pypi: g | Projects | Ecosyste.ms: Papers

10.12688/f1000research.24956.2

gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
Cited by: 274
Author(s): Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson
Software Mentions: 14
Published: almost 4 years ago

10.7554/eLife.58705

Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants
Cited by: 23
Author(s): Liis Kolberg, Nurlan Kerimov, Hedi Peterson, Kaur Alasoo
Software Mentions: 11
Published: about 4 years ago

10.1371/journal.pone.0153680

Viral Evolved Inhibition Mechanism of the RNA Dependent Protein Kinase PKR's Kinase Domain, a Structural Perspective
Cited by: 4
Author(s): K. Hari Krishna, Yallamandayya Vadlamudi, Mithilesh Kumar
Software Mentions: 9
Published: over 8 years ago

10.1186/1471-2105-15-224

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
Cited by: 275
Author(s): Krishna R. Kalari, Asha Nair, Jaysheel Bhavsar, Daniel R. O’Brien, Jaime Davila, Matthew A. Bockol, Jinfu Nie, Xiaojia Tang, Saurabh Baheti, Jay B. Doughty, Sumit Middha, Hugues Sicotte, E. Aubrey Thompson, Yan W. Asmann, Jean-Pierre A. Kocher
Software Mentions: 8
Published: about 10 years ago

10.7717/peerj.8522

Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells
Cited by: 8
Author(s): Phongsakorn Chuammitri, Soulasack Vannamahaxay, Benjaporn Sornpet, Kidsadagon Pringproa, Prapas Patchanee
Software Mentions: 8
Published: over 4 years ago

10.5334/jors.319

CMakeCatchTemplate: A C++ template project
Cited by: 1
Author(s): Thomas Dowrick, Mian Ahmed, Stephen A. Thompson, James Hetherington, Jonathan Cooper, Matthew J. Clarkson
Software Mentions: 7
Published: over 3 years ago

10.1002/ece3.6927

Disjunction between canola distribution and the genetic structure of its recently described pest, the canola flower midge (Contarinia brassicola)
Cited by: 5
Author(s): Erin O. Campbell, Julian R. Dupuis, Jennifer Holowachuk, Shane Hladun, Meghan A. Vankosky, Boyd A. Mori
Software Mentions: 6
Published: almost 4 years ago

10.1093/jmcb/mjaa061

RNF219 interacts with CCR4–NOT in regulating stem cell differentiation
Cited by: 6
Author(s): Hao Du, Chen Chen, Yan Wang, Yang Yang, Zhuanzhuan Che, Xiaoxu Liu, Siyan Meng, Chenghao Guo, Manman Xu, Haitong Fang, Fengchao Wang, Chengqi Lin, Zhuojuan Luo
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pcbi.1007904

Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites
Cited by: 7
Author(s): Agata P. Perlinska, Adam Stasiulewicz, Ewa K. Nawrocka, Krzysztof Kazimierczuk, Piotr Setny, Joanna I. Sułkowska
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1006648

Adaptation of A-to-I RNA editing in Drosophila
Cited by: 56
Author(s): Yuange Duan, Shengqian Dou, Shiqi Luo, Hong Zhang, Jian Lü
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.51139

Diversification of the Caenorhabditis heat shock response by Helitron transposable elements
Cited by: 19
Author(s): Jacob M. Garrigues, Brian V Tsu, Matthew D. Daugherty, Amy E. Pasquinelli
Software Mentions: 4
Published: almost 5 years ago

10.1126/sciadv.abf8660

FUS-ALS mutants alter FMRP phase separation equilibrium and impair protein translation
Cited by: 32
Author(s): Nicol Birsa, Agnieszka M Ule, Maria Giovanna Garone, Brian Tsang, Francesca Mattedi, P. Andrew Chong, Jack Humphrey, Seth Jarvis, Melis Pisiren, Oscar G. Wilkins, Micheal L Nosella, Anny Devoy, Cristian Bodo, Rafaela Fernandez de la Fuente, Elizabeth Fisher, Alessandro Rosa, Gabriella Viero, Julie D. Forman-Kay, Giampietro Schiavo, Pietro Fratta
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0225368

