Ecosyste.ms: Papers

10.1186/s12859-014-0389-8

VTBuilder: a tool for the assembly of multi isoform transcriptomes
Cited by: 29
Author(s): John Archer, Gareth Whiteley, Nicholas R. Casewell, Robert A. Harrison, Simon C. Wagstaff
Software Mentions: 1
Published: about 10 years ago

10.1186/1742-4682-8-5

Disruption of cell wall fatty acid biosynthesis in Mycobacterium tuberculosis using a graph theoretic approach
Cited by: 4
Author(s): Veeky Baths, Utpal Roy, Talvinder Singh
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0013326

A Minimal Model for Multiple Epidemics and Immunity Spreading
Cited by: 24
Author(s): Kim Sneppen, Ala Trusina, Mogens H. Jensen, Stefan Bornholdt
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0160315

Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms
Cited by: 17
Author(s): Jhih-Wei Jian, Elumalai Pavadai, Thejkiran Pitti, Cheng-Shong Wu, Keng‐Chang Tsai, Jeng-Yih Chang, Hung-Pin Peng, An‐Suei Yang
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.22457

Characterization of miRNA and their target gene during chicken embryo skeletal muscle development
Cited by: 20
Author(s): Endashaw Jebessa, Hongjia Ouyang, Bahareldin Ali Abdalla, Zhenhui Li, A. Y. Abdullahi, Liu Qing-shen, Qinghua Nie, Xiquan Zhang
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0044631

Integrating Constitutive Gene Expression and Chemoactivity: Mining the NCI60 Anticancer Screen
Cited by: 10
Author(s): David G. Covell
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-12-S13-S6

PB1-F2 Finder: scanning influenza sequences for PB1-F2 encoding RNA segments
Cited by: 4
Author(s): David S. DeLuca, Derin B. Keskin, Guanglan Zhang, Ellis L. Reinherz, Vladimir Brusic
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2105-6-136

Cited by: 38
Author(s): Taijiao Jiang, Amy E. Keating
Software Mentions: 1
Published: almost 20 years ago

10.1186/s12859-015-0798-3

miRA: adaptable novel miRNA identification in plants using small RNA sequencing data
Cited by: 73
Author(s): M. Evers, Michael Huttner, Anne Dueck, Gunter Meister, Julia C. Engelmann
Software Mentions: 1
Published: about 9 years ago

10.3390/cells10051166

Small-RNA Sequencing Reveals Altered Skeletal Muscle microRNAs and snoRNAs Signatures in Weanling Male Offspring from Mouse Dams Fed a Low Protein Diet during Lactation
Cited by: 3
Author(s): Ioannis Kanakis, Moussira Alameddine, Leighton Folkes, Simon Moxon, Ioanna Myrtziou, Susan E. Ozanne, Mandy J. Peffers, Katarzyna Goljanek‐Whysall, Aphrodite Vasilaki
Software Mentions: 1
Published: over 3 years ago

10.1016/j.dib.2018.12.038

Data on Vulnerability Detection in Android
Cited by: 12
Author(s): Shivi Garg, Niyati Baliyan
Software Mentions: 1
Published: almost 6 years ago

10.1007/s00125-020-05128-1

One-leg inactivity induces a reduction in mitochondrial oxidative capacity, intramyocellular lipid accumulation and reduced insulin signalling upon lipid infusion: a human study with unilateral limb suspension
Cited by: 15
Author(s): Lena Bilet, Esther Phielix, Tineke van de Weijer, Anne Gemmink, Madeleen Bosma, Esther Moonen‐Kornips, Johanna A. Jörgensen, Gert Schaart, Dongyan Zhang, Kenneth Meijer, Maria T. E. Hopman, Matthijs K. C. Hesselink, D.M. Ouwens, Gerald I. Shulman, Vera B. Schrauwen‐Hinderling, Patrick Schrauwen
Software Mentions: 1
Published: over 4 years ago

