pypi: Scaffold | Projects | Ecosyste.ms: Papers

10.14814/phy2.12988

Reduced mitochondrial mass and function add to age-related susceptibility toward diet-induced fatty liver in C57BL/6J mice
Cited by: 27
Author(s): Kerstin Lohr, Fiona Pachl, Amin Moghaddas Gholami, Kerstin E. Geillinger, Hannelore Daniel, Bernhard Küster, Martin Klingenspor
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0218360

Candida utilis yeast as a functional protein source for Atlantic salmon (Salmo salar L.): Local intestinal tissue and plasma proteome responses
Cited by: 14
Author(s): Felipe Eduardo Reveco-Urzua, Mette Hofossæter, Mallikarjuna Rao Kovi, Liv Torunn Mydland, Ragnhild Ånestad, Randi Sørby, Charles McL. Press, Leidy Lagos, Margareth Øverland
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0121055

Scalable Production in Human Cells and Biochemical Characterization of Full-Length Normal and Mutant Huntingtin
Cited by: 36
Author(s): Bin Huang, Tanja Lucas, Claudia Kueppers, Xiaomin Dong, Maike Krause, Alexander Bepperling, Johannes Büchner, Hans Voshol, Andreas Weiss, Bertran Gerrits, Stefan Kochanek
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0100263

Insight into PreImplantation Factor (PIF*) Mechanism for Embryo Protection and Development: Target Oxidative Stress and Protein Misfolding (PDI and HSP) through Essential RIPK Binding Site
Cited by: 30
Author(s): Eytan R. Barnea, David M. Lubman, Yan Hui Liu, V. Absalon-Medina, Soren Hayrabedyan, Krassimira Todorova, R.O. Gilbert, Joy Guingab, Timothy J. Barder
Software Mentions: 2
Published: about 11 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: over 8 years ago

10.1074/mcp.RA118.000973

Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks (Gasterosteus aculeatus)
Cited by: 22
Author(s): Johnathon Li, Bryn Levitan, Silvia Gómez‐Jiménez, Dietmar Kültz
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0018724

Temperature-Induced Protein Secretion by Leishmania mexicana Modulates Macrophage Signalling and Function
Cited by: 84
Author(s): Kasra Hassani, Elisabeth Antoniak, Armando Jardim, Martin Olivier
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-9-595

Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species
Cited by: 53
Author(s): Hernán Lorenzi, Mathangi Thiagarajan, Brian J. Haas, Jennifer Wortman, Neil Hall, Elisabet Caler
Software Mentions: 2
Published: over 16 years ago

10.1093/pcp/pcaa170

A Novel Signaling Pathway Required for Arabidopsis Endodermal Root Organization Shapes the Rhizosphere Microbiome
Cited by: 11
Author(s): Julius Dürr, Guilhem Reyt, Stijn Spaepen, Sally Hilton, Cathal Meehan, Qi Wu, Takehiro Kamiya, Paulina Flis, H. G. Dickinson, Attila Fehér, Shivshankar Umashankar, Shruti Pavagadhi, Sanjay Swarup, David E. Salt, Gary D. Bending, José Gutierrez-Marcos
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0185125

Biochemical and biomechanical properties of the pacemaking sinoatrial node extracellular matrix are distinct from contractile left ventricular matrix
Cited by: 19
Author(s): Jessica M. Gluck, Anthony W. Herren, Sergey Yechikov, Hillary K.J. Kao, Ambereen Khan, Brett S. Phinney, Nipavan Chiamvimonvat, James W. Chan, Deborah K. Lieu
Software Mentions: 2
Published: almost 8 years ago

10.1074/mcp.M115.054064

Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry
Cited by: 148
Author(s): He Huang, Sophie Alvarez, Rebecca K. Bindbeutel, Zhouxin Shen, Michael J. Naldrett, Bradley S. Evans, Steven P. Briggs, Leslie M. Hicks, Steve A. Kay, Dmitri A. Nusinow
Software Mentions: 2
Published: over 9 years ago

10.1111/tpj.13743

Multiple marker abundance profiling: combining selected reaction monitoring and data‐dependent acquisition for rapid estimation of organelle abundance in subcellular samples
Cited by: 13
Author(s): Cornelia M. Hooper, Tim J. Stevens, Anna Maija Saukkonen, Ian Castleden, Pragya Singh, Gregory W. Mann, Bertrand Fabre, Jun Ito, Michael J. Deery, Kathryn S. Lilley, Young-Mo Kim, A. Harvey Millar, Joshua L. Heazlewood, Harriet T. Parsons
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1009506

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

10.1371/journal.pone.0004501

Two Chromogranin A-Derived Peptides Induce Calcium Entry in Human Neutrophils by Calmodulin-Regulated Calcium Independent Phospholipase A2
Cited by: 87
Author(s): Dandan Zhang, Peiman Shooshtarizadeh, Benoît‐Joseph Laventie, Didier Colin, Jean-François Chich, Jasmina Vidić, Jean de Barry, Sylvette Chasserot‐Golaz, François Delalande, Alain Van Dorsselaer, Francis Schneider, Karen B. Helle, Dominique Aunis, Gilles Prévost, Marie‐Hélène Metz‐Boutigue
Software Mentions: 2
Published: over 16 years ago

