pypi: Scaffold | Projects | Ecosyste.ms: Papers

10.7554/eLife.53375

Integrated analysis of H2A.Z isoforms function reveals a complex interplay in gene regulation
Cited by: 29
Author(s): Assala Lamaa, Jonathan Humbert, Marion Aguirrebengoa, Xue Cheng, Estelle Nicolas, Jacques Côté, Didier Trouche
Software Mentions: 3
Published: over 5 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: over 4 years ago

10.7554/eLife.54812

CB1-receptor-mediated inhibitory LTD triggers presynaptic remodeling via protein synthesis and ubiquitination
Cited by: 16
Author(s): Hannah R. Monday, Mathieu Bourdenx, Bryen A. Jordan, Pablo E. Castillo
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms141020658

Absolute Quantification of Selected Proteins in the Human Osteoarthritic Secretome
Cited by: 44
Author(s): Mandy J. Peffers, Robert J. Beynon, Peter Clegg
Software Mentions: 3
Published: about 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: over 4 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: over 9 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: over 8 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: about 8 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: about 7 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: almost 14 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: over 5 years ago

10.7554/eLife.22693

The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels
Cited by: 77
Author(s): A. J. Miles, Stephen P. Burr, GL Grice, James A. Nathan
Software Mentions: 3
Published: over 8 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: almost 5 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: almost 6 years ago

10.7554/eLife.58362

Structural basis of mitochondrial translation
Cited by: 61
Author(s): Shintaro Aibara, Vivek P. Singh, A. Modelska, Alexey Amunts
Software Mentions: 3
Published: about 5 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: almost 7 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: over 7 years ago

10.7554/eLife.28270

Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition
Cited by: 42
Author(s): Vivek Mahadevan, C. Sahara Khademullah, Zahra Dargaei, Jonah Chevrier, Pavel Uvarov, Julian Kwan, Richard D. Bagshaw, Tony Pawson, Andrew Emili, Yves De Koninck, Victor Anggono, Matti S. Airaksinen, Melanie A. Woodin
Software Mentions: 3
Published: about 8 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: about 7 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: almost 7 years ago

10.7554/eLife.62621

miR-125-chinmo pathway regulates dietary restriction-dependent enhancement of lifespan in Drosophila
Cited by: 12
Author(s): Manish Pandey, Sakshi Bansal, Sudipta Bar, Amit Kumar Yadav, Nicholas S. Sokol, Jason M. Tennessen, Pankaj Kapahi, Geetanjali Chawla
Software Mentions: 3
Published: over 4 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: almost 18 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: about 9 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: over 8 years ago

10.1186/s13321-017-0212-4

Comparative analyses of structural features and scaffold diversity for purchasable compound libraries
Cited by: 24
Author(s): Jun Shang, Huiyong Sun, Hui Liu, Chen Fu, Sheng Tian, Peichen Pan, Dan Li, De-Xin Kong, Tingjun Hou
Software Mentions: 3
Published: over 8 years ago

10.1016/j.jbc.2021.100456

Binding of Gtf2i-β/δ transcription factors to the ARMS2 gene leads to increased circulating HTRA1 in AMD patients and in vitro
Cited by: 6
Author(s): Yang Pan, Daisuke Iejima, Mao Nakayama, Akiko Suga, Tomoyuki Noda, Inderjeet Kaur, Taraprasad Das, Subhabrata Chakrabarti, Robyn H. Guymer, Margaret M. DeAngelis, Megumi Yamamoto, Paul N. Baird, Takeshi Iwata
Software Mentions: 3
Published: almost 5 years ago

10.1093/gigascience/giaa050

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome
Cited by: 64
Author(s): Annarita Marrano, Monica Britton, Paulo A. Zaini, Aleksey V. Zimin, Rachael E. Workman, Daniela Puiu, Luca Bianco, Erica A. Di Pierro, Brian Allen, Sandeep Chakraborty, Michela Troggio, Charles A. Leslie, Winston Timp, Abhaya M. Dandekar, Steven L. Salzberg, David B. Neale
Software Mentions: 3
Published: over 5 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: over 14 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: about 4 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: over 8 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: almost 5 years ago

