi: 10.1016/j.ebiom.2022.104430. Epub 2023 Jan 10.
Bernuzzi F, Maertens A, Saha S, Troncoso-Rey P, Ludwig T, Hiller K, Mithen RF, Korcsmaros T, Traka MH.: Sulforaphane rewires central metabolism to support antioxidant response and achieve glucose homeostasis. Redox Biol. 2023 Sep 7;67:102878. doi: 10.1016/j.redox.2023.102878.
Corpas M, de Mendoza C, Moreno-Torres V, Pintos I, Seoane P, Perkins JR, Ranea JAG, Fatumo S, Korcsmaros T, Martín-Villa JM, Barreiro P, Corral O, Soriano V.: Genetic signature detected in T cell receptors from patients with severe COVID-19. iScience. 2023 Aug 25;26(10):107735. doi: 10.1016/j.isci.2023.107735. eCollection 2023 Oct 20.
Csabai L, Bohár B, Türei D, Prabhu S, Földvári-Nagy L, Madgwick M, Fazekas D, Módos D, Ölbei M, Halka T, Poletti M, Kornilova P, Kadlecsik T, Demeter A, Szalay-Bekő M, Kapuy O, Lenti K, Vellai T, Gul L, Korcsmáros T.: AutophagyNet: high-resolution data source for the analysis of autophagy and its regulation. Autophagy. 2023 Aug 17:1-15. doi: 10.1080/15548627.2023.2247737.
Hajdú B, Csabai L, Márton M, Holczer M, Korcsmáros T, Kapuy O.: Oscillation of Autophagy Induction under Cellular Stress and What Lies behind It, a Systems Biology Study. Int J Mol Sci. 2023 Apr 21;24(8):7671. doi: 10.3390/ijms24087671.
Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I, Farr E, Fernandez-Torras A, Gyori BM, Hartung M, Hoyt CT, Klein C, Korcsmaros T, Maier A, Mann M, Ochoa D, Pareja-Lorente E, Popp F, Preusse M, Probul N, Schwikowski B, Sen B, Strauss MT, Turei D, Ulusoy E, Waltemath D, Wodke JAH, Saez-Rodriguez J.: Democratizing knowledge representation with BioCypher. Nat Biotechnol. 2023 Aug;41(8):1056-1059. doi: 10.1038/s41587-023-01848-y.
Ray N, Park SJ, Jung H, Kim J, Korcsmaros T, Moon Y.: Stress-responsive Gdf15 counteracts renointestinal toxicity via autophagic and microbiota reprogramming. Commun Biol. 2023 Jun 3;6(1):602. doi: 10.1038/s42003-023-04965-1.
2022
Brooks-Warburton J, Modos D, Sudhakar P, Madgwick M, Thomas JP, Bohar B, Fazekas D, Zoufir A, Kapuy O, Szalay-Beko M, Verstockt B, Hall LJ, Watson A, Tremelling M, Parkes M, Vermeire S, Bender A, Carding SR, Korcsmaros T.: A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis. Nat Commun. 2022 Apr 28;13(1):2299. doi: 10.1038/s41467-022-29998-8.
Csabai L, Fazekas D, Kadlecsik T, Szalay-Bekő M, Bohár B, Madgwick M, Módos D, Ölbei M, Gul L, Sudhakar P, Kubisch J, Oyeyemi OJ, Liska O, Ari E, Hotzi B, Billes VA, Molnár E, Földvári-Nagy L, Csályi K, Demeter A, Pápai N, Koltai M, Varga M, Lenti K, Farkas IJ, Türei D, Csermely P, Vellai T, Korcsmáros T.: SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. Nucleic Acids Res. 2022 Jan 7;50(D1):D701-D709. doi: 10.1093/nar/gkab909.
Demeter A, Jacomin AC, Gul L, Lister A, Lipscombe J, Invernizzi R, Branchu P, Macaulay I, Nezis IP, Kingsley RA, Korcsmaros T, Hautefort I.: Computational prediction and experimental validation of Salmonella Typhimurium SopE-mediated fine-tuning of autophagy in intestinal epithelial cells. Front Cell Infect Microbiol. 2022 Aug 17;12:834895. doi: 10.3389/fcimb.2022.834895.
