10.3390/microorganisms8050653

Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae
Cited by: 33
Author(s): Jamie McGowan, Richard O’Hanlon, Rebecca A. Owens, David A. Fitzpatrick
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-70324-3

The integral spliceosomal component CWC15 is required for development in Arabidopsis
Cited by: 8
Author(s): Daniel Slane, Cameron H. Lee, Martina Kolb, Craig Dent, Yingjing Miao, Mirita Franz‐Wachtel, Steffen Lau, Boris Maček, Sureshkumar Balasubramanian, Martin Bayer, Gerd Jürgens
Software Mentions: 3
Published: almost 6 years ago

10.1084/jem.20201011

The T cell CD6 receptor operates a multitask signalosome with opposite functions in T cell activation
Cited by: 33
Author(s): Daiki Mori, Claude Grégoire, Guillaume Voisinne, Javier Celis-Gutierrez, Rudy Aussel, Laura Girard, Mylène Camus, Marlène Marcellin, Jérémy Argenty, Odile Burlet‐Schiltz, Frédéric Di Fiore, Anne Gonzalez de Peredo, Marie Malissen, Romain Roncagalli, Bernard Malissen
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-26343-2

Acrylamide acute neurotoxicity in adult zebrafish
Cited by: 56
Author(s): Melissa Faria, Tamar Ziv, Cristian Gómez‐Canela, Shani Ben-Lulu, Eva Prats, Karen Adriana Novoa-Luna, Arie Admon, Benjamı́n Piña, Romà Tauler, Leobardo Manuel Gómez-Oliván, Demetrio Raldúa
Software Mentions: 3
Published: about 8 years ago

10.1186/s12860-020-00331-9

Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages
Cited by: 18
Author(s): Sabin Bhandari, Ruomei Li, Jaione Simón-Santamaría, Peter McCourt, Steinar Johansen, Bård Smedsrød, Iñigo Martínez-Zubiaurre, Karen Kristine Sørensen
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-26639-3

Hit-Gel: Streamlining in-gel protein digestion for high-throughput proteomics experiments
Cited by: 11
Author(s): Corné Swart, Silvia Martínez-Jaime, Michał Górka, Kerstin Zander, Alexander Graf
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-19351-9

Visualization of human karyopherin beta-1/importin beta-1 interactions with protein partners in mitotic cells by co-immunoprecipitation and proximity ligation assays
Cited by: 13
Author(s): Laura Di Francesco, Annalisa Verrico, Italia Anna Asteriti, Paola Rovella, Pietro Cirigliano, Giulia Guarguaglini, Maria Eugenia Schininà, Patrizia Lavia
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-20458-2

SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses
Cited by: 10
Author(s): Dominik Dornfeld, Alexandra H. Dudek, Thibaut Vausselin, Sira C. Günther, Judd F. Hultquist, Sebastian Giese, Daria Khokhlova-Cubberley, Yap Ching Chew, Lars Pache, Nevan J. Krogan, Adolfo Garcı́a-Sastre, Martin Schwemmle, Megan L. Shaw
Software Mentions: 3
Published: over 8 years ago

10.1016/j.molcel.2019.02.031

MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation
Cited by: 79
Author(s): Apoorva Baluapuri, Julia Hofstetter, Nevenka Dudvarski Stanković, Theresa Endres, Pranjali Bhandare, Seychelle M. Vos, Bikash Adhikari, Jessica Denise Schwarz, Ashwin Narain, Markus Vogt, Shuangyan Wang, Robert Düster, Lisa Anna Jung, Jens T. Vanselow, Armin Wiegering, Matthias Geyer, Hans Michael Maric, Peter Gallant, Susanne Walz, Andreas Schlösser, Patrick Cramer, Martin Eilers, Elmar Wolf
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-021-96635-7

Multi-layered proteogenomic analysis unravels cancer metastasis directed by MMP-2 and focal adhesion kinase signaling
Cited by: 11
Author(s): Yumi Kwon, Seongjun Park, Binh Thanh Nguyen, Mi Jeong Kim, Sejin Oh, Hwanho Lee, Narae Park, Hyun‐Seok Kim, Min‐Jung Kang, Byung Soh Min, Jinwon Lee, Eun Gyeong Yang, Cheolju Lee
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-018-30578-4

Snake Venom Extracellular vesicles (SVEVs) reveal wide molecular and functional proteome diversity
Cited by: 18
Author(s): Victor Corassolla Carregari, Lívia Rosa-Fernandes, Paulo A. Baldasso, Sérgio Paulo Bydlowski, Sérgio Marangoni, Martin R. Larsen, Giuseppe Palmisano
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0237981

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

10.3390/cancers13020348

Discovery of Functional Alternatively Spliced PKM Transcripts in Human Cancers
Cited by: 6
Author(s): Xiangyu Li, Woonghee Kim, Muhammad Arif, Chunxia Gao, Andreas Hober, David Kotol, Linnéa Strandberg, Björn Forsström, Åsa Sivertsson, Per Oksvold, Hasan Türkez, Morten Grötli, Yusuke Sato, Haruki Kume, Seishi Ogawa, Jan Borén, Jens Nielsen, Mathias Uhlén, Cheng Cheng Zhang, Adil Mardinoğlu
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0198442

