Ecosyste.ms: Papers

10.1371/journal.pone.0121358

No Evidence of Enemy Release in Pathogen and Microbial Communities of Common Wasps (Vespula vulgaris) in Their Native and Introduced Range
Cited by: 30
Author(s): Philip J. Lester, Peter Bösch, Monica A. M. Gruber, Eugene A. Kapp, Lifeng Peng, Evan C. Brenton-Rule, Joe Buchanan, W. L. Stanislawek, Michael Archer, Juan C. Corley, Maité Masciocchi, Annette Van Oystaeyen, Tom Wenseleers
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0038283

Molecular Characterization of Podoviral Bacteriophages Virulent for Clostridium perfringens and Their Comparison with Members of the Picovirinae
Cited by: 40
Author(s): Nikolay V. Volozhantsev, Brian B. Oakley, Cesar A. Morales, Vladimir V. Verevkin, Vasily A. Bannov, Valentina M. Krasilnikova, Anastasiya V. Popova, Е. Л. Жиленков, Johnna K. Garrish, Kathleen M. Schegg, Rebekah Woolsey, David R. Quilici, J. Eric Line, Kelli L. Hiett, Gregory R. Siragusa, Э. А. Светоч, Bruce S. Seal
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0031858

Functional Complexity of the Axonal Growth Cone: A Proteomic Analysis
Cited by: 38
Author(s): Adriana Estrada-Bernal, Staci D. Sanford, Lucas J. Sosa, Glenn C. Simon, Kirk C. Hansen, Karl H. Pfenninger
Software Mentions: 3
Published: about 12 years ago

10.1186/1471-2164-14-830

HOXC9 directly regulates distinct sets of genes to coordinate diverse cellular processes during neuronal differentiation
Cited by: 23
Author(s): Xiangwei Wang, Jeong-Hyeon Choi, Jane Ding, Liqun Yang, Lambert C. M. Ngoka, Mi Kyung Lee, Yunhong Zha, Ling Mao, Boquan Jin, Mingqiang Ren, John K. Cowell, Shuang Huang, Huidong Shi, Hongjuan Cui, Han‐Fei Ding
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-018-36048-1

Molecular evolution of juvenile hormone esterase-like proteins in a socially exchanged fluid
Cited by: 25
Author(s): Adria C LeBoeuf, Amir B. Cohanim, Céline Stoffel, Colin S. Brent, Patrice Waridel, Eyal Privman, Laurent Keller, Richard Benton
Software Mentions: 3
Published: over 5 years ago

10.1186/s12915-015-0128-2

The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers
Cited by: 14
Author(s): Sarah K. Harten, Harald Oey, Lauren M. Bourke, Vandhana Bharti, Luke Isbel, Lucia Daxinger, Pierre Faou, Neil O. Robertson, Jacqueline M. Matthews, Emma Whitelaw
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-018-34864-z

Interactome determination of a Long Noncoding RNA implicated in Embryonic Stem Cell Self-Renewal
Cited by: 14
Author(s): Keriayn N. Smith, Joshua Starmer, Terry Magnuson
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0009828

Mining nematode protein secretomes to explain lifestyle and host specificity
Cited by: 9
Author(s): Lucienne Tritten, Cristina Ballesteros, Robin N. Beech, Timothy G. Geary, Yovany Moreno
Software Mentions: 3
Published: over 2 years ago

10.1371/journal.pone.0026495

New Inflammation-Related Biomarkers during Malaria Infection
Cited by: 44
Author(s): Fikregabrail Aberra Kassa, Marina Tiemi Shio, Marie-Josée Bellemare, Babacar Faye, Momar Ndao, Martin Olivier
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pntd.0008439

Unravelling the proteomic signature of extracellular vesicles released by drug-resistant Leishmania infantum parasites
Cited by: 33
Author(s): Noélie Douanne, George Dong, Mélanie Douanne, Martin Olivier, Christopher Fernández-Prada
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijms22168631

The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales
Cited by: 5
Author(s): Marie-Caroline Müller, T. Wagner
Software Mentions: 3
Published: almost 3 years ago

10.1371/journal.pone.0160160

Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument
Cited by: 20
Author(s): Chengjian Tu, Jun Li, Shichen Shen, Quanhu Sheng, Yu Shyr, Jun Qu
Software Mentions: 3
Published: almost 8 years ago