10.1186/1746-1596-9-S1-S3

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images
Cited by: 20
Author(s): David Ameisen, Christophe Deroulers, Valérie Perrier, Fatiha Bouhidel, Maxime Battistella, Luc Legrès, Anne Janin, Philippe Bertheau, Jean-Baptiste Yunès
Software Mentions: 1
Published: about 10 years ago

10.1002/ece3.3208

Diversity and distribution of genetic variation in gammarids: Comparing patterns between invasive and non‐invasive species
Cited by: 16
Author(s): Miguel Baltazar‐Soares, Filipa Paiva, Yiyong Chen, Aibin Zhan, Elizabeta Briski
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-11-478

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development
Cited by: 10
Author(s): Sébastien Terrat, Éric Peyretaillade, Olivier Gonçalves, Éric Dugat-Bony, Fabrice N. Gravelat, Anne Moné, Corinne Biderre‐Petit, Delphine Boucher, Julien Troquet, Pierre Peyret
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2105-15-258

GMOseek: a user friendly tool for optimized GMO testing
Cited by: 20
Author(s): Dany Morisset, Petra Kralj Novak, Darko Zupanič, Kristina Gruden, Nada Lavrač, Jana Žel
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-7-531

The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases
Cited by: 15
Author(s): Gully A. P. C. Burns, Wei-Cheng Cheng, Richard H. Thompson, Larry W. Swanson
Software Mentions: 1
Published: about 18 years ago

10.1186/1476-072X-7-22

Using GPS-enabled cell phones to track the travel patterns of adolescents
Cited by: 121
Author(s): Sarah E. Wiehe, Aaron E. Carroll, Gilbert C. Liu, Kelly L. Haberkorn, Shawn C. Hoch, Jeffery S. Wilson, J.Dennis Fortenberry
Software Mentions: 1
Published: almost 17 years ago

10.3389/fpls.2015.01101

A Comprehensive Approach to Assess Arabidopsis Survival Phenotype in Water-Limited Condition Using a Non-invasive High-Throughput Phenomics Platform
Cited by: 8
Author(s): Emilio Vello, Akiko Tomita, Amadou Oury Diallo, Thomas E. Bureau
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2105-6-221

GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures
Cited by: 23
Author(s): Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
Software Mentions: 1
Published: about 19 years ago

10.1007/s12553-016-0169-8

Automatic classification of histopathological diagnoses for building a large scale tissue catalogue
Cited by: 1
Author(s): Robert Reihs, Heimo Müller, Stefan Sauer, Kurt Zatloukal
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-12-484

Morphometic analysis of TCGA glioblastoma multiforme
Cited by: 47
Author(s): Hang Chang, Gerald Fontenay, Ju Han, Ge Cong, Frederick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin
Software Mentions: 1
Published: about 13 years ago

10.1016/j.heliyon.2019.e01998

A real-time virtual machine for task placement in loosely-coupled computer systems
Cited by: 1
Author(s): Mohamed O. Elsedfy, Wael A. Murtada, Ezz F. Abdulqawi, Mahmoud Gadallah
Software Mentions: 1
Published: over 5 years ago

10.1186/s12981-016-0125-8

Infection of rhesus macaques with a pool of simian immunodeficiency virus with the envelope genes from acute HIV-1 infections
Cited by: 4
Author(s): Kendall Krebs, Mingxing Tian, Mohammed Asmal, Binhua Ling, Kenneth N. Nelson, Kenneth R. Henry, Richard Gibson, Yuejin Li, Wenling Han, Robin J. Shattock, Ronald S. Veazey, Norman L. Letvin, Eric J. Arts, Yong Gao
Software Mentions: 1
Published: about 8 years ago

10.1186/1758-2946-1-16

Shape: automatic conformation prediction of carbohydrates using a genetic algorithm
Cited by: 23
Author(s): Jimmy Rosen, Laurence Miguet, Serge Pérez
Software Mentions: 1
Published: about 15 years ago

10.1186/2043-9113-3-7

TUMIR: an experimentally supported database of microRNA deregulation in various cancers
Cited by: 11
Author(s): Lei Dong, Min Luo, Fang Wang, Ruoyu Zhang, Tingting Li, Jia Yu
Software Mentions: 1
Published: almost 12 years ago