Computational analysis of functional single nucleotide polymorphisms associated with SLC26A4 gene
Cited by: 18
Author(s): Mirza Jawad ul Hasnain, Muhammad Shoaib, Salman Qadri, Bakhtawar Afzal, Tehreem Anwar, Syed Hassan Abbas, Amina Sarwar, Hafiz Muhammad Talha Malik, Muhammad Tariq Pervez
Software Mentions: 4
Published: over 4 years ago

10.1038/srep37680

Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers
Cited by: 13
Author(s): Wei Zhu, Le Xiong, Jinming Peng, Xin Deng, Jun Gao, Chunmei Li
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pcbi.1005991

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
Cited by: 280
Author(s): Ahmadreza Ghaffarizadeh, Randy Heiland, Samuel H. Friedman, Shannon M. Mumenthaler, Paul Macklin
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0044000

GPU-FS-kNN: A Software Tool for Fast and Scalable kNN Computation Using GPUs
Cited by: 62
Author(s): Ahmed Shamsul Arefin, Carlos Riveros, Regina Berretta, Pablo Moscato
Software Mentions: 4
Published: about 12 years ago

10.1186/s12864-016-2896-7

Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data
Cited by: 8
Author(s): Yongsheng Bai, Jeff Kinne, Brandon Donham, Feng Jiang, Lizhong Ding, Justin Hassler, Randal J. Kaufman
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-017-17678-3

Comprehensive analysis of the catalytic and structural properties of a mu-class glutathione s-transferase from Fasciola gigantica
Cited by: 20
Author(s): Jupitara Kalita, Rohit Shukla, Harish Shukla, Kundlik Gadhave, Rajanish Giri, Timir Tripathi
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12859-020-03614-2

Extending rnaSPAdes functionality for hybrid transcriptome assembly
Cited by: 13
Author(s): Andrey D. Prjibelski, G. Puglia, Dmitry Antipov, Elena Bushmanova, Daniela Giordano, Alla Mikheenko, Domenico Vitale, Alla Lapidus
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-30420-x

Targeting Nucleotide Binding Domain of Multidrug Resistance-associated Protein-1 (MRP1) for the Reversal of Multi Drug Resistance in Cancer
Cited by: 12
Author(s): Divya Dhasmana, Ashutosh Singh, Rohit Shukla, Timir Tripathi, Neha Garg
Software Mentions: 3
Published: about 6 years ago

10.1155/2020/1872962

Development of Autophagy Signature-Based Prognostic Nomogram for Refined Glioma Survival Prognostication
Cited by: 5
Author(s): Yuxiang Fan, Xinyu Peng, Baoqin Li, Gang Zhao
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-61132-w

Long-range replica exchange molecular dynamics guided drug repurposing against tyrosine kinase PtkA of Mycobacterium tuberculosis
Cited by: 10
Author(s): Priya Nagpal, Salma Jamal, Hina Singh, Waseem Ali, Sana Tanweer, Rahul Sharma, Abhinav Grover, Sonam Grover
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-70202-y

Identification and characterization of cytosolic malate dehydrogenase from the liver fluke Fasciola gigantica
Cited by: 6
Author(s): Purna B Chetri, Rohit Shukla, Timir Tripathi
Software Mentions: 3
Published: about 4 years ago

10.1155/2013/697051

In SilicoScreening and Molecular Dynamics Simulation of Disease-Associated nsSNP in TYRP1 Gene and Its Structural Consequences in OCA3
Cited by: 63
Author(s): Balu Kamaraj, Rituraj Purohit
Software Mentions: 3
Published: over 11 years ago

10.1186/s12859-020-03590-7

SPAligner: alignment of long diverged molecular sequences to assembly graphs
Cited by: 12
Author(s): Tatiana Dvorkina, Dmitry Antipov, Anton Korobeynikov, Sergey Nurk
Software Mentions: 3
Published: about 4 years ago

10.3389/fmolb.2020.603983

Identification of the Interactions Interference Between the PH and START Domain of CERT by Limonoid and HPA Inhibitors
Cited by: 1
Author(s): Mariem Ghoula, Axelle Le Marec, Christophe Magnan, Hervé Le Stunff, Olivier Taboureau
Software Mentions: 3
Published: almost 4 years ago