10.1016/j.molcel.2012.05.004

A Death Effector Domain Chain DISC Model Reveals a Crucial Role for Caspase-8 Chain Assembly in Mediating Apoptotic Cell Death
Cited by: 267
Author(s): Laura S. Dickens, Robert S. Boyd, Rebekah Jukes-Jones, Michelle A. Hughes, Gemma L. Robinson, Louise Fairall, John W. R. Schwabe, Kelvin Cain, Marion MacFarlane
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2164-12-267

Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: Role of the LINE-encoded endonuclease
Cited by: 13
Author(s): Vandana Kumari, Rahul Sharma, Vijay Pal Yadav, Abhishek Kumar Gupta, Alok Bhattacharya, Sudha Bhattacharya
Software Mentions: 2
Published: about 14 years ago

10.3390/antiox8120605

The Disulfide Stress Response and Protein S-thioallylation Caused by Allicin and Diallyl Polysulfanes in Bacillus subtilis as Revealed by Transcriptomics and Proteomics
Cited by: 21
Author(s): Bui Khanh, Nguyen Thi Thu Huyen, Vu Van Loi, Martin C. H. Gruhlke, Marc Schaffer, Ulrike Mäder, Sandra Maaß, Dörte Becher, Jörg Bernhardt, Miriam Arbach, Chris J. Hamilton, Alan Slusarenko, Haike Antelmann
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.3001081

Molecular characterization of the conoid complex in Toxoplasma reveals its conservation in all apicomplexans, including Plasmodium species
Cited by: 49
Author(s): Luděk Kořený, Mohammad Zeeshan, Konstantin Barylyuk, Eelco C. Tromer, Jolien J. E. van Hooff, Declan Brady, Huiling Ke, Sara Chelaghma, David J. P. Ferguson, Laura Eme, Rita Tewari, Ross F. Waller
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pbio.3000373

N-terminal β-strand underpins biochemical specialization of an ATG8 isoform
Cited by: 43
Author(s): Erin K. Zess, Cassandra Jensen, Neftaly Cruz-Mireles, Juan Carlos De la Concepcion, Jan Sklenář, Madlen Stephani, Richard Imre, Elisabeth Roitinger, Richard K. Hughes, Khaoula Belhaj, Karl Mechtler, Frank L.H. Menke, Tolga O. Bozkurt, Mark J. Banfield, Sophien Kamoun, Abbas Maqbool, Yasin Dagdas
Software Mentions: 2
Published: about 6 years ago

10.1016/j.xpro.2021.100417

Identifying cytokine signaling signatures in primary human Th-1 cells by phospho-proteomics analysis
Cited by: 0
Author(s): Jonathan Martínez-Fábregas, Elizabeth Pöhler, Ignacio Moraga
Software Mentions: 2
Published: about 4 years ago

10.1126/sciadv.aba8397

The structures of natively assembled clathrin-coated vesicles
Cited by: 38
Author(s): Mohammadreza Paraan, Joshua H. Mendez, Savanna R. Sharum, Danielle L. Kurtin, Huan He, Scott M. Stagg
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0208352

Characterization of longitudinal canal tissue in the acorn barnacle Amphibalanus amphitrite
Cited by: 8
Author(s): Chenyue Wang, Janna N. Schultzhaus, Chris R. Taitt, Dagmar H. Leary, Lisa C. Shriver‐Lake, Daniel A. Snellings, Samantha L Sturiale, Stella H. North, Beatriz Orihuela, Daniel Rittschof, Kathryn J. Wahl, Christopher M. Spillmann
Software Mentions: 2
Published: over 6 years ago

10.1038/srep29417

Identification of cyclins A1, E1 and vimentin as downstream targets of heme oxygenase-1 in vascular endothelial growth factor-mediated angiogenesis
Cited by: 16
Author(s): Andrea S. Bauer, Hayley Mylroie, Clare Thornton, Damien Calay, Graeme M. Birdsey, Allan Kiprianos, Garrick K. Wilson, Miguel P. Soares, Xiaoke Yin, Manuel Mayr, Anna M. Randi, Justin C. Mason
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0040695

Integrated Metabolo-Proteomic Approach to Decipher the Mechanisms by Which Wheat QTL (Fhb1) Contributes to Resistance against Fusarium graminearum
Cited by: 212
Author(s): Raghavendra Gunnaiah, Ajjamada C. Kushalappa, Raj Duggavathi, S. L. Fox, Daryl J. Somers
Software Mentions: 2
Published: about 13 years ago

