cran: Andromeda | Projects | Ecosyste.ms: Papers

10.1084/jem.20201011

The T cell CD6 receptor operates a multitask signalosome with opposite functions in T cell activation
Cited by: 33
Author(s): Daiki Mori, Claude Grégoire, Guillaume Voisinne, Javier Celis-Gutierrez, Rudy Aussel, Laura Girard, Mylène Camus, Marlène Marcellin, Jérémy Argenty, Odile Burlet‐Schiltz, Frédéric Di Fiore, Anne Gonzalez de Peredo, Marie Malissen, Romain Roncagalli, Bernard Malissen
Software Mentions: 3
Published: over 3 years ago

10.1107/S2052252519007668

Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder
Cited by: 10
Author(s): Jeong Kuk Park, Keon Young Kim, Yeo Won Sim, Young Dong Kim, Jin Kyun Kim, Cheol Lee, Jeongran Han, Chae Un Kim, J. Eugene Lee, SangYoun Park
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.50777

Single-cell proteomics reveals changes in expression during hair-cell development
Cited by: 77
Author(s): Ying Zhu, Mirko Scheibinger, Daniel C. Ellwanger, Jocelyn F. Krey, Dong‐Hee Choi, Ryan Kelly, Stefan Heller, Peter G. Barr-Gillespie
Software Mentions: 3
Published: over 4 years ago

10.1128/mSphere.00129-19

Combined Transcriptome and Proteome Analysis of Immortalized Human Keratinocytes Expressing Human Papillomavirus 16 (HPV16) Oncogenes Reveals Novel Key Factors and Networks in HPV-Induced Carcinogenesis
Cited by: 21
Author(s): Ruwen Yang, Jana Klimentová, Elke Göckel-Krzikalla, Regina Ly, Nadine Gmelin, Agnes Hotz‐Wagenblatt, Helena Řehulková, Jiřı́ Stulı́k, Frank Rösl, Martina Niebler
Software Mentions: 3
Published: about 5 years ago

10.1128/mSphere.00476-20

Characterization of Extracellular Vesicles Produced by Aspergillus fumigatus Protoplasts
Cited by: 41
Author(s): Juliana Rizzo, Thibault Chaze, Kildare Miranda, Robert W. Roberson, Olivier Gorgette, Leonardo Nimrichter, Mariette Matondo, Jean Paul Latgé, Anne Beauvais, Márcio L. Rodrigues
Software Mentions: 3
Published: over 3 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: over 6 years ago

10.1007/978-1-4939-7493-1_6

Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells
Cited by: 24
Author(s): Jakob Wirbel, Pedro R. Cutillas, Julio Sáez-Rodríguez
Software Mentions: 3
Published: over 6 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: over 4 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: almost 4 years ago

10.1590/0074-02760170385

NS1 codon usage adaptation to humans in pandemic Zika virus
Cited by: 11
Author(s): Caio César de Melo Freire, Giuseppe Palmisano, Carla Torres Braconi, Fernanda R. Cugola, Fabiele Baldino Russo, Patrícia Cristina Baleeiro Beltrão-Braga, Atila Iamarino, Daniel Ferreira de Lima Neto, Amadou Alpha Sall, Lívia Rosa-Fernandes, Martin R. Larsen, Paolo Marinho de Andrade Zanotto
Software Mentions: 3
Published: about 6 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: about 4 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: about 3 years ago

10.1128/mSystems.00612-20

A Mutation Upstream of the rplN-rpsD Ribosomal Operon Downregulates Bordetella pertussis Virulence Factor Production without Compromising Bacterial Survival within Human Macrophages
Cited by: 4
Author(s): Jakub Novák, David Jurnečka, Irena Linhartová, Jana Holubová, Ondřej Staněk, Daniel Štipl, Ana Dienstbier, Branislav Večerek, Nayara Azevedo, Jan Provazník, Vladimı́r Beneš, Peter Šebo
Software Mentions: 3
Published: over 3 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: almost 6 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: almost 3 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: over 3 years ago