10.3389/fninf.2012.00026

Supercomputers Ready for Use as Discovery Machines for Neuroscience
Cited by: 54
Author(s): Moritz Helias, Susanne Kunkel, Gen Masumoto, Jun Igarashi, Jochen Martin Eppler, Shin Ishii, Tomoki Fukai, Abigail Morrison, Markus Diesmann
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pcbi.1007913

Two-step mechanism of J-domain action in driving Hsp70 function
Cited by: 16
Author(s): Bartłomiej Tomiczek, Wojciech Delewski, Łukasz Nierzwicki, Milena Stolarska, Igor Grochowina, Brenda Schilke, Rafał Dutkiewicz, Marta A. Uzarska, Szymon J. Ciesielski, Jacek Czub, Elizabeth A. Craig, Jarosław Marszałek
Software Mentions: 3
Published: over 4 years ago

10.1007/s41109-017-0027-2

Efficient orbit-aware triad and quad census in directed and undirected graphs
Cited by: 17
Author(s): Mark Ortmann, Ulrik Brandes
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2021.682841

MONTI: A Multi-Omics Non-negative Tensor Decomposition Framework for Gene-Level Integrative Analysis
Cited by: 6
Author(s): Il Bong Jung, Minsu Kim, Sungmin Rhee, Sangsoo Lim, Kai Sun
Software Mentions: 3
Published: about 3 years ago

10.1186/s12864-018-5176-x

funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data
Cited by: 5
Author(s): Liis Kolberg, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson
Software Mentions: 3
Published: almost 6 years ago

10.3389/fchem.2020.00493

Binding of the Anti-FIV Peptide C8 to Differently Charged Membrane Models: From First Docking to Membrane Tubulation
Cited by: 2
Author(s): Daniele Di Marino, Annalisa Bruno, Manuela Grimaldi, Mario Scrima, Ilaria Stillitano, Giuseppina Amodio, Grazia Della Sala, Alice Romagnoli, Augusta De Santis, Ornella Moltedo, Paolo Remondelli, Giovanni Boccia, Gerardino D’Errico, Anna Maria D’Ursi, Vittorio Limongelli
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0190942

Structural investigations on mechanism of lapatinib resistance caused by HER-2 mutants
Cited by: 6
Author(s): Subhash Verma, Sumit Goyal, Anchala Kumari, Aditi Singh, Salma Jamal, Abhinav Grover
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0163688

Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic
Cited by: 1
Author(s): Amirhossein Manzourolajdad, Mileidy Gonzalez, John L. Spouge
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2105-15-273

A new method for modeling coalescent processes with recombination
Cited by: 16
Author(s): Ying Wang, Ying Zhou, Linfeng Li, Xian Chen, Yuting Liu, Zhiming Ma, Shuhua Xu
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-015-1977-3

Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses
Cited by: 96
Author(s): Julia Metzger, Matthias Karwath, Raúl Tonda, Sergi Beltrán, Lídia Águeda, Marta Gut, Ivo Gut, O. Distl
Software Mentions: 3
Published: almost 9 years ago

10.3389/fphar.2015.00248

Molecular features of interaction between VEGFA and anti-angiogenic drugs used in retinal diseases: a computational approach
Cited by: 69
Author(s): Chiara Bianca Maria Platania, Luisa Di Paola, Gian Marco Leggio, Giovanni Luca Romano, Filippo Drago, Salvatore Salomone, Claudio Bucolo
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2164-10-420

Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation
Cited by: 13
Author(s): Tamara Aid-Pavlidis, Pavlos Pavlidis, Tõnis Timmusk
Software Mentions: 3
Published: over 15 years ago

10.3390/cancers13153716

Primary Aldosteronism: Metabolic Reprogramming and the Pathogenesis of Aldosterone-Producing Adenomas
Cited by: 6
Author(s): Siyuan Gong, Martina Tetti, Martín Reincke, Tracy Ann Williams
Software Mentions: 3
Published: about 3 years ago

