Márton Olbei

Oct 2021

Csabai L,Fazekas D,Kadlecsik T,Szalay-Beko M,Bohár B,Madgwick M,Módos D,Olbei 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 research

Publishers version: doi:10.1093/nar/gkab909

Aug 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

Publishers version: doi:10.3390/cells10092242

Mar 2021

Turei D, Valdeolivas A, Gul L, Palacio-Escat N, Klein M, Ivanova O, Olbei M, Gabor A, Theis F, Modos D, Korcsmaros T, Saez-Rodriguez J

Integrated intra- and intercellular signaling knowledge for multicellular omics analysis

Molecular Systems Biology

Publishers version: doi:10.15252/msb.20209923

Feb 2021

Olbei M, Hautefort I, Modos D, Treveil A, Poletti M, Gul L, Shannon-Lowe C, Korcsmaros

SARS-CoV-2 causes a different cytokine response compared to other cytokine storm-causing respiratory viruses in severely ill patients

Frontiers in Immunology

Publishers version: doi:https://doi.org/10.3389/fimmu.2021.629193

Feb 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 Computational Biology

Publishers version: doi:10.1371/journal.pcbi.1008685

Jan 2021

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 biology

Publishers version: doi:10.1186/s13059-020-02208-8

Oct 2020

Ostaszewski M,Niarakis A,Mazein A,Kuperstein I,Phair R,Orta-Resendiz A,Aghamiri SS,Acencio ML,Glaab E,Ruepp A,Fobo G,Montrone C,Brauner B,Frischman G,Gómez LCM,Somers J,Hoch M,Gupta SK,Scheel J,Borlinghaus H,Czauderna T,Schreiber F,Montagud A,de Leon MP,Funahashi A,Hiki Y,Hiroi N,Yamada TG,Dräger A,Renz A,Naveez M,Bocskei Zs,Messina F,Börnigen D,Fergusson L,Conti M,Rameil M,Nakonecnij V,Vanhoefer J,Schmiester L,Wang M,Ackerman EE,Shoemaker J,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,Haw R,Jassal B,Matthews L,Orlic-Milacic M,Ribeiro AS,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,Soliman S,Valdeolivas A,Esteban-Medina M,Peña-Chilet M,Helikar T,Lal Puniya,Modos D,Treveil S,Olbei M,De Meulder B,Dugourd A,Naldi A,Noel V,Calzone L,Sander C,Demir E,Korcsmaros T,Freeman TC,Augé F,Beckmann JS,Hasenauer J,Wolkenhauer O,Wilighagen EL,Pico AR,Evelo CT,Gillespie ML,Stein LD,Hermjakob H,DEustachio P,Saez-Rodriguez J,Dopazo J,Valencia A,Kitano H,Barillot E,Auffray C,Balling R,Schneider R,The COVID idsease map community .

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

bioRxiv

Publishers version: doi:10.1101/2020.10.26.356014

Jul 2020

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.

Scientific reports

Publishers version: doi:10.1038/s41598-020-67780-2

Dec 2019

Treveil A., Sudhakar P., Matthews Z., Wrzesinski T., Jones E., Brooks J., Olbei M., Hautefort I., Hall L., Carding S., Mayer U., Powell P., Wileman T., Di Palma F., Haerty W., Korcsmaros T.

Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches.

Molecular omics

Publishers version: doi:10.1039/c9mo00130a

Jan 2019

Olbei M., Kingsley R. A., Korcsmaros T., Sudhakar P.

Network Biology Approaches to Identify Molecular and Systems-Level Differences Between Salmonella Pathovars.

Publishers version: doi:10.1007/978-1-4939-9000-9_21

Dec 2018

Mehta T. K., Koch C., Nash W., Knaack S. A., Sudhakar P., Olbei M., Bastkowski S., Penso Dolfin L., Korcsmaros T., Haerty W., Roy S., Di Palma F.

Evolution of regulatory networks controlling adaptive traits in cichlids

biorxiv

Publishers version: doi:10.1101/496034

Nov 2018

Csabai L., Olbei M., Budd A., Korcsmaros T., Fazekas D.

SignaLink: Multilayered Regulatory Networks.

Publishers version: doi:10.1007/978-1-4939-8618-7_3

Nov 2018

Csabai L., Olbei M., Budd A., Korcsmaros T., Fazekas D.

SignaLink: Multilayered Regulatory Networks.

Methods in molecular biology (Clifton, N.J.)

Publishers version: doi:10.1007/978-1-4939-8618-7_3

Oct 2017

Metris A., Sudhakar P., Fazekas D., Demeter A., Eszter A., Olbei M., Branchu P., Kingsley R., Baranyi J., Korcsmaros T.

SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation

Nature Partner Journals Systems Biology and Applications

Publishers version: doi:doi:10.1038/s41540-017-0034-z

Feb 2022

Thomas JP, Olbei M, Brooks J, Korcsmaros T, Modos

Analysing miRNA-Target Gene Networks in Inflammatory Bowel Disease and Other Complex Diseases Using Transcriptomic Data

Genes

Publishers version: doi:https://doi.org/10.3390/genes13020370

Dec 2021

Olbei M, Bohar B, Fazekas D, Madgwick M, Sudhakar P, Hautefort I, Metris A, Baranyi J, Kingsley RA, Korcsmaros

Multi-layered networks of SalmoNet2 enable strain comparisons of theSalmonellagenus on a molecular level

bioRxiv

Publishers version: doi:https://doi.org/10.1101/2021.12.20.473597

Oct 2021

Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frischman G, Gómez LCM, Somers J, Hoch M, Gupta SK, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, de Leon MP, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Zs, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker J, 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, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Ribeiro AS, 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, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Helikar T, Lal Puniya, Modos D (QIB), Treveil S (EI), Olbei M (EI), De Meulder B, Dugourd A, Naldi A, Noel V, Calzone L, Sander C, Demir E, Korcsmaros T (EI), Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ML, Stein LD, Hermjakob H, DEustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms

Molecular Systems Biology

Publishers version: doi:https://doi.org/10.15252/msb.202110387