10.7554/eLife.50705

Cardiac mitochondrial function depends on BUD23 mediated ribosome programming
Cited by: 10
Author(s): Matthew Baxter, Maria Voronkov, Toryn Poolman, Gina L. J. Galli, Christian Pinali, Laurence Goosey, Abigail Knight, Karolina Krakowiak, Robert Maidstone, Mudassar Iqbal, Min Zi, Sukhpal Prehar, Elizabeth J. Cartwright, Julie Gibbs, Laura Matthews, Antony Adamson, Neil Humphreys, Pedro Rebelo-Guiomar, Michal Minczuk, David A. Bechtold, A. S. I. Loudon, David Ray
Software Mentions: 3
Published: over 4 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: almost 3 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 8 years ago

10.1186/s12864-019-5456-0

Global host molecular perturbations upon in situ loss of bacterial endosymbionts in the deep-sea mussel Bathymodiolus azoricus assessed using proteomics and transcriptomics
Cited by: 9
Author(s): Camille Détrée, Iman Haddad, Emmanuelle Demey-Thomas, Joëlle Vinh, François H. Lallier, Arnaud Tanguy, Jean Mary
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: almost 4 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 6 years ago

10.1083/jcb.202106115

GOLPH3 and GOLPH3L are broad-spectrum COPI adaptors for sorting into intra-Golgi transport vesicles
Cited by: 24
Author(s): Lawrence G. Welch, Sew‐Yeu Peak‐Chew, Farida Begum, Tim J. Stevens, Sean Munro
Software Mentions: 3
Published: over 2 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: about 4 years ago

10.18632/oncotarget.27462

Identification of molecular targets for the targeted treatment of gastric cancer using dasatinib
Cited by: 26
Author(s): Raquel Carvalho Montenegro, Alison Howarth, Alessandro Ceroni, Vita Fedele, Batoul Farran, Felipe Pantoja Mesquita, Martin Frejno, Benedict‐Tilman Berger, S. Heinzlmeir, Heba Sailem, Roberta Tesch, Daniel Ebner, S. Knapp, Rommel Rodríguez Burbano, Bernhard Küster, Susanne Müller
Software Mentions: 3
Published: over 4 years ago

10.1242/jcs.221606

The N-cadherin interactome in primary cardiomyocytes as defined by quantitative proximity proteomics
Cited by: 39
Author(s): Li Yang, Chelsea D. Merkel, Xuemei Zeng, Jonathon A. Heier, Pamela S. Cantrell, Mai Sun, Donna B. Stolz, Simon C. Watkins, Nathan A. Yates, Adam V. Kwiatkowski
Software Mentions: 3
Published: over 5 years ago

10.26508/lsa.202000660

Metabolic reprogramming of fibro/adipogenic progenitors facilitates muscle regeneration
Cited by: 34
Author(s): Alessio Reggio, Marco Rosina, Natalie Krahmer, Alessandro Palma, Lucia Lisa Petrilli, Giuliano Maiolatesi, Giorgia Massacci, Illari Salvatori, Cristiana Valle, Stefano Testa, Cesare Gargioli, Claudia Fuoco, Luisa Castagnoli, Gianni Cesareni
Software Mentions: 3
Published: over 4 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: about 7 years ago

10.1371/journal.ppat.1004183

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis
Cited by: 116
Author(s): Luis Solans, Jesús Gonzalo-Asensio, Claudia Sala, Andrej Benjak, Swapna Uplekar, Jacques Rougemont, Christophe Guilhot, Wladimir Malaga, Carlos Martı́n, Stewart T. Cole
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-018-4907-3

Novel proteome and acetylome of Bemisia tabaci Q in response to Cardinium infection
Cited by: 10
Author(s): Hongran Li, James D. Harwood, Tong‐Xian Liu, Dong Chu
Software Mentions: 3
Published: almost 6 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: about 6 years ago

10.1371/journal.pgen.1009600

Antagonistic fungal enterotoxins intersect at multiple levels with host innate immune defences
Cited by: 10
Author(s): Xing Zhang, Benjamin W. Harding, Dina Aggad, Damien Courtine, Jia‐Xuan Chen, Nathalie Pujol, Jonathan J. Ewbank
Software Mentions: 3
Published: almost 3 years ago

10.1083/jcb.202005130

SUMOylation stabilizes sister kinetochore biorientation to allow timely anaphase
Cited by: 4
Author(s): Shaowu Xue, Menglu Wang, Claudia Schaffner, Olga O. Nerusheva, Dean Clift, Christos Spanos, David A. Kelly, Michael H. Tatham, Andreas U. Wallek, Yehui Wu, Juri Rappsilber, A. Arockia Jeyaprakash, Zuzana Storchová, Ronald T. Hay, Adèle L. Marston
Software Mentions: 3
Published: about 3 years ago