10.1128/mBio.02048-16

Making Home Sweet and Sturdy:<i>Toxoplasma gondii</i>ppGalNAc-Ts Glycosylate in Hierarchical Order and Confer Cyst Wall Rigidity
Cited by: 48
Author(s): Tadakimi Tomita, Tatsuki Sugi, Rama R. Yakubu, Vincent Tu, Yanfen Ma, Louis M. Weiss
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0133751

Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes
Cited by: 43
Author(s): Moon Young Lee, Chanjae Park, Robyn M. Berent, Paul J. Park, Robert Fuchs, Syn Hannah, Chin Albert, Jared Townsend, Craig C. Benson, Doug Redelman, Tong Shen, Sang-Youel Park, Joseph M. Miano, Kenton M. Sanders, Seungil Ro
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2105-8-483

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system
Cited by: 17
Author(s): Arnaud Droit, Joanna M. Hunter, Michèle Rouleau, Chantal Éthier, Aude Picard-Cloutier, David Bourgais, Guy G. Poirier
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2164-13-361

Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species
Cited by: 85
Author(s): Emily A. Hornett, Christopher W. Wheat
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0252711

The Goto Kakizaki rat: Impact of age upon changes in cardiac and renal structure, function
Cited by: 5
Author(s): Patrick Meagher, Robert Civitarese, Xavier Lee, Mark Forrest Gordon, Antoinette Bugyei-Twum, Jean-François Desjardins, Golam Kabir, Yanling Zhang, Hari Kosanam, Aylin Visram, Howard Leong‐Poi, Andrew Advani, Kim A. Connelly
Software Mentions: 3
Published: almost 3 years ago

10.1186/1751-0473-8-23

Combining de novo and reference-guided assembly with scaffold_builder
Cited by: 54
Author(s): Genivaldo Gueiros Z. Silva, Bas E. Dutilh, T. David Matthews, Keri Elkins, Robert Schmieder, Elizabeth A. Dinsdale, Robert A. Edwards
Software Mentions: 3
Published: over 10 years ago

10.1128/JVI.00980-17

ZIC2 Is Essential for Maintenance of Latency and Is a Target of an Immediate Early Protein during Kaposi's Sarcoma-Associated Herpesvirus Lytic Reactivation
Cited by: 10
Author(s): Yuanzhi Lyu, K. Nakano, Ryan R. Davis, Clifford G. Tepper, Mel Campbell, Yoshihiro Izumiya
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0018880

Arabidopsis Plasmodesmal Proteome
Cited by: 222
Author(s): Lourdes Fernández‐Calvino, Christine Faulkner, John Walshaw, Gerhard Saalbach, Emmanuelle Bayer, Yoselin Benitez‐Alfonso, Andrew J. Maule
Software Mentions: 3
Published: about 13 years ago

10.1038/s41598-021-89996-6

Proteomic and genomic analysis of acid dentin lysate with focus on TGF-β signaling
Cited by: 7
Author(s): Jila Nasirzade, Zahra Kargarpour, Goran Mitulović, Franz Josef Strauß, Layla Panahipour, Frank Schwarz, Reinhard Gruber
Software Mentions: 3
Published: almost 3 years ago

10.1038/s41598-019-55896-z

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster
Cited by: 7
Author(s): Julia Bespyatykh, Egor Shitikov, Andrei Guliaev, Alexander Smolyakov, Ksenia M. Klimina, Vladimir A. Veselovsky, М В Малахова, Georgij Arapidi, Marine Dogonadze, Olga Manicheva, Dmitry Bespiatykh, Igor Mokrousov, Viacheslav Zhuravlev, Elena N. Ilina, Vadim M. Govorun
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009708

Ras/ERK and PI3K/AKT signaling differentially regulate oncogenic ERG mediated transcription in prostate cells
Cited by: 6
Author(s): Brady G. Strittmatter, Travis J. Jerde, Peter C. Hollenhorst
Software Mentions: 3
Published: almost 3 years ago

10.1111/acel.13124

Proteomic signatures of in vivo muscle oxidative capacity in healthy adults
Cited by: 12
Author(s): Fatemeh Adelnia, Ceereena Ubaida‐Mohien, Ruin Moaddel, Michelle Shardell, Alexey E. Lyashkov, Kenneth W. Fishbein, Miguel A. Aon, Richard G. Spencer, Luigi Ferrucci
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-33943-5

Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation
Cited by: 33
Author(s): Erich Hofmann, Rhett M. Rautsaw, Jason L. Strickland, Matthew L. Holding, Michael Hogan, Andrew J. Mason, Darin R. Rokyta, Christopher L. Parkinson
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-67665-4

