bioconductor: MSstats | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections
Cited by: 9
Author(s): Matineh Rahmatbakhsh, Alla Gagarinova, Mohan Babu
Software Mentions: 21
Published: over 3 years ago

10.3389/fncel.2020.612560

Proteomic Characterization of Human Neural Stem Cells and Their Secretome During in vitro Differentiation
Cited by: 19
Author(s): Jakub Červenka, Jiřina Tylečková, Helena Kupcová Skalníková, Kateřina Vodičková Kepková, Ievgeniia Poliakh, Ivona Valeková, Lucie Pfeiferová, Michal Kolář, Michaela Vaškovičová, Tereza Pánková, Petr Vodička
Software Mentions: 7
Published: almost 4 years ago

10.1074/mcp.RA120.002105

MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures
Cited by: 70
Author(s): Ting Huang, Meena Choi, Manuel Tzouros, Sabrina Golling, Nikhil J. Pandya, Balázs Bánfai, Tom Dunkley, Olga Vitek
Software Mentions: 7
Published: about 4 years ago

10.1038/s41598-021-94256-8

Proteomics and metabonomics analyses of Covid-19 complications in patients with pulmonary fibrosis
Cited by: 10
Author(s): Jianrong Yang, Chunxia Chen, Wan Chen, Luying Huang, Zhao Fu, Kun Ye, Liwen Lv, Zhihuang Nong, Xing Zhou, Wensheng Lu, Ming Zhong
Software Mentions: 6
Published: over 3 years ago

10.1128/AAC.00504-21

Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance
Cited by: 4
Author(s): Andrej Trauner, Amir Banaei‐Esfahani, Sebastian M. Gygli, Philipp Warmer, Julia Feldmann, Mattia Zampieri, Sònia Borrell, Ben C. Collins, Christian Beisel, Ruedi Aebersold, Sébastien Gagneux
Software Mentions: 6
Published: over 3 years ago

10.1016/j.celrep.2019.06.046

Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry
Cited by: 68
Author(s): Pavel Bouchal, Olga T. Schubert, Jakub Faktor, Lenka Čápková, Hana Imrichová, Karolína Zoufalová, Vendula Páralová, Roman Hrstka, Yansheng Liu, H. Alexander Ebhardt, Eva Budínská, Rudolf Nenutil, Ruedi Aebersold
Software Mentions: 6
Published: over 5 years ago

10.3389/fnmol.2019.00272

DYRK1A Overexpression Alters Cognition and Neural-Related Proteomic Pathways in the Hippocampus That Are Rescued by Green Tea Extract and/or Environmental Enrichment
Cited by: 18
Author(s): Ilario De Toma, Mireia Ortega, Patrick Aloy, Eduard Sabidó, Mara Dierssen
Software Mentions: 5
Published: about 5 years ago

10.1021/acsomega.1c03681

Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells
Cited by: 5
Author(s): Ankitha Shetty, Santosh D. Bhosale, Subhash Tripathi, Tanja Buchacher, Rahul Biradar, Omid Rasool, Robert Moulder, Sanjeev Galande, Riitta Lahesmaa
Software Mentions: 5
Published: over 3 years ago

10.15252/emmm.201404874

Non‐invasive prognostic protein biomarker signatures associated with colorectal cancer
Cited by: 42
Author(s): Silvia Šurinová, Lenka Radová, Meena Choi, Josef Srovnal, Hermann Brenner, Olga Vitek, Marián Hajdúch, Ruedi Aebersold
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0153160

SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools
Cited by: 39
Author(s): Peter Blattmann, Moritz Heusel, Ruedi Aebersold
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-019-43091-z

A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model
Cited by: 10
Author(s): Tatjana Sajic, Rodolfo Ciuffa, Vera Lemos, Pan Xu, Valentina Leone, Chen Li, Evan G. Williams, Georgios Makris, Amir Banaei‐Esfahani, Mathias Heikenwälder, Kristina Schoonjans, Ruedi Aebersold
Software Mentions: 5
Published: over 5 years ago

10.3389/fphys.2021.652799

Proteomics and Machine Learning Approaches Reveal a Set of Prognostic Markers for COVID-19 Severity With Drug Repurposing Potential
Cited by: 45
Author(s): Kruthi Suvarna, Deeptarup Biswas, Medha Gayathri J Pai, Arup Acharjee, Renuka Bankar, Viswanthram Palanivel, Akanksha Salkar, Ayushi Verma, Amrita Mukherjee, Manisha Choudhury, Saicharan Ghantasala, Susmita Ghosh, Avinash Singh, Arghya Banerjee, Apoorva Badaya, Surbhi Bihani, Gaurish Loya, Krishi Mantri, Ananya Burli, Jyotirmoy Roy, Alisha Srivastava, Sachee Agrawal, Om Shrivastav, Jayanthi Shastri, Sanjeeva Srivastava
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0249771

OptiMissP: A dashboard to assess missingness in proteomic data-independent acquisition mass spectrometry
Cited by: 6
Author(s): Angelica Arioli, Arianna Dagliati, Bethany Geary, Niels Peek, Philip A. Kalra, Anthony D. Whetton, Nophar Geifman
Software Mentions: 4
Published: over 3 years ago

