pypi: workbench | Projects | Ecosyste.ms: Papers

10.12688/f1000research.12974.1

Using bio.tools to generate and annotate workbench tool descriptions
Cited by: 8
Author(s): Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Helena Rasche, Michael R. Crusoe, Hedi Peterson, Jon C. Ison, Hervé Ménager
Software Mentions: 8
Published: about 7 years ago

10.1093/gigascience/giaa162

Lilikoi V2.0: a deep learning–enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data
Cited by: 10
Author(s): Xinying Fang, Yu Liu, Zhijie Ren, Yuheng Du, Qizhao Huang, Lana X. Garmire
Software Mentions: 7
Published: almost 4 years ago

10.12688/f1000research.28608.2

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
Cited by: 6
Author(s): Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø. Arntzen, Benoît J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 6
Published: over 3 years ago

10.3389/fbioe.2014.00061

Improving Collaboration by Standardization Efforts in Systems Biology
Cited by: 49
Author(s): Andreas Dräger, Bernhard Ø. Palsson
Software Mentions: 6
Published: about 10 years ago

10.1007/s11306-015-0879-3

Data standards can boost metabolomics research, and if there is a will, there is a way
Cited by: 89
Author(s): Philippe Rocca-Serra, Reza M. Salek, Masanori Arita, Elon Correa, Saravanan Dayalan, Alejandra González-Beltrán, Timothy M. D. Ebbels, Royston Goodacre, Janna Hastings, Kenneth Haug, Albert Koulman, Macha Nikolski, Matej Orešič, Susanna-Assunta Sansone, Daniel Schober, James M. Smith, Christoph Steinbeck, Mark R. Viant, Steffen Neumann
Software Mentions: 5
Published: about 9 years ago

10.3389/fmicb.2016.00398

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow
Cited by: 48
Author(s): Anna Lopatina, Sofia Medvedeva, Sergey Shmakov, Maria D. Logacheva, В. А. Крыленков, Konstantin Severinov
Software Mentions: 5
Published: over 8 years ago

10.1002/pro.3783

The Dundee Resource for Sequence Analysis and Structure Prediction
Cited by: 11
Author(s): Stuart A. MacGowan, Fábio Madeira, Thiago Britto‐Borges, Mateusz Warowny, Alexey Drozdetskiy, James B. Procter, Geoffrey J. Barton
Software Mentions: 5
Published: about 5 years ago

10.1111/tpj.14795

The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit
Cited by: 30
Author(s): Yury Tikunov, Raana Roohanitaziani, Fien Meijer‐Dekens, Jos Molthoff, João Paulo, Richard Finkers, Iris Capel, Fátima Carvajal Moreno, Chris Maliepaard, Mariska Nijenhuis-de Vries, C.W. Labrie, W. Verkerke, A.W. van Heusden, Fred van Eeuwijk, R.G.F. Visser, Arnaud Bovy
Software Mentions: 4
Published: over 4 years ago

10.1186/1752-0509-1-13

Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery
Cited by: 59
Author(s): William J. Bosl
Software Mentions: 4
Published: almost 18 years ago

10.1093/gbe/evu073

An Expanded Genomic Representation of the Phylum Cyanobacteria
Cited by: 260
Author(s): Rochelle M. Soo, Connor T. Skennerton, Yuji Sekiguchi, Michael Imelfort, Samuel J. Paech, Paul G. Dennis, Jason A. Steen, Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 4
Published: over 10 years ago

10.3390/microorganisms9061310

Meropenem Pharmacokinetics and Target Attainment in Critically Ill Patients Are Not Affected by Extracorporeal Membrane Oxygenation: A Matched Cohort Analysis
Cited by: 12
Author(s): Matthias Gijsen, Erwin Dreesen, Pieter Annaert, Johan Nicolaï, Yves Debaveye, Joost Wauters, Isabel Spriet
Software Mentions: 4
Published: over 3 years ago

10.1107/S090744491201863X

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography
Cited by: 36
Author(s): Sándor Brockhauser, Olof Svensson, Matthew W. Bowler, Max H. Nanao, E. Gordón, Ricardo M. F. Leal, А. Н. Попов, Matthew Gerring, A.A. McCarthy, Andrew Götz
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0140829

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud
Cited by: 99
Author(s): Enis Afgan, Clare Sloggett, Nuwan Goonasekera, Igor V. Makunin, Derek Benson, Mark L. Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie
Software Mentions: 4
Published: about 9 years ago

