Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: Scaffold
https://packages.ecosyste.ms/registries/pypi.org/packages/Scaffold
Simple project scaffolding for Python
5 versions
Latest release: 9 months ago
343 downloads last month
Papers Mentioning Scaffold 1,866
10.3389/fmicb.2019.00330
Transcriptional and Proteomic Choreography Under Phosphorus Deficiency and Re-supply in the N2 Fixing Cyanobacterium Trichodesmium erythraeumCited by: 11
Author(s): Kyle R. Frischkorn, Sheean T. Haley, Sonya T. Dyhrman
Software Mentions: 2
Published: about 5 years ago
10.3389/fmicb.2012.00393
Current Approaches on Viral Infection: Proteomics and Functional ValidationsCited by: 7
Author(s): Jie Zheng, Boon Huan Tan, Richard J. Sugrue, Kai Tang
Software Mentions: 2
Published: over 12 years ago
10.3389/fimmu.2021.625649
Complement-Opsonized HIV Modulates Pathways Involved in Infection of Cervical Mucosal Tissues: A Transcriptomic and Proteomic StudyCited by: 2
Author(s): Cecilia Svanberg, Rada Ellegård, Elisa Crisci, Mohammad Khalid, Ninnie Borendal Wodlin, Maria Svenvik, Sofia Nyström, Kenzie Birse, Adam Burgener, Esaki M. Shankar, Marie Larsson
Software Mentions: 2
Published: about 3 years ago
10.3389/fimmu.2014.00067
Pancreatic Cancer Cells Isolated from Muc1-Null Tumors Favor the Generation of a Mature Less Suppressive MDSC PopulationCited by: 11
Author(s): Amritha Kidiyoor, Jorge Schettini, Dahlia M. Besmer, Stephen L. Rego, Sritama Nath, Jennifer M. Curry, Lopamudra Das Roy, Didier Dréau, Pinku Mukherjee
Software Mentions: 2
Published: over 10 years ago
10.3389/fevo.2019.00085
Alternative Transcription at Venom Genes and Its Role as a Complementary Mechanism for the Generation of Venom Complexity in the Common House SpiderCited by: 13
Author(s): Robert A. Haney, Taylor Matte, FitzAnthony S. Forsyth, Jessica E. Garb
Software Mentions: 2
Published: about 5 years ago
10.3389/fimmu.2021.621744
In Vitro Culture Expansion Shifts the Immune Phenotype of Human Adipose-Derived Mesenchymal Stem CellsCited by: 25
Author(s): Richard Jeske, Xuegang Yuan, Qin Fu, Bruce A. Bunnell, Timothy M. Logan, Yan Li
Software Mentions: 2
Published: about 3 years ago
10.3389/fmicb.2018.01397
The Role of Mass Spectrometry in Structural Studies of Flavin-Based Electron Bifurcating EnzymesCited by: 8
Author(s): Monika Tokmina‐Lukaszewska, Angela Patterson, Luke Berry, Liam W. Scott, Narayanaganesh Balasubramanian, Brian Bothner
Software Mentions: 2
Published: almost 6 years ago
10.3389/fcell.2020.00700
Tubular ER Associates With Diacylglycerol-Rich Structures During Lipid Droplet ConsumptionCited by: 4
Author(s): Suriakarthiga Ganesan, Marjan Tavassoli, Brittney Shabits, Vanina Zaremberg
Software Mentions: 2
Published: almost 4 years ago
10.3389/fcell.2020.616706
Identification of the Myogenetic Oligodeoxynucleotides (myoDNs) That Promote Differentiation of Skeletal Muscle Myoblasts by Targeting NucleolinCited by: 11
Author(s): Sayaka Shinji, Koji Umezawa, Yuma Nihashi, Shun‐ichi Nakamura, Takeshi Shimosato, Tomohide Takaya
Software Mentions: 2
Published: over 3 years ago
10.1002/2211-5463.12997
Cystatin C regulates the cytotoxicity of infection‐induced endothelial‐derived β‐amyloidCited by: 2
Author(s): Ron Balczon, K. Adam Morrow, Silas J. Leavesley, C.M. Francis, T. Stevens, Ezinne Agwaramgbo, Christopher Williams, R.P. Stevens, Geri Langham, S.B. Voth, Eugene A. Cioffi, Susan E Weintraub, Troy Stevens
Software Mentions: 2
Published: over 3 years ago
10.15252/embr.201744807
<scp>PAWS</scp> 1 controls Wnt signalling through association with casein kinase 1αCited by: 24
Author(s): Polyxeni Bozatzi, Kevin S. Dingwell, Kevin Z. L. Wu, Fay Cooper, Timothy D. Cummins, Luke D. Hutchinson, J. Vogt, Nicola T. Wood, Thomas Macartney, Joby Varghese, Robert Gourlay, David G. Campbell, James C. Smith, Gopal P. Sapkota
Software Mentions: 2
Published: about 6 years ago
10.1186/1471-2164-15-945
Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding effortsCited by: 25