10.1186/s40478-019-0796-1

Composition of the Intranuclear Inclusions of Fragile X-associated Tremor/Ataxia Syndrome
Cited by: 45
Author(s): Lisa Ma, Anthony W. Herren, Glenda Espinal, Jamie L. Randol, Bridget McLaughlin, Verónica Martínez‐Cerdeño, Isaac N. Pessah, Randi J. Hagerman, Paul J. Hagerman
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0018497

A Mighty Small Heart: The Cardiac Proteome of Adult Drosophila melanogaster
Cited by: 81
Author(s): Anthony Cammarato, Christian H. Ahrens, Nakissa N. Alayari, Ermir Qeli, Jasma Rucker, Mary C. Reedy, Christian M. Zmasek, Marjan Guček, Robert N. Cole, Jennifer E. Van Eyk, Rolf Bodmer, Brian O’Rourke, Sanford I. Bernstein, D. Brian Foster
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pbio.3001136

Plant pathogens convergently evolved to counteract redundant nodes of an NLR immune receptor network
Cited by: 56
Author(s): Lida Derevnina, Mauricio P Contreras, Hiroaki Adachi, Jessica Upson, Angel Vergara Cruces, Rongrong Xie, Jan Sklenář, Frank L.H. Menke, Sam T. Mugford, Dan MacLean, Wenbo Ma, Saskia A. Hogenhout, A. Goverse, Abbas Maqbool, Chih‐Hang Wu, Sophien Kamoun
Software Mentions: 2
Published: almost 4 years ago

10.1038/srep36699

Insights into a novel nuclear function for Fascin in the regulation of the amino-acid transporter SLC3A2
Cited by: 21
Author(s): Amine Saad, Krikor Bijian, Dinghong Qiu, Sabrina Daniela da Silva, Maud Marques, Chia-Hao Chang, Hassan Nassour, Dindial Ramotar, Sambasivarao Damaraju, John R. Mackey, Tarek A. Bismar, Michael Witcher, Moulay A. Alaoui‐Jamali
Software Mentions: 2
Published: over 8 years ago

10.1038/srep37643

Nucleoside-Diphosphate-Kinase of P. gingivalis is Secreted from Epithelial Cells In the Absence of a Leader Sequence Through a Pannexin-1 Interactome
Cited by: 25
Author(s): Kalina R. Atanasova, Jungnam Lee, JoAnn S. Roberts, Kyulim Lee, David M. Ojcius, Özlem Yılmaz
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0228134

Proteomic profiling of proteins in the dorsal horn of the spinal cord in dairy cows with chronic lameness
Cited by: 2
Author(s): Daniel Herzberg, Pablo Strobel, Heine Yacob Müller, Constanza Meneses, Mads Werner, Hedie Bustamante
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0156543

A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site
Cited by: 11
Author(s): Erin Becker, Andrew I. Yao, Phillip Seitzer, Tobias Kind, Ting Wang, Rich Eigenheer, Katie S. Y. Shao, Vladimir Yarov‐Yarovoy, Marc T. Facciotti
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0015004

Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery
Cited by: 1,153
Author(s): Larry Gold, Deborah Ayers, Jennifer Bertino, C. Bock, Ashley Bock, Edward N. Brody, Jeff Carter, Andrew B. Dalby, Bruce E. Eaton, Tim Fitzwater, Dylan Flather, Ashley Forbes, Trudi Foreman, Cate Fowler, Bharat Gawande, Meredith Goss, Magda Gunn, Shashi Gupta, Dennis Halladay, Jim Heil, Joe Heilig, Brian J. Hicke, Gregory M. Husar, Nebojša Janjić, Thale C. Jarvis, Susan D. Jennings, Evaldas Katilius, Tracy R. Keeney, Nancy Kim, Tad H. Koch, Stephan Kräemer, Luke Kroiss, Ngan Le, Daniel M. Levine, Wes Lindsey, Bridget Lollo, Wes Mayfield, Mike Mehan, Robert Mehler, Sally K. Nelson, Michele Nelson, Dan Nieuwlandt, Malti Nikrad, Urs A. Ochsner, Rachel Ostroff, Matt Otis, Thomas S. Parker, Steve Pietrasiewicz, Daniel I. Resnicow, John C. Rohloff, Glenn M. Sanders, Sarah Sattin, Daniel J. Schneider, Britta Swebilius Singer, Martin Stanton, Alana Sterkel, A. Keith Stewart, Suzanne Stratford, Jonathan D. Vaught, Mike Vrkljan, Jeffrey J. Walker, Mike Watrobka, Sheela Waugh, Allison Weiss, Sheri K. Wilcox, Alexey D. Wolfson, Steven K. Wolk, Chi Zhang, Dom Zichi
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0026542

A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface
Cited by: 73
Author(s): Xiaoxiao Li, James F. LeBlanc, Amy Truong, Ravi Vuthoori, Sharon S. Chen, Jonathan L. Lustgarten, Bennett E. Roth, Jeff Allard, Andrew Ippoliti, Laura L. Presley, James Borneman, William L. Bigbee, Vanathi Gopalakrishnan, Thomas G. Graeber, David Elashoff, Jonathan Braun, Lee Goodglick
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0190836

Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds
Cited by: 7
Author(s): Clifford G. Clark, Chih-Yu Chen, Chrystal Berry, Matthew Walker, Stuart McCorrister, Patrick Chong, Garrett Westmacott
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0037034

Comparative Proteomic Analysis of Aedes aegypti Larval Midgut after Intoxication with Cry11Aa Toxin from Bacillus thuringiensis
Cited by: 48
Author(s): Angeles Cancino-Rodezno, Luis Lozano, Cris Oppert, Julieta Ivonne Castro, Humberto Lánz-Mendoza, Sergio Encarnación, Amy Evans, Sarjeet S. Gill, Mário Soberón, Juan Luís Jurat-Fuentes, Alejandra Bravo
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0124473

Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features
Cited by: 29
Author(s): Abhinay Ramaprasad, Tobias Mourier, Raeece Naeem, Tareq B. Malas, Ehab M. Moussa, Aswini K. Panigrahi, Sarah J. Vermont, Thomas D. Otto, Jonathan M. Wastling, Arnab Pain
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pbio.3000566

Cilia-based peptidergic signaling
Cited by: 45
Author(s): Raj Luxmi, Dhivya Kumar, Richard E. Mains, Stephen M. King, Betty A. Eipper
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0027811

Radiation–Induced Signaling Results in Mitochondrial Impairment in Mouse Heart at 4 Weeks after Exposure to X-Rays
Cited by: 130
Author(s): Žarko Barjaktarović, Dominik Schmaltz, Alena Shyla, Omid Azimzadeh, Sabine Schulz, Julia Haagen, Wolfgang Dörr, Hakan Sarioglu, Alexander Schäfer, Michael J. Atkinson, Hans Zischka, Soile Tapio
Software Mentions: 2
Published: over 13 years ago

10.1186/1476-4598-12-62

Biochemical and biological characterization of exosomes containing prominin-1/CD133
Cited by: 90
Author(s): Germana Rappa, Javier Mercapide, Fabio Anzanello, R. Marshall Pope, Aurelio Lorico
Software Mentions: 2
Published: about 12 years ago

10.1186/1756-6606-4-28

Impairment of adult hippocampal neural progenitor proliferation by methamphetamine: role for nitrotyrosination
Cited by: 49
Author(s): Arun Venkatesan, Lerna Uzasci, Zhaohui Chen, Labchan Rajbhandari, Carol Anderson, Myoung Hwa Lee, M.A. Bianchet, Robert J. Cotter, Hongjun Song, Avindra Nath
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0064621

Transcriptome and Proteome Data Reveal Candidate Genes for Pollinator Attraction in Sexually Deceptive Orchids
Cited by: 44
Author(s): Khalid E. M. Sedeek, Weihong Qi, Monica A. Schauer, Alok Gupta, Lucy Poveda, Shuqing Xu, Zhong‐Jian Liu, Ueli Grossniklaus, Florian P. Schiestl, Philipp M. Schlüter
Software Mentions: 2
Published: about 12 years ago

10.1186/1471-2164-15-S12-S2

Time-course human urine proteomics in space-flight simulation experiments
Cited by: 22
Author(s): Hans Binder, Henry Wirth, Arsen Arakelyan, Kathrin Lembcke, Evgeny S. Tiys, В. А. Иванисенко, Н. А. Колчанов, Alexey Kononikhin, Igor Popov, E. N. Nikolaev, Л. Х. Пастушкова, И. М. Ларина
Software Mentions: 2
Published: over 10 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: over 6 years ago

10.1038/s41598-019-53268-1

Elemental Zn and its Binding Protein Zinc-α2-Glycoprotein are Elevated in HPV-Positive Oropharyngeal Squamous Cell Carcinoma
Cited by: 8
Author(s): Kate Poropatich, Tatjana Paunesku, Alia Zander, Brian Wray, Matthew J. Schipma, Prarthana Dalal, Mark Agulnik, Si Chen, Barry Lai, Olga Antipova, Evan Maxey, Koshonna Brown, Michael Beau Wanzer, Demirkan Gursel, Hanli Fan, Alfred Rademaker, Gayle E. Woloschak, Bharat B. Mittal
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0012671

Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae
Cited by: 150
Author(s): Nikoleta G. Tsvetanova, Daniel M. Klass, Julia Salzman, Patrick O. Brown
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0080737

PRICKLE1 Interaction with SYNAPSIN I Reveals a Role in Autism Spectrum Disorders
Cited by: 37
Author(s): Lily Paemka, Vinit B. Mahajan, Jessica M. Skeie, Levi P. Sowers, Salleh N. Ehaideb, Pedro González-Alegre, Toshikuni Sasaoka, Hirotaka Tao, Asuka Miyagi, Naoto Ueno, Keizo Takao, Tsuyoshi Miyakawa, Shu Wu, Benjamin W. Darbro, Polly J. Ferguson, Andrew A. Pieper, Jeremiah K. Britt, John A. Wemmie, Danielle S. Rudd, Thomas H. Wassink, Hatem El‐Shanti, Heather C Mefford, Gemma L. Carvill, J. Robert Manak, Alexander G. Bassuk
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0094166