10.7717/peerj.4075

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion.
Cited by: 17
Author(s): Miriam E. Shiffman, Rochelle M. Soo, Paul G. Dennis, Mark Morrison, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 4
Published: almost 8 years ago

10.1186/1471-2105-13-S4-S5

An ICT infrastructure to integrate clinical and molecular data in oncology research
Cited by: 29
Author(s): Daniele Segagni, Valentina Tibollo, Arianna Dagliati, Alberto Zambelli, Silvia G. Priori, Riccardo Bellazzi
Software Mentions: 4
Published: over 12 years ago

10.3389/fgene.2016.00206

A Network Approach of Gene Co-expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways
Cited by: 30
Author(s): Bryan Musungu, Deepak Bhatnagar, Robert L. Brown, Gary A. Payne, Greg O'Brian, Ahmad M. Fakhoury, Matt Geisler
Software Mentions: 3
Published: about 8 years ago

10.3390/v12080801

Determining the Suitability of MinION’s Direct RNA and DNA Amplicon Sequencing for Viral Subtype Identification
Cited by: 10
Author(s): Deborah M. Leigh, Christopher Schefer, Carolina Cornejo
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2014.00031

Shotgun metagenomic data reveals significant abundance but low diversity of “Candidatus Scalindua” marine anammox bacteria in the Arabian Sea oxygen minimum zone
Cited by: 28
Author(s): Laura Villanueva, Daan R. Speth, Theo van Alen, Alexander Hoischen, Mike S. M. Jetten
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0229326

Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (mSNV) analysis during an influenza A/H5N8 outbreak
Cited by: 1
Author(s): Marjolein J Poen, Anne Pohlmann, Clara Amid, Theo M. Bestebroer, Sharon M Brookes, Ian H. Brown, Helen Everett, Claudia M. E. Schapendonk, Rachel D Scheuer, Saskia L. Smits, Martin Beer, Ron A. M. Fouchier, Richard J. Ellis
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1002502

Computational Prediction and Molecular Characterization of an Oomycete Effector and the Cognate Arabidopsis Resistance Gene
Cited by: 58
Author(s): Sandra Goritschnig, Ksenia V. Krasileva, Douglas Dahlbeck, Brian J. Staskawicz
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12870-018-1501-4

Genome-wide transcriptome analysis reveals small RNA profiles involved in early stages of stolon-to-tuber transitions in potato under photoperiodic conditions
Cited by: 22
Author(s): Kirtikumar R. Kondhare, Nilam N Malankar, Ravi Suresh Devani, Anjan K. Banerjee
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-020-07086-9

In vitro resynthesis of lichenization reveals the genetic background of symbiosis-specific fungal-algal interaction in Usnea hakonensis
Cited by: 26
Author(s): Mieko Kono, Yoshiaki Kon, Yoshihito Ohmura, Yoko Satta, Yohey Terai
Software Mentions: 3
Published: about 4 years ago

10.1007/s10270-020-00798-2

Behavioral interfaces for executable DSLs
Cited by: 8
Author(s): D. J. LeRoy, Erwan Bousse, Manuel Wimmer, Tanja Mayerhofer, Benôıt Combemale, Wieland Schwinger
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.70119

The BigBrainWarp toolbox for integration of BigBrain 3D histology with multimodal neuroimaging
Cited by: 33
Author(s): Casey Paquola, Jessica Royer, Lindsay B. Lewis, Claude Lepage, Tristan Glatard, Konrad Wagstyl, Jordan DeKraker, Paule-Joanne Toussaint, Sofie L. Valk, D. Louis Collins, Ali Raza Khan, Katrin Amunts, Alan C. Evans, Timo Dickscheid, Boris C. Bernhardt
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-016-1045-2

Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower
Cited by: 26
Author(s): Sebastián Moschen, Janet Higgins, Julio A. Di Rienzo, Ruth Amelia Heinz, Norma Paniego, Paula Fernández
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pbio.3000979

A multi-scale cortical wiring space links cellular architecture and functional dynamics in the human brain
Cited by: 61
Author(s): Casey Paquola, Jakob Seidlitz, Oualid Benkarim, Jessica Royer, Petr Klimeš, Richard A. I. Bethlehem, Sara Larivière, Reinder Vos de Wael, Raúl Rodríguez‐Cruces, Jeffery A. Hall, Birgit Frauscher, Jonathan Smallwood, Boris C. Bernhardt
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0027297