10.1101/2021.06.06.446826

Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant
Cited by: 84
Author(s): Lucy Thorne, Mehdi Bouhaddou, Ann-Kathrin Reuschl, Lorena Zuliani-Alvarez, Benjamin J. Polacco, Adrian Pelin, Jyoti Batra, Matt Whelan, Manisha R. Ummadi, Ajda Roic, Jane Turner, Kirsten Obernier, Hannes Braberg, Margaret Soucheray, Alicia Richards, Kuei‐Ho Chen, Bhavya Harjai, Danish Memon, Myra Hosmillo, Joseph Hiatt, Aminu S. Jahun, Ian Goodfellow, Mahdad Noursadeghi, Jacqueline M. Fabius, Kevan M. Shokat, Natalia Jura, Kliment A. Verba, Pedro Beltrão, Danielle L. Swaney, Adolfo Garcı́a-Sastre, Clare Jolly, Greg J. Towers, Nevan J. Krogan
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms22158251

DIA-Based Quantitative Proteomics Reveals the Protein Regulatory Networks of Floral Thermogenesis in Nelumbo nucifera
Cited by: 5
Author(s): Yueyang Sun, Yu Zeng, Jing Jin, Hao Chen, Zhiying Liu, Qinru Zi, Zeyang Xiong, Ying Wang, Qian Li, Jing Peng, Yi Ding
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-72625-z

Re-establishment of the epigenetic state and rescue of kinome deregulation in Ts65Dn mice upon treatment with green tea extract and environmental enrichment
Cited by: 13
Author(s): Ilario De Toma, Mireia Ortega, Silvina Catuara-Solarz, Cesar Sierra, Eduard Sabidó, Mara Dierssen
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-017-05949-y

Enhanced differential expression statistics for data-independent acquisition proteomics
Cited by: 29
Author(s): Tomi Suomi, Laura L. Elo
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2020.589005

Elucidation of the miR164c-Guided Gene/Protein Interaction Network Controlling Seed Vigor in Rice
Cited by: 5
Author(s): Kerui Huang, Shiqi Zhou, Kaimin Shen, Yan Zhou, Feng Wang, Xiaocheng Jiang
Software Mentions: 4
Published: about 4 years ago

10.1093/bioinformatics/btw580

DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics
Cited by: 212
Author(s): Samuel Wieczorek, Florence Combes, Cosmin Lazar, Quentin Giai Gianetto, Laurent Guy, Alexia Dorffer, Anne-Marie Hesse, Yohann Couté, Myriam Ferro, Christophe Bruley, Thomas Bürger
Software Mentions: 4
Published: over 8 years ago

10.1093/bioinformatics/btz961

<i>iq</i>: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
Cited by: 42
Author(s): Thang V. Pham, Alex A. Henneman, Connie R. Jiménez
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-13-S16-S6

Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs
Cited by: 103
Author(s): Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek
Software Mentions: 3
Published: about 12 years ago

10.1186/2040-2392-5-38

Integrative proteomic analysis of the NMDA NR1 knockdown mouse model reveals effects on central and peripheral pathways associated with schizophrenia and autism spectrum disorders
Cited by: 31
Author(s): Hendrik Wesseling, Paul C. Guest, Chi-Ming Lee, Erik H. F. Wong, Hassan Rahmoune, Sabine Bahn
Software Mentions: 3
Published: over 10 years ago

10.1016/j.mcpro.2021.100077

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs
Cited by: 127
Author(s): Fengchao Yu, Sarah E. Haynes, Alexey I. Nesvizhskii
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13024-020-00398-0

Cerebrospinal fluid profile of NPTX2 supports role of Alzheimer’s disease-related inhibitory circuit dysfunction in adults with Down syndrome
Cited by: 18
Author(s): Olivia Belbin, Mei Fang Xiao, Desheng Xu, María Carmona-Iragui, Jordi Malé i Pegueroles, Bessy Benejam, Laura Videla, Susana Fernández, Isabel Barroeta, Raúl Nuñez‐Llaves, Víctor Montal, Eduard Vilaplana, Miren Altuna, Jordi Clarimón, Daniel Alcolea, Rafael Blesa, Alberto Lleó, Paul F. Worley, Juan Fortea
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008840

The kinase Isr1 negatively regulates hexosamine biosynthesis in S. cerevisiae
Cited by: 3
Author(s): Emma B Alme, Erica Stevenson, Nevan J. Krogan, Danielle L. Swaney, David P. Toczyski
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pntd.0005104

Differential Protein Expression in the Hemolymph of Bithynia siamensis goniomphalos Infected with Opisthorchis viverrini
Cited by: 11
Author(s): Kulwadee Suwannatrai, Apiporn Suwannatrai, Pairat Tabsripair, Jariya Umka Welbat, Sirikachorn Tangkawattana, Cinzia Cantacessi, Jason Mulvenna, Smarn Tesana, Alex Loukas, Javier Sotillo
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0121314

