Not logged in PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways Vande Moortele, Tibo; Verschaffelt, Pieter; Huang, Qingyao; Doncheva, Nadezhda T.; Holstein, Tanja; Jachmann, Caroline; Dawyndt, Peter; Martens, Lennart; Mesuere, Bart; van den Bossche, Tim Share Save
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The STRING database in 2025: protein networks with directionality of regulation Szklarczyk, Damian; Nastou, Katerina; Koutrouli, Mikaela; Kirsch, Rebecca; Mehryary, Farrokh; Hachilif, Radja; Hu, Dewei; Peluso, Matteo E.; Huang, Qingyao; Fang, Tao; Doncheva, Nadezhda T.; Pyysalo, Sampo; Bork, Peer; Jensen, Lars J.; von Mering, Christian Share Save
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A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates Rebak, Alexandra S.; Hendriks, Ivo A.; Elsborg, Jonas D.; Buch-Larsen, Sara C.; Nielsen, Claus H.; Terslev, Lene; Kirsch, Rebecca; Damgaard, Dres; Doncheva, Nadezhda T.; Lennartsson, Caroline; Rykaer, Martin; Jensen, Lars J.; Christophorou, Maria A.; Nielsen, Michael L. Share Save
Alteration of microglial metabolism and inflammatory profile contributes to neurotoxicity in a hiPSC-derived microglia model of frontotemporal dementia 3 Haukedal, Henriette; Lorenzen, Signe Syshoj; Westi, Emil Winther; Corsi, Giulia I.; Gadekar, Veerendra P.; McQuade, Amanda; Davtyan, Hayk; Doncheva, Nadezhda T.; Schmid, Benjamin; Chandrasekaran, Abinaya; Seemann, Stefan E.; Cirera, Susanna; Blurton-Jones, Mathew; Meyer, Morten; Gorodkin, Jan; Aldana, Blanca I.; Freude, Kristine Share Save
Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration Kokoli, Maria; Karatzas, Evangelos; Baltoumas, Fotis A.; Schneider, Reinhard; Pafilis, Evangelos; Paragkamian, Savvas; Doncheva, Nadezhda T.; Jensen, Lars Juhl; Pavlopoulos, Georgios A. Share Save
The transcriptomic landscape of neurons carrying PSEN1 mutations reveals changes in extracellular matrix components and non-coding gene expression Corsi, Giulia I.; Gadekar, Veerendra P.; Haukedal, Henriette; Doncheva, Nadezhda T.; Anthon, Christian; Ambardar, Sheetal; Palakodeti, Dasaradhi; Hyttel, Poul; Freude, Kristine; Seemann, Stefan E.; Gorodkin, Jan Share Save
Golgi fragmentation - One of the earliest organelle phenotypes in Alzheimer's disease neurons Haukedal, Henriette; Corsi, Giulia I.; Gadekar, Veerendra P.; Doncheva, Nadezhda T.; Kedia, Shekhar; de Haan, Noortje; Chandrasekaran, Abinaya; Jensen, Pia; Schionning, Pernille; Vallin, Sarah; Marlet, Frederik Ravnkilde; Poon, Anna; Pires, Carlota; Agha, Fawzi Khoder; Wandall, Hans H.; Cirera, Susanna; Simonsen, Anja Hviid; Nielsen, Troels Tolstrup; Nielsen, Jorgen Erik; Hyttel, Poul; Muddashetty, Ravi; Aldana, Blanca I.; Gorodkin, Jan; Nair, Deepak; Meyer, Morten; Larsen, Martin Rossel; Freude, Kristine Share Save
Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis Yarani, Reza; Palasca, Oana; Doncheva, Nadezhda T.; Anthon, Christian; Pilecki, Bartosz; Svane, Cecilie A. S.; Mirza, Aashiq H.; Litman, Thomas; Holmskov, Uffe; Bang-Berthelsen, Claus H.; Vilien, Mogens; Jensen, Lars J.; Gorodkin, Jan; Pociot, Flemming Share Save
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest Szklarczyk, Damian; Kirsch, Rebecca; Koutrouli, Mikaela; Nastou, Katerina; Mehryary, Farrokh; Hachilif, Radja; Gable, Annika L.; Fang, Tao; Doncheva, Nadezhda T.; Pyysalo, Sampo; Bork, Peer; Jensen, Lars J.; von Mering, Christian Share Save
The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production Geissler, Adrian S.; Poulsen, Line D.; Doncheva, Nadezhda T.; Anthon, Christian; Seemann, Stefan E.; Gonzalez-Tortuero, Enrique; Breuener, Anne; Jensen, Lars J.; Hjort, Carsten; Vinther, Jeppe; Gorodkin, Jan Share Save
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Astrocytic reactivity triggered by defective autophagy and metabolic failure causes neurotoxicity in frontotemporal dementia type 3 Chandrasekaran, Abinaya; Dittlau, Katarina Stoklund; Corsi, Giulia, I; Haukedal, Henriette; Doncheva, Nadezhda T.; Ramakrishna, Sarayu; Ambardar, Sheetal; Salcedo, Claudia; Schmidt, Sissel, I; Zhang, Yu; Cirera, Susanna; Pihl, Maria; Schmid, Benjamin; Nielsen, Troels Tolstrup; Nielsen, Jorgen E.; Kolko, Miriam; Kobolak, Julianna; Dinnyes, Andras; Hyttel, Poul; Palakodeti, Dasaradhi; Gorodkin, Jan; Muddashetty, Ravi S.; Meyer, Morten; Aldana, Blanca, I; Freude, Kristine K. Share Save
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets (vol 49, pg D605, 2021) Szklarczyk, Damian; Gable, Annika L.; Nastou, Katerina C.; Lyon, David; Kirsch, Rebecca; Pyysalo, Sampo; Doncheva, Nadezhda T.; Legeay, Marc; Fang, Tao; Bork, Peer; Jensen, Lars J.; von Mering, Christian Share Save
Epistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability Dultz, Georg; Srikakulam, Sanjay K.; Konetschnik, Michael; Shimakami, Tetsuro; Doncheva, Nadezhda T.; Dietz, Julia; Sarrazin, Christoph; Biondi, Ricardo M.; Zeuzem, Stefan; Tampe, Robert; Kalinina, Olga, V; Welsch, Christoph Share Save
Human pathways in animal models: possibilities and limitations Doncheva, Nadezhda T.; Palasca, Oana; Yarani, Reza; Litman, Thomas; Anthon, Christian; Groenen, Martien A. M.; Stadler, Peter F.; Pociot, Flemming; Jensen, Lars J.; Gorodkin, Jan Share Save
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets Szklarczyk, Damian; Gable, Annika L.; Nastou, Katerina C.; Lyon, David; Kirsch, Rebecca; Pyysalo, Sampo; Doncheva, Nadezhda T.; Legeay, Marc; Fang, Tao; Bork, Peer; Jensen, Lars J.; von Mering, Christian Share Save
Transcriptome landscape of protein-coding genes and long noncoding RNAs in the colon and blood of DSS-induced mouse model of Acute ulcerative colitis Yarani, R.; Palasca, O.; Doncheva, N. Tsankova; Anthon, C.; Pilecki, B.; Litman, T.; Holmskov, U.; Jensen, L. J.; Gorodkin, J.; Pociot, F. Share Save
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Szklarczyk, Damian; Gable, Annika L.; Lyon, David; Junge, Alexander; Wyder, Stefan; Huerta-Cepas, Jaime; Simonovic, Milan; Doncheva, Nadezhda T.; Morris, John H.; Bork, Peer; Jensen, Lars J.; Mering, Christianvon Share Save
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