10.3390/biomedicines9070795

Antisense Oligonucleotide-Based Therapeutic against Menin for Triple-Negative Breast Cancer Treatment
Cited by: 5
Author(s): Dang Tan Nguyen, Thi Khanh Le, Clément Paris, Chaïma Cherif, Stéphane Audebert, Sandra Oluchi Udu-Ituma, Sébastien Benizri, Philippe Barthélemy, François Bertucci, David Taïeb, Palma Rocchi
Software Mentions: 3
Published: about 3 years ago

10.1016/j.csbj.2020.08.009

Designing custom CRISPR libraries for hypothesis-driven drug target discovery
Cited by: 11
Author(s): Vaishnavi Srinivasan Iyer, Long Jiang, Yunbing Shen, Sanjaykumar V. Boddul, Santanu Panda, Zsolt Kasza, Bernhard Schmierer, Fredrik Wermeling
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-10-35

The Genome Reverse Compiler: an explorative annotation tool
Cited by: 13
Author(s): Andrew S. Warren, João Carlos Setúbal
Software Mentions: 3
Published: over 15 years ago

10.1016/j.dib.2020.106350

Data analysis of molecular dynamics simulation trajectories of β-sitosterol, sonidegib and cholesterol in smoothened protein with the CHARMM36 force field
Cited by: 7
Author(s): Che Omar
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0061908

p.Arg82Leu von Hippel-Lindau (VHL) Gene Mutation among Three Members of a Family with Familial Bilateral Pheochromocytoma in India: Molecular Analysis and In Silico Characterization
Cited by: 9
Author(s): Anulekha Mary John, George Priya Doss C, Andrew Ebenazer, M. S. Seshadri, Aravindan Nair, Simon Rajaratnam, Rekha Pai
Software Mentions: 2
Published: over 11 years ago

10.3389/fchem.2020.581058

On the Efficient Evaluation of the Exchange Correlation Potential on Graphics Processing Unit Clusters
Cited by: 10
Author(s): David B. Williams‐Young, Wibe A. de Jong, Hubertus J. J. van Dam, Chao Yang
Software Mentions: 2
Published: almost 4 years ago

10.1186/1475-925X-11-30

Ischemia episode detection in ECG using kernel density estimation, support vector machine and feature selection
Cited by: 21
Author(s): Jinho Park, Witold Pedrycz, Moongu Jeon
Software Mentions: 2
Published: over 12 years ago

10.1155/2014/895831

IntegratingIn SilicoPrediction Methods, Molecular Docking, and Molecular Dynamics Simulation to Predict the Impact of ALK Missense Mutations in Structural Perspective
Cited by: 30
Author(s): C. George Priya Doss, Chiranjib Chakraborty, Luonan Chen, Hailong Zhu
Software Mentions: 2
Published: over 10 years ago

10.3389/fnins.2017.00684

Conformational Ensembles of α-Synuclein Derived Peptide with Different Osmolytes from Temperature Replica Exchange Sampling
Cited by: 16
Author(s): Salma Jamal, Anchala Kumari, Aditi Singh, Sumit Goyal, Abhinav Grover
Software Mentions: 2
Published: almost 7 years ago

10.3389/fonc.2020.01032

Biliary Tract Carcinogenesis Model Based on Bile Metaproteomics
Cited by: 3
Author(s): Ariel A. Arteta, Miryan Margot Sánchez‐Jiménez, Diego F. Dávila, Olga Palacios, Nora Cardona‐Castro
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2013.00530

Tubulin tyrosine nitration regulates microtubule organization in plant cells
Cited by: 33
Author(s): Ya. B. Blume, Yuliya Krasylenko, Oleg M. Demchuk, А. І. Yemets
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-015-0598-9

MANTIS: an R package that simulates multilocus models of pathogen evolution
Cited by: 10
Author(s): José Lourenço, Paul S. Wikramaratna, Sunetra Gupta
Software Mentions: 2
Published: over 9 years ago

