Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: shell
https://packages.ecosyste.ms/registries/pypi.org/packages/shell
A better way to run shell commands in Python.
2 versions
Latest release: almost 11 years ago
1 dependent package
30,144 downloads last month
Papers Mentioning shell 207
10.1093/gbe/evaa153
The Identification and Evolutionary Trends of the Solute Carrier Superfamily in ArthropodsCited by: 9
Author(s): Shane Denecke, Olympia Driva, Hằng Ngọc Bảo Lương, Panagiotis Ioannidis, Marc Linka, Ralf Nauen, Sven Geibel, John Vontas
Software Mentions: 3
Published: over 4 years ago
10.1093/gigascience/gix099
An architecture for genomics analysis in a clinical setting using Galaxy and DockerCited by: 9
Author(s): William Digan, Hector Countouris, Marc Barritault, David Baudoin, Pierre Laurent‐Puig, Hélène Blons, Anita Burgun, Bastien Rance
Software Mentions: 3
Published: about 7 years ago
10.1038/s41597-019-0020-y
A 204-subject multimodal neuroimaging dataset to study language processingCited by: 53
Author(s): Jan Mathijs Schoffelen, Robert Oostenveld, Nietzsche H. L. Lam, Julia Uddén, Annika Hultén, Peter Hagoort
Software Mentions: 3
Published: over 5 years ago
10.1038/srep15839
Littoral lichens as a novel source of potentially bioactive ActinobacteriaCited by: 51
Author(s): Delphine Parrot, Sanjay Antony-Babu, Laurent Intertaglia, Martín Grube, Sophie Tomasi, Marcelino T. Suzuki
Software Mentions: 3
Published: about 9 years ago
10.1038/s41598-019-38682-9
Unexpected population fragmentation in an endangered seabird: the case of the Peruvian diving-petrelCited by: 17
Author(s): Robin Cristofari, Paula Plaza, Claudia E. Fernández, Emiliano Trucchi, Nicolás Gouin, Céline Le Bohec, Carlos B. Zavalaga, Joanna Alfaro‐Shigueto, Guillermo Luna‐Jorquera
Software Mentions: 3
Published: over 5 years ago
10.1155/2014/692893
Dynamic Interactive Educational Diabetes Simulations Using the World Wide Web: An Experience of More Than 15 Years with AIDA OnlineCited by: 2
Author(s): Eldon D. Lehmann, Dennis K. DeWolf, Christopher A. Novotny, Karen L. Reed, Robert Gotwals
Software Mentions: 3
Published: almost 11 years ago
10.18632/oncotarget.12390
Meta-analysis of gene expression and integrin-associated signaling pathways in papillary renal cell carcinoma subtypesCited by: 4
Author(s): Kai Zhang, Hang-Mao Lee, Gong-Hong Wei, Aki Manninen
Software Mentions: 3
Published: about 8 years ago
10.1098/rsob.140133
Bacterial genospecies that are not ecologically coherent: population genomics of<i>Rhizobium leguminosarum</i>Cited by: 118
Author(s): Nitin Kumar, Ganesh Lad, Elisa Giuntini, Maria Kaye, Piyachat Udomwong, N. Jannah Shamsani, J. Peter W. Young, Xavier Bailly
Software Mentions: 3
Published: almost 10 years ago
10.1371/journal.pone.0082751
Global Assessment of Antrodia cinnamomea-Induced MicroRNA Alterations in Hepatocarcinoma CellsCited by: 10
Author(s): Yen–Ju Chen, Mike W.C. Thang, Yu Tzu Chan, Yu-Feng Huang, Nianhan Ma, Alice L. Yu, Ching‐Yi Wu, Miao Hu, Kuo Ping Chiu
Software Mentions: 2
Published: almost 11 years ago
10.1186/s40064-016-1828-y
An evaluation and selection problems of OSS-LMS packagesCited by: 63
Author(s): Belal Najeh Abdullateef, Nur Fazidah Elias, Hazura Mohamed, A. A. Zaidan, B. B. Zaidan
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0048381
Fluorescence Behavioral Imaging (FBI) Tracks Identity in Heterogeneous Groups of DrosophilaCited by: 13
Author(s): Pavan Ramdya, Thomas Schaffter, Dario Floreano, Richard Benton
Software Mentions: 2
