cran: Andromeda | Projects | Ecosyste.ms: Papers

10.1128/AEM.02091-17

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum T
Cited by: 64
Author(s): Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti‐Dinh, Igor V. Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Software Mentions: 2
Published: over 8 years ago

10.3389/fendo.2019.00674

Glucocorticoid Treatment Leads to Aberrant Ion and Macromolecular Transport in Regenerating Zebrafish Fins
Cited by: 18
Author(s): Johannes R. Schmidt, Karina Geurtzen, Martin von Bergen, Kristin Schubert, Franziska Knopf
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2020.551495

Systematic Identification of Hub Genes in Placenta Accreta Spectrum Based on Integrated Transcriptomic and Proteomic Analysis
Cited by: 5
Author(s): Bingnan Chen, Di Wang, Yue Bian, Jiapo Li, Tian Yang, Na Li, Chong Qiao
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.molcel.2019.08.005

Polyamines Control eIF5A Hypusination, TFEB Translation, and Autophagy to Reverse B Cell Senescence
Cited by: 189
Author(s): Hanlin Zhang, Ghada Alsaleh, Jack Feltham, Yizhe Sun, Gennaro Napolitano, Thomas Riffelmacher, P. David Charles, Lisa Frau, Philip Hublitz, Zhanru Yu, Shabaz Mohammed, Andrea Ballabio, Stefan Balabanov, Jane Mellor, Anna Katharina Simon
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1009583

RIOK2 phosphorylation by RSK promotes synthesis of the human small ribosomal subunit
Cited by: 6
Author(s): Emilie L. Cerezo, Thibault Houlès, Oriane Lié, Marie-Kerguelen Sarthou, Charlotte Audoynaud, Geneviève Lavoie, Maral Halladjian, Sylvain Cantaloube, Carine Froment, Odile Burlet‐Schiltz, Y. Henry, Philippe P. Roux, Anthony K. Henras, Yves Roméo
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2020.581070

Plasma Proteome Responses in Salmonid Fish Following Immunization
Cited by: 8
Author(s): Fiona K. Bakke, Milena Mira Monte, David Stead, Dwight R. Causey, Alex Douglas, Daniel J. Macqueen, Helen Dooley
Software Mentions: 2
Published: over 5 years ago

10.3389/fcimb.2020.00443

Investigating Non-sterilizing Cure in TB Patients at the End of Successful Anti-TB Therapy
Cited by: 20
Author(s): Caroline G. G. Beltran, Tiaan Heunis, James Gallant, Rouxjeane Venter, Nelita du Plessis, André G. Loxton, Matthias Trost, Jill Winter, Stephanus T. Malherbe, Bavesh D Kana, Gerhard Walzl
Software Mentions: 2
Published: almost 6 years ago

10.3390/cancers13061472

Persistent Inflammatory Stimulation Drives the Conversion of MSCs to Inflammatory CAFs That Promote Pro-Metastatic Characteristics in Breast Cancer Cells
Cited by: 17
Author(s): Linor Rubinstein-Achiasaf, Dina Morein, Hagar Ben-Yaakov, Yulia Liubomirski, Tsipi Meshel, Eti Elbaz, Orly Dorot, Edward Pichinuk, Michael Gershovits, Miguel Weil, Adit Ben‐Baruch
Software Mentions: 2
Published: about 5 years ago

10.3389/fcimb.2018.00145

The Loss of Expression of a Single Type 3 Effector (CT622) Strongly Reduces Chlamydia trachomatis Infectivity and Growth
Cited by: 14
Author(s): Mathilde M. Cossé, Michael L. Barta, Derek J. Fisher, Lena K. Oesterlin, Béatrice Niragire, Stéphanie Perrinet, Gaël A. Millot, P. Scott Hefty, Agathe Subtil
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-019-6058-6

A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana
Cited by: 40
Author(s): Jiorgos Kourelis, Farnusch Kaschani, Friederike Grosse‐Holz, Felix Homma, Markus Kaiser, Renier A. L. van der Hoorn
Software Mentions: 2
Published: over 6 years ago

10.1186/s40478-019-0847-7

Comparative profiling of the synaptic proteome from Alzheimer’s disease patients with focus on the APOE genotype
Cited by: 50
Author(s): Raphael Hesse, Maica Llavero Hurtado, Rosemary J. Jackson, Samantha L. Eaton, Abigail G. Herrmann, Martí Colom‐Cadena, Makis Tzioras, Declan King, Jamie Rose, Jane Tulloch, Chris-Anne McKenzie, Colin Smith, Christopher M. Henstridge, Douglas J. Lamont, Thomas M. Wishart, Tara L. Spires‐Jones
Software Mentions: 2
Published: over 6 years ago

10.3389/fcell.2020.544043

Comparative Transcriptional Profiling of Motor Neuron Disorder-Associated Genes in Various Human Cell Culture Models
Cited by: 8
Author(s): Stefan Hauser, Stefanie Schuster, Elena Heuten, Philip Höflinger, Jakob Admard, Yvonne Schelling, Ana Velić, Boris Maček, Stephan Ossowski, Lüdger Schöls
Software Mentions: 2
Published: over 5 years ago

