pypi: Comet | Projects | Ecosyste.ms: Papers

10.12688/f1000research.15140.2

Recommendations for the packaging and containerizing of bioinformatics software
Cited by: 32
Author(s): Bjoern Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian D. O’Connor, Fábio Madeira, Victoria Domínguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jiménez, BioContainers Community, Yasset Perez‐Riverol
Software Mentions: 14
Published: over 5 years ago

10.3389/fonc.2020.01767

Ovarian Blood Sampling Identifies Junction Plakoglobin as a Novel Biomarker of Early Ovarian Cancer
Cited by: 6
Author(s): Florian Weiland, Noor A. Lokman, Manuela Klingler‐Hoffmann, Thomas W. Jobling, Andrew N. Stephens, Karin Sundfeldt, Peter Hoffmann, Martin K. Oehler
Software Mentions: 13
Published: about 4 years ago

10.1126/sciadv.1600760

Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia
Cited by: 85
Author(s): S. Picaud, Katharina Leonards, Jean-Philippe Lambert, Oliver M. Dovey, Christopher Wells, Oleg Fedorov, Octovia Monteiro, Takao Fujisawa, Chenyi Wang, Hannah Lingard, C. Tallant, Nikzad Nikbin, Lucie Guetzoyan, Richard J. Ingham, Steven V. Ley, P.E. Brennan, Susanne Müller, Anastasia Samsonova, Anne‐Claude Gingras, Juerg Schwaller, George S. Vassiliou, Stefan Knapp, P. Filippakopoulos
Software Mentions: 10
Published: about 8 years ago

10.1016/j.molcel.2018.11.006

Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains
Cited by: 117
Author(s): Jean-Philippe Lambert, S. Picaud, Takao Fujisawa, Huayun Hou, P. Savitsky, Liis Uusküla-Reimand, Gagan D. Gupta, Hala Abdouni, Zhen‐Yuan Lin, Monika Tucholska, James D.R. Knight, Beatriz Gonzalez-Badillo, Nicole St‐Denis, Joseph A. Newman, Manuel Stucki, Laurence Pelletier, Nuno Bandeira, Michael D. Wilson, P. Filippakopoulos, Anne‐Claude Gingras
Software Mentions: 9
Published: almost 6 years ago

10.1186/s13059-016-1043-8

Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders
Cited by: 184
Author(s): Liis Uusküla-Reimand, Huayun Hou, Payman Samavarchi-Tehrani, Matteo Vietri Rudan, Minggao Liang, Alejandra Medina-Rivera, Hisham Mohammed, Dominic Schmidt, Petra Schwalie, Edwin J. Young, Jüri Reimand, Suzana Hadjur, Anne‐Claude Gingras, Michael D. Wilson
Software Mentions: 8
Published: about 8 years ago

10.1128/mSystems.00632-19

Early-Stage <i>Staphylococcus aureus</i> Bloodstream Infection Causes Changes in the Concentrations of Lipoproteins and Acute-Phase Proteins and Is Associated with Low Antibody Titers against Bacterial Virulence Factors
Cited by: 7
Author(s): Stephan Michalik, Nandakumar Sundaramoorthy, Annette Murr, Maren Depke, Uwe Völker, Barbara M. Bröker, Hege Vangstein Aamot, Frank Schmidt
Software Mentions: 7
Published: almost 5 years ago

10.15252/embj.2018101220

The interactome of <scp>KRAB</scp> zinc finger proteins reveals the evolutionary history of their functional diversification
Cited by: 58
Author(s): Pierre-Yves Helleboid, Moritz Heusel, Julien Duc, Cécile Piot, Christian W. Thorball, Andrea Coluccio, Julien Pontis, Michaël Imbeault, Priscilla Turelli, Ruedi Aebersold, Didier Trono
Software Mentions: 7
Published: over 5 years ago

10.1016/j.celrep.2019.11.026

Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome
Cited by: 53
Author(s): Edward Lau, Yu Han, Damon R. Williams, Cody T Thomas, Rajani Shrestha, Joseph C. Wu, Maggie Lam
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12859-016-1298-9

Evaluating tools for transcription factor binding site prediction
Cited by: 75
Author(s): Narayan Jayaram, Daniel Usvyat, Andrew C.R. Martin
Software Mentions: 6
Published: about 8 years ago