Pseudomonas syringae pv. actinidiae Draft Genomes Comparison Reveal Strain-Specific Features Involved in Adaptation and Virulence to Actinidia Species
Cited by: 118
Author(s): Simone Marcelletti, Patrizia Ferrante, Milena Petriccione, Giuseppe Firrao, M. Scortichini
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0150273

De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq
Cited by: 27
Author(s): Shivanjali Kotwal, Sanjana Kaul, Pooja Sharma, Manik Gupta, Rama Shankar, Mukesh Jain, Manoj K. Dhar
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2105-13-89

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art
Cited by: 75
Author(s): Rasna R. Walia, Cornelia Caragea, Benjamin A. Lewis, Fadi Towfic, Michael Terribilini, Yasser EL-Manzalawy, Drena Dobbs, Vasant Honavar
Software Mentions: 2
Published: over 12 years ago

10.1038/s41598-018-25089-1

The quest for identifiability in human functional connectomes
Cited by: 173
Author(s): Enrico Amico, Joaquín Goñi
Software Mentions: 2
Published: over 6 years ago

10.3390/biom10060864

Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains
Cited by: 9
Author(s): Woori Kim, Namil Lee, Soonkyu Hwang, Yong Jae Lee, Jihun Kim, Suhyung Cho, Bernhard Ø. Palsson, Byung-Kwan Cho
Software Mentions: 2
Published: over 4 years ago

10.1093/database/bau064

Processing biological literature with customizable Web services supporting interoperable formats
Cited by: 12
Author(s): Rafał Rak, Riza Theresa Batista-Navarro, Jacob Carter, Andrew Rowley, Sophia Ananiadou
Software Mentions: 2
Published: over 10 years ago

10.1098/rstb.2018.0092

Natural diversity of CRISPR spacers of Thermus : evidence of local spacer acquisition and global spacer exchange
Cited by: 19
Author(s): Anna Lopatina, Sofia Medvedeva, Daria Artamonova, Matvey Kolesnik, Vasily Sitnik, Iaroslav Ispolatov, Konstantin Severinov
Software Mentions: 2
Published: over 5 years ago

10.1038/emi.2016.140

Discovery and genetic analysis of novel coronaviruses in least horseshoe bats in southwestern China
Cited by: 27
Author(s): Lin‐Fa Wang, Shihong Fu, Yanghui Cao, Hailin Zhang, Yue Feng, Wei Yang, Kai Nie, Xuejun Ma, Guodong Liang
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-020-60190-4

Dissecting the Genetic Complexity of Fusarium Crown Rot Resistance in Wheat
Cited by: 10
Author(s): Shree R. Pariyar, Gül Erginbaş-Orakci, Said Dadshani, Oyiga Benedict Chijioke, Jens Léon, Abdelfattah A. Dababat, Florian M. W. Grundler
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-021-86671-8

Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis
Cited by: 3
Author(s): Nelson Martinez‐Matias, Nataliya Chorna, Sahily González-Crespo, Lilliam Villanueva, Ingrid M. Montes-Rodríguez, Loyda M. Melendez-Aponte, Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Ednalise Santiago‐Cartagena, Brian C. Rymond, Mohan Babu, Igor Štagljar, José R. Rodríguez‐Medina
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-017-3989-7

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery
Cited by: 30
Author(s): Maryam Moazzzam Jazi, Seyed Mahdi Seyedi, Esmaeil Ebrahimie, Mansour Ebrahimi, Gianluca De Moro, Christopher Botanga
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1009232

Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region
Cited by: 10
Author(s): Dheeraj Prakaash, Graham P. Cook, Oreste Acuto, Antreas C. Kalli
Software Mentions: 2
Published: over 3 years ago

10.1042/BSR20202269

Computational analysis of Cyclin D1 gene SNPs and association with breast cancer
Cited by: 9
Author(s): Ayesha Aftab, Ranjha Khan, Wasim Shah, Muhammad Azhar, Ahsanullah Unar, Hafiz Muhammad Jafar Hussain, Ahmed Waqas
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0012078

Deep Sequencing of the Vaginal Microbiota of Women with HIV
Cited 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: over 14 years ago

10.1186/2049-2618-1-25

An in vitrobiofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
Cited by: 103
Author(s): Anna Edlund, Youngik Yang, Adam P. Hall, Lihong Guo, Renate Lux, Xuesong He, Karen E. Nelson, Kenneth H. Nealson, Shibu Yooseph, Wenyuan Shi, Jeffrey S. McLean
Software Mentions: 2
Published: about 11 years ago