10.1155/2013/495134

The Development of Models Based on Linear and Nonlinear Multivariate Methods to Predict ADME/PK Properties Using Physicochemical Properties of Kinase, Protease Inhibitors, and GPCR Antagonists
Cited by: 0
Author(s): Deepu Bakasta, M. G. Shambhu
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-11-381

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results
Cited by: 124
Author(s): Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, Chi Zhang
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-7-103

SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools
Cited by: 15
Author(s): Arthur Chun-Chieh Shih, D. T. Lee, Laurent Lin, Chin Lin Peng, Shiang Heng Chen, Yu Wei Wu, Chun Yi Wong, Meng Yuan Chou, Tze Chang Shiao, Mu Fen Hsieh
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2105-10-302

Prediction of antigenic epitopes on protein surfaces by consensus scoring
Cited by: 94
Author(s): Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias
Software Mentions: 1
Published: about 15 years ago

10.1038/srep18209

Increased co-expression of genes harboring the damaging de novo mutations in Chinese schizophrenic patients during prenatal development
Cited by: 38
Author(s): Qiang Wang, Miaoxin Li, Zhenxing Yang, Xun Hu, Hei-Man Wu, Peiyan Ni, Hongyan Ren, Wei Deng, Mingli Li, Xiaohong Ma, Wanjun Guo, Liansheng Zhao, Yingcheng Wang, Bo Xiang, Wei Lei, Pak C. Sham, Tao Li
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-019-42858-8

CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing
Cited by: 16
Author(s): John Markham, Satwica Yerneni, Georgina L Ryland, Huei San Leong, Andrew Fellowes, Ella R. Thompson, Wasanthi De Silva, Amit Kumar, Richard Lupat, Jason Li, Jason Ellul, Stephen B. Fox, Michael Dickinson, Anthony T. Papenfuss, Piers Blombery
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-7-207

Development and implementation of an algorithm for detection of protein complexes in large interaction networks
Cited by: 429
Author(s): Md. Altaf-Ul-Amin, Yoko Shinbo, Kenji Mihara, Ken Kurokawa, Shigehiko Kanaya
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2105-7-S4-S25

SVM Classifier – a comprehensive java interface for support vector machine classification of microarray data
Cited by: 38
Author(s): Mehdi Pirooznia, Youping Deng
Software Mentions: 1
Published: about 18 years ago

10.3892/ijmm.2013.1582

Comparison of gene expression profiles and related pathways in chronic thromboembolic pulmonary hypertension
Cited by: 17
Author(s): Song Gu, Pixiong Su, Jun Yan, Xitao Zhang, Xiangguang An, Jie Gao, Rui Xin, Yan Liu
Software Mentions: 1
Published: almost 11 years ago

10.1155/2013/736386

TIPdb: A Database of Anticancer, Antiplatelet, and Antituberculosis Phytochemicals from Indigenous Plants in Taiwan
Cited by: 33
Author(s): Ying Lin, Chia-Chi Wang, Ih Sheng Chen, Jhao Liang Jheng, Jih Heng Li, Chun Wei Tung
Software Mentions: 1
Published: almost 12 years ago

10.1155/2015/545308

Composition of Web Services Using Markov Decision Processes and Dynamic Programming
Cited by: 11
Author(s): Víctor Uc-Cetina, Francisco Moo-Mena, Rafael Hernández-Ucán
Software Mentions: 1
Published: almost 10 years ago

10.3390/s130709183

Optimal Placement of Accelerometers for the Detection of Everyday Activities
Cited by: 308
Author(s): Ian Cleland, Basel Kikhia, Chris Nugent, Andrey Boytsov, Josef Hallberg, Kåre Synnes, Sally McClean, Dewar Finlay
Software Mentions: 1
Published: over 11 years ago

10.3390/s141222372

A Cloud-Based Car Parking Middleware for IoT-Based Smart Cities: Design and Implementation
Cited by: 146
Author(s): Zhanlin Ji, Иван Ганчев, Máirtín O’Dróma, Li Zhao, Xueji Zhang
Software Mentions: 1
Published: about 10 years ago