Published: about 12 years ago
10.1371/journal.pone.0143247
Learning Predictive Interactions Using Information Gain and Bayesian Network ScoringCited by: 18
Author(s): Xia Jiang, Jeremy Jao, Richard E. Neapolitan
Software Mentions: 2
Published: almost 9 years ago
10.1016/j.cels.2020.04.003
nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style TransferCited by: 137
Author(s): Réka Hollandi, Ábel Szkalisity, Tímea Tóth, Ervin Tasnádi, Csaba Molnár, Botond Mathe, István Grexa, J. Molnár, Árpád Bálind, Mate Gorbe, Mária Kovács, Ede Migh, Allen Goodman, Tamás Balassa, Krisztián Koós, Wenyu Wang, Juan C. Caicedo, Norbert Bara, Ferenc Kovács, Lassi Paavolainen, Tivadar Danka, András Kriston, Anne E. Carpenter, Kevin Smith, Péter Horváth
Software Mentions: 2
Published: over 4 years ago
10.1016/j.dib.2021.107208
Packet-level and IEEE 802.11 MAC frame-level network traffic traces data of the D-Link IoT devicesCited by: 6
Author(s): Rajarshi Roy Chowdhury, Sandhya Aneja, Nagender Aneja, Pg Emeroylariffion Abas
Software Mentions: 2
Published: over 3 years ago
10.1016/j.dib.2021.107333
Dataset of whole-brain resting-state fMRI of 227 young and elderly adults acquired at 3TCited by: 3
Author(s): Xia Li, Håkan Fischer, Amirhossein Manzouri, Kristoffer Månsson, Tie‐Qiang Li
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pgen.1000913
Natural Single-Nucleosome Epi-Polymorphisms in YeastCited by: 14
Author(s): Muniyandi Nagarajan, Jean‐Baptiste Veyrieras, Maud de Dieuleveult, Hélène Bottin, Steffen Fehrmann, Anne-Laure Abraham, Séverine Croze, Lars M. Steinmetz, Xavier Gidrol, Gaël Yvert
Software Mentions: 2
Published: over 14 years ago
10.1371/journal.pcbi.1006959
Ten quick tips for using a Raspberry PiCited by: 10
Author(s): Anthony C. Fletcher, Cameron Mura
Software Mentions: 2
Published: over 5 years ago
10.3389/fncom.2019.00074
Neuronal Morphology and Synapse Count in the Nematode WormCited by: 2
Author(s): Robert M. Friedman
Software Mentions: 2
Published: about 5 years ago
10.7717/peerj.241
Composable languages for bioinformatics: the NYoSh experimentCited by: 7
Author(s): Maria Simi, Fabien Campagne
Software Mentions: 2
Published: almost 11 years ago
10.3389/fgene.2013.00288
Sequencing quality assessment tools to enable data-driven informatics for high throughput genomicsCited by: 134
Author(s): Richard M. Leggett, Ricardo H. Ramírez-González, Bernardo Clavijo, Darren Waite, Robert P. Davey
Software Mentions: 2
Published: almost 12 years ago
10.3389/fgene.2013.00199
The spliced leader trans-splicing mechanism in different organisms: molecular details and possible biological rolesCited by: 28
Author(s): Mainá Bitar, Mariana Boroni, Andréa Mara Macedo, Carlos Renato Machado, Glória Regina Franco
Software Mentions: 2
Published: almost 12 years ago
10.3389/fimmu.2021.629193
SARS-CoV-2 Causes a Different Cytokine Response Compared to Other Cytokine Storm-Causing Respiratory Viruses in Severely Ill PatientsCited by: 85
Author(s): Márton Ölbei, Isabelle Hautefort, Dezső Módos, Agatha Treveil, Martina Poletti, Lejla Gul, Claire Shannon-Lowe, Tamás Korcsmáros
Software Mentions: 2
Published: over 3 years ago
10.21769/BioProtoc.3539
mRNA Extraction from Gill Tissue for RNA-sequencingCited by: 0
Author(s): Jukka‐Pekka Verta, Felicity C. Jones
Software Mentions: 2
Published: almost 5 years ago
10.1107/S0907444911007530
Evaluating the solution from<i>MrBUMP</i>and<i>BALBES</i>Cited by: 20
Author(s): Ronan Keegan, Fei Long, Vincent J. Fazio, Martyn Winn, Garib N. Murshudov, A.A. Vagin