10.1038/s41598-019-41336-5

Female novelty and male status dynamically modulate ejaculate expenditure and seminal fluid proteome over successive matings in red junglefowl
Cited by: 9
Author(s): Aitor Álvarez-Fernández, Kirill Borziak, Grant C. McDonald, Steve Dorus, Tommaso Pizzari
Software Mentions: 6
Published: over 5 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

10.1186/s12864-018-4980-7

Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes
Cited by: 3
Author(s): Katja R Kasimatis, Megan Moerdyk-Schauwecker, Nadine Timmermeyer, Patrick C. Phillips
Software Mentions: 6
Published: over 6 years ago

10.1093/bioinformatics/bty646

Automated workflow composition in mass spectrometry-based proteomics
Cited by: 37
Author(s): Magnus Palmblad, Anna‐Lena Lamprecht, Jon C. Ison, Veit Schwämmle
Software Mentions: 6
Published: over 6 years ago

10.1186/s13073-017-0454-9

Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines
Cited by: 45
Author(s): Javier A. Alfaro, Alexandr Ignatchenko, Vladimir Ignatchenko, Ankit Sinha, Paul C. Boutros, Thomas Kislinger
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-020-75505-8

Proteomic signatures of acute oxidative stress response to paraquat in the mouse heart
Cited by: 12
Author(s): Vishantie Dostal, Silas D. Wood, Cody T Thomas, Yu Han, Edward Lau, Maggie P. Y. Lam
Software Mentions: 6
Published: about 4 years ago

10.7717/peerj.1401

An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64
Cited by: 18
Author(s): Robert Winkler
Software Mentions: 6
Published: about 9 years ago

10.1038/s41598-021-91684-4

Peptide profiling in cow urine reveals molecular signature of physiology-driven pathways and in-silico predicted bioactive properties
Cited by: 6
Author(s): Rohit Kumar, Syed Azmal Ali, Sumit Kumar Singh, Vanya Bhushan, Jai K. Kaushik, Ashok Kumar Mohanty, Sanjay Kumar
Software Mentions: 5
Published: over 3 years ago

10.1074/mcp.O115.050229

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets
Cited by: 129
Author(s): Yasset Perez‐Riverol, Qing Wei Xu, Rui Wang, Julian Uszkoreit, Johannes Griss, Aniel Sánchez, Florian Reisinger, Attila Csordás, Tobias Ternent, Noemi del-Toro, José A. Dianes, Martin Eisenacher, Henning Hermjakob, Juan Antonio Vizcaíno
Software Mentions: 5
Published: almost 9 years ago

10.3390/foods10061331

Chemoprotective Effects of Xanthohumol against the Carcinogenic Mycotoxin Aflatoxin B1
Cited by: 15
Author(s): Alja Štern, Veronika Furlan, Matjaž Novak, Martina Štampar, Zala Kolenc, Katarina Kores, Metka Filipič, Urban Bren, Bojana Žegura
Software Mentions: 5
Published: over 3 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

10.3390/proteomes8030015

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
Cited by: 9
Author(s): Subina Mehta, Caleb Easterly, Ray Sajulga, Robert Millikin, Andrea Argentini, Ignacio Eguinoa, Lennart Martens, Michael R. Shortreed, Lloyd M. Smith, Thomas McGowan, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-021-81740-4

Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
Cited by: 3
Author(s): Ching-Tai Chen, Jen-Hung Wang, Cheng-Wei Cheng, Wei-Che Hsu, Chu-Ling Ko, Wai-Kok Choong, Ting‐Yi Sung
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pgen.1008511

JMJD6 participates in the maintenance of ribosomal DNA integrity in response to DNA damage
Cited by: 11
Author(s): Jérémie Fages, Catherine Chailleux, Jonathan Humbert, Suk-Min Jang, Jérémy Loehr, Jean-Philippe Lambert, Jacques Côté, Didier Trouche, Yvan Canitrot
Software Mentions: 5
Published: over 4 years ago

10.15252/msb.20209844

Integrative characterization of the near‐minimal bacterium <i>Mesoplasma florum</i>
Cited by: 8
Author(s): Dominick Matteau, Jean-Christophe Lachance, Frédéric Grenier, Samuel Gauthier, James M. Daubenspeck, Kevin Dybvig, Daniel Garneau, Thomas F. Knight, Pierre-Étienne Jacques, Sébastien Rodrigue
Software Mentions: 5
Published: almost 4 years ago