10.1016/j.mcpro.2021.100119

Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs
Cited by: 16
Author(s): Tomoya Niinae, Koshi Imami, Naoyuki Sugiyama, Yasushi Ishihama
Software Mentions: 2
Published: over 5 years ago

10.1074/mcp.RA120.002359

Plasma Proteomes Can Be Reidentifiable and Potentially Contain Personally Sensitive and Incidental Findings
Cited by: 17
Author(s): Philipp E. Geyer, Sebastian Porsdam Mann, Peter V. Treit, Matthias Mann
Software Mentions: 2
Published: over 5 years ago

10.3389/fbioe.2018.00019

Phosphoproteome of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395, under Nitrogen-Replete and -Deplete Conditions
Cited by: 1
Author(s): Michael T. Guarnieri, Alida T. Gerritsen, Calvin A. Henard, Eric P. Knoshaug
Software Mentions: 2
Published: over 8 years ago

10.1074/mcp.M115.053926

Novel Molecular Insights into Classical and Alternative Activation States of Microglia as Revealed by Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-based Proteomics*
Cited by: 45
Author(s): Harris Bell-Temin, Ashley E. Culver‐Cochran, Dale Chaput, Christina M. Carlson, Melanie N. Kuehl, Brant R. Burkhardt, Paula C. Bickford, Bin Liu, Stanley M. Stevens
Software Mentions: 2
Published: over 10 years ago

10.3390/foods9091150

Living the Sweet Life: How Liquorilactobacillus hordei TMW 1.1822 Changes Its Behavior in the Presence of Sucrose in Comparison to Glucose
Cited by: 7
Author(s): Julia Bechtner, Christina Ludwig, Michael Kiening, Frank Jakob, Rudi F. Vogel
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-018-4517-0

Liver proteome response of pre-harvest Atlantic salmon following exposure to elevated temperature
Cited by: 37
Author(s): Waldo G. Nuez-Ortín, Chris Carter, Peter D. Nichols, Ira Cooke, Richard Wilson
Software Mentions: 2
Published: over 8 years ago

10.3390/foods9091147

An Artificial Intelligence Characterised Functional Ingredient, Derived from Rice, Inhibits TNF-α and Significantly Improves Physical Strength in an Inflammaging Population
Cited by: 13
Author(s): Kathy Kennedy, Brian Keogh, Cyril Lopez, Alessandro Adelfio, Brendan Molloy, Alish Kerr, Audrey Wall, Gaël Jalowicki, Thérèse A. Holton, Nora Khaldi
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12861-018-0177-1

Short term optical defocus perturbs normal developmental shifts in retina/RPE protein abundance
Cited by: 11
Author(s): Nina Riddell, Pierre Faou, Sheila G. Crewther
Software Mentions: 2
Published: almost 8 years ago

10.3389/fncel.2021.662035

Integrative Cell Type-Specific Multi-Omics Approaches Reveal Impaired Programs of Glial Cell Differentiation in Mouse Culture Models of DM1
Cited by: 10
Author(s): Anchel González-Barriga, Louison Lallemant, Diana Mihaela Dincã, Sandra Bráz, Hélène Polvèche, Paul Magneron, Cédric Pionneau, Aline Huguet-Lachon, Jean‐Baptiste Claude, Cérina Chhuon, Ida Chiara Guerrera, Cyril F. Bourgeois, Didier Auboeuf, Geneviève Gourdon, Mário Gomes‐Pereira
Software Mentions: 2
Published: about 5 years ago

10.1038/s41426-018-0210-2

Associating H2O2-and NO-related changes in the proteome of Mycobacterium smegmatis with enhanced survival in macrophage
Cited by: 9
Author(s): Naadir Ganief, Jessica Sjouerman, Claudia Albeldas, Kehilwe C. Nakedi, Clemens Hermann, Bridget Calder, Jonathan M. Blackburn, Nelson C. Soares
Software Mentions: 2
Published: over 7 years ago

10.15252/embr.202052289

Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER‐phagy, and Collagen quality control
Cited by: 42
Author(s): Alessio Reggio, Viviana Buonomo, Rayene Berkane, Ramachandra M Bhaskara, Mariana Edith Tellechea, Ilaria Peluso, Elena Polishchuk, Giorgia Di Lorenzo, Carmine Cirillo, Marianna Esposito, Adeela Hussain, Antje K. Huebner, Christian A. Hübner, Carmine Settembre, Gerhard Hummer, Paolo Grumati, Alexandra Stolz
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13072-021-00382-y

Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex
Cited by: 4
Author(s): Martina Weigt, Qingsong Gao, Hyoju Ban, Haijin He, Guido Mastrobuoni, Stefan Kempa, Wei Chen, Fēi Li
Software Mentions: 2
Published: over 5 years ago

10.1074/mcp.M115.050401

Translating Proteomic Into Functional Data: An High Mobility Group A1 (HMGA1) Proteomic Signature Has Prognostic Value in Breast Cancer
Cited by: 30
Author(s): E Maurizio, Jacek R. Wiśniewski, Yari Ciani, Antonella Amato, Laura Arnoldo, Carlotta Penzo, Silvia Pegoraro, Vincenzo Giancotti, Alberto Zambelli, Silvano Piazza, Guidalberto Manfioletti, Riccardo Sgarra
Software Mentions: 2
Published: over 10 years ago

