cran: Andromeda | Projects | Ecosyste.ms: Papers

10.1186/s13068-016-0608-9

Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose
Cited by: 91
Author(s): Jaana Kuuskeri, Mari Häkkinen, Pia Laine, Olli‐Pekka Smolander, Fitsum Tamene, Sini Miettinen, Paula Nousiainen, Marianna Kemell, Petri Auvinen, Taina Lundell
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pgen.1008551

Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance
Cited by: 32
Author(s): Patrícia Alves de Castro, Ana Cristina Colabardini, Adriana Oliveira Manfiolli, Jéssica Chiaratto, Lilian Pereira Silva, Eliciane Cevolani Mattos, Giuseppe Palmisano, Fausto Almeida, Gabriela Félix Persinoti, Laure Nicolas Annick Ries, Laura Mellado, Marina Campos Rocha, Michael Bromley, Roberto Nascimento Silva, Gabriel Scalini de Souza, Flávio Vieira Loures, Iran Malavazi, Neil Andrew Brown, Gustavo H. Goldman
Software Mentions: 4
Published: almost 7 years ago

10.3389/fpls.2019.00473

Proteases Underground: Analysis of the Maize Root Apoplast Identifies Organ Specific Papain-Like Cysteine Protease Activity
Cited by: 15
Author(s): Jan Schulze Hüynck, Farnusch Kaschani, Karina van der Linde, Sebastian Ziemann, André N. Müller, Thomas Colby, Markus Kaiser, Johana C. Misas-Villamil, Gunther Doehlemann
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.ppat.1009824

pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spread
Cited by: 12
Author(s): Tomasz H. Benedyk, Julia Muenzner, Viv Connor, Yue Han, Katherine A. Brown, Kaveesha J. Wijesinghe, Yunhui Zhuang, Susanna Colaco, Guido A. Stoll, Owen S. Tutt, Stanislava Svobodova, Dmitri I. Svergun, Neil Bryant, Janet E. Deane, Andrew E. Firth, Cy M. Jeffries, Colin M. Crump, Stephen C. Graham
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-020-07118-4

Transcriptome-IPMS analysis reveals a tissue-dependent miR156/SPL13 regulatory mechanism in alfalfa drought tolerance
Cited by: 6
Author(s): Biruk A. Feyissa, Justin B. Renaud, Vida Nasrollahi, Susanne E. Kohalmi, Abdelali Hannoufa
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.56554

Cytotoxic T cells swarm by homotypic chemokine signalling
Cited by: 32
Author(s): Jorge Luis Galeano Niño, Sophie V. Pageon, Szun S. Tay, Feyza Colakoglu, Daryan Kempe, Jack D. Hywood, Jessica K Mazalo, James Cremasco, Matt Govendir, Laura F. Dagley, Ku‐Lung Hsu, Simone Rizzetto, Jerzy Zieba, Gregory Rice, Victoria Prior, Geraldine M. O’Neill, Richard J. Williams, David R. Nisbet, Belinda Kramer, Andrew I. Webb, Fabio Luciani, Mark Read, Maté Biro
Software Mentions: 4
Published: about 6 years ago

10.3390/antibiotics10030325

The Phosin PptA Plays a Negative Role in the Regulation of Antibiotic Production in Streptomyces lividans
Cited by: 7
Author(s): Noriyasu Shikura, Emmanuelle Darbon, Catherine Esnault, Ariane Deniset‐Besseau, Delin Xu, Clara Lejeune, Éric Jacquet, Naïma Nhiri, Laila Sago, David Cornu, Sebastiaan Werten, Cécile Martel, Marie‐Joëlle Virolle
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2016.00427

Proteogenomic Analysis of Mycobacterium smegmatis Using High Resolution Mass Spectrometry
Cited by: 16
Author(s): Potgieter Mg, Kehilwe C. Nakedi, Jon Ambler, Andrew J. M. Nel, Shaun Garnett, Nelson C. Soares, Nicola Mulder, Jonathan M. Blackburn
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2019.01410

On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics
Cited by: 6
Author(s): K.C.T. Machado, Suereta Fortuin, Gisele G. Tomazella, André Fonseca, Robin M. Warren, Harald G. Wiker, Sandro J. de Souza, Gustavo Souza
Software Mentions: 4
Published: over 7 years ago

10.1111/tpj.15250

The chemical compound ‘Heatin’ stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1‐subfamily of nitrilases
Cited by: 7
Author(s): Lennard van der Woude, Markus Piotrowski, Gruson Klaasse, Judith K Paulus, Daniel Krahn, Sabrina Ninck, Farnusch Kaschani, Markus Kaiser, Ondřej Novák, Karin Ljung, Suzanne Bulder, Marcel van Verk, L. Basten Snoek, Martijn Fiers, Nathaniel I. Martin, R.A.L. van der Hoorn, Stéphanie Robert, Sjef Smeekens, Martijn van Zanten
Software Mentions: 4
Published: over 5 years ago