10.3390/ijms22094864

Characterization of Extracellular Vesicle Cargo in Sjögren’s Syndrome through a SWATH-MS Proteomics Approach
Cited by: 11
Author(s): Francesco Finamore, Antonella Cecchettini, Elisa Ceccherini, Giovanni Signore, Francesco Ferro, Silvia Rocchiccioli, Chiara Baldini
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-82569-7

Physiological and molecular responses of lobe coral indicate nearshore adaptations to anthropogenic stressors
Cited by: 16
Author(s): Kaho H. Tisthammer, Emma Timmins‐Schiffman, François O. Seneca, Brook L. Nunn, Robert H. Richmond
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-018-27650-4

MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides
Cited by: 4
Author(s): Emma Timmins‐Schiffman, Molly P. Mikan, Ying S. Ting, H. Rodger Harvey, Brook L. Nunn
Software Mentions: 4
Published: over 6 years ago

10.3390/molecules26072027

Discovery of Post-Translational Modifications in Emiliania huxleyi
Cited by: 2
Author(s): Van-An Duong, Onyou Nam, EonSeon Jin, Jong Park, Hookeun Lee
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-017-3800-9

A comprehensive proteogenomic study of the human Brucella vaccine strain 104 M
Cited by: 12
Author(s): Xiaodong Zai, Qiaoling Yang, Kun Liu, Ruihua Li, Mengying Qian, Taoran Zhao, Yaohui Li, Ying Yin, Dayong Dong, Ling Fu, Shanhu Li, Junjie Xu, Wei Chen
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-021-81986-y

Proteome-wide profiling and mapping of post translational modifications in human hearts
Cited by: 15
Author(s): Navratan Bagwan, Henrik H. El Ali, Alicia Lundby
Software Mentions: 4
Published: almost 4 years ago

10.18632/aging.103516

ASNEO: Identification of personalized alternative splicing based neoantigens with RNA-seq
Cited by: 18
Author(s): Zhanbing Zhang, Chi Zhou, Lihua Tang, Yukang Gong, Zhiting Wei, Gongchen Zhang, Feng Wang, Qi Liu, Jing Yu
Software Mentions: 4
Published: over 4 years ago

10.1074/mcp.RA118.001141

Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition
Cited by: 45
Author(s): Piotr Grabowski, Sebastian Hesse, Sebastian Hollizeck, Meino Rohlfs, Uta Behrends, Roya Sherkat, Hannah Tamary, Ekrem Ünal, Raz Somech, Türkan Patıroğlu, Stefan Canzar, Jutte van der Werff ten Bosch, Christoph Klein, Juri Rappsilber
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0251820

Embryonic developmental arrest in the annual killifish Austrolebias charrua: A proteomic approach to diapause III
Cited by: 5
Author(s): Cora Chalar, Graciela Clivio, Jimena Montagne, Alicia Costábile, Analı́a Lima, Nicolás Papa, Nora Berois, María José Arezo
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0228503

Lumenal calcification and microvasculopathy in fetuin-A-deficient mice lead to multiple organ morbidity
Cited by: 33
Author(s): Marietta Herrmann, Anne Babler, Irina Moshkova, Felix Gremse, Fabian Kießling, Ulrike Kusebauch, Valentin Nelea, Rafael Kramann, Robert L. Moritz, Marc D. McKee, Willi Jahnen‐Dechent
Software Mentions: 4
Published: almost 5 years ago

10.3389/fnut.2020.00150

High-Resolution Mass Spectrometer–Based Ultra-Deep Profile of Milk Whey Proteome in Indian Zebu (Sahiwal) Cattle
Cited by: 17
Author(s): Alka Chopra, Syed Azmal Ali, Shveta Bathla, Preeti Rawat, Vikas Vohra, Sudarshan Kumar, Ashok Kumar Mohanty
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2019.01410

On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics
Cited by: 6
Author(s): K.C.T. Machado, Suereta Fortuin, Gisele G. Tomazella, André Fonseca, Robin M. Warren, Harald G. Wiker, Sandro J. de Souza, Gustavo Souza
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0181680

Probing the compartmentalization of HIV-1 in the central nervous system through its neutralization properties
Cited by: 18
Author(s): Karl Stéfic, Antoine Chaillon, Mélanie Bouvin-Pley, Alain Moreau, Martine Braibant, Frédéric Bastides, Guillaume Gras, Louis Bernard, Françis Barin
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms20143425

Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network
Cited by: 17
Author(s): Lan Gongqiang, Jiyun Zhou, Ruifeng Xu, Qin Lu, Hongpeng Wang
Software Mentions: 4
Published: over 5 years ago