Gul L, Korcsmaros T, Hall N.: Flaviviruses hijack the host microbiota to
facilitate their transmission. Cell. 2022 Jul 7;185(14):2395-2397. doi:
10.1016/j.cell.2022.06.019.
Gul L, Modos D, Fonseca S, Madgwick M, Thomas JP, Sudhakar P, Booth C, Stentz R, Carding SR, Korcsmaros T.: Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease. J Extracell Vesicles. 2022 Jan;11(1):e12189. doi: 10.1002/jev2.12189.
Hautefort I, Poletti M, Papp D, Korcsmaros T.: Everything You Always Wanted to Know About Organoid-Based Models (and Never Dared to Ask). Cell Mol Gastroenterol Hepatol. 2022;14(2):311-331. doi: 10.1016/j.jcmgh.2022.04.012. Epub 2022 May 25.
Kapuy O, Korcsmáros T.: Chloroquine and COVID-19-A systems biology model uncovers the drug's detrimental effect on autophagy and explains its failure. PLoS One. 2022 Apr 7;17(4):e0266337. doi: 10.1371/journal.pone.0266337. eCollection 2022.
Kubinski R, Djamen-Kepaou JY, Zhanabaev T, Hernandez-Garcia A, Bauer S, Hildebrand F, Korcsmaros T, Karam S, Jantchou P, Kafi K, Martin RD.: Benchmark of Data Processing Methods and Machine Learning Models for Gut Microbiome-Based Diagnosis of Inflammatory Bowel Disease. Front Genet. 2022 Feb 14;13:784397. doi: 10.3389/fgene.2022.784397. eCollection 2022.
Liska O, Bohár B, Hidas A, Korcsmáros T, Papp B, Fazekas D, Ari E.: TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species. Database (Oxford). 2022 Sep 16;2022:baac083. doi: 10.1093/database/baac083.
Olbei M, Bohar B, Fazekas D, Madgwick M, Sudhakar P, Hautefort I, Métris A, Baranyi J, Kingsley RA, Korcsmaros T.: Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level. mSystems. 2022 Aug 30;7(4):e0149321. doi: 10.1128/msystems.01493-21. Epub 2022 Aug 1.
Pavlidis P, Tsakmaki A, Pantazi E, Li K, Cozzetto D, Digby-Bell J, Yang F, Lo
JW, Alberts E, Sa ACC, Niazi U, Friedman J, Long AK, Ding Y, Carey CD, Lamb C,
Saqi M, Madgwick M, Gul L, Treveil A, Korcsmaros T, Macdonald TT, Lord GM,
Bewick G, Powell N.: Interleukin-22 regulates neutrophil recruitment in
ulcerative colitis and is associated with resistance to ustekinumab therapy. Nat Commun. 2022 Oct 3;13(1):5820. doi: 10.1038/s41467-022-33331-8.
Pavlidis P, Tsakmaki A, Treveil A, Li K, Cozzetto D, Yang F, Niazi U, Hayee BH, Saqi M, Friedman J, Korcsmaros T, Bewick G, Powell N.: Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease. Cell Rep. 2022 Sep 27;40(13):111439. doi: 10.1016/j.celrep.2022.111439.
Poletti M, Treveil A, Csabai L, Gul L, Modos D, Madgwick M, Olbei M, Bohar B, Valdeolivas A, Turei D, Verstockt B, Triana S, Alexandrov T, Saez-Rodriguez J, Stanifer ML, Boulant S, Korcsmaros T.: Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways. NPJ Syst Biol Appl. 2022 May 2;8(1):15. doi: 10.1038/s41540-022-00224-x.
Stentz R, Jones E, Juodeikis R, Wegmann U, Guirro M, Goldson AJ, Brion A, Booth C, Sudhakar P, Brown IR, Korcsmáros T, Carding SR.: The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors. Appl Environ Microbiol. 2022 Aug 23;88(16):e0053322. doi: 10.1128/aem.00533-22. Epub 2022 Aug 2.