The proteome of perilymph in patients with vestibular schwannoma. A possibility to identify biomarkers for tumor associated hearing loss?
Cited by: 26
Author(s): Jesper Edvardsson Rasmussen, Göran Laurell, Helge Rask‐Andersen, Jonas Bergquist, Per Eriksson
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-30587-3

A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes
Cited by: 2
Author(s): Brett W. Engelmann, Chiaowen Joyce Hsiao, John Blischak, Yannick Fourne, Zia Khan, Michael J. Ford, Yoav Gilad
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12859-019-3337-9

Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations
Cited by: 8
Author(s): Antoine Buetti‐Dinh, Malte Herold, Stephan Christel, Mohamed El Hajjami, Francesco Delogu, Olga Ilie, Sören Bellenberg, Paul Wilmes, Ansgar Poetsch, Wolfgang Sand, Mario Vera, Igor V. Pivkin, Ran Friedman, Mark Dopson
Software Mentions: 3
Published: over 6 years ago

10.1186/s12866-020-01877-6

Proteomic analysis of Rickettsia akari proposes a 44 kDa-OMP as a potential biomarker for Rickettsialpox diagnosis
Cited by: 5
Author(s): František Csicsay, Gabriela Flores‐Ramírez, Fernando Zúñiga-Navarrete, Mária Bartošová, Alena Fučíková, Petr Pajer, Jiří Dresler, Ľudovít Škultéty, Marco Antonio Quevedo-Diaz
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-017-12021-2

Differential regulation of vaginal lipocalins (OBP, MUP) during the estrous cycle of the house mouse
Cited by: 25
Author(s): Martina Černá, Barbora Kuntová, Pavel Talacko, Romana Stopková, Pavel Stopka
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0160160

Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument
Cited by: 20
Author(s): Chengjian Tu, Jun Li, Shichen Shen, Quanhu Sheng, Yu Shyr, Jun Qu
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.redox.2020.101491

Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin
Cited by: 55
Author(s): Amir Ata Saei, Hjalmar Gullberg, Pierre Sabatier, Christian M. Beusch, Katarina Johansson, Bo Lundgren, Per I. Arvidsson, Elias S.J. Arnér, Roman A. Zubarev
Software Mentions: 3
Published: about 6 years ago

10.1126/sciadv.abg3013

<i>C9orf72</i> -derived arginine-containing dipeptide repeats associate with axonal transport machinery and impede microtubule-based motility
Cited by: 51
Author(s): Laura Fumagalli, Florence L. Young, Steven Boeynaems, Mathias De Decker, Arpan R. Mehta, Ann Swijsen, Raheem Fazal, Wenting Guo, Matthieu Moisse, Jimmy Beckers, Lieselot Dedeene, Bhuvaneish T. Selvaraj, Tijs Vandoorne, Vanesa Madan, Marka van Blitterswijk, Denitza Raitcheva, Alexander McCampbell, Koen Poesen, Aaron D. Gitler, Philipp Koch, Pieter Vanden Berghe, Dietmar Rudolf Thal, Cathérine Verfaillie, Siddharthan Chandran, Ludo Van Den Bosch, Simon L. Bullock, Philip Van Damme
Software Mentions: 3
Published: about 5 years ago

10.1007/s00018-016-2401-0

Multi-OMIC profiling of survival and metabolic signaling networks in cells subjected to photodynamic therapy
Cited by: 24
Author(s): Ruud Weijer, Séverine Clavier, Esther A. Zaal, Maud M. E. Pijls, Robert T. van Kooten, Klaas Vermaas, René Leen, Aldo Jongejan, Perry D. Moerland, Antoine H. C. van Kampen, André B. P. Kuilenburg, Celia R. Berkers, Simone Lemeer, Michal Heger
Software Mentions: 3
Published: over 9 years ago

10.1038/s41597-020-0519-2

Systems biology of acidophile biofilms for efficient metal extraction
Cited by: 7
Author(s): Antoine Buetti‐Dinh, Malte Herold, Stephan Christel, Mohamed El Hajjami, Sören Bellenberg, Olga Ilie, Paul Wilmes, Ansgar Poetsch, Wolfgang Sand, Mario Vera, Igor V. Pivkin, Mark Dopson
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-017-16633-6

A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community
Cited by: 45
Author(s): Jakob Herschend, Zacharias Brimnes Visby Damholt, Andrea Marion Marquard, Birte Svensson, Søren J. Sørensen, Per Hägglund, Mette Burmølle
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-43512-z

Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: about 7 years ago

10.3390/proteomes9030034

Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric
Cited by: 11
Author(s): Benjamin C. Orsburn
Software Mentions: 3
Published: almost 5 years ago

10.1002/pmic.201700388

Integrative Analysis of Proteome and Ubiquitylome Reveals Unique Features of Lysosomal and Endocytic Pathways in Gefitinib‐Resistant Non‐Small Cell Lung Cancer Cells
Cited by: 19
Author(s): Wang Li, Heyong Wang, Yan Yang, Tian Zhao, Zhixiong Zhang, Ye Tian, Zhaomie Shi, Xiaojun Peng, Fēi Li, Yonghong Feng, Lei Zhang, Gening Jiang, Fan Zhang
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12953-016-0092-y