10.1016/j.ccell.2017.03.001

Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia
Cited by: 85
Author(s): Sebastian Mohr, Carmen Doebele, Federico Comoglio, Tobias Berg, Julia Beck, Hanibal Bohnenberger, Gabriela Alexe, Jasmin Corso, Philipp Ströbel, Astrid Wachter, Tim Beißbarth, Frank Schnütgen, Anjali Cremer, Nadine Haetscher, Stefanie Göllner, A. Maureen Rouhi, Lars Palmqvist, Michael A. Rieger, Timm Schroeder, Halvard Bönig, Carsten Müller‐Tidow, Florian Kuchenbauer, Ekkehard Schütz, Anthony Green, Henning Urlaub, Kimberly Stegmaier, R. Keith Humphries, Hubert Serve, Thomas Oellerich
Software Mentions: 4
Published: over 9 years ago

10.1111/all.14694

Comparative proteomics of common allergenic tree pollens of birch, alder, and hazel
Cited by: 5
Author(s): Barbara Darnhofer, Tamara Tomin, Laura Liesinger, Matthias Schittmayer, Peter Valentin Tomazic, Ruth Birner‐Gruenberger
Software Mentions: 4
Published: almost 6 years ago

10.15252/embr.201846557

Tamoxifen mechanically reprograms the tumor microenvironment via <scp>HIF</scp> ‐1A and reduces cancer cell survival
Cited by: 55
Author(s): Ernesto Cortés, Dariusz Lachowski, Benjamin Robinson, Müge Sarper, Jaakko Teppo, Stephen D. Thorpe, Tyler J Lieberthal, Kenji Iwamoto, David A. Lee, Mariko Okada‐Hatakeyama, Markku Varjosalo, Armando E. del Río Hernández
Software Mentions: 4
Published: almost 8 years ago

10.3390/molecules26072027

Discovery of Post-Translational Modifications in Emiliania huxleyi
Cited by: 2
Author(s): Van-An Duong, Onyou Nam, EonSeon Jin, Jong Park, Hookeun Lee
Software Mentions: 4
Published: over 5 years ago

10.15252/emmm.201708202

A proteomic network approach across the <scp>ALS</scp> ‐ <scp>FTD</scp> disease spectrum resolves clinical phenotypes and genetic vulnerability in human brain
Cited by: 115
Author(s): Mfon Umoh, Eric B. Dammer, Jingting Dai, Duc M. Duong, James J. Lah, Aĺlan I. Levey, Marla Gearing, Jonathan D. Glass, Nicholas T. Seyfried
Software Mentions: 4
Published: almost 9 years ago

10.15252/embj.201899559

Phosphoproteomic screening identifies physiological substrates of the <scp>CDKL</scp> 5 kinase
Cited by: 52
Author(s): Iván Muñoz, Michael Morgan, Julien Peltier, Florian Weiland, Mateusz Gregorczyk, Fiona Brown, Thomas Macartney, Rachel Toth, Matthias Trost, John Rouse
Software Mentions: 4
Published: about 8 years ago

10.15252/embr.201744884

The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics
Cited by: 34
Author(s): Thomas O’Loughlin, Thomas A. Masters, Folma Buß
Software Mentions: 4
Published: over 8 years ago

10.1074/mcp.O117.067728

Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences
Cited by: 62
Author(s): Bo Zhang, Mohammad Pirmoradian, Roman A. Zubarev, Lukas Käll
Software Mentions: 4
Published: over 9 years ago

10.1016/j.dib.2015.11.063

Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods
Cited by: 29
Author(s): Claire Ramus, Agnès Hovasse, Marlène Marcellin, Anne-Marie Hesse, Emmanuelle Mouton-Barbosa, David Bouyssié, Sebastian Vaca, Christine Carapito, Karima Chaoui, Christophe Bruley, Jérôme Garin, Sarah Cianférani, Myriam Ferro, Alain Van Dorssaeler, Odile Burlet‐Schiltz, Christine Schaeffer, Yohann Couté, Anne Gonzalez de Peredo
Software Mentions: 4
Published: over 10 years ago

10.15252/emmm.201708428

Comparative proteomics reveals a diagnostic signature for pulmonary head‐and‐neck cancer metastasis
Cited by: 41
Author(s): Hanibal Bohnenberger, Lars Kaderali, Philipp Ströbel, Diego Yepes, Uwe Plessmann, Neekesh V. Dharia, Sha Yao, Carina Heydt, Sabine Merkelbach‐Bruse, Alexander Emmert, Jonatan F. Hoffmann, Julius Bodemeyer, Kirsten Reuter‐Jessen, Anna‐Maria Lois, Leif Hendrik Dröge, Philipp Baumeister, Christoph Walz, Lorenz Biggemann, Roland B. Walter, Björn Häupl, Federico Comoglio, Kuan‐Ting Pan, Sebastian Scheich, Christof Lenz, Stefan Küffer, Felix Bremmer, Julia Kitz, Maren Sitte, Tim Beißbarth, Marc Hinterthaner, Martin Sebastian, Joachim Lotz, Hans‐Ulrich Schildhaus, Hendrik A. Wolff, Bernhard C. Danner, Christian Brandts, Reinhard Büttner, Martin Canis, Kimberly Stegmaier, Hubert Serve, Henning Urlaub, Thomas Oellerich
Software Mentions: 4
Published: about 8 years ago