10.1186/1471-2164-15-249

Characterization of the pigmented shell-forming proteome of the common grove snail Cepaea nemoralis
Cited by: 73
Author(s): Karlheinz Mann, Daniel J. Jackson
Software Mentions: 3
Published: over 10 years ago

10.1016/j.jbc.2021.100295

The cytoprotective protein MANF promotes neuronal survival independently from its role as a GRP78 cofactor
Cited by: 27
Author(s): Ave Eesmaa, Li-Ying Yu, Helka Göös, Kristofer Nõges, Vera Kovaleva, Maarit Hellman, Richard Zimmermann, Martin Jung, Perttu Permi, Markku Varjosalo, Päivi Lindholm, Märt Saarma
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-019-0636-8

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma
Cited by: 92
Author(s): Markus Löffler, Christopher Mohr, Leon Bichmann, Lena Katharina Freudenmann, Mathias Walzer, Christopher Schroeder, Nico Trautwein, Franz J. Hilke, Raphael S. Zinser, Lena Mühlenbruch, Daniel J. Kowalewski, Heiko Schuster, Marc Sturm, Jakob Matthes, Olaf Rieß, Stefan Czemmel, Sven Nahnsen, Ingmar Königsrainer, Karolin Thiel, Silvio Nadalin, Stefan Beckert, Hans Bösmüller, Falko Fend, Ana Velić, Boris Maček, Sebastian P. Haen, Luigi Buonaguro, Oliver Kohlbacher, Stefan Stevanović, Alfred Königsrainer, Hans‐Georg Rammensee
Software Mentions: 3
Published: about 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: almost 3 years ago

10.1172/jci.insight.135544

PDX-derived organoids model in vivo drug response and secrete biomarkers
Cited by: 55
Author(s): Ling Huang, Bruno Bockorny, Indranil Paul, Dipikaa Akshinthala, Pierre‐Olivier Frappart, Omar Gandarilla, Arindam Bose, Veronica Sanchez‐Gonzalez, Emily E Rouse, Sylvain Lehoux, Nicole Pandell, Christine Lim, John G. Clohessy, Joseph E. Grossman, Raúl González, Sofia Perea Del Pino, George Daaboul, Mandeep S. Sawhney, Steven D. Freedman, Alexander Kleger, Richard D. Cummings, Andrew Emili, Lakshmi Muthuswamy, Manuel Hidalgo, Senthil K. Muthuswamy
Software Mentions: 3
Published: over 3 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: almost 6 years ago

10.1186/s13059-019-1799-8

Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency
Cited by: 43
Author(s): Taolan Zhao, Qing Huan, Jing Sun, Chunyan Liu, Xiuli Hou, Xiang Yu, Ian M. Silverman, Yi Zhang, Brian D. Gregory, Chunming Liu, Wenfeng Qian, Xiaofeng Cao
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-019-1814-0

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation
Cited by: 26
Author(s): Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, Susan Boerner, Jan B. Heidelberger, Anke Busch, Heike Hänel, Andrea Voigt, Martin Möckel, Stefanie Ebersberger, Anica Scholz, Annabelle Dold, Tobias Schmid, Ingo Ebersberger, Jean‐Yves Roignant, Kathi Zarnack, Julian König, Petra Beli
Software Mentions: 3
Published: over 4 years ago

10.1128/AEM.01319-20

Editing of the Proteolytic System of Lactococcus lactis Increases Its Bioactive Potential
Cited by: 6
Author(s): Chenxi Huang, Jan Kok
Software Mentions: 3
Published: over 3 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: about 5 years ago

10.1186/s13058-020-01367-7

Combined the SMAC mimetic and BCL2 inhibitor sensitizes neoadjuvant chemotherapy by targeting necrosome complexes in tyrosine aminoacyl-tRNA synthase-positive breast cancer
Cited by: 5
Author(s): Kyung Min Lee, Hyebin Lee, Dohyun Han, Woo Kyung Moon, Kwangsoo Kim, Hyeon Jeong Oh, Jin-Hwan Choi, Eunmi Hwang, Seong Eun Kang, Seock Ah Im, Han Suk Ryu
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1008155

