Ecosyste.ms: Papers

10.1371/journal.pone.0243241

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis
Cited by: 15
Author(s): Sebastian Hupfauf, Mohammad Etemadi, Marina Fernández-Delgado Juárez, María Gómez-Brandòn, Heribert Insam, Sabine Marie Podmirseg
Software Mentions: 13
Published: almost 4 years ago

10.1111/mec.15735

Phylogenetic and geographical analysis of a retrovirus during the early stages of endogenous adaptation and exogenous spread in a new host
Cited by: 11
Author(s): Bonnie Chaban, Faye Wedrowicz, Fiona Hogan, Peter Timms
Software Mentions: 9
Published: almost 4 years ago

10.1002/cam4.4035

The prognostic value of sarcopenia combined with preoperative fibrinogen–albumin ratio in patients with intrahepatic cholangiocarcinoma after surgery: A multicenter, prospective study
Cited by: 10
Author(s): Haitao Yu, Mingxun Wang, Yi Wang, Jinhuan Yang, Liming Deng, Wenming Bao, Bangjie He, Lin Zou, Zi-Yan Chen, Kaiyu Chen, Baofu Zhang, Fangting Liu, Zhengping Yu, Long‐Yun Ye, Bin Jin, Gang Chen
Software Mentions: 8
Published: over 3 years ago

10.1111/jcmm.16275

Identification of key candidate biomarkers for severe influenza infection by integrated bioinformatical analysis and initial clinical validation
Cited by: 7
Author(s): Shuai Liu, Zhisheng Huang, Xiaoyan Deng, Xiaohui Zou, Hui Li, Shengrui Mu, Bin Cao
Software Mentions: 7
Published: almost 4 years ago

10.3390/antiox10040627

The Human 2-Cys Peroxiredoxins form Widespread, Cysteine-Dependent- and Isoform-Specific Protein-Protein Interactions
Cited by: 16
Author(s): Loes van Dam, Marc Pagès-Gallego, Paulien E. Polderman, Robert M. van Es, Boudewijn M.T. Burgering, Harmjan R. Vos, Tobias B. Dansen
Software Mentions: 7
Published: over 3 years ago

10.1002/1878-0261.12385

Genome‐wide identification of a novel mi <scp>RNA</scp> ‐based signature to predict recurrence in patients with gastric cancer
Cited by: 26
Author(s): Yongmei Yang, Ailin Qu, Rui Zhao, Mengmeng Hua, Xin Zhang, Zhaogang Dong, Guixi Zheng, Hongwei Pan, Hongchun Wang, Xiaoyun Yang, Yi Zhang
Software Mentions: 6
Published: about 6 years ago

10.1089/ast.2018.1912

Assessing the Acceptability of Science Operations Concepts and the Level of Mission Enhancement of Capabilities for Human Mars Exploration Extravehicular Activity
Cited by: 11
Author(s): K. Beaton, Steven P. Chappell, Andrew F. J. Abercromby, Matthew J. Miller, S. E. Kobs Nawotniak, A. L. Brady, Adam H. Stevens, Samuel J. Payler, S. S. Hughes, D. S. S. Lim
Software Mentions: 5
Published: over 5 years ago

10.1128/mBio.02333-17

Multisystem Analysis of <i>Mycobacterium tuberculosis</i> Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface
Cited by: 49
Author(s): Xavier Carette, John Platig, David C. Young, Michaela Helmel, A. E. Young, Zhe Wang, Lakshmi-Prasad Potluri, Cameron Stuver Moody, Jumei Zeng, Sladjana Prisic, Joseph N. Paulson, Jan Muntel, Ashoka V. R. Madduri, Jorge J. Velarde, Jacob A. Mayfield, Christopher P. Locher, Tiansheng Wang, John Quackenbush, Kyu Y. Rhee, D. Branch Moody, Hanno Steen, Robert N. Husson
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-017-3978-x