Biochemical Properties and Atomic Resolution Structure of a Proteolytically Processed β-Mannanase from Cellulolytic Streptomyces sp. SirexAA-E
Cited by: 16
Author(s): Taichi E. Takasuka, Justin Acheson, C.M. Bianchetti, Ben M. Prom, Lai F. Bergeman, Adam J. Book, Cameron R. Currie, Brian G. Fox
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1005018

The Ribosome Biogenesis Factor Nol11 Is Required for Optimal rDNA Transcription and Craniofacial Development in Xenopus
Cited by: 36
Author(s): John N. Griffin, Samuel B. Sondalle, Florencia Del Viso, Susan J. Baserga, Mustafa K. Khokha
Software Mentions: 2
Published: over 10 years ago

10.1186/s12862-021-01910-w

Odorant-binding proteins in canine anal sac glands indicate an evolutionarily conserved role in mammalian chemical communication
Cited by: 5
Author(s): Sunita Janssenswillen, Kim Roelants, Sébastien Carpentier, H. de Rooster, Mieke Metzemaekers, Bram Vanschoenwinkel, Paul Proost, Franky Bossuyt
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0168913

Conserved Lysine Acetylation within the Microtubule-Binding Domain Regulates MAP2/Tau Family Members
Cited by: 16
Author(s): Andrew Hwang, Hanna Trzeciakiewicz, Dave Friedmann, Chao Yuan, Ronen Marmorstein, Virginia M.‐Y. Lee, Todd J. Cohen
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0186461

Software-aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry
Cited by: 14
Author(s): Tatiana Radchenko, Andreas Brink, Yves Siegrist, Christopher J. Kochansky, Alison Bateman, Fabien Fontaine, Luca Morettoni, Ismael Zamora
Software Mentions: 2
Published: over 7 years ago

10.1007/s00401-020-02178-y

SFPQ and Tau: critical factors contributing to rapid progression of Alzheimer’s disease
Cited by: 41
Author(s): Neelam Younas, Saima Zafar, Mohsin Shafiq, Aneeqa Noor, Anna Siegert, Amandeep Singh Arora, А. П. Галкин, Ayesha Zafar, Mathias Schmitz, Christine Stadelmann, Olivier Andréoletti, Isidre Ferrer, Inga Zerr
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1006592

β-Integrin de-phosphorylation by the Density-Enhanced Phosphatase DEP-1 attenuates EGFR signaling in C. elegans
Cited by: 15
Author(s): Michael Walser, Christoph Alois Umbricht, Erika Fröhli, Paolo Nanni, Alex Hajnal
Software Mentions: 2
Published: over 8 years ago

10.3390/microorganisms9081593

Glucosidase Inhibitors Screening in Microalgae and Cyanobacteria Isolated from the Amazon and Proteomic Analysis of Inhibitor Producing Synechococcus sp. GFB01
Cited by: 6
Author(s): Diana Gomes Gradíssimo, Vivian Cássia Oliveira da Silva, Luciana Pereira Xavier, Sidney Vasconcelos do Nascimento, Rafael Borges da Silva Valadares, Sílvia Maria Mathes Faustino, Maria Paula Cruz Schneider, Agenor Valadares Santos
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0250296

Sodium butyrate modulates chicken macrophage proteins essential for Salmonella Enteritidis invasion
Cited by: 3
Author(s): Anamika Gupta, Mohit Bansal, Rohana Liyanage, Abhinav Upadhyay, N. C. Rath, Annie Donoghue, Xiaolun Sun
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0075446

A Purine Analog Synergizes with Chloroquine (CQ) by Targeting Plasmodium falciparum Hsp90 (PfHsp90)
Cited by: 23
Author(s): Dea Shahinas, Asongna Folefoc, Tony Taldone, Gabriela Chiosis, Ian Crandall, Dylan R. Pillai
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0028949

Proteome Changes Driven by Phosphorus Deficiency and Recovery in the Brown Tide-Forming Alga Aureococcus anophagefferens
Cited by: 60
Author(s): Louie L. Wurch, Erin M. Bertrand, Mak A. Saito, Benjamin A. S. Van Mooy, Sonya T. Dyhrman
Software Mentions: 2
Published: over 13 years ago

10.1016/j.dib.2014.09.006

Data set for the proteomic inventory and quantitative analysis of chicken uterine fluid during eggshell biomineralization
Cited by: 12
Author(s): Pauline Marie, Valérie Labas, Aurélien Brionne, Grégoire Harichaux, Christelle Hennequet-Antier, Yves Nys, Joël Gautron
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.45916

In vivo identification of GTPase interactors by mitochondrial relocalization and proximity biotinylation
Cited by: 60
Author(s): Alison K. Gillingham, Jessie Bertram, Farida Begum, Sean Munro
Software Mentions: 2
Published: about 6 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 5 years ago

