Ecosyste.ms: Papers

10.1186/s12859-015-0453-z

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
Cited by: 41
Author(s): Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido
Software Mentions: 13
Published: almost 10 years ago

10.1155/2021/6616908

Interpreting the Molecular Mechanisms of Yinchenhao Decoction on Hepatocellular Carcinoma through Absorbed Components Based on Network Pharmacology
Cited by: 5
Author(s): Jijia Sun, Tao Han, Tao Yang, Yunhui Chen, Jihan Huang
Software Mentions: 11
Published: over 3 years ago

10.1093/gigascience/giz147

Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa
Cited by: 16
Author(s): Miriam Payá‐Milans, Laura Poza‐Viejo, Patxi San Martín-Úriz, David Lara‐Astiaso, Mark D. Wilkinson, Pedro Crevillén
Software Mentions: 8
Published: almost 5 years ago

10.3390/ijms22094917

The Cellular Composition of Bovine Coccygeal Intervertebral Discs: A Comprehensive Single-Cell RNAseq Analysis
Cited by: 24
Author(s): Martina Caliò, Benjamin Gantenbein, Marcel Egli, Lucy Poveda, Fabian Ille
Software Mentions: 7
Published: over 3 years ago

10.15252/embj.2020107100

<i>De novo</i> DNA methylation controls neuronal maturation during adult hippocampal neurogenesis
Cited by: 17
Author(s): Sara Zocher, Rupert W. Overall, Gabriel Berdugo-Vega, Nicole Rund, Anne Karasinsky, Vijay S. Adusumilli, Christina Steinhauer, Sina Scheibenstock, Kristian Händler, Joachim L. Schultze, Federico Calegari, Gerd Kempermann
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1007337

Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets
Cited by: 15
Author(s): M. Vijayabaskar, Debbie K. Goode, Nadine Obier, Monika Lichtinger, Amber M.L. Emmett, Fatin N Zainul Abidin, Nisar Ahmed Shar, Rebecca Hannah, Salam A. Assi, Michael Lie-A-Ling, Berthold Göttgens, Georges Lacaud, Valérie Kouskoff, Constanze Bonifer, David R. Westhead
Software Mentions: 6
Published: about 5 years ago

10.3389/fpls.2021.675208

Differential Regulation of Maize and Sorghum Orthologs in Response to the Fungal Pathogen Exserohilum turcicum
Cited by: 5
Author(s): Pragya Adhikari, Santiago X. Mideros, Tiffany M. Jamann
Software Mentions: 6
Published: over 3 years ago

10.3390/genes11040434

Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups
Cited by: 5
Author(s): Daniil S. Wiebe, N. A. Omelyanchuk, Aleksey M. Mukhin, Ivo Große, Sergey A. Lashin, Elena V. Zemlyanskaya, В. В. Миронова
Software Mentions: 6
Published: over 4 years ago

10.1093/molbev/msv282

Population Structure Shapes Copy Number Variation in Malaria Parasites
Cited by: 43
Author(s): Ian H. Cheeseman, Becky A. Miller, John C. Tan, Aiping Tan, Shalini Nair, Standwell C. Nkhoma, Marcos De Donato, Hectorina Rodulfo, Arjen M. Dondorp, OraLee H. Branch, Lastenia Ruiz Mesía, Paul N. Newton, Mayfong Mayxay, Alfred Amambua-Ngwa, David J. Conway, François Nosten, Michael T. Ferdig, Tim Anderson
Software Mentions: 5
Published: almost 9 years ago

10.1155/2021/6641838

Analysis of Molecular Mechanism of Erxian Decoction in Treating Osteoporosis Based on Formula Optimization Model
Cited by: 22
Author(s): Lang Yang, Liuyi Fan, Kexin Wang, Yu-peng Chen, Liuqin Liang, Xuemei Qin, Aiping Lü, Peng Cao, Bin Yu, Daogang Guan, Junxiang Peng
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0106298

Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines
Cited by: 56
Author(s): Montiago X. LaBute, Xiaohua Zhang, Jason Lenderman, Brian J. Bennion, Sergio E. Wong, Felice C. Lightstone
Software Mentions: 5
Published: about 10 years ago

10.3389/fgene.2020.00654

Gene Set Analysis: Challenges, Opportunities, and Future Research
Cited by: 98
Author(s): Farhad Maleki, Katie Ovens, Daniel J. Hogan, Anthony Kusalik
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-017-1586-z