10.1111/jipb.12742

Involvement of sweet pepperCaLOX2in jasmonate-dependent induced defence against Western flower thrips
Cited by: 28
Author(s): Sandeep J. Sarde, Klaas Bouwmeester, Jhon Venegas‐Molina, Anja David, Wilhelm Boland, Marcel Dicke
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.36652

Functional gradients of the cerebellum
Cited by: 264
Author(s): Xavier Guell, Jeremy D. Schmahmann, John D. E. Gabrieli, Samik Ghosh
Software Mentions: 2
Published: over 6 years ago

10.3389/fphar.2019.00642

Transcriptome Profiling Reveals Pro-Inflammatory Cytokines and Matrix Metalloproteinase Activation in Zika Virus Infected Human Umbilical Vein Endothelial Cells
Cited by: 18
Author(s): Svetlana F. Khaiboullina, Timsy Uppal, Konstatin Kletenkov, Stephen C. St. Jeor, Ekaterina Garanina, Albert A. Rizvanov, Subhash C. Verma
Software Mentions: 2
Published: over 5 years ago

10.1186/2041-1480-3-S1-S7

OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia
Cited by: 24
Author(s): Olga Tcheremenskaia, Romualdo Benigni, Ivelina Nikolova, Nina Jeliazkova, Sylvia Escher, Monika Batke, Thomas Baier, Vladimir Poroikov, Alexey Lagunin, Micha Rautenberg, Barry Hardy
Software Mentions: 2
Published: almost 13 years ago

10.1186/2041-1480-2-4

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
Cited by: 17
Author(s): Toshiaki Katayama, Mark D. Wilkinson, Rutger A. Vos, Takeshi Kawashima, Seiichiro Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong‐Woo Chun, Atsuko Yamaguchi, Shin Kawano, Jan Aerts, Kiyoko F. Aoki‐Kinoshita, Kazuharu Arakawa, Bruno Aranda, Raoul Jean Pierre Bonnal, José Marı́a Fernández, Takatomo Fujisawa, Paul M. Gordon, Naohisa Goto, Syed Haider, Todd W. Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Gregory Von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, Erin McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas H. Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12864-016-2710-6

Genome sequence and comparative analysis of clavicipitaceous insect-pathogenic fungus Aschersonia badia with Metarhizium spp.
Cited by: 12
Author(s): Yamini Agrawal, Tarun Jairaj Narwani, S. Subramanian
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-021-07455-y

Early transcriptome changes induced by the Geminivirus C4 oncoprotein: setting the stage for oncogenesis
Cited by: 5
Author(s): C. M. Deom, Magdy S. Alabady, Li Yang
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2020.00598

Elucidating the Regulon of a Fur-like Protein in Mycobacterium avium subsp. paratuberculosis (MAP)
Cited by: 6
Author(s): Fernanda Miyagaki Shoyama, Taveesak Janetanakit, John P. Bannantine, Raúl G. Barletta, Srinand Sreevatsan
Software Mentions: 2
Published: over 4 years ago

10.3389/fphar.2016.00153

Therapeutics Insight with Inclusive Immunopharmacology Explication of Human Rotavirus A for the Treatment of Diarrhea
Cited by: 6
Author(s): Mohammad Uzzal Hossain, Abu Hashem, Chaman Ara Keya, Md. Salimullah
Software Mentions: 2
Published: over 8 years ago

10.1080/21505594.2016.1237333

What's a SNP between friends: The influence of single nucleotide polymorphisms on virulence and phenotypes ofClostridium difficilestrain 630 and derivatives
Cited by: 34
Author(s): Mark M. Collery, Sarah A. Kuehne, Shonna M. McBride, Michelle L. Kelly, Marc Monot, Alan Cockayne, Bruno Dupuy, Nigel P. Minton
Software Mentions: 2
Published: over 8 years ago

10.3390/v12020243

Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix)
Cited by: 12
Author(s): Alexandru Tomazatos, Rachel E. Marschang, Iulia Maranda, Heike von Baum, Alexandra Bialonski, Marina Spînu, Renke Lühken, Jonas Schmidt‐Chanasit, Dániel Cadar
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0161390