Succinyl-proteome profiling of Dendrobium officinale, an important traditional Chinese orchid herb, revealed involvement of succinylation in the glycolysis pathway
Cited by: 37
Author(s): Shi Feng, Kaili Jiao, Hong Guo, Min Jiang, Juan Hao, Huizhong Wang, Chenjia Shen
Software Mentions: 5
Published: about 7 years ago

10.1098/rsfs.2019.0119

Towards blood flow in the virtual human: efficient self-coupling of HemeLB
Cited by: 9
Author(s): J. W. S. McCullough, Robin A. Richardson, Alex Patronis, René Halver, Ryan Marshall, Martin Ruefenacht, Brian J. N. Wylie, Thomas Odaker, Michael Wiedemann, Bryn Lloyd, Esra Neufeld, Godehard Sutmann, Anthony Skjellum, Dieter Kranzlmüller, Peter V. Coveney
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-018-36984-y

Comparative transcriptome analysis reveals relationship of three major domesticated varieties of Auricularia auricula-judae
Cited by: 15
Author(s): Yuhui Zhao, Liang Wang, Dongshan Zhang, Rong Li, Tianyou Cheng, Yibi Zhang, Liu Xue-ju, Gary Wong, Yuguo Tang, Hui Wang, Shan Gao
Software Mentions: 4
Published: almost 6 years ago

10.1111/zph.12827

Zoonotic <i>Bartonella</i> species in Eurasian wolves and other free‐ranging wild mammals from Italy
Cited by: 15
Author(s): Grazia Greco, Aya Attia Koraney Zarea, Giovanni Sgroi, Maria Tempesta, Nicola D’Alessio, Gianvito Lanave, Marcos Antônio Bezerra‐Santos, Roberta Iatta, Vincenzo Veneziano, Domenico Otranto, Bruno B Chomel
Software Mentions: 3
Published: over 3 years ago

10.3389/fneur.2018.00684

Thigh-Derived Inertial Sensor Metrics to Assess the Sit-to-Stand and Stand-to-Sit Transitions in the Timed Up and Go (TUG) Task for Quantifying Mobility Impairment in Multiple Sclerosis
Cited by: 27
Author(s): Harry J. Witchel, Cäcilia Oberndorfer, Robert Needham, Aoife Healy, Carina E. I. Westling, Joseph H. Guppy, Jake Bush, Jens Barth, Chantal Herberz, Daniel Roggen, Bjoern M. Eskofier, Waqar Rashid, Nachiappan Chockalingam, Jochen Klucken
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms20020451

Comparative Phosphoproteomic Analysis of Barley Embryos with Different Dormancy during Imbibition
Cited by: 10
Author(s): Shin-­nosuke Ishikawa, José M. Barrero, Fumiyuki Takahashi, Scott C. Peck, Frank Gubler, Kazuo Shinozaki, Taishi Umezawa
Software Mentions: 3
Published: almost 6 years ago

10.1111/jipb.12862

Identification of plant genes putatively involved in the perception of fungal ergosterol‐squalene
Cited by: 15
Author(s): Laura Lindo, Rosa E. Cardoza, Alicia Lorenzana de la Varga, Pedro A. Casquero, Santiago Gutiérrez
Software Mentions: 3
Published: almost 5 years ago

10.3389/fneur.2018.00029

Predictive Capability of an iPad-Based Medical Device (medx) for the Diagnosis of Vertigo and Dizziness
Cited by: 17
Author(s): Katharina Feil, Regina Feuerecker, Nicolina Goldschagg, Ralf Strobl, Thomas Brandt, A. Müller, Eva Grill, Michael Strupp
Software Mentions: 2
Published: over 6 years ago

10.1002/aps3.1228

Testing Hopkins’ Bioclimatic Law with PhenoCam data
Cited by: 30
Author(s): Andrew D. Richardson, Koen Hufkens, Xiaolu Li, Toby R. Ault
Software Mentions: 2
Published: over 5 years ago

10.3390/ma6104737

Surface Roughness and Morphology Customization of Additive Manufactured Open Porous Ti6Al4V Structures
Cited by: 178
Author(s): Grzegorz Pyka, Greet Kerckhofs, Ioannis Papantoniou, Mathew Speirs, Jan Schrooten, Martine Wevers
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0130887