10.3389/fcell.2021.568660

Transcriptional Repression of MFG-E8 Causes Disturbance in the Homeostasis of Cell Cycle Through DOCK/ZP4/STAT Signaling in Buffalo Mammary Epithelial Cells
Cited by: 5
Author(s): Arvind Verma, Syed Azmal Ali, Parul Singh, Sanjay Kumar, Ashok Kumar Mohanty
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pbio.3000358

Global proteomic analyses define an environmentally contingent Hsp90 interactome and reveal chaperone-dependent regulation of stress granule proteins and the R2TP complex in a fungal pathogen
Cited by: 30
Author(s): Teresa R. O’Meara, Matthew J. O’Meara, Elizabeth J. Polvi, Mohammad Reza Pourhaghighi, Sean D. Liston, Zhen‐Yuan Lin, Amanda O. Veri, Andrew Emili, Anne‐Claude Gingras, Leah E. Cowen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0006351

Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc-STAMS2)
Cited by: 9
Author(s): Gilberto Santos de Oliveira, Rebeca Kawahara, Lívia Rosa-Fernandes, Simon Ngao Mule, Carla Cristi Avila, Marta Maria Geraldes Teixeira, Martin R. Larsen, Giuseppe Palmisano
Software Mentions: 4
Published: over 6 years ago

10.1016/j.cels.2017.11.002

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines
Cited by: 18
Author(s): Peter Blattmann, David Henriques, Michael Zimmermann, Fabian Frommelt, Uwe Sauer, Julio Sáez-Rodríguez, Ruedi Aebersold
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pntd.0005791

Proteogenomic analysis of the total and surface-exposed proteomes of Plasmodium vivax salivary gland sporozoites
Cited by: 65
Author(s): Kristian E. Swearingen, Scott E. Lindner, Erika L. Flannery, Ashley M. Vaughan, Robert Morrison, Rapatbhorn Patrapuvich, Cristian Koepfli, Ivan Müller, Aaron R. Jex, Robert L. Moritz, Stefan H. I. Kappe, Jetsumon Sattabongkot, Sebastian A. Mikolajczak
Software Mentions: 4
Published: over 7 years ago

10.1074/mcp.RA118.000877

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome*
Cited by: 86
Author(s): Roman Mylonas, Ilan Beer, Christian Iseli, Chloé Chong, Hui Song Pak, David Gfeller, George Coukos, Ioannis Xénarios, Markus Müller, Michal Bassani-Sternberg
Software Mentions: 4
Published: almost 6 years ago

10.1152/physiolgenomics.00044.2018

Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways
Cited by: 14
Author(s): Stephanie J. Valberg, Sudeep Perumbakkam, Erica C. McKenzie, Carrie J. Finno
Software Mentions: 4
Published: almost 6 years ago

10.3390/proteomes5030020

mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data
Cited by: 18
Author(s): Scott B. Ficarro, William M. Alexander, Jarrod A. Marto
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pntd.0008237

Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms
Cited by: 20
Author(s): Jayden Logan, Mark S. Pearson, Srikanth S. Manda, Young Jun Choi, Matthew A. Field, Ramon M. Eichenberger, Jason Mulvenna, Shivashankar H. Nagaraj, Ricardo Toshio Fujiwara, Pedro Henrique Gazzinelli-Guimarães, Lilian Lacerda Bueno, Vitor Luís Tenório Mati, Jeffrey M. Bethony, Makedonka Mitreva, Javier Sotillo, Alex Loukas
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-019-2845-y

HOME: a histogram based machine learning approach for effective identification of differentially methylated regions
Cited by: 29
Author(s): Akanksha Srivastava, Yuliya V. Karpievitch, Steven R. Eichten, Justin O. Borevitz, Ryan Lister
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-67525-1

Machine learning analysis identifies genes differentiating triple negative breast cancers
Cited by: 22
Author(s): Charu Kothari, Mazid Abiodoun Osseni, Lynda Agbo, Geneviève Ouellette, Maxime Déraspe, François Laviolette, Jacques Corbeil, Jean-Philippe Lambert, Caroline Diorio, Francine Durocher
Software Mentions: 3
Published: over 4 years ago

10.1128/AEM.01319-20

Editing of the Proteolytic System of Lactococcus lactis Increases Its Bioactive Potential
Cited by: 6
Author(s): Chenxi Huang, Jan Kok
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-017-08436-6