Author(s): Amanda M. Hulse‐Kemp, Hamid Ashrafi, Xiuting Zheng, Fei Wang, Kevin A. Hoegenauer, Andrea Maeda, Shanshan Yang, Kevin Stoffel, Marta Matvienko, Kimberly Clemons, Joshua A. Udall, Allen Van Deynze, Don C. Jones, David M. Stelly
Software Mentions: 2
Published: over 9 years ago
10.3389/fbioe.2020.00882
Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation SystemsCited by: 26
Author(s): K. M. Shakirova, Viktoriia Y. Ovchinnikova, Э. Б. Дашинимаев
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12864-018-4890-8
A high-density genetic map of extra-long staple cotton (Gossypium barbadense) constructed using genotyping-by-sequencing based single nucleotide polymorphic markers and identification of fiber traits-related QTL in a recombinant inbred line populationCited by: 24
Author(s): Fan Lü, Liping Wang, Xinyi Wang, Haiyan Zhang, Yanfei Zhu, Jiayan Guo, Wenwei Gao, Hao Geng, Quanjia Chen, Yanying Qu
Software Mentions: 2
Published: almost 6 years ago
10.1186/s12915-017-0439-6
Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)Cited by: 54
Author(s): Peter A. Larsen, R. Alan Harris, Yue Liu, Shwetha C. Murali, C. Ryan Campbell, Adam D. Brown, Beth A. Sullivan, Jennifer Shelton, Susan J. Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C. Durand, Muhammad S. Shamim, E Aiden, Donna M. Muzny, Richard A. Gibbs, Anne D. Yoder, Jeffrey Rogers, Kim C. Worley
Software Mentions: 2
Published: over 6 years ago
10.15252/embj.201798714
Evidence for the nuclear import of histones H3.1 and H4 as monomersCited by: 39
Author(s): Michael James Apta‐Smith, Juan R. Hernández-Fernaud, Andrew Bowman
Software Mentions: 2
Published: over 5 years ago
10.3934/Neuroscience.2019.4.299
Brain proteomics links oxidative stress with metabolic and cellular stress response proteins in behavioural alteration of Alzheimer’s disease model ratsCited by: 3
Author(s): Mohammad Azizur Rahman, Shahdat Hossain, Noorlidah Abdullah, Norhaniza Aminudin
Software Mentions: 2
Published: over 5 years ago
10.1016/j.dib.2020.106064
Tandem mass tagged dataset used to characterize muscle-specific proteome changes in beef during early postmortem periodCited by: 2
Author(s): Chaoyu Zhai, B. A. Djimsa, Kitty Brown, Jessica E. Prenni, D. R. Woerner, K. E. Belk, Mahesh N. Nair
Software Mentions: 2
Published: over 3 years ago
10.1016/j.dib.2015.02.013
Supporting data for comparative proteomic analysis of Listeria monocytogenes ATCC 7644 exposed to a sublethal concentration of nisinCited by: 0
Author(s): Kendi Nishino Miyamoto, Karina Mariante Monteiro, Karin da Silva Caumo, Karina Rodrigues Lorenzatto, Henrique Bunselmeyer Ferreira, Adriano Brandelli
Software Mentions: 2
Published: almost 9 years ago
10.1093/database/bav056
Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applicationsCited by: 24
Author(s): Tamás Hegedűs, Pururawa Mayank Chaubey, György Várady, Edit Szabó, Hajnalka Sarankó, Lia Hofstetter, Bernd Roschitzki, Bruno Stieger, Balázs Sarkadi
Software Mentions: 2
Published: almost 9 years ago
10.1186/1471-2164-15-S12-S2
Time-course human urine proteomics in space-flight simulation experimentsCited 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 9 years ago
10.1186/s12014-019-9228-2
Rapid detection of colistin resistance protein MCR-1 by LC–MS/MSCited by: 11
Author(s): Honghui Wang, Yong Chen, Jeffrey R Strich, Steven K. Drake, Jung Ho Youn, Avi Z. Rosenberg, Marjan Guček, Patrick T. McGann, Anthony F. Suffredini, John P. Dekker
Software Mentions: 2
Published: about 5 years ago
10.1038/s42003-019-0426-2
15-deoxy-Δ12,14-Prostaglandin J2 inhibits human soluble epoxide hydrolase by a dual orthosteric and allosteric mechanismCited by: 14
Author(s): Giancarlo Abis, Rebecca L. Charles, J. Kopec, Wyatt W. Yue, R. Andrew Atkinson, Tam T. Bui, Steven Lynham, Popova Sn, Yin-Biao Sun, Franca Fraternali, Philip Eaton, Maria R. Conte
Software Mentions: 2
Published: about 5 years ago
10.3390/cells7120269
Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium StressCited by: 15