A Mass Spectrometric-Derived Cell Surface Protein Atlas
Cited by: 306
Author(s): Damaris Bausch-Fluck, Andreas Hofmann, Thomas Bock, Andreas P. Frei, Ferdinando Cerciello, Andrea Jacobs, Hansjoerg Moest, Ulrich Omasits, Rebekah L. Gundry, Charles Yoon, Ralph Schiess, Alexander Schmidt, Paulina Mirkowska, Anetta Härtlová, Jennifer E. Van Eyk, Jean‐Pierre Bourquin, Ruedi Aebersold, Kenneth R. Boheler, Peter W. Zandstra, Bernd Wollscheid
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0214110

The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification
Cited by: 43
Author(s): Mona Abed, Erik Verschueren, Hanna G. Budayeva, Peter Liu, Donald S. Kirkpatrick, Rohit Reja, Sarah Kummerfeld, Joshua D. Webster, Sarah Gierke, Mike Reichelt, Keith R. Anderson, Robert J. Newman, Merone Roose‐Girma, Zora Modrušan, Hazal Pektas, Emin Maltepe, Kim Newton, Vishva M. Dixit
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-020-01384-4

Multiplexed quantitative proteomics provides mechanistic cues for malaria severity and complexity
Cited by: 15
Author(s): Vipin Kumar, Ray S, Shalini Aggarwal, Deeptarup Biswas, Manali Jadhav, Radha Yadav, Sanjeev Sabnis, Soumaditya Banerjee, Arunansu Talukdar, Sanjay Kumar Kochar, Suvin Shetty, Kunal Sehgal, Swati Patankar, Sanjeeva Srivastava
Software Mentions: 3
Published: about 4 years ago

10.3389/fpls.2020.01278

Combined Proteome and Transcriptome Analysis of Heat-Primed Azalea Reveals New Insights Into Plant Heat Acclimation Memory
Cited by: 14
Author(s): Xiuyun Wang, Li Zheng, Bing Liu, Hong Zhou, Mohamed S. Elmongy, Yiping Xia
Software Mentions: 3
Published: over 4 years ago

10.3390/jcm8081253

Multi-Omics Characterization of the Spontaneous Mesenchymal–Epithelial Transition in the PMC42 Breast Cancer Cell Lines
Cited by: 22
Author(s): Sugandha Bhatia, James Monkman, Tony Blick, Pascal H.G. Duijf, Shivashankar H. Nagaraj, Erik W. Thompson
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-32314-4

Separation of blood microsamples by exploiting sedimentation at the microscale
Cited by: 22
Author(s): David Forchelet, Steve Béguin, Tatjana Sajic, Nasim Bararpour, Zoltan Pataky, Miguel Frias, Silke Grabherr, Marc Augsburger, Y. Liu, Mirren Charnley, Julien Déglon, Ruedi Aebersold, Aurélien Thomas, Philippe Renaud
Software Mentions: 3
Published: over 6 years ago

10.21203/rs.3.rs-515215/v1

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes
Cited by: 6
Author(s): Kliment A. Verba, Meghna Gupta, Caleigh M. Azumaya, Michelle Moritz, Sergei Pourmal, Amy Diallo, Gregory E. Merz, Gwendolyn Μ. Jang, Mehdi Bouhaddou, Andrea Fossati, Axel F. Brilot, Devan Diwanji, Evelyn Hernandez, Nadia Herrera, Huong T. Kratochvil, Victor Lam, Fēi Li, Yang Li, Henry C. Nguyen, Carlos Nowotny, Tristan W. Owens, Jessica K. Peters, Alexandrea N. Rizo, Ursula Schulze‐Gahmen, Amber M. Smith, Iris D. Young, Zanlin Yu, Daniel Asarnow, Christian B. Billesbølle, Melody G. Campbell, Jen Chen, Kuei‐Ho Chen, Un Seng Chio, Miles Sasha Dickinson, Loan Doan, Mingliang Jin, Kate Kim, Junrui Li, Yen-Li Li, Edmond M. Linossi, Yanxin Liu, Megan Lo, Jocelyne Lopez, Kyle E. Lopez, Adamo Mancino, Frank R. Moss, Michael Paul, Komal Ishwar Pawar, Adrian Pelin, Thomas H. Pospiech, Cristina Puchades, Soumya G. Remesh, Maliheh Safari, Kaitlin Schaefer, Ming Sun, Mariano Tabios, Aye C. Thwin, Erron W. Titus, Raphael Trenker, Eric Tse, Tsz Kin Martin Tsui, Feng Feng, Kaihua Zhang, Yang Zhang, Jianhua Zhao, Fengbo Zhou, Yuan Zhou, Lorena Zuliani-Alvarez, David A. Agard, Yifan Cheng, James S. Fraser, Natalia Jura, Tanja Kortemme, Aashish Manglik, Daniel R. Southworth, Robert M. Stroud, Danielle L. Swaney, Nevan J. Krogan, Adam Frost, Oren S. Rosenberg
Software Mentions: 2
Published: over 3 years ago

10.1126/sciadv.abc6479

Structural basis for heme-dependent NCoR binding to the transcriptional repressor REV-ERBβ
Cited by: 12
Author(s): Sarah A. Mosure, Timothy S. Strutzenberg, Jinsai Shang, Paola Munoz-Tello, Laura A. Solt, Patrick R. Griffin, D.J. Kojetin
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0149418

Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways
Cited by: 28
Author(s): Kapil Dev Singh, Bernd Roschitzki, L. Basten Snoek, Jonas Grossmann, Xue Zheng, Mark Elvin, Polina Kamkina, Sabine Schrimpf, Gino Poulin, J.E. Kammenga, Michael O. Hengartner
Software Mentions: 2
Published: almost 9 years ago

10.1038/srep46567

Sirtuins in the phylum Basidiomycota: A role in virulence in Cryptococcus neoformans
Cited by: 15
Author(s): Samantha D. M. Arras, Jessica L. Chitty, Maha S.I. Wizrah, Paige E. Erpf, Benjamin L. Schulz, Miloš Tanurdžić, James A. Fraser
Software Mentions: 2
Published: over 7 years ago

10.1016/j.cels.2019.08.005

High-Throughput Assessment of Kinome-wide Activation States
Cited by: 30
Author(s): Thierry Schmidlin, Donna O. Debets, Charlotte A.G.H. van Gelder, Kelly E. Stecker, Stamatia Rontogianni, Bart L. van den Eshof, Kristel Kemper, Esther H. Lips, Maartje van den Biggelaar, Daniel S. Peeper, Albert J. R. Heck, Maarten Altelaar
Software Mentions: 2
Published: about 5 years ago

10.1186/s12918-018-0656-9

Analysis of significant protein abundance from multiple reaction-monitoring data
Cited by: 0
Author(s): Jongsu Jun, Jungsoo Gim, Yongkang Kim, Hyunsoo Kim, Su Jong Yu, Injun Yeo, Jiyoung Park, Jeong‐Ju Yoo, Young Youn Cho, Dong Hoon Lee, Eun Ju Cho, Jeong Hoon Lee, Yoon Jun Kim, Seungyeoun Lee, Jung Hwan Yoon, Youngsoo Kim, Taesung Park
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-017-08306-1

Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival
Cited by: 39
Author(s): Teresa Cortes, Olga T. Schubert, Amir Banaei‐Esfahani, Ben C. Collins, Ruedi Aebersold, Douglas Young
Software Mentions: 2
Published: over 7 years ago

10.1186/s12014-018-9209-x

Quality assessment and interference detection in targeted mass spectrometry data using machine learning
Cited by: 15
Author(s): Shadi Toghi Eshghi, Paul Auger, W R Mathews
Software Mentions: 2
Published: about 6 years ago

10.1186/s12014-018-9189-x

Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases
Cited by: 15
Author(s): Nina Zila, Andrea Bileck, Besnik Muqaku, Lukas Janker, Ossia M. Eichhoff, Phil F. Cheng, Reinhard Dummer, Mitchell P. Levesque, Christopher Gerner, Verena Paulitschke
Software Mentions: 2
Published: almost 7 years ago

10.15252/msb.20178126

Data‐independent acquisition‐based <scp>SWATH</scp> ‐ <scp>MS</scp> for quantitative proteomics: a tutorial
Cited by: 646
Author(s): Christina Ludwig, Ludovic Gillet, George Rosenberger, Sabine Amon, Ben C. Collins, Ruedi Aebersold
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.51461

Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages
Cited by: 39
Author(s): Jonathan M. Budzik, Danielle L. Swaney, David Jimenez-Morales, Jeffrey R. Johnson, Nicholas E Garelis, Teresa Repasy, Allison Roberts, Lauren M. Popov, Trevor J. Parry, Dexter Pratt, Trey Ideker, Nevan J. Krogan, Jeffery S. Cox
Software Mentions: 2
Published: almost 5 years ago

10.3390/mps2010008

Fast Proteome Identification and Quantification from Data-Dependent Acquisition–Tandem Mass Spectrometry (DDA MS/MS) Using Free Software Tools
Cited by: 15
Author(s): Jesse G. Meyer
Software Mentions: 2
Published: almost 6 years ago

10.3389/fpls.2021.716114

Quantitative Proteomics and Relative Enzymatic Activities Reveal Different Mechanisms in Two Peanut Cultivars (Arachis hypogaea L.) Under Waterlogging Conditions
Cited by: 5
Author(s): Dengwang Liu, Jicheng Zhan, Zinan Luo, Ningbo Zeng, Wei Zhang, Hao Zhang, Li Lin
Software Mentions: 2
Published: over 3 years ago

10.3390/life10080143

Applications of Proteomic Tools to Study Insect Vector–Plant Virus Interactions
Cited by: 4
Author(s): Priyanka Mittapelly, Swapna Priya Rajarapu
Software Mentions: 2
Published: over 4 years ago

10.1038/s41438-019-0194-7

Integrated analysis of transcriptomic and proteomic data from tree peony (P. ostii) seeds reveals key developmental stages and candidate genes related to oil biosynthesis and fatty acid metabolism
Cited by: 61
Author(s): Xiaojing Wang, Haiying Liang, Da‐Long Guo, Lili Guo, Xiangguang Duan, Qishi Jia, Xiaogai Hou
Software Mentions: 2
Published: about 5 years ago