Disrupting glutamine metabolic pathways to sensitize gemcitabine-resistant pancreatic cancer
Cited by: 65
Author(s): Ru Chen, Lisa A. Lai, Yumi Sullivan, Melissa H. Wong, Lei Wang, Jonah Riddell, L. Jung, Venu G. Pillarisetty, Teresa A. Brentnall, Sheng Pan
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-10059-w

A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions
Cited by: 39
Author(s): Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiß, Laura M Palma Medina, Melanie Gutjahr, Elke Hammer, Dörte Becher, T Pribýl, Sven Hammerschmidt, Eric W. Deutsch, Samuel L. Bader, Michael Hecker, Robert L. Moritz, Ulrike Mäder, Uwe Völker, Frank Schmidt
Software Mentions: 3
Published: about 7 years ago

10.1074/mcp.RA118.001218

PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms
Cited by: 39
Author(s): Steven Verbruggen, Elvis Ndah, Wim Van Criekinge, Siegfried Gessulat, Bernhard Küster, Mathias Wilhelm, Petra Van Damme, Gerben Menschaert
Software Mentions: 3
Published: over 5 years ago

10.1016/j.celrep.2019.09.060

Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes
Cited by: 47
Author(s): Anna L. Mallam, Wisath Sae-Lee, Jeffrey M. Schaub, Fan Tu, Anna M. Battenhouse, Yu Jin Jang, Jonghwan Kim, John B. Wallingford, Ilya J. Finkelstein, Edward M. Marcotte, Kevin Drew
Software Mentions: 3
Published: about 5 years ago

10.1074/mcp.TIR119.001431

Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry
Cited by: 41
Author(s): Sabine Amon, Fabienne Meier-Abt, Ludovic Gillet, Slavica Dimitrieva, Alexandre Theocharides, Markus G. Manz, Ruedi Aebersold
Software Mentions: 3
Published: over 5 years ago

10.1038/sdata.2019.11

Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins
Cited by: 38
Author(s): Peter Blattmann, Vivienne Stutz, Giulia Lizzo, J. Wall Richard, Philipp Gut, Ruedi Aebersold
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.ppat.1005672

A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles
Cited by: 297
Author(s): Katja Koeppen, Thomas H. Hampton, Michael Jarek, Maren Scharfe, Scott A. Gerber, Daniel W. Mielcarz, Elora G. Demers, Emily L. Dolben, John H. Hammond, Deborah A. Hogan, Bruce A. Stanton
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.ppat.1009603

Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay
Cited by: 20
Author(s): Lara Contu, Giuseppe Balistreri, Michal Domanski, Anne-Christine Uldry, Oliver Mühlemann
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0217105

Identification of key modules and hub genes for small-cell lung carcinoma and large-cell neuroendocrine lung carcinoma by weighted gene co-expression network analysis of clinical tissue-proteomes
Cited by: 21
Author(s): Hiroki Nakamura, Kiyonaga Fujii, Vipul Gupta, Hiroko Hata, Hirotaka Koizumu, Masahiro Hoshikawa, Saeko Naruki, Yuka Miyata, Ikuya Takahashi, Tomoki Miyazawa, Hiroki Sakai, Kouhei Tsumoto, Masayuki Takagi, Hisashi Saji, Toshihide Nishimura
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-017-4293-2

Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera
Cited by: 16
Author(s): Emma Whittington, Desiree Forsythe, Kirill Borziak, Timothy L. Karr, James R. Walters, Steve Dorus
Software Mentions: 3
Published: almost 7 years ago

10.1186/gb-2010-11-1-r7

Genome-wide prediction of transcription factor binding sites using an integrated model
Cited by: 111
Author(s): Kyoung Jae Won, Bing Ren, Weiwei Wang
Software Mentions: 3
Published: almost 15 years ago

10.1186/s12859-014-0441-8

APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools
Cited by: 14
Author(s): Erik Malm, Vaibhav Srivastava, Gustav Sundqvist, Vincent Bulone
Software Mentions: 3
Published: almost 10 years ago

10.1002/pmic.202000319

DDASSQ: An open‐source, multiple peptide sequencing strategy for label free quantification based on an OpenMS pipeline in the KNIME analytics platform
Cited by: 5
Author(s): M. Svecla, G Garrone, Fiorenza Farè, Giacomo Aletti, Giuseppe Danilo Norata, Giangiacomo Beretta
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0221837