Author(s): Meenakshi Agarwal, Ashish Pathak, Rajesh Rathore, Om Prakash, Rakesh Singh, Rajneesh Jaswal, John C. Seaman, Ashvini Chauhan
Software Mentions: 2
Published: over 5 years ago
10.3390/cells8020192
In-Depth Proteome Analysis Highlights HepaRG Cells as a Versatile Cell System Surrogate for Primary Human HepatocytesCited by: 35
Author(s): Georg Tascher, Audrey Burban, Sandrine Camus, Marine Plumel, Stéphanie Chanon, Rémy Le Guével, В. П. Шевченко, Alain Van Dorsselaer, Étienne Lefai, Christiane Guguen‐Guillouzo, Fabrice Bertile
Software Mentions: 2
Published: about 5 years ago
10.1186/1559-0275-11-23
Deciphering the peptidome of urine from ovarian cancer patients and healthy controlsCited by: 36
Author(s): Christopher R. Smith, Ihor Batruch, Josep Miquel Bauça, Hari Kosanam, Julia Ridley, Marcus Q. Bernardini, Felix Leung, Eleftherios P. Diamandis, Vathany Kulasingam
Software Mentions: 2
Published: almost 10 years ago
10.1038/s42003-021-02214-x
Placental secretome characterization identifies candidates for pregnancy complicationsCited by: 16
Author(s): Tina Napso, Xiaohui Zhao, Marta Ibañez-Lligoña, Ionel Sandovici, Richard G. Kay, Amy L. George, Fiona M. Gribble, Frank Reimann, Claire L Meek, Russell S. Hamilton, Amanda N. Sferruzzi‐Perri
Software Mentions: 2
Published: almost 3 years ago
10.1186/s40478-019-0796-1
Composition of the Intranuclear Inclusions of Fragile X-associated Tremor/Ataxia SyndromeCited 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: over 4 years ago
10.3390/cells9092070
Dynamic High-Sensitivity Quantitation of Procollagen-I by Endogenous CRISPR-Cas9 NanoLuciferase TaggingCited by: 7
Author(s): Ben Calverley, Karl E. Kadler, Adam Pickard
Software Mentions: 2
Published: over 3 years ago
10.1038/s41419-021-03589-9
Non-canonical role of wild-type SEC23B in the cellular stress response pathwayCited by: 3
Author(s): Lamis Yehia, Darren Liu, Shuai Fu, Pranav Iyer, Charis Eng
Software Mentions: 2
Published: about 3 years ago
10.1186/s12864-015-2262-1
Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red SeaCited by: 13
Author(s): Kondethimmanahalli H. Chandramouli, Sarah Al-Aqeel, Taewoo Ryu, Huoming Zhang, Loqmane Seridi, Yanal Ghosheh, Pei‐Yuan Qian, Timothy Ravasi
Software Mentions: 2
Published: over 8 years ago
10.1002/btpr.2978
Multiplexed clonality verification of cell lines for protein biologic productionCited by: 4
Author(s): Sofie A. O’Brien, Juhi Ojha, Paul Y K Wu, Wei Shou Hu
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-019-5817-8
Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungiCited by: 16
Author(s): Mari Mäkinen, Jaana Kuuskeri, Pia Laine, Olli‐Pekka Smolander, Andriy Kovalchuk, Zhen Zeng, Fred O. Asiegbu, Lars Paulín, Petri Auvinen, Taina Lundell
Software Mentions: 2
Published: almost 5 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 endonucleaseCited by: 13
Author(s): Vandana Kumari, Rahul Sharma, Vijay Pal Yadav, Abhishek Kumar Gupta, Alok Bhattacharya, Sudha Bhattacharya
Software Mentions: 2
Published: almost 13 years ago
10.1186/s12014-017-9172-y
A proteomic approach to understanding the pathogenesis of idiopathic macular hole formationCited by: 10
Author(s): Pingbo Zhang, Mingyan Zhu, Yuming Zhao, Jiang Qian, Craig Dufresne, Randi Turner, Richard D. Semba, Sharon D. Solomon
Software Mentions: 2
Published: over 6 years ago
10.1186/s13068-018-1350-2
Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profilesCited by: 19
Author(s): Jiaxi Miao, Mengmeng Wang, Lei Ma, Tuo Li, Qiwei Huang, Dongyang Liu, Qirong Shen
Software Mentions: 2
Published: over 5 years ago
10.1038/s42003-020-1091-1
Genomic insights of body plan transitions from bilateral to pentameral symmetry in EchinodermsCited by: 25