Software Mentions: 2
Published: over 13 years ago
10.1128/mBio.01348-21
Inhibiting Type VI Secretion System Activity with a Biomimetic Peptide Designed To Target the Baseplate Wedge ComplexCited by: 5
Author(s): Yassine Cherrak, Isaac Filella-Merce, Victoria Schmidt, Deborah Byrne, V. Sgoluppi, R. Chaiaheloudjou, S. Betzi, Xavier Morelli, Michaël Nilges, Riccardo Pellarin, Éric Durand
Software Mentions: 2
Published: about 3 years ago
10.1534/g3.118.200134
Programmable Single and Multiplex Base-Editing in <i>Bombyx mori</i> Using RNA-Guided Cytidine DeaminasesCited by: 14
Author(s): Yufeng Li, Sanyuan Ma, Le Sun, Tong Zhang, Jiasong Chang, Wei Lu, Xiaoxu Chen, Yue Liu, Xiaogang Wang, Run Shi, Ping Zhao, Qingyou Xia
Software Mentions: 2
Published: over 6 years ago
10.1186/s12859-015-0466-7
Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and samplingCited by: 16
Author(s): Ramón Dı́az-Uriarte
Software Mentions: 2
Published: over 9 years ago
10.3390/genes8110308
Gene Regulatory Network Rewiring in the Immune Cells Associated with CancerCited by: 13
Author(s): Ping Han, Chandrasekhar Gopalakrishnan, Hao Yu, Edwin Wang
Software Mentions: 2
Published: about 7 years ago
10.1186/gb-2009-10-4-r43
The bovine lactation genome: insights into the evolution of mammalian milkCited by: 174
Author(s): Danielle G. Lemay, David J. Lynn, William Martin, Margaret C. Neville, Theresa Casey, Gonzalo Rincón, Evgenia V. Kriventseva, Wesley C. Barris, Angie S. Hinrichs, Adrian Molenaar, Katherine S. Pollard, Nauman J. Maqbool, Kuljeet Singh, R. Murney, Evgeny M. Zdobnov, Ross L. Tellam, Juan F. Medrano, J. Bruce German, Monique Rijnkels
Software Mentions: 2
Published: almost 16 years ago
10.1186/s13073-015-0147-1
Ultradeep analysis of tumor heterogeneity in regions of somatic hypermutationCited by: 5
Author(s): Janice M. Spence, John P. Spence, Andrew Abumoussa, W. Richard Burack
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2164-12-S4-S6
FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selectionCited by: 11
Author(s): Karina Machado, E. Schroeder, Duncan D. Ruiz, Elisângela Machado Leal Cohen, Osmar Norberto de Souza
Software Mentions: 2
Published: almost 13 years ago
10.1186/1471-2164-15-423
CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing dataCited by: 134
Author(s): Zhifu Sun, Jared M. Evans, Aditya Bhagwate, Sumit Middha, Matthew A. Bockol, Huihuang Yan, Jean Pierre A. Kocher
Software Mentions: 2
Published: almost 11 years ago
10.1186/s12864-016-2883-z
Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic cladeCited by: 49
Author(s): Jasna Kovač, Robert W. Miller, Laura M. Carroll, David J. Kent, Jiahui Jian, Sarah M. Beno, Martin Wiedmann
Software Mentions: 2
Published: over 8 years ago
10.1186/1471-2148-10-123
Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approachCited by: 52
Author(s): Ajna S. Rivera, M. Sabrina Pankey, David C. Plachetzki, Carlos Darwin Angulo Villacorta, Anna Syme, Jeanne M. Serb, Angela R. Omilian, Todd H. Oakley
Software Mentions: 2
Published: over 14 years ago
10.1186/1471-2148-13-150
Exploring signatures of positive selection in pigmentation candidate genes in populations of East Asian ancestryCited by: 55
Author(s): Jessica Hider, Rachel M. Gittelman, Tapan Shah, Melissa Edwards, Arnold Rosenbloom, Joshua M. Akey, Esteban J. Parra
Software Mentions: 2
Published: over 11 years ago
10.1186/s12859-021-04282-6
SPLICE-q: a Python tool for genome-wide quantification of splicing efficiencyCited by: 5
