pypi: Scaffold | Projects | Ecosyste.ms: Papers

10.1016/j.xcrm.2020.100096

Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV Infection
Cited by: 11
Author(s): Sean M. Hughes, Claire Levy, Fernanda Calienes, Joanne D. Stekler, Urvashi Pandey, Lucia Vojtech, Alicia R. Berard, Kenzie Birse, Laura Noël‐Romas, Brian Richardson, Jackelyn B. Golden, Michael Cartwright, Ann C. Collier, Claire E. Stevens, Marcel E. Curlin, Timothy H. Holtz, Nelly Mugo, Elizabeth Irungu, Elly Katabira, Timothy Muwonge, Javier R. Lama, Jared M. Baeten, Adam Burgener, Jairam R. Lingappa, M. Juliana McElrath, Romel D. Mackelprang, Ian McGowan, Ross D. Cranston, Mark J. Cameron, Florian Hladik
Software Mentions: 21
Published: over 3 years ago

10.1128/mBio.02699-19

The Toxoplasma gondii Cyst Wall Interactome
Cited by: 24
Author(s): Vincent Tu, Tadakimi Tomita, Tatsuki Sugi, Joshua Mayoral, Bing Han, Rama R. Yakubu, Tere Williams, Aline Luciano Horta, Yanfen Ma, Louis M. Weiss
Software Mentions: 11
Published: about 4 years ago

10.3390/microorganisms8121887

A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function
Cited by: 13
Author(s): Laurin Christopher Gierse, Alexander Meene, Daniel Schultz, Theresa Schwaiger, Claudia Karte, Charlotte Schröder, Haitao Wang, Christine Wünsche, Karen Methling, Bernd Kreikemeyer, Stephan Fuchs, Jörg Bernhardt, Dörte Becher, Michael Lalk, Tim Urich, Katharina Riedel
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0199274

Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats
Cited by: 25
Author(s): Boris Zybailov, Galina Glazko, Yasir Rahmatallah, Dmitri S. Andreyev, Taylor McElroy, Oleg Karaduta, Stephanie D. Byrum, Lisa Orr, Alan J. Tackett, Samuel G. Mackintosh, Ricky D. Edmondson, Dorothy A. Kieffer, Roy J. Martin, Sean H. Adams, Nosratola D. Vaziri, John M. Arthur
Software Mentions: 9
Published: over 5 years ago

10.7554/eLife.54756

ATR expands embryonic stem cell fate potential in response to replication stress
Cited by: 34
Author(s): Sina Atashpaz, Sara Samadi Shams, Javier Martín‐González, Endre Sebestyén, Negar Arghavanifard, Andrea Gnocchi, Eliene Albers, Simone Minardi, Giovanni Fagà, Paolo Soffientini, E. Allievi, Valeria Cancila, Ángela Bachi, Óscar Fernández-Capetillo, Claudio Tripodo, Francesco Ferrari, Andrés J. López-Contreras, Vincenzo Costanzo
Software Mentions: 9
Published: about 4 years ago

10.7554/eLife.59442

Collagen-rich omentum is a premetastatic niche for integrin α2-mediated peritoneal metastasis
Cited by: 33
Author(s): Yen‐Lin Huang, Ching-Yeu Liang, Danilo Ritz, Ruimário Inácio Coelho, Dedy Septiadi, Manuela Estermann, Cécile Cumin, Natalie Rimmer, Andreas Schötzau, Mónica Núñez López, André Fedier, Martina Konantz, Tatjana Vlajnic, Diego Calabrese, Claudia Lengerke, Leonor David, Barbara Rothen‐Rutishauser, Francis Jacob, Viola Heinzelmann‐Schwarz
Software Mentions: 8
Published: over 3 years ago

10.1093/gigascience/giz003

Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
Cited by: 21
Author(s): Stefan Prost, Ellie E. Armstrong, Johan A. A. Nylander, Gregg W.C. Thomas, Alexander Suh, Bent Petersen, Love Dalén, Brett W. Benz, Mozes P. K. Blom, Eleftheria Palkopoulou, Per G. P. Ericson, Martin Irestedt
Software Mentions: 8
Published: over 5 years ago

10.1186/gb-2013-14-2-r18

The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila
Cited by: 29
Author(s): Tobias Kockmann, Moritz Gerstung, Tommy Beat Schlumpf, Zhu Xhinzhou, Daniel Heß, Niko Beerenwinkel, Christian Beisel, Renato Paro
Software Mentions: 7
Published: over 11 years ago

10.7554/eLife.49874

Discovery proteomics in aging human skeletal muscle finds change in spliceosome, immunity, proteostasis and mitochondria
Cited by: 114
Author(s): Ceereena Ubaida‐Mohien, Alexey E. Lyashkov, Marta González-Freire, Ravi Tharakan, Michelle Shardell, Ruin Moaddel, Richard D. Semba, Chee W. Chia, Myriam Gorospe, Ranjan Sen, Luigi Ferrucci
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0208561

Open source software in quantum computing
Cited by: 87
Author(s): Mark Fingerhuth, Tomáš Babej, Peter Wittek
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-019-2990-3

Analysis of networks of host proteins in the early time points following HIV transduction
Cited by: 8
Author(s): Éva Csősz, Ferenc Tóth, Mohamed Mahdi, George Tsaprailis, Miklós Emri, József Tözsér
Software Mentions: 7
Published: almost 5 years ago