Thomas JP, Modos D, Rushbrook SM, Powell N, Korcsmaros T.: The Emerging Role of Bile Acids in the Pathogenesis of Inflammatory Bowel Disease. Front Immunol. 2022 Feb 3;13:829525. doi: 10.3389/fimmu.2022.829525. eCollection 2022.
Thomas JP, Ölbei M, Brooks-Warburton J, Korcsmaros T, Modos D.: Analysing miRNA-Target Gene Networks in Inflammatory Bowel Disease and Other Complex Diseases Using Transcriptomic Data. Genes (Basel). 2022 Feb 18;13(2):370. doi: 10.3390/genes13020370.
2021
Bohár B, Fazekas D, Madgwick M, Csabai L, Olbei M, Korcsmaros T, Szalay-Beko M.: Sherlock: an open-source data platform to store, analyze and integrate Big Data for biology [version 1; peer review: 2 approved with reservations]. F1000Research 2021, 10:409. doi: 10.12688/f1000research.52791.1
Földvári-Nagy L, Schnabel T, Dörnyei G, Korcsmáros T, Lenti K.: On the role of bacterial metalloproteases in COVID-19 associated cytokine storm. Cell Commun Signal. 2021 Jan 13;19(1):7. doi: 10.1186/s12964-020-00699-3.
Kapuy O, Holczer M, Márton M, Korcsmáros T.: Autophagy-dependent survival is controlled with a unique regulatory network upon various cellular stress events. Cell Death Dis. 2021 Mar 23;12(4):309. doi: 10.1038/s41419-021-03599-7.
Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, Abeliovich H, Abildgaard MH, Abudu YP, Acevedo-Arozena A, Adamopoulos IE, Adeli K, Adolph TE, Adornetto A, Aflaki E, Agam G, Agarwal A, Aggarwal BB, Agnello M, Agostinis P, Agrewala JN, Agrotis A, Aguilar PV, Ahmad ST, Ahmed ZM, Ahumada-Castro U, Aits S, Aizawa S, Akkoc Y, Akoumianaki T, Akpinar HA, Al-Abd AM, Al-Akra L, Al-Gharaibeh A, Alaoui-Jamali MA, Alberti S, Alcocer-Gómez E, Alessandri C, Ali M, Alim Al-Bari MA, Aliwaini S, Alizadeh J, Almacellas E, Almasan A, Alonso A, Alonso GD, Altan-Bonnet N, Altieri DC, Álvarez ÉMC, Alves S, Alves da Costa C, Alzaharna MM, Amadio M, Amantini C, Amaral C, Ambrosio S, Amer AO, Ammanathan V, An Z, Andersen SU, Andrabi SA, Andrade-Silva M, Andres AM, Angelini S, Ann D, Anozie UC, Ansari MY, Antas P, Antebi A, Antón Z, Anwar T, Apetoh L, Apostolova N, Araki T, Araki Y, Arasaki K, Araújo WL, Araya J, Arden C, Arévalo MA, Arguelles S, Arias E, Arikkath J, Arimoto H, Ariosa AR, Armstrong-James D, Arnauné-Pelloquin L, Aroca A, Arroyo DS, Arsov I, Artero R, Asaro DML, Aschner M, Ashrafizadeh M, Ashur-Fabian O, Atanasov AG, Au AK, Auberger P, Auner HW, Aurelian L, et al.: Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)(1). Autophagy. 2021 Jan;17(1):1-382. doi: 10.1080/15548627.2020.1797280. Epub 2021 Feb 8.
McKee AM, Kirkup BM, Madgwick M, Fowler WJ, Price CA, Dreger SA, Ansorge R, Makin KA, Caim S, Le Gall G, Paveley J, Leclaire C, Dalby M, Alcon-Giner C, Andrusaite A, Feng TY, Di Modica M, Triulzi T, Tagliabue E, Milling SWF, Weilbaecher KN, Rutkowski MR, Korcsmáros T, Hall LJ, Robinson SD.: Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumor growth. iScience. 2021 Aug 20;24(9):103012. doi: 10.1016/j.isci.2021.103012. eCollection 2021 Sep 24.
Mehta TK, Koch C, Nash W, Knaack SA, Sudhakar P, Olbei M, Bastkowski S, Penso-Dolfin L, Korcsmaros T, Haerty W, Roy S, Di-Palma F.: Evolution of regulatory networks associated with traits under selection in cichlids. Genome Biol. 2021 Jan 8;22(1):25. doi: 10.1186/s13059-020-02208-8.