The alternative cap-binding complex is required for antiviral defense in vivo
Cited by: 18
Author(s): Anna Gebhardt, Valter Bergant, Daniel Schnepf, Markus Moser, Arno Meiler, Dieudonnée Togbe, Claire Mackowiak, Line S. Reinert, Søren R. Paludan, Bernhard Ryffel, Alexey Stukalov, Peter Staeheli, Andreas Pichlmair
Software Mentions: 3
Published: over 4 years ago

10.3389/fpls.2017.01961

Rhizobium Impacts on Seed Productivity, Quality, and Protection of Pisum sativum upon Disease Stress Caused by Didymella pinodes: Phenotypic, Proteomic, and Metabolomic Traits
Cited by: 37
Author(s): Nima Ranjbar Sistani, Hans‐Peter Kaul, Getinet Desalegn, Stefanie Wienkoop
Software Mentions: 3
Published: over 6 years ago

10.1074/mcp.RA119.001769

Dynamic Transcriptomic and Phosphoproteomic Analysis During Cell Wall Stress in Aspergillus nidulans
Cited by: 5
Author(s): Cynthia Chelius, Walker Huso, Samantha Reese, Alexander Doan, Stephen R. Lincoln, Kelsi Lawson, Bao Tran, Raj Purohit, Trevor Glaros, Ranjan Srivastava, Steven D. Harris, Mark R. Marten
Software Mentions: 3
Published: almost 4 years ago

10.1007/s00018-019-03434-5

Integrative genomics reveal a role for MCPIP1 in adipogenesis and adipocyte metabolism
Cited by: 12
Author(s): Magdalena Łośko, Dobrochna Dolicka, Natalia Pydyn, Urszula Jankowska, Sylwia Kędracka–Krok, Maria Kulecka, Agnieszka Paziewska, Michał Mikuła, Piotr Major, Marek Winiarski, Andrzej Budzyński, Jolanta Jura
Software Mentions: 3
Published: over 4 years ago

10.1007/s00018-016-2401-0

Multi-OMIC profiling of survival and metabolic signaling networks in cells subjected to photodynamic therapy
Cited by: 24
Author(s): Ruud Weijer, Séverine Clavier, Esther A. Zaal, Maud M. E. Pijls, Robert T. van Kooten, Klaas Vermaas, René Leen, Aldo Jongejan, Perry D. Moerland, Antoine H. C. van Kampen, André B. P. Kuilenburg, Celia R. Berkers, Simone Lemeer, Michal Heger
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2021.722802

Effect and Response of Quercus ilex subsp. ballota [Desf.] Samp. Seedlings From Three Contrasting Andalusian Populations to Individual and Combined Phytophthora cinnamomi and Drought Stresses
Cited by: 18
Author(s): Bonoso San-Eufrasio, María Ángeles Castillejo, Mónica Labella-Ortega, Francisco J. Ruíz-Gómez, Rafael M. Navarro-Cerrillo, Marta Tienda-Parrilla, Jesús V. Jorrín‐Novo, María‐Dolores Rey
Software Mentions: 3
Published: almost 3 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: almost 3 years ago

10.1038/s41416-019-0659-3

Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer
Cited by: 14
Author(s): Nikolaus Berndt, Antje Egners, Guido Mastrobuoni, Olga Vvedenskaya, Athanassios Fragoulis, Aurélien Dugourd, Sascha Bulik, Matthias Pietzke, Chris Bielow, Rob J. J. van Gassel, Steven W. M. Olde Damink, Merve Erdem, Julio Sáez-Rodríguez, Hermann‐Georg Holzhütter, Stefan Kempa, Thorsten Cramer
Software Mentions: 3
Published: over 4 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: over 3 years ago

10.1074/mcp.RA118.001218

PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms
Cited by: 39
Author(s): Steven Verbruggen, Elvis Ndah, Wim Van Criekinge, Siegfried Gessulat, Bernhard Küster, Mathias Wilhelm, Petra Van Damme, Gerben Menschaert
Software Mentions: 3
Published: almost 5 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: over 2 years ago