10.3389/fmicb.2021.631889

DWV Infection in vitro Using Honey Bee Pupal Tissue
Cited by: 3
Author(s): Yunfei Wu, Xuye Yuan, Jing Li, Tatsuhiko Kadowaki
Software Mentions: 7
Published: about 3 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: almost 6 years ago

10.1186/s12915-019-0713-x

Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi
Cited by: 31
Author(s): Yuanning Li, Michael G. Tassia, Damien S. Waits, Viktoria E. Bogantes, Kyle T. David, Kenneth M. Halanych
Software Mentions: 6
Published: over 4 years ago

10.3390/v11010053

Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus
Cited by: 13
Author(s): Florian Pfaff, Sara Hägglund, Martina Zoli, Sandra Blaise‐Boisseau, Eve Laloy, Susanne Koethe, Daniela Zühlke, Katharina Riedel, Stéphan Zientara, Labib Bakkali‐Kassimi, J. F. Valarcher, Dirk W. Höper, Martin Beer, Michael Eschbaumer
Software Mentions: 6
Published: over 5 years ago

10.1093/gbe/evab069

Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus
Cited by: 13
Author(s): Fernando Seixas, Nathaniel B. Edelman, James Mallet
Software Mentions: 6
Published: about 3 years ago

10.1186/s13059-019-1857-2

eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5′UTR
Cited by: 34
Author(s): Ania Wilczynska, Sarah L. Gillen, Tobias Schmidt, Hedda A. Meijer, Rebekah Jukes-Jones, Claudia Langlais, Kari Kopra, Wei-Ting Lu, Jack D. Godfrey, Ben R Hawley, Kelly Hodge, Sara Zanivan, Kelvin Cain, John Le Quesne, Martin Bushell
Software Mentions: 5
Published: over 4 years ago

10.3390/jcm9092930

Proteomic Profiles of Exosomes of Septic Patients Presenting to the Emergency Department Compared to Healthy Controls
Cited by: 8
Author(s): Daniel C. Morris, Anja Kathrin Jaehne, Michael Chopp, Zhanggang Zhang, Laila Poisson, Yalei Chen, Indrani Datta, Emanuel P. Rivers
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22042046

Dysregulated Provision of Oxidisable Substrates to the Mitochondria in ME/CFS Lymphoblasts
Cited by: 20
Author(s): Daniel Missailidis, Oana Sanislav, Claire Y. Allan, Paige K. Smith, Sarah J. Annesley, Paul R. Fisher
Software Mentions: 5
Published: about 3 years ago

10.1074/mcp.RA120.002175

Transcriptome and Secretome Analysis of Intra-Mammalian Life-Stages of Calicophoron daubneyi Reveals Adaptation to a Unique Host Environment
Cited by: 3
Author(s): Kathryn M. Huson, Erwan Atcheson, Nicola A.M. Oliver, Philip M. Best, J.P. Barley, R.E.B. Hanna, Tom N. McNeilly, Yongxiang Fang, Sam Haldenby, Steve Paterson, Mark W. Robinson
Software Mentions: 5
Published: over 3 years ago

10.3389/fphar.2018.00084

Proteomic Analysis of Combined Gemcitabine and Birinapant in Pancreatic Cancer Cells
Cited by: 15
Author(s): Xu Zhu, Xiaomeng Shen, Jun Qu, Robert M. Straubinger, William J. Jusko
Software Mentions: 5
Published: about 6 years ago

10.3389/fcell.2021.655866

Proteomic Changes Associated With Sperm Fertilizing Ability in Meat-Type Roosters
Cited by: 4
Author(s): Anaïs Vitorino Carvalho, Laura Soler, Aurore Thélie, Isabelle Grasseau, Luiz Cordeiro, Daniel Tomas, Ana-Paula Teixeira-Gomes, Valérie Labas, Elisabeth Blesblois
Software Mentions: 5
Published: about 3 years ago

10.7554/eLife.03346

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network
Cited by: 82
Author(s): Carine Gubelmann, Petra Schwalie, Sunil K. Raghav, Eva Röder, Tenagne Delessa, Elke Kiehlmann, Sebastian M. Waszak, Andrea Corsinotti, Gilles Udin, Wiebke Holcombe, Gottfried Rudofsky, Didier Trono, Christian Wolfrum, Bart Deplancke
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.20375

Oral transfer of chemical cues, growth proteins and hormones in social insects
Cited by: 96
Author(s): Adria C LeBoeuf, Patrice Waridel, Colin S. Brent, André Nicolau Aquime Gonçalves, Laure Menin, Daniel Ortiz, Oksana Riba‐Grognuz, Atsuo Koto, Zamira Guerra Soares, Eyal Privman, Eric A. Miska, Richard Benton, Laurent Keller
Software Mentions: 5
Published: over 7 years ago

10.3389/fcimb.2020.588155

Proteome and Microbiome Mapping of Human Gingival Tissue in Health and Disease
Cited by: 14
Author(s): Kai Bao, Xiaofei Li, Lucy Poveda, Weihong Qi, Nathalie Selevsek, Pınar Gümüş, Gülnur Emingil, Jonas Grossmann, Patricia I. Diaz, George Hajishengallis, Nagihan Bostancı, Georgios N. Belibasakis
Software Mentions: 5
Published: over 3 years ago