Author(s): Veronica Costa, Julianus Pfeuffer, Annita Louloupi, Ulf Andersson Ørom, Rosario M. Piro
Software Mentions: 2
Published: over 3 years ago
10.1007/s11948-020-00197-2
“Ethics When You Least Expect It”: A Modular Approach to Short Course Data Ethics InstructionCited by: 5
Author(s): Louise Bezuidenhout, Robert Quick, H. P. Shanahan
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2105-7-205
SIMAGE: si mulation of DNA-m icroa rray g ene e xpression dataCited by: 23
Author(s): Casper J. Albers, Ritsert C. Jansen, Jan Kok, Oscar P. Kuipers, Sacha A. F. T. van Hijum
Software Mentions: 2
Published: over 18 years ago
10.1038/s41598-017-15199-7
Serial dependence is absent at the time of perception but increases in visual working memoryCited by: 130
Author(s): Daniel P. Bliss, Jerome J. Sun, Mark D’Esposito
Software Mentions: 2
Published: about 7 years ago
10.1186/1471-2105-9-126
DOVIS: an implementation for high-throughput virtual screening using AutoDockCited by: 78
Author(s): Shuxing Zhang, Kamal Kumar, Xiaohui Jiang, Anders Wallqvist, Jaques Reifman
Software Mentions: 2
Published: over 16 years ago
10.1038/s41598-020-62880-5
Asymmetric participation of defenders and critics of vaccines to debates on French-speaking TwitterCited by: 20
Author(s): Floriana Gargiulo, Florian Cafiero, Paul Guille-Escuret, Valérie Seror, Jeremy K. Ward
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2105-8-246
Simcluster: clustering enumeration gene expression data on the simplex spaceCited by: 15
Author(s): Ricardo Z. N. Vêncio, Leonardo Varuzza, Carlos Alberto de Bragança Pereira, Helena Brentani, Ilya Shmulevich
Software Mentions: 2
Published: over 17 years ago
10.1186/s12859-017-1945-9
Explorative visual analytics on interval-based genomic data and their metadataCited by: 4
Author(s): Vahid Jalili, Matteo Matteucci, Marco Masseroli, Stefano Ceri
Software Mentions: 2
Published: almost 7 years ago
10.3390/s16081306
A Self-Provisioning Mechanism in OpenStack for IoT DevicesCited by: 15
Author(s): Antonio Solano, Raquel Dormido, N. Duro, Juan Miguel Sánchez
Software Mentions: 2
Published: about 8 years ago
10.3390/s21144714
Method to Increase Dependability in a Cloud-Fog-Edge EnvironmentCited by: 4
Author(s): Ovidiu Stan, Szilárd Enyedi, Cosmina Corches, Stelian Flonta, Iulia Ștefan, Dan-Ioan Gota, Liviu Miclea
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0063673
Fine De Novo Sequencing of a Fungal Genome Using only SOLiD Short Read Data: Verification on Aspergillus oryzae RIB40Cited by: 21
Author(s): Myco Umemura, Yoshinori Koyama, Itaru Takeda, Hiroko Hagiwara, Tsutomu Ikegami, Hideaki Koike, Masayuki Machida
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0232981
Active Notch signaling is required for arm regeneration in a brittle starCited by: 15
Author(s): Vladimir Mashanov, Jennifer Akiona, Maleana Khoury, Jacob W. Ferrier, Robert W. Reid, Denis Jacob Machado, Olga Zueva, Daniel Janies
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0206154
In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattleCited by: 11
Author(s): Quratulain Hanif, Muhammad Farooq, Imran Amin, Shahid Mansoor, Yi Zhang, Qaiser M. Khan
Software Mentions: 2
Published: about 6 years ago
10.1186/s12859-018-2576-5
iRODS metadata management for a cancer genome analysis workflowCited by: 3
Author(s): Lech Nieroda, Lukas Maas, Scott Thiebes, Ulrich Lang, Ali Sunyaev, Viktor Achter, Martin Peifer
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0255078