Author(s): Yongxin Li, Akihito Omori, Rachel L. Flores, Sheri Satterfield, Christine Nguyen, Tomomi Ota, Toko Tsurugaya, Tetsuro Ikuta, Kazuho Ikeo, Mani Kikuchi, Jason Cheok Kuan Leong, Adrian Reich, Hao Meng, Wenting Wan, Yang Dong, Yaondong Ren, Si Zhang, Tao Zeng, Masahiro Uesaka, Yui Uchida, Xueyan Li, Tomoko Shibata, Takahiro Bino, Kota Ogawa, Shuji Shigenobu, Mariko Kondo, Fayou Wang, Luonan Chen, Gary M. Wessel, Hidetoshi Saiga, R. Andrew Cameron, Brian T. Livingston, Cynthia A. Bradham, Wen Wang, Naoki Irie
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12859-017-1563-6
ProteoModlR for functional proteomic analysisCited by: 5
Author(s): Paolo Cifani, Mojdeh Shakiba, Sagar Chhangawala, Alex Kentsis
Software Mentions: 2
Published: about 7 years ago
10.1016/j.celrep.2021.109230
Integrin intra-heterodimer affinity inversely correlates with integrin activatabilityCited by: 11
Author(s): Guangyu Sun, Emilie Guillon, Scott A. Holley
Software Mentions: 2
Published: almost 3 years ago
10.3390/cells9061423
Chromatin Trapping of Factors Involved in DNA Replication and Repair Underlies Heat-Induced Radio- and ChemosensitizationCited by: 3
Author(s): Artem V. Luzhin, Bogdan Avanesyan, Artem K. Velichko, Victoria О. Shender, Natalia Ovsyannikova, Georgij Arapidi, Polina V. Shnaider, Nadezhda V. Petrova, Igor I. Kireev, Sergey V. Razin, Omar L. Kantidze
Software Mentions: 2
Published: almost 4 years ago
10.1016/j.dib.2014.09.006
Data set for the proteomic inventory and quantitative analysis of chicken uterine fluid during eggshell biomineralizationCited by: 12
Author(s): Pauline Marie, Valérie Labas, Aurélien Brionne, Grégoire Harichaux, Christelle Hennequet-Antier, Yves Nys, Joël Gautron
Software Mentions: 2
Published: over 9 years ago
10.3389/fcimb.2021.724569
An Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis SputumCited by: 6
Author(s): Alexander C. Graf, Johanna Striesow, Jan Pané‐Farré, Thomas Sura, Martina Wurster, Michael Lalk, Dietmar H. Pieper, Dörte Becher, Barbara C. Kahl, Katharina Riedel
Software Mentions: 2
Published: over 2 years ago
10.1242/dev.185421
Ykt6-dependent endosomal recycling is required for Wnt secretion in the <i>Drosophila</i> wing epitheliumCited by: 13
Author(s): Karen Linnemannstöns, Leonie Witte, Pradhipa Karuna, Jeanette Clarissa Kittel, Adi Danieli, Denise Madeddu, Lena Nitsch, Mona Honemann‐Capito, Ferdi Grawe, Andreas Wodarz, Julia Christina Gross
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.ppat.1005640
Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus Colletotrichum higginsianumCited by: 71
Author(s): Sonia Campo, Kerrigan B. Gilbert, James C. Carrington
Software Mentions: 2
Published: almost 8 years ago
10.1186/2045-3701-3-37
Proteomic analysis of mismatch repair-mediated alkylating agent-induced DNA damage responseCited by: 4
Author(s): Xi Chen, Yong Zhao, Guo Min Li, Lin Guo
Software Mentions: 2
Published: over 10 years ago
10.1186/1471-2164-9-595
Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba speciesCited by: 53
Author(s): Hernán Lorenzi, Mathangi Thiagarajan, Brian J. Haas, Jennifer Wortman, Neil Hall, Elisabet Caler
Software Mentions: 2
Published: over 15 years ago
10.3390/cancers13143618
TRAF6 Phosphorylation Prevents Its Autophagic Degradation and Re-Shapes LPS-Triggered Signaling NetworksCited by: 3
Author(s): Julia Busch, Rita Moreno, Laureano de la Vega, Vera V. Saul, Susanne Bacher, Felix von Zweydorf, Marius Ueffing, Axel Weber, Christian Johannes Gloeckner, Uwe Linne, Michael Kracht, M. Lienhard Schmitz
Software Mentions: 2
Published: almost 3 years ago
10.1111/1462-2920.13930
Transcriptome and proteome dynamics in chemostat culture reveal how<i>Campylobacter jejuni</i>modulates metabolism, stress responses and virulence factors upon changes in oxygen availabilityCited by: 28
Author(s): Edward Guccione, John J. Kendall, Andrew Hitchcock, Nitanshu Garg, Michael A. White, Francis Mulholland, Robert K. Poole, David J. Kelly
Software Mentions: 2
Published: over 6 years ago
10.1186/s13072-016-0087-z
Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancersCited by: 23
Author(s): Jian Sun, Yilin Zhao, Rebecca McGreal, Yamit Cohen‐Tayar, Shira Rockowitz, Carola Wilczek, Ruth Ashery‐Padan, David Shechter, Deyou Zheng, Aleš Cvekl