Beta-nerve growth factor stimulates spontaneous electrical activity of in vitro embryonic mouse GnRH neurons through a P75 mediated-mechanism
Cited by: 8
Author(s): Caroline Pinet, Renaud Fleurot, Flavie Derouin-Tochon, S.P. de Graaf, Xavier Druart, Guillaume Tsikis, Catherine Taragnat, Ana-Paula Teixeira-Gomes, Valérie Labas, Thierry Moreau, Xavier Cayla, Anne Duittoz
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-81000-5

EBF1 drives hallmark B cell gene expression by enabling the interaction of PAX5 with the MLL H3K4 methyltransferase complex
Cited by: 12
Author(s): Charles E. Bullerwell, Philippe Pierre Robichaud, Pierre Deprez, Andrew P. Joy, Gabriel Wajnberg, Darwin D’souza, Simi Chacko, Sébastien Fournier, Nicolas Crapoulet, David A. Barnett, Stephen M. Lewis, Rodney J. Ouellette
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009215

Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae
Cited by: 12
Author(s): Joshua J. Black, Richa Sardana, Ezzeddine W. Elmir, Arlen Johnson
Software Mentions: 3
Published: over 3 years ago

10.1128/mSphere.00207-17

The Effector TepP Mediates Recruitment and Activation of Phosphoinositide 3-Kinase on Early Chlamydia trachomatis Vacuoles
Cited by: 27
Author(s): Victoria K. Carpenter, Yi-Shan Chen, Lee Dolat, Raphael H. Valdivia
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-04423-z

Metabolic changes in Medaka fish induced by cyanobacterial exposures in mesocosms: an integrative approach combining proteomic and metabolomic analyses
Cited by: 12
Author(s): Benoît. Sotton, Alain Paris, Séverine Le Manach, Alain Blond, Gérard Lacroix, Alexis Millot, Clément Duval, Hélène Huet, Qun Qiao, Sophie Labrut, Giovanni Chiapetta, Joëlle Vinh, Arnaud Catherine, Benjamin Marie
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12974-017-0840-7

Proteomic analysis of aged microglia: shifts in transcription, bioenergetics, and nutrient response
Cited by: 71
Author(s): Antwoine Flowers, Harris Bell-Temin, Ahmad Jalloh, Stanley M. Stevens, Paula C. Bickford
Software Mentions: 3
Published: about 7 years ago

10.3390/nu11020418

Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids
Cited by: 40
Author(s): Nijiati Abulizi, Candice Quin, Kirsty Brown, Yee Kwan Chan, S K Gill, Deanna L. Gibson
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0237981

Cancer proteome and metabolite changes linked to SHMT2
Cited by: 16
Author(s): Jiefei Tong, Jonathan R. Krieger, Paul Taylor, Richard D. Bagshaw, Jae Seung Kang, Swathi P. Jeedigunta, Leanne E. Wybenga‐Groot, Wen Zhang, Heba Badr, Shideh Mirhadi, Nhu-An Pham, Étienne Coyaud, Man Yu, Ming Li, Michael Cabanero, Brian Raught, Jason T. Maynes, Cynthia Hawkins, Ming‐Sound Tsao, Michael F. Moran
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-018-4982-5

Deciphering the oviductal extracellular vesicles content across the estrous cycle: implications for the gametes-oviduct interactions and the environment of the potential embryo
Cited by: 91
Author(s): Carmen Almiñana, Guillaume Tsikis, Valérie Labas, Rustem Uzbekov, Juliano Coelho da Silveira, Stefan Bauersachs, Pascal Mermillod
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-13-308

Estimating relative abundances of proteins from shotgun proteomics data
Cited by: 88
Author(s): Sean J. McIlwain, Michael Mathews, Michael S. Bereman, Edwin W. Rubel, Michael J. MacCoss, William Stafford Noble
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-018-26313-8

Impact of the griffithsin anti-HIV microbicide and placebo gels on the rectal mucosal proteome and microbiome in non-human primates
Cited by: 26
Author(s): Lauren Girard, Kenzie Birse, Johanna B. Holm, Pawel Gajer, Mike Humphrys, David Garber, Patricia C. Guenthner, Laura Noël‐Romas, Max Abou, Stuart McCorrister, Garrett Westmacott, Lin Wang, Lisa C. Rohan, Nobuyuki Matoba, Janet M. McNicholl, Kenneth E. Palmer, Jacques Ravel, Adam Burgener
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2164-12-177