10.1080/21505594.2017.1325064

Signatures of cytoplasmic proteins in the exoproteome distinguish community- and hospital-associated methicillin-resistantStaphylococcus aureusUSA300 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: over 8 years ago

10.1186/s13073-015-0208-5

Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance
Cited by: 74
Author(s): William R. Swindell, Henriette A. Remmer, Mrinal K. Sarkar, Xianying Xing, Drew H. Barnes, Liza Wolterink, John J. Voorhees, Rajan P. Nair, Andrew Johnston, James T. Elder, Jóhann E. Guðjónsson
Software Mentions: 3
Published: about 10 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: over 9 years ago

10.3390/genes10070522

Sperm Proteome Analysis and Identification of Fertility-Associated Biomarkers in Unexplained Male Infertility
Cited by: 36
Author(s): Manesh Kumar Panner Selvam, Ashok Agarwal, Peter Natesan Pushparaj, Saradha Baskaran, Hocine Bendou
Software Mentions: 3
Published: over 6 years ago

10.1111/mmi.14398

Protein kinase B controls Mycobacterium tuberculosis 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: about 6 years ago

10.1093/gigascience/giz070

Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome
Cited by: 42
Author(s): Quanxin Bi, Yang Zhao, Wei Du, Ying Lu, Gui Liu, Zhimin Zheng, Haiyan Yu, Yubo Cui, Zhi Liu, Tianpeng Cui, Deshi Cui, Xiaojuan Liu, Yingchao Li, Fan Siqi, Xiaoyu Hu, Guanghui Fu, Jian Ding, Chengjiang Ruan, Libing Wang
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): BenoÃ®t. 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: over 8 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: over 5 years ago

10.3389/fmicb.2019.00127

The Selection of a Hepatocyte Cell Line Susceptible to Plasmodium falciparum Sporozoite Invasion That Is Associated With Expression of Glypican-3
Cited by: 13
Author(s): Rebecca E. Tweedell, Dingyin Tao, Timothy Hamerly, Tanisha M. Robinson, Simon J. Larsen, Alexander G B Grønning, Alessandra M. Norris, J. W. B. King, Henry C.-H. Law, Jan Baumbach, Elke S. Bergmann‐Leitner, Rhoel R. Dinglasan
Software Mentions: 3
Published: over 6 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: over 6 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: about 6 years ago

10.3389/fmicb.2018.02371

A Metabolic Labeling Strategy for Relative Protein Quantification in Clostridioides difficile
Cited by: 4
Author(s): Anke Trautwein-Schult, Sandra Maaß, Kristina Plate, Andreas Otto, Dörte Becher
Software Mentions: 3
Published: about 7 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: almost 5 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 5 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: over 4 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: over 4 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: about 4 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: over 5 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: about 9 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: over 6 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: almost 14 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: over 4 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: almost 5 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: over 5 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: almost 5 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: over 10 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: almost 10 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: about 9 years ago

10.1371/journal.ppat.1001328

A Novel Toxoplasma gondii Nuclear Factor TgNF3 Is a Dynamic Chromatin-Associated Component, Modulator of Nucleolar Architecture and Parasite Virulence
Cited by: 36
Author(s): Alejandro Olguin-Lamas, Edwige Madec, Agnès Hovasse, Elisabeth Werkmeister, Isabelle Callebaut, Christian Slomianny, Stéphane Delhaye, Thomas Mouveaux, Christine Schaeffer-Reiss, Alain Van Dorsselaer, Stanislas Tomavo
Software Mentions: 3
Published: over 14 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: about 8 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: over 4 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: over 4 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: about 4 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: almost 12 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: almost 4 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: almost 5 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: about 6 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: over 8 years ago

10.1128/mBio.02048-16

Making Home Sweet and Sturdy:Toxoplasma gondiippGalNAc-Ts Glycosylate in Hierarchical Order and Confer Cyst Wall Rigidity
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Author(s): Tadakimi Tomita, Tatsuki Sugi, Rama R. Yakubu, Vincent Tu, Yanfen Ma, Louis M. Weiss
Software Mentions: 3
Published: over 8 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: about 8 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: about 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: over 5 years ago

10.3390/proteomes9010015

Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics
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Author(s): Benjamin C. Orsburn
Software Mentions: 3
Published: over 4 years ago