A Parallel Population Genomic and Hydrodynamic Approach to Fishery Management of Highly-Dispersive Marine Invertebrates: The Case of the Fijian Black-Lip Pearl Oyster Pinctada margaritifera
Cited by: 18
Author(s): Monal M. Lal, Paul C. Southgate, Dean R. Jerry, Cyprien Bosserelle, Kyall R. Zenger
Software Mentions: 2
Published: over 8 years ago

10.3389/fpls.2016.01564

Soybean TIP Gene Family Analysis and Characterization of GmTIP1;5 and GmTIP2;5 Water Transport Activity
Cited by: 28
Author(s): Li Song, Na Nguyen, Rupesh Deshmukh, Gunvant Patil, Silvas J. Prince, Babu Valliyodan, Raymond N. Mutava, Sharon Pike, Walter Gassmann, Henry T. Nguyen
Software Mentions: 1
Published: about 8 years ago

10.3390/genes8090212

Chloroplast Genome Sequence of Clusterbean (Cyamopsis tetragonoloba L.): Genome Structure and Comparative Analysis
Cited by: 42
Author(s): Tanvi Kaila, Pavan K. Chaduvla, Hukam C. Rawal, Swati Saxena, Anshika Tyagi, S. V. Amitha Mithra, Amolkumar U. Solanke, Pritam Kalia, Tilak Raj Sharma, Nagendra Singh, Kishor Gaikwad
Software Mentions: 1
Published: over 7 years ago

10.1128/genomeA.00467-14

Draft Genome Sequence of Lactobacillus plantarum wikim18, Isolated from Korean Kimchi
Cited by: 3
Author(s): Ja Young Jang, Hyeong In Lim, Hae Woong Park, Hak-Jong Choi, Tae-Woon Kim, Mi Jeong Kang, Jong Hee Lee
Software Mentions: 1
Published: over 10 years ago

10.1128/genomeA.01350-17

Complete Genome Sequences of Plasmid-Bearing Campylobacter coli and Campylobacter jejuni Strains Isolated from Retail Chicken Liver
Cited by: 6
Author(s): Daya Marasini, Mohamed K. Fakhr
Software Mentions: 1
Published: about 7 years ago

10.1002/hbm.24381

Spatial parcellations, spectral filtering, and connectivity measures in fMRI: Optimizing for discrimination
Cited by: 29
Author(s): Roser Sala‐Llonch, Stephen M. Smith, Mark W. Woolrich, Eugene Duff
Software Mentions: 1
Published: about 6 years ago

10.1002/jcsm.12506

Uniform sarcolemmal dystrophin expression is required to prevent extracellular microRNA release and improve dystrophic pathology
Cited by: 22
Author(s): van Westering Tle., Yulia Lomonosova, Anna M.L. Coenen-Stass, Corinne Betts, Amarjit Bhomra, Margriet Hulsker, Lucy E Clark, Graham McClorey, Annemieke Aartsma‐Rus, Maaike van Putten, Matthew J. Wood, Thomas C. Roberts
Software Mentions: 1
Published: about 5 years ago

10.1186/s13321-018-0266-y

HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors
Cited by: 22
Author(s): Abid Qureshi, Abhishek Rajput, Guneet Kaur, Manoj Kumar
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.jcv.2018.03.005

The current landscape of nucleic acid tests for filovirus detection
Cited by: 13
Author(s): David J. Clark, John J. Tyson, Andrew D. Sails, Sanjeev Krishna, Henry M. Staines
Software Mentions: 1
Published: over 6 years ago

10.1038/srep09448

Phylogenomic analysis uncovers the evolutionary history of nutrition and infection mode in rice blast fungus and other Magnaporthales
Cited by: 31
Author(s): Jing Luo, Huan Qiu, Guohong Cai, Nicole Wagner, Debashish Bhattacharya, Ning Zhang
Software Mentions: 1
Published: over 9 years ago

10.1038/srep28060

A Genome-wide Study of “Non-3UTR” Polyadenylation Sites in Arabidopsis thaliana
Cited by: 25
Author(s): Cheng Guo, Matthew Spinelli, Man Liu, Qingshun Quinn Li, Chun Liang
Software Mentions: 1
Published: over 8 years ago

10.1038/srep30381

Haplotyping the human leukocyte antigen system from single chromosomes
Cited by: 5
Author(s): Nicholas M. Murphy, Matthew D. Burton, David Powell, Fernando Rossello, Don Cooper, Abha Chopra, Ming Je Hsieh, D. Sayer, Lavinia Gordon, Mark D. Pertile, Brian D. Tait, Helen Ruth Irving, Colin W. Pouton
Software Mentions: 1
Published: over 8 years ago