Expansion and functional diversification of a leucyl aminopeptidase family that encodes the major protein constituents of Drosophila sperm
Cited by: 35
Author(s): Steve Dorus, Elaine C. Wilkin, Timothy L. Karr
Software Mentions: 3
Published: about 13 years ago

10.1038/srep32459

Deep sexual dimorphism in adult medaka fish liver highlighted by multi-omic approach
Cited by: 39
Author(s): Qun Qiao, Séverine Le Manach, Benoît Sotton, Hélène Huet, Evelyne Duvernois-Berthet, Alain Paris, Clément Duval, Loïc Ponger, Arul Marie, Alain Blond, L. Matheron, Joëlle Vinh, G. Bolbach, Chakib Djédiat, Cécile Bernard, Marc Edery, Benjamin Marie
Software Mentions: 3
Published: over 7 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

10.1038/s41598-017-02970-z

Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens
Cited by: 16
Author(s): Igor Fesenko, Regina Khazigaleeva, Ilya Kirov, Andrey Kniazev, Oksana Glushenko, Konstantin Babalyan, Georgij Arapidi, Tatiana I. Shashkova, Ivan Butenko, Victor G. Zgoda, Ksenia S. Anufrieva, A. V. Seredina, Anna Filippova, Vadim M. Govorun
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-33068-9

Spider silk proteome provides insight into the structural characterization of Nephila clavipes flagelliform spidroin
Cited by: 26
Author(s): José Roberto Aparecido dos Santos-Pinto, Helen Andrade Arcuri, Franciele Grego Esteves, Mário Sérgio Palma, Gert Lübec
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0183975

Biophysical analysis of the effect of chemical modification by 4-oxononenal on the structure, stability, and function of binding immunoglobulin protein (BiP)
Cited by: 4
Author(s): Dinen D. Shah, Surinder Singh, Monika Dzieciątkowska, Krishna Mallela
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-73847-x

Differentiating Staphylococcus infection-associated glomerulonephritis and primary IgA nephropathy: a mass spectrometry-based exploratory study
Cited by: 9
Author(s): Anjali A. Satoskar, John P. Shapiro, Mikayla Jones, Cherri Bott, Samir Parikh, Sergey V. Brodsky, Lianbo Yu, Haikady N. Nagaraja, Daniel W. Wilkey, Michael L. Merchant, Jon B. Klein, Tibor Nádasdy, Brad H. Rovin
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-98454-2

Protein expression reveals a molecular sexual identity of avian primordial germ cells at pre-gonadal stages
Cited by: 9
Author(s): Laura Soler, Sabine Alves, Aurélien Brionne, Aurore Jacques, Vanessa Guérin, Maëva Cherif--Feildel, Lucie Combes‐Soia, Sophie Fouchécourt, Aurore Thélie, Élisabeth Blesbois, Michael J. McGrew, Valérie Labas, Marina Govoroun
Software Mentions: 3
Published: over 2 years ago

10.1371/journal.ppat.1005811

The Arabidopsis Protein Phosphatase PP2C38 Negatively Regulates the Central Immune Kinase BIK1
Cited by: 106
Author(s): Daniel Couto, Roda Niebergall, Xiangxiu Liang, Christoph A. Bücherl, Jan Sklenář, Alberto P. Macho, Vardis Ntoukakis, Paul Derbyshire, Denise Altenbach, Dan MacLean, Silke Robatzek, Joachim F. Uhrig, Frank L.H. Menke, Jian‐Min Zhou, Cyril Zipfel
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-017-3608-7

Sex differences in the molecular signature of the developing mouse hippocampus
Cited by: 40
Author(s): Joseph L. Bundy, Cynthia Vied, Richard S. Nowakowski
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.ppat.1006448

Structure of the Neisseria Adhesin Complex Protein (ACP) and its role as a novel lysozyme inhibitor
Cited by: 18
Author(s): María Victoria Humbert, Amaka M. Awanye, Lu Lian, Jeremy P. Derrick, Myron Christodoulides
Software Mentions: 3
Published: almost 7 years ago

10.3389/fphys.2019.00312

Physical Activity Associated Proteomics of Skeletal Muscle: Being Physically Active in Daily Life May Protect Skeletal Muscle From Aging
Cited by: 68
Author(s): Ceereena Ubaida‐Mohien, Marta González-Freire, Alexey E. Lyashkov, Ruin Moaddel, Chee W. Chia, Eleanor M. Simonsick, Ranjan Sen, Luigi Ferrucci
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1002742