10.1099/ijsem.0.001755

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies
Cited by: 5,104
Author(s): Seok Hwan Yoon, Seung Min Ha, Soon‐Jae Kwon, Jeongmin Lim, Yeseul Kim, Hyungseok Seo, Jongsik Chun
Software Mentions: 1
Published: over 7 years ago

10.1093/bioinformatics/btw096

Reaction Decoder Tool (RDT): extracting features from chemical reactions
Cited by: 70
Author(s): Syed Asad Rahman, Gilliean Torrance, Lorenzo Baldacci, Sergio Martínez Cuesta, Franz Fenninger, Nimish Gopal, Saket Choudhary, John W. May, Gemma L. Holliday, Christoph Steinbeck, Janet M. Thornton
Software Mentions: 1
Published: almost 9 years ago

10.6026/97320630013073

Analysis of EAWAG-BBD pathway prediction system for the identification of malathion degrading microbes
Cited by: 23
Author(s): Subramaniam Sivakumar, Palanivel Anitha, Balsubramanian Ramesh, Gopal Suresh
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-12-52

RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis
Cited by: 17
Author(s): Barry R. Zeebèrg, Hongfang Liu, A Kahn, Martin Ehler, Vinodh N. Rajapakse, Robert F. Bonner, Jacob D. Brown, Brian P. Brooks, Vladimir Larionov, William C. Reinhold, John N. Weinstein, Yves Pommier
Software Mentions: 1
Published: almost 14 years ago

10.1186/1475-925X-10-62

Pulsatile ex vivo perfusion of human saphenous vein grafts under controlled pressure conditions increases MMP-2 expression
Cited by: 18
Author(s): Sara Dummler, Stefan Eichhorn, Christian Tesche, Ulrich Schreiber, Bernhard Voß, Marcus-André Deutsch, Hans Hauner, Harald Lahm, Rüdiger Lange, Markus Krane
Software Mentions: 1
Published: almost 14 years ago

10.3390/s17102408

Command Disaggregation Attack and Mitigation in Industrial Internet of Things
Cited by: 12
Author(s): Peng Xun, Peidong Zhu, Yifan Hu, Pengshuai Cui, Yan Zhang
Software Mentions: 1
Published: about 7 years ago

10.3390/microorganisms8081132

Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents
Cited by: 10
Author(s): Maxime Allioux, Stéven Yvenou, G. B. Slobodkina, A. I. Slobodkin, Zongze Shao, Mohamed Jebbar, Karine Alain
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms8121876

Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics
Cited by: 4
Author(s): Karim Hayoun, Emilie Geersens, Cédric Christian Laczny, Rashi Halder, Carmen Lázaro Sánchez, Abhijit Manna, Françoise Bringel, Michaël Ryckelynck, Paul Wilmes, Emilie Muller, Béatrice Alpha-Bazin, Jean Armengaud, Stéphane Vuilleumier
Software Mentions: 1
Published: about 4 years ago

10.1186/1756-0500-4-384

Medusa: A tool for exploring and clustering biological networks
Cited by: 51
Author(s): Georgios A. Pavlopoulos, Sean D. Hooper, Alejandro Sifrim, Reinhard Schneider, Jan Aerts
Software Mentions: 1
Published: about 13 years ago

10.1186/1743-422X-4-123

Viroporin potential of the lentivirus lytic peptide (LLP) domains of the HIV-1 gp41 protein
Cited by: 31
Author(s): Joshua M. Costin, Joshua M. Rausch, Robert F. Garry, William C. Wimley
Software Mentions: 1
Published: almost 18 years ago

10.1186/1756-0500-1-67

GPCRTree: online hierarchical classification of GPCR function
Cited by: 39
Author(s): Matthew N. Davies, Andrew Secker, Mark Halling‐Brown, David S. Moss, Alex A. Freitas, Jon Timmis, Edward Clark, Darren R. Flower
Software Mentions: 1
Published: almost 17 years ago