10.1186/s12964-019-0326-6

Glucose-dependent phosphorylation signaling pathways and crosstalk to mitochondrial respiration in insulin secreting cells
Cited by: 11
Author(s): Jaime Santo‐Domingo, Antonio Núñez Galindo, Ornella Cominetti, Umberto De Marchi, Pedro R. Cutillas, Loïc Dayon, Andreas Wiederkehr
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0204234

Large scale changes in the transcriptome of Eisenia fetida during regeneration
Cited by: 28
Author(s): Aksheev Bhambri, Neeraj Dhaunta, Surendra Singh Patel, Mitali Hardikar, Abhishek Bhatt, Nagesh Srikakulam, Shruti Shridhar, Shamsudheen Karuthedath Vellarikkal, Rajesh Pandey, Rijith Jayarajan, Ankit Verma, Vikram Kumar, Pradeep Gautam, Yukti Khanna, Jameel Ahmed Khan, Bastian Fromm, Kevin J. Peterson, Vinod Scaria, Sridhar Sivasubbu, Beena Pillai
Software Mentions: 5
Published: over 5 years ago

10.1007/s00401-021-02299-y

Single-cell profiling of myasthenia gravis identifies a pathogenic T cell signature
Cited by: 21
Author(s): Florian Ingelfinger, Sinduya Krishnarajah, Michael H. Kramer, Sebastian G. Utz, Edoardo Galli, Mirjam Lutz, Pascale Zwicky, Ayse U. Akarca, Nicole Puertas Jurado, Can Ulutekin, David Bamert, Corinne C. Widmer, Luca Piccoli, Federica Sallusto, Nicolás Gonzalo Núñez, Teresa Marafioti, Didier Schneiter, Isabelle Opitz, Antonio Lanzavecchia, Hans H. Jung, Donatella De Feo, Sarah Mundt, Bettina Schreiner, Burkhard Becher
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0245710

Isolation of the Buchnera aphidicola flagellum basal body complexes from the Buchnera membrane
Cited by: 1
Author(s): Matthew J. Schepers, James N. Yelland, Nancy A. Moran, David W. Taylor
Software Mentions: 5
Published: almost 3 years ago

10.15252/embr.202050078

The actin modulator <scp>hMENA</scp> regulates <scp>GAS</scp> 6‐ <scp>AXL</scp> axis and pro‐tumor cancer/stromal cell cooperation
Cited by: 18
Author(s): Roberta Melchionna, Sheila Spada, Francesca Di Modugno, Daniel D’Andrea, Anna Di Carlo, Mariangela Panetta, Anna Maria Mileo, Isabella Sperduti, Barbara Antoniani, Enzo Gallo, Rita T. Lawlor, Lorenzo Piemonti, Paolo Visca, Michèle Milella, Gian Luca Grazi, Francesco Facciolo, Emily Chen, Aldo Scarpa, Paola Nisticò
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.56474

A divergent cyclin/cyclin-dependent kinase complex controls the atypical replication of a malaria parasite during gametogony and transmission
Cited by: 42
Author(s): Aurélia C. Balestra, Mohammad Zeeshan, Edward Rea, Carla Pasquarello, Lorenzo Brusini, Tobias Mourier, Amit Kumar Subudhi, Natacha Klages, Patrizia Arboit, Rajan Kumar Pandey, Declan Brady, Sue Vaughan, Anthony A. Holder, Arnab Pain, David Ferguson, Alexandre Hainard, Rita Tewari, Mathieu Brochet
Software Mentions: 5
Published: almost 4 years ago

10.3389/fimmu.2021.643298

Immunomodulation of T Helper Cells by Tumor Microenvironment in Oral Cancer Is Associated With CCR8 Expression and Rapid Membrane Vitamin D Signaling Pathway
Cited by: 14
Author(s): Marco Fraga, Milly Yáñez, Macarena Sherman, Faryd Llerena, Mauricio Hernández, Guillermo Nourdin, Francisco Álvarez, Joaquín Urrizola, César Rivera, Liliana Lamperti, Lorena Nova, S Rojas Castro, Olga Zambrano, Alejandro Cifuentes, León Campos, Sergio Moya, J. Pastor, Marcelo Nuñez, Jorge Gatica, Jorge Figueroa, Felipe Zúñiga, Carlos Salomón, Gustavo Cerda, Ricardo Puentes, Gonzalo Labarca, Mabel Vidal, Reuben McGregor, Estefanía Nova-Lamperti
Software Mentions: 5
Published: about 3 years ago

10.7554/eLife.64940

DIPPER, a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics
Cited by: 32
Author(s): Vivian Tam, Peikai Chen, Anita Yee, Nestor Solis, Théo Klein, Mateusz Kudelko, Rakesh Sharma, Wing‐Lok Chan, Christopher M. Overall, Lisbet Haglund, Pak C. Sham, Kathryn S.E. Cheah, Danny Chan
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-017-08094-8

CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo
Cited by: 14
Author(s): D. Craig Ayre, Ian C. Chute, Andrew P. Joy, David A. Barnett, Andrew M. Hogan, Marc P. Grüll, Lourdes Peña‐Castillo, Andrew S. Lang, Stephen M. Lewis, Sherri L. Christian
Software Mentions: 5
Published: over 6 years ago