Integrative proteomic and glycoproteomic profiling of Mycobacterium tuberculosis culture filtrate
Cited by: 18
Author(s): Paula Tucci, Madelón Portela, Carlos Rivas Chetto, Gualberto González‐Sapienza, Mónica Marı́n
Software Mentions: 3
Published: over 4 years ago

10.1016/j.isci.2021.102950

Comparative proteomic investigation of multiple methicillin-resistant Staphylococcus aureus strains generated through adaptive laboratory evolution
Cited by: 10
Author(s): Jordy Evan Sulaiman, Lexin Long, Long Wu, Pei‐Yuan Qian, Henry Lam
Software Mentions: 3
Published: about 3 years ago

10.7554/eLife.54993

NuRD subunit CHD4 regulates super-enhancer accessibility in rhabdomyosarcoma and represents a general tumor dependency
Cited by: 30
Author(s): Joana G. Marques, Berkley E. Gryder, Blaz Pavlovic, Yeonjoo Chung, Quy A. Ngo, Fabian Frommelt, Matthias Gstaiger, Young K. Song, Katharina Benischke, Dominik Laubscher, Marco Wachtel, Javed Khan, Beat W. Schäfer
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.28270

Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition
Cited by: 42
Author(s): Vivek Mahadevan, C. Sahara Khademullah, Zahra Dargaei, Jonah Chevrier, Pavel Uvarov, Julian Kwan, Richard D. Bagshaw, Tony Pawson, Andrew Emili, Yves De Koninck, Victor Anggono, Matti S. Airaksinen, Melanie A. Woodin
Software Mentions: 3
Published: about 7 years ago

10.1021/acs.jproteome.1c00243

Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance
Cited by: 12
Author(s): Tommaso De Marchi, Paul Theodor Pyl, Martin Sjöström, Stina Klasson, Hanna Sartor, Lena Tran, Gyula Pekár, Johan Malmström, Lars Malmström, Emma Niméus
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.70560

Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36
Cited by: 5
Author(s): Jasmin van den Heuvel, Caroline Ashiono, Ludovic Gillet, Kerstin Dörner, Emanuel Wyler, Ivo Zemp, Ulrike Kutay
Software Mentions: 3
Published: over 3 years ago

10.3390/toxins11030167

The Dual Prey-Inactivation Strategy of Spiders—In-Depth Venomic Analysis of Cupiennius salei
Cited by: 31
Author(s): Lucia Kuhn‐Nentwig, Nicolas Langenegger, Manfred Heller, Dominique Koua, Wolfgang Nentwig
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.64159

Cerebrospinal fluid proteome maps detect pathogen-specific host response patterns in meningitis
Cited by: 11
Author(s): Anahita Bakochi, Tirthankar Mohanty, Paul Theodor Pyl, Carlos Gueto-Tettay, Lars Malmström, Adam Linder, Johan Malmström
Software Mentions: 3
Published: over 3 years ago

10.1016/j.csbj.2020.10.010

Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses
Cited by: 6
Author(s): Sébastien Leblanc, Marie-Christine Brunet
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.07661

An open-source computational and data resource to analyze digital maps of immunopeptidomes
Cited by: 92
Author(s): Étienne Caron, Lucia Espona Pernas, Daniel J. Kowalewski, Heiko Schuster, Nicola Ternette, Adán Alpízar, Ralf B. Schittenhelm, Sri H. Ramarathinam, Cecilia S. Lindestam Arlehamn, Ching Chiek Koh, Ludovic Gillet, Armin Rabsteyn, Pedro J. Navarro, Sangtae Kim, Henry H N Lam, Theo Sturm, Miguel Marcilla, Alessandro Sette, D. S. Campbell, Eric W. Deutsch, Robert L. Moritz, Anthony W. Purcell, Hans‐Georg Rammensee, Stefan Stevanović, Ruedi Aebersold
Software Mentions: 3
Published: over 9 years ago

10.1016/j.celrep.2018.08.085

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data
Cited by: 27
Author(s): Ali Sinan Köksal, Kirsten Beck, Dylan Cronin, Aaron McKenna, Nathan D. Camp, Saurabh Srivastava, Matthew E. MacGilvray, Rastislav Bodík, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher, Anthony Gitter
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.58828

EDF1 coordinates cellular responses to ribosome collisions
Cited by: 79
Author(s): Niladri K. Sinha, Alban Ordureau, Katharina Best, James A. Saba, Boris Zinshteyn, Elayanambi Sundaramoorthy, Amit Fulzele, Danielle M. Garshott, T. Denk, Matthias Thoms, João A. Paulo, J. Wade Harper, Eric J. Bennett, Roland Beckmann, Rachel Green
Software Mentions: 3
Published: over 4 years ago