10.1186/s13068-019-1506-8

Transcriptomic and proteomic responses to very low CO2 suggest multiple carbon concentrating mechanisms in Nannochloropsis oceanica
Cited by: 40
Author(s): Li Wei, Mohamed El Hajjami, Chen Shen, Wuxin You, Yandu Lu, Jing Li, Xiaoyan Jing, Qiang Hu, Wenxu Zhou, Ansgar Poetsch, Jian Xu
Software Mentions: 3
Published: almost 5 years ago

10.3389/fbioe.2021.640419

Extracellular Vesicles Derived From Adult and Fetal Bone Marrow Mesenchymal Stromal Cells Differentially Promote ex vivo Expansion of Hematopoietic Stem and Progenitor Cells
Cited by: 8
Author(s): Corina Adriana Ghebes, Jess Morhayim, Marion Kleijer, Merve Koroglu, Stefan J. Erkeland, Remco M. Hoogenboezem, Eric Bindels, Floris P.J. van Alphen, Maartje van den Biggelaar, Martijn A. Nolte, Bram C. J. van der Eerden, Eric Braakman, Carlijn Voermans, Jeroen van de Peppel
Software Mentions: 3
Published: about 3 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: over 3 years ago

10.3389/fpls.2018.01248

Microscopic and Proteomic Analysis of Dissected Developing Barley Endosperm Layers Reveals the Starchy Endosperm as Prominent Storage Tissue for ER-Derived Hordeins Alongside the Accumulation of Barley Protein Disulfide Isomerase (HvPDIL1-1)
Cited by: 13
Author(s): Valentin Roustan, Pierre-Jean Roustan, Marieluise Weidinger, Siegfried Reipert, Eszter Kapusi, Azita Shabrangy, Eva Stöger, Wolfram Weckwerth, Verena Ibl
Software Mentions: 3
Published: over 5 years ago

10.1016/j.mcpro.2021.100118

A Reductionist Approach Using Primary and Metastatic Cell–Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis
Cited by: 10
Author(s): Ariane F. Busso-Lopes, Carolina Moretto Carnielli, Flávia Vischi Winck, Fábio Malta de Sá Patroni, Ana Karina de Oliveira, Daniela Campos Granato, Rute Alves Pereira e Costa, Romênia R. Domingues, Bianca Alves Pauletti, Diego Mauricio Riaño-Pachón, Juliana Aparecida Aricetti, Camila Caldana, Edgard Graner, Ricardo D. Coletta, Kelly A. Dryden, Jay W. Fox, Adriana Franco Paes Leme
Software Mentions: 3
Published: over 3 years ago

10.1016/j.mcpro.2021.100092

The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development
Cited by: 7
Author(s): Karsten Cirksena, Hermann J. Hütte, Aleksandra Shcherbakova, Thomas Thumberger, Roman Sakson, Stefan Weiß, Lars Riff Jensen, Alina Friedrich, Daniel Todt, Andreas W. Kuß, Thomas Ruppert, Joachim Wittbrodt, Hans Bakker, Falk F. R. Buettner
Software Mentions: 3
Published: over 3 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: over 4 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: almost 6 years ago

10.3390/molecules25061396

Mass Spectrometry Advances and Perspectives for the Characterization of Emerging Adoptive Cell Therapies
Cited by: 10
Author(s): Camille Lombard‐Banek, John E. Schiel
Software Mentions: 3
Published: about 4 years ago

10.1074/mcp.O115.049460

A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day*
Cited by: 39
Author(s): Fabian Hosp, Richard A. Scheltema, H. Christian Eberl, Nils A. Kulak, Eva C. Keilhauer, Korbinian Mayr, Matthias Mann
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.mcpro.2021.100125

Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network
Cited by: 6
Author(s): Cristian V. A. Munteanu, Gabriela Chirițoiu, Marioara Chirițoiu, Simona Ghenea, Andrei-José Petrescu, Ștefana M. Petrescu
Software Mentions: 3
Published: over 3 years ago

10.1074/mcp.O115.055467

Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling
Cited by: 61
Author(s): Mark Larance, Kathryn J. Kirkwood, Michele Tinti, Alejandro Brenes Murillo, Michael A. J. Ferguson, Angus I. Lamond
Software Mentions: 3
Published: almost 8 years ago

10.3390/molecules26092587

Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma Cells
Cited by: 5
Author(s): Doungdean Tummanatsakun, Tanakorn Proungvitaya, Sittiruk Roytrakul, Siriporn Proungvitaya
Software Mentions: 3
Published: about 3 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: about 7 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: about 3 years ago