10.1186/s12859-017-1563-6

ProteoModlR for functional proteomic analysis
Cited by: 5
Author(s): Paolo Cifani, Mojdeh Shakiba, Sagar Chhangawala, Alex Kentsis
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-021-95228-8

Salivary proteome of aphthous stomatitis reveals the participation of vitamin metabolism, nutrients, and bacteria
Cited by: 4
Author(s): Romina Hernández-Olivos, Mariagrazia Muñoz, Esteban Núñez, Paola Andrea Camargo-Ayala, Jenaro Garcia-Huidobro, Alfredo Pereira, Fabiane M. Nachtigall, Leonardo S. Santos, César Rivera
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers13102443

Discovery and Evaluation of Protein Biomarkers as a Signature of Wellness in Late-Stage Cancer Patients in Early Phase Clinical Trials
Cited by: 4
Author(s): Bethany Geary, Erin Peat, S. Dransfield, Natalie Cook, Fiona Thistlethwaite, Donna M. Graham, Louise Carter, Andrew Hughes, Matthew Krebs, Anthony D. Whetton
Software Mentions: 2
Published: over 3 years ago

10.1007/s13361-018-2122-8

Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows
Cited by: 84
Author(s): Dario Amodei, Jarrett D. Egertson, Brendan MacLean, Richard S. Johnson, Gennifer E. Merrihew, Austin W. Keller, D. C. B. Marsh, Olga Vitek, Parag Mallick, Michael J. MacCoss
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13229-017-0151-y

A brain proteomic investigation of rapamycin effects in the Tsc1 +/− mouse model
Cited by: 18
Author(s): Hendrik Wesseling, Ype Elgersma, Sabine Bahn
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms21134754

A Comprehensive Proteomic SWATH-MS Workflow for Profiling Blood Extracellular Vesicles: A New Avenue for Glioma Tumour Surveillance
Cited by: 33
Author(s): Susannah Hallal, Ali Azimi, Heng Wei, Nicholas Ho, Maggie Yuk Ting Lee, Hao‐Wen Sim, Joanne Sy, Brindha Shivalingam, Michael E. Buckland, Kimberley Alexander-Kaufman
Software Mentions: 2
Published: over 4 years ago

10.15252/emmm.201404873

Prediction of colorectal cancer diagnosis based on circulating plasma proteins
Cited by: 74
Author(s): Silvia Šurinová, Meena Choi, Sha Tao, Peter J. Schüffler, Chiung‐Yun Chang, Timothy Clough, K Vysloužil, Marta Khoylou, Josef Srovnal, Yansheng Liu, Mariette Matondo, Ruth Hüttenhain, Hendrik Weisser, Joachim M. Buhmann, Marián Hajdúch, Hermann Brenner, Olga Vitek, Ruedi Aebersold
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms21217944

Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations
Cited by: 60
Author(s): Daniele Mattei, Andranik Ivanov, Marc van Oostrum, Stanislav Pantelyushin, Juliet Richetto, F Mueller, Michał Beffinger, Linda Schellhammer, Johannes vom Berg, Bernd Wollscheid, Dieter Beule, Rosa Chiara Paolicelli, Urs Meyer
Software Mentions: 2
Published: about 4 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: about 6 years ago

10.1186/1755-8794-7-58

Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea
Cited by: 13
Author(s): Joseph N. Brown, Heather M. Brewer, Carrie Nicora, Karl K. Weitz, Michael J. Morris, Andrew Skabelund, Joshua N. Adkins, Richard Smith, Ji Hoon Cho, Richard Gelinas
Software Mentions: 2
Published: about 10 years ago

10.1099/mgen.0.000163

Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli
Cited by: 46
Author(s): Kerri M. Malone, Kévin Rue-Albrecht, David A. Magee, Kevin M. Conlon, Olga T. Schubert, Nicolas C. Nalpas, John A. Browne, Alicia Smyth, Eamonn Gormley, Ruedi Aebersold, David E. MacHugh, Stephen V. Gordon
Software Mentions: 2
Published: almost 7 years ago

10.1128/mSphere.00522-17

BioID Reveals Novel Proteins of the <i>Plasmodium</i> Parasitophorous Vacuole Membrane
Cited by: 39
Author(s): Cilly Bernardette Schnider, Damaris Bausch-Fluck, Francis Brühlmann, Volker Heussler, Paul‐Christian Burda
Software Mentions: 2
Published: almost 7 years ago

10.1074/mcp.TIR120.002048

Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant
Cited by: 120
Author(s): Fengchao Yu, Sarah E. Haynes, Guo Ci Teo, Dmitry M. Avtonomov, Daniel A. Polasky, Alexey I. Nesvizhskii
Software Mentions: 2
Published: over 4 years ago

10.1074/mcp.O115.048181

MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments
Cited by: 54
Author(s): Matthew J. Rardin, Birgit Schilling, Lin Chen, Brendan MacLean, Dan Sørensen, Alexandria K. Sahu, Michael J. MacCoss, Olga Vitek, Bradford W. Gibson
Software Mentions: 2
Published: over 9 years ago