Software Mentions: 2
Published: over 7 years ago
10.1186/s12964-018-0257-7
Kv1.3 channel blockade with the Vm24 scorpion toxin attenuates the CD4+ effector memory T cell response to TCR stimulationCited by: 19
Author(s): José Ignacio Veytia-Bucheli, Juana María Jiménez-Vargas, Erika Melchy-Pérez, Monserrat Alba Sandoval-Hernández, Lourival D. Possani, Yvonne Rosenstein
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0140650
Sperm Proteome Maturation in the Mouse EpididymisCited by: 83
Author(s): Sheri Skerget, Matthew Rosenow, Konstantinos Pétritis, Timothy L. Karr
Software Mentions: 2
Published: over 8 years ago
10.1186/s12864-019-5981-x
Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traitsCited by: 14
Author(s): Jitao Li, Jianjian Lv, Ping Liu, Ping Chen, Jiajia Wang, Jian Li
Software Mentions: 2
Published: almost 5 years ago
10.3389/fcell.2021.634355
Recovery of Depleted miR-146a in ALS Cortical Astrocytes Reverts Cell Aberrancies and Prevents Paracrine Pathogenicity on Microglia and Motor NeuronsCited by: 20
Author(s): Marta Barbosa, Cátia Gomes, Catarina Sequeira, Joana Gonçalves-Ribeiro, Carolina Campos Pina, Luís A. R. Carvalho, Rui Moreira, Sandra H. Vaz, Ana Rita Vaz, Dora Brites
Software Mentions: 2
Published: about 3 years ago
10.1186/1471-2164-15-95
Characterization of the membrane proteome and N-glycoproteome in BV-2 mouse microglia by liquid chromatography-tandem mass spectrometryCited by: 17
Author(s): Dohyun Han, Seong-Yong Moon, Yikwon Kim, Hophil Min, Youngsoo Kim
Software Mentions: 2
Published: over 10 years ago
10.1007/s00726-021-03006-7
Gamma-gliadin specific celiac disease antibodies recognize p31-43 and p57-68 alpha gliadin peptides in deamidation related manner as a result of cross-reactionCited by: 7
Author(s): Ádám Diós, Rita Elek, Ildikò Szabó, Szilvia Horváth, Judit Gyimesi, Róbert Király, Katharina Werkstetter, Sibylle Koletzko, László Fésüs, Ilma Rita Korponay-Szabó
Software Mentions: 2
Published: almost 3 years ago
10.3390/cancers6031464
Phosphorylation of Large T Antigen Regulates Merkel Cell Polyomavirus ReplicationCited by: 19
Author(s): José Ángel Menéndez Díaz, Xin Wang, Sabrina H. Tsang, Jing Jiao, Jianxin You
Software Mentions: 2
Published: almost 10 years ago
10.1186/s13075-019-1961-4
Proteomic and histopathological characterisation of sicca subjects and primary Sjögren’s syndrome patients reveals promising tear, saliva and extracellular vesicle disease biomarkersCited by: 58
Author(s): Lara A. Aqrawi, Hilde Kanli Galtung, Eduarda Guerreiro, Reidun Øvstebø, Bernd Thiede, Tor Paaske Utheim, Xiangjun Chen, Øygunn Aass Utheim, Øyvind Palm, Kathrine Skarstein, Janicke Liaaen Jensen
Software Mentions: 2
Published: almost 5 years ago
10.3389/fimmu.2017.00358
Human Melanoma-Derived Extracellular Vesicles Regulate Dendritic Cell MaturationCited 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: about 7 years ago
10.3389/fmed.2017.00080
Assessment of Circulating Protein Signatures for Kidney Transplantation in Pediatric RecipientsCited by: 9
Author(s): Tara K. Sigdel, Minnie M. Sarwal
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pone.0115213
Microtubule-Dependent Modulation of Adhesion Complex CompositionCited by: 37
Author(s): Daniel Ng, Jonathan D. Humphries, Adam Byron, Angélique Millon‐Frémillon
Software Mentions: 2
Published: over 9 years ago
10.1016/j.mbplus.2020.100027
Proteomic fingerprints of damage in extracellular matrix assembliesCited by: 18
Author(s): Alexander Eckersley, Matiss Ozols, Ronan O’Cualain, Emma-Jayne Keevill, April Foster, Suzanne M. Pilkington, David Knight, Christopher E.M. Griffiths, Rachel Watson, Michael J. Sherratt
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-021-07678-z
ddRAD sequencing: an emerging technology added to the biosecurity toolbox for tracing the origin of brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae)Cited by: 6
