pypi: Scaffold | Projects | Ecosyste.ms: Papers

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

10.3390/ijms21031074

An Isolated Complex V Inefficiency and Dysregulated Mitochondrial Function in Immortalized Lymphocytes from ME/CFS Patients
Cited by: 48
Author(s): Daniel Missailidis, Sarah J. Annesley, Claire Y. Allan, Oana Sanislav, Brett A. Lidbury, Donald P. Lewis, Paul R. Fisher
Software Mentions: 3
Published: over 5 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 4 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: about 13 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: almost 5 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: almost 8 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: almost 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 11 years ago

10.7554/eLife.28482

A comprehensive analysis of coregulator recruitment, androgen receptor function and gene expression in prostate cancer
Cited by: 44
Author(s): Song Liu, Sangeeta Kumari, Qiang Hu, Dhirodatta Senapati, Varadha Balaji Venkadakrishnan, Dan Wang, Adam DePriest, Simon Schlanger, Salma Ben-Salem, Malyn May Asuncion Valenzuela, Belinda Willard, Shaila Mudambi, Wendy M. Swetzig, Gokul M. Das, Mojgan Shourideh, Shahriah Koochekpour, Sara M. Falzarano, Cristina Magi‐Galluzzi, Neelu Yadav, Xiwei Chen, Changshi Lao, Jianmin Wang, Jean Noël Billaud, Hannelore V. Heemers
Software Mentions: 3
Published: almost 8 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: over 6 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 12 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

10.7554/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: about 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: almost 9 years ago

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

10.3390/ijms21030965

The Cannabis Proteome Draft Map Project
Cited by: 13
Author(s): Conor Jenkins, Benjamin C. Orsburn
Software Mentions: 3
Published: over 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: over 6 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: 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: 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: about 8 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: over 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: over 5 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

10.1080/21505594.2017.1325064

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: about 8 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: 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 9 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: almost 7 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: almost 6 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

10.1093/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: about 5 years ago

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: over 10 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: over 4 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: almost 9 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: about 10 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: almost 10 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: almost 6 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: about 6 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 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: over 5 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 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: almost 8 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: almost 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: about 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 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: over 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: almost 5 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 4 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: almost 8 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: over 6 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 4 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 13 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 9 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 8 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 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: about 5 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 8 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 11 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 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 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 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: almost 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 4 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: almost 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: about 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

10.1371/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

10.3390/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 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: about 8 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

10.1371/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: about 13 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

10.1371/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 9 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 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: about 4 years ago

10.3389/fmicb.2018.02371

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

10.1371/journal.pone.0211582

A rapid methods development workflow for high-throughput quantitative proteomic applications
Cited by: 16
Author(s): Yan Chen, Jonathan T. Vu, Mitchell G. Thompson, William A. Sharpless, Leanne Jade G. Chan, Jennifer Gin, Jay D. Keasling, Paul D. Adams, Young-Mo Kim
Software Mentions: 3
Published: over 6 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: about 5 years ago

10.3389/fimmu.2017.00358

Human Melanoma-Derived Extracellular Vesicles Regulate Dendritic Cell Maturation
Cited by: 44
Author(s): Rachel L.G. Maus, James W. Jakub, Wendy K. Nevala, Trace Christensen, Klara E. Noble-Orcutt, Zohar Sachs, Tina J. Hieken, Svetomir N. Markovic
Software Mentions: 2
Published: over 8 years ago

10.1038/s41419-021-03589-9

Non-canonical role of wild-type SEC23B in the cellular stress response pathway
Cited by: 3
Author(s): Lamis Yehia, Darren Liu, Shuai Fu, Pranav Iyer, Charis Eng
Software Mentions: 2
Published: over 4 years ago

10.1038/s41419-018-0423-2

A multi-omic analysis reveals the role of fumarate in regulating the virulence of enterohemorrhagic Escherichia coli
Cited by: 20
Author(s): Chengi Kuo, Sin Tian Wang, Chia Mei Lin, Hao-Chieh Chiu, Cheng Huang, Der Yen Lee, Geen Dong Chang, Tse‐Chuan Chou, Jenn Wei Chen, Chang Shi Chen
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.00330

Transcriptional and Proteomic Choreography Under Phosphorus Deficiency and Re-supply in the N2 Fixing Cyanobacterium Trichodesmium erythraeum
Cited by: 11
Author(s): Kyle R. Frischkorn, Sheean T. Haley, Sonya T. Dyhrman
Software Mentions: 2
Published: over 6 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 9 years ago