MOST: most-similar ligand based approach to target prediction
Cited by: 25
Author(s): Tao Huang, Hong Mi, Chengyuan Lin, Ling Zhao, Linda L. D. Zhong, Fengbin Liu, Ge Zhang, Aiping Lu, Zhaoxiang Bian
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0151697

Comparative RNA-Seq Analysis Reveals That Regulatory Network of Maize Root Development Controls the Expression of Genes in Response to N Stress
Cited by: 19
Author(s): Xiujing He, Hui Ma, Xing Zhao, Shujun Nie, Yuhua Li, Zhiming Zhang, Yaou Shen, Qi Chen, Yanli Lu, Hai Long, Shufeng Zhou, Shibin Gao, Guangtang Pan, Hung-Ching Lin
Software Mentions: 4
Published: over 8 years ago

10.3390/molecules22071128

DeCAF—Discrimination, Comparison, Alignment Tool for 2D PHarmacophores
Cited by: 5
Author(s): Marta M. Stepniewska-Dziubinska, Piotr Zielenkiewicz, Paweł Siedlecki
Software Mentions: 4
Published: over 7 years ago

10.3390/molecules24213942

A Chemometric Analysis of Deep-Sea Natural Products
Cited by: 16
Author(s): Lisa I. Pilkington
Software Mentions: 4
Published: about 5 years ago

10.1016/j.mex.2019.100775

PHARMIP: An insilico method to predict genetics that underpin adverse drug reactions
Cited by: 6
Author(s): Ahmad Zidan, Eman A. Saad, Nasser E. Ibrahim, Amal Mahmoud, Medhat H. Hashem, Alaa A. Hemeida
Software Mentions: 4
Published: almost 5 years ago

10.3390/plants10061240

Cleaning the Medicago Microarray Database to Improve Gene Function Analysis
Cited by: 1
Author(s): Francesca Marzorati, Chu Wang, Giulio Pavesi, Luca Mizzi, Piero Morandini
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pcbi.1004153

Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens
Cited by: 61
Author(s): Yu‐Chen Lo, Silvia Senese, Chien-Ming Li, Qi Hu, Yong Huang, Robert Damoiseaux, Jorge Z. Torres
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2014.00035

The analytical landscape of static and temporal dynamics in transcriptome data
Cited by: 26
Author(s): Sangwon Oh, Seongho Song, Nupur Dasgupta, Gregory A. Grabowski
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12859-017-1772-z

Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum
Cited by: 13
Author(s): Daniel Amsel, Andreas Vilcinskas, André Billion
Software Mentions: 4
Published: over 7 years ago

10.1093/bib/bbv037

Building a virtual ligand screening pipeline using free software: a survey
Cited by: 68
Author(s): Enrico Glaab
Software Mentions: 4
Published: over 9 years ago

10.3389/fcell.2021.694633

Bioinformatic Analyses Identify a Prognostic Autophagy-Related Long Non-coding RNA Signature Associated With Immune Microenvironment in Diffuse Gliomas
Cited by: 10
Author(s): Shengchao Xu, Lu Tang, Zhixiong Liu, Kui Yang, Quan Cheng
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pbio.1002576

Prefrontal Markers and Cognitive Performance Are Dissociated during Progressive Dopamine Lesion
Cited by: 8
Author(s): Charles R.E. Wilson, Julien Vezoli, Frederic M. Stoll, Maïlys C. M. Faraut, Vincent Leviel, Kenneth Knoblauch, Emmanuel Procyk
Software Mentions: 3
Published: about 8 years ago

10.1038/srep27357

Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development
Cited by: 16
Author(s): Lorenzo Ricci, Ankita Chaurasia, Pascal Lapébie, Philippe Dru, Rebecca R. Helm, Richard R. Copley, Stefano Tiozzo
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms21155248

Drug Discovery Targeting the Disorder-To-Order Transition Regions through the Conformational Diversity Mimicking and Statistical Analysis
Cited by: 5
Author(s): Insung Na, Sungwoo Choi, Sang Jun Son, Vladimir N. Uversky, Chul Geun Kim
Software Mentions: 3
Published: over 4 years ago