Moon Y, Korcsmáros T, Nagappan A, Ray N.: MicroRNA target-based network predicts androgen receptor-linked mycotoxin stress. Ecotoxicol Environ Saf. 2021 Dec 27;230:113130. doi: 10.1016/j.ecoenv.2021.113130. Online ahead of print.
Olbei M, Hautefort I, Modos D, Treveil A, Poletti M, Gul L, Shannon-Lowe CD, Korcsmaros T.: SARS-CoV-2 Causes a Different Cytokine Response Compared to Other Cytokine Storm-Causing Respiratory Viruses in Severely Ill Patients. Front Immunol. 2021 Mar 1;12:629193. doi: 10.3389/fimmu.2021.629193. eCollection 2021.
Olbei M, Thomas JP, Hautefort I, Treveil A, Bohar B, Madgwick M, Gul L, Csabai L, Modos D, Korcsmaros T.: CytokineLink: A Cytokine Communication Map to Analyse Immune Responses-Case Studies in Inflammatory Bowel Disease and COVID-19. Cells. 2021 Aug 29;10(9):2242. doi: 10.3390/cells10092242.
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, et al.: COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Oct;17(10):e10387. doi: 10.15252/msb.202110387.
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff-Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, et al.: COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Dec;17(12):e10851. doi: 10.15252/msb.202110851.
Poletti M, Arnauts K, Ferrante M, Korcsmaros T.: Organoid-based Models to Study the Role of Host-microbiota Interactions in IBD. J Crohns Colitis. 2021 Jul 5;15(7):1222-1235. doi: 10.1093/ecco-jcc/jjaa257.
Sudhakar P, Machiels K, Verstockt B, Korcsmaros T, Vermeire S.: Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. Front Microbiol. 2021 May 11;12:618856. doi: 10.3389/fmicb.2021.618856. eCollection 2021.
Thomas JP, Modos D, Korcsmaros T, Brooks-Warburton J.: Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease. Front Genet. 2021 Oct 21;12:760501. doi: 10.3389/fgene.2021.760501. eCollection 2021.
Treveil A, Bohar B, Sudhakar P, Gul L, Csabai L, Olbei M, Poletti M, Madgwick M, Andrighetti T, Hautefort I, Modos D, Korcsmaros T.: ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PLoS Comput Biol. 2021 Feb 3;17(2):e1008685. doi: 10.1371/journal.pcbi.1008685. eCollection 2021 Feb.
Türei D, Valdeolivas A, Gul L, Palacio-Escat N, Klein M, Ivanova O, Ölbei M, Gábor A, Theis F, Módos D, Korcsmáros T, Saez-Rodriguez J.: Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. Mol Syst Biol. 2021 Mar;17(3):e9923. doi: 10.15252/msb.20209923.
2020
Andrighetti T, Bohar B, Lemke N, Sudhakar P, Korcsmaros T.: MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions. Cells. 2020 May 21;9(5):1278. doi: 10.3390/cells9051278.
Demeter A, Romero-Mulero MC, Csabai L, Ölbei M, Sudhakar P, Haerty W, Korcsmáros T.: ULK1 and ULK2 are less redundant than previously thought: computational analysis uncovers distinct regulation and functions of these autophagy induction proteins. Sci Rep. 2020 Jul 2;10(1):10940. doi: 10.1038/s41598-020-67780-2.
Frioux C, Singh D, Korcsmaros T, Hildebrand F.: From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. Comput Struct Biotechnol J. 2020 Jun 25;18:1722-1734. doi: 10.1016/j.csbj.2020.06.028. eCollection 2020.
Kiu R, Treveil A, Harnisch LC, Caim S, Leclaire C, van Sinderen D, Korcsmaros T, Hall LJ.: Bifidobacterium breve UCC2003 Induces a Distinct Global Transcriptomic Program in Neonatal Murine Intestinal Epithelial Cells. iScience. 2020 Jul 24;23(7):101336. doi: 10.1016/j.isci.2020.101336. Epub 2020 Jul 2.