10.3390/genes12040608

Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles
Cited by: 2
Author(s): Sofia M. Kolchanova, Aleksey Komissarov, Sergei Kliver, Anyi Mazo‐Vargas, Yashira Afanador, Jafet Vélez-Valentín, Ricardo Valentín de la Rosa, Stephanie O Castro-Marquez, Israel Rivera-Colon, Audrey J. Majeske, Walter Wolfsberger, Taylor Hains, André Corvelo, Juan-Carlos Martinez-Cruzado, Travis C. Glenn, Orlando Robinson, Klaus Peter Koepfli, Tarás K. Oleksyk
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-016-1212-5

Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets
Cited by: 48
Author(s): Yalchin Oytam, Fariborz Sobhanmanesh, Konsta Duesing, Joshua C. Bowden, Megan Osmond, Jason P. Ross
Software Mentions: 2
Published: about 8 years ago

10.3390/molecules21050588

In Silico Investigation of Traditional Chinese Medicine for Potential Lead Compounds as SPG7 Inhibitors against Coronary Artery Disease
Cited by: 4
Author(s): Kuen‐Bao Chen, Kuan‐Chung Chen, Yajie Chang, Kun-Lung Chang, Pei-Chun Chang, Tung-Ti Chang, Calvin Yu-Chian Chen
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-017-4101-z

Patterns of host gene expression associated with harboring a foregut microbial community
Cited by: 3
Author(s): Kevin D. Kohl, Kelly F. Oakeson, Diane M. Dunn, David K. Meyerholz, Colin Dale, Robert B. Weiss, M. Denise Dearing
Software Mentions: 2
Published: about 7 years ago

10.1155/2014/502618

Computational Analysis Reveals the Association of Threonine 118 Methionine Mutation in PMP22 Resulting in CMT-1A
Cited by: 78
Author(s): Chundi Vinay Kumar, Rayapadi G. Swetha, Anand Anbarasu, Sudha Ramaiah
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-017-01235-z

Distant Phe345 mutation compromises the stability and activity of Mycobacterium tuberculosis isocitrate lyase by modulating its structural flexibility
Cited by: 61
Author(s): Harish Shukla, Rohit Shukla, Amit Sonkar, Tripti Pandey, Timir Tripathi
Software Mentions: 2
Published: over 7 years ago

10.1038/srep44301

Fabrication of cerebral aneurysm simulator with a desktop 3D printer
Cited by: 47
Author(s): Yu Liu, Qing Gao, Shiyu Du, Zichen Chen, Jianzhong Fu, Bing Chen, Zhenjie Liu, Yong He
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-18102-6

Structure and Interactions of A Host Defense Antimicrobial Peptide Thanatin in Lipopolysaccharide Micelles Reveal Mechanism of Bacterial Cell Agglutination
Cited by: 67
Author(s): Sheetal Sinha, Lihe Zheng, Yuguang Mu, Wun Jern Ng, Surajit Bhattacharjya
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-44013-9

Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance
Cited by: 34
Author(s): Muhammad Tahir Khan, Abbas Khan, Ashfaq Ur Rehman, Yanjie Wang, Khalid Pervaiz Akhtar, Shaukat Iqbal Malik, Dong‐Qing Wei
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-93266-w

An immunoinformatics approach to design a multi-epitope vaccine against Mycobacterium tuberculosis exploiting secreted exosome proteins
Cited by: 14
Author(s): Rahul Sharma, Vikrant Singh Rajput, Salma Jamal, Abhinav Grover, Sonam Grover
Software Mentions: 2
Published: about 3 years ago

10.1038/s41598-021-95814-w

Intra- and interspecific variability among congeneric Pagellus otoliths
Cited by: 27
Author(s): Claudio D’Iglio, Marco Albano, Sergio Famulari, Serena Savoca, Giuseppe Panarello, Davide Di Paola, Anna Perdichizzi, Paola Rinelli, Giovanni Lanteri, Nunziacarla Spanò, Gioele Capillo
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pcbi.1005202

Induced Fit in Protein Multimerization: The HFBI Case
Cited by: 5
Author(s): Laura Riccardi, Paolo Mereghetti
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pcbi.1002844

Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
Cited by: 48
Author(s): Federica Chiappori, Ivan Merelli, Giorgio Colombo, Luciano Milanesi, Giulia Morra
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pcbi.1004496

Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding
Cited by: 11
Author(s): Suhani Nagpal, Satyam Tiwari, Koyeli Mapa, Lipi Thukral
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms17122116

Discovery of a New Class of Cathepsin K Inhibitors in Rhizoma Drynariae as Potential Candidates for the Treatment of Osteoporosis
Cited by: 17
Author(s): Zuo-Cheng Qiu, Xiaoli Dong, Yi Dai, Gao Keng Xiao, Xin Luan Wang, Ka-Chun Wong, Man Sau Wong, Xin Yao
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1008245

A gene co-expression network-based analysis of multiple brain tissues reveals novel genes and molecular pathways underlying major depression
Cited by: 71
Author(s): Zachary Gerring, Eric R. Gamazon, Eske M. Derks
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0147348

DNA Repair Gene (XRCC1) Polymorphism (Arg399Gln) Associated with Schizophrenia in South Indian Population: A Genotypic and Molecular Dynamics Study
Cited by: 15
Author(s): S Sujitha, Dileep Kumar, George Priya Doss C, Kumar Aavula, R. Ramésh, Srinivasan Lakshmanan, Soosiah Gunasekaran, Gopinathan Anilkumar
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-15-S7-S5

Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics
Cited by: 12
Author(s): Maurício G. S. Costa, Técio G Benetti-Barbosa, Nathan Desdouits, Arnaud Blondel, Paulo Mascarello Bisch, Pedro Geraldo Pascutti, Paulo Ricardo Batista
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0131754

Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA
Cited by: 56
Author(s): S. Y. Mashayak, Mara Jochum, Konstantin Koschke, N. R. Aluru, Victor Rühle, Christoph Junghans
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0244820

Are the new mobile wireless EEG headsets reliable for the evaluation of musical pleasure?
Cited by: 8
Author(s): Thibault Chabin, Damien Gabriel, Emmanuel Haffen, Thierry Moulin, Lionel Pazart
Software Mentions: 2
Published: over 3 years ago

10.3390/cells9010232

Intragenic MicroRNAs Autoregulate Their Host Genes in Both Direct and Indirect Ways—A Cross-Species Analysis
Cited by: 12
Author(s): Maximilian Zeidler, Alexander Hüttenhofer, Michaela Kress, Kai K. Kummer
Software Mentions: 2
Published: over 4 years ago

10.1016/j.dib.2016.11.003

Data set of Aspergillus flavus induced alterations in tear proteome: Understanding the pathogen-induced host response to fungal infection
Cited by: 7
Author(s): Jeyalakshmi Kandhavelu, Naveen Luke Demonte, Venkatesh Prajna Namperumalsamy, Prajna Lalitha, Chitra Thangavel, Jeya Maheshwari Jayapal, Kuppamuthu Dharmalingam
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12900-019-0103-1

QRNAS: software tool for refinement of nucleic acid structures
Cited by: 42
Author(s): Juliusz Stasiewicz, Sunandan Mukherjee, Chandran Nithin, Janusz M. Bujnicki
Software Mentions: 2
Published: over 5 years ago

10.3390/nu11081795

Identification of the Secreted Proteins Originated from Primary Human Hepatocytes and HepG2 Cells
Cited by: 23
Author(s): András Frankó, Sonja Hartwig, Jörg Kotzka, Marc Ruoß, Andreas K. Nüssler, Alfred Königsrainer, Hans‐Ulrich Häring, Stefan Lehr, Andreas Peter
Software Mentions: 1
Published: about 5 years ago

10.1002/advs.201901878

A 3D‐Printed Hybrid Nasal Cartilage with Functional Electronic Olfaction
Cited by: 55
Author(s): Yasamin A. Jodat, Kiavash Kiaee, Daniel Vela Jarquin, Rosakaren Ludivina De la Garza Hernández, Ting Wang, Sudeep Joshi, Zahra Rezaei, Bruna Alice Gomes de Melo, David H. Ge, Su Ryon Shin
Software Mentions: 1
Published: over 4 years ago

10.1186/1748-7188-1-22

SMOTIF: efficient structured pattern and profile motif search
Cited by: 23
Author(s): Yongqiang Zhang, Mohammed J. Zaki
Software Mentions: 1
Published: almost 18 years ago