10.18632/aging.103461

Quantitative proteomics analysis of young and elderly skin with DIA mass spectrometry reveals new skin aging-related proteins
Cited by: 18
Author(s): Jing Ma, Mengting Liu, Yaochi Wang, Cong Xin, Hui Zhang, Shirui Chen, Xiaodong Zheng, Xuejun Zhang, Feng‐Li Xiao, Sen Yang
Software Mentions: 1
Published: over 4 years ago

10.1186/s12866-019-1675-4

iTRAQ-based proteomic analysis reveals the mechanisms of Botrytis cinerea controlled with Wuyiencin
Cited by: 9
Author(s): Liming Shi, Beibei Ge, Jinzi Wang, Binghua Liu, Jinjin Ma, Qiuhe Wei, Kecheng Zhang
Software Mentions: 1
Published: about 5 years ago

10.3390/genes10110923

Proteomics Recapitulates Ovarian Proteins Relevant to Puberty and Fertility in Brahman Heifers (Bos indicus L.)
Cited by: 13
Author(s): Muhammad S. Tahir, Loan Nguyen, Benjamin L. Schulz, G. Boe-Hansen, M. G. Thomas, S. S. Moore, Li Yieng Lau, M. R. S. Fortes
Software Mentions: 1
Published: about 5 years ago

10.1128/IAI.00955-19

Neisseria meningitidis Induces Pathology-Associated Cellular and Molecular Changes in Trigeminal Schwann Cells
Cited by: 9
Author(s): Ali Delbaz, Mo Chen, Freda E.-C. Jen, Benjamin L. Schulz, Alain-Dominique Gorse, Michael P. Jennings, James St John, Jenny Ekberg
Software Mentions: 1
Published: almost 5 years ago

10.18632/oncotarget.24632

Characterization of increasing stages of invasiveness identifies stromal/cancer cell crosstalk in rat models of mesothelioma
Cited by: 9
Author(s): Joëlle S. Nader, Jérôme Abadie, Sophie Deshayes, Alice Boissard, Stéphanie Blandin, Christophe Blanquart, Nicolas Boisgerault, Olivier Coqueret, Catherine Guette, Marc Grégoire, Daniel Pouliquen
Software Mentions: 1
Published: almost 7 years ago

10.3390/jcm10163659

Changes in the Proteome Profile of People Achieving Remission of Type 2 Diabetes after Bariatric Surgery
Cited by: 4
Author(s): Zohaib Iqbal, Helene Fachim, John M. Gibson, Ivona Baričević-Jones, Amy E. Campbell, Bethany Geary, Rachelle Donn, Dashne Hamarashid, Akheel A. Syed, Anthony D. Whetton, Handrean Soran, Adrian Heald
Software Mentions: 1
Published: over 3 years ago

10.1186/s12953-019-0153-0

Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs
Cited by: 0
Author(s): Suxiang Lu, Qian Xiong, Kang Du, Xiangchao Gan, Xuzhen Wang, Liandong Yang, Ying Wang, Feng Ge, Shunping He
Software Mentions: 1
Published: about 5 years ago

10.1038/srep39985

Phosphoproteomic comparison of Pik3ca and Pten signalling identifies the nucleotidase NT5C as a novel AKT substrate
Cited by: 17
Author(s): Larissa S. Moniz, Silvia Šurinová, Essam Ghazaly, Lorena Gonzalez Velasco, Syed Haider, Juan Carlos Rodríguez-Prados, Inma M. Berenjeno, Claude Chelala, Bart Vanhaesebroeck
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-019-5523-6

Proteome profiling of triple negative breast cancer cells overexpressing NOD1 and NOD2 receptors unveils molecular signatures of malignant cell proliferation
Cited by: 21
Author(s): Fernando Janczur Velloso, Alexandre Rosa Campos, Mari Cleide Sogayar, Ricardo G. Correa
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-017-08333-y

Statistical characterization of therapeutic protein modifications
Cited by: 4
Author(s): Tsung-Heng Tsai, Zhiqi Hao, Qiuting Hong, Benjamin Moore, Cinzia Stella, Jeffrey H. Zhang, Yan Chen, Michael T. Kim, Theo Koulis, Gregory A. Ryslik, Erik Verschueren, Fred Jacobson, William E. Haskins, Olga Vitek
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-09691-3

Serum fibronectin distinguishes the early stages of hepatocellular carcinoma
Cited by: 35
Author(s): Hyunsoo Kim, Jiyoung Park, Yongkang Kim, Areum Sohn, Injun Yeo, Su Jong Yu, Jung Hwan Yoon, Taesung Park, Youngsoo Kim
Software Mentions: 1
Published: over 7 years ago

10.3390/nu11020219

Proteomics Analysis Reveals the Implications of Cytoskeleton and Mitochondria in the Response of the Rat Brain to Starvation
Cited by: 6
Author(s): Beatriz Cuevas-Fernández, Carlos Fuentes-Almagro, Juan Peragón
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-018-35038-7

Changes in canine serum N-glycosylation as a result of infection with the heartworm parasite Dirofilaria immitis
Cited by: 3
Author(s): Anna‐Janina Behrens, Rebecca M. Duke, Laudine M. C. Petralia, Sylvain Lehoux, Clotilde K. S. Carlow, Christopher H. Taron, Jeremy M. Foster
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-017-3601-1