Achieving High Resolution Timer Events in Virtualized Environment
Cited by: 5
Author(s): Błażej Adamczyk, Andrzej Chydziński
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0235316

Non-destructive lock-picking of a historical treasure chest by means of X-ray computed tomography
Cited by: 1
Author(s): Eva Zikmundová, Tomáš Zikmund, Vladimı́r Sládek, Jozef Kaiser
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0075992

Ligand Pose and Orientational Sampling in Molecular Docking
Cited by: 123
Author(s): Ryan G. Coleman, Michael Carchia, Teague Sterling, John J. Irwin, Brian K. Shoichet
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0098522

Identification of Different Varieties of Sesame Oil Using Near-Infrared Hyperspectral Imaging and Chemometrics Algorithms
Cited by: 23
Author(s): Chuanqi Xie, Qiao-Nan Wang, Yong He
Software Mentions: 2
Published: over 10 years ago

10.1155/2017/9284856

The Association of Quantitative Facial Color Features with Cold Pattern in Traditional East Asian Medicine
Cited by: 4
Author(s): Sujeong Mun, Ilkoo Ahn, Si-Woo Lee
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-020-01974-9

Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k-mer-based multiplexing
Cited by: 5
Author(s): Alexander Dilthey, Sebastian Meyer, Achim J. Kaasch
Software Mentions: 2
Published: over 4 years ago

10.1242/jcs.181842

Fast and precise targeting of single tumor cells <i>in vivo</i> by multimodal correlative microscopy
Cited by: 80
Author(s): Matthia A. Karreman, Luc Mercier, Nicole L. Schieber, Gergely Solecki, Guillaume Allio, Frank Winkler, Bernhard Ruthensteiner, Jacky G. Goetz, Yannick Schwab
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep31478

Histological response of soda-lime glass-ceramic bactericidal rods implanted in the jaws of beagle dogs
Cited by: 8
Author(s): José S. Moya, A. Martínez, Roberto López‐Píriz, Francisco Guitián, Luis A. Díaz, Leticia Esteban-Tejeda, Belén Cabal, F. Sket, Elisa Fernández-García, Antoni P. Tomsia, Ramón Torrecillas
Software Mentions: 2
Published: about 8 years ago

10.3390/s18010130

The Effect of the Accelerometer Operating Range on Biomechanical Parameters: Stride Length, Velocity, and Peak Tibial Acceleration during Running
Cited by: 26
Author(s): Christian Mitschke, Pierre Kiesewetter, Thomas L. Milani
Software Mentions: 2
Published: almost 7 years ago

10.3390/s21165279

Rapid Foreign Object Detection System on Seaweed Using VNIR Hyperspectral Imaging
Cited by: 6
Author(s): Donghoon Kwak, Guk-Jin Son, Mi‐Kyung Park, Young-Duk Kim
Software Mentions: 2
Published: over 3 years ago

10.1155/2019/5153136

Robocasting of Bioactive SiO₂-P₂O₅-CaO-MgO-Na₂O-K₂O Glass Scaffolds
Cited by: 31
Author(s): Francesco Baino, Jacopo Barberi, Elisa Fiume, Gissur Örlygsson, Jonathan Massera, Enrica Verné
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.34465

Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage
Cited by: 24
Author(s): Markéta Kaucká, Julian Petersen, Markéta Tesařová, Bára Szarowská, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, Karl Annusver, Maria Kasper, Orsolya Symmons, Leslie Pan, François Spitz, Jozef Kaiser, Mária Hovořáková, Tomáš Zikmund, Kazunori Sunadome, Michael P. Matise, Hui Wang, Ulrika Marklund, Hind Abdo, Patrik Ernfors, Pascal Maire, Maud Wurmser, Andrei S. Chagin, Kaj Fried, Igor Adameyko
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.5954