How did the characteristics of the growing season change during the past 100 years at a steep river basin in Japan?Cited by: 4
Author(s): Shin Nagai, Taku M. Saitoh, Kenlo Nishida Nasahara
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0049774
Onset of Immune Senescence Defined by Unbiased Pyrosequencing of Human Immunoglobulin mRNA RepertoiresCited by: 32
Author(s): Florian Rubelt, Volker Sievert, Florian Knaust, Christian Diener, Theam Soon Lim, Karl Skriner, Edda Klipp, Richard Reinhardt, Hans Lehrach, Zoltán Konthur
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0012078
Deep Sequencing of the Vaginal Microbiota of Women with HIVCited by: 241
Author(s): Ruben Hummelen, Andrew D. Fernandes, Jean M. Macklaim, Russell J. Dickson, John Changalucha, Gregory B. Gloor, Gregor Reid
Software Mentions: 2
Published: about 14 years ago
10.1371/journal.pone.0164325
Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)Cited by: 26
Author(s): Ajay Kumar Mahato, Nimisha Sharma, Akshay Singh, Manish Srivastav, Jaiprakash, Sanjay Kumar Singh, Anand Kumar Singh, Tilak Raj Sharma, Nagendra Singh
Software Mentions: 2
Published: about 8 years ago
10.1128/genomeA.01084-16
Draft Genome Sequence of Enterococcus faecalis Strain F165 Isolated from a Urinary Tract InfectionCited by: 0
Author(s): Thiago G. S. Paim, Luiza Pieta, Janira Prichula, Gustavo Enck Sambrano, Renata Oliveira Soares, Aline Dall Bello, Jeverson Frazzon, Pedro Alves d’Azevedo
Software Mentions: 1
Published: about 8 years ago
10.1038/s41598-018-22478-4
Oat evolution revealed in the maternal lineages of 25 Avena speciesCited by: 25
Author(s): Yong‐Bi Fu
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2105-6-196
COPASAAR – A database for proteomic analysis of single amino acid repeatsCited by: 24
Author(s): Daniel P. Depledge, Andrew R. Dalby
Software Mentions: 1
Published: over 19 years ago
10.1186/1471-2105-14-201
Bioinformatic pipelines in Python with LeafCited by: 6
Author(s): Francesco Napolitano, Renato Mariani-Costantini, Roberto Tagliaferri
Software Mentions: 1
Published: over 11 years ago
10.1186/1471-2229-8-17
Cross-species EST alignments reveal novel and conserved alternative splicing events in legumesCited by: 54
Author(s): Bing Bing Wang, Mike O'toole, Volker Brendel, Nevin D. Young
Software Mentions: 1
Published: over 16 years ago
10.1093/jhered/esaa001
Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 WorkshopCited by: 3
Author(s): Amanda R. Stahlke, Donavan Bell, Tashi Dhendup, Brooke Kern, Samuel Pannoni, Zachary L. Robinson, Jeffrey Strait, Seth Smith, Brian K. Hand, Paul A. Hohenlohe, Gordon Luikart
Software Mentions: 1
Published: over 4 years ago
10.1186/s12859-020-03602-6
Bioinformatics recipes: creating, executing and distributing reproducible data analysis workflowsCited by: 1
Author(s): Natay Aberra, Aswathy Sebastian, Aaron P. Maloy, Christopher B. Rees, Meredith L. Bartron, István Albert
Software Mentions: 1
Published: over 4 years ago
10.1186/s12864-016-2895-8
Benchmarking of de novo assembly algorithms for Nanopore data reveals optimal performance of OLC approachesCited by: 18
Author(s): Yesesri Cherukuri, Sarath Chandra Janga
Software Mentions: 1
Published: over 8 years ago
10.1186/1471-2164-7-300
Pfarao: a web application for protein family analysis customized for cytoskeletal and motor proteins (CyMoBase)Cited by: 28
Author(s): Florian Odronitz, Martin Kollmar
Software Mentions: 1
Published: almost 18 years ago
10.1186/1471-2164-7-120
Effect of 5'UTR introns on gene expression in Arabidopsis thalianaCited by: 183