10.3390/ijms22115858

Calreticulin Deficiency Disturbs Ribosome Biogenesis and Results in Retardation in Embryonic Kidney Development
Cited by: 4
Author(s): Nazli Serin, Gry H. Dihazi, Asima Tayyeb, Christof Lenz, Gerhard A. Müller, Michael Zeisberg, Hassan Dihazi
Software Mentions: 5
Published: almost 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: over 8 years ago

10.1371/journal.ppat.1009097

Vaginal microbiome-hormonal contraceptive interactions associate with the mucosal proteome and HIV acquisition
Cited by: 17
Author(s): Laura Noël‐Romas, Michelle Perner, Refilwe P. Molatlhegi, Christina Farr Zuend, Amanda Mabhula, Sarah Hoger, Alana Lamont, Kenzie Birse, Alicia R. Berard, Stuart McCorrister, Garett Westmacott, Al Leslie, Vanessa Poliquin, Renee Heffron, Lyle R. McKinnon, Adam Burgener
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.49558

Long non-coding RNA GRASLND enhances chondrogenesis via suppression of the interferon type II signaling pathway
Cited by: 23
Author(s): Nguyen P.T. Huynh, Catherine C. Gloss, Jeremiah Lorentz, Ruhang Tang, Jonathan M. Brunger, Audrey McAlinden, Bo Zhang, Farshid Guilak
Software Mentions: 5
Published: about 4 years ago

10.3390/antibiotics10030325

The Phosin PptA Plays a Negative Role in the Regulation of Antibiotic Production in Streptomyces lividans
Cited by: 7
Author(s): Noriyasu Shikura, Emmanuelle Darbon, Catherine Esnault, Ariane Deniset‐Besseau, Delin Xu, Clara Lejeune, Éric Jacquet, Naïma Nhiri, Laila Sago, David Cornu, Sebastiaan Werten, Cécile Martel, Marie‐Joëlle Virolle
Software Mentions: 4
Published: about 3 years ago

10.1093/jxb/erx247

Delaying chloroplast turnover increases water-deficit stress tolerance through the enhancement of nitrogen assimilation in rice
Cited by: 35
Author(s): Nir Sade, Kamolchanok Umnajkitikorn, María del Mar Rubio Wilhelmi, Matthew Wright, Songhu Wang, Eduardo Blumwald
Software Mentions: 4
Published: almost 7 years ago

10.1038/srep46553

Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism
Cited by: 60
Author(s): Ling Yin, Yunhe An, Junjie Qu, Xinlong Li, Yali Zhang, Ian B. Dry, Huijuan Wu, Jiang Lu
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2019.00715

Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Quorum Sensing Molecule N-3-Oxododecanoyl Homoserine Lactone
Cited by: 16
Author(s): Joseph R. Spangler, Scott N. Dean, Dagmar H. Leary, Scott A. Walper
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.00495

Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator
Cited by: 7
Author(s): Natalia M. Vior, Eva Cea-Torrescassana, Tom H. Eyles, Govind Chandra, Andrew W. Truman
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2018.03183

Iron Regulation in Clostridioides difficile
Cited by: 42
Author(s): Mareike Berges, Annika-Marisa Michel, Christian Lassek, Aaron M. Nuss, Michael Beckstette, Petra Dersch, Katharina Riedel, Susanne Sievers, Dörte Becher, Andreas Otto, Sandra Maaß, Manfred Rohde, Denitsa Eckweiler, José Manuel Borrero‐de Acuña, Martina Jahn, Meina Neumann‐Schaal, Dieter Jahn
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.44889

Identification of compounds that rescue otic and myelination defects in the zebrafish adgrg6 (gpr126) mutant
Cited by: 19
Author(s): Elvira Diamantopoulou, Sarah Baxendale, Antonio de la Vega de León, Anzar Asad, Celia J. Holdsworth, Leïla Abbas, Valerie J. Gillet, Giselle R. Wiggin, Tanya T. Whitfield
Software Mentions: 4
Published: almost 5 years ago

10.1016/j.dib.2015.11.063

Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods
Cited by: 29
Author(s): Claire Ramus, Agnès Hovasse, Marlène Marcellin, Anne-Marie Hesse, Emmanuelle Mouton-Barbosa, David Bouyssié, Sebastian Vaca, Christine Carapito, Karima Chaoui, Christophe Bruley, Jérôme Garin, Sarah Cianférani, Myriam Ferro, Alain Van Dorssaeler, Odile Burlet‐Schiltz, Christine Schaeffer, Yohann Couté, Anne Gonzalez de Peredo
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-018-4783-x

The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum
Cited by: 27
Author(s): Chuanlin Yin, Meizhen Li, Jian Hu, Kun Lang, Qiming Chen, Jinding Liu, Dan Guo, Kang He, Yipei Dong, Jiapeng Luo, Zhenkun Song, James R. Walters, Wenqing Zhang, Fĕi Li, Xue-Xin Chen
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.celrep.2019.06.049

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy
Cited by: 81
Author(s): Felix J. Hartmann, Joël Babdor, Pier Federico Gherardini, El-ad David Amir, Kyle Jones, Bita Sahaf, Diana M. Márquez, Peter O. Krutzik, Erika O’Donnell, Natalia Sigal, Holden T. Maecker, Everett Meyer, Matthew H. Spitzer, Sean C. Bendall
Software Mentions: 4
Published: almost 5 years ago