10.3390/plants8090335

Infections of the Xylella fastidiosa subsp. pauca Strain “De Donno” in Alfalfa (Medicago sativa) Elicits an Overactive Immune Response
Cited by: 10
Author(s): Raied Abou Kubaa, Annalisa Giampetruzzi, Giuseppe Altamura, María Saponari, P. Saldarelli
Software Mentions: 3
Published: about 5 years ago

10.1186/1758-2946-6-33

In Silicotarget fishing: addressing a “Big Data” problem by ligand-based similarity rankings with data fusion
Cited by: 46
Author(s): Xian Liu, Xu Yue, Shanshan Li, Yulan Wang, Jiantang Peng, Cheng Luo, Xiaomin Luo, Mingyue Zheng, Kaixian Chen, Hualiang Jiang
Software Mentions: 3
Published: over 10 years ago

10.1186/s40360-017-0128-7

Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects
Cited by: 42
Author(s): Matthieu Chartier, Louis–Philippe Morency, María Inés Zylber, Rafaël Najmanovich
Software Mentions: 3
Published: over 7 years ago

10.3389/fdata.2019.00025

Novel Computational Approach to Predict Off-Target Interactions for Small Molecules
Cited by: 50
Author(s): Mohan Rao, Rishi Gupta, Michael J. Liguori, Mufeng Hu, Xin Huang, Srinivasa R. Mantena, Scott W. Mittelstadt, Eric A.G. Blomme, Terry R. Van Vleet
Software Mentions: 3
Published: over 5 years ago

10.1186/s12940-017-0265-x

Comparison of methods for calculating the health costs of endocrine disrupters: a case study on triclosan
Cited by: 1
Author(s): Radka Přichystalová, Jean-Baptiste Fini, Leonardo Trasande, Martine Bellanger, Barbara Demeneix, Laura Maxim
Software Mentions: 3
Published: over 7 years ago

10.1093/database/bav087

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME
Cited by: 13
Author(s): George Nicola, Michael R. Berthold, Michael Hedrick, Michael K. Gilson
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0094031

Disruption of the Homogentisate Solanesyltransferase Gene Results in Albino and Dwarf Phenotypes and Root, Trichome and Stomata Defects in Arabidopsis thaliana
Cited by: 12
Author(s): Yuehui Chao, Junmei Kang, Tiejun Zhang, Qingchuan Yang, Margaret Y. Gruber, Yan Sun
Software Mentions: 3
Published: over 10 years ago

10.3389/fpls.2020.00346

Exploration of the Yield Potential of Mesoamerican Wild Common Beans From Contrasting Eco-Geographic Regions by Nested Recombinant Inbred Populations
Cited by: 14
Author(s): Jorge C. Berny Mier y Teran, Enéas Ricardo Konzen, Antonia Palkovic, Siu Mui Tsai, Paul Gepts
Software Mentions: 3
Published: over 4 years ago

10.1038/srep28288

Function-specific virtual screening for GPCR ligands using a combined scoring method
Cited by: 71
Author(s): Albert J. Kooistra, Henry F. Vischer, Daniel A. McNaught-Flores, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf
Software Mentions: 3
Published: over 8 years ago

10.1155/2020/6628641

An Investigation of the Molecular Mechanisms Underlying the Analgesic Effect of Jakyak-Gamcho Decoction: A Network Pharmacology Study
Cited by: 8
Author(s): Ho-Sung Lee, In-Hee Lee, Kyung‐Won Kang, Sang‐In Park, Tae-Wook Kwon, Ho-Sung Lee
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pntd.0009813

Morphological, molecular and MALDI-TOF MS identification of ticks and tick-associated pathogens in Vietnam
Cited by: 9
Author(s): Ly Na Huynh, Adama Zan Diarra, Quang Luan Pham, Nhiem Le-Viet, Jean-Michel Bérenger, Van Hoang Ho, Xuan Quang Nguyen, Philippe Parola
Software Mentions: 3
Published: about 3 years ago

10.1186/s13058-014-0482-y

A novel phosphatidylinositol 3-kinase (PI3K) inhibitor directs a potent FOXO-dependent, p53-independent cell cycle arrest phenotype characterized by the differential induction of a subset of FOXO-regulated genes
Cited by: 29
Author(s): Richard Hill, Ravi Kiran Reddy Kalathur, Sergio Callejas, Laura Colaço, Ricardo Brandão, Beatriz G. Serelde, Antonio Cebriá, Carmen Blanco‐Aparicio, Joaquı́n Pastor, Matthias E. Futschik, Ana Dopazo, Wolfgang Link
Software Mentions: 3
Published: almost 10 years ago