10.15252/embj.2019104202

Systematic analysis of the <scp>IL</scp> ‐17 receptor signalosome reveals a robust regulatory feedback loop
Cited by: 14
Author(s): Helena Draberova, Sarka Janusova, Daniela Knizkova, Tereza Šemberová, Michaela Přibíková, Andrea Ujevic, Karel Harant, Sofija Knápková, Matouš Hrdinka, Viola Fanfani, Giovanni Stracquadanio, Ales Drobek, Klara Ruppova, Ondřej Štěpánek, Peter Dráber
Software Mentions: 4
Published: over 6 years ago

10.15252/emmm.201505344

Characterization and quantification of proteins secreted by single human embryos prior to implantation
Cited by: 34
Author(s): Maurizio Poli, Alessandro Ori, Tim Child, S. Jaroudi, K Spath, Martin Beck, Dagan Wells
Software Mentions: 4
Published: about 11 years ago

10.1186/1471-2105-12-439

SCFIA: a statistical corresponding feature identification algorithm for LC/MS
Cited by: 8
Author(s): Jian Cui, Xuepo Ma, Long Chen, Jianqiu Zhang
Software Mentions: 4
Published: almost 15 years ago

10.15252/emmm.202013131

Synaptic disruption and CREB‐regulated transcription are restored by K + channel blockers in ALS
Cited by: 19
Author(s): Alberto Catanese, Sandeep Rajkumar, Daniel Sommer, Dennis Freisem, Alexander Wirth, Amr Aly, David Massa-López, Andrea Olivieri, Federica Torelli, Valentin Ioannidis, Joanna Lipecka, Ida Chiara Guerrera, Daniel Zytnicki, Albert C. Ludolph, Edor Kabashi, Medhanie Mulaw, Francesco Roselli, Tobias M. Böckers
Software Mentions: 4
Published: over 5 years ago

10.15252/emmm.201911659

<scp>FBXL</scp> 4 deficiency increases mitochondrial removal by autophagy
Cited by: 34
Author(s): David Alsina, Oleksandr Lytovchenko, Aleksandra Schab, Ilian Atanassov, F. Schober, Min Jiang, Camilla Koolmeister, Anna Wedell, Robert W. Taylor, Anna Wredenberg, Nils-Göran Larsson
Software Mentions: 4
Published: over 6 years ago

10.1074/mcp.RA119.001392

Cathepsin L Regulates Metabolic Networks Controlling Rapid Cell Growth and Proliferation
Cited by: 7
Author(s): Tommy Weiss-Sadan, Gal Itzhak, Farnusch Kaschani, Zhanru Yu, Mohamed Mahameed, Adi Anaki, Yael Ben-Nun, Emmanuelle Merquiol, Boaz Tirosh, Benedikt M. Kessler, Markus Kaiser, Galia Blum
Software Mentions: 4
Published: over 7 years ago

10.1007/s00401-020-02217-8

Extrinsic immune cell-derived, but not intrinsic oligodendroglial factors contribute to oligodendroglial differentiation block in multiple sclerosis
Cited by: 47
Author(s): Laura Starost, Maren Lindner, Martin Herold, Yu Xu, Hannes C.A. Drexler, Katharina Heß, Marc Ehrlich, Linda Ottoboni, Francesca Ruffini, Martin Stehling, Albrecht Röpke, Christian Thomas, Hans R. Schöler, Jack Antel, Jürgen Winkler, Gianvito Martino, Luisa Klotz, Tanja Kuhlmann
Software Mentions: 4
Published: about 6 years ago

10.1016/j.celrep.2021.109583

Dynamic bi-directional phosphorylation events associated with the reciprocal regulation of synapses during homeostatic up- and down-scaling
Cited by: 19
Author(s): Kristina Desch, Julian D. Langer, Erin M. Schuman
Software Mentions: 4
Published: about 5 years ago

10.1007/s12035-019-01643-4

Altered Levels of Proteins and Phosphoproteins, in the Absence of Early Causative Transcriptional Changes, Shape the Molecular Pathogenesis in the Brain of Young Presymptomatic Ki91 SCA3/MJD Mouse
Cited by: 14
Author(s): Kalina Wiatr, Piotr Piasecki, Łukasz Marczak, Paweł Wojciechowski, Małgorzata Kurkowiak, Rafał Płoski, Małgorzata Rydzanicz, Luiza Handschuh, Johannes Jungverdorben, Oliver Brüstle, Marek Figlerowicz, Maciej Figiel
Software Mentions: 4
Published: over 7 years ago

10.3389/fcell.2021.568660

Transcriptional Repression of MFG-E8 Causes Disturbance in the Homeostasis of Cell Cycle Through DOCK/ZP4/STAT Signaling in Buffalo Mammary Epithelial Cells
Cited by: 5
Author(s): Arvind Verma, Syed Azmal Ali, Parul Singh, Sanjay Kumar, Ashok Kumar Mohanty
Software Mentions: 4
Published: over 5 years ago

10.1152/physiolgenomics.00044.2018

Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways
Cited by: 14
Author(s): Stephanie J. Valberg, Sudeep Perumbakkam, Erica C. McKenzie, Carrie J. Finno
Software Mentions: 4
Published: almost 8 years ago

10.3390/ijms22158251

DIA-Based Quantitative Proteomics Reveals the Protein Regulatory Networks of Floral Thermogenesis in Nelumbo nucifera
Cited by: 5
Author(s): Yueyang Sun, Yu Zeng, Jing Jin, Hao Chen, Zhiying Liu, Qinru Zi, Zeyang Xiong, Ying Wang, Qian Li, Jing Peng, Yi Ding
Software Mentions: 4
Published: about 5 years ago