10.1186/s40478-019-0796-1

Composition of the Intranuclear Inclusions of Fragile X-associated Tremor/Ataxia Syndrome
Cited by: 45
Author(s): Lisa Ma, Anthony W. Herren, Glenda Espinal, Jamie L. Randol, Bridget McLaughlin, Verónica Martínez‐Cerdeño, Isaac N. Pessah, Randi J. Hagerman, Paul J. Hagerman
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13072-019-0265-x

Citrullination of HP1γ chromodomain affects association with chromatin
Cited by: 17
Author(s): Meike Wiese, Andrew J. Bannister, Srinjan Basu, Wayne Boucher, Kai J. Wohlfahrt, Maria A. Christophorou, Michael L. Nielsen, David Klenerman, Ernest D. Laue, Tony Kouzarides
Software Mentions: 2
Published: about 7 years ago

10.1074/mcp.M114.042499

Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs)
Cited by: 24
Author(s): Marie‐Therese Mackmull, Murat Iskar, Luca Parca, Stephan Singer, Peer Bork, Alessandro Ori, Martin Beck
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0091433

Detection of Viral Proteins in Human Cells Lines by Xeno-Proteomics: Elimination of the Last Valid Excuse for Not Testing Every Cellular Proteome Dataset for Viral Proteins
Cited by: 3
Author(s): Alexey Chernobrovkin, Roman A. Zubarev
Software Mentions: 2
Published: over 12 years ago

10.1074/mcp.RA119.001766

Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor
Cited by: 11
Author(s): Sylwia Magdalena Struk, Carolien De Cuyper, Anni Jacobs, Lukas Braem, Alan Walton, Annick De Keyser, Stephen Depuydt, Lam Dai Vu, Ive De Smet, François‐Didier Boyer, Dominique Eeckhout, Geert Persiau, Kris Gevaert, Geert De Jaeger, Sofie Goormachtig
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0149637

Proteome Based Construction of the Lymphocyte Function-Associated Antigen 1 (LFA-1) Interactome in Human Dendritic Cells
Cited by: 2
Author(s): Christina Eich, Edwin Lasonder, Luis J. Cruz, Inge Reinieren-Beeren, Alessandra Cambi, Carl G. Figdor, Sonja I. Buschow
Software Mentions: 2
Published: over 10 years ago

10.1074/mcp.RA119.001400

A Label-free Mass Spectrometry Method to Predict Endogenous Protein Complex Composition*
Cited by: 27
Author(s): Zachary McBride, Donglai Chen, Youngwoo Lee, Uma K. Aryal, Jun Xie, Daniel B. Szymanski
Software Mentions: 2
Published: almost 7 years ago

10.15252/embj.2019102731

CLUH granules coordinate translation of mitochondrial proteins with mTORC1 signaling and mitophagy
Cited by: 36
Author(s): David Pla‐Martín, Désirée Schatton, Janica L. Wiederstein, Marie‐Charlotte Marx, Salim Khiati, Marcus Krüger, Elena I. Rugarli
Software Mentions: 2
Published: over 6 years ago

10.15252/embj.2020107182

Reciprocal priming between receptor tyrosine kinases at recycling endosomes orchestrates cellular signalling outputs
Cited by: 9
Author(s): Michael P. Smith, Harriet R. Ferguson, Jennifer Ferguson, Egor Zindy, Katarzyna M. Kowalczyk, Thomas Kedward, Christian Bates, Joseph Parsons, Joanne Watson, Sarah Chandler, Paul Fullwood, Stacey Warwood, David Knight, Robert B. Clarke, Chiara Francavilla
Software Mentions: 2
Published: about 5 years ago

10.1155/2013/275390

The Application of SILAC Mouse in Human Body Fluid Proteomics Analysis Reveals Protein Patterns Associated with IgA Nephropathy
Cited by: 10
Author(s): Shilin Zhao, Rongxia Li, Xiaoyan Cai, Wan-Jia Chen, Qingrun Li, Tao Xing, Zhu Wang, Y. Eugene Chen, Rong Zeng, Deng Yueyi
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0177408

Ubiquitylation of the acetyltransferase MOF in Drosophila melanogaster
Cited by: 10
Author(s): Sarah Schunter, Raffaella Villa, Victoria K. Flynn, Jan B. Heidelberger, Anne-Kathrin Classen, Petra Beli, Peter B. Becker
Software Mentions: 2
Published: about 9 years ago

10.15252/embj.2020104419

Cyclin A triggers Mitosis either via the Greatwall kinase pathway or Cyclin B
Cited by: 47
Author(s): Nadia Hégarat, Adrijana Crncec, Maria F. Suarez Peredo Rodriguez, Fabio Echegaray Iturra, Yan Gu, Oliver Busby, Paul Lang, Alexis R. Barr, Chris Bakal, Masato T. Kanemaki, Angus I. Lamond, Béla Novák, Tony Ly, Helfrid Hochegger
Software Mentions: 2
Published: about 6 years ago

10.1242/dmm.045096

CHIP mutations affect the heat shock response differently in human fibroblasts and iPSC-derived neurons
Cited by: 5
Author(s): Stefanie Schuster, Elena Heuten, Ana Velić, Jakob Admard, Matthis Synofzik, Stephan Ossowski, Boris Maček, Stefan Hauser, Lüdger Schöls
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0235118

Time-series proteomic study of the response of HK-2 cells to hyperglycemic, hypoxic diabetic-like milieu
Cited by: 4
Author(s): Alberto Valdés, María Castro-Puyana, Coral García-Pastor, Javier Lucio-Cazaña, Marı́a Luisa Marina
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0244493

Comparative proteomics provides insights into diapause program of Bactrocera minax (Diptera: Tephritidae)
Cited by: 20
Author(s): Jia Wang, Li-Lin Ran, Ying Li, Ying‐Hong Liu
Software Mentions: 2
Published: over 5 years ago

10.1242/dmm.033092

Fetal articular cartilage regeneration versus adult fibrocartilaginous repair: secretome proteomics unravels molecular mechanisms in an ovine model
Cited by: 16
Author(s): Iris Ribitsch, Rupert L. Mayer, Monika Egerbacher, Simone Gabner, Maciej M. Kańduła, Julie Rosser, Eva Haltmayer, Ulrike Auer, Sinan Gültekin, Johann Huber, Andrea Bileck, David P. Kreil, Christopher Gerner, Florien Jenner
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.dib.2015.08.010

Dataset from the global phosphoproteomic mapping of early mitotic exit in human cells
Cited by: 8
Author(s): Samuel Rogers, Rachael A. McCloy, Benjamin L. Parker, Rima Chaudhuri, Velimir Gayevskiy, Nolan J. Hoffman, D. Neil Watkins, Roger J. Daly, David E. James, Andrew Burgess
Software Mentions: 2
Published: over 10 years ago

10.1038/s42003-020-0795-6

An isothermal shift assay for proteome scale drug-target identification
Cited by: 38
Author(s): Kerri A. Ball, Kristofor Webb, S. J. Coleman, Kira A. Cozzolino, Jeremy Jacobsen, Kevin R. Jones, Michael H. B. Stowell, William M. Old
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-021-01797-9

Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics
Cited by: 38
Author(s): Chia‐Feng Tsai, Peng Fei Zhang, David Scholten, Kendall J. Martin, Yiting Wang, Rui Zhao, William B. Chrisler, Dhwani Patel, Maowei Dou, Yuzhi Jia, Carolina Reduzzi, Xia Liu, Ronald J. Moore, Kristin Burnum-Johnson, Miao-Hsia Lin, Chuan‐Chih Hsu, Jon Jacobs, Jacob Kagan, Sudhir Srivastava, Karin D. Rodland, H. Steven Wiley, Weijun Qian, Richard Smith, Ying Zhu, Massimo Cristofanilli, Tao Liu, Huiping Liu, Tujin Shi
Software Mentions: 2
Published: over 5 years ago

10.3390/antiox10030378

Nitrosative Redox Homeostasis and Antioxidant Response Defense in Disused Vastus lateralis Muscle in Long-Term Bedrest (Toulouse Cocktail Study)
Cited by: 7
Author(s): Dieter Blottner, Daniele Capitanio, Gabor Trautmann, Sandra Furlan, Guido Gambara, Manuela Moriggi, Katharina Block, Pietro Barbacini, Enrica Torretta, Guillaume Py, Angèle Chopard, Imre Vida, Pompeo Volpe, Cecilia Gelfi, Michele Salanova
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-020-0817-4

pH-responsive high stability polymeric nanoparticles for targeted delivery of anticancer therapeutics
Cited by: 137
Author(s): L. Palanikumar, Sumaya Al-Hosani, Mona Kalmouni, Vanessa P. Nguyen, Liaqat Ali, Renu Pasricha, Francisco N. Barrera, Mazin Magzoub
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-021-02364-y

HLA-B and cysteinylated ligands distinguish the antigen presentation landscape of extracellular vesicles
Cited by: 8
Author(s): Julia Bauzá‐Martinez, Albert J. R. Heck, Wei Wu
Software Mentions: 2
Published: almost 5 years ago

10.1096/fj.202002484R

Sperm proteins and cancer‐testis antigens are released by the seminiferous tubules in mice and men
Cited by: 14
Author(s): Liza O’Donnell, Diane Rebourcet, Laura F. Dagley, Raouda Sgaier, Giuseppe Infusini, Peter J. O’Shaughnessy, Frédéric Chalmel, Daniela Fietz, W. Weidner, Julien M. D. Legrand, Robin M. Hobbs, Robert I McLachlan, Andrew I. Webb, Adrian Pilatz, Thorsten Diemer, Lee B. Smith, Peter G. Stanton
Software Mentions: 2
Published: over 5 years ago

10.1074/mcp.RA118.000593

The Protein Coded by a Short Open Reading Frame, Not by the Annotated Coding Sequence, Is the Main Gene Product of the Dual-Coding Gene MIEF1
Cited by: 44
Author(s): Vivian Delcourt, Mylène Brunelle, Annie Roy, Jean-François Jacques, Michel Salzet, Isabelle Fournier, Xavier Roucou
Software Mentions: 2
Published: over 7 years ago

10.1186/s12014-018-9189-x

Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases
Cited by: 15
Author(s): Nina Zila, Andrea Bileck, Besnik Muqaku, Lukas Janker, Ossia M. Eichhoff, Phil F. Cheng, Reinhard Dummer, Mitchell P. Levesque, Christopher Gerner, Verena Paulitschke
Software Mentions: 2
Published: over 8 years ago

10.1186/s12014-016-9124-y

Cardiovascular proteomics in the era of big data: experimental and computational advances
Cited by: 9
Author(s): Maggie P. Y. Lam, Edward Lau, Dominic C. M. Ng, Ding Wang, Peipei Ping
Software Mentions: 2
Published: over 9 years ago

10.1074/mcp.M114.044289

Global Proteomics Analysis of the Response to Starvation in C. elegans*
Cited by: 29
Author(s): Mark Larance, Ehsan Pourkarimi, Bin Wang, Alejandro Brenes Murillo, Robert E. Kent, Angus I. Lamond, Anton Gartner
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0234918

ZapE/Afg1 interacts with Oxa1 and its depletion causes a multifaceted phenotype
Cited by: 7
Author(s): Jan Pyrih, Vendula Rašková, Ingrid Škodová-Sveráková, Tomáš Pánek, Julius Lukeš
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0168183

Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis
Cited by: 8
Author(s): Daniela Beißer, Farnusch Kaschani, Nadine Graupner, Lars Großmann, Manfred Jensen, Sabrina Ninck, Florian Schulz, Sven Rahmann, Jens Boenigk, Markus Kaiser
Software Mentions: 2
Published: over 9 years ago

10.3390/cells9051191

Super-Resolution Localisation of Nuclear PI(4)P and Identification of Its Interacting Proteome
Cited by: 14
Author(s): Veronika Fáberová, Ilona Kalasová, Alžběta Krausová, Pavel Hozák
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0231681

Laser capture microdissection in combination with mass spectrometry: Approach to characterization of tissue-specific proteomes of Eudiplozoon nipponicum (Monogenea, Polyopisthocotylea)
Cited by: 6
Author(s): Pavel Roudnický, David Potěšil, Zbyněk Zdráhal, Milan Gelnar, Martin Kašný
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0248415

Membrane particles from mesenchymal stromal cells reduce the expression of fibrotic markers on pulmonary cells
Cited by: 1
Author(s): Ana Merino, Martin J. Hoogduijn, María Molina-Molina, Elena G Arias-Salgado, Sander S. Korevaar, Carla C. Baan, Ana Montes-Worboys
Software Mentions: 2
Published: over 5 years ago

10.1186/s12014-019-9243-3

Elucidating the endogenous synovial fluid proteome and peptidome of inflammatory arthritis using label-free mass spectrometry
Cited by: 15
Author(s): Shalini M. Mahendran, Edward Keystone, Roman Krawetz, Kun Liang, Eleftherios P. Diamandis, Vinod Chandran
Software Mentions: 2
Published: about 7 years ago

10.3390/cells8020192

In-Depth Proteome Analysis Highlights HepaRG Cells as a Versatile Cell System Surrogate for Primary Human Hepatocytes
Cited by: 35
Author(s): Georg Tascher, Audrey Burban, Sandrine Camus, Marine Plumel, Stéphanie Chanon, Rémy Le Guével, В. П. Шевченко, Alain Van Dorsselaer, Étienne Lefai, Christiane Guguen‐Guillouzo, Fabrice Bertile
Software Mentions: 2
Published: over 7 years ago

10.3390/cells9040984

Characterization of RNP Networks of PUM1 and PUM2 Post-Transcriptional Regulators in TCam-2 Cells, a Human Male Germ Cell Model
Cited by: 4
Author(s): Maciej Jerzy Smialek, Erkut Ilaslan, Marcin Sajek, Aleksandra Świercz, Damian Mikolaj Janecki, Kamila Kusz-Zamelczyk, Tomasz Woźniak, Maciej Kotecki, Luiza Handschuh, Marek Figlerowicz, Jadwiga Jaruzelska
Software Mentions: 2
Published: about 6 years ago

10.3390/cells10010068

Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome
Cited by: 18
Author(s): Martin Sztacho, Barbora Šalovská, Jakub Červenka, Can Balaban, Peter Hoboth, Pavel Hozák
Software Mentions: 2
Published: over 5 years ago

10.3390/cells10071701

Phosphorylation in the Charged Linker Modulates Interactions and Secretion of Hsp90β
Cited by: 5
Author(s): Lorenz Weidenauer, Manfredo Quadroni
Software Mentions: 2
Published: almost 5 years ago

10.1074/mcp.M114.043489

The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer
Cited by: 278
Author(s): Richard A. Scheltema, Jan-Peter Hauschild, Oliver Lange, Daniel Hornburg, Eduard Denisov, Eugen Damoc, A. Kuehn, Alexander Makarov, Matthias Mann
Software Mentions: 2
Published: over 11 years ago

10.3390/cells9081817

Cyclopamine and Rapamycin Synergistically Inhibit mTOR Signalling in Mouse Hepatocytes, Revealing an Interaction of Hedgehog and mTor Signalling in the Liver
Cited by: 4
Author(s): Luise Spormann, Christiane Rennert, Erik Kolbe, Fritzi Ott, Carolin Lossius, Robert Lehmann, Rolf Gebhardt, Thomas Berg, Madlen Matz‐Soja
Software Mentions: 2
Published: almost 6 years ago

10.3390/cells9071666

Disclosing the Interactome of Leukemogenic NUP98-HOXA9 and SET-NUP214 Fusion Proteins Using a Proteomic Approach
Cited by: 9
Author(s): Adélia Mendes, Ramona Jühlen, Sabrina Bousbata, Birthe Fahrenkrog
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0150672

Analysis of the Cerebrospinal Fluid Proteome in Alzheimer's Disease
Cited by: 77
Author(s): Payam Emami Khoonsari, Anna Häggmark, Maria Lönnberg, Maria Mikus, Lena Kilander, Lars Lannfelt, Jonas Bergquist, Martin Ingelsson, Peter Nilsson, Kim Kultima, Ganna Shevchenko
Software Mentions: 2
Published: over 10 years ago

10.1074/mcp.TIR118.001131

MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides
Cited by: 87
Author(s): Christoph Wichmann, Florian Meier, Sebastian Virreira Winter, Andreas-David Brunner, Jürgen Cox, Matthias Mann
Software Mentions: 2
Published: about 7 years ago

10.3390/cells9102272

Small-Molecule Chemical Knockdown of MuRF1 in Melanoma Bearing Mice Attenuates Tumor Cachexia Associated Myopathy
Cited by: 13
Author(s): Volker Adams, Victoria Gußen, Sergey Zozulya, André Cruz, Anselmo Sigari Moriscot, Axel Linke, Siegfried Labeit
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0201480

Dissecting the subcellular membrane proteome reveals enrichment of H+ (co-)transporters and vesicle trafficking proteins in acidic zones of Chara internodal cells
Cited by: 16
Author(s): Heidi Pertl-Obermeyer, Peter Lackner, Waltraud X. Schulze, Marion C. Hoepflinger, Margit Hoeftberger, Ilse Foissner, Gerhard Obermeyer
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.celrep.2019.04.025

Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection
Cited by: 66
Author(s): Edward Jd Greenwood, James C Williamson, Agata Sienkiewicz, Adi Naamati, Nicholas J Matheson, Paul J. Lehner
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-016-3361-3

Systematic analysis of the lysine acetylome in Fusarium graminearum
Cited by: 39
Author(s): Shanyue Zhou, Qiwen Yang, Changfa Yin, Lin Liu, Wenxing Liang
Software Mentions: 2
Published: over 9 years ago

10.1016/j.celrep.2019.09.080

MitoRibo-Tag Mice Provide a Tool for In Vivo Studies of Mitoribosome Composition
Cited by: 22
Author(s): Jakob D. Busch, Miriam Cipullo, Ilian Atanassov, Ana Bratić, Eduardo Silva Ramos, Thomas Schöndorf, Xinping Li, Sarah F Pearce, Dusanka Milenkovic, Joanna Rorbach, Nils‐Göran Larsson
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0162317

LBD1 of Vitellogenin Receptor Specifically Binds to the Female-Specific Storage Protein SP1 via LBR1 and LBR3
Cited by: 10
Author(s): Lina Liu, Yejing Wang, Yu Liu, Ying Lin, Yong Hou, Yan Zhang, Shuguang Wei, Peng Zhao, Ping Zhao, Huawei He
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41419-021-03436-x

Alternative splicing of ceramide synthase 2 alters levels of specific ceramides and modulates cancer cell proliferation and migration in Luminal B breast cancer subtype
Cited by: 16
Author(s): Trishna Pani, Kajal Rajput, Animesh Kar, Harsh Sharma, Rituparna Basak, Nihal Medatwal, Sandhini Saha, Gagan Dev, Satish Kumar, Shweta Gupta, Arnab Mukhopadhyay, Dipankar Malakar, Tushar Kanti Maiti, Aneeshkumar G. Arimbasseri, Svs Deo, Ravi Datta Sharma, Avinash Bajaj, Ujjaini Dasgupta
Software Mentions: 2
Published: over 5 years ago

10.1038/s41421-021-00278-x

Discovery of a cooperative mode of inhibiting RIPK1 kinase
Cited by: 11
Author(s): Huyan Meng, Guowei Wu, Xinsuo Zhao, Anhui Wang, Dekang Li, Yilun Tong, Teng Jin, Ye Cao, Bing Shan, Shichen Hu, Ying Liu, Lifeng Pan, Xiaoxu Tian, Ping Wu, Chao Peng, Junying Yuan, Guohui Li, Tan Li, Zhaoyin Wang, Ying Li
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-15-95

Characterization of the membrane proteome and N-glycoproteome in BV-2 mouse microglia by liquid chromatography-tandem mass spectrometry
Cited by: 17
Author(s): Dohyun Han, Seong-Yong Moon, Yikwon Kim, Hophil Min, Youngsoo Kim
Software Mentions: 2
Published: over 12 years ago

10.3390/cancers11101478

Protein Expression Profiling Identifies Key Proteins and Pathways Involved in Growth Inhibitory Effects Exerted by Guggulsterone in Human Colorectal Cancer Cells
Cited by: 13
Author(s): Rari Leo, Lubna Therachiyil, Sivaraman K Siveen, Shahab Uddin, Michał Kuliński, Joerg Buddenkotte, Martin Steinhoff, Roopesh Krishnankutty
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0198404

Investigation of lignocellulolytic enzymes during different growth phases of Ganoderma lucidum strain G0119 using genomic, transcriptomic and secretomic analyses
Cited by: 23
Author(s): Shuai Zhou, Jingsong Zhang, Fuying Ma, Chuanhong Tang, Qingjiu Tang, Xiaoyu Zhang
Software Mentions: 2
Published: about 8 years ago

10.1038/cr.2017.36

Baf60b-mediated ATM-p53 activation blocks cell identity conversion by sensing chromatin opening
Cited by: 18
Author(s): Shuyi Ji, Linying Zhu, Yimeng Gao, Xiaoran Zhang, Yupeng Yan, Jin Cen, Rongxia Li, Rong Zeng, Lujian Liao, Chaoqi Hou, Yawei Gao, Shaorong Gao, Gang Wei, Lijian Hui
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2020.00209

Comparative Proteomics of Meat Spoilage Bacteria Predicts Drivers for Their Coexistence on Modified Atmosphere Packaged Meat
Cited by: 18
Author(s): Sandra Kolbeck, Christina Ludwig, Chen Meng, Maik Hilgarth, Rudi F. Vogel
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2018.00775

Using RT-qPCR, Proteomics, and Microscopy to Unravel the Spatio-Temporal Expression and Subcellular Localization of Hordoindolines Across Development in Barley Endosperm
Cited by: 12
Author(s): Azita Shabrangy, Valentin Roustan, Siegfried Reipert, Marieluise Weidinger, Pierre-Jean Roustan, Eva Stöger, Wolfram Weckwerth, Verena Ibl
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-021-92931-4

Overlapping regions of Caf20 mediate its interactions with the mRNA-5′cap-binding protein eIF4E and with ribosomes
Cited by: 4
Author(s): Ebelechukwu C. Nwokoye, Eiman AlNaseem, Robert A. Crawford, Lydia M. Castelli, Martin D. Jennings, Christopher J. Kershaw, Graham D. Pavitt
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-018-25059-7

Trafficking, localization and degradation of the Na+,HCO3− co-transporter NBCn1 in kidney and breast epithelial cells
Cited by: 8
Author(s): Christina W. Olesen, Jens Vogensen, Ida Axholm, Marc Severin, Julie Schnipper, Isabella Skandorff Pedersen, Jakob Hjorth von Stemann, Jacob M. Schrøder, Dan Ploug Christensen, Stine Falsig Pedersen
Software Mentions: 2
Published: about 8 years ago

10.1111/jcmm.12407

Establishment of a proteome profile and identification of molecular markers for mouse spermatogonial stem cells
Cited by: 27
Author(s): Quan Zhou, Yueshuai Guo, Bo Zheng, Binbin Shao, Min Jiang, Gaigai Wang, Tao Zhou, Lei Wang, Zuomin Zhou, Xuejiang Guo, Xiaoyan Huang
Software Mentions: 2
Published: over 11 years ago

10.1186/s13395-020-00226-5

High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers
Cited by: 24
Author(s): Sebastian Kallabis, Lena Abraham, Stefan Müller, Verena Dzialas, Clara Türk, Janica L. Wiederstein, Theresa Bock, Hendrik Nolte, Leonardo Nogara, Bert Blaauw, Thomas Braun, Marcus Krüger
Software Mentions: 2
Published: about 6 years ago

10.1002/glia.24032

Regulation of aquaporin‐4 expression in the central nervous system investigated using M23‐AQP4 null mouse
Cited by: 10
Author(s): Francesco Pisani, Laura Simone, Maria Grazia Mola, Manuela De Bellis, Antonio Frigeri, Grazia Paola Nicchia, María Svelto
Software Mentions: 2
Published: about 5 years ago

10.1186/s13287-018-0867-4

Early passaging of mesenchymal stem cells does not instigate significant modifications in their immunological behavior
Cited by: 26
Author(s): Niketa Sareen, Glen Lester Sequiera, Rakesh Chaudhary, Ejlal Abu‐El‐Rub, Subir Roy Chowdhury, Vikram Sharma, Arun Surendran, Meenal Moudgil, Paul Fernyhough, Amir Ravandi, Sanjiv Dhingra
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-23505-0