Quantitative succinylome analysis in the liver of non-alcoholic fatty liver disease rat model
Cited by: 32
Author(s): Yang Cheng, Tianlu Hou, Ping Jian, Xianhai Zeng, Jianjie Chen
Software Mentions: 3
Published: over 10 years ago

10.1007/978-1-4939-7493-1_6

Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells
Cited by: 24
Author(s): Jakob Wirbel, Pedro R. Cutillas, Julio Sáez-Rodríguez
Software Mentions: 3
Published: over 8 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: almost 5 years ago

10.1186/s12864-019-6213-0

Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts
Cited by: 27
Author(s): Andrew L. Garfoot, Gary Wilson, Joshua J. Coon, Laura J. Knoll
Software Mentions: 3
Published: over 6 years ago

10.1007/s00412-019-00700-0

The molecular basis of monopolin recruitment to the kinetochore
Cited by: 15
Author(s): Rebecca Plowman, Namit Singh, Eelco C. Tromer, Angel Payan, Eris Duro, Christos Spanos, Juri Rappsilber, Berend Snel, Geert J.P.L. Kops, K.D. Corbett, Adèle L. Marston
Software Mentions: 3
Published: about 7 years ago

10.3390/biomedicines9020107

Breast Cancer-Derived Microvesicles Are the Source of Functional Metabolic Enzymes as Potential Targets for Cancer Therapy
Cited by: 4
Author(s): Yousef Risha, Vanessa Susevski, Nico Hüttmann, Suttinee Poolsup, Zoran Minić, Maxim V. Berezovski
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.ppat.1008155

The alternative cap-binding complex is required for antiviral defense in vivo
Cited by: 18
Author(s): Anna Gebhardt, Valter Bergant, Daniel Schnepf, Markus Moser, Arno Meiler, Dieudonnée Togbe, Claire Mackowiak, Line S. Reinert, Søren R. Paludan, Bernhard Ryffel, Alexey Stukalov, Peter Staeheli, Andreas Pichlmair
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1009410

Macrophage-specific responses to human- and animal-adapted tubercle bacilli reveal pathogen and host factors driving multinucleated cell formation
Cited by: 18
Author(s): Christophe J. Queval, Antony Fearns, Laure Botella, Alicia Smyth, Laura Schnettger, Morgane Mitermite, Esen Wooff, Bernardo Villarreal‐Ramos, Waldo L. García-Jiménez, Tiaan Heunis, Matthias Trost, Dirk Werling, Francisco J. Salguero, Stephen V. Gordon, Maximiliano G. Gutiérrez
Software Mentions: 3
Published: over 5 years ago

10.1186/s12014-017-9159-8

Distinct proteome pathology of circulating microparticles in systemic lupus erythematosus
Cited by: 18
Author(s): Ole Østergaard, Christoffer Tandrup Nielsen, Julia T. Tanassi, Line V. Iversen, Søren Jacobsen, Niels H. H. Heegaard
Software Mentions: 3
Published: almost 9 years ago

10.1074/mcp.RA120.002227

Peptidomics-Driven Strategy Reveals Peptides and Predicted Proteases Associated With Oral Cancer Prognosis
Cited by: 9
Author(s): Leandro Xavier Neves, Daniela Campos Granato, Ariane F. Busso-Lopes, Carolina Moretto Carnielli, Fabio M. de Sá Patroni, Tatiane De Rossi, Ana Karina de Oliveira, Ana Carolina Prado Ribeiro, Thaís Bianca Brandão, André Nimtz Rodrigues, Pammela A. Lacerda, Miyuki Uno, Nilva K. Cervigne, Alan Roger Santos‐Silva, Luiz Paulo Kowalski, Márcio Ajudarte Lopes, Adriana Franco Paes Leme
Software Mentions: 3
Published: over 5 years ago

10.1590/0074-02760170385

NS1 codon usage adaptation to humans in pandemic Zika virus
Cited by: 11
Author(s): Caio César de Melo Freire, Giuseppe Palmisano, Carla Torres Braconi, Fernanda R. Cugola, Fabiele Baldino Russo, Patrícia Cristina Baleeiro Beltrão-Braga, Atila Iamarino, Daniel Ferreira de Lima Neto, Amadou Alpha Sall, Lívia Rosa-Fernandes, Martin R. Larsen, Paolo Marinho de Andrade Zanotto
Software Mentions: 3
Published: about 8 years ago

10.1242/jcs.221606

The N-cadherin interactome in primary cardiomyocytes as defined by quantitative proximity proteomics
Cited by: 39
Author(s): Li Yang, Chelsea D. Merkel, Xuemei Zeng, Jonathon A. Heier, Pamela S. Cantrell, Mai Sun, Donna B. Stolz, Simon C. Watkins, Nathan A. Yates, Adam V. Kwiatkowski
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.ppat.1004183

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis
Cited by: 116
Author(s): Luis Solans, Jesús Gonzalo-Asensio, Claudia Sala, Andrej Benjak, Swapna Uplekar, Jacques Rougemont, Christophe Guilhot, Wladimir Malaga, Carlos Martı́n, Stewart T. Cole
Software Mentions: 3
Published: about 12 years ago