10.1186/s13015-017-0094-z

On avoided words, absent words, and their application to biological sequence analysis
Cited by: 22
Author(s): Yannis Almirantis, Panagiotis Charalampopoulos, Gao Jia, Costas S. Iliopoulos, Manal Mohamed, Solon P. Pissis, Dimitris Polychronopoulos
Software Mentions: 1
Published: over 7 years ago

10.1186/s13613-019-0594-8

Use of MIRUS™ for MAC-driven application of isoflurane, sevoflurane, and desflurane in postoperative ICU patients: a randomized controlled trial
Cited by: 10
Author(s): Martin Bellgardt, Adrian-Iustin Georgevici, Mitja Klutzny, Dominik Drees, Andreas Meiser, Philipp Gude, Heike Vogelsang, Thomas P. Weber, Jennifer Herzog‐Niescery
Software Mentions: 1
Published: almost 5 years ago

10.1007/s10484-020-09490-z

Cardiovascular Biomarkers’ Inherent Timescales in Mental Workload Assessment During Simulated Air Traffic Control Tasks
Cited by: 6
Author(s): Thea Radüntz, Thorsten Mühlhausen, Marion Freyer, Norbert Fürstenau, Beate Meffert
Software Mentions: 1
Published: almost 4 years ago

10.1007/s00204-020-02788-1

Molecular basis of mood and cognitive adverse events elucidated via a combination of pharmacovigilance data mining and functional enrichment analysis
Cited by: 5
Author(s): Christos Andronis, João Pedro Silva, Eftychia Lekka, Vassilis Virvilis, Helena Carmo, Konstantina Bampali, Margot Ernst, Yang Hu, Irena Loryan, Jacques Richard, Félix Carvalho, Miroslav M. Savić
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2105-12-201

CAPL: an efficient association software package using family and case-control data and accounting for population stratification
Cited by: 3
Author(s): Ren Hua Chung, Michael A. Schmidt, Eden R. Martin
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-11-642

Genome-wide promoter analysis of histone modifications in human monocyte-derived antigen presenting cells
Cited by: 29
Author(s): Liina Tserel, Raivo Kolde, Ana Rebane, Kai Kisand, Tõnis Org, Hedi Peterson, Jaak Vilo, Pärt Peterson
Software Mentions: 1
Published: almost 14 years ago

10.1186/s12864-018-4804-9

Stratification of candidate genes for Parkinson’s disease using weighted protein-protein interaction network analysis
Cited by: 34
Author(s): Raffaele Ferrari, Demis A. Kia, James E. Tomkins, John Hardy, Nicholas W. Wood, Ruth C. Lovering, Patrick A. Lewis, Claudia Manzoni
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-16-S5-S8

Structural investigations of T854A mutation in EGFR and identification of novel inhibitors using structure activity relationships
Cited by: 27
Author(s): Sumit Goyal, Salma Jamal, Asheesh Shanker, Abhinav Grover
Software Mentions: 1
Published: over 9 years ago

10.1186/s12870-016-0946-6

Combined transcriptome and metabolome analyses to understand the dynamic responses of rice plants to attack by the rice stem borer Chilo suppressalis (Lepidoptera: Crambidae)
Cited by: 53
Author(s): Qingsong Liu, Xingyun Wang, Vered Tzin, Jörg Romeis, Yufa Peng, Yunhe Li
Software Mentions: 1
Published: almost 8 years ago

10.3390/biology10060451

Anchored Phylogenomics, Evolution and Systematics of Elateridae: Are All Bioluminescent Elateroidea Derived Click Beetles?
Cited by: 35
Author(s): Hume Douglas, Robin Kundrata, Adam Brunke, Hermes E. Escalona, Julie T. Chapados, Jackson Eyres, Robin Richter, Karine Savard, Adam Ślipiński, Duane D. McKenna, Jeremy R. Dettman
Software Mentions: 1
Published: over 3 years ago

10.1002/brb3.1735

Identifying interactive biological pathways associated with reading disability
Cited by: 5
Author(s): Hope Sparks Lancaster, Xiaonan Liu, Valentin Dinu, Jing Li
Software Mