pypi: Scaffold | Projects | Ecosyste.ms: Papers

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 7 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 8 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 4 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: over 13 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 11 years ago

10.3390/ijms21010179

Analysis of the Barley Malt Rootlet Proteome
Cited by: 8
Author(s): Ramamurthy Mahalingam
Software Mentions: 3
Published: almost 5 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 7 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: over 4 years ago

10.1128/mBio.02048-16

Making Home Sweet and Sturdy:Toxoplasma gondiippGalNAc-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: over 7 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 11 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 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: 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 3 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 4 years ago

10.1002/pmic.202000319

DDASSQ: An open‐source, multiple peptide sequencing strategy for label free quantification based on an OpenMS pipeline in the KNIME analytics platform
Cited by: 5
Author(s): M. Svecla, G Garrone, Fiorenza Farè, Giacomo Aletti, Giuseppe Danilo Norata, Giangiacomo Beretta
Software Mentions: 3
Published: over 3 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 4 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 13 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: 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: almost 4 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: over 3 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 4 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: over 4 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 3 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 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: almost 9 years ago

10.7717/peerj.4691

Sexually dimorphic venom proteins in long-jawed orb-weaving spiders (Tetragnatha) comprise novel gene families
Cited by: 18
Author(s): Pamela A. Zobel-Thropp, Emily A. Bulger, Matthew Cordes, Greta J. Binford, Rosemary G. Gillespie, Michael S. Brewer
Software Mentions: 3
Published: over 6 years ago

10.3390/pathogens9020131

Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy
Cited by: 9
Author(s): Julia Bespyatykh, Egor Shitikov, Dmitry Bespiatykh, Andrei Guliaev, Ksenia M. Klimina, Vladimir A. Veselovsky, Georgij Arapidi, Marine Dogonadze, Viacheslav Zhuravlev, Elena Ilina, Vadim M. Govorun
Software Mentions: 3
Published: almost 5 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 5 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 4 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 7 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: over 9 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 8 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 5 years ago

10.1371/journal.pone.0209856

BioID identifies proteins involved in the cell biology of caveolae
Cited by: 6
Author(s): Carolina Mendoza-Topaz, Ivana Yeow, Kirsi Riento, Benjamin J. Nichols
Software Mentions: 3
Published: almost 6 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: over 12 years ago

10.1186/s13059-015-0696-z

FOXM1 binds directly to non-consensus sequences in the human genome
Cited by: 47
Author(s): Deborah A. Sanders, Michael V. Gormally, Giovanni Marsico, Dario Beraldi, David Tannahill, Shankar Balasubramanian
Software Mentions: 3
Published: over 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 13 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 7 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 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: over 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: about 5 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 5 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 4 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: almost 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 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: over 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: almost 3 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 8 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 5 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 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 13 years ago

10.1074/mcp.RA117.000445

Infection by the Helminth Parasite Fasciola hepatica Requires Rapid Regulation of Metabolic, Virulence, and Invasive Factors to Adjust to Its Mammalian Host
Cited by: 70
Author(s): Krystyna Cwiklinski, Heather Jewhurst, Paul McVeigh, Tara Barbour, Aaron G. Maule, José F. Tort, Sandra M. O’Neill, Mark W. Robinson, Sheila Donnelly, John P. Dalton
Software Mentions: 3
Published: over 6 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 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: almost 4 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 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: over 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: almost 17 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 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 5 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 6 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 5 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 5 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: over 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: over 7 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 7 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 4 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 7 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: over 3 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 4 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 6 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 8 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: about 6 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 6 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 7 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 6 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 6 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: almost 6 years ago

10.3389/fmicb.2019.02708

Vesicles From Vibrio cholerae Contain AT-Rich DNA and Shorter mRNAs That Do Not Correlate With Their Protein Products
Cited by: 15
Author(s): Petter Langlete, Anders K. Krabberød, Hanne C. Winther‐Larsen
Software Mentions: 2
Published: almost 5 years ago

