pypi: Scaffold | Projects | Ecosyste.ms: Papers

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: almost 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 5 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: about 6 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 13 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 8 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 15 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 9 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: almost 14 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 9 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 10 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 9 years ago

10.1038/s41598-018-34864-z

Interactome determination of a Long Noncoding RNA implicated in Embryonic Stem Cell Self-Renewal
Cited by: 14
Author(s): Keriayn N. Smith, Joshua Starmer, Terry Magnuson
Software Mentions: 3
Published: over 7 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 5 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 5 years ago

10.1371/journal.pone.0183975

Biophysical analysis of the effect of chemical modification by 4-oxononenal on the structure, stability, and function of binding immunoglobulin protein (BiP)
Cited by: 4
Author(s): Dinen D. Shah, Surinder Singh, Monika Dzieciątkowska, Krishna Mallela
Software Mentions: 3
Published: almost 9 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 5 years ago

10.1186/s12915-015-0128-2

The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers
Cited by: 14
Author(s): Sarah K. Harten, Harald Oey, Lauren M. Bourke, Vandhana Bharti, Luke Isbel, Lucia Daxinger, Pierre Faou, Neil O. Robertson, Jacqueline M. Matthews, Emma Whitelaw
Software Mentions: 3
Published: over 11 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 6 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 9 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 15 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 7 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 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: over 7 years ago

10.1371/journal.pone.0237981

Cancer proteome and metabolite changes linked to SHMT2
Cited by: 16
Author(s): Jiefei Tong, Jonathan R. Krieger, Paul Taylor, Richard D. Bagshaw, Jae Seung Kang, Swathi P. Jeedigunta, Leanne E. Wybenga‐Groot, Wen Zhang, Heba Badr, Shideh Mirhadi, Nhu-An Pham, Étienne Coyaud, Man Yu, Ming Li, Michael Cabanero, Brian Raught, Jason T. Maynes, Cynthia Hawkins, Ming‐Sound Tsao, Michael F. Moran
Software Mentions: 3
Published: almost 6 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 11 years ago

10.1111/tpj.14495

Phosphoproteomic analysis reveals plant <scp>DNA</scp> damage signalling pathways with a functional role for histone H2<scp>AX</scp> phosphorylation in plant growth under genotoxic stress
Cited by: 29
Author(s): Wanda M. Waterworth, Michael Wilson, Dapeng Wang, Thomas S. Nühse, Stacey Warward, Julian N. Selley, Claudia West
Software Mentions: 3
Published: almost 7 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 9 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: almost 13 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 7 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 6 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 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 6 years ago

10.12688/wellcomeopenres.16031.2

Large CRISPR-Cas-induced deletions in the oxamniquine resistance locus of the human parasite Schistosoma mansoni
Cited by: 7
Author(s): Geetha Sankaranarayanan, Avril Coghlan, Patrick Driguez, Magda E. Lotkowska, Mandy Sanders, Nancy Holroyd, Alan S. Tracey, Matthew Berriman, Gabriel Rinaldi
Software Mentions: 3
Published: over 5 years ago

10.1080/21505594.2017.1325064

Signatures of cytoplasmic proteins in the exoproteome distinguish community- and hospital-associated methicillin-resistant<i>Staphylococcus aureus</i>USA300 lineages
Cited by: 18
Author(s): Solomon Mekonnen, Laura M Palma Medina, Corinna Glasner, Eleni Tsompanidou, Anne de Jong, Stefano Grasso, Marc Schaffer, Ulrike Mäder, Anders Rhod Larsen, Heidi Gumpert, Henrik Westh, Uwe Völker, Andreas Otto, Dörte Becher, Jan Maarten van Dijl
Software Mentions: 3
Published: over 9 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 8 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: about 10 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 5 years ago

10.1111/mmi.14398

Protein kinase B controls <i>Mycobacterium tuberculosis</i> growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112
Cited by: 14
Author(s): Kawther Alqaseer, Obolbek Turapov, Philippe Barthe, Heena Jagatia, Angélique De Visch, Christian Roumestand, Malgorzata Wegrzyn, Iona L. Bartek, Martin I. Voskuil, Helen M. O’Hare, Paul Ajuh, Andrew R. Bottrill, Adam A. Witney, Martin Cohen‐Gonsaud, Simon J. Waddell, Galina V. Mukamolova
Software Mentions: 3
Published: almost 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: about 11 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 9 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: about 6 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 7 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 7 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: almost 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: over 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 6 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 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: over 5 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 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: almost 10 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 7 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 7 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 14 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 8 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 5 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 5 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 5 years ago

10.1186/1471-2164-13-361

Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species
Cited by: 85
Author(s): Emily A. Hornett, Christopher W. Wheat
Software Mentions: 3
Published: over 14 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 9 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 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 11 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 10 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 6 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 13 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 6 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 5 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 10 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 9 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: about 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 6 years ago

10.3390/ijms21010179

Analysis of the Barley Malt Rootlet Proteome
Cited by: 8
Author(s): Ramamurthy Mahalingam
Software Mentions: 3
Published: over 6 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 6 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 6 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 5 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 9 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: about 5 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 15 years ago

10.1371/journal.ppat.1009351

A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum
Cited by: 19
Author(s): Jun Miao, Chengqi Wang, Amuza Byaruhanga Lucky, Xiaoying Liang, Hui Min, Swamy Rakesh Adapa, Rays H. Y. Jiang, Kami Kim, Liwang Cui
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.59288

Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism
Cited by: 41
Author(s): Robert J. Nichols, Benjamin LaFrance, Naiya R Phillips, Devon Radford, Luke M. Oltrogge, Luis E. Valentin-Alvarado, Amanda J. Bischoff, Eva Nogales, David F. Savage
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.32952

SIRT2 deacetylase regulates the activity of GSK3 isoforms independent of inhibitory phosphorylation
Cited by: 36
Author(s): Mohsen Sarikhani, Sneha Mishra, Sangeeta Maity, Chaithanya Kotyada, Donald J. Wolfgeher, Mahesh P. Gupta, Mahavir Singh, Nagalingam R. Sundaresan
Software Mentions: 2
Published: over 8 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 7 years ago

10.3390/ijms19102912

Porcine Breast Extracellular Matrix Hydrogel for Spatial Tissue Culture
Cited by: 14
Author(s): Girdhari Rijal, Jing Wang, Ilhan Yu, David R. Gang, Roland Chen, Weimin Li
Software Mentions: 2
Published: almost 8 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 7 years ago

10.7554/eLife.04525

Mucosal effects of tenofovir 1% gel
Cited by: 40
Author(s): Florian Hladik, Adam Burgener, Lamar Ballweber, Raphaël Gottardo, Lucia Vojtech, Slim Fourati, Jiyan Dai, Mark J. Cameron, Johanna Strobl, Sean M. Hughes, Craig Hoesley, P. Andrew, Sherri Johnson, Jeanna Piper, David R. Friend, T. Blake Ball, Ross D. Cranston, Kenneth H. Mayer, M. Juliana McElrath, Ian McGowan
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.01299

A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 Å resolution
Cited by: 47
Author(s): Xing Zhang, Haixun Guo, Lei Jin, Elizabeth Czornyj, Asher Hodes, Wong H. Hui, Angela W Nieh, Jeff F. Miller, Z. Hong Zhou
Software Mentions: 2
Published: over 12 years ago

10.7554/eLife.32866

Mfn2 ubiquitination by PINK1/parkin gates the p97-dependent release of ER from mitochondria to drive mitophagy
Cited by: 243
Author(s): Gian‐Luca McLelland, Thomas Goiran, Wei Yi, Geneviève Dorval, Carol X Chen, Nadine Lauinger, Andrea I Krahn, Sepideh Valimehr, Aleksandar Raković, Isabelle Rouiller, Thomas M. Durcan, Jean‐François Trempe, Edward A. Fon
Software Mentions: 2
Published: over 8 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 5 years ago

10.3390/proteomes8030014

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field
Cited by: 133
Author(s): Emmalyn J. Dupree, Madhuri Jayathirtha, Hannah Yorkey, Marius Mihăşan, Brîndușa Alina Petre, Costel C. Darie
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.49953

Kv2.1 mediates spatial and functional coupling of L-type calcium channels and ryanodine receptors in mammalian neurons
Cited by: 55
Author(s): Nicholas C. Vierra, Michael Kirmiz, Deborah van der List, Luis Fernando Santana, James S. Trimmer
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.ppat.1006001

The Listeria monocytogenes PASTA Kinase PrkA and Its Substrate YvcK Are Required for Cell Wall Homeostasis, Metabolism, and Virulence
Cited by: 61
Author(s): Daniel A. Pensinger, Kyle Boldon, Grischa Y. Chen, William J.B. Vincent, Sherman Kyle, Min Xiong, Adam J. Schaenzer, Emily R. Forster, Jörn Coers, Rob Striker, John-Demian Sauer
Software Mentions: 2
Published: almost 10 years ago

10.3390/ijms20236041

Dead Cas Systems: Types, Principles, and Applications
Cited by: 66
Author(s): Sergey Brezgin, Anastasiya Kostyusheva, Dmitry Kostyushev, Vladimir Chulanov
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.20882

Constitutive scaffolding of multiple Wnt enhanceosome components by Legless/BCL9
Cited by: 61
Author(s): Laurens M. van Tienen, Juliusz Mieszczanek, Marc Fiedler, Trevor J. Rutherford, Mariann Bienz
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms21020466

Identification of 56 Proteins Involved in Embryo–Maternal Interactions in the Bovine Oviduct
Cited by: 13
Author(s): Charles Banliat, Guillaume Tsikis, Valérie Labas, Ana-Paula Teixeira-Gomes, Emmanuelle Com, Régis Lavigne, Charles Pineau, Benoît Guyonnet, Pascal Mermillod, Marie Saint‐Dizier
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1008917

Novel Babesia bovis exported proteins that modify properties of infected red blood cells
Cited by: 15
Author(s): Hassan Hakimi, Thomas J. Templeton, Minoru Sakaguchi, Junya Yamagishi, Shuichi Miyazaki, Kazuhide Yahata, Takayuki Uchihashi, Shin-ichiro Kawazu, O. Kaneko, Masahito Asada
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.60126

Autoregulatory control of microtubule binding in doublecortin-like kinase 1
Cited by: 14
Author(s): Regina L. Agulto, Melissa M Rogers, Tracy Tan, Amrita Ramkumar, Ashlyn M Downing, Hannah Bodin, Julia Castro, Dan W. Nowakowski, Kassandra M. Ori-McKenney
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.32660

Intracellular antibody signalling is regulated by phosphorylation of the Fc receptor TRIM21
Cited by: 53
Author(s): Claire F. Dickson, Adam J. Fletcher, Marina Vaysburd, Ji‐Chun Yang, Donna L. Mallery, Jingwei Zeng, Christopher M. Johnson, Stephen H. McLaughlin, Mark Skehel, Sarah Maslen, James Cruickshank, Nicolas Huguenin‐Dezot, Jason W. Chin, David Neuhaus, Leo C. James
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms22105392

α-Synuclein A53T Binds to Transcriptional Adapter 2-Alpha and Blocks Histone H3 Acetylation
Cited by: 13
Author(s): Ji-Yeong Lee, Hanna Kim, Areum Jo, Rin Khang, Chi-Hu Park, Soo-Jeong Park, Eunsang Kwag, Joo‐Ho Shin
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21051729

Tuberous Sclerosis Complex Axis Controls Renal Extracellular Vesicle Production and Protein Content
Cited by: 16
Author(s): Fahad Zadjali, Prashant Kumar, Ying Yao, Daniel L. Johnson, Aristotelis Astrinidis, Peter Vogel, Kenneth W. Gross, John J. Bissler
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1006379

Calmodulin-like proteins localized to the conoid regulate motility and cell invasion by Toxoplasma gondii
Cited by: 84
Author(s): Shaojun Long, Kevin M. Brown, Lisa L. Drewry, Bryan A. Anthony, Isabelle Phan, L. David Sibley
Software Mentions: 2
Published: over 9 years ago

10.1038/srep15443

Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations
Cited by: 75
Author(s): Abdallah Abdallah, Grant A. Hill-Cawthorne, Thomas D. Otto, Francesc Español i Coll, José Afonso Guerra-Assunção, Ge Gao, Raeece Naeem, Hifzur Rahman Ansari, Tareq B. Malas, Sabir A. Adroub, Theo Verboom, Roy Ummels, Huoming Zhang, Aswini K. Panigrahi, Ruth McNerney, Roland Brosch, Taane G. Clark, Marcel A. Behr, Wilbert Bitter, Arnab Pain
Software Mentions: 2
Published: almost 11 years ago

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