10.1038/s42003-021-02166-2

Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease
Cited by: 5
Author(s): Mayar Allam, Thomas Hu, Shuangyi Cai, Krishnan Laxminarayanan, Robert B. Hughley, Ahmet F. Coşkun
Software Mentions: 4
Published: almost 3 years ago

10.1186/s12859-015-0818-3

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads
Cited by: 11
Author(s): Xiao Zhu, Ho-fung Leung, Rongjie Wang, Francis Y. L. Chin, Siu Ming Yiu, Guangri Quan, Yajie Li, Rui Zhang, Qinghua Jiang, Bo Liu, Yucui Dong, Guohui Zhou, Yadong Wang
Software Mentions: 4
Published: over 8 years ago

10.15252/embj.2019103922

Prevention of dsRNA‐induced interferon signaling by AGO1x is linked to breast cancer cell proliferation
Cited by: 18
Author(s): Souvik Ghosh, Joao C. Guimaraes, Manuela Lanzafame, Alexander Schmidt, Afzal Pasha Syed, Beatrice Dimitriades, Anastasiya Börsch, Shreemoyee Ghosh, Nitish Mittal, Thomas Montavon, Ana Luísa Correia, Johannes Danner, Gunter Meister, Luigi Terracciano, Sébastien Pfeffer, Salvatore Piscuoglio, Mihaela Zavolan
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-020-6672-3

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly
Cited by: 19
Author(s): Anthony Bayega, Haïg Djambazian, Konstantina T. Tsoumani, Maria‐Eleni Gregoriou, Efthimia Sagri, Elena Drosopoulou, Penelope Mavragani-Tsipidou, Kristina Giorda, George Tsiamis, Kostas Bourtzis, Spyridon Oikonomopoulos, Ken Dewar, Deanna M. Church, Alexie Papanicolaou, Kostas D. Mathiopoulos, Jiannis Ragoussis
Software Mentions: 4
Published: about 4 years ago

10.1021/acs.jproteome.0c00992

Human Bone Proteomes before and after Decomposition: Investigating the Effects of Biological Variation and Taphonomic Alteration on Bone Protein Profiles and the Implications for Forensic Proteomics
Cited by: 21
Author(s): Hayley L. Mickleburgh, Ed C. Schwalbe, Andrea Bonicelli, Haruka Mizukami, Federica Sellitto, Sefora Starace, Daniel J. Wescott, David Carter, Noemi Procopio
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0025851

Examination of Triacylglycerol Biosynthetic Pathways via De Novo Transcriptomic and Proteomic Analyses in an Unsequenced Microalga
Cited by: 200
Author(s): Michael T. Guarnieri, Ambarish Nag, Sharon Smolinski, Al Darzins, Michael Seibert, Philip T. Pienkos
Software Mentions: 4
Published: over 12 years ago

10.1038/s41598-020-60623-0

First evidence of production of the lantibiotic nisin P
Cited by: 29
Author(s): Enriqueta García-Gutiérrez, Paula M. O’Connor, Gerhard Saalbach, Calum J. Walsh, James W. Hegarty, Caitriona M. Guinane, Melinda J. Mayer, Arjan Narbad, Paul D. Cotter
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.60645

Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation
Cited by: 28
Author(s): Christian Brion, Sheila Lutz, Frank W. Albert
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pbio.3001306

Dynamic landscape of protein occupancy across the Escherichia coli chromosome
Cited by: 18
Author(s): Peter L. Freddolino, Haley M. Amemiya, Thomas J. Goss, Saeed Tavazoie
Software Mentions: 4
Published: almost 3 years ago

10.1038/s41598-017-01179-4

Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress
Cited by: 42
Author(s): Mélanie Hillion, Jörg Bernhardt, Tobias Busche, Martina Rossius, Sandra Maaß, Dörte Becher, Mamta Rawat, Markus Wirtz, Rüdiger Hell, Christian Rückert, Jörn Kalinowski, Haike Antelmann
Software Mentions: 4
Published: about 7 years ago

10.15252/embr.201948882

Mitochondrial protein biogenesis in the synapse is supported by local translation
Cited by: 56
Author(s): Bożena Kuźniewska, Dominik Cysewski, Michał Wasilewski, Paulina Sakowska, Jacek Miłek, Tomasz M. Kuliński, M. Winiarski, Paweł Kozielewicz, Ewelina Knapska, Michał Dadlez, Agnieszka Chacińska, Andrzej Dziembowski, Magdalena Dziembowska
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0102495

Loss of Sirt1 Function Improves Intestinal Anti-Bacterial Defense and Protects from Colitis-Induced Colorectal Cancer
Cited by: 44
Author(s): Giuseppe Lo Sasso, Dongryeol Ryu, Laurent Mouchiroud, Samodha C. Fernando, Christopher L. Anderson, Elena Katsyuba, Alessandra Piersigilli, Michael O. Hottiger, Kristina Schoonjans, Johan Auwerx
Software Mentions: 4
Published: almost 10 years ago

10.3389/fbioe.2020.00155

Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
Cited by: 9
Author(s): Richou Han, Katie Haning, Juan C. Gonzalez-Rivera, Yongqiang Yang, Runxia Li, Seung Hee Cho, Ju Huang, Bobi A. Simonsen, Shihui Yang, Lydia M. Contreras
Software Mentions: 4
Published: about 4 years ago