10.1111/jnc.14845

NYX‐2925 induces metabotropicN‐methyl‐<scp>d</scp>‐aspartate receptor (NMDAR) signaling that enhances synaptic NMDAR and α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid receptor
Cited by: 6
Author(s): M. Scott Bowers, Luisa P. Cacheaux, Srishti U. Sahu, Matthew Schmidt, Joseph A. Sennello, Katherine Leaderbrand, M. Amin Khan, Roger A. Kroes, Joseph R. Moskal
Software Mentions: 2
Published: about 5 years ago

10.1186/1866-1955-6-36

PreImplantation factor (PIF*) promotes embryotrophic and neuroprotective decidual genes: effect negated by epidermal growth factor
Cited by: 17
Author(s): Christina M. Duzyj, Michael J. Paidas, Lellean JeBailey, Jing Huang, Eytan R. Barnea
Software Mentions: 2
Published: about 10 years ago

10.3389/fmicb.2017.01772

Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling
Cited by: 21
Author(s): Sergio Triana, Hans de Cock, Robin A. Ohm, Giovanna Danies, Han A. B. Wösten, Silvia Restrepo, Andrés Fernando González Barrios, Adriana Celis
Software Mentions: 2
Published: about 7 years ago

10.1186/1479-5876-10-35

Hyperglycemic conditions inhibit C3-mediated immunologic control of Staphylococcus aureus
Cited by: 37
Author(s): Pamela S. Hair, Charlene G. Echague, Reuben D. Rohn, Neel K. Krishna, Julius O. Nyalwidhe, Kenji M. Cunnion
Software Mentions: 2
Published: over 12 years ago

10.3389/fmicb.2018.00755

The Membrane-Bound C Subunit of Reductive Dehalogenases: Topology Analysis and Reconstitution of the FMN-Binding Domain of PceC
Cited by: 19
Author(s): Géraldine Florence Buttet, Mathilde Stéphanie Willemin, Romain Hamelin, Aamani Rupakula, Julien Maillard
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2019.00384

Mixotrophic Growth Under Micro-Oxic Conditions in the Purple Sulfur Bacterium “Thiodictyon syntrophicum”
Cited by: 14
Author(s): Samuel M. Luedin, Nicola Storelli, Francesco Danza, Samuele Roman, Matthias Wittwer, Joël F. Pothier, Mauro Tonolla
Software Mentions: 2
Published: over 5 years ago

10.3389/fcell.2020.00700

Tubular ER Associates With Diacylglycerol-Rich Structures During Lipid Droplet Consumption
Cited by: 4
Author(s): Suriakarthiga Ganesan, Marjan Tavassoli, Brittney Shabits, Vanina Zaremberg
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2020.01227

Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class “Acidobacteriia”
Cited by: 14
Author(s): Ohana Y.A. Costa, Chidinma Oguejiofor, Daniela Zühlke, Cristine Chaves Barreto, Christine Wünsche, Katharina Riedel, Eiko E. Kuramae
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-017-06680-4

Mass spectrometry-based determination of Kallikrein-related peptidase 7 (KLK7) cleavage preferences and subsite dependency
Cited by: 5
Author(s): Lakmali Munasinghage Silva, Thomas Stoll, Thomas Kryza, Carson Stephens, Marcus L. Hastie, Helen F. Irving-Rodgers, Ying Dong, Jeffrey J. Gorman, Judith A. Clements
Software Mentions: 2
Published: over 7 years ago

10.3389/fcimb.2021.724569

An Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis Sputum
Cited by: 6
Author(s): Alexander C. Graf, Johanna Striesow, Jan Pané‐Farré, Thomas Sura, Martina Wurster, Michael Lalk, Dietmar H. Pieper, Dörte Becher, Barbara C. Kahl, Katharina Riedel
Software Mentions: 2
Published: about 3 years ago

10.18632/oncotarget.14272

CD147: a small molecule transporter ancillary protein at the crossroad of multiple hallmarks of cancer and metabolic reprogramming
Cited by: 34
Author(s): Agnieszka A. Kendrick, Johnathon Schafer, Monika Dzieciątkowska, Travis Nemkov, Angelo D’Alessandro, Deepika Neelakantan, Heide L. Ford, Chad G. Pearson, Colin D. Weekes, Kirk C. Hansen, Elan Eisenmesser
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2020.00448