10.1128/mSphere.00135-17

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

10.1128/mSphere.00100-20

MAG2, a Toxoplasma gondii Bradyzoite Stage-Specific Cyst Matrix Protein
Cited by: 8
Author(s): Vincent Tu, Joshua Mayoral, Rama R. Yakubu, Tadakimi Tomita, Tatsuki Sugi, Bing Han, Tere Williams, Yanfen Ma, Louis M. Weiss
Software Mentions: 2
Published: over 5 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

10.1534/g3.115.017053

The Mosaic Mutants of Cucumber: A Method to Produce Knock-Downs of Mitochondrial Transcripts
Cited by: 9
Author(s): Angel R. Del Valle-Echevarria, Agnieszka Kiełkowska, Grzegorz Bartoszewski, Michael J. Havey
Software Mentions: 2
Published: about 10 years ago

10.1128/mSystems.01095-20

Single-Cell RNA Sequencing Reveals that the Switching of the Transcriptional Profiles of Cysteine-Related Genes Alters the Virulence of Entamoeba histolytica
Cited by: 4
Author(s): Min Feng, Yuhan Zhang, Hang Zhou, Xia Li, Yongfeng Fu, Hiroshi Tachibana, Xunjia Cheng
Software Mentions: 2
Published: over 4 years ago

10.1128/mSystems.00397-21

The DNA Sensor IFIX Drives Proteome Alterations To Mobilize Nuclear and Cytoplasmic Antiviral Responses, with Its Acetylation Acting as a Localization Toggle
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Author(s): Timothy R. Howard, Marni S. Crow, Todd M. Greco, Krystal K. Lum, Tuo Li, Ileana M. Cristea
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-021-83395-7

A Casz1–NuRD complex regulates temporal identity transitions in neural progenitors
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Author(s): Pierre Mattar, Christine Jolicoeur, Dang Thanh Chung, Sujay Shah, Brian S. Clark, Michel Cayouette
Software Mentions: 2
Published: over 4 years ago

10.1186/gb-2012-13-2-r11

Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells
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Author(s): Najeeb U. Siddiqui, Xiao Li, Hua Luo, Angelo Karaiskakis, Huayun Hou, Thomas Kislinger, J. Timothy Westwood, Quaid Morris, Howard D. Lipshitz
Software Mentions: 2
Published: over 13 years ago

10.1038/s41598-021-86284-1

Ibuprofen alters epoxide hydrolase activity and epoxy-oxylipin metabolites associated with different metabolic pathways in murine livers
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Author(s): Shuchita Tiwari, Jun Yang, Christophe Morisseau, Blythe Durbin‐Johnson, Bruce D. Hammock, Aldrin V. Gomes
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-89907-9

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

10.1038/s41598-021-91756-5

Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives
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Author(s): Mana Iwata, Ana Gutiérrez, Gisela Marques, Grzegorz Sabat, Philip J. Kersten, Daniel Cullen, Jennifer M. Bhatnagar, J. S. Yadav, Anna Lipzen, Yuko Yoshinaga, Aarti Sharma, Catherine Adam, Christopher Daum, Vivian Ng, Igor V. Grigoriev, Chiaki Hori
Software Mentions: 2
Published: about 4 years ago

10.3389/fvets.2020.584948

Protein Cargo of Extracellular Vesicles From Bovine Follicular Fluid and Analysis of Their Origin From Different Ovarian Cells
Cited by: 19
Author(s): Svetlana Uzbekova, Carmen Almiñana, Valérie Labas, Ana-Paula Teixeira-Gomes, Lucie Combes‐Soia, Guillaume Tsikis, Anaïs Vitorino Carvalho, Rustem Uzbekov, Г. Н. Сингина
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-92931-4

Overlapping regions of Caf20 mediate its interactions with the mRNA-5′cap-binding protein eIF4E and with ribosomes
Cited by: 4
Author(s): Ebelechukwu C. Nwokoye, Eiman AlNaseem, Robert A. Crawford, Lydia M. Castelli, Martin D. Jennings, Christopher J. Kershaw, Graham D. Pavitt
Software Mentions: 2
Published: about 4 years ago

10.3390/jof6030148

Proteomic and Transcriptomic Analyses Indicate Metabolic Changes and Reduced Defense Responses in Mycorrhizal Roots of Oeceoclades maculata (Orchidaceae) Collected in Nature
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Author(s): Rafael Borges da Silva Valadares, Silvia Perotto, Adriano Reis Lucheta, Eder C. Santos, Renato R. M. Oliveira, Márcio Rodrigues Lambais
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-021-95060-0

Proteomic study of Desulfovibrio ferrophilus IS5 reveals overexpressed extracellular multi-heme cytochrome associated with severe microbiologically influenced corrosion
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Author(s): Mohor Chatterjee, Yu Fan, Fang Cao, A. A. Jones, Giovanni Pilloni, Xiaozhou Zhang
Software Mentions: 2
Published: almost 4 years ago