Maternal nutrition modulates fetal development by inducing placental efficiency changes in gilts
Cited by: 34
Author(s): Long Che, Zhenguo Yang, Mengmeng Xu, Shengyu Xu, Lianqiang Che, Yan Lin, Zhengfeng Fang, Jian Li, Shuai Chen, De Wu
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-019-57153-9

Targeting of EGFR by a combination of antibodies mediates unconventional EGFR trafficking and degradation
Cited by: 21
Author(s): S. V. P. Jones, Peter King, Costin N. Antonescu, Michael G. Sugiyama, Amandeep Bhamra, Silvia Šurinová, Nicos Angelopoulos, Michael Kragh, Mikkel W. Pedersen, John A. Hartley, Clare E. Futter, Daniel Hochhauser
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-016-3146-8

Comparative proteomics reveals that central metabolism changes are associated with resistance against Sporisorium scitamineum in sugarcane
Cited by: 48
Author(s): Yachun Su, Liping Xu, Zhuqing Wang, Qiong Peng, Yuting Yang, Yun Chen, Youxiong Que
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-020-79459-9

Quantitative proteomics analysis of Angiostrongylus vasorum-induced alterations in dog serum sheds light on the pathogenesis of canine angiostrongylosis
Cited by: 11
Author(s): Lucienne Tritten, Nina Gillis-Germitsch, Tobias Kockmann, Manuela Schnyder
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-80442-7

Benchtop micro-mashing: high-throughput, robust, experimental beer brewing
Cited by: 5
Author(s): Edward D. Kerr, Christopher H. Caboche, Peter Josh, Benjamin L. Schulz
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13195-021-00861-0

VAMP-2 is a surrogate cerebrospinal fluid marker of Alzheimer-related cognitive impairment in adults with Down syndrome
Cited by: 4
Author(s): Alberto Lleó, María Carmona-Iragui, Laura Videla, Susana Fernández, Bessy Benejam, Jordi Malé i Pegueroles, Isabel Barroeta, Miren Altuna, Sílvia Valldeneu, Mei Fang Xiao, Desheng Xu, Raúl Nuñez‐Llaves, Marta Querol‐Vilaseca, Sònia Sirisi, Alexandre Bejanin, M. Florencia Iulita, Jordi Clarimón, Rafael Blesa, Paul F. Worley, Daniel Alcolea, Juan Fortea, Olivia Belbin
Software Mentions: 1
Published: over 3 years ago

10.1186/2040-2392-5-41

Proteomic analysis of post mortem brain tissue from autism patients: evidence for opposite changes in prefrontal cortex and cerebellum in synaptic connectivity-related proteins
Cited by: 49
Author(s): Jantine A.C. Broek, Paul C. Guest, Hassan Rahmoune, Sabine Bahn
Software Mentions: 1
Published: over 10 years ago

10.1128/mBio.00658-21

Targeted Quantification of Phosphorylation Sites Identifies STRIPAK-Dependent Phosphorylation of the Hippo Pathway-Related Kinase SmKIN3
Cited by: 2
Author(s): Valentina Stein, Bernhard Blank‐Landeshammer, Ramona Märker, Albert Sickmann, Ulrich Kück
Software Mentions: 1
Published: over 3 years ago

10.1186/s13229-016-0080-1

Synaptic vesicle dynamic changes in a model of fragile X
Cited by: 18
Author(s): Jantine A.C. Broek, Lin Zhu, H. Martijn de Gruiter, Heleen van ‘t Spijker, Elize D. Haasdijk, David A. Cox, Süreyya Özcan, Gert W. A. van Cappellen, Adriaan B. Houtsmuller, Rob Willemsen, Chris I. De Zeeuw, Sabine Bahn
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.molcel.2017.01.021

The TRAIL-Induced Cancer Secretome Promotes a Tumor-Supportive Immune Microenvironment via CCR2
Cited by: 160
Author(s): Torsten Hartwig, Antonella Montinaro, Silvia von Karstedt, Alexandra Sevko, Silvia Šurinová, Ankur Chakravarthy, Lucia Taraborrelli, Peter Dráber, Élodie Lafont, Frederick Arce Vargas, Mona El‐Bahrawy, Sergio A. Quezada, Henning Walczak
Software Mentions: 1
Published: almost 8 years ago

10.1074/mcp.M114.044305

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues
Cited by: 774
Author(s): Roland Bruderer, Oliver M. Bernhardt, Tejas Gandhi, Saša M. Miladinović, Lin-Yang Cheng, Simon Messner, Tobias Ehrenberger, Vito Riccardo Tomaso Zanotelli, Yulia Butscheid, Claudia Escher, Olga Vitek, Oliver Rinner, Lukas Reiter
Software Mentions: 1
Published: over 9 years ago

10.1074/mcp.RA119.001496

Proteomic Profiling of Human Prostate Cancer-associated Fibroblasts (CAF) Reveals LOXL2-dependent Regulation of the Tumor Microenvironment
Cited by: 58
Author(s): Elizabeth V. Nguyen, Brooke A. Pereira, Mitchell G. Lawrence, Xiuquan Ma, Richard J. Rebello, Howard Chan, Birunthi Niranjan, Yunjian Wu, Stuart John Ellem, Xiaoqing Guan, Jianmin Wu, Joanna N. Skhinas, Thomas R. Cox, Gail P. Risbridger, Renea A. Taylor, Natalie Lister, Roger J. Daly
Software Mentions: 1
Published: over 5 years ago