10.1093/database/bay141

EnhancerDB: a resource of transcriptional regulation in the context of enhancers
Cited by: 24
Author(s): Ran Kang, Yiming Zhang, Qingqing Huang, Meng Ji, Ruofan Ding, Yunjian Chang, Lili Xiong, Zhiyun Guo
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41431-019-0557-4

The paternal and maternal genetic history of Vietnamese populations
Cited by: 20
Author(s): Enrico Macholdt, Liliana Arias, Nguyễn Thùy Dương, Nguyễn Đăng Tôn, Nguyễn Văn Phòng, Roland Schröder, Brigitte Pakendorf, Nông Văn Hải, Mark Stoneking
Software Mentions: 3
Published: almost 5 years ago

10.1098/rsif.2018.0413

Biarticular muscles in light of template models, experiments and robotics: a review
Cited by: 26
Author(s): Christian Schumacher, Maziar Ahmad Sharbafi, André Seyfarth, Christian Rode
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-021-07640-z

Buffalo sperm surface proteome profiling reveals an intricate relationship between innate immunity and reproduction
Cited by: 6
Author(s): Vipul Batra, Vanya Bhushan, Syed Azmal Ali, Parul Sarwalia, Ankit Pal, Seema Karanwal, Subhash Solanki, A. Kumaresan, Rakesh Kumar, Tirtha Kumar Datta
Software Mentions: 2
Published: over 3 years ago

10.18632/oncotarget.18473

NiaoDuQing granules relieve chronic kidney disease symptoms by decreasing renal fibrosis and anemia
Cited by: 28
Author(s): Xu Wang, Suyun Yu, Qi Jia, Li-Chuan Chen, Jinqiu Zhong, Yan-Hong Pan, Pengfei Shen, Yuchen Shen, Siliang Wang, Zhonghong Wei, Yuzhu Cao, Yin Lu
Software Mentions: 2
Published: over 7 years ago

10.1002/minf.201200141

Chemically Advanced Template Search (CATS) for Scaffold‐Hopping and Prospective Target Prediction for ‘Orphan’ Molecules
Cited by: 125
Author(s): Michael Reutlinger, Christian P. Koch, Daniel Reker, Nickolay Todoroff, Petra Schneider, Tiago Rodrigues, Gisbert Schneider
Software Mentions: 2
Published: almost 12 years ago

10.3390/ijms21051868

Reveals of New Candidate Active Components in Hemerocallis Radix and Its Anti-Depression Action of Mechanism Based on Network Pharmacology Approach
Cited by: 23
Author(s): Hsin-Yi Lin, Jen-Chieh Tsai, Lung‐Yuan Wu, Wen-Huang Peng
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21197102

Finding New Molecular Targets of Familiar Natural Products Using In Silico Target Prediction
Cited by: 10
Author(s): Fabian Mayr, Gabriele Möller, Ulrike Garscha, Jana Fischer, Patricia Rodríguez Castaño, Silvia G. Inderbinen, Veronika Temml, Birgit Waltenberger, Stefan Schwaiger, Rolf W. Hartmann, Christian Gege, Stefan Martens, Alex Odermatt, Amit V. Pandey, Oliver Werz, Jerzy Adamski, Hermann Stuppner, Daniela Schuster
Software Mentions: 2
Published: about 4 years ago

10.1186/s12906-020-02900-z

Effect of Gallic acid and Myricetin on ovarian cancer models: a possible alternative antitumoral treatment
Cited by: 28
Author(s): Luis Varela-Rodríguez, Blanca Sánchez‐Ramírez, Verónica Ivonne Hernández‐Ramírez, Hugo Varela-Rodríguez, Rodrigo Daniel Castellanos-Mijangos, Carmen González-Horta, Bibiana Chávez‐Munguía, Patricia Talamás-Rohana
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms8040528

Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus
Cited by: 19
Author(s): Ángela Paulina Arce-Leal, Rocí­o Bautista, Edgar A. Rodríguez-Negrete, Miguel Ángel Manzanilla-Ramírez, José Joaquín Velázquez-Monreal, María Elena Santos-Cervantes, Jesús Méndez-Lozano, Carmen R. Beuzón, Eduardo R. Bejarano, Araceli G. Castillo, M. Gonzalo Claros, Norma Elena Leyva-López
Software Mentions: 2
Published: over 4 years ago

10.1186/s12870-021-02932-8

Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize
Cited by: 11
Author(s): Zhengjie Chen, Danling Tang, Jixing Ni, Peng Li, Le Wang, Jinhong Zhou, Chenyang Li, Hai Long, Lujiang Li, Jian Liu
Software Mentions: 2
Published: over 3 years ago

10.3390/ijerph18084073

Application of Combined Analyses of Stable Isotopes and Stomach Contents for Understanding Ontogenetic Niche Shifts in Silver Croaker (Pennahia argentata)
Cited by: 4
Author(s): Bong Kyu Choi, Won‐Seok Kim, Changwei Ji, Min-Seob Kim, Ihn–Sil Kwak
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-06335-4

Deficient glutamate biosynthesis triggers a concerted upregulation of ribosomal protein genes in Arabidopsis
Cited by: 9
Author(s): Tamara Muñoz-Nortes, José Manuel Pérez-Pérez, Raquel Sarmiento-Mañús, Héctor Candela, José Luis Micol
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0140507

Comparative De Novo Transcriptome Analysis of Fertilized Ovules in Xanthoceras sorbifolium Uncovered a Pool of Genes Expressed Specifically or Preferentially in the Selfed Ovule That Are Potentially Involved in Late-Acting Self-Incompatibility
Cited by: 20
Author(s): Quan Zhou, Yun Zheng
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-020-80780-6

Network pharmacology integrated molecular docking reveals the bioactive components and potential targets of Morinda officinalis–Lycium barbarum coupled-herbs against oligoasthenozoospermia
Cited by: 16
Author(s): Xue Bai, Yu-Wen Tang, Qiang Li, Yafei Chen, Dan Liú, Guimin Liu, Xiaolei Fan, Ru Ma, Shuyan Wang, Lingru Li, Kailin Zhou, Yanfei Zheng, Zhenquan Liu
Software Mentions: 2
Published: almost 4 years ago

10.3390/molecules25092135

Phenylpyrazalopyrimidines as Tyrosine Kinase Inhibitors: Synthesis, Antiproliferative Activity, and Molecular Simulations
Cited by: 10
Author(s): Bhupender S. Chhikara, Sajda Ashraf, Saghar Mozaffari, Nicole St. Jeans, Dindyal Mandal, Rakesh Tiwari, Zaheer Ul-Haq, Keykavous Parang
Software Mentions: 2
Published: over 4 years ago

10.1002/anie.201604336

Unveiling (−)‐Englerin A as a Modulator of L‐Type Calcium Channels
Cited by: 37
Author(s): Tiago Rodrigues, Florian Sieglitz, Víctor J. Somovilla, Pedro M. S. D. Cal, Antony Galione, Francisco Corzana, Gonçalo J. L. Bernardes
Software Mentions: 2
Published: over 8 years ago

10.1098/rspa.2020.0228

Wireless power distributions in multi-cavity systems at high frequencies
Cited by: 2
Author(s): Farasatul Adnan, Valon Blakaj, Sendy Phang, Thomas M. Antonsen, Stephen C. Creagh, Gabriele Gradoni, Gregor Tanner
Software Mentions: 2
Published: almost 4 years ago

10.3390/medicines4040093

Patient Safety in Complementary Medicine through the Application of Clinical Risk Management in the Public Health System
Cited by: 8
Author(s): Elio Rossi, Tommaso Bellandi, Marco Picchi, Sonia Baccetti, Maria Valeria Monechi, Vuono Catia, Federica Sabatini, Antonella Traversi, Mariella Di Stefano, Fabio Firenzuoli, Sara Albolino, Riccardo Tartaglia
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12900-018-0080-9

Molecular mechanisms underlying the impact of mutations in SOD1 on its conformational properties associated with amyotrophic lateral sclerosis as revealed with molecular modelling
Cited by: 16
Author(s): Н. А. Алемасов, Nikita V. Ivanisenko, Srinivasan Ramachandran, В. А. Иванисенко
Software Mentions: 2
Published: almost 7 years ago