Genome-Wide Analysis of GLD-1–Mediated mRNA Regulation Suggests a Role in mRNA Storage
Cited by: 43
Author(s): Claudia Scheckel, Dimos Gaidatzis, Jane E. Wright, Rafal Ciosk
Software Mentions: 3
Published: almost 12 years ago

10.3389/fmicb.2020.01179

Analysis of Virus and Host Proteomes During Productive HSV-1 and VZV Infection in Human Epithelial Cells
Cited by: 14
Author(s): Werner J. D. Ouwendijk, Lennard J. M. Dekker, Henk-Jan van den Ham, Tihana Lenac Roviš, Erik Haefner, Stipan Jonjić, Jürgen Haas, Theo M. Luider, Georges M. G. M. Verjans
Software Mentions: 3
Published: almost 4 years ago

10.1093/jxb/erv532

Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins
Cited by: 27
Author(s): Kyla J. Morton, Shangang Jia, Chi Zhang, David R. Holding
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.ppat.1009023

Epstein-Barr virus LMP1 manipulates the content and functions of extracellular vesicles to enhance metastatic potential of recipient cells
Cited by: 12
Author(s): Dingani Nkosi, Sun Lee, Leanne C. Duke, David G. Meckes
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1004809

Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses
Cited by: 94
Author(s): Benjamin Schwessinger, Ofir Bahar, Nicholas Thomas, Nicholas Holton, Vladimir Nekrasov, Deling Ruan, Patrick E. Canlas, Arsalan Daudi, Young-Mo Kim, Vasanth Singan, Rita C. Kuo, Mansi Chovatia, Christopher Daum, Joshua L. Heazlewood, Cyril Zipfel, Pamela C. Ronald
Software Mentions: 3
Published: about 9 years ago

10.12688/wellcomeopenres.16031.2

Large CRISPR-Cas-induced deletions in the oxamniquine resistance locus of the human parasite Schistosoma mansoni
Cited by: 7
Author(s): Geetha Sankaranarayanan, Avril Coghlan, Patrick Driguez, Magda E. Lotkowska, Mandy Sanders, Nancy Holroyd, Alan S. Tracey, Matthew Berriman, Gabriel Rinaldi
Software Mentions: 3
Published: over 3 years ago

10.1080/21505594.2017.1325064

Signatures of cytoplasmic proteins in the exoproteome distinguish community- and hospital-associated methicillin-resistant<i>Staphylococcus aureus</i>USA300 lineages
Cited by: 18
Author(s): Solomon Mekonnen, Laura M Palma Medina, Corinna Glasner, Eleni Tsompanidou, Anne de Jong, Stefano Grasso, Marc Schaffer, Ulrike Mäder, Anders Rhod Larsen, Heidi Gumpert, Henrik Westh, Uwe Völker, Andreas Otto, Dörte Becher, Jan Maarten van Dijl
Software Mentions: 3
Published: about 7 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

10.3389/fcimb.2020.00217

Extracellular Vesicle-Contained microRNA of C. elegans as a Tool to Decipher the Molecular Basis of Nematode Parasitism
Cited by: 9
Author(s): Thomas Duguet, Julien Soichot, Rostyslav Kuzyakiv, Lars Malmström, Lucienne Tritten
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12870-016-0858-5

Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease
Cited by: 43
Author(s): Federico Martinelli, Russell L. Reagan, David Dolan, Veronica Fileccia, Abhaya M. Dandekar
Software Mentions: 3
Published: almost 8 years ago

10.3389/fcimb.2021.662404

Proteomic Analysis of Copper Toxicity in Human Fungal Pathogen Cryptococcus neoformans
Cited by: 4
Author(s): Tianshu Sun, Yanjian Li, Yingxing Li, Hailong Li, Yiyi Gong, Jianhuang Wu, Ya-Ting Ning, Chen Ding, Yingchun Xu
Software Mentions: 3
Published: almost 3 years ago

10.1111/mmi.14398

Protein kinase B controls <i>Mycobacterium tuberculosis</i> growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112
Cited by: 14
Author(s): Kawther Alqaseer, Obolbek Turapov, Philippe Barthe, Heena Jagatia, Angélique De Visch, Christian Roumestand, Malgorzata Wegrzyn, Iona L. Bartek, Martin I. Voskuil, Helen M. O’Hare, Paul Ajuh, Andrew R. Bottrill, Adam A. Witney, Martin Cohen‐Gonsaud, Simon J. Waddell, Galina V. Mukamolova
Software Mentions: 3
Published: over 4 years ago

10.15252/embj.201797038

Isoform‐specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands
Cited by: 88
Author(s): Massimiliano Manzo, Joël Wirz, Christina M. Ambrosi, Rodrigo Villaseñor, Bernd Roschitzki, Tuncay Baubec
Software Mentions: 3
Published: over 6 years ago

10.1074/mcp.RA120.002028

A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria
Cited by: 36
Author(s): Andreas Linden, Markus Deckers, Iwan Parfentev, Ralf Pflanz, Bettina Homberg, Piotr Neumann, Ralf Ficner, Peter Rehling, Henning Urlaub
Software Mentions: 3
Published: almost 4 years ago

10.15252/embj.2018100825

Diverse roles of TssA‐like proteins in the assembly of bacterial type VI secretion systems
Cited by: 34
Author(s): Johannes Schneider, Sergey Nazarov, Ricardo Adaixo, Martina Liuzzo, Peter David Ringel, Henning Stahlberg, Marek Basler
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.molcel.2019.07.022

Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk
Cited by: 140
Author(s): James A. Letts, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, L.A. Sazanov
Software Mentions: 3
Published: over 4 years ago

10.1038/s42003-019-0594-0

Mycobacterium tuberculosis sensor kinase DosS modulates the autophagosome in a DosR-independent manner
Cited by: 18
Author(s): Uma S. Gautam, Smriti Mehra, Priyanka Kumari, Xavier Álvarez, Tianhua Niu, Jaya Sivaswami Tyagi, Deepak Kaushal
Software Mentions: 3
Published: over 4 years ago

10.1016/j.mcpro.2021.100064

Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner
Cited by: 8
Author(s): Lauriane Vélot, Frédéric Lessard, Félix-Antoine Bérubé-Simard, Christophe Tav, Bertrand Neveu, Valentine Teyssier, Imène Boudaoud, Ugo Dionne, Noémie Lavoie, Steve Bilodeau, Frédéric Pouliot, Nicolas Bisson
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms8020244

Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses
Cited by: 5
Author(s): Ohana Y.A. Costa, Marcelo M. Zerillo, Daniela Zühlke, Anna M. Kielak, Agata Pijl, Katharina Riedel, Eiko E. Kuramae
Software Mentions: 3
Published: over 4 years ago

10.1038/s41419-021-03731-7

GIPC2 is an endocrine-specific tumor suppressor gene for both sporadic and hereditary tumors of RET- and SDHB-, but not VHL-associated clusters of pheochromocytoma/paraganglioma
Cited by: 8
Author(s): Yeqing Dong, Yongsheng Huang, Chengyan Fan, Liang Wang, Ran Zhang, Wenhua Li, Zhengguang Guo, Dong Wang, Zhi Zheng
Software Mentions: 3
Published: about 3 years ago

10.3390/microorganisms9050980

Metaproteomics—An Advantageous Option in Studies of Host-Microbiota Interaction
Cited by: 10
Author(s): Oleg Karaduta, Zeljko Dvanajscak, Boris Zybailov
Software Mentions: 3
Published: about 3 years ago

10.1016/j.tcsw.2021.100052

Biochemical and phenotypic characterisation of the Mycobacterium smegmatis transporter UspABC
Cited by: 0
Author(s): Magdalena Karlikowska, Ajit Singh, Apoorva Bhatt, Sascha Ott, Andrew R. Bottrill, Gurdyal S. Besra, Elizabeth Fullam
Software Mentions: 3
Published: over 2 years ago

10.1371/journal.pone.0165504

MALDI-TOF Mass Spectrometry Enables a Comprehensive and Fast Analysis of Dynamics and Qualities of Stress Responses of Lactobacillus paracasei subsp. paracasei F19
Cited by: 10
Author(s): Ann-Sophie Schott, Jürgen Behr, Jennifer J. Quinn, Rudi F. Vogel
Software Mentions: 3
Published: over 7 years ago

10.3390/medicines6030071

Effect of Sulforaphane and 5-Aza-2’-Deoxycytidine on Melanoma Cell Growth
Cited by: 5
Author(s): Tung-Chin Chiang, Brian Koss, L. Joseph Su, Charity L. Washam, Stephanie D. Byrum, Aaron J. Storey, Alan J. Tackett
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.cell.2011.12.029

RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3
Cited by: 504
Author(s): Lígia Tavares, Emilia Dimitrova, David Oxley, Judith Webster, Raymond A. Poot, Jeroen Demmers, Karel Bezstarosti, Stephen Taylor, Hiroki Ura, Hiroshi Koide, Anton Wutz, Miguel Vidal, Sarah Elderkin, Neil Brockdorff
Software Mentions: 3
Published: over 12 years ago