10.1186/s12610-016-0043-6

Sperm DNA damage and its role in IVF and ICSI
Cited by: 46
Author(s): Phil Bach, Peter N. Schlegel
Software Mentions: 2
Published: almost 8 years ago

10.15252/msb.20167295

An atlas of human kinase regulation
Cited by: 87
Author(s): David Ochoa, Mindaugas Jonikas, Robert Lawrence, Bachir El Debs, Joel Selkrig, Athanasios Typas, Judit Villén, Silvia Santos, Pedro Beltrão
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-018-27500-3

In planta proximity dependent biotin identification (BioID)
Cited by: 56
Author(s): Madiha Khan, Ji‐Young Youn, Anne‐Claude Gingras, Rajagopal Subramaniam, Darrell Desveaux
Software Mentions: 2
Published: over 6 years ago

10.1038/s41597-020-00744-3

A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics
Cited by: 10
Author(s): Harshi Weerakoon, Jeremy Potriquet, Alok K. Shah, Sarah Reed, Buddhika A. Jayakody, Charu Kapil, Mukul K. Midha, Robert L. Moritz, Ailin Lepletier, Jason Mulvenna, John J. Miles, Michelle M. Hill
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41597-019-0308-y

Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi
Cited by: 2
Author(s): Dasha Krayushkina, Emma Timmins‐Schiffman, Jessica F. Faux, Damon May, Michael Riffle, H. Rodger Harvey, Brook L. Nunn
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41597-020-00724-7

A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS
Cited by: 25
Author(s): Mukul K. Midha, Ulrike Kusebauch, David Shteynberg, Charu Kapil, Samuel L. Bader, Panga Jaipal Reddy, D. S. Campbell, Nitin S. Baliga, Robert L. Moritz
Software Mentions: 2
Published: about 4 years ago

10.1007/s00018-020-03528-5

The secreted inhibitor of invasive cell growth CREG1 is negatively regulated by cathepsin proteases
Cited by: 2
Author(s): Alejandro Gomez-Auli, Larissa E. Hillebrand, D. Christen, Sira C. Günther, Martin L. Biniossek, Christoph Peters, Oliver Schilling, Thomas Reinheckel
Software Mentions: 2
Published: over 4 years ago

10.1038/sdata.2014.31

A repository of assays to quantify 10,000 human proteins by SWATH-MS
Cited by: 373
Author(s): George Rosenberger, Ching Chiek Koh, Tiannan Guo, Hannes L. Röst, Petri Kouvonen, Ben C. Collins, Moritz Heusel, Yansheng Liu, Étienne Caron, Anton Vichalkovski, Marco Faini, Olga T. Schubert, Pouya Faridi, H. Alexander Ebhardt, Mariette Matondo, Henry Lam, Samuel L. Bader, D. S. Campbell, Eric W. Deutsch, Robert L. Moritz, Stephen Tate, Ruedi Aebersold
Software Mentions: 2
Published: about 10 years ago

10.1038/sdata.2015.74

Hair-bundle proteomes of avian and mammalian inner-ear utricles
Cited by: 12
Author(s): Phillip A. Wilmarth, Jocelyn F. Krey, Jung Bum Shin, Dongseok Choi, Larry L. David, Peter G. Barr-Gillespie
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-018-22610-4

Cost-effective generation of precise label-free quantitative proteomes in high-throughput by microLC and data-independent acquisition
Cited by: 65
Author(s): Jakob Vowinckel, Aleksej Zelezniak, Roland Bruderer, Michael Mülleder, Lukas Reiter, Markus Ralser
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers13153754

Cloud Computing Based Immunopeptidomics Utilizing Community Curated Variant Libraries Simplifies and Improves Neo-Antigen Discovery in Metastatic Melanoma
Cited by: 2
Author(s): Amol Prakash, Keira E. Mahoney, Benjamin C. Orsburn
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.ppat.1006256

Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism
Cited by: 51
Author(s): Zoi Sychev, Alex Hu, Terri A. DiMaio, Anthony Gitter, Nathan D. Camp, William Stafford Noble, Alejandro Wolf-Yadlin, Michael Lagunoff
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1009293