Author(s): Betty Y.-W. Chung, Cas Simons, Andrew E. Firth, Chris M. Brown, Roger P. Hellens
Software Mentions: 1
Published: over 18 years ago
10.1186/1471-2164-7-73
A high-throughput screen identifying sequence and promiscuity characteristics of the loxP spacer region in Cre-mediated recombinationCited by: 61
Author(s): Perseus I. Missirlis, Duane E. Smailus, Robert A. Holt
Software Mentions: 1
Published: over 18 years ago
10.1038/s41598-019-45835-3
Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencersCited by: 68
Author(s): Jiayun Chen, Xingsong Li, Zhong Huang, Yuhuan Meng, Hongli Du
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0037538
Chondrocyte Deformations as a Function of Tibiofemoral Joint Loading Predicted by a Generalized High-Throughput Pipeline of Multi-Scale SimulationsCited by: 39
Author(s): Scott C. Sibole, Ahmet Erdemir
Software Mentions: 1
Published: over 12 years ago
10.1093/jamiaopen/ooaa043
Facilitating reproducible research through direct connection of data analysis with manuscript preparation: StatTag for connecting statistical software to Microsoft WordCited by: 2
Author(s): Leah J. Welty, Luke V. Rasmussen, Abigail S. Baldridge, Eric W. Whitley
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pone.0041827
NEXCADE: Perturbation Analysis for Complex NetworksCited by: 23
Author(s): Gitanjali Yadav, Suresh Babu
Software Mentions: 1
Published: over 12 years ago
10.1186/1471-2105-15-S10-P2
Automating deployment of several GBrowse instancesCited by: 0
Author(s): Neil Moore, Jerzy W. Jaromczyk, Christopher L. Schardl, J D Hill, Devin Wright
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0136574
Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is IntactCited by: 29
Author(s): Puya G. Yazdi, Brian Pedersen, Jared F. Taylor, Omar Khattab, Yuhan Chen, Steven E. Jacobsen, Ping H. Wang
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pone.0163174
The High-Risk Human Papillomavirus E6 Oncogene Exacerbates the Negative Effect of Tryptophan Starvation on the Development of Chlamydia trachomatisCited by: 10
Author(s): Shardulendra P. Sherchand, Joyce A. Ibana, Arnold H. Zea, Alison J. Quayle, Ashok Aiyar
Software Mentions: 1
Published: about 8 years ago
10.1371/journal.pgen.1003411
The Role of the Arabidopsis Exosome in siRNA–Independent Silencing of Heterochromatic LociCited by: 27
Author(s): Jeong Hee Shin, Hsiao-Lin Wang, Jinwon Lee, Brandon L. Dinwiddie, Dmitry A. Belostotsky, Julia A. Chekanova
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0119317
T346Hunter: A Novel Web-Based Tool for the Prediction of Type III, Type IV and Type VI Secretion Systems in Bacterial GenomesCited by: 54
Author(s): Pedro Manuel Martínez-García, Cayo Ramos, Pablo Rodrı́guez-Palenzuela
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0131166
Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical CenterCited by: 10
Author(s): Albert Geskin, Elizabeth Legowski, Anish Chakka, Uma Chandran, M. Michael Barmada, William A. LaFramboise, Jeremy M. Berg, Rebecca S. Jacobson
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.ppat.1006861
Switching and loss of cellular cytokine producing capacity characterize in vivo viral infection and malignant transformation in human T- lymphotropic virus type 1 infectionCited by: 22
Author(s): Huseini Kagdi, Maria Piera Demontis, Juan Carlos Ramos, Graham P. Taylor
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2164-12-125
Consistency of gene starts among Burkholderia genomesCited by: 10