10.1074/mcp.RA118.000877

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome*
Cited by: 86
Author(s): Roman Mylonas, Ilan Beer, Christian Iseli, Chloé Chong, Hui Song Pak, David Gfeller, George Coukos, Ioannis Xénarios, Markus Müller, Michal Bassani-Sternberg
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41419-021-04057-0

TRAIP modulates the IGFBP3/AKT pathway to enhance the invasion and proliferation of osteosarcoma by promoting KANK1 degradation
Cited by: 14
Author(s): Mi Li, Wei Wu, Sisi Deng, Zengwu Shao, Xin Jin
Software Mentions: 4
Published: about 5 years ago

10.1016/j.isci.2021.102807

Identification of response signatures for tankyrase inhibitor treatment in tumor cell lines
Cited by: 6
Author(s): Line Mygland, Jo Waaler, Martin Frank Strand, Petter Olsen, Aleksandra Aizenshtadt, Kaja Lund, Nina Solberg, Max Lycke, Tor Espen Thorvaldsen, Sandra Espada, Dorna Misaghian, Christian M. Page, Oleg Agafonov, Ståle Nygård, Nai‐Wen Chi, Eva Lin, Jenille Tan, Yihong Yu, Mike Costa, Stefan Krauß, Jo Waaler
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers13092143

Proteomic Studies of Primary Acute Myeloid Leukemia Cells Derived from Patients Before and during Disease-Stabilizing Treatment Based on All-Trans Retinoic Acid and Valproic Acid
Cited by: 5
Author(s): Maria Hernandez-Valladares, Rebecca Wangen, Elise Aasebø, Håkon Reikvam, Frode S. Berven, Frode Selheim, Øystein Bruserud
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers11020263

Integrative Omic Profiling Reveals Unique Hypoxia Induced Signatures in Gastric Cancer Associated Myofibroblasts
Cited by: 2
Author(s): Hanna Najgebauer, Andrew F. Jarnuczak, Andrea Varró, Christopher M. Sanderson
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms21082873

Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis
Cited by: 115
Author(s): Chen Chen, Jie Hou, John J. Tanner
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.66014

Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses
Cited by: 18
Author(s): Stephan Wilmes, Polly-Anne Jeffrey, Jonathan Martínez-Fábregas, Maximillian Hafer, Paul K. Fyfe, Elizabeth Pöhler, Silvia Gaggero, Martín López‐García, Grant Lythe, Charles Taylor, Thomas Guerrier, David Launay, Suman Mitra, Jacob Piehler, Carmen Molina-Parı́s, Ignacio Moraga
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers12030709

Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia
Cited by: 30
Author(s): Elise Aasebø, Frode S. Berven, Sushma Bartaula-Brevik, Tomasz Stokowy, Randi Hovland, Marc Vaudel, Stein Ove Døskeland, Emmet McCormack, Tanveer S. Batth, Jesper V. Olsen, Øystein Bruserud, Frode Selheim, Maria Hernandez-Valladares
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms22020736

Omics Analysis of Blood-Responsive Regulon in Bordetella pertussis Identifies a Novel Essential T3SS Substrate
Cited by: 2
Author(s): Jakub Držmíšek, Daniel Štipl, Denisa Petráčková, Branislav Večerek, Ana Dienstbier
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0228108

Community-intrinsic properties enhance keratin degradation from bacterial consortia
Cited by: 15
Author(s): Poonam Nasipuri, Jakob Herschend, Asker Brejnrod, Jonas Stenløkke Madsen, Roall Espersen, Birte Svensson, Mette Burmølle, Samuel Jacquiod, Søren J. Sørensen
Software Mentions: 4
Published: over 6 years ago

10.1074/mcp.RA117.000189

Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC)
Cited by: 63
Author(s): Katarzyna Buczak, Alessandro Ori, Joanna Kirkpatrick, Kerstin Hölzer, Daniel Dauch, Stephanie Roessler, Volker Endris, Felix Lasitschka, Luca Parca, Alexander Schmidt, Lars Zender, Peter Schirmacher, Jeroen Krijgsveld, Stephan Singer, Martin Beck
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-021-87759-x

SIRT1 promotes lipid metabolism and mitochondrial biogenesis in adipocytes and coordinates adipogenesis by targeting key enzymatic pathways
Cited by: 58
Author(s): Yasser Majeed, Najeeb Halabi, Aisha Madani, Rudolf Engelke, Aditya Bhagwat, Houari Abdesselem, Maha Victor Agha, Muneera Vakayil, Raphael Jean Courjaret, Neha Goswami, Hisham Ben Hamidane, Mohamed A. Elrayess, Arash Rafii, Johannes Graumann, Frank Schmidt, Nayef Mazloum
Software Mentions: 4
Published: over 5 years ago

10.1016/j.molcel.2019.04.002

Functional Landscape of PCGF Proteins Reveals Both RING1A/B-Dependent-and RING1A/B-Independent-Specific Activities
Cited by: 116
Author(s): Andrea Scelfo, Daniel Fernández-Pérez, Simone Tamburri, Marika Zanotti, Elisa Lavarone, Monica Soldi, Tiziana Bonaldi, Karin Johanna Ferrari, Diego Pasini
Software Mentions: 4
Published: over 7 years ago

10.1074/mcp.RA118.001141

Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition
Cited by: 45
Author(s): Piotr Grabowski, Sebastian Hesse, Sebastian Hollizeck, Meino Rohlfs, Uta Behrends, Roya Sherkat, Hannah Tamary, Ekrem Ünal, Raz Somech, Türkan Patıroğlu, Stefan Canzar, Jutte van der Werff ten Bosch, Christoph Klein, Juri Rappsilber
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0178603

Proteome-wide profiling of protein lysine acetylation in Aspergillus flavus
Cited by: 17
Author(s): Yangyong Lv
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-020-72625-z

Re-establishment of the epigenetic state and rescue of kinome deregulation in Ts65Dn mice upon treatment with green tea extract and environmental enrichment
Cited by: 13
Author(s): Ilario De Toma, Mireia Ortega, Silvina Catuara-Solarz, Cesar Sierra, Eduard Sabidó, Mara Dierssen
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-021-81986-y

Proteome-wide profiling and mapping of post translational modifications in human hearts
Cited by: 15
Author(s): Navratan Bagwan, Henrik H. El Ali, Alicia Lundby
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0235263

Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications
Cited by: 2
Author(s): George W. Preston, Liping Yang, David H. Phillips, Claudia S. Maier
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-64623-y

Comparative analysis of MACROD1, MACROD2 and TARG1 expression, localisation and interactome
Cited by: 20
Author(s): Roko Žaja, Gülcan Aydin, Barbara E. Lippok, Regina Feederle, Bernhard Lüscher, Karla L. H. Feijs
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0206317

Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress
Cited by: 11
Author(s): Kayode T. Adu, Richard Wilson, David S. Nichols, Anthony L. Baker, John P. Bowman, ML Britz
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-019-44542-3

Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes
Cited by: 9
Author(s): Bénédicte Gnangnon, Aline Fréville, Kátia Cailliau, Catherine Leroy, Caroline De Witte, David Tulasne, Alain Martoriarti, Vincent Jung, Ida Chiara Guerrera, Sabrina Marion, Jamal Khalife, Christine Pierrot
Software Mentions: 4
Published: over 7 years ago

10.1016/j.molcel.2021.06.016

Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination
Cited by: 31
Author(s): Ashwin Narain, Pranjali Bhandare, Bikash Adhikari, Simone Backes, Martin Eilers, Lars Dölken, Andreas Schlösser, Florian Erhard, Apoorva Baluapuri, Elmar Wolf
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-49817-3

An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo
Cited by: 35
Author(s): Steffen Israel, Markus Ernst, Olympia E. Psathaki, Hannes C.A. Drexler, Ellen Casser, Yutaka Suzuki, Wojciech Makałowski, Michele Boiani, Georg Fuellen, Leila Taher
Software Mentions: 4
Published: about 7 years ago

10.3390/biom11060843

Nucleoside Analogues Are Potent Inducers of Pol V-mediated Mutagenesis
Cited by: 2
Author(s): Balagra Kasim Sumabe, Synnøve Brandt Ræder, Lisa Marie Røst, Animesh Sharma, Eric S Donkor, Lydia Mosi, Samuel Duodu, Per Bruheim, Marit Otterlei
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-017-3977-y

The first succinylome profile of Trichophyton rubrum reveals lysine succinylation on proteins involved in various key cellular processes
Cited by: 24
Author(s): Xingye Xu, Tao Liu, Jian Yang, Lihong Chen, Bo Liu, Candong Wei, Lingling Wang, Qi Jin
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-12021-2

Differential regulation of vaginal lipocalins (OBP, MUP) during the estrous cycle of the house mouse
Cited by: 25
Author(s): Martina Černá, Barbora Kuntová, Pavel Talacko, Romana Stopková, Pavel Stopka
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-16633-6

A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community
Cited by: 45
Author(s): Jakob Herschend, Zacharias Brimnes Visby Damholt, Andrea Marion Marquard, Birte Svensson, Søren J. Sørensen, Per Hägglund, Mette Burmølle
Software Mentions: 3
Published: almost 9 years ago

10.1126/sciadv.abg3013

C9orf72 -derived arginine-containing dipeptide repeats associate with axonal transport machinery and impede microtubule-based motility
Cited by: 51
Author(s): Laura Fumagalli, Florence L. Young, Steven Boeynaems, Mathias De Decker, Arpan R. Mehta, Ann Swijsen, Raheem Fazal, Wenting Guo, Matthieu Moisse, Jimmy Beckers, Lieselot Dedeene, Bhuvaneish T. Selvaraj, Tijs Vandoorne, Vanesa Madan, Marka van Blitterswijk, Denitza Raitcheva, Alexander McCampbell, Koen Poesen, Aaron D. Gitler, Philipp Koch, Pieter Vanden Berghe, Dietmar Rudolf Thal, Cathérine Verfaillie, Siddharthan Chandran, Ludo Van Den Bosch, Simon L. Bullock, Philip Van Damme
Software Mentions: 3
Published: over 5 years ago