10.1093/molbev/msab103

The Evolution of Calcification in Reef-Building Corals
Cited by: 15
Author(s): Xin Wang, Didier Zoccola, Yi Jin Liew, Éric Tambutté, Guoxin Cui, Denis Allemand, Sylvie Tambutté, Manuel Aranda
Software Mentions: 3
Published: about 3 years ago

10.1186/s12862-020-01734-0

The skeletome of the red coral Corallium rubrum indicates an independent evolution of biomineralization process in octocorals
Cited by: 35
Author(s): Nathalie Le Roy, Philippe Ganot, Manuel Aranda, Denis Allemand, Sylvie Tambutté
Software Mentions: 3
Published: over 3 years ago

10.3390/cells10030646

Identification of Ku70 Domain-Specific Interactors Using BioID2
Cited by: 2
Author(s): Sanna Abbasi, Caroline Schild-Poulter
Software Mentions: 3
Published: about 3 years ago

10.3390/proteomes9010015

Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics
Cited by: 92
Author(s): Benjamin C. Orsburn
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0221669

Cholinergic-like neurons carrying PSEN1 E280A mutation from familial Alzheimer’s disease reveal intraneuronal sAPPβ fragments accumulation, hyperphosphorylation of TAU, oxidative stress, apoptosis and Ca2+ dysregulation: Therapeutic implications
Cited by: 16
Author(s): Viviana Soto-Mercado, Miguel Mendivil-Perez, Carlos Vélez-Pardo, Francisco Lopera, Marlene Jiménez-Del-Río
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0115213

Microtubule-Dependent Modulation of Adhesion Complex Composition
Cited by: 37
Author(s): Daniel Ng, Jonathan D. Humphries, Adam Byron, Angélique Millon‐Frémillon
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0220568

Delineating the role of FANCA in glucose-stimulated insulin secretion in β cells through its protein interactome
Cited by: 6
Author(s): Dragana Lagundžin, Wen Feng Hu, Henry C.-H. Law, Kimiko L. Krieger, Fangfang Qiao, Emalie J. Clement, Andjela Drincic, Olgica Nedić, Michael J. Naldrett, Sophie Alvarez, Nicholas T. Woods
Software Mentions: 2
Published: over 4 years ago

10.1107/S2059798315022482

Initiating heavy-atom-based phasing by multi-dimensional molecular replacement
Cited by: 3
Author(s): Bjørn Panyella Pedersen, Pontus Gourdon, Xiangyu Liu, Jesper Lykkegaard Karlsen, Poul Nissen
Software Mentions: 2
Published: about 8 years ago

10.1186/s12866-019-1387-9

Functional characterization and proteomic analysis of lolA in Xanthomonas campestris pv. campestris
Cited by: 14
Author(s): Chao‐Tsai Liao, Ying-Chuan Chiang, Yi‐Min Hsiao
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0188105

Profiling of proteins secreted in the bovine oviduct reveals diverse functions of this luminal microenvironment
Cited by: 36
Author(s): Viju Vijayan Pillai, Darren Weber, Brett S. Phinney, Vimal Selvaraj
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0215267

Muscle fiber hypertrophy in response to 6 weeks of high-volume resistance training in trained young men is largely attributed to sarcoplasmic hypertrophy
Cited by: 52
Author(s): Cody T. Haun, Christopher G. Vann, Shelby C. Osburn, Petey W. Mumford, Paul A. Roberson, Matthew A. Romero, Carlton D. Fox, Christopher Johnson, Hailey A. Parry, Andreas N. Kavazis, Jordan R. Moon, Veera L.D. Badisa, Benjamin M. Mwashote, Victor Ibeanusi, Kaelin C. Young, Michael D. Roberts
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0140650

Sperm Proteome Maturation in the Mouse Epididymis
Cited by: 83
Author(s): Sheri Skerget, Matthew Rosenow, Konstantinos Pétritis, Timothy L. Karr
Software Mentions: 2
Published: over 8 years ago

10.1002/acn3.51242

Elevated levels of extracellular vesicles in progranulin‐deficient mice and FTD‐ GRN Patients
Cited by: 7
Author(s): Andrew E. Arrant, Skylar E. Davis, Rachael M Vollmer, Charles Murchison, James A. Mobley, Alissa L. Nana, Salvatore Spina, Lea T. Grinberg, Anna Karydas, Bruce L. Miller, William W. Seeley, Erik D. Roberson
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0028532