10.1073/pnas.2019145118

Global hydroclimatic response to tropical volcanic eruptions over the last millennium
Cited by: 29
Author(s): Ernesto Tejedor, Nathan J. Steiger, Jason E. Smerdon, Roberto Serrano‐Notivoli, Mathias Vuille
Software Mentions: 2
Published: over 3 years ago

10.1186/s12966-016-0411-9

A quasi-experimental examination of how school-based physical activity changes impact secondary school student moderate- to vigorous- intensity physical activity over time in the COMPASS study
Cited by: 13
Author(s): Stephen Hunter, Scott T. Leatherdale, Kate Storey, Valerie Carson
Software Mentions: 2
Published: over 8 years ago

10.3390/ijerph18189454

The Potential of Strategic Environmental Assessment to Improve Urban Planning in Sierra Leone
Cited by: 1
Author(s): Prince T. Mabey, Wei Li, Abu James Sundufu, Akhtar Hussain Lashari
Software Mentions: 2
Published: about 3 years ago

10.3390/ph14090856

Hypoglycemic Activity of Aqueous Extract of Latex from Hancornia speciosa Gomes: A Study in Zebrafish and In Silico
Cited by: 1
Author(s): Rosana Tomazi, Ângela Costa Figueira, Adriana Maciel Ferreira, Diego Quaresma Ferreira, Gisele Custódio de Souza, Wandson Braamcamp de Souza Pinheiro, José Rodrigues Pinheiro Neto, Geilson Alcantara da Silva, Henrique Barros de Lima, Lorane Izabel da Silva Hage‐Melim, Arlindo César Matias Pereira, José Carlos Tavares Carvalho, Sheylla Susan Moreira da Silva de Almeida
Software Mentions: 2
Published: about 3 years ago

10.1186/1758-2946-3-40

Mining chemical information from open patents
Cited by: 29
Author(s): David Jessop, Sam Adams, Peter Murray‐Rust
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2229-13-153

Transcriptome analysis of heat stress response in switchgrass (Panicum virgatumL.)
Cited by: 82
Author(s): Yongfang Li, Yixing Wang, Yuhong Tang, Vijaya Gopal Kakani, Ramamurthy Mahalingam
Software Mentions: 2
Published: about 11 years ago

10.1186/1758-2946-3-43

The semantics of Chemical Markup Language (CML): dictionaries and conventions
Cited by: 33
Author(s): Peter Murray‐Rust, J.E. Townsend, Sam Adams, Weerapong Phadungsukanan, Jens M. H. Thomas
Software Mentions: 2
Published: about 13 years ago

10.3389/fpls.2017.01647

Transcriptome Profiling Reveals the Negative Regulation of Multiple Plant Hormone Signaling Pathways Elicited by Overexpression of C-Repeat Binding Factors
Cited by: 19
Author(s): Aixin Li, Mingqi Zhou, Donghui Wei, Chen Hu, Chenjiang You, Juan Lin
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2016.00567

Trait Specific Expression Profiling of Salt Stress Responsive Genes in Diverse Rice Genotypes as Determined by Modified Significance Analysis of Microarrays
Cited by: 20
Author(s): Mohammad Rashed Hossain, George W. Bassel, Jeremy Pritchard, Garima P Sharma, B. V. Ford‐Lloyd
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-9-499

Natural computation meta-heuristics for the in silico optimization of microbial strains
Cited by: 101
Author(s): Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha
Software Mentions: 2
Published: almost 16 years ago

10.1002/cam4.3492

New small‐molecule compound Hu‐17 inhibits estrogen biosynthesis by aromatase in human ovarian granulosa cancer cells
Cited by: 1
Author(s): Xi Yang, Jiansheng Liu, Haiwei Wang, Shang Li, Yang‐Hua Yi, Yanzhi Du
Software Mentions: 2
Published: about 4 years ago

10.3389/fphar.2018.00613

Extending in Silico Protein Target Prediction Models to Include Functional Effects
Cited by: 4
Author(s): Lewis Mervin, Avid M. Afzal, Lars Brive, Ola Engkvist, Andreas Bender
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0177225

Changes in gene expression between a soybean F1 hybrid and its parents are associated with agronomically valuable traits
Cited by: 7
Author(s): Earl Taliercio, David Eickholt, Rakin Rouf, Thomas Carter
Software Mentions: 2
Published: over 7 years ago

10.3389/fchem.2018.00138

Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds
Cited by: 84
Author(s): Huichao Huang, Guigui Zhang, Yuquan Zhou, Chenru Lin, Suling Chen, Yutong Lin, Shangkang Mai, Zunnan Huang
Software Mentions: 2
Published: over 6 years ago

10.3389/fphar.2017.00681

Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach
Cited by: 21
Author(s): Grace Mugumbate, V. Mendes, M. Błaszczyk, Mohamad Sabbah, George Papadatos, Joël Lelièvre, Lluís Ballell, David Barros, C. Abell, Tom L. Blundell, John P. Overington
Software Mentions: 2
Published: about 7 years ago

10.1186/s13321-017-0199-x

The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data
Cited by: 76
Author(s): Mahendra Awale, Jean‐Louis Reymond
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1004073

Comparative Evolutionary and Developmental Dynamics of the Cotton (Gossypium hirsutum) Fiber Transcriptome
Cited by: 134
Author(s): Mi‐Jeong Yoo, Jonathan F. Wendel
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-15-741

Transcriptomic complexity in young maize primary roots in response to low water potentials
Cited by: 68
Author(s): Nina Opitz, Anja Paschold, Caroline Marcon, Waqas Ahmed Malik, Christa Lanz, Hans‐Peter Piepho, Frank Hochholdinger
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pcbi.1002574

Assessing Drug Target Association Using Semantic Linked Data
Cited by: 132
Author(s): Bin Chen, Ying Ding, David Wild
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pcbi.1002326

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding
Cited by: 59
Author(s): Tianyun Liu, Russ B. Altman
Software Mentions: 2
Published: almost 13 years ago

10.3390/biom10091252

Computational Methods and Software Tools for Functional Analysis of miRNA Data
Cited by: 7
Author(s): Adrián García-Moreno, Pedro Carmona-Sáez
Software Mentions: 2
Published: about 4 years ago

10.1016/j.ejmech.2015.04.017

Prospective performance evaluation of selected common virtual screening tools. Case study: Cyclooxygenase (COX) 1 and 2
Cited by: 16
Author(s): Teresa Kaserer, Veronika Temml, Zsófia Kutil, Tomáš Vaněk, Přemysl Landa, Daniela Schuster
Software Mentions: 2
Published: over 9 years ago

10.1093/database/bay140

RAEdb: a database of enhancers identified by high-throughput reporter assays
Cited by: 13
Author(s): Zena Cai, Ya Cui, Zhiying Tan, Gaihua Zhang, Zhongyang Tan, Xinlei Zhang, Yousong Peng
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-13-23

Markov Chain Ontology Analysis (MCOA)
Cited by: 12
Author(s): H. Robert Frost, Alexa T. McCray
Software Mentions: 2
Published: almost 13 years ago

10.1155/2014/325697

MPINet: Metabolite Pathway Identification via Coupling of Global Metabolite Network Structure and Metabolomic Profile
Cited by: 9
Author(s): Feng Li, Yanjun Xu, Desi Shang, Haixiu Yang, Wei Liu, Junwei Han, Zeguo Sun, Qianlan Yao, Chunlong Zhang, Jing Ma, Fei Su, Feng Li, Xinrui Shi, Yunpeng Zhang, Jing Li, Qi Gu, Xia Li, Chunquan Li
Software Mentions: 2
Published: almost 11 years ago

10.1093/database/bax041

TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species
Cited by: 5
Author(s): Sony Malhotra, Grace Mugumbate, Tom L. Blundell, Alícia P. Higueruelo
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2164-14-889

Functional analyses of cotton (Gossypium hirsutum L.) immature fiber (im) mutant infer that fiber cell wall development is associated with stress responses
Cited by: 44
Author(s): Hee Jin Kim, Yuhong Tang, Hong S. Moon, Christopher D. Delhom, David D. Fang
Software Mentions: 2
Published: almost 12 years ago

10.1093/database/bav123

ChemProt-3.0: a global chemical biology diseases mapping
Cited by: 81
Author(s): Jens Vindahl Kringelum, Sonny Kim Kjærulff, Søren Brunak, Ole Lund, Tudor I. Oprea, Olivier Taboureau
Software Mentions: 2
Published: almost 9 years ago