10.3390/molecules25051244

Proteomic Analysis of the Early Development of the Phalaenopsis amabilis Flower Bud under Low Temperature Induction Using the iTRAQ/MRM Approach
Cited by: 6
Author(s): Cong Chen, Lanting Zeng, Haiyi Zhao, Qingsheng Ye
Software Mentions: 1
Published: almost 5 years ago

10.1128/mSphere.00069-21

Streptococcus suis Encodes Multiple Allelic Variants of a Phase-Variable Type III DNA Methyltransferase, ModS, That Control Distinct Phasevarions
Cited by: 5
Author(s): Greg Tram, Freda E.-C. Jen, Zachary N. Phillips, Jamie Timms, Asma-Ul Husna, Michael P. Jennings, P. J. Blackall, John M. Atack
Software Mentions: 1
Published: over 3 years ago

10.15252/msb.20167062

Proteomics and integrative omic approaches for understanding host–pathogen interactions and infectious diseases
Cited by: 140
Author(s): Pierre M. Jean Beltran, Joel D. Federspiel, Xuanyu Sheng, Ileana M. Cristea
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13071-019-3403-1

Qualitative and quantitative proteomic analyses of Schistosoma japonicum eggs and egg-derived secretory-excretory proteins
Cited by: 29
Author(s): Carolina De Marco Veríssimo, Jeremy Potriquet, Hong You, Donald P. McManus, Jason Mulvenna, Malcolm K. Jones
Software Mentions: 1
Published: over 5 years ago

10.3390/pathogens10070883

Reduced Level of Tear Antimicrobial and Immunomodulatory Proteins as a Possible Reason for Higher Ocular Infections in Diabetic Patients
Cited by: 1
Author(s): Gergő Kalló, Anita Varga, Judit Szabó, Miklós Emri, József Tőzsér, Adrienne Csutak, Éva Csősz
Software Mentions: 1
Published: over 3 years ago

10.1038/s41390-020-1035-y

Biomarkers of neonatal skin barrier adaptation reveal substantial differences compared to adult skin
Cited by: 7
Author(s): Marty O. Visscher, Andrew N. Carr, Jason M. Winget, Thomas G. Huggins, Charles C. Bascom, Robert J. Isfort, Karen M. Lammers, Vivek Narendran
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.6699

MetaMSD: meta analysis for mass spectrometry data
Cited by: 2
Author(s): Seok Chang Ryu, George A. Wendt
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.3001191

Smoothened transduces Hedgehog signals via activity-dependent sequestration of PKA catalytic subunits
Cited by: 32
Author(s): Corvin D. Arveseth, John T. Happ, Danielle Hedeen, Jü Zhu, Jacob L. Capener, Dana Klatt Shaw, Ishan Deshpande, Jiahao Liang, Jiewei Xu, Sara L. Stubben, Isaac Nelson, Madison F. Walker, Kouki Kawakami, Asuka Inoue, Nevan J. Krogan, David J. Grunwald, Ruth Hüttenhain, Aashish Manglik, Benjamin R. Myers
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.1004898

Non-degradative Ubiquitination of Protein Kinases
Cited by: 30
Author(s): K. Aurelia Ball, Jeffrey R. Johnson, Mary K. Lewinski, John Guatelli, Erik Verschueren, Nevan J. Krogan, Matthew P. Jacobson
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1007694

Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles
Cited by: 28
Author(s): Ruth E. Thomas, Evelyn S. Vincow, Gennifer E. Merrihew, Michael J. MacCoss, Marie Y. Davis, Leo J. Pallanck
Software Mentions: 1
Published: over 6 years ago

10.1038/s41396-018-0275-x

Antiepileptic drug carbamazepine promotes horizontal transfer of plasmid-borne multi-antibiotic resistance genes within and across bacterial genera
Cited by: 225
Author(s): Yue Wang, Ji Lu, Likai Mao, Jie Li, Zhiguo Yuan, Philip L. Bond, Jianhua Guo
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0167474

iTRAQ-Based Quantitative Proteomic Comparison of Early- and Late-Passage Human Dermal Papilla Cell Secretome in Relation to Inducing Hair Follicle Regeneration
Cited by: 21
Author(s): Huan Zhang, Ningxia Zhu, Keng Huang, Bin Cai, Yang Zeng, Yan‐Ming Xu, Yang Liu, Yanping Yuan, Cheng Huang Lin
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0240453

SWATH-MS based proteomic profiling of pancreatic ductal adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways
Cited by: 6
Author(s): Ekene Emmanuel Nweke, Previn Naicker, Shaun Aron, Stoyan Stoychev, John Devar, David L. Tabb, J. Omoshoro-Jones, Martin D. Smith, G. Candy
Software Mentions: 1
Published: about 4 years ago

Projects: bioconductor: MSstats

Papers Mentioning MSstats 115