10.1016/j.redox.2020.101491

Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin
Cited by: 55
Author(s): Amir Ata Saei, Hjalmar Gullberg, Pierre Sabatier, Christian M. Beusch, Katarina Johansson, Bo Lundgren, Per I. Arvidsson, Elias S.J. Arnér, Roman A. Zubarev
Software Mentions: 3
Published: over 6 years ago

10.1002/pmic.202000319

DDASSQ: An open‐source, multiple peptide sequencing strategy for label free quantification based on an OpenMS pipeline in the KNIME analytics platform
Cited by: 5
Author(s): M. Svecla, G Garrone, Fiorenza Farè, Giacomo Aletti, Giuseppe Danilo Norata, Giangiacomo Beretta
Software Mentions: 3
Published: about 5 years ago

10.1038/s41597-020-0519-2

Systems biology of acidophile biofilms for efficient metal extraction
Cited by: 7
Author(s): Antoine Buetti‐Dinh, Malte Herold, Stephan Christel, Mohamed El Hajjami, Sören Bellenberg, Olga Ilie, Paul Wilmes, Ansgar Poetsch, Wolfgang Sand, Mario Vera, Igor V. Pivkin, Mark Dopson
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-19351-9

Visualization of human karyopherin beta-1/importin beta-1 interactions with protein partners in mitotic cells by co-immunoprecipitation and proximity ligation assays
Cited by: 13
Author(s): Laura Di Francesco, Annalisa Verrico, Italia Anna Asteriti, Paola Rovella, Pietro Cirigliano, Giulia Guarguaglini, Maria Eugenia Schininà, Patrizia Lavia
Software Mentions: 3
Published: over 8 years ago

10.1186/s12953-016-0092-y

Quantitative succinylome analysis in the liver of non-alcoholic fatty liver disease rat model
Cited by: 32
Author(s): Yang Cheng, Tianlu Hou, Ping Jian, Xianhai Zeng, Jianjie Chen
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0191682

The long noncoding RNA lncR492 inhibits neural differentiation of murine embryonic stem cells
Cited by: 15
Author(s): Maria Winzi, Núria Casas-Vila, Maciej Paszkowski‐Rogacz, Li Ding, Svenja Noack, Mirko Theis, Falk Butter, Frank Buchholz
Software Mentions: 3
Published: over 8 years ago

10.3390/biomedicines9020107

Breast Cancer-Derived Microvesicles Are the Source of Functional Metabolic Enzymes as Potential Targets for Cancer Therapy
Cited by: 4
Author(s): Yousef Risha, Vanessa Susevski, Nico Hüttmann, Suttinee Poolsup, Zoran Minić, Maxim V. Berezovski
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-6213-0

Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts
Cited by: 27
Author(s): Andrew L. Garfoot, Gary Wilson, Joshua J. Coon, Laura J. Knoll
Software Mentions: 3
Published: almost 7 years ago

10.3390/proteomes9030034

Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric
Cited by: 11
Author(s): Benjamin C. Orsburn
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1008681

The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)
Cited by: 20
Author(s): Christos N. Velanis, Pumi Perera, Bennett Thomson, Erica de Leau, Shih Chieh Liang, Ben Hartwig, Alexander Förderer, Harry Thornton, Pedro Arêde, Jiawen Chen, Kimberly M. Webb, Serin Gümüs, Geert De Jaeger, Clinton A. Page, C. Nathan Hancock, Christos Spanos, Juri Rappsilber, Philipp Voigt, Franziska Turck, Frank Wellmer, Justin Goodrich
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1009410

Macrophage-specific responses to human- and animal-adapted tubercle bacilli reveal pathogen and host factors driving multinucleated cell formation
Cited by: 18
Author(s): Christophe J. Queval, Antony Fearns, Laure Botella, Alicia Smyth, Laura Schnettger, Morgane Mitermite, Esen Wooff, Bernardo Villarreal‐Ramos, Waldo L. García-Jiménez, Tiaan Heunis, Matthias Trost, Dirk Werling, Francisco J. Salguero, Stephen V. Gordon, Maximiliano G. Gutiérrez
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1006656

Novel insights into SLC25A46-related pathologies in a genetic mouse model
Cited by: 32
Author(s): Maria Eirini Terzenidou, Aikaterini Segklia, Toshimi Kano, Florentia Papastefanaki, Alexandros Karakostas, Maria Charalambous, Fotis Ioakeimidis, Maria Papadaki, Ismini Kloukina, Margarita Chrysanthou‐Piterou, Martina Samiotaki, George Panayotou, Rebecca Matsas, Eleni Douni
Software Mentions: 3
Published: over 9 years ago

10.1002/pmic.201700388

Integrative Analysis of Proteome and Ubiquitylome Reveals Unique Features of Lysosomal and Endocytic Pathways in Gefitinib‐Resistant Non‐Small Cell Lung Cancer Cells
Cited by: 19
Author(s): Wang Li, Heyong Wang, Yan Yang, Tian Zhao, Zhixiong Zhang, Ye Tian, Zhaomie Shi, Xiaojun Peng, Fēi Li, Yonghong Feng, Lei Zhang, Gening Jiang, Fan Zhang
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-20458-2

SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses
Cited by: 10
Author(s): Dominik Dornfeld, Alexandra H. Dudek, Thibaut Vausselin, Sira C. Günther, Judd F. Hultquist, Sebastian Giese, Daria Khokhlova-Cubberley, Yap Ching Chew, Lars Pache, Nevan J. Krogan, Adolfo Garcı́a-Sastre, Martin Schwemmle, Megan L. Shaw
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2018.02371

A Metabolic Labeling Strategy for Relative Protein Quantification in Clostridioides difficile
Cited by: 4
Author(s): Anke Trautwein-Schult, Sandra Maaß, Kristina Plate, Andreas Otto, Dörte Becher
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2019.02709

Label-Free Proteomic Approach to Study the Non-lethal Effects of Silver Nanoparticles on a Gut Bacterium
Cited by: 4
Author(s): Guido Domingo, Federica Villa, Candida Vannini, Elisa Garuglieri, Elisabetta Onelli, Marcella Bracale, Francesca Cappitelli
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1006620

Mutations in mitochondrial DNA causing tubulointerstitial kidney disease
Cited by: 47
Author(s): Thomas M. Connor, Simon Hoer, Andrew Mallett, Daniel P. Gale, Aurora Gómez-Durán, Viktor Posse, Robin Antrobus, Pablo Moreno, Marco Sciacovelli, Christian Frezza, Jennifer Duff, Neil Sheerin, John A. Sayer, Margaret Ashcroft, Michael S. Wiesener, Gavin Hudson, Claes M. Gustafsson, Patrick F. Chinnery, Patrick H. Maxwell
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2019.00325

Proteomic Analysis of Lactobacillus nagelii in the Presence of Saccharomyces cerevisiae Isolated From Water Kefir and Comparison With Lactobacillus hordei
Cited by: 16
Author(s): Julia Bechtner, Di Xu, Jürgen Behr, Christina Ludwig, Rudi F. Vogel
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1006088

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
Cited by: 21
Author(s): Matthew E. MacGilvray, Evgenia Shishkova, Deborah Chasman, Michael Place, Anthony Gitter, Joshua J. Coon, Audrey P. Gasch
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2019.00378

High-Throughput Proteomics Identifies Proteins With Importance to Postantibiotic Recovery in Depolarized Persister Cells
Cited by: 23
Author(s): Daniel-Timon Spanka, Anne Konzer, Daniel Edelmann, Bork A. Berghoff
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1008649

Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress
Cited by: 49
Author(s): Alexandro Rodríguez‐Rojas, Joshua Jay Kim, Paul R. Johnston, Olga Makarova, Murat Eravci, Christoph Weise, Regine Hengge, Jens Rolff
Software Mentions: 3
Published: over 6 years ago

10.1111/pce.13481

Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis
Cited by: 24
Author(s): Sebastian Schneider, Arno Schintlmeister, Manuel Becana, Michael Wagner, Dagmar Woebken, Stefanie Wienkoop
Software Mentions: 3
Published: over 7 years ago

10.1111/pbi.12916

Three unrelated protease inhibitors enhance accumulation of pharmaceutical recombinant proteins in Nicotiana benthamiana
Cited by: 53
Author(s): Friederike Grosse‐Holz, Luisa Madeira, Muhammad Awais Zahid, Molly Songer, Jiorgos Kourelis, Mary Fesenko, Sabrina Ninck, Farnusch Kaschani, Markus Kaiser, Renier A. L. van der Hoorn
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2020.594824

The Active Constituent From Gynostemma Pentaphyllum Prevents Liver Fibrosis Through Regulation of the TGF-β1/NDRG2/MAPK Axis
Cited by: 8
Author(s): Hui Huang, Kuifeng Wang, Qian Liu, Feihong Ji, Hu Zhou, Shanhua Fang, Jiansheng Zhu
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcell.2020.549451

Pex14p Phosphorylation Modulates Import of Citrate Synthase 2 Into Peroxisomes in Saccharomyces cerevisiae
Cited by: 17
Author(s): Andreas Schummer, Renate Maier, Shiran Gabay-Maskit, Tobias Hansen, Wignand W. D. Mühlhäuser, Ida Suppanz, Amir Fadel, Maya Schuldiner, Wolfgang Girzalsky, Silke Oeljeklaus, Einat Zalckvar, Ralf Erdmann, Bettina Warscheid
Software Mentions: 3
Published: about 6 years ago

10.1111/pbi.13092

Activity‐based proteomics reveals nine target proteases for the recombinant protein‐stabilizing inhibitor Sl <scp>CYS</scp> 8 in Nicotiana benthamiana
Cited by: 12
Author(s): Philippe V. Jutras, Friederike Grosse‐Holz, Farnusch Kaschani, Markus Kaiser, Dominique Michaud, Renier A. L. van der Hoorn
Software Mentions: 3
Published: over 7 years ago

10.3389/fcimb.2021.619981

Innate Immune Responses of Galleria mellonella to Mycobacterium bovis BCG Challenge Identified Using Proteomic and Molecular Approaches
Cited by: 8
Author(s): Masanori Asai, Gerard Sheehan, Yanwen Li, Brian Robertson, Kevin Kavanagh, Paul Langford, Sandra M. Newton
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pbio.3001344