Püngel D, Treveil A, Dalby MJ, Caim S, Colquhoun IJ, Booth C, Ketskemety J, Korcsmaros T, van Sinderen D, Lawson MA, Hall LJ.: Bifidobacterium breve UCC2003 Exopolysaccharide Modulates the Early Life Microbiota by Acting as a Potential Dietary Substrate. Nutrients. 2020 Mar 29;12(4):948. doi: 10.3390/nu12040948.
Seyed Tabib NS, Madgwick M, Sudhakar P, Verstockt B, Korcsmaros T, Vermeire S.: Big data in IBD: big progress for clinical practice. Gut. 2020 Aug;69(8):1520-1532. doi: 10.1136/gutjnl-2019-320065. Epub 2020 Feb 28.
2019
Jones EJ, Matthews ZJ, Gul L, Sudhakar P, Treveil A, Divekar D, Buck J, Wrzesinski T, Jefferson M, Armstrong SD, Hall LJ, Watson AJM, Carding SR, Haerty W, Di Palma F, Mayer U, Powell PP, Hautefort I, Wileman T, Korcsmaros T.: Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. Dis Model Mech. 2019 Mar 18;12(3):dmm037069. doi: 10.1242/dmm.037069.
Kosztelnik M, Kurucz A, Papp D, Jones E, Sigmond T, Barna J, Traka MH, Lorincz T, Szarka A, Banhegyi G, Vellai T, Korcsmaros T, Kapuy O.: Suppression of AMPK/aak-2 by NRF2/SKN-1 down-regulates autophagy during prolonged oxidative stress. FASEB J. 2019 Feb;33(2):2372-2387. doi: 10.1096/fj.201800565RR. Epub 2018 Oct 2.
New M, Van Acker T, Sakamaki JI, Jiang M, Saunders RE, Long J, Wang VM, Behrens A, Cerveira J, Sudhakar P, Korcsmaros T, Jefferies HBJ, Ryan KM, Howell M, Tooze SA.: MDH1 and MPP7 Regulate Autophagy in Pancreatic Ductal Adenocarcinoma. Cancer Res. 2019 Apr 15;79(8):1884-1898. doi: 10.1158/0008-5472.CAN-18-2553. Epub 2019 Feb 14.
Olbei M, Kingsley RA, Korcsmaros T, Sudhakar P.: Network Biology Approaches to Identify Molecular and Systems-Level Differences Between Salmonella Pathovars. Methods Mol Biol. 2019;1918:265-273. doi: 10.1007/978-1-4939-9000-9_21.
Sudhakar P, Jacomin AC, Hautefort I, Samavedam S, Fatemian K, Ari E, Gul L, Demeter A, Jones E, Korcsmaros T, Nezis IP.: Targeted interplay between bacterial pathogens and host autophagy. Autophagy. 2019 Sep;15(9):1620-1633. doi: 10.1080/15548627.2019.1590519. Epub 2019 Mar 25.
Sun D, Ren X, Ari E, Korcsmaros T, Csermely P, Wu LY.: Discovering cooperative biomarkers for heterogeneous complex disease diagnoses. Brief Bioinform. 2019 Jan 18;20(1):89-101. doi: 10.1093/bib/bbx090.
2018
Billes V, Kovács T, Manzéger A, Lőrincz P, Szincsák S, Regős Á, Kulcsár PI, Korcsmáros T, Lukácsovich T, Hoffmann G, Erdélyi M, Mihály J, Takács-Vellai K, Sass M, Vellai T.: Developmentally regulated autophagy is required for eye formation in Drosophila. Autophagy. 2018;14(9):1499-1519. doi: 10.1080/15548627.2018.1454569. Epub 2018 Aug 9.
Csabai L, Ölbei M, Budd A, Korcsmáros T, Fazekas D.: SignaLink: Multilayered Regulatory Networks. Methods Mol Biol. 2018;1819:53-73. doi: 10.1007/978-1-4939-8618-7_3.
Jacomin AC, Gul L, Sudhakar P, Korcsmaros T, Nezis IP.: What We Learned From Big Data for Autophagy Research. Front Cell Dev Biol. 2018 Aug 17;6:92. doi: 10.3389/fcell.2018.00092. eCollection 2018.