10.1007/s00535-021-01802-2

Alteration of protein expression and spliceosome pathway activity during Barrett’s carcinogenesis
Cited by: 1
Author(s): Christoph Stingl, Angela Bureo Gonzalez, Coşkun Güzel, Kai Yi N. Phoa, Michail Doukas, Gerben E. Breimer, Sybren L. Meijer, Jacques Bergman, Theo M. Luider
Software Mentions: 2
Published: about 4 years ago

10.1099/jgv.0.001607

Identification of protein interactions of grapevine fanleaf virus RNA-dependent RNA polymerase during infection of Nicotiana benthamiana by affinity purification and tandem mass spectrometry
Cited by: 2
Author(s): Larissa J. Osterbaan, Victoria Hoyle, Michelle Curtis, Stacy L. DeBlasio, Keith Rivera, Michelle Heck, Marc Fuchs
Software Mentions: 2
Published: about 4 years ago

10.1242/jcs.154880

Tyrosine phosphorylation of WIP releases bound WASP and impairs podosome assembly in macrophages
Cited by: 15
Author(s): Vineetha Vijayakumar, James Monypenny, Xing Judy Chen, Laura M. Machesky, Sérgio Lilla, Adrian J. Thrasher, Inés M. Antón, Yolanda Calle, Gareth E. Jones
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-016-0951-y

OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
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Author(s): Song Gao, Denis Bertrand, Burton K. Chia, Niranjan Nagarajan
Software Mentions: 2
Published: about 9 years ago

10.1155/2013/581862

iTRAQ-Based and Label-Free Proteomics Approaches for Studies of Human Adenovirus Infections
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Author(s): Hung V. Trinh, Jonas Grossmann, Peter Gehrig, Bernd Roschitzki, Ralph Schlapbach, Urs F. Greber, Silvio Hemmi
Software Mentions: 2
Published: over 12 years ago

10.1186/1758-2946-5-5

Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines
Cited by: 23
Author(s): Sheng Tian, Youyong Li, Junmei Wang, Xiaojie Xu, Lei Xu, Xiaohong Wang, Lei Chen, Tingjun Hou
Software Mentions: 2
Published: over 12 years ago

10.1155/2013/293782

Proteomic Analysis and Label-Free Quantification of the Large <i>Clostridium difficile</i> Toxins
Cited by: 17
Author(s): Hércules Moura, Rebecca R. Terilli, Adrian R. Woolfitt, Yulanda M. Williamson, Glauber Wagner, Thomas A. Blake, Maria I. Solano, John R. Barr
Software Mentions: 2
Published: almost 12 years ago

10.7150/thno.47893

Analysis of mesenchymal stem cell proteomes <i>in situ</i> in the ischemic heart
Cited by: 11
Author(s): Dunzheng Han, Junjie Yang, Eric Zhang, Yanwen Liu, Chan Boriboun, Aijun Qiao, Yang Yu, Shuyuan Xu, Yang Liu, Wenying Yan, Biao Luo, Dagang Lü, Chunxiang Zhang, Chunfa Jie, James A. Mobley, Jianyi Zhang, Gangjian Qin
Software Mentions: 2
Published: over 5 years ago

10.3390/toxins8040105

Quantitative Proteomic Analysis of Venoms from Russian Vipers of Pelias Group: Phospholipases A2 are the Main Venom Components
Cited by: 29
Author(s): Sergey I. Kovalchuk, Rustam H. Ziganshin, Vladislav G. Starkov, Victor I. Tsetlin, Yuri N. Utkin
Software Mentions: 2
Published: over 9 years ago

10.3389/fpls.2017.01292

Stress-Related Mitogen-Activated Protein Kinases Stimulate the Accumulation of Small Molecules and Proteins in Arabidopsis thaliana Root Exudates
Cited by: 13
Author(s): Nadine Strehmel, Wolfgang Hoehenwarter, Susann Mönchgesang, Petra Majovsky, Sylvia Krüger, Dierk Scheel, Justin Lee
Software Mentions: 2
Published: about 8 years ago

10.1186/s13321-019-0391-2

Dataset’s chemical diversity limits the generalizability of machine learning predictions
Cited by: 59
Author(s): Marta Glavatskikh, Jules Leguy, Gilles Hunault, Thomas Cauchy, Benoit Da Mota
Software Mentions: 2
Published: over 5 years ago

10.1074/jbc.M116.729806

Composition and Activity of the Non-canonical Gram-positive SecY2 Complex
Cited by: 8
Author(s): Mikaila Bandara, Robin A. Corey, Remy Martin, J. Mark Skehel, Ariel Blocker, Howard F. Jenkinson, Ian Collinson
Software Mentions: 2
Published: almost 9 years ago