Author(s): Yan Ji, Gábor Vétek, Chandan Pal, Jinping Zhang, Rania Gmati, Qing-Hai Fan, Disna N. Gunawardana, Allan Burne, Diane Anderson, K. B. Rebijith, Sherly George, Péter Farkas, Dongmei Li
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0215267
Muscle fiber hypertrophy in response to 6 weeks of high-volume resistance training in trained young men is largely attributed to sarcoplasmic hypertrophyCited by: 52
Author(s): Cody T. Haun, Christopher G. Vann, Shelby C. Osburn, Petey W. Mumford, Paul A. Roberson, Matthew A. Romero, Carlton D. Fox, Christopher Johnson, Hailey A. Parry, Andreas N. Kavazis, Jordan R. Moon, Veera L.D. Badisa, Benjamin M. Mwashote, Victor Ibeanusi, Kaelin C. Young, Michael D. Roberts
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0221669
Cholinergic-like neurons carrying PSEN1 E280A mutation from familial Alzheimer’s disease reveal intraneuronal sAPPβ fragments accumulation, hyperphosphorylation of TAU, oxidative stress, apoptosis and Ca2+ dysregulation: Therapeutic implicationsCited by: 16
Author(s): Viviana Soto-Mercado, Miguel Mendivil-Perez, Carlos Vélez-Pardo, Francisco Lopera, Marlene Jiménez-Del-Río
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0188105
Profiling of proteins secreted in the bovine oviduct reveals diverse functions of this luminal microenvironmentCited by: 36
Author(s): Viju Vijayan Pillai, Darren Weber, Brett S. Phinney, Vimal Selvaraj
Software Mentions: 2
Published: over 6 years ago
10.1002/acn3.51242
Elevated levels of extracellular vesicles in progranulin‐deficient mice and FTD‐ GRN PatientsCited by: 7
Author(s): Andrew E. Arrant, Skylar E. Davis, Rachael M Vollmer, Charles Murchison, James A. Mobley, Alissa L. Nana, Salvatore Spina, Lea T. Grinberg, Anna Karydas, Bruce L. Miller, William W. Seeley, Erik D. Roberson
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2020.00598
Elucidating the Regulon of a Fur-like Protein in Mycobacterium avium subsp. paratuberculosis (MAP)Cited by: 6
Author(s): Fernanda Miyagaki Shoyama, Taveesak Janetanakit, John P. Bannantine, Raúl G. Barletta, Srinand Sreevatsan
Software Mentions: 2
Published: about 4 years ago
10.3389/fmicb.2017.01772
Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic ModelingCited by: 21
Author(s): Sergio Triana, Hans de Cock, Robin A. Ohm, Giovanna Danies, Han A. B. Wösten, Silvia Restrepo, Andrés Fernando González Barrios, Adriana Celis
Software Mentions: 2
Published: over 6 years ago
10.3390/mps3010015
A Fast and Accurate Method to Identify and Quantify Enzymes in Brush-Border Membranes: In Situ Hydrolysis Followed by Nano LC-MS/MSCited by: 7
Author(s): Antonio Brun, Melisa E Magallanes, Carlos Martı́nez del Rio, Gregory A. Barrett-Wilt, William H. Karasov, Enrique Caviedes‐Vidal
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2164-15-536
Characterization and potential evolutionary impact of transposable elements in the genome of Cochliobolus heterostrophusCited by: 27
Author(s): Mateus Ferreira Santana, José Cleydson Ferreira da Silva, Eduardo S. G. Mizubuti, Elza Fernandes de Araújo, Bradford Condon, B. Gillian Turgeon, Marisa Vieira de Queiroz
Software Mentions: 2
Published: almost 10 years ago
10.3389/fmicb.2014.00259
Interactions of proteins with biogenic iron oxyhydroxides and a new culturing technique to increase biomass yields of neutrophilic, iron-oxidizing bacteriaCited by: 4
Author(s): Roman A. Barco, Katrina J. Edwards
Software Mentions: 2
Published: almost 10 years ago
10.3390/biology9090294
A Poplar Rust Effector Protein Associates with Protein Disulfide Isomerase and Enhances Plant SusceptibilityCited by: 8
Author(s): Mst Hur Madina, Saifur Rahman, Xiaoqiang Huang, Yang Zhang, Huanquan Zheng, Hugo Germain
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-015-2076-1
Molt-dependent transcriptomic analysis of cement proteins in the barnacle Amphibalanus amphitriteCited by: 31
Author(s): Wenxu Zheng, Dagmar H. Leary, Jinny Liu, Robert E. Settlage, Kenan P. Fears, Stella H. North, Anahita Mostaghim, Tara Essock‐Burns, Sarah E. Haynes, Kathryn J. Wahl, Christopher M. Spillmann