Kapuy O, Papp D, Vellai T, Bánhegyi G, Korcsmáros T.: Systems-Level Feedbacks of NRF2 Controlling Autophagy upon Oxidative Stress Response. Antioxidants (Basel). 2018 Mar 5;7(3):39. doi: 10.3390/antiox7030039.
2017
Brooks J, Watson A, Korcsmaros T.: Omics Approaches to Identify Potential Biomarkers of Inflammatory Diseases in the Focal Adhesion Complex. Genomics Proteomics Bioinformatics. 2017 Apr;15(2):101-109. doi: 10.1016/j.gpb.2016.12.003. Epub 2017 Apr 1.
Jones EJ, Korcsmaros T, Carding SR.: Mechanisms and pathways of Toxoplasma gondii transepithelial migration. Tissue Barriers. 2017 Jan 2;5(1):e1273865. doi: 10.1080/21688370.2016.1273865. Epub 2016 Dec 20.
Korcsmaros T, Schneider MV, Superti-Furga G.: Next generation of network medicine: interdisciplinary signaling approaches. Integr Biol (Camb). 2017 Feb 20;9(2):97-108. doi: 10.1039/c6ib00215c.
Lamprinaki D, Beasy G, Zhekova A, Wittmann A, James S, Dicks J, Iwakura Y, Saijo S, Wang X, Chow CW, Roberts I, Korcsmaros T, Mayer U, Wileman T, Kawasaki N.: LC3-Associated Phagocytosis Is Required for Dendritic Cell Inflammatory Cytokine Response to Gut Commensal Yeast Saccharomyces cerevisiae. Front Immunol. 2017 Oct 25;8:1397. doi: 10.3389/fimmu.2017.01397. eCollection 2017.
Métris A, Sudhakar P, Fazekas D, Demeter A, Ari E, Olbei M, Branchu P, Kingsley RA, Baranyi J, Korcsmáros T.: SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. NPJ Syst Biol Appl. 2017 Oct 18;3:31. doi: 10.1038/s41540-017-0034-z. eCollection 2017.
Módos D, Bulusu KC, Fazekas D, Kubisch J, Brooks J, Marczell I, Szabó PM, Vellai T, Csermely P, Lenti K, Bender A, Korcsmáros T.: Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. NPJ Syst Biol Appl. 2017 Jan 24;3:2. doi: 10.1038/s41540-017-0003-6.
2016
Csályi K, Fazekas D, Kadlecsik T, Türei D, Gul L, Horváth B, Módos D, Demeter A, Pápai N, Lenti K, Csermely P, Vellai T, Korcsmáros T, Varga M.: SignaFish: A Zebrafish-Specific Signaling Pathway Resource. Zebrafish. 2016 Dec;13(6):541-544. doi: 10.1089/zeb.2016.1277. Epub 2016 Apr 20.
Csermely P, Korcsmáros T, Nussinov R.: Intracellular and intercellular signaling networks in cancer initiation, development and precision anti-cancer therapy: RAS acts as contextual signaling hub. Semin Cell Dev Biol. 2016 Oct;58:55-9. doi: 10.1016/j.semcdb.2016.07.005. Epub 2016 Jul 6.
Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, Adams CM, Adams PD, Adeli K, Adhihetty PJ, Adler SG, Agam G, Agarwal R, Aghi MK, Agnello M, Agostinis P, Aguilar PV, Aguirre-Ghiso J, Airoldi EM, Ait-Si-Ali S, Akematsu T, Akporiaye ET, Al-Rubeai M, Albaiceta GM, Albanese C, Albani D, Albert ML, Aldudo J, Algül H, Alirezaei M, Alloza I, Almasan A, Almonte-Beceril M, Alnemri ES, Alonso C, Altan-Bonnet N, Altieri DC, Alvarez S, Alvarez-Erviti L, Alves S, Amadoro G, Amano A, Amantini C, Ambrosio S, Amelio I, Amer AO, Amessou M, Amon A, An Z, Anania FA, Andersen SU, Andley UP, Andreadi CK, Andrieu-Abadie N, Anel A, Ann DK, Anoopkumar-Dukie S, Antonioli M, Aoki H, Apostolova N, Aquila S, Aquilano K, Araki K, Arama E, Aranda A, Araya J, Arcaro A, Arias E, Arimoto H, Ariosa AR, Armstrong JL, Arnould T, Arsov I, Asanuma K, Askanas V, Asselin E, Atarashi R, Atherton SS, Atkin JD, Attardi LD, Auberger P, Auburger G, Aurelian L, Autelli R, Avagliano L, Avantaggiati ML, Avrahami L, Awale S, Azad N, Bachetti T, Backer JM, Bae DH, Bae JS, Bae ON, Bae SH, Baehrecke EH, Baek SH, Baghdiguian S, Bagniewska-Zadworna A, et al.: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy. 2016;12(1):1-222. doi: 10.1080/15548627.2015.1100356.