10.1093/dnares/dsy044

A unique life-strategy of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1—a comparative genomics viewpoint
Cited by: 24
Author(s): Diya Sen, Karnelia Paul, Chinmay Saha, G. N. Mukherjee, Mayurakshi Nag, Samrat Ghosh, A. K. Das, A. Seal, Sucheta Tripathy
Software Mentions: 3
Published: almost 7 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: 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: about 6 years ago

10.3390/proteomes7020014

Extracellular Vesicle Integrins Distinguish Unique Cancers
Cited by: 43
Author(s): Stephanie N. Hurwitz, David G. Meckes
Software Mentions: 2
Published: over 6 years ago

10.3389/fbioe.2020.00882

Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems
Cited by: 26
Author(s): K. M. Shakirova, Viktoriia Y. Ovchinnikova, Э. Б. Дашинимаев
Software Mentions: 2
Published: over 5 years ago

10.1186/s12014-019-9228-2

Rapid detection of colistin resistance protein MCR-1 by LC–MS/MS
Cited by: 11
Author(s): Honghui Wang, Yong Chen, Jeffrey R Strich, Steven K. Drake, Jung Ho Youn, Avi Z. Rosenberg, Marjan Guček, Patrick T. McGann, Anthony F. Suffredini, John P. Dekker
Software Mentions: 2
Published: over 6 years ago

10.1016/j.dib.2020.106064

Tandem mass tagged dataset used to characterize muscle-specific proteome changes in beef during early postmortem period
Cited by: 2
Author(s): Chaoyu Zhai, B. A. Djimsa, Kitty Brown, Jessica E. Prenni, D. R. Woerner, K. E. Belk, Mahesh N. Nair
Software Mentions: 2
Published: about 5 years ago

10.3390/cells7120269

Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress
Cited by: 15
Author(s): Meenakshi Agarwal, Ashish Pathak, Rajesh Rathore, Om Prakash, Rakesh Singh, Rajneesh Jaswal, John C. Seaman, Ashvini Chauhan
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.redox.2019.101265

Oxygen-dependent bond formation with FIH regulates the activity of the client protein OTUB1
Cited by: 13
Author(s): Christina Pickel, Julia Günter, Amalia Ruiz-Serrano, Patrick Spielmann, Jacqueline-Alba Fabrizio, Witold Wolski, Daniel J. Peet, Roland H. Wenger, Carsten C. Scholz
Software Mentions: 2
Published: about 6 years ago

10.1038/s42003-021-02214-x

Placental secretome characterization identifies candidates for pregnancy complications
Cited by: 16
Author(s): Tina Napso, Xiaohui Zhao, Marta Ibañez-Lligoña, Ionel Sandovici, Richard G. Kay, Amy L. George, Fiona M. Gribble, Frank Reimann, Claire L Meek, Russell S. Hamilton, Amanda N. Sferruzzi‐Perri
Software Mentions: 2
Published: over 4 years ago

10.1016/j.celrep.2021.109230

Integrin intra-heterodimer affinity inversely correlates with integrin activatability
Cited by: 11
Author(s): Guangyu Sun, Emilie Guillon, Scott A. Holley
Software Mentions: 2
Published: over 4 years ago

10.1186/s13072-016-0087-z

Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers
Cited by: 23
Author(s): Jian Sun, Yilin Zhao, Rebecca McGreal, Yamit Cohen‐Tayar, Shira Rockowitz, Carola Wilczek, Ruth Ashery‐Padan, David Shechter, Deyou Zheng, Aleš Cvekl
Software Mentions: 2
Published: about 9 years ago

10.1111/1462-2920.13930

Transcriptome and proteome dynamics in chemostat culture reveal howCampylobacter jejunimodulates metabolism, stress responses and virulence factors upon changes in oxygen availability
Cited by: 28
Author(s): Edward Guccione, John J. Kendall, Andrew Hitchcock, Nitanshu Garg, Michael A. White, Francis Mulholland, Robert K. Poole, David J. Kelly
Software Mentions: 2
Published: about 8 years ago

10.1128/mBio.01137-19

Identification of Extracellular DNA-Binding Proteins in the Biofilm Matrix
Cited by: 89
Author(s): J.S. Kavanaugh, Caralyn E. Flack, Jessica Lister, Erica B. Ricker, Carolyn B. Ibberson, Christian Jenul, Derek E. Moormeier, Elizabeth Delmain, Kenneth W. Bayles, Alexander R. Horswill
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1005640

Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus Colletotrichum higginsianum
Cited by: 71
Author(s): Sonia Campo, Kerrigan B. Gilbert, James C. Carrington
Software Mentions: 2
Published: over 9 years ago

10.1128/mSphere.00135-17

Heparin Mimics Extracellular DNA in Binding to Cell Surface-Localized Proteins and Promoting Staphylococcus aureus Biofilm Formation
Cited by: 31
Author(s): Sharad Mishra, Alexander R. Horswill
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-021-89907-9

Continual proteomic divergence of HepG2 cells as a consequence of long-term spheroid culture
Cited by: 2
Author(s): Andrea Antonio Ellero, Iman van den Bout, Maré Vlok, Allan Duncan Cromarty, Tracey Hurrell
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-66286-1

A new brilliantly blue-emitting luciferin-luciferase system from Orfelia fultoni and Keroplatinae (Diptera)
Cited by: 16
Author(s): Vadim R. Viviani, Jaqueline R. Silva, Danilo T. Amaral, Vanessa R. Bevilaqua, Fábio Camargo Abdalla, Bruce R. Branchini, Carl Hirschie Johnson
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-76052-y

Human perinatal stem cell derived extracellular matrix enables rapid maturation of hiPSC-CM structural and functional phenotypes
Cited by: 21
Author(s): Travis J. Block, Jeffery Creech, A.M. Rocha, Milos Marinkovic, Daniela Ponce-Balbuena, Eric N. Jiménez-Vázquez, Sy Griffey, Todd J. Herron
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.ppat.1008307

An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing
Cited by: 7
Author(s): Raymond Wong, Ahalya Balachandran, Peter K. Cheung, Ran Cheng, Qun Pan, Peter Stoilov, P. Richard Harrigan, Benjamin J. Blencowe, Donald R. Branch, Alan Cochrane
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009506

The antiviral sirtuin 3 bridges protein acetylation to mitochondrial integrity and metabolism during human cytomegalovirus infection
Cited by: 16
Author(s): Xuanyu Sheng, Ileana M. Cristea
Software Mentions: 2
Published: over 4 years ago

10.1002/2211-5463.12997

Cystatin C regulates the cytotoxicity of infection‐induced endothelial‐derived β‐amyloid
Cited by: 2
Author(s): Ron Balczon, K. Adam Morrow, Silas J. Leavesley, C.M. Francis, T. Stevens, Ezinne Agwaramgbo, Christopher Williams, R.P. Stevens, Geri Langham, S.B. Voth, Eugene A. Cioffi, Susan E Weintraub, Troy Stevens
Software Mentions: 2
Published: about 5 years ago

10.3390/proteomes7010010

Comparative Proteomic Analysis Unveils Critical Pathways Underlying the Role of Nitrogen Fertilizer Treatment in American Elderberry
Cited by: 1
Author(s): Bo Yang, Andrew L. Thomas, C. Michael Greenlief
Software Mentions: 2
Published: over 6 years ago

10.1186/1477-5956-7-9

A novel approach to denoising ion trap tandem mass spectra
Cited by: 27
Author(s): Jiarui Ding, Jinhong Shi, Guy G. Poirier, Fang‐Xiang Wu
Software Mentions: 2
Published: over 16 years ago

10.3390/cells9061423

Chromatin Trapping of Factors Involved in DNA Replication and Repair Underlies Heat-Induced Radio- and Chemosensitization
Cited by: 3
Author(s): Artem V. Luzhin, Bogdan Avanesyan, Artem K. Velichko, Victoria О. Shender, Natalia Ovsyannikova, Georgij Arapidi, Polina V. Shnaider, Nadezhda V. Petrova, Igor I. Kireev, Sergey V. Razin, Omar L. Kantidze
Software Mentions: 2
Published: over 5 years ago

10.15252/embj.201798714

Evidence for the nuclear import of histones H3.1 and H4 as monomers
Cited by: 39
Author(s): Michael James Apta‐Smith, Juan R. Hernández-Fernaud, Andrew Bowman
Software Mentions: 2
Published: about 7 years ago

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