Software Mentions: 2
Published: over 8 years ago
10.3389/fmicb.2019.00384
Mixotrophic Growth Under Micro-Oxic Conditions in the Purple Sulfur Bacterium “Thiodictyon syntrophicum”Cited by: 14
Author(s): Samuel M. Luedin, Nicola Storelli, Francesco Danza, Samuele Roman, Matthias Wittwer, Joël F. Pothier, Mauro Tonolla
Software Mentions: 2
Published: about 5 years ago
10.3389/fmicb.2020.01227
Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class “Acidobacteriia”Cited by: 14
Author(s): Ohana Y.A. Costa, Chidinma Oguejiofor, Daniela Zühlke, Cristine Chaves Barreto, Christine Wünsche, Katharina Riedel, Eiko E. Kuramae
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12934-019-1243-5
Redesigning the Aspergillus nidulans xylanase regulatory pathway to enhance cellulase production with xylose as the carbon and inducer sourceCited by: 4
Author(s): P. Ballmann, Jorge D. Lightfoot, Majon Muller, Stefan Dröge, Rolf A. Prade
Software Mentions: 2
Published: over 4 years ago
10.3389/fneur.2018.00465
Environmental Enrichment Upregulates Striatal Synaptic Vesicle-Associated Proteins and Improves Motor FunctionCited by: 6
Author(s): Suk Young Song, Minji Chae, Ji Hea Yu, Min Young Lee, Soonil Pyo, Yeseul Shin, Ahreum Baek, Jung Won Park, Eun Sook Park, Ja Young Choi, Sung Rae Cho
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0220568
Delineating the role of FANCA in glucose-stimulated insulin secretion in β cells through its protein interactomeCited by: 6
Author(s): Dragana Lagundžin, Wen Feng Hu, Henry C.-H. Law, Kimiko L. Krieger, Fangfang Qiao, Emalie J. Clement, Andjela Drincic, Olgica Nedić, Michael J. Naldrett, Sophie Alvarez, Nicholas T. Woods
Software Mentions: 2
Published: over 4 years ago
10.1186/s12964-016-0133-2
The arabidopsis cyclic nucleotide interactomeCited by: 34
Author(s): Lara Donaldson, Stuart Meier, Chris Gehring
Software Mentions: 2
Published: about 8 years ago
10.1242/bio.037937
Physiological profile of undifferentiated bovine blastocyst-derived trophoblastsCited by: 13
Author(s): Viju Vijayan Pillai, L. G. B. Siqueira, Moubani Das, Tiffany G. Kei, Lan N. Tu, Anthony W. Herren, Brett S. Phinney, Soon Hon Cheong, Peter J. Hansen, Vimal Selvaraj
Software Mentions: 2
Published: over 5 years ago
10.1107/S2059798315022482
Initiating heavy-atom-based phasing by multi-dimensional molecular replacementCited by: 3
Author(s): Bjørn Panyella Pedersen, Pontus Gourdon, Xiangyu Liu, Jesper Lykkegaard Karlsen, Poul Nissen
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0028532
Conserved BK Channel-Protein Interactions Reveal Signals Relevant to Cell Death and SurvivalCited by: 38
Author(s): Bernd Sokolowski, Sandra Orchard, Margaret Harvey, Settu Sridhar, Yoshihisa Sakai
Software Mentions: 2
Published: over 12 years ago
10.3389/fpls.2019.01657
A LysR-Type Transcriptional Regulator LcrX Is Involved in Virulence, Biofilm Formation, Swimming Motility, Siderophore Secretion, and Growth in Sugar Sources in Xanthomonas axonopodis Pv. glycinesCited by: 14
Author(s): Hanbi Park, Eunsoo Do, Minyoung Kim, Hye-Jee Park, Jong-Chan Lee, Sang-Wook Han
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0228134
Proteomic profiling of proteins in the dorsal horn of the spinal cord in dairy cows with chronic lamenessCited by: 2
Author(s): Daniel Herzberg, Pablo Strobel, Heine Yacob Müller, Constanza Meneses, Mads Werner, Hedie Bustamante
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0028949
Proteome Changes Driven by Phosphorus Deficiency and Recovery in the Brown Tide-Forming Alga Aureococcus anophagefferensCited 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 12 years ago
10.1093/bioinformatics/btaa288
HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-CCited by: 11
Author(s): Ryo Nakabayashi, Shinichi Morishita
Software Mentions: 2
Published: about 4 years ago
10.1186/s12864-019-5750-x
Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticepsCited by: 14
Author(s): Alexander Capraro, Denis O’Meally, Shafagh A. Waters, Hardip R. Patel, Arthur Georges, Paul D. Waters
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0007050
Barrier-to-Autointegration Factor Proteome Reveals Chromatin-Regulatory PartnersCited by: 93
Author(s): Rocío Montes de, Christopher J. Shoemaker, Marjan Guček, Robert N. Cole, Katherine L. Wilson
Software Mentions: 2
Published: over 14 years ago
10.1016/j.bbapap.2013.04.004
A tutorial for software development in quantitative proteomics using PSI standard formatsCited by: 5
Author(s): Faviel F. Gonzalez-Galarza, Da Qi, Jun Fan, Conrad Bessant, Andrew R. Jones
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0136362
Proteins with Intrinsically Disordered Domains Are Preferentially Recruited to Polyglutamine AggregatesCited by: 30
Author(s): Maggie P. Wear, Dmitry Kryndushkin, Robert N. O’Meally, Jason L. Sonnenberg, Robert N. Cole, Frank Shewmaker
Software Mentions: 2
Published: over 8 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 responsesCited 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 4 years ago
10.1371/journal.pone.0064044
Urine Proteins Identified by Two-Dimensional Differential Gel Electrophoresis Facilitate the Differential Diagnoses of ScrapieCited 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: almost 11 years ago
10.1042/BJ20130579
Nogo-A couples with Apg-1 through interaction and co-ordinate expression under hypoxic and oxidative stressCited by: 13
Author(s): Florian Kern, Ruslan I. Stanika, Bettina Sarg, Martin Offterdinger, Daniel Heß, Gerald J. Obermair, Herbert Lindner, Christine E. Bandtlow, Ludger Hengst, Rüdiger Schweigreiter
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0119523
Experimental Study on Differences in Clivus Chordoma Bone Invasion: An iTRAQ-Based Quantitative Proteomic AnalysisCited by: 16
Author(s): Zhen Wu, Liang Wang, Zhengguang Guo, Ke Wang, Yang Zhang, Kaibing Tian, Junting Zhang, Wei Sun, Chunmei Yu
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pone.0021991
A Novel Role of Protein Tyrosine Kinase2 in Mediating Chloride Secretion in Human Airway Epithelial CellsCited by: 7
Author(s): Lianchun Liang, Owen M. Woodward, Zhaohui Chen, Robert J. Cotter, William B. Guggino
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0018497
A Mighty Small Heart: The Cardiac Proteome of Adult Drosophila melanogasterCited 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: about 13 years ago
10.1371/journal.pone.0150239
Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID)Cited by: 30
Author(s): Christoph Schweingruber, Paolo Soffientini, Marc‐David Ruepp, Ángela Bachi, Oliver Mühlemann
Software Mentions: 2
Published: about 8 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 SiteCited 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: almost 10 years ago
10.1007/s00401-021-02285-4
Age-associated insolubility of parkin in human midbrain is linked to redox balance and sequestration of reactive dopamine metabolitesCited by: 26
Author(s): Jacqueline M. Tokarew, Daniel N. El-Kodsi, Nathalie A. Lengacher, Travis K. Fehr, Antoinette Nguyen, Bojan Shutinoski, Brian O’Nuallain, Ming Jin, Jasmine Khan, Andy Cheuk-Him Ng, Juan Li, Quan Jiang, Mei Zhang, Liqun Wang, Rajib Sengupta, Kathryn R. Barber, An Tran, Doo Soon Im, Steve Callaghan, David Park, Stéphanie Zandee, Xiajun Dong, Clemens R. Scherzer, Alexandre Prat, Eve C. Tsai, Masashi Takanashi, Nobutaka Hattori, Jennifer A. Chan, Luigi Zecca, Andrew B. West, Arne Holmgren, Lawrence G. Puente, Gary S. Shaw, Gergely Tóth, John Woulfe, Peggy Taylor, Julianna J. Tomlinson, Michael G. Schlossmacher
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0185125
Biochemical and biomechanical properties of the pacemaking sinoatrial node extracellular matrix are distinct from contractile left ventricular matrixCited 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: over 6 years ago