10.1186/s13007-017-0174-6

A nondestructive method to estimate the chlorophyll content of Arabidopsis seedlings
Cited by: 73
Author(s): Ying Liang, Daisuke Urano, Kang Liao, Tyson L. Hedrick, Yajun Gao, Alan M. Jones
Software Mentions: 1
Published: over 7 years ago

10.1186/s13104-015-1190-0

BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services
Cited by: 3
Author(s): Henrique Velloso, Ricardo Assunção Vialle, José Miguel Ortega
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pcbi.1002800

Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures
Cited by: 15
Author(s): Niels Röckendorf, Markus Borschbach, Andreas Frey
Software Mentions: 1
Published: almost 12 years ago

10.1177/2041669515593019

Cognitive Bias for Learning Speech Sounds From a Continuous Signal Space Seems Nonlinguistic
Cited by: 3
Author(s): Sabine van der Ham, Bart de Boer
Software Mentions: 1
Published: about 9 years ago

10.3390/ijerph16193593

Principal Component Analysis of Categorized Polytomous Variable-Based Classification of Diabetes and Other Chronic Diseases
Cited by: 11
Author(s): Musa Uba Muhammad, Jiadong Ren, Noman Sohail Muhammad, Munawar Hussain, Muhammad Irshad
Software Mentions: 1
Published: about 5 years ago

10.1186/s40679-016-0026-x

Structural damage reduction in protected gold clusters by electron diffraction methods
Cited by: 5
Author(s): Eduardo Ortega, Arturo Ponce, Ulises Santiago, Diego Alducin, Alfredo Benítez-Lara, Germán Plascencia-Villa, Miguel José–Yacamán
Software Mentions: 1
Published: about 8 years ago

10.1186/1472-6947-6-12

Development and evaluation of an open source software tool for deidentification of pathology reports
Cited by: 93
Author(s): Bruce A. Beckwith, Rajeshwarri Mahaadevan, Ulysses J. Balis, Frank C. Kuo
Software Mentions: 1
Published: over 18 years ago

10.1515/jib-2020-0033

BioDWH2: an automated graph-based data warehouse and mapping tool
Cited by: 8
Author(s): Marcel Friedrichs
Software Mentions: 1
Published: almost 4 years ago

10.3390/s20010207

Data Query Mechanism Based on Hash Computing Power of Blockchain in Internet of Things
Cited by: 70
Author(s): Yongjun Ren, Fujian Zhu, Pradip Kumar Sharma, Tian Wang, Jin Wang, Osama Alfarraj, Amr Tolba
Software Mentions: 1
Published: almost 5 years ago

10.1186/1755-8794-3-43

LNCaP Atlas: Gene expression associated with in vivoprogression to castration-recurrent prostate cancer
Cited by: 71
Author(s): Tammy L Romanuik, Gang Wang, Olena Morozova, Allen Delaney, Marco A. Marra, Marianne D. Sadar
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0154324

Converging Work-Talk Patterns in Online Task-Oriented Communities
Cited by: 9
Author(s): Qi Xuan, Prémkumar Dévanbu, Vladimir Filkov
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0074918

Assessing Species Distribution Using Google Street View: A Pilot Study with the Pine Processionary Moth
Cited by: 56
Author(s): Jérôme Rousselet, Charles-Edouard Imbert, Anissa Dekri, Jacques García, Francis Goussard, B. Vincent, Olivier Denux, Christelle Robinet, Franck Dorkeld, Alain Roques, Jean‐Pierre Rossi
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2105-13-21

Fast automatic quantitative cell replication with fluorescent live cell imaging
Cited by: 3
Author(s): Ching-Wei Wang
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2156-9-13

Prevalence of common disease-associated variants in Asian Indians
Cited by: 39
Author(s): Trevor J. Pemberton, Niyati Mehta, David B. Witonsky, Anna Di Rienzo, Hooman Allayee, David V. Conti, Pragna I. Patel
Software Mentions: 1
Published: almost 17 years ago