Conserved BK Channel-Protein Interactions Reveal Signals Relevant to Cell Death and Survival
Cited by: 38
Author(s): Bernd Sokolowski, Sandra Orchard, Margaret Harvey, Settu Sridhar, Yoshihisa Sakai
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-021-07758-0

Integrated proteomic and transcriptomic profiling identifies aberrant gene and protein expression in the sarcomere, mitochondrial complex I, and the extracellular matrix in Warmblood horses with myofibrillar myopathy
Cited by: 8
Author(s): Zoë J. Williams, Deborah Velez‐Irizarry, Keri Gardner, Stephanie J. Valberg
Software Mentions: 2
Published: almost 3 years ago

10.1186/1471-2164-15-306

Proteomic analysis of Daphnia magna hints at molecular pathways involved in defensive plastic responses
Cited by: 35
Author(s): Kerstin Otte, Thomas Fröhlich, Georg J. Arnold, Christian Laforsch
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2407-11-368

Purine Nucleoside Phosphorylase mediated molecular chemotherapy and conventional chemotherapy: A tangible union against chemoresistant cancer
Cited by: 11
Author(s): Preetinder Singh, Swapna Joshi, Pamela J. Russell, Sham V. Nair, Aparajita Khatri
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-019-6194-z

The olfactory secretome varies according to season in female sheep and goat
Cited by: 7
Author(s): P A Cann, Malika Chabi, Aliénor Delsart, Chrystelle Le Danvic, Jean‐Michel Saliou, Manon Chasles, Matthieu Keller, Patricia Nagnan‐Le Meillour
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0218360

Candida utilis yeast as a functional protein source for Atlantic salmon (Salmo salar L.): Local intestinal tissue and plasma proteome responses
Cited by: 14
Author(s): Felipe Eduardo Reveco-Urzua, Mette Hofossæter, Mallikarjuna Rao Kovi, Liv Torunn Mydland, Ragnhild Ånestad, Randi Sørby, Charles McL. Press, Leidy Lagos, Margareth Øverland
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0228134

Proteomic profiling of proteins in the dorsal horn of the spinal cord in dairy cows with chronic lameness
Cited by: 2
Author(s): Daniel Herzberg, Pablo Strobel, Heine Yacob Müller, Constanza Meneses, Mads Werner, Hedie Bustamante
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0136362

Proteins with Intrinsically Disordered Domains Are Preferentially Recruited to Polyglutamine Aggregates
Cited by: 30
Author(s): Maggie P. Wear, Dmitry Kryndushkin, Robert N. O’Meally, Jason L. Sonnenberg, Robert N. Cole, Frank Shewmaker
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0007050

Barrier-to-Autointegration Factor Proteome Reveals Chromatin-Regulatory Partners
Cited by: 93
Author(s): Rocío Montes de, Christopher J. Shoemaker, Marjan Guček, Robert N. Cole, Katherine L. Wilson
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0028949

Proteome Changes Driven by Phosphorus Deficiency and Recovery in the Brown Tide-Forming Alga Aureococcus anophagefferens
Cited by: 60
Author(s): Louie L. Wurch, Erin M. Bertrand, Mak A. Saito, Benjamin A. S. Van Mooy, Sonya T. Dyhrman
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0064044

Urine Proteins Identified by Two-Dimensional Differential Gel Electrophoresis Facilitate the Differential Diagnoses of Scrapie
Cited by: 9
Author(s): Lise Lamoureux, Sharon L R Simon, Margot Plews, Viola Ruddat, Simone Brunet, Catherine Graham, Stefanie Czub, J. David Knox
Software Mentions: 2
Published: almost 11 years ago

10.3390/cancers6031464

Phosphorylation of Large T Antigen Regulates Merkel Cell Polyomavirus Replication
Cited by: 19
Author(s): José Ángel Menéndez Díaz, Xin Wang, Sabrina H. Tsang, Jing Jiao, Jianxin You
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-019-5981-x

Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits
Cited by: 14
Author(s): Jitao Li, Jianjian Lv, Ping Liu, Ping Chen, Jiajia Wang, Jian Li
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0134014

Flux Balance Analysis with Objective Function Defined by Proteomics Data—Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine
Cited by: 21
Author(s): Daniel Montezano, Laura Meek, Rashmi Gupta, Luiz E. Bermudez, J.C.M. Bermudez
Software Mentions: 2
Published: almost 9 years ago