10.3390/genes9120579

Integrated Proteomic and Transcriptomic Analysis of Differential Expression of Chicken Lung Tissue in Response to NDV Infection during Heat Stress
Cited by: 19
Author(s): Perot Saelao, Ying Wang, Ganrea Chanthavixay, Vivian M. Yu, Rodrigo A. Gallardo, Jack C. M. Dekkers, Susan J. Lamont, T. Ross Kelly, Huaijun Zhou
Software Mentions: 4
Published: over 5 years ago

10.1172/jci.insight.143289

LncRNA DRAIR is downregulated in diabetic monocytes and modulates inflammatory phenotype via epigenetic mechanisms
Cited by: 15
Author(s): Marpadga A. Reddy, Vishnu Amaram, Sadhan Das, Vinay Singh Tanwar, Rituparna Ganguly, Mei Wang, Linda Lanting, Lingxiao Zhang, Maryam Abdollahi, Zhuo Chen, Xiwei Wu, Sridevi Devaraj, Rama Natarajan
Software Mentions: 4
Published: about 3 years ago

10.3390/jof2010006

Proteomic Analysis of Pathogenic Fungi Reveals Highly Expressed Conserved Cell Wall Proteins
Cited by: 41
Author(s): Jackson Champer, James I. Ito, Karl V. Clemons, David A. Stevens, Markus Kalkum
Software Mentions: 4
Published: over 8 years ago

10.1016/j.gpb.2020.06.004

The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells
Cited by: 4
Author(s): Monika Hiller, M Geissler, George M.C. Janssen, Peter A. van Veelen, Annemieke Aartsma‐Rus, Pietro Spitali
Software Mentions: 4
Published: almost 4 years ago

10.3389/fpls.2016.01661

The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation
Cited by: 13
Author(s): Igor Fesenko, A. V. Seredina, Georgij Arapidi, Vasily V. Ptushenko, Anatoly S. Urban, Ivan Butenko, Sergey I. Kovalchuk, Konstantin Babalyan, Andrey Knyazev, Regina Khazigaleeva, Elena N. Pushkova, Nikolay Anikanov, В. Т. Иванов, Vadim M. Govorun
Software Mentions: 4
Published: over 7 years ago

10.1093/jhered/esaa057

Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis)
Cited by: 22
Author(s): Kevin R. Bredemeyer, Andrew Harris, Gang Li, Li-Jun Zhao, Nicole M. Foley, Melody Roelke‐Parker, Stephen J. O’Brien, Leslie A. Lyons, Wesley C. Warren, William J. Murphy
Software Mentions: 4
Published: over 3 years ago

10.3390/insects12070618

Genetic Screening to Identify Candidate Resistance Alleles to Cry1F Corn in Fall Armyworm Using Targeted Sequencing
Cited by: 10
Author(s): Katrina Schlum, Kurt Lamour, P. A. Tandy, Scott J. Emrich, Caroline Placidi De Bortoli, Tejas Rao, Diego M Viteri Dillon, Angela M. Linares‐Ramírez, Juan Luís Jurat-Fuentes
Software Mentions: 4
Published: almost 3 years ago

10.3390/toxins12010004

Alteration of Bumblebee Venom Composition toward Higher Elevation
Cited by: 7
Author(s): Nezahat Pınar Barkan, Mathieu Chevalier, Jean‐Nicolas Pradervand, Antoine Guisan
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-92053-x

Jejunal mucosa proteomics unravel metabolic adaptive processes to mild chronic heat stress in dairy cows
Cited by: 11
Author(s): Franziska Koch, Dirk Albrecht, Solvig Görs, Björn Kuhla
Software Mentions: 4
Published: almost 3 years ago

10.1128/mSphere.00207-17

The Effector TepP Mediates Recruitment and Activation of Phosphoinositide 3-Kinase on Early Chlamydia trachomatis Vacuoles
Cited by: 27
Author(s): Victoria K. Carpenter, Yi-Shan Chen, Lee Dolat, Raphael H. Valdivia
Software Mentions: 3
Published: over 6 years ago

10.1186/s13321-017-0212-4

Comparative analyses of structural features and scaffold diversity for purchasable compound libraries
Cited by: 24
Author(s): Jun Shang, Huiyong Sun, Hui Liu, Chen Fu, Sheng Tian, Peichen Pan, Dan Li, De-Xin Kong, Tingjun Hou
Software Mentions: 3
Published: about 7 years ago

10.3390/genes10070522

Sperm Proteome Analysis and Identification of Fertility-Associated Biomarkers in Unexplained Male Infertility
Cited by: 36
Author(s): Manesh Kumar Panner Selvam, Ashok Agarwal, Peter Natesan Pushparaj, Saradha Baskaran, Hocine Bendou
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13073-015-0208-5

Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance
Cited by: 74
Author(s): William R. Swindell, Henriette A. Remmer, Mrinal K. Sarkar, Xianying Xing, Drew H. Barnes, Liza Wolterink, John J. Voorhees, Rajan P. Nair, Andrew Johnston, James T. Elder, Jóhann E. Guðjónsson
Software Mentions: 3
Published: almost 9 years ago

10.1093/gigascience/giaa050

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome
Cited by: 64
Author(s): Annarita Marrano, Monica Britton, Paulo A. Zaini, Aleksey V. Zimin, Rachael E. Workman, Daniela Puiu, Luca Bianco, Erica A. Di Pierro, Brian Allen, Sandeep Chakraborty, Michela Troggio, Charles A. Leslie, Winston Timp, Abhaya M. Dandekar, Steven L. Salzberg, David B. Neale
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-021-89996-6