10.1093/database/bax095

PTS: a pharmaceutical target seeker
Cited by: 5
Author(s): Peng Ding, Xin Yan, Zhihong Liu, Jiewen Du, Yunfei Du, Yutong Lu, Di Wu, Yiru Xu, Huihao Zhou, Qiong Gu, Jing Xu
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13020-020-00369-z

Development of simultaneous interaction prediction approach (SiPA) for the expansion of interaction network of traditional Chinese medicine
Cited by: 1
Author(s): Mengjie Rui, Pang Hui, Wei Ji, Siqi Wang, Xiaoduo Yu, Lilong Wang, Chunlai Feng
Software Mentions: 2
Published: about 4 years ago

10.1007/s41116-017-0011-z

Solar wind stream interaction regions throughout the heliosphere
Cited by: 179
Author(s): I. G. Richardson
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0084646

Using Expression Profiling to Understand the Effects of Chronic Cadmium Exposure on MCF-7 Breast Cancer Cells
Cited by: 15
Author(s): Zelmina Lubovac-Pilav, Daniel Borràs, Esmeralda Ponce, Maggie C. Louie
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0243215

Supportive consensus
Cited by: 1
Author(s): Alberto Palomares, Miguel Rebollo, Carlos Carrascosa
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0204378

The integration of pharmacophore-based 3D QSAR modeling and virtual screening in safety profiling: A case study to identify antagonistic activities against adenosine receptor, A2A, using 1,897 known drugs
Cited by: 19
Author(s): Fan Fan, Dora Toledo Warshaviak, Hisham K. Hamadeh, Robert T. Dunn
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.jbc.2021.100562

Integrating 3D structural information into systems biology
Cited by: 17
Author(s): Diana Murray, Donald Petrey, Barry Honig
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0256837

Geographic proximity, supply chain and organizational glocalized survival: China’s e-commerce investments in Indonesia
Cited by: 2
Author(s): Jinsheng Zhu, Weidian Lan, Xian‐Chun Zhang
Software Mentions: 2
Published: about 3 years ago

10.1093/database/bav060

SInCRe—structural interactome computational resource for<i>Mycobacterium tuberculosis</i>
Cited by: 9
Author(s): Rahul Metri, Sridhar Hariharaputran, Gayatri Ramakrishnan, Praveen Anand, Upadhyayula S. Raghavender, Bernardo Ochoa‐Montaño, Alícia P. Higueruelo, Ramanathan Sowdhamini, Nagasuma Chandra, Tom L. Blundell, Narayanaswamy Srinivasan
Software Mentions: 2
Published: almost 10 years ago

10.1093/jxb/eru173

Salt stress and senescence: identification of cross-talk regulatory components
Cited by: 107
Author(s): Annapurna Devi Allu, Aleksandra Maria Soja, Anhui Wu, Jędrzej Szymański, Salma Balazadeh
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj-cs.633

Dynamic sampling of images from various categories for classification based incremental deep learning in fog computing
Cited by: 0
Author(s): Swaraj Dube, Yee Wan Wong, Hanung Adi Nugroho
Software Mentions: 1
Published: over 3 years ago

10.3762/bjnano.8.108

Optical response of heterogeneous polymer layers containing silver nanostructures
Cited by: 3
Author(s): Miriam Carlberg, Florent Pourcin, Olivier Margeat, Judikaël Le Rouzo, Gérard Berginc, Rose-Marie Sauvage, Jörg Ackermann, Ludovic Escoubas
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.184

Gooseneck barnacles (<i>Lepas</i>spp.) ingest microplastic debris in the North Pacific Subtropical Gyre
Cited by: 169
Author(s): Miriam C. Goldstein, Deborah S. Goodwin
Software Mentions: 1
Published: about 11 years ago

10.3390/pathogens10070821

Rhipicephalus Tick: A Contextual Review for Southeast Asia
Cited by: 8
Author(s): Li Tan, Ruhil Hayati Hamdan, Basripuzi Nurul Hayyan Hassan, Mohd Farhan Hanif Reduan, Ibrahim Abdul-Azeez Okene, Shih Keng Loong, Jing Jing Khoo, Samsuddin Ahmad Syazwan, Seng Hua Lee
Software Mentions: 1
Published: over 3 years ago