10.1038/srep31721

New evidence for grain specific C4 photosynthesis in wheat
Cited by: 59
Author(s): Parimalan Rangan, Agnelo Furtado, Robert J. Henry
Software Mentions: 1
Published: over 8 years ago

10.1038/srep41052

The sRNAome mining revealed existence of unique signature small RNAs derived from 5.8SrRNA from Piper nigrum and other plant lineages
Cited by: 12
Author(s): S Asha, E. V. Soniya
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep45228

Quasispecies of Hepatitis C Virus Participate in Cell-Specific Infectivity
Cited by: 5
Author(s): Takasuke Fukuhara, Seiji Yamamoto, Chikako Ono, Shota Nakamura, Daisuke Motooka, Haruhiko Mori, Takeshi Kurihara, Asuka Sato, Tomokazu Tamura, Takashi Mizutani, Tomoyoshi Okamoto, Michio Imamura, Toru Ikegami, Tomoharu Yoshizumi, Yuji Soejima, Yoshihiko Maehara, Kazuaki Chayama, Yoshiharu Matsuura
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-07022-0

A deletion affecting an LRR-RLK gene co-segregates with the fruit flat shape trait in peach
Cited by: 26
Author(s): Elena López‐Girona, Yu Zhang, Iban Eduardo, José Ramón Hernández Mora, Konstantinos G. Alexiou, Pere Arús, María José Aranzana
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-12845-y

Fasciclin-like arabinogalactan protein gene expression is associated with yield of flour in the milling of wheat
Cited by: 18
Author(s): Ravi Chandrabhan Nirmal, Agnelo Furtado, Parimalan Rangan, Robert J. Henry
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-017-16072-3

ZIKV infection regulates inflammasomes pathway for replication in monocytes
Cited by: 29
Author(s): Svetlana F. Khaiboullina, Timsy Uppal, Rupa Sarkar, Andrew Gorzalski, Stephen St. Jeor, Subhash C. Verma
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-22987-2

Adipokinetic hormone signaling determines dietary fatty acid preference through maintenance of hemolymph fatty acid composition in the cricket Gryllus bimaculatus
Cited by: 14
Author(s): Kazuya Fukumura, Takahiro Konuma, Yusuke Tsukamoto, Shinji Nagata
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-37465-y

Modulation of miRNA expression in natural populations of A. thaliana along a wide altitudinal gradient of Indian Himalayas
Cited by: 11
Author(s): Alok Tripathi, Akanksha Singh, Rajneesh Singh, Ashwani Kumar Verma, Sribash Roy
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-40197-2

Circatidal gene expression in the mangrove cricket Apteronemobius asahinai
Cited by: 16
Author(s): Ayumi Satoh, Yohey Terai
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-51922-2

Reticular Dysgenesis and Mitochondriopathy Induced by Adenylate Kinase 2 Deficiency with Atypical Presentation
Cited by: 11
Author(s): Lina Ghaloul‐Gonzalez, Al‐Walid Mohsen, Anuradha Karunanidhi, Bianca Seminotti, Hey Chong, Suneeta Madan‐Khetarpal, Jessica Sebastian, Catherine Walsh Vockley, Miguel Reyes‐Múgica, Mark T. Vander Lugt, Jerry Vockley
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-57736-x

Divergence across mitochondrial genomes of sympatric members of the Schistosoma indicum group and clues into the evolution of Schistosoma spindale
Cited by: 14
Author(s): Ben P. Jones, Billie F. Norman, Hannah E. Borrett, Stephen W. Attwood, M. M. H. Mondal, Anthony J. Walker, Joanne P. Webster, Jayanthe Rajapakse, Scott P Lawton
Software Mentions: 1
Published: almost 5 years ago

10.3390/s151229789

Abnormal Condition Monitoring of Workpieces Based on RFID for Wisdom Manufacturing Workshops
Cited by: 7
Author(s): Cunji Zhang, Xifan Yao, Jianming Zhang
Software Mentions: 1
Published: about 9 years ago

10.3390/s20143966

A Smartphone Crowdsensing System Enabling Environmental Crowdsourcing for Municipality Resource Allocation with LSTM Stochastic Prediction
Cited by: 2
Author(s): Theodoros Anagnostopoulos, Theodoros Xanthopoulos, Yannis Psaromiligkos
Software Mentions: 1
Published: over 4 years ago