Modos D, Brooks J, Fazekas D, Ari E, Vellai T, Csermely P, Korcsmaros T, Lenti K.: Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. Sci Rep. 2016 Dec 6;6:38588. doi: 10.1038/srep38588.
Nussinov R, Tsai CJ, Jang H, Korcsmáros T, Csermely P.: Oncogenic KRAS signaling and YAP1/β-catenin: Similar cell cycle control in tumor initiation. Semin Cell Dev Biol. 2016 Oct;58:79-85. doi: 10.1016/j.semcdb.2016.04.001. Epub 2016 Apr 4.
Türei D, Korcsmáros T, Saez-Rodriguez J.: OmniPath: guidelines and gateway for literature-curated signaling pathway resources. Nat Methods. 2016 Nov 29;13(12):966-967. doi: 10.1038/nmeth.4077.
2015
Alexeyenko A, Alkasalias T, Pavlova T, Szekely L, Kashuba V, Rundqvist H, Wiklund P, Egevad L, Csermely P, Korcsmaros T, Guven H, Klein G.: Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth. J Exp Clin Cancer Res. 2015 Jun 18;34(1):62. doi: 10.1186/s13046-015-0178-x.
Csermely P, Hódsági J, Korcsmáros T, Módos D, Perez-Lopez ÁR, Szalay K, Veres DV, Lenti K, Wu LY, Zhang XS.: Cancer stem cells display extremely large evolvability: alternating plastic and rigid networks as a potential Mechanism: network models, novel therapeutic target strategies, and the contributions of hypoxia, inflammation and cellular senescence. Semin Cancer Biol. 2015 Feb;30:42-51. doi: 10.1016/j.semcancer.2013.12.004. Epub 2014 Jan 8.
Lewis R, Guha R, Korcsmaros T, Bender A.: Synergy Maps: exploring compound combinations using network-based visualization. J Cheminform. 2015 Aug 1;7:36. doi: 10.1186/s13321-015-0090-6. eCollection 2015.
Perez-Lopez ÁR, Szalay KZ, Türei D, Módos D, Lenti K, Korcsmáros T, Csermely P.: Targets of drugs are generally, and targets of drugs having side effects are specifically good spreaders of human interactome perturbations. Sci Rep. 2015 May 11;5:10182. doi: 10.1038/srep10182.
Türei D, Földvári-Nagy L, Fazekas D, Módos D, Kubisch J, Kadlecsik T, Demeter A, Lenti K, Csermely P, Vellai T, Korcsmáros T.: Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. Autophagy. 2015;11(1):155-65. doi: 10.4161/15548627.2014.994346.
Veres DV, Gyurkó DM, Thaler B, Szalay KZ, Fazekas D, Korcsmáros T, Csermely P.: ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis. Nucleic Acids Res. 2015 Jan;43(Database issue):D485-93. doi: 10.1093/nar/gku1007. Epub 2014 Oct 27.
2014
2013
Bozóky B, Savchenko A, Csermely P, Korcsmáros T, Dúl Z, Pontén F, Székely L, Klein G.: Novel signatures of cancer-associated fibroblasts. Int J Cancer. 2013 Jul 15;133(2):286-93. doi: 10.1002/ijc.28035. Epub 2013 Feb 12.
Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R.: Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther. 2013 Jun;138(3):333-408. doi: 10.1016/j.pharmthera.2013.01.016. Epub 2013 Feb 4.