10.1172/JCI86924

Extracellular matrix proteomics identifies molecular signature of symptomatic carotid plaques
Cited by: 108
Author(s): Sarah R. Langley, Karin Willeit, Athanasios Didangelos, Ljubica Matic, Philipp Skroblin, Javier Barallobre-Barreiro, Mariette Lengquist, Gregor Rungger, Alexander Kapustin, Ludmilla Kedenko, Chris Molenaar, Ruifang Lu, Temo Barwari, Gonca Suna, Xiaoke Yin, Bernhard Iglseder, Bernhard Paulweber, Peter Willeit, Joseph Shalhoub, Gérard Pasterkamp, Alun H. Davies, Claudia Monaco, Ulf Hedin, Catherine M. Shanahan, Johann Willeit, Stefan Kiechl, Manuel Mayr
Software Mentions: 2
Published: over 8 years ago

10.1074/jbc.M116.763243

Autophosphorylation-based Calcium (Ca2+) Sensitivity Priming and Ca2+/Calmodulin Inhibition of Arabidopsis thaliana Ca2+-dependent Protein Kinase 28 (CPK28)
Cited by: 44
Author(s): Kyle W. Bender, R. Kevin Blackburn, Jacqueline Monaghan, Paul Derbyshire, Frank L.H. Menke, Cyril Zipfel, Michael B. Goshe, Raymond E. Zielinski, Steven C. Huber
Software Mentions: 2
Published: over 8 years ago

10.3389/fpls.2017.01416

Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis
Cited by: 12
Author(s): Zhijian Jiang, Manoj Kumar, Matthew P. Padula, Mathieu Pernice, Tim Kahlke, Mikael Kim, Peter J. Ralph
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41398-020-00966-4

Integration of postmortem amygdala expression profiling, GWAS, and functional cell culture assays: neuroticism-associated synaptic vesicle glycoprotein 2A (SV2A) gene is regulated by miR-133a and miR-218
Cited by: 9
Author(s): Magdalena Jurkiewicz, Dirk Moser, Antonius Koller, Lei Yu, Emily I. Chen, David A. Bennett, Turhan Canli
Software Mentions: 2
Published: almost 5 years ago

10.3390/jcm10112446

Characteristics of the Urinary Proteome in Women with Overactive Bladder Syndrome: A Case-Control Study
Cited by: 1
Author(s): Marianne Koch, Pavel Lyatoshinsky, Goran Mitulović, Barbara Bodner‐Adler, Sören Lange, Engelbert Hanzal, Wolfgang Umek
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2020.01230

Big Genes, Small Effectors: Pea Aphid Cassette Effector Families Composed From Miniature Exons
Cited by: 6
Author(s): Matthew Dommel, Jong‐Nam Oh, José C. Huguet‐Tapia, Endrick Guy, Hélène Boulain, Akiko Sugio, M. Murugan, Fabrice Legeai, Michelle Heck, Charlotte M. Smith, Frank F. White
Software Mentions: 2
Published: almost 5 years ago

10.1038/hortres.2014.39

Dynamic changes in the date palm fruit proteome during development and ripening
Cited by: 35
Author(s): Claudius Marondedze, Chris Gehring, Ludivine Thomas
Software Mentions: 2
Published: almost 11 years ago

10.1074/jbc.RA119.007504

The priming factor CAPS1 regulates dense-core vesicle acidification by interacting with rabconnectin3β/WDR7 in neuroendocrine cells
Cited by: 7
Author(s): Ellen Crummy, Muralidharan Mani, John C. Thellman, Thomas F.J. Martin
Software Mentions: 2
Published: about 6 years ago

10.1074/jbc.RA119.010486

Moonlighting matrix metalloproteinase substrates: Enhancement of proinflammatory functions of extracellular tyrosyl-tRNA synthetase upon cleavage
Cited by: 14
Author(s): Parker G. Jobin, Nestor Solis, Yoan Machado, Peter A. Bell, K. Simran, Nam Hoon Kwon, Sung Hoon Kim, Christopher M. Overall, Georgina S. Butler
Software Mentions: 2
Published: over 5 years ago

10.1074/jbc.RA119.012517

Phosphorylation of the overlooked tyrosine 310 regulates the structure, aggregation, and microtubule- and lipid-binding properties of Tau
Cited by: 27
Author(s): Nadine Ait-Bouziad, Anass Chiki, Galina Limorenko, Shifeng Xiao, David Eliezer, Hilal A. Lashuel
Software Mentions: 2
Published: about 5 years ago

10.1038/hortres.2016.29

Relative quantification of phosphoproteomic changes in grapevine (Vitis vinifera L.) leaves in response to abscisic acid
Cited by: 14
Author(s): Supakan Rattanakan, Iniga S. George, Paul A. Haynes, Grant R. Cramer
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-020-66286-1

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

10.1128/mBio.02146-17

A Phosphorylation Switch on Lon Protease Regulates Bacterial Type III Secretion System in Host
Cited by: 23
Author(s): Xiaofeng Zhou, Doron Teper, Maxuel O. Andrade, Tong Zhang, Sixue Chen, Wenlei Song, Nian Wang
Software Mentions: 2
Published: over 7 years ago

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