DockerBIO: web application for efficient use of bioinformatics Docker images
Cited by: 1
Author(s): Chang‐Hyuk Kwon, Jason Kim, Jaegyoon Ahn
Software Mentions: 1
Published: almost 6 years ago

10.1002/acm2.12494

A study of positioning orientation effect on segmentation accuracy using convolutional neural networks for rectal cancer
Cited by: 9
Author(s): Kuo Men, Pamela J. Boimel, James Janopaul‐Naylor, Charles Ching-An Cheng, Haoyu Zhong, Mingyan Huang, H. Geng, Yong Fan, John P. Plastaras, Edgar Ben‐Josef, Ying Xiao
Software Mentions: 1
Published: almost 6 years ago

10.1099/mic.0.052555-0

Taxon-specific metagenomics of Trichoderma reveals a narrow community of opportunistic species that regulate each other’s development
Cited by: 45
Author(s): Martina A. Friedl, Irina S. Druzhinina
Software Mentions: 1
Published: almost 13 years ago

10.7554/eLife.40179

Unique morphogenetic signatures define mammalian neck muscles and associated connective tissues
Cited by: 45
Author(s): Églantine Heude, Markéta Tesařová, Elizabeth M. Sefton, Estelle Jullian, Noritaka Adachi, Alexandre Grimaldi, Tomáš Zikmund, Jozef Kaiser, Gabrielle Kardon, Robert G. Kelly
Software Mentions: 1
Published: almost 6 years ago

10.1111/jeu.12501

Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free-living Giant Amoebae
Cited by: 19
Author(s): Georgia M. Ward, Sigrid Neuhauser, R. Groben, Stefan Ciaghi, Cédric Berney, Sarah Romac, David Bass
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41597-020-0369-y

The first high-resolution meteorological forcing dataset for land process studies over China
Cited by: 589
Author(s): Jie He, Kun Yang, Wenjun Tang, Hui Lu, Jun Qin, Yingying Chen, Xin Li
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms19030885

Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids
Cited by: 13
Author(s): Zanxia Cao, Yunqiang Bian, Guodong Hu, Liling Zhao, Zhenzhen Kong, Yuedong Yang, Jihua Wang, Yaoqi Zhou
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-01214-4

Expandable Mg-based Helical Stent Assessment using Static, Dynamic, and Porcine Ex Vivo Models
Cited by: 17
Author(s): Youngmi Koo, Tarannum Tiasha, Vesselin Shanov, Yeoheung Yun
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-15766-y

A necessary criterion for obtaining accurate lattice parameters by Rietveld method
Cited by: 34
Author(s): Masami Tsubota, Jiro Kitagawa
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-36958-0

The impact of carbon addition on the organisation of rhizosheath of chickpea
Cited by: 12
Author(s): Sheikh M.F. Rabbi, Matthew Tighe, Oliver Knox, Iain M. Young
Software Mentions: 1
Published: almost 6 years ago

10.3390/ma14175009

Mechanical Performance of Chairside Ceramic CAD/CAM Restorations and Zirconia Abutments with Different Internal Implant Connections: In Vitro Study and Finite Element Analysis
Cited by: 2
Author(s): Sergio Torres‐Giner, José F. Bartolomé, Pablo Gómez-Cogolludo, Carlos Castellote, Guillermo Pradíes
Software Mentions: 1
Published: about 3 years ago

10.3390/ma10070735

Improving the Strength of ZTA Foams with Different Strategies: Immersion Infiltration and Recoating
Cited by: 10
Author(s): Xiao Chen, Ulf Betke, Stefan Rannabauer, Paul Clemens Peters, Gerrit Maximilian Söffker, Michael Scheffler
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22147736

A Bioglass-Based Antibiotic (Vancomycin) Releasing Bone Void Filling Putty to Treat Osteomyelitis and Aid Bone Healing
Cited by: 13
Author(s): Raquib Hasan, Kambri Schaner, Pranothi Mulinti, Amanda E. Brooks
Software Mentions: 1
Published: over 3 years ago