Proteomic analysis of plasma extracellular vesicles reveals mitochondrial stress upon HTLV-1 infection
Cited by: 22
Author(s): Patricia Jeannin, Thibault Chaze, Quentin Giai Gianetto, Mariette Matondo, Olivier Gout, Antoine Gessain, Philippe V. Afonso
Software Mentions: 2
Published: about 8 years ago

10.1242/jcs.154880

Tyrosine phosphorylation of WIP releases bound WASP and impairs podosome assembly in macrophages
Cited by: 15
Author(s): Vineetha Vijayakumar, James Monypenny, Xing Judy Chen, Laura M. Machesky, Sérgio Lilla, Adrian J. Thrasher, Inés M. Antón, Yolanda Calle, Gareth E. Jones
Software Mentions: 2
Published: over 12 years ago

10.3389/fpls.2020.625507

Transcriptomic and Proteomic Analyses of Nepenthes ampullaria and Nepenthes rafflesiana Reveal Parental Molecular Expression in the Pitchers of Their Hybrid, Nepenthes × hookeriana
Cited by: 11
Author(s): Muhammad Mu′izzuddin Zulkapli, Nur Syatila Ab Ghani, Tiew Yik Ting, Wan Mohd Aizat, Hoe-Han Goh
Software Mentions: 2
Published: over 5 years ago

10.1109/ACCESS.2020.3047588

Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey
Cited by: 12
Author(s): Muhammad Usman Tariq, Muhammad Haseeb, Mohammed Aledhari, Rehma Razzak, Reza M. Parizi, Fahad Saeed
Software Mentions: 2
Published: over 5 years ago

10.1016/j.str.2017.04.005

The Architecture of the Anbu Complex Reflects an Evolutionary Intermediate at the Origin of the Proteasome System
Cited by: 11
Author(s): Adrian C. D. Fuchs, Vikram Alva, Lorena Maldoner, R. Albrecht, M.D. Hartmann, Joerg Martin
Software Mentions: 2
Published: about 9 years ago

10.1016/j.immuni.2017.11.016

Oncogenic RAS Signaling Promotes Tumor Immunoresistance by Stabilizing PD-L1 mRNA
Cited by: 416
Author(s): Matthew A. Coelho, Sophie de Carné Trécesson, Sareena Rana, Davide Zecchin, Christopher Moore, Míriam Molina‐Arcas, Philip East, Bradley Spencer‐Dene, Emma Nye, Karin Barnouin, Ambrosius P. Snijders, Wi S. Lai, Perry J. Blackshear, Julian Downward
Software Mentions: 2
Published: over 8 years ago

10.7150/thno.37623

Comprehensive characterization of the phosphoproteome of gastric cancer from endoscopic biopsy specimens
Cited by: 19
Author(s): Yuichi Abe, Hidekazu Hirano, Hirokazu Shoji, Asa Tada, Junko Isoyama, Akemi Kakudo, Daigo Gunji, Kazufumi Honda, Narikazu Boku, Jun Adachi, Takeshi Tomonaga
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2021.635550

SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS
Cited by: 19
Author(s): Kamil Mikulášek, Hana Konečná, David Potěšil, Renata Holánková, Jan Havliš, Zbyněk Zdráhal
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.61816

Proteomics reveals synergy between biomass degrading enzymes and inorganic Fenton chemistry in leaf-cutting ant colonies
Cited by: 7
Author(s): Morten Schiøtt, Jacobus J. Boomsma
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.60480

Chemical genetics and proteome-wide site mapping reveal cysteine MARylation by PARP-7 on immune-relevant protein targets
Cited by: 37
Author(s): Kelsie M Rodriguez, Sara C. Buch-Larsen, Ilsa T Kirby, Ivan Rodriguez Siordia, David Hutin, Marit Rasmussen, Denis M. Grant, Larry L. David, Jason Matthews, Michael L. Nielsen, Michael S. Cohen
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.143474

Identification of Wee1 as a target in combination with avapritinib for gastrointestinal stromal tumor treatment
Cited by: 5
Author(s): Shuai Ye, Dinara Sharipova, Marya Kozinova, Lilli Klug, Jimson D’Souza, Martin G. Belinsky, Katherine J. Johnson, Margret B. Einarson, Karthik Devarajan, Yan Zhou, Samuel Litwin, Michael C. Heinrich, Ronald P. DeMatteo, Margaret von Mehren, James S. Duncan, Lori Rink
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2021.716114

Quantitative Proteomics and Relative Enzymatic Activities Reveal Different Mechanisms in Two Peanut Cultivars (Arachis hypogaea L.) Under Waterlogging Conditions
Cited by: 5
Author(s): Dengwang Liu, Jicheng Zhan, Zinan Luo, Ningbo Zeng, Wei Zhang, Hao Zhang, Li Lin
Software Mentions: 2
Published: almost 5 years ago

10.1242/jcs.257188

Ribosome quality control activity potentiates vaccinia virus protein synthesis during infection
Cited by: 17
Author(s): Elayanambi Sundaramoorthy, Andrew P Ryan, Amit Fulzele, Marilyn Leonard, Matthew D. Daugherty, Eric J. Bennett
Software Mentions: 2
Published: about 5 years ago

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