Proteomic and genomic analysis of acid dentin lysate with focus on TGF-β signaling
Cited by: 7
Author(s): Jila Nasirzade, Zahra Kargarpour, Goran Mitulović, Franz Josef Strauß, Layla Panahipour, Frank Schwarz, Reinhard Gruber
Software Mentions: 3
Published: almost 3 years ago

10.1016/j.jbc.2021.100456

Binding of Gtf2i-β/δ transcription factors to the ARMS2 gene leads to increased circulating HTRA1 in AMD patients and in vitro
Cited by: 6
Author(s): Yang Pan, Daisuke Iejima, Mao Nakayama, Akiko Suga, Tomoyuki Noda, Inderjeet Kaur, Taraprasad Das, Subhabrata Chakrabarti, Robyn H. Guymer, Margaret M. DeAngelis, Megumi Yamamoto, Paul N. Baird, Takeshi Iwata
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-73847-x

Differentiating Staphylococcus infection-associated glomerulonephritis and primary IgA nephropathy: a mass spectrometry-based exploratory study
Cited by: 9
Author(s): Anjali A. Satoskar, John P. Shapiro, Mikayla Jones, Cherri Bott, Samir Parikh, Sergey V. Brodsky, Lianbo Yu, Haikady N. Nagaraja, Daniel W. Wilkey, Michael L. Merchant, Jon B. Klein, Tibor Nádasdy, Brad H. Rovin
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-98454-2

Protein expression reveals a molecular sexual identity of avian primordial germ cells at pre-gonadal stages
Cited by: 9
Author(s): Laura Soler, Sabine Alves, Aurélien Brionne, Aurore Jacques, Vanessa Guérin, Maëva Cherif--Feildel, Lucie Combes‐Soia, Sophie Fouchécourt, Aurore Thélie, Élisabeth Blesbois, Michael J. McGrew, Valérie Labas, Marina Govoroun
Software Mentions: 3
Published: over 2 years ago

10.1038/s41598-021-81000-5

EBF1 drives hallmark B cell gene expression by enabling the interaction of PAX5 with the MLL H3K4 methyltransferase complex
Cited by: 12
Author(s): Charles E. Bullerwell, Philippe Pierre Robichaud, Pierre Deprez, Andrew P. Joy, Gabriel Wajnberg, Darwin D’souza, Simi Chacko, Sébastien Fournier, Nicolas Crapoulet, David A. Barnett, Stephen M. Lewis, Rodney J. Ouellette
Software Mentions: 3
Published: over 3 years ago

10.1186/1751-0473-8-23

Combining de novo and reference-guided assembly with scaffold_builder
Cited by: 54
Author(s): Genivaldo Gueiros Z. Silva, Bas E. Dutilh, T. David Matthews, Keri Elkins, Robert Schmieder, Elizabeth A. Dinsdale, Robert A. Edwards
Software Mentions: 3
Published: over 10 years ago

10.1093/gigascience/giz070

Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome
Cited by: 42
Author(s): Quanxin Bi, Yang Zhao, Wei Du, Ying Lu, Gui Liu, Zhimin Zheng, Haiyan Yu, Yubo Cui, Zhi Liu, Tianpeng Cui, Deshi Cui, Xiaojuan Liu, Yingchao Li, Fan Siqi, Xiaoyu Hu, Guanghui Fu, Jian Ding, Chengjiang Ruan, Libing Wang
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-015-0696-z

FOXM1 binds directly to non-consensus sequences in the human genome
Cited by: 47
Author(s): Deborah A. Sanders, Michael V. Gormally, Giovanni Marsico, Dario Beraldi, David Tannahill, Shankar Balasubramanian
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-020-67665-4

Beta-nerve growth factor stimulates spontaneous electrical activity of in vitro embryonic mouse GnRH neurons through a P75 mediated-mechanism
Cited by: 8
Author(s): Caroline Pinet, Renaud Fleurot, Flavie Derouin-Tochon, S.P. de Graaf, Xavier Druart, Guillaume Tsikis, Catherine Taragnat, Ana-Paula Teixeira-Gomes, Valérie Labas, Thierry Moreau, Xavier Cayla, Anne Duittoz
Software Mentions: 3
Published: almost 4 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: over 2 years ago

10.1128/mBio.02048-16

Making Home Sweet and Sturdy:Toxoplasma gondiippGalNAc-Ts Glycosylate in Hierarchical Order and Confer Cyst Wall Rigidity
Cited by: 48
Author(s): Tadakimi Tomita, Tatsuki Sugi, Rama R. Yakubu, Vincent Tu, Yanfen Ma, Louis M. Weiss
Software Mentions: 3
Published: about 7 years ago

10.1093/jxb/erv532

Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins
Cited by: 27
Author(s): Kyla J. Morton, Shangang Jia, Chi Zhang, David R. Holding
Software Mentions: 3
Published: over 8 years ago

10.3389/fphys.2019.00312

Physical Activity Associated Proteomics of Skeletal Muscle: Being Physically Active in Daily Life May Protect Skeletal Muscle From Aging
Cited by: 68
Author(s): Ceereena Ubaida‐Mohien, Marta González-Freire, Alexey E. Lyashkov, Ruin Moaddel, Chee W. Chia, Eleanor M. Simonsick, Ranjan Sen, Luigi Ferrucci
Software Mentions: 3
Published: about 5 years ago