10.1016/j.jbc.2021.100295

The cytoprotective protein MANF promotes neuronal survival independently from its role as a GRP78 cofactor
Cited by: 27
Author(s): Ave Eesmaa, Li-Ying Yu, Helka Göös, Kristofer Nõges, Vera Kovaleva, Maarit Hellman, Richard Zimmermann, Martin Jung, Perttu Permi, Markku Varjosalo, Päivi Lindholm, Märt Saarma
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-019-0461-z

C/EBPβ-LIP induces cancer-type metabolic reprogramming by regulating the let-7/LIN28B circuit in mice
Cited by: 11
Author(s): Tobias Ackermann, Götz Hartleben, Christine Müller, Guido Mastrobuoni, Marco Groth, Britt A. Sterken, Mohamad Amr Zaini, Sameh A. Youssef, Hidde R. Zuidhof, Sara Russo Krauss, Gertrud Kortman, Gerald de Haan, Alain de Bruin, Zhao Qi Wang, Matthias Platzer, Stefan Kempa, Cornelis F. Calkhoven
Software Mentions: 3
Published: about 7 years ago

10.1074/mcp.RA117.000400

Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment
Cited by: 47
Author(s): Thomas Worzfeld, Florian Finkernagel, Silke Reinartz, Anne Konzer, Till Adhikary, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Mario Looso, Johannes Graumann, Rolf Müller
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-019-5456-0

Global host molecular perturbations upon in situ loss of bacterial endosymbionts in the deep-sea mussel Bathymodiolus azoricus assessed using proteomics and transcriptomics
Cited by: 9
Author(s): Camille Détrée, Iman Haddad, Emmanuelle Demey-Thomas, Joëlle Vinh, François H. Lallier, Arnaud Tanguy, Jean Mary
Software Mentions: 3
Published: over 7 years ago

10.1083/jcb.202005130

SUMOylation stabilizes sister kinetochore biorientation to allow timely anaphase
Cited by: 4
Author(s): Shaowu Xue, Menglu Wang, Claudia Schaffner, Olga O. Nerusheva, Dean Clift, Christos Spanos, David A. Kelly, Michael H. Tatham, Andreas U. Wallek, Yehui Wu, Juri Rappsilber, A. Arockia Jeyaprakash, Zuzana Storchová, Ronald T. Hay, Adèle L. Marston
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1008681

The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)
Cited by: 20
Author(s): Christos N. Velanis, Pumi Perera, Bennett Thomson, Erica de Leau, Shih Chieh Liang, Ben Hartwig, Alexander Förderer, Harry Thornton, Pedro Arêde, Jiawen Chen, Kimberly M. Webb, Serin Gümüs, Geert De Jaeger, Clinton A. Page, C. Nathan Hancock, Christos Spanos, Juri Rappsilber, Philipp Voigt, Franziska Turck, Frank Wellmer, Justin Goodrich
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0191682

The long noncoding RNA lncR492 inhibits neural differentiation of murine embryonic stem cells
Cited by: 15
Author(s): Maria Winzi, Núria Casas-Vila, Maciej Paszkowski‐Rogacz, Li Ding, Svenja Noack, Mirko Theis, Falk Butter, Frank Buchholz
Software Mentions: 3
Published: over 8 years ago

10.1083/jcb.202106115

GOLPH3 and GOLPH3L are broad-spectrum COPI adaptors for sorting into intra-Golgi transport vesicles
Cited by: 24
Author(s): Lawrence G. Welch, Sew‐Yeu Peak‐Chew, Farida Begum, Tim J. Stevens, Sean Munro
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-019-1814-0

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation
Cited by: 26
Author(s): Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, Susan Boerner, Jan B. Heidelberger, Anke Busch, Heike Hänel, Andrea Voigt, Martin Möckel, Stefanie Ebersberger, Anica Scholz, Annabelle Dold, Tobias Schmid, Ingo Ebersberger, Jean‐Yves Roignant, Kathi Zarnack, Julian König, Petra Beli
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1008649

Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress
Cited by: 49
Author(s): Alexandro Rodríguez‐Rojas, Joshua Jay Kim, Paul R. Johnston, Olga Makarova, Murat Eravci, Christoph Weise, Regine Hengge, Jens Rolff
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-017-3977-y

The first succinylome profile of Trichophyton rubrum reveals lysine succinylation on proteins involved in various key cellular processes
Cited by: 24
Author(s): Xingye Xu, Tao Liu, Jian Yang, Lihong Chen, Bo Liu, Candong Wei, Lingling Wang, Qi Jin
Software Mentions: 3
Published: almost 9 years ago

10.26508/lsa.202000660

Metabolic reprogramming of fibro/adipogenic progenitors facilitates muscle regeneration
Cited by: 34
Author(s): Alessio Reggio, Marco Rosina, Natalie Krahmer, Alessandro Palma, Lucia Lisa Petrilli, Giuliano Maiolatesi, Giorgia Massacci, Illari Salvatori, Cristiana Valle, Stefano Testa, Cesare Gargioli, Claudia Fuoco, Luisa Castagnoli, Gianni Cesareni
Software Mentions: 3
Published: over 6 years ago