Author(s): John Dunbar, Judith D. Cohn, Michael E. Wall
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.pone.0061386
IMACULAT — An Open Access Package for the Quantitative Analysis of Chromosome Localization in the NucleusCited by: 9
Author(s): Ishita Mehta, Sandeep Chakraborty, Basuthkar J. Rao
Software Mentions: 1
Published: over 11 years ago
10.1002/ejic.201701413
Formation of Mono Oxo Molybdenum(IV) PNP Pincer Complexes: Interplay between Water and Molecular OxygenCited by: 6
Author(s): Sara R. M. M. de Aguiar, Özgür Öztopçu, Anna Troiani, Giulia de Petris, Matthias Weil, Berthold Stöger, Ernst Pittenauer, Günter Allmaier, Luı́s F. Veiros, Karl Kirchner
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0169370
Whole Genome Sequencing of 39 Invasive Streptococcus pneumoniae Sequence Type 199 Isolates Revealed Switches from Serotype 19A to 15BCited by: 19
Author(s): Oliwia Makarewicz, Marie‐Odile Lucas, Christian Brandt, Leonie Herrmann, Andreas Albersmeier, Christian Rückert, Jochen Blom, Alexander Goesmann, Mark van der Linden, Jörn Kalinowski, Mathias W. Pletz
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.pcbi.1005898
MAGPIE: Simplifying access and execution of computational models in the life sciencesCited by: 5
Author(s): Christoph Baldow, Sebastian Salentin, Michael Schroeder, Ingo Roeder, Ingmar Glauche
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.pbio.1001325
Bet Hedging in Yeast by Heterogeneous, Age-Correlated Expression of a Stress ProtectantCited by: 317
Author(s): Sasha F. Levy, Naomi Ziv, Mark L. Siegal
Software Mentions: 1
Published: over 12 years ago
10.1186/s13007-017-0269-0
Terzyme: a tool for identification and analysis of the plant terpenomeCited by: 24
Author(s): Piyush Priya, Archana Yadav, Jyoti Chand, Gitanjali Yadav
Software Mentions: 1
Published: almost 7 years ago
10.7717/peerj.10487
Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophsCited by: 2
Author(s): Aline B. M. Vaz, Paula Luize Camargos Fonseca, Felipe F. Silva, Gabriel Quintanilha-Peixoto, Inmaculada Sampedro, J.A. Siles, Anderson Oliveira do Carmo, Rodrigo Bentes Kato, Vasco Azevedo, Fernanda Badotti, J. A. Ocampo, Carlos A. Rosa, Aristóteles Goés-Neto
Software Mentions: 1
Published: almost 4 years ago
10.3389/fcimb.2019.00447
Network-Based Metabolism-Centered Screening of Potential Drug Targets in Klebsiella pneumoniae at Genome ScaleCited by: 27
Author(s): Müberra Fatma Cesur, Bushra Siraj, Reaz Uddin, Saliha Durmuş, Tunahan Çakır
Software Mentions: 1
Published: almost 5 years ago
10.3390/s130506687
IPv6 Addressing Proxy: Mapping Native Addressing from Legacy Technologies and Devices to the Internet of Things (IPv6)Cited by: 31
Author(s): Antonio J. Jara, Pedro Moreno-Sanchez, Antonio F. Skarmeta, Socrates Varakliotis, Peter T. Kirstein
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0097589
fcGENE: A Versatile Tool for Processing and Transforming SNP DatasetsCited by: 45
Author(s): Nab Raj Roshyara, Markus Scholz
Software Mentions: 1
Published: over 10 years ago
10.1038/srep10182
Targets of drugs are generally and targets of drugs having side effects are specifically good spreaders of human interactome perturbationsCited by: 21
Author(s): Áron R. Perez-Lopez, Kristóf Z. Szalay, Dénes Türei, Dezső Módos, Katalin Lenti, Tamás Korcsmáros, Péter Csermely
Software Mentions: 1
Published: over 9 years ago
10.3390/ijms20205142
Exploring the Binding Mechanism and Dynamics of EndoMS/NucS to Mismatched dsDNACited by: 2
Author(s): Yanjun Zhang, Sheng‐You Huang