Csermely P, Korcsmáros T.: Cancer-related networks: a help to understand, predict and change malignant transformation. Semin Cancer Biol. 2013 Aug;23(4):209-12. doi: 10.1016/j.semcancer.2013.06.011. Epub 2013 Jul 2.
Fazekas D, Koltai M, Türei D, Módos D, Pálfy M, Dúl Z, Zsákai L, Szalay-Bekő M, Lenti K, Farkas IJ, Vellai T, Csermely P, Korcsmáros T.: SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. BMC Syst Biol. 2013 Jan 18;7:7. doi: 10.1186/1752-0509-7-7.
Gyurkó DM, Veres DV, Módos D, Lenti K, Korcsmáros T, Csermely P.: Adaptation and learning of molecular networks as a description of cancer development at the systems-level: potential use in anti-cancer therapies. Semin Cancer Biol. 2013 Aug;23(4):262-9. doi: 10.1016/j.semcancer.2013.06.005. Epub 2013 Jun 21.
Korcsmaros T, Dunai ZA, Vellai T, Csermely P.: Teaching the bioinformatics of signaling networks: an integrated approach to facilitate multi-disciplinary learning. Brief Bioinform. 2013 Sep;14(5):618-32. doi: 10.1093/bib/bbt024. Epub 2013 May 2.
Kubisch J, Türei D, Földvári-Nagy L, Dunai ZA, Zsákai L, Varga M, Vellai T, Csermely P, Korcsmáros T.: Complex regulation of autophagy in cancer - integrated approaches to discover the networks that hold a double-edged sword. Semin Cancer Biol. 2013 Aug;23(4):252-61. doi: 10.1016/j.semcancer.2013.06.009. Epub 2013 Jun 28.
Pálfy M, Farkas IJ, Vellai T, Korcsmáros T.: Uniform curation protocol of metazoan signaling pathways to predict novel signaling components. Methods Mol Biol. 2013;1021:285-97. doi: 10.1007/978-1-62703-450-0_15.
Türei D, Papp D, Fazekas D, Földvári-Nagy L, Módos D, Lenti K, Csermely P, Korcsmáros T.: NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. Oxid Med Cell Longev. 2013;2013:737591. doi: 10.1155/2013/737591. Epub 2013 Apr 17.
2012
Dunai ZA, Imre G, Barna G, Korcsmaros T, Petak I, Bauer PI, Mihalik R.: Staurosporine induces necroptotic cell death under caspase-compromised conditions in U937 cells. PLoS One. 2012;7(7):e41945. doi: 10.1371/journal.pone.0041945. Epub 2012 Jul 31.
Farkas IJ, Szántó-Várnagy A, Korcsmáros T.: Linking proteins to signaling pathways for experiment design and evaluation. PLoS One. 2012;7(4):e36202. doi: 10.1371/journal.pone.0036202. Epub 2012 Apr 27.
Pálfy M, Reményi A, Korcsmáros T.: Endosomal crosstalk: meeting points for signaling pathways. Trends Cell Biol. 2012 Sep;22(9):447-56. doi: 10.1016/j.tcb.2012.06.004. Epub 2012 Jul 14.
Papp D, Lenti K, Módos D, Fazekas D, Dúl Z, Türei D, Földvári-Nagy L, Nussinov R, Csermely P, Korcsmáros T.: The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops. FEBS Lett. 2012 Jun 21;586(13):1795-802. doi: 10.1016/j.febslet.2012.05.016. Epub 2012 May 26.
2011
Farkas IJ, Korcsmáros T, Kovács IA, Mihalik Á, Palotai R, Simkó GI, Szalay KZ, Szalay-Beko M, Vellai T, Wang S, Csermely P.: Network-based tools for the identification of novel drug targets. Sci Signal. 2011 May 17;4(173):pt3. doi: 10.1126/scisignal.2001950.
Korcsmáros T, Szalay MS, Rovó P, Palotai R, Fazekas D, Lenti K, Farkas IJ, Csermely P, Vellai T.: Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PLoS One. 2011 May 3;6(5):e19240. doi: 10.1371/journal.pone.0019240.
2010