Structure of the human C9orf72-SMCR8 complex reveals a multivalent protein interaction architecture
Cited by: 6
Author(s): Julia Nörpel, Simone Cavadini, Andreas Schenk, Alexandra Graff-Meyer, Daniel Heß, Jan Seebacher, Jeffrey A. Chao, Varun Bhaskar
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms8050653

Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae
Cited by: 33
Author(s): Jamie McGowan, Richard O’Hanlon, Rebecca A. Owens, David A. Fitzpatrick
Software Mentions: 3
Published: over 6 years ago

10.3389/fcvm.2021.713983

Pan-Cancer Analysis of Atrial-Fibrillation-Related Innate Immunity Gene ANXA4
Cited by: 6
Author(s): Tao Yan, Shijie Zhu, Yu Shi, Changming Xie, Miao Zhu, Yangyang Zhang, Chunsheng Wang, Changfa Guo
Software Mentions: 3
Published: about 5 years ago

10.3389/fcimb.2021.595554

Protein and Microbial Biomarkers in Sputum Discern Acute and Latent Tuberculosis in Investigation of Pastoral Ethiopian Cohort
Cited by: 4
Author(s): Milkessa HaileMariam, Yu Yoshida, Harinder Singh, Takele Teklu, Biniam Wondale, Adane Worku, Aboma Zewude, Stephanie Mounaud, Tamara Tsitrin, Mengistu Legesse, Gobena Ameni, Rembert Pieper
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2021.707298

Effects of Combinatorial Ubiquitinated Protein-Based Nanovaccine and STING Agonist in Mice With Drug-Resistant and Metastatic Breast Cancer
Cited by: 4
Author(s): Fang Huang, Ning Pan, Yi-ting Wei, Jinjin Zhao, Mohanad Aldarouish, Xuru Wang, Xiaotong Sun, Wen Zhang, Yongqiang Chen, Lixin Wang
Software Mentions: 3
Published: about 5 years ago

10.3389/fnmol.2018.00454

Effects of APOE Genotype on Brain Proteomic Network and Cell Type Changes in Alzheimer's Disease
Cited by: 48
Author(s): Jingting Dai, Erik C. B. Johnson, Eric B. Dammer, Duc M. Duong, Marla Gearing, James J. Lah, Aĺlan I. Levey, Thomas S. Wingo, Nicholas T. Seyfried
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-26343-2

Acrylamide acute neurotoxicity in adult zebrafish
Cited by: 56
Author(s): Melissa Faria, Tamar Ziv, Cristian Gómez‐Canela, Shani Ben-Lulu, Eva Prats, Karen Adriana Novoa-Luna, Arie Admon, Benjamı́n Piña, Romà Tauler, Leobardo Manuel Gómez-Oliván, Demetrio Raldúa
Software Mentions: 3
Published: over 8 years ago

10.1186/s12860-020-00331-9

Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages
Cited by: 18
Author(s): Sabin Bhandari, Ruomei Li, Jaione Simón-Santamaría, Peter McCourt, Steinar Johansen, Bård Smedsrød, Iñigo Martínez-Zubiaurre, Karen Kristine Sørensen
Software Mentions: 3
Published: almost 6 years ago

10.15252/msb.20209730

Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses
Cited by: 63
Author(s): Aurélien Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gábor, Kristina B. Emdal, Vítor Vieira, Dorte B. Bekker-Jensen, Jennifer Kranz, Eric Bindels, Ana S.H. Costa, Abel Sousa, Pedro Beltrão, Miguel Rocha, Jesper V. Olsen, Christian Frezza, Rafael Kramann, Julio Sáez-Rodríguez
Software Mentions: 3
Published: almost 6 years ago

10.15252/embr.201745642

Negative feedback via <scp>RSK</scp> modulates Erk‐dependent progression from naïve pluripotency
Cited by: 25
Author(s): Isabelle Nett, Carla Mulas, Laurent Guy, Kathryn S. Lilley, Austin Smith
Software Mentions: 3
Published: over 8 years ago

10.15252/emmm.201910427

Plasma Proteome Profiling to detect and avoid sample‐related biases in biomarker studies
Cited by: 141
Author(s): Philipp E. Geyer, Eugenia Voytik, Peter V. Treit, Sophia Doll, Alisa Kleinhempel, Lili Niu, Johannes B. Müller-Reif, Marie-Luise Buchholtz, Jakob Bader, Daniel Teupser, Lesca M. Holdt
Software Mentions: 3
Published: about 7 years ago

10.1186/s12859-019-3337-9

Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations
Cited by: 8
Author(s): Antoine Buetti‐Dinh, Malte Herold, Stephan Christel, Mohamed El Hajjami, Francesco Delogu, Olga Ilie, Sören Bellenberg, Paul Wilmes, Ansgar Poetsch, Wolfgang Sand, Mario Vera, Igor V. Pivkin, Ran Friedman, Mark Dopson
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12866-020-01877-6

Proteomic analysis of Rickettsia akari proposes a 44 kDa-OMP as a potential biomarker for Rickettsialpox diagnosis
Cited by: 5
Author(s): František Csicsay, Gabriela Flores‐Ramírez, Fernando Zúñiga-Navarrete, Mária Bartošová, Alena Fučíková, Petr Pajer, Jiří Dresler, Ľudovít Škultéty, Marco Antonio Quevedo-Diaz
Software Mentions: 3
Published: over 6 years ago

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