10.12688/wellcomeopenres.15403.2

Pathogenic FAM83G palmoplantar keratoderma mutations inhibit the PAWS1:CK1α association and attenuate Wnt signalling.
Cited by: 4
Author(s): Kevin Z. L. Wu, Rebecca A. Jones, Theresa Tachie-Menson, Thomas Macartney, Nicola T. Wood, Joby Varghese, Robert Gourlay, Renata Soares, James C. Smith, Gopal P. Sapkota
Software Mentions: 3
Published: about 4 years ago

10.1111/mmi.14398

Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112
Cited by: 14
Author(s): Kawther Alqaseer, Obolbek Turapov, Philippe Barthe, Heena Jagatia, Angélique De Visch, Christian Roumestand, Malgorzata Wegrzyn, Iona L. Bartek, Martin I. Voskuil, Helen M. O’Hare, Paul Ajuh, Andrew R. Bottrill, Adam A. Witney, Martin Cohen‐Gonsaud, Simon J. Waddell, Galina V. Mukamolova
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2019.00127

The Selection of a Hepatocyte Cell Line Susceptible to Plasmodium falciparum Sporozoite Invasion That Is Associated With Expression of Glypican-3
Cited by: 13
Author(s): Rebecca E. Tweedell, Dingyin Tao, Timothy Hamerly, Tanisha M. Robinson, Simon J. Larsen, Alexander G B Grønning, Alessandra M. Norris, J. W. B. King, Henry C.-H. Law, Jan Baumbach, Elke S. Bergmann‐Leitner, Rhoel R. Dinglasan
Software Mentions: 3
Published: about 5 years ago

10.1016/j.mcpro.2021.100064

Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner
Cited by: 8
Author(s): Lauriane Vélot, Frédéric Lessard, Félix-Antoine Bérubé-Simard, Christophe Tav, Bertrand Neveu, Valentine Teyssier, Imène Boudaoud, Ugo Dionne, Noémie Lavoie, Steve Bilodeau, Frédéric Pouliot, Nicolas Bisson
Software Mentions: 3
Published: over 3 years ago

10.1080/21505594.2017.1325064

Signatures of cytoplasmic proteins in the exoproteome distinguish community- and hospital-associated methicillin-resistantStaphylococcus aureusUSA300 lineages
Cited by: 18
Author(s): Solomon Mekonnen, Laura M Palma Medina, Corinna Glasner, Eleni Tsompanidou, Anne de Jong, Stefano Grasso, Marc Schaffer, Ulrike Mäder, Anders Rhod Larsen, Heidi Gumpert, Henrik Westh, Uwe Völker, Andreas Otto, Dörte Becher, Jan Maarten van Dijl
Software Mentions: 3
Published: about 7 years ago

10.1186/s40478-020-00982-x

C9orf72-associated SMCR8 protein binds in the ubiquitin pathway and with proteins linked with neurological disease
Cited by: 15
Author(s): John Goodier, Alisha O. Soares, Gavin Pereira, Lauren DeVine, Laura Sánchez, Robert N. Cole, José L. García‐Pérez
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2020.01179

Analysis of Virus and Host Proteomes During Productive HSV-1 and VZV Infection in Human Epithelial Cells
Cited by: 14
Author(s): Werner J. D. Ouwendijk, Lennard J. M. Dekker, Henk-Jan van den Ham, Tihana Lenac Roviš, Erik Haefner, Stipan Jonjić, Jürgen Haas, Theo M. Luider, Georges M. G. M. Verjans
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.ppat.1001328

A Novel Toxoplasma gondii Nuclear Factor TgNF3 Is a Dynamic Chromatin-Associated Component, Modulator of Nucleolar Architecture and Parasite Virulence
Cited by: 36
Author(s): Alejandro Olguin-Lamas, Edwige Madec, Agnès Hovasse, Elisabeth Werkmeister, Isabelle Callebaut, Christian Slomianny, Stéphane Delhaye, Thomas Mouveaux, Christine Schaeffer-Reiss, Alain Van Dorsselaer, Stanislas Tomavo
Software Mentions: 3
Published: about 13 years ago

10.1186/s12915-015-0128-2

The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers
Cited by: 14
Author(s): Sarah K. Harten, Harald Oey, Lauren M. Bourke, Vandhana Bharti, Luke Isbel, Lucia Daxinger, Pierre Faou, Neil O. Robertson, Jacqueline M. Matthews, Emma Whitelaw
Software Mentions: 3
Published: about 9 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 5 years ago

10.1074/mcp.RA120.002028

A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria
Cited by: 36
Author(s): Andreas Linden, Markus Deckers, Iwan Parfentev, Ralf Pflanz, Bettina Homberg, Piotr Neumann, Ralf Ficner, Peter Rehling, Henning Urlaub
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-8-483

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system
Cited by: 17
Author(s): Arnaud Droit, Joanna M. Hunter, Michèle Rouleau, Chantal Éthier, Aude Picard-Cloutier, David Bourgais, Guy G. Poirier
Software Mentions: 3
Published: over 16 years ago

Projects: pypi: Scaffold

Papers Mentioning Scaffold 1,866