10.1186/s40793-016-0208-0

Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T
Cited by: 22
Author(s): Slimane Khayi, Pauline Blin, Teik Min Chong, Kok‐Gan Chan, Denis Faure
Software Mentions: 1
Published: about 8 years ago

10.3390/toxins12110673

Genomics and Proteomics Analyses Revealed Novel Candidate Pesticidal Proteins in a Lepidopteran-Toxic Bacillus thuringiensis Strain
Cited by: 6
Author(s): Ayda Khorramnejad, Joaquín Gomis-Cebolla, Reza Talaei‐Hassanlouei, Yolanda Bel, Baltasar Escriche
Software Mentions: 1
Published: about 4 years ago

10.1128/mSystems.00139-16

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen
Cited by: 32
Author(s): Neha Garg, Yi Zeng, Anna Edlund, Alexey V. Melnik, Laura M. Sanchez, Hosein Mohimani, Alexey Gurevich, Vivian Miao, Stefan Schiffler, Yan Wei Lim, Tal Luzzatto-Knaan, Shengxin Cai, Forest Rohwer, Pavel A. Pevzner, Robert H. Cichewicz, Theodore Alexandrov, Pieter C. Dorrestein
Software Mentions: 1
Published: almost 8 years ago

10.1186/s43141-020-00064-4

Light/heat effects on RNA editing in chloroplast NADH-plastoquinone oxidoreductase subunit 2 (ndhB) gene of Calotropis (Calotropis procera)
Cited by: 3
Author(s): Ahmed M. Ramadan
Software Mentions: 1
Published: over 4 years ago

10.7554/eLife.25327

ER assembly of SNARE complexes mediating formation of partitioning membrane in Arabidopsis cytokinesis
Cited by: 20
Author(s): Matthias Karnahl, Misoon Park, Ulríke Mayer, Ulrike Hiller, Gerd Jürgens
Software Mentions: 1
Published: over 7 years ago

10.1186/1743-0003-11-117

The feasibility of using haptic devices to engage people with chronic traumatic brain injury in virtual 3D functional tasks
Cited by: 10
Author(s): Lynn H. Gerber, Cody Narber, Nalini Vishnoi, Sidney L. Johnson, Leighton Chan, Zoran Đurić
Software Mentions: 1
Published: almost 11 years ago

10.1016/j.jplph.2020.153351

Genomic resources in plant breeding for sustainable agriculture
Cited by: 75
Author(s): Mahendar Thudi, Palakurthi Ramesh, James C. Schnable, Annapurna Chitikineni, Susanne Dreisigacker, Emma Mace, Rakesh K. Srivastava, C. Tara Satyavathi, Damaris Achieng Odeny, Vijay K. Tiwari, Hon‐Ming Lam, Yan Hu, Vikas K. Singh, Guowei Li, Yunbi Xu, Xiaoping Chen, Sanjay Kaila, Henry T. Nguyen, S. Sivasankar, Scott A. Jackson, Timothy J. Close, Shungang Wan, Rajeev K. Varshney
Software Mentions: 1
Published: almost 4 years ago

10.1007/s13205-016-0471-1

Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture (Xaj-pitha) of Assam, India
Cited by: 47
Author(s): Sudipta Sankar Bora, Jyotshna Keot, Saurav Das, K. K. Sarma, Madhumita Barooah
Software Mentions: 1
Published: over 8 years ago

10.1016/j.jsb.2017.02.007

SuRVoS: Super-Region Volume Segmentation workbench
Cited by: 68
Author(s): Imanol Luengo, Michele C. Darrow, Matthew C. Spink, Ying Sun, Wei Dai, Cynthia Y. He, Wah Chiu, Tony Pridmore, Alun Ashton, Elizabeth Duke, Mark Basham, A. P. French
Software Mentions: 1
Published: over 7 years ago

10.3390/antibiotics9040164

Acquisition of Colistin Resistance Links Cell Membrane Thickness Alteration with a Point Mutation in the lpxD Gene in Acinetobacter baumannii
Cited by: 9
Author(s): N. Saleh, Marwa S Hesham, Magdy A. Amin, Reham Samir Mohamed
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-016-3159-3

Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare)
Cited by: 39
Author(s): Hiroshi Hisano, Mai Tsujimura, Hideya Yoshida, Toru Terachi, Kazuhiro Sato
Software Mentions: 1
Published: about 8 years ago