A redox-active crosslinker reveals an essential and inhibitable oxidative folding network in the endoplasmic reticulum of malaria parasites
Cited by: 8
Author(s): David W. Cobb, Heather M. Kudyba, Alejandra Villegas, Michael R. Hoopmann, Rodrigo P. Baptista, Baylee Bruton, Michelle Krakowiak, Robert L. Moritz, Vasant Muralidharan
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.ppat.1005606

Interrogating the Plasmodium Sporozoite Surface: Identification of Surface-Exposed Proteins and Demonstration of Glycosylation on CSP and TRAP by Mass Spectrometry-Based Proteomics
Cited by: 144
Author(s): Kristian E. Swearingen, Scott E. Lindner, Lirong Shi, Melanie J. Shears, Anke Harupa, Christine S. Hopp, Ashley M. Vaughan, Timothy A. Springer, Robert L. Moritz, Stefan H. I. Kappe, Photini Sinnis
Software Mentions: 2
Published: over 8 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: over 4 years ago

10.1186/s12864-021-07640-z

Buffalo sperm surface proteome profiling reveals an intricate relationship between innate immunity and reproduction
Cited by: 6
Author(s): Vipul Batra, Vanya Bhushan, Syed Azmal Ali, Parul Sarwalia, Ankit Pal, Seema Karanwal, Subhash Solanki, A. Kumaresan, Rakesh Kumar, Tirtha Kumar Datta
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0198523

Recombinant purified buffalo leukemia inhibitory factor plays an inhibitory role in cell growth
Cited by: 4
Author(s): Syed Azmal Ali, Dhruba Malakar, Jai K. Kaushik, Ashok Kumar Mohanty, Sanjay Kumar
Software Mentions: 2
Published: over 6 years ago

10.1109/ACCESS.2020.3047588

Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey
Cited by: 12
Author(s): Muhammad Usman Tariq, Muhammad Haseeb, Mohammed Aledhari, Rehma Razzak, Reza M. Parizi, Fahad Saeed
Software Mentions: 2
Published: almost 4 years ago

10.3389/fonc.2020.593989

Systematically Characterizing A-to-I RNA Editing Neoantigens in Cancer
Cited by: 18
Author(s): Chi Zhou, Zhiting Wei, Liye Zhang, Zhaoyi Yang, Qi Liu
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2017.02658

Quantitative Proteomic Analysis of Four Developmental Stages of Saprolegnia parasitica
Cited by: 17
Author(s): Vaibhav Srivastava, Svetlana Rezinciuc, Vincent Bulone
Software Mentions: 2
Published: almost 7 years ago

10.1093/g3journal/jkab218

The amino acid substitution affects cellular response to mistranslation
Cited by: 8
Author(s): Matthew D. Berg, Yi Zhu, Bianca Y. Ruiz, Raphaël Loll-Krippleber, Joshua Isaacson, Bryan-Joseph San Luis, Julie Genereaux, Charles Boone, Judit Villén, Grant W. Brown, Christopher J. Brandl
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

10.1371/journal.pone.0205446

HIV-genetic diversity and drug resistance transmission clusters in Gondar, Northern Ethiopia, 2003-2013
Cited by: 19
Author(s): Dawit Assefa Arimide, Almaz Abebe, Yenew Kebede, Fekadu Adugna, Tesfaye Tilahun, Desta Kassa, Yibeltal Assefa, Taye Tolera Balcha, Per Björkman, Patri K. Medstrand
Software Mentions: 2
Published: about 6 years ago

10.15252/emmm.201910880

Phosphorylation of TFCP2L1 by CDK1 is required for stem cell pluripotency and bladder carcinogenesis
Cited by: 43
Author(s): Jinbeom Heo, Byeong‐Joo Noh, Seungun Lee, Hye‐Yeon Lee, YongHwan Kim, Jisun Lim, Hyein Ju, Hwan Yeul Yu, Chae‐Min Ryu, Peter Cw Lee, Hee Jong Jeong, Yumi Oh, Kyunggon Kim, Sangjin Kim, Jaekyoung Son, Bumsik Hong, Jong Soo Kim, Yong Mee Cho, Dong‐Myung Shin
Software Mentions: 2
Published: about 5 years ago

10.1186/s40793-021-00376-z

Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery
Cited by: 6
Author(s): Emma Timmins‐Schiffman, Samuel J. White, Rhonda Elliott Thompson, Brent Vadopalas, Benoït Eudeline, Brook L. Nunn, Susan Jo Roberts
Software Mentions: 2
Published: over 3 years ago

Projects: pypi: Comet

Papers Mentioning Comet 248