10.3390/ijms21114045

Gut–Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization
Cited by: 43
Author(s): Bruno Tilocca, Luisa Pieroni, Alessio Soggiu, Domenico Britti, L. Bonizzi, Paola Roncada, Viviana Greco
Software Mentions: 3
Published: almost 4 years ago

10.18632/oncotarget.7248

MicroRNA-34a promotes genomic instability by a broad suppression of genome maintenance mechanisms downstream of the oncogene KSHV-vGPCR
Cited by: 14
Author(s): Claudia J. Krause, Oliver Popp, Nanthakumar Thirunarayanan, Gunnar Dittmar, Martin Lipp, Gerd Müller
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.5876

KIAA0101 is associated with human renal cell carcinoma proliferation and migration induced by erythropoietin
Cited by: 27
Author(s): Shengjun Fan, Xin Li, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 3
Published: over 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: almost 6 years ago

10.3390/ijms20010016

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools
Cited by: 34
Author(s): Dana Pascovici, Jemma X. Wu, Matthew J. McKay, Chitra Joseph, Zainab Noor, Karthik Shantharam Kamath, Yunqi Wu, Shoba Ranganathan, Vivek Gupta, Mehdi Mirzaei
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-64483-6

Salivary proteome signatures in the early and middle stages of human pregnancy with term birth outcome
Cited by: 14
Author(s): Amit Dey, Bhoj Kumar, Abhishek Kumar Singh, Prakash Ranjan, Ramachandran Thiruvengadam, Bapu Koundinya Desiraju, Pallavi Kshetrapal, Nitya Wadhwa, Shinjini Bhatnagar, Faraz Rashid, Dipankar Malakar, Dinakar M. Salunke, Tushar Kanti Maiti
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-021-87955-9

Induced pluripotent stem cells from subjects with Lesch-Nyhan disease
Cited by: 5
Author(s): Diane Sutcliffe, Ashok R. Dinasarapu, Jasper E. Visser, Joery den Hoed, Fatemeh Seifar, Piyush Joshi, Irène Ceballos-Picot, Tejas Sardar, Ellen J. Hess, Yan V. Sun, Zhexing Wen, Michael E. Zwick, Hyder A. Jinnah
Software Mentions: 3
Published: about 3 years ago

10.18632/oncotarget.13569

Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers
Cited by: 187
Author(s): Stephanie N. Hurwitz, Mark A. Rider, Joseph L. Bundy, Xia Liu, Rakesh Kumar Singh, David G. Meckes
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-020-66051-4

Tiered approach for the identification of Mal d 1 reduced, well tolerated apple genotypes
Cited by: 19
Author(s): Emilia Romer, Soraya Chebib, Karl‐Christian Bergmann, Katrin Plate, Sylvia Becker, Christina Ludwig, Chen Meng, Thilo C. Fischer, Werner Dierend, Wilfried Schwab
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-018-26639-3

Hit-Gel: Streamlining in-gel protein digestion for high-throughput proteomics experiments
Cited by: 11
Author(s): Corné Swart, Silvia Martínez-Jaime, Michał Górka, Kerstin Zander, Alexander Graf
Software Mentions: 3
Published: almost 6 years ago

10.18632/oncotarget.14605

Probing the prostate tumour microenvironment I: impact of glucose deprivation on a cell model of prostate cancer progression
Cited by: 7
Author(s): Claire Tonry, John G. Armstrong, Stephen R. Pennington
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-020-70324-3

The integral spliceosomal component CWC15 is required for development in Arabidopsis
Cited by: 8
Author(s): Daniel Slane, Cameron H. Lee, Martina Kolb, Craig Dent, Yingjing Miao, Mirita Franz‐Wachtel, Steffen Lau, Boris Maček, Sureshkumar Balasubramanian, Martin Bayer, Gerd Jürgens
Software Mentions: 3
Published: almost 4 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: over 5 years ago

10.3390/ijms21197404

Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana
Cited by: 5
Author(s): Yanqiao Zhu, Oliver Berkowitz, Jennifer Selinski, Andreas Hartmann, Reena Narsai, Yan Wang, Peisheng Mao, James Whelan
Software Mentions: 3
Published: over 3 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: over 6 years ago