10.1186/1755-8794-8-S2-S9

Network-based prediction and knowledge mining of disease genes
Cited by: 19
Author(s): Matthew B. Carson, Hui Lu
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2180-12-130

Analysis of a Clostridium difficile PCR ribotype 078 100 kilobase island reveals the presence of a novel transposon, Tn6164
Cited by: 35
Author(s): Jeroen Corver, Dennis Bakker, Michael S. M. Brouwer, Céline Harmanus, M.P.M. Hensgens, Adam P. Roberts, L.J.A. Lipman, Ed J. Kuijper, Hans C. van Leeuwen
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12883-019-1319-1

Leukoencephalopathia, demyelinating peripheral neuropathy and dural ectasia explained by a not formerly described de novo mutation in the SAMD9L gene, ends 27 years of investigations – a case report
Cited by: 10
Author(s): Sofia Thunström, Markus Axelsson
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2210-12-1

Computational models for in-vitro anti-tubercular activity of molecules based on high-throughput chemical biology screening datasets
Cited by: 29
Author(s): Vinita Periwal, Shireesha Kishtapuram, Vinod Scaria
Software Mentions: 1
Published: over 12 years ago

10.1186/s12870-017-1088-1

Identification of a methyltransferase catalyzing the final step of methyl anthranilate synthesis in cultivated strawberry
Cited by: 24
Author(s): Jérémy Pillet, Alan H. Chambers, Christopher R. Barbey, Zhilong Bao, Anne Plotto, Jinhe Bai, Michael L. Schwieterman, Timothy S. Johnson, Benjamin J. Harrison, Vance M. Whitaker, Thomas A. Colquhoun, Kevin M. Folta
Software Mentions: 1
Published: over 7 years ago

10.1186/s12917-016-0830-5

Evidence for the presence of African swine fever virus in an endemic region of Western Kenya in the absence of any reported outbreak
Cited by: 28
Author(s): Lian F. Thomas, Richard P. Bishop, Cynthia Onzere, Michael T. McIntosh, Karissa A. Lemire, William A. de Glanville, Elizabeth A. J. Cook, Eric M. Fèvre
Software Mentions: 1
Published: over 8 years ago

10.3897/BDJ.2.e4221

A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control
Cited by: 32
Author(s): Mathew Cherian, Anton Güntsch, Matthias Obst, Saverio Vicario, Robert Haines, Alan Williams, Yde de Jong, Carole Goble
Software Mentions: 1
Published: about 10 years ago

10.1093/bioinformatics/bty045

JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure
Cited by: 21
Author(s): Peter V Troshin, James B. Procter, Alexander Sherstnev, Daniel L. Barton, Fábio Madeira, Geoffrey J. Barton
Software Mentions: 1
Published: almost 7 years ago

10.1155/2020/2316369

Miniaturized Water-Jet Ultrasound Indentation System for Quantitative Assessment of Articular Cartilage Degeneration: A Validation Study
Cited by: 0
Author(s): Y. P. Huang, Yongping Zheng
Software Mentions: 1
Published: over 4 years ago

10.1155/2014/352862

Clonality and Resistome Analysis of KPC-ProducingKlebsiella pneumoniaeStrain Isolated in Korea Using Whole Genome Sequencing
Cited by: 23
Author(s): Yangsoon Lee, Bong Soo Kim, Jongsik Chun, Ji Hyun Yong, Yeong Seon Lee, Jung Sik Yoo, Dongeun Yong, Seong Geun Hong, Roshan D’Souza, Kenneth S. Thomson, Kyungwon Lee
Software Mentions: 1
Published: almost 11 years ago

10.3390/ma12091545

Reliability-Based Low Fatigue Life Analysis of Turbine Blisk with Generalized Regression Extreme Neural Network Method
Cited by: 26
Author(s): Chunyi Zhang, Jingshan Wei, Hui-Zhe Jing, Chengwei Fei, Wenzhong Tang
Software Mentions: 1
Published: over 5 years ago

10.1128/MRA.00315-20

Draft Genome Sequences of Two Acidophilic, Mesophilic Verrucomicrobial Methanotrophs Contain Only One pmoCAB Operon
Cited by: 1
Author(s): Geert Cremers, Arjan Pol, Mike S. M. Jetten, Huub J. M. Op den Camp
Software Mentions: 1
Published: over 4 years ago

Projects: pypi: workbench

Papers Mentioning workbench 139