Combination Analysis of Metatranscriptome and Metagenome Reveal the Composition and Functional Response of Coral Symbionts to Bleaching During an El Niño Event
Cited by: 9
Author(s): Fu-Lin Sun, Hongqiang Yang, Guan Wang, Quan Shi
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2018.00818

Proteomic Profiling and Epitope Analysis of the Complex α-, γ-, and ω-Gliadin Families in a Commercial Bread Wheat
Cited by: 12
Author(s): Kyoungwon Cho, Hye-Rang Beom, You-Ran Jang, Susan B. Altenbach, William H. Vensel, Annamaria Simon-Buss, Sung-Hun Lim, Min Kim, Jong-Yeol Lee
Software Mentions: 2
Published: over 6 years ago

10.3389/fevo.2019.00085

Alternative Transcription at Venom Genes and Its Role as a Complementary Mechanism for the Generation of Venom Complexity in the Common House Spider
Cited by: 13
Author(s): Robert A. Haney, Taylor Matte, FitzAnthony S. Forsyth, Jessica E. Garb
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-38492-z

Animal species identification in parchments by light
Cited by: 8
Author(s): Ángel Martín Fernández Alvarez, Julie Bouhy, Marc Dieu, Cathérine Charles, Olivier Deparis
Software Mentions: 2
Published: almost 6 years ago

10.3389/fnmol.2018.00243

Use of Proteomic Imaging Coupled With Transcriptomic Analysis to Identify Biomolecules Responsive to Cochlear Injury
Cited by: 2
Author(s): Kenyaria V. Noble, Michelle L. Reyzer, Jeremy L. Barth, Hayes McDonald, Michael Tuck, Kevin L. Schey, Edward L. Krug, Hainan Lang
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.16835

Upregulation of minichromosome maintenance complex component 3 during epithelial-to-mesenchymal transition in human prostate cancer
Cited by: 25
Author(s): Paul A. Stewart, Zahraa I. Khamis, Haiyen E. Zhau, Peng Duan, Quan‐Lin Li, Leland W.K. Chung, Qing‐Xiang Amy Sang
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2017.01134

Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode
Cited by: 13
Author(s): Fan Lin, Brad J. Williams, Padmavathi A V Thangella, Adam Ladak, Athena Schepmoes, Hernando J. Olivos, Kangmei Zhao, Stephen Callister, Laura E. Bartley
Software Mentions: 2
Published: over 7 years ago

10.3389/fcell.2020.616706

Identification of the Myogenetic Oligodeoxynucleotides (myoDNs) That Promote Differentiation of Skeletal Muscle Myoblasts by Targeting Nucleolin
Cited by: 11
Author(s): Sayaka Shinji, Koji Umezawa, Yuma Nihashi, Shun‐ichi Nakamura, Takeshi Shimosato, Tomohide Takaya
Software Mentions: 2
Published: almost 4 years ago

10.3389/fpls.2019.01657

A LysR-Type Transcriptional Regulator LcrX Is Involved in Virulence, Biofilm Formation, Swimming Motility, Siderophore Secretion, and Growth in Sugar Sources in Xanthomonas axonopodis Pv. glycines
Cited by: 14
Author(s): Hanbi Park, Eunsoo Do, Minyoung Kim, Hye-Jee Park, Jong-Chan Lee, Sang-Wook Han
Software Mentions: 2
Published: almost 5 years ago

10.3389/fneur.2018.00465

Environmental Enrichment Upregulates Striatal Synaptic Vesicle-Associated Proteins and Improves Motor Function
Cited by: 6
Author(s): Suk Young Song, Minji Chae, Ji Hea Yu, Min Young Lee, Soonil Pyo, Yeseul Shin, Ahreum Baek, Jung Won Park, Eun Sook Park, Ja Young Choi, Sung Rae Cho
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2014.00067

Pancreatic Cancer Cells Isolated from Muc1-Null Tumors Favor the Generation of a Mature Less Suppressive MDSC Population
Cited by: 11
Author(s): Amritha Kidiyoor, Jorge Schettini, Dahlia M. Besmer, Stephen L. Rego, Sritama Nath, Jennifer M. Curry, Lopamudra Das Roy, Didier Dréau, Pinku Mukherjee
Software Mentions: 2
Published: almost 11 years ago

Projects: pypi: Scaffold

Papers Mentioning Scaffold 1,866