10.3390/ma14154113

Cyclic Mechanical Fatigue Lifetime of Bi0.5Na0.5TiO3-Based Eco-Piezoceramics
Cited by: 0
Author(s): José F. Bartolomé, Luis E. Fuentes-Cobas, Álvaro López García, Alfredo Jacas-Rodríguez, L. Pardo
Software Mentions: 1
Published: over 3 years ago

10.1186/1757-1146-7-S1-A109

Development and performance evaluation of slip-resistant agricultural work shoes
Cited by: 0
Author(s): Kyungsuk Lee, Young-soon Oh, Do-hee Kim, Hye-Seon Chae, Kyung-ran Kim
Software Mentions: 1
Published: over 10 years ago

10.1098/rsif.2018.0039

Neutron scanning reveals unexpected complexity in the enamel thickness of an herbivorous Jurassic reptile
Cited by: 18
Author(s): Marc E. H. Jones, Peter W. Lucas, Abigail S. Tucker, Amy P. Watson, Joseph J. W. Sertich, John Foster, Ruth Williams, Ulf Garbe, Joseph J. Bevitt, Filomena Salvemini
Software Mentions: 1
Published: over 6 years ago

10.1007/s10670-014-9648-3

X-Phi and Carnapian Explication
Cited by: 46
Author(s): Joshua Shepherd, James Justus
Software Mentions: 1
Published: over 10 years ago

10.3390/ma13225080

An Antibiotic-Releasing Bone Void Filling (ABVF) Putty for the Treatment of Osteomyelitis
Cited by: 4
Author(s): Raquib Hasan, Abbey Wohlers, Jacob Shreffler, Pranothi Mulinti, Hunter Ostlie, Codi Schaper, Benjamin D. Brooks, Amanda E. Brooks
Software Mentions: 1
Published: almost 4 years ago

10.1002/2211-5463.12831

Deregulation of miR‐27a may contribute to canine fibroblast activation after coculture with a mast cell tumour cell line
Cited by: 4
Author(s): Matias Aguilera-Rojas, Soroush Sharbati, Torsten Stein, Ralf Einspanier
Software Mentions: 1
Published: over 4 years ago

10.3389/fcell.2020.00572

Polarized Sonic Hedgehog Protein Localization and a Shift in the Expression of Region-Specific Molecules Is Associated With the Secondary Palate Development in the Veiled Chameleon
Cited by: 2
Author(s): Marek Hampl, Jana Dumková, Michaela Kavková, Hana Dosedělová, Anna Bryjova, Oldřich Zahradníček, Martin Pyszko, Miloš Macholán, Tomáš Zikmund, Jozef Kaiser, Marcela Buchtová
Software Mentions: 1
Published: over 4 years ago

10.1021/acsearthspacechem.0c00238

Sulfur Molecules in Space by X-rays: A Computational Study
Cited by: 2
Author(s): Goranka Bilalbegović, Aleksandar Maksimović, Lynne Valencic, Susi Lehtola
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pbio.3000902

Local retinoic acid signaling directs emergence of the extraocular muscle functional unit
Cited by: 17
Author(s): Glenda Comai, Markéta Tesařová, Valérie Dupé, Muriel Rhinn, Pedro Vallecillo-García, Fabio da Silva, Betty Féret, Katherine Exelby, Pascal Dollé, Leif Carlsson, Brian A. Pryce, François Spitz, Sigmar Stricker, Tomáš Zikmund, Jozef Kaiser, James Briscoe, Andreas Schedl, Norbert B. Ghyselinck, Ronen Schweitzer, Shahragim Tajbakhsh
Software Mentions: 1
Published: almost 4 years ago

10.3389/fonc.2021.619929

On the Importance of Individualized, Non-Coplanar Beam Configurations in Mediastinal Lymphoma Radiotherapy, Optimized With Automated Planning
Cited by: 8
Author(s): L. Rossi, P. Cambraia Lopes, Joana Leitão, Cécile P.M. Janus, M. van de Pol, S. Breedveld, J. Penninkhof, B. Heijmen
Software Mentions: 1
Published: over 3 years ago