10.3390/biom11060843

Nucleoside Analogues Are Potent Inducers of Pol V-mediated Mutagenesis
Cited by: 2
Author(s): Balagra Kasim Sumabe, Synnøve Brandt Ræder, Lisa Marie Røst, Animesh Sharma, Eric S Donkor, Lydia Mosi, Samuel Duodu, Per Bruheim, Marit Otterlei
Software Mentions: 3
Published: about 5 years ago

10.1074/mcp.RA118.001288

Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance
Cited by: 133
Author(s): Roland Bruderer, Jan Muntel, Sebastian Müller, Oliver M. Bernhardt, Tejas Gandhi, Ornella Cominetti, Charlotte Macron, Jérôme Carayol, Oliver Rinner, Arne Astrup, Wim H. M. Saris, Jörg Hager, Armand Valsesia, Loïc Dayon, Lukas Reiter
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1006620

Mutations in mitochondrial DNA causing tubulointerstitial kidney disease
Cited by: 47
Author(s): Thomas M. Connor, Simon Hoer, Andrew Mallett, Daniel P. Gale, Aurora Gómez-Durán, Viktor Posse, Robin Antrobus, Pablo Moreno, Marco Sciacovelli, Christian Frezza, Jennifer Duff, Neil Sheerin, John A. Sayer, Margaret Ashcroft, Michael S. Wiesener, Gavin Hudson, Claes M. Gustafsson, Patrick F. Chinnery, Patrick H. Maxwell
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-018-4907-3

Novel proteome and acetylome of Bemisia tabaci Q in response to Cardinium infection
Cited by: 10
Author(s): Hongran Li, James D. Harwood, Tong‐Xian Liu, Dong Chu
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1006088

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
Cited by: 21
Author(s): Matthew E. MacGilvray, Evgenia Shishkova, Deborah Chasman, Michael Place, Anthony Gitter, Joshua J. Coon, Audrey P. Gasch
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pgen.1009600

Antagonistic fungal enterotoxins intersect at multiple levels with host innate immune defences
Cited by: 10
Author(s): Xing Zhang, Benjamin W. Harding, Dina Aggad, Damien Courtine, Jia‐Xuan Chen, Nathalie Pujol, Jonathan J. Ewbank
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-019-1799-8

Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency
Cited by: 43
Author(s): Taolan Zhao, Qing Huan, Jing Sun, Chunyan Liu, Xiuli Hou, Xiang Yu, Ian M. Silverman, Yi Zhang, Brian D. Gregory, Chunming Liu, Wenfeng Qian, Xiaofeng Cao
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13073-019-0636-8

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma
Cited by: 92
Author(s): Markus Löffler, Christopher Mohr, Leon Bichmann, Lena Katharina Freudenmann, Mathias Walzer, Christopher Schroeder, Nico Trautwein, Franz J. Hilke, Raphael S. Zinser, Lena Mühlenbruch, Daniel J. Kowalewski, Heiko Schuster, Marc Sturm, Jakob Matthes, Olaf Rieß, Stefan Czemmel, Sven Nahnsen, Ingmar Königsrainer, Karolin Thiel, Silvio Nadalin, Stefan Beckert, Hans Bösmüller, Falko Fend, Ana Velić, Boris Maček, Sebastian P. Haen, Luigi Buonaguro, Oliver Kohlbacher, Stefan Stevanović, Alfred Königsrainer, Hans‐Georg Rammensee
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2164-15-249

Characterization of the pigmented shell-forming proteome of the common grove snail Cepaea nemoralis
Cited by: 73
Author(s): Karlheinz Mann, Daniel J. Jackson
Software Mentions: 3
Published: over 12 years ago

10.3389/fpls.2018.01248

Microscopic and Proteomic Analysis of Dissected Developing Barley Endosperm Layers Reveals the Starchy Endosperm as Prominent Storage Tissue for ER-Derived Hordeins Alongside the Accumulation of Barley Protein Disulfide Isomerase (HvPDIL1-1)
Cited by: 13
Author(s): Valentin Roustan, Pierre-Jean Roustan, Marieluise Weidinger, Siegfried Reipert, Eszter Kapusi, Azita Shabrangy, Eva Stöger, Wolfram Weckwerth, Verena Ibl
Software Mentions: 3
Published: almost 8 years ago

10.3389/fpls.2017.01961

Rhizobium Impacts on Seed Productivity, Quality, and Protection of Pisum sativum upon Disease Stress Caused by Didymella pinodes: Phenotypic, Proteomic, and Metabolomic Traits
Cited by: 37
Author(s): Nima Ranjbar Sistani, Hans‐Peter Kaul, Getinet Desalegn, Stefanie Wienkoop
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pbio.3001344

Structure of the human C9orf72-SMCR8 complex reveals a multivalent protein interaction architecture
Cited by: 6
Author(s): Julia Nörpel, Simone Cavadini, Andreas Schenk, Alexandra Graff-Meyer, Daniel Heß, Jan Seebacher, Jeffrey A. Chao, Varun Bhaskar
Software Mentions: 3
Published: almost 5 years ago