10.3390/ijms21239162

Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives
Cited by: 18
Author(s): Galina Smolikova, Daria Gorbach, Elena Lukasheva, Gregory Mavropolo-Stolyarenko, Tatiana Bilova, Alena Soboleva, Alexander Tsarev, E. V. Romanovskaya, Е. P. Podolskaya, Vladimir A. Zhukov, И. А. Тихонович, С.С. Медведев, Wolfgang Hoehenwarter, Andrej Frolov
Software Mentions: 3
Published: over 3 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: over 4 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: about 5 years ago

10.1038/s41598-019-55053-6

Integrative proteomics and phosphoproteomics in pulmonary arterial hypertension
Cited by: 36
Author(s): Weiling Xu, Suzy Comhair, Ruoying Chen, Bo Hu, Yuan Hou, Yadi Zhou, Lori Mavrakis, Allison J. Janocha, Ling Li, Dongmei Zhang, Belinda Willard, Kewal Asosingh, Feixiong Cheng, Serpil C. Erzurum
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-96635-7

Multi-layered proteogenomic analysis unravels cancer metastasis directed by MMP-2 and focal adhesion kinase signaling
Cited by: 11
Author(s): Yumi Kwon, Seongjun Park, Binh Thanh Nguyen, Mi Jeong Kim, Sejin Oh, Hwanho Lee, Narae Park, Hyun‐Seok Kim, Min‐Jung Kang, Byung Soh Min, Jinwon Lee, Eun Gyeong Yang, Cheolju Lee
Software Mentions: 3
Published: over 2 years ago

10.3390/ijms22062957

Implication of EZH2 in the Pro-Proliferative and Apoptosis-Resistant Phenotype of Pulmonary Artery Smooth Muscle Cells in PAH: A Transcriptomic and Proteomic Approach
Cited by: 9
Author(s): Karima Habbout, Junichi Omura, Charifa Awada, Alice Bourgeois, Yann Grobs, Vinod Krishna, Sandra Breuils‐Bonnet, Éve Tremblay, Ghada Mkannez, Sandra Martineau, Valérie Nadeau, Florence Roux‐Dalvai, Mark Orcholski, Jey Jeyaseelan, David E. Gutstein, François Potus, Steeve Provencher, Sébastien Bonnet, Roxane Paulin, Olivier Boucherat
Software Mentions: 3
Published: about 3 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: about 5 years ago

10.1038/s41598-019-43512-z

Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: about 5 years ago

10.3390/s141121213

iMuseumA: An Agent-Based Context-Aware Intelligent Museum System
Cited by: 9
Author(s): Inmaculada Ayala, Mercedes Amor, Mónica Pinto, Lidia Fuentes, Nadia Gámez
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms21031074

An Isolated Complex V Inefficiency and Dysregulated Mitochondrial Function in Immortalized Lymphocytes from ME/CFS Patients
Cited by: 48
Author(s): Daniel Missailidis, Sarah J. Annesley, Claire Y. Allan, Oana Sanislav, Brett A. Lidbury, Donald P. Lewis, Paul R. Fisher
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-45764-1

Varroa destructor parasitism has a greater effect on proteome changes than the deformed wing virus and activates TGF-β signaling pathways
Cited by: 20
Author(s): Tomáš Erban, B. Sopko, Klara Kadlikova, Pavel Talacko, Karel Harant
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms22136806

Proteomics Analysis of Andrographolide-Induced Apoptosis via the Regulation of Tumor Suppressor p53 Proteolysis in Cervical Cancer-Derived Human Papillomavirus 16-Positive Cell Lines
Cited by: 5
Author(s): Pariyakorn Udomwan, Chamsai Pientong, Panwad Tongchai, Ati Burassakarn, Nuchsupha Sunthamala, Sittiruk Roytrakul, Supawadee Suebsasana, Tipaya Ekalaksananan
Software Mentions: 3
Published: almost 3 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 6 years ago

10.3390/ijms22158172

Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins
Cited by: 9
Author(s): Orarat Ginsawaeng, Michał Górka, Alexander Erban, Carolin Heise, Franziska Brueckner, Rainer Hoefgen, Joachim Kopka, Aleksandra Skirycz, Dirk K. Hincha, Ellen Zuther
Software Mentions: 3
Published: almost 3 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 6 years ago

Projects: cran: Andromeda

Papers Mentioning Andromeda 1,724