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.pone.0120520
Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina PlatformCited by: 95
Author(s): Abhishek Mitra, Magdalena Skrzypczak, Krzysztof Ginalski, Maga Rowicka
Software Mentions: 1
Published: over 9 years ago
10.1007/s00706-016-1731-9
High-spin iron(II) complexes with mono-phosphorylated 2,6-diaminopyridine ligandsCited by: 9
Author(s): Christan Schröder-Holzhacker, Berthold Stöger, Ernst Pittenauer, Günther Allmaier, Luı́s F. Veiros, Karl Kirchner
Software Mentions: 1
Published: over 8 years ago
10.1002/mgg3.502
Dysfunctional DNA repair pathway via defective <i>FANCD2</i> gene engenders multifarious exomic and transcriptomic effects in Fanconi anemiaCited by: 2
Author(s): Karthik Raja Velmurugan, Pawel Michalak, Lin Kang, Natalie C. Fonville, Harold R. Garner
Software Mentions: 1
Published: about 6 years ago
10.3389/fmicb.2020.528051
Teaching Microbiome Analysis: From Design to Computation Through InquiryCited by: 2
Author(s): Gail Rosen, Penny L. Hammrich
Software Mentions: 1
Published: about 4 years ago
10.1186/s40168-018-0541-1
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysisCited by: 906
Author(s): Gherman Uritskiy, Jocelyne DiRuggiero, James Taylor
Software Mentions: 1
Published: about 6 years ago
10.3390/ma13112601
Flexural Damage of Honeycomb Paperboard—A Numerical and Experimental StudyCited by: 6
Author(s): L. Czechowski, Wojciech Śmiechowicz, Gabriela Kmita-Fudalej, W. Szewczyk
Software Mentions: 1
Published: over 4 years ago
10.3390/biom9050199
Computational Simulation of Adapter Length-Dependent LASSO Probe Capture EfficiencyCited by: 2
Author(s): Jingqian Liu, Syukri Shukor, Shuxiang Li, Alfred Tamayo, Lorenzo Tosi, Benjamin Larman, Vikas Nanda, Wilma K. Olson, Biju Parekkadan
Software Mentions: 1
Published: over 5 years ago
10.3389/fneur.2017.00496
Fatigue and Cognitive Fatigability in Mild Traumatic Brain Injury are Correlated with Altered Neural Activity during Vigilance Test PerformanceCited by: 32
Author(s): Marika Möller, Love Engström Nordin, Aniko Bartfai, Per Julin, Tie‐Qiang Li
Software Mentions: 1
Published: about 7 years ago
10.3389/fnins.2020.00238
Peak Width of Skeletonized Mean Diffusivity as a Marker of Diffuse Cerebrovascular DamageCited by: 22
Author(s): Audrey Low, Elijah Mak, James D. Stefaniak, Maura Malpetti, Nicolas Nicastro, George Savulich, Leonidas Chouliaras, Hugh S. Markus, James B. Rowe
Software Mentions: 1
Published: over 4 years ago
10.1038/srep30308
A novel alignment-free method for detection of lateral genetic transfer based on TF-IDFCited by: 34
Author(s): Yingnan Cong, Yao-ban Chan, Mark A. Ragan
Software Mentions: 1
Published: over 8 years ago
10.1038/srep35068
Three-dimensional electron microscopy reveals the evolution of glomerular barrier injuryCited by: 50
Author(s): Michael J. Randles, Sophie Collinson, Tobias Starborg, Aleksandr Mironov, Mira Krendel, Eva Königshausen, Lorenz Sellin, Ian Roberts, Karl E. Kadler, Jeffrey H. Miner, Rachel Lennon
Software Mentions: 1
Published: about 8 years ago
10.1038/srep44790
A Ras GTPase associated protein is involved in the phototropic and circadian photobiology responses in fungiCited by: 21
Author(s): Silvia Polaino, José Manuel Villalobos-Escobedo, Viplendra P. S. Shakya, Alejandro Miralles-Durán, Suman Chaudhary, Catalina Sanz, Mahdi Shahriari, Eva M. Luque, Arturo P. Eslava, Luis M. Corrochano, Alfredo Herrera-Estrella, Alexander Idnurm
Software Mentions: 1
Published: over 7 years ago