10.3389/fpls.2021.722802

Effect and Response of Quercus ilex subsp. ballota [Desf.] Samp. Seedlings From Three Contrasting Andalusian Populations to Individual and Combined Phytophthora cinnamomi and Drought Stresses
Cited by: 18
Author(s): Bonoso San-Eufrasio, María Ángeles Castillejo, Mónica Labella-Ortega, Francisco J. Ruíz-Gómez, Rafael M. Navarro-Cerrillo, Marta Tienda-Parrilla, Jesús V. Jorrín‐Novo, María‐Dolores Rey
Software Mentions: 3
Published: almost 5 years ago

10.1111/pbi.12916

Three unrelated protease inhibitors enhance accumulation of pharmaceutical recombinant proteins in <i>Nicotiana benthamiana</i>
Cited by: 53
Author(s): Friederike Grosse‐Holz, Luisa Madeira, Muhammad Awais Zahid, Molly Songer, Jiorgos Kourelis, Mary Fesenko, Sabrina Ninck, Farnusch Kaschani, Markus Kaiser, Renier A. L. van der Hoorn
Software Mentions: 3
Published: about 8 years ago

10.1111/pce.13481

Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis
Cited by: 24
Author(s): Sebastian Schneider, Arno Schintlmeister, Manuel Becana, Michael Wagner, Dagmar Woebken, Stefanie Wienkoop
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2019.00325

Proteomic Analysis of Lactobacillus nagelii in the Presence of Saccharomyces cerevisiae Isolated From Water Kefir and Comparison With Lactobacillus hordei
Cited by: 16
Author(s): Julia Bechtner, Di Xu, Jürgen Behr, Christina Ludwig, Rudi F. Vogel
Software Mentions: 3
Published: over 7 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: almost 6 years ago

10.1111/pbi.13092

Activity‐based proteomics reveals nine target proteases for the recombinant protein‐stabilizing inhibitor <i>Sl</i> <scp>CYS</scp> 8 in <i>Nicotiana benthamiana</i>
Cited by: 12
Author(s): Philippe V. Jutras, Friederike Grosse‐Holz, Farnusch Kaschani, Markus Kaiser, Dominique Michaud, Renier A. L. van der Hoorn
Software Mentions: 3
Published: over 7 years ago

10.1186/s13058-020-01367-7

Combined the SMAC mimetic and BCL2 inhibitor sensitizes neoadjuvant chemotherapy by targeting necrosome complexes in tyrosine aminoacyl-tRNA synthase-positive breast cancer
Cited by: 5
Author(s): Kyung Min Lee, Hyebin Lee, Dohyun Han, Woo Kyung Moon, Kwangsoo Kim, Hyeon Jeong Oh, Jin-Hwan Choi, Eunmi Hwang, Seong Eun Kang, Seock Ah Im, Han Suk Ryu
Software Mentions: 3
Published: over 5 years ago

10.3389/fnmol.2018.00454

Effects of APOE Genotype on Brain Proteomic Network and Cell Type Changes in Alzheimer's Disease
Cited by: 48
Author(s): Jingting Dai, Erik C. B. Johnson, Eric B. Dammer, Duc M. Duong, Marla Gearing, James J. Lah, Aĺlan I. Levey, Thomas S. Wingo, Nicholas T. Seyfried
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2021.707298

Effects of Combinatorial Ubiquitinated Protein-Based Nanovaccine and STING Agonist in Mice With Drug-Resistant and Metastatic Breast Cancer
Cited by: 4
Author(s): Fang Huang, Ning Pan, Yi-ting Wei, Jinjin Zhao, Mohanad Aldarouish, Xuru Wang, Xiaotong Sun, Wen Zhang, Yongqiang Chen, Lixin Wang
Software Mentions: 3
Published: almost 5 years ago

10.1074/mcp.RA119.001769

Dynamic Transcriptomic and Phosphoproteomic Analysis During Cell Wall Stress in Aspergillus nidulans
Cited by: 5
Author(s): Cynthia Chelius, Walker Huso, Samantha Reese, Alexander Doan, Stephen R. Lincoln, Kelsi Lawson, Bao Tran, Raj Purohit, Trevor Glaros, Ranjan Srivastava, Steven D. Harris, Mark R. Marten
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2019.00378

High-Throughput Proteomics Identifies Proteins With Importance to Postantibiotic Recovery in Depolarized Persister Cells
Cited by: 23
Author(s): Daniel-Timon Spanka, Anne Konzer, Daniel Edelmann, Bork A. Berghoff
Software Mentions: 3
Published: over 7 years ago

10.3389/fcimb.2021.619981

Innate Immune Responses of Galleria mellonella to Mycobacterium bovis BCG Challenge Identified Using Proteomic and Molecular Approaches
Cited by: 8
Author(s): Masanori Asai, Gerard Sheehan, Yanwen Li, Brian Robertson, Kevin Kavanagh, Paul Langford, Sandra M. Newton
Software Mentions: 3
Published: over 5 years ago

10.3389/fcimb.2021.595554

Protein and Microbial Biomarkers in Sputum Discern Acute and Latent Tuberculosis in Investigation of Pastoral Ethiopian Cohort
Cited by: 4
Author(s): Milkessa HaileMariam, Yu Yoshida, Harinder Singh, Takele Teklu, Biniam Wondale, Adane Worku, Aboma Zewude, Stephanie Mounaud, Tamara Tsitrin, Mengistu Legesse, Gobena Ameni, Rembert Pieper
Software Mentions: 3
Published: about 5 years ago

10.1038/s41416-019-0659-3

Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer
Cited by: 14
Author(s): Nikolaus Berndt, Antje Egners, Guido Mastrobuoni, Olga Vvedenskaya, Athanassios Fragoulis, Aurélien Dugourd, Sascha Bulik, Matthias Pietzke, Chris Bielow, Rob J. J. van Gassel, Steven W. M. Olde Damink, Merve Erdem, Julio Sáez-Rodríguez, Hermann‐Georg Holzhütter, Stefan Kempa, Thorsten Cramer
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.594824

The Active Constituent From Gynostemma Pentaphyllum Prevents Liver Fibrosis Through Regulation of the TGF-β1/NDRG2/MAPK Axis
Cited by: 8
Author(s): Hui Huang, Kuifeng Wang, Qian Liu, Feihong Ji, Hu Zhou, Shanhua Fang, Jiansheng Zhu
Software Mentions: 3
Published: over 5 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: almost 7 years ago

10.3389/fcvm.2021.713983

Pan-Cancer Analysis of Atrial-Fibrillation-Related Innate Immunity Gene ANXA4
Cited by: 6
Author(s): Tao Yan, Shijie Zhu, Yu Shi, Changming Xie, Miao Zhu, Yangyang Zhang, Chunsheng Wang, Changfa Guo
Software Mentions: 3
Published: almost 5 years ago

10.15252/msb.20209730

Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses
Cited by: 63
Author(s): Aurélien Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gábor, Kristina B. Emdal, Vítor Vieira, Dorte B. Bekker-Jensen, Jennifer Kranz, Eric Bindels, Ana S.H. Costa, Abel Sousa, Pedro Beltrão, Miguel Rocha, Jesper V. Olsen, Christian Frezza, Rafael Kramann, Julio Sáez-Rodríguez
Software Mentions: 3
Published: over 5 years ago

10.1186/s13068-019-1506-8

Transcriptomic and proteomic responses to very low CO2 suggest multiple carbon concentrating mechanisms in Nannochloropsis oceanica
Cited by: 40
Author(s): Li Wei, Mohamed El Hajjami, Chen Shen, Wuxin You, Yandu Lu, Jing Li, Xiaoyan Jing, Qiang Hu, Wenxu Zhou, Ansgar Poetsch, Jian Xu
Software Mentions: 3
Published: almost 7 years ago

10.3389/fbioe.2021.640419

Extracellular Vesicles Derived From Adult and Fetal Bone Marrow Mesenchymal Stromal Cells Differentially Promote ex vivo Expansion of Hematopoietic Stem and Progenitor Cells
Cited by: 8
Author(s): Corina Adriana Ghebes, Jess Morhayim, Marion Kleijer, Merve Koroglu, Stefan J. Erkeland, Remco M. Hoogenboezem, Eric Bindels, Floris P.J. van Alphen, Maartje van den Biggelaar, Martijn A. Nolte, Bram C. J. van der Eerden, Eric Braakman, Carlijn Voermans, Jeroen van de Peppel
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2020.549451

Pex14p Phosphorylation Modulates Import of Citrate Synthase 2 Into Peroxisomes in Saccharomyces cerevisiae
Cited by: 17
Author(s): Andreas Schummer, Renate Maier, Shiran Gabay-Maskit, Tobias Hansen, Wignand W. D. Mühlhäuser, Ida Suppanz, Amir Fadel, Maya Schuldiner, Wolfgang Girzalsky, Silke Oeljeklaus, Einat Zalckvar, Ralf Erdmann, Bettina Warscheid
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2018.02371

A Metabolic Labeling Strategy for Relative Protein Quantification in Clostridioides difficile
Cited by: 4
Author(s): Anke Trautwein-Schult, Sandra Maaß, Kristina Plate, Andreas Otto, Dörte Becher
Software Mentions: 3
Published: over 7 years ago

10.1016/j.mcpro.2021.100118

A Reductionist Approach Using Primary and Metastatic Cell–Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis
Cited by: 10
Author(s): Ariane F. Busso-Lopes, Carolina Moretto Carnielli, Flávia Vischi Winck, Fábio Malta de Sá Patroni, Ana Karina de Oliveira, Daniela Campos Granato, Rute Alves Pereira e Costa, Romênia R. Domingues, Bianca Alves Pauletti, Diego Mauricio Riaño-Pachón, Juliana Aparecida Aricetti, Camila Caldana, Edgard Graner, Ricardo D. Coletta, Kelly A. Dryden, Jay W. Fox, Adriana Franco Paes Leme
Software Mentions: 3
Published: over 5 years ago

10.1016/j.mcpro.2021.100092

The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development
Cited by: 7
Author(s): Karsten Cirksena, Hermann J. Hütte, Aleksandra Shcherbakova, Thomas Thumberger, Roman Sakson, Stefan Weiß, Lars Riff Jensen, Alina Friedrich, Daniel Todt, Andreas W. Kuß, Thomas Ruppert, Joachim Wittbrodt, Hans Bakker, Falk F. R. Buettner
Software Mentions: 3
Published: over 5 years ago