10.3389/fmed.2017.00080

Assessment of Circulating Protein Signatures for Kidney Transplantation in Pediatric Recipients
Cited by: 9
Author(s): Tara K. Sigdel, Minnie M. Sarwal
Software Mentions: 2
Published: about 8 years ago

10.1038/cdd.2015.22

XLS (c9orf142) is a new component of mammalian DNA double-stranded break repair
Cited by: 61
Author(s): Andrew Craxton, Joanna Somers, Deeksha Munnur, Rebekah Jukes-Jones, Kelvin Cain, Michal Malewicz
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2018.01397

The Role of Mass Spectrometry in Structural Studies of Flavin-Based Electron Bifurcating Enzymes
Cited by: 8
Author(s): Monika Tokmina‐Lukaszewska, Angela Patterson, Luke Berry, Liam W. Scott, Narayanaganesh Balasubramanian, Brian Bothner
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-020-79545-y

Surface hydrophobics mediate functional dimerization of CYP121A1 of Mycobacterium tuberculosis
Cited by: 5
Author(s): Amit Kumar, Christopher S. Campomizzi, Natalie Jay, Shaun Ferguson, Emelie‐Jo Scheffler, James Lioi, Chengjian Tu, Jun Qu, Claire Simons, D. Fernando Estrada
Software Mentions: 2
Published: over 4 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: over 4 years ago

10.3389/fmicb.2012.00393

Current Approaches on Viral Infection: Proteomics and Functional Validations
Cited by: 7
Author(s): Jie Zheng, Boon Huan Tan, Richard J. Sugrue, Kai Tang
Software Mentions: 2
Published: over 13 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: about 12 years ago

10.1186/s12964-016-0133-2

The arabidopsis cyclic nucleotide interactome
Cited by: 34
Author(s): Lara Donaldson, Stuart Meier, Chris Gehring
Software Mentions: 2
Published: about 9 years ago

10.2196/13780

Generative Participatory Design Methodology to Develop Electronic Health Interventions: Systematic Literature Review
Cited by: 53
Author(s): Pieter Vandekerckhove, Marleen de Mul, Wichor M. Bramer, Antoinette de Bont
Software Mentions: 2
Published: over 5 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 13 years ago

10.1186/2045-3701-3-37

Proteomic analysis of mismatch repair-mediated alkylating agent-induced DNA damage response
Cited by: 4
Author(s): Xi Chen, Yong Zhao, Guo Min Li, Lin Guo
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13023-019-1192-4

New insights on congenital pulmonary airways malformations revealed by proteomic analyses
Cited by: 9
Author(s): Constance Barazzone-Argiroffo, J. Lascano Maillard, Isabelle Vidal, Marie‐Luce Bochaton‐Piallat, Sanja Blaskovic, Yves Donati, Barbara E. Wildhaber, Anne‐Laure Rougemont, Christophe Delacourt, Isabelle Ruchonnet-Métrailler
Software Mentions: 2
Published: over 5 years ago

10.4172/jpb.1000384

Proteome Dynamics of the Specialist Oxalate Degrader Oxalobacter formigenes
Cited by: 13
Author(s): Mellissa L Ellis, James A. Mobley, Ross P. Holmes, John Knight
Software Mentions: 2
Published: over 9 years ago

10.3390/jpm10030083

Protein Expression Analysis of an In Vitro Murine Model of Prostate Cancer Progression: Towards Identification of High-Potential Therapeutic Targets
Cited by: 6
Author(s): Hisham F. Bahmad, Wenjing Peng, Rui Zhu, Farah Ballout, Alissar Monzer, Mohamad K. Elajami, Firas Kobeissy, Wassim Abou-Kheir, Yehia Mechref
Software Mentions: 2
Published: almost 5 years ago

10.1098/rsob.170024

SUMOylation pathway alteration coupled with downregulation of SUMO E2 enzyme at mucosal epithelium modulates inflammation in inflammatory bowel disease
Cited by: 32
Author(s): Salman Ahmad Mustfa, Mukesh Kumar Singh, Aamir Suhail, Gayatree Mohapatra, Smriti Verma, Debangana Chakravorty, Sarika Rana, Ritika Rampal, Atika Dhar, Sudipto Saha, Vineet Ahuja, Chittur V. Srikanth
Software Mentions: 2
Published: about 8 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 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 5 years ago

10.18632/oncotarget.25106

Proteomic screening identifies the zonula occludens protein ZO-1 as a new partner for ADAM12 in invadopodia-like structures
Cited by: 10
Author(s): Bassil Dekky, Michael W. Ruff, Dominique Bonnier, Vincent Legagneux, Nathalie Théret
Software Mentions: 2
Published: over 7 years ago

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