10.15252/emmm.201910427

Plasma Proteome Profiling to detect and avoid sample‐related biases in biomarker studies
Cited by: 141
Author(s): Philipp E. Geyer, Eugenia Voytik, Peter V. Treit, Sophia Doll, Alisa Kleinhempel, Lili Niu, Johannes B. Müller-Reif, Marie-Luise Buchholtz, Jakob Bader, Daniel Teupser, Lesca M. Holdt
Software Mentions: 3
Published: over 6 years ago

10.15252/embr.201745642

Negative feedback via <scp>RSK</scp> modulates Erk‐dependent progression from naïve pluripotency
Cited by: 25
Author(s): Isabelle Nett, Carla Mulas, Laurent Guy, Kathryn S. Lilley, Austin Smith
Software Mentions: 3
Published: about 8 years ago

10.1074/mcp.O115.048777

Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics*
Cited by: 28
Author(s): Jun Fan, Shyamasree Saha, Gary Barker, Kate J Heesom, Fawaz Ghali, Andrew R. Jones, David A. Matthews, Conrad Bessant
Software Mentions: 3
Published: over 10 years ago

10.3390/molecules25061396

Mass Spectrometry Advances and Perspectives for the Characterization of Emerging Adoptive Cell Therapies
Cited by: 10
Author(s): Camille Lombard‐Banek, John E. Schiel
Software Mentions: 3
Published: about 6 years ago

10.1074/mcp.O115.049460

A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day*
Cited by: 39
Author(s): Fabian Hosp, Richard A. Scheltema, H. Christian Eberl, Nils A. Kulak, Eva C. Keilhauer, Korbinian Mayr, Matthias Mann
Software Mentions: 3
Published: almost 11 years ago

10.1016/j.mcpro.2021.100125

Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network
Cited by: 6
Author(s): Cristian V. A. Munteanu, Gabriela Chirițoiu, Marioara Chirițoiu, Simona Ghenea, Andrei-José Petrescu, Ștefana M. Petrescu
Software Mentions: 3
Published: over 5 years ago

10.1074/mcp.O115.055467

Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling
Cited by: 61
Author(s): Mark Larance, Kathryn J. Kirkwood, Michele Tinti, Alejandro Brenes Murillo, Michael A. J. Ferguson, Angus I. Lamond
Software Mentions: 3
Published: almost 10 years ago

10.3390/molecules26092587

Bioinformatic Prediction of Signaling Pathways for Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) and Its Role in Cholangiocarcinoma Cells
Cited by: 5
Author(s): Doungdean Tummanatsakun, Tanakorn Proungvitaya, Sittiruk Roytrakul, Siriporn Proungvitaya
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1006656

Novel insights into SLC25A46-related pathologies in a genetic mouse model
Cited by: 32
Author(s): Maria Eirini Terzenidou, Aikaterini Segklia, Toshimi Kano, Florentia Papastefanaki, Alexandros Karakostas, Maria Charalambous, Fotis Ioakeimidis, Maria Papadaki, Ismini Kloukina, Margarita Chrysanthou‐Piterou, Martina Samiotaki, George Panayotou, Rebecca Matsas, Eleni Douni
Software Mentions: 3
Published: about 9 years ago

10.3389/fpls.2021.624365

A Multi-OMICs Approach Sheds Light on the Higher Yield Phenotype and Enhanced Abiotic Stress Tolerance in Tobacco Lines Expressing the Carrot lycopene β-cyclase1 Gene
Cited by: 13
Author(s): Juan C. Moreno, Silvia Martínez-Jaime, Monika Kosmacz, Ewelina Sokołowska, Philipp Schulz, Axel Fischer, Urszula Luzarowska, Michel Havaux, Aleksandra Skirycz
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2019.02709

Label-Free Proteomic Approach to Study the Non-lethal Effects of Silver Nanoparticles on a Gut Bacterium
Cited by: 4
Author(s): Guido Domingo, Federica Villa, Candida Vannini, Elisa Garuglieri, Elisabetta Onelli, Marcella Bracale, Francesca Cappitelli
Software Mentions: 3
Published: over 6 years ago

10.1172/jci.insight.135544

PDX-derived organoids model in vivo drug response and secrete biomarkers
Cited by: 55
Author(s): Ling Huang, Bruno Bockorny, Indranil Paul, Dipikaa Akshinthala, Pierre‐Olivier Frappart, Omar Gandarilla, Arindam Bose, Veronica Sanchez‐Gonzalez, Emily E Rouse, Sylvain Lehoux, Nicole Pandell, Christine Lim, John G. Clohessy, Joseph E. Grossman, Raúl González, Sofia Perea Del Pino, George Daaboul, Mandeep S. Sawhney, Steven D. Freedman, Alexander Kleger, Richard D. Cummings, Andrew Emili, Lakshmi Muthuswamy, Manuel Hidalgo, Senthil K. Muthuswamy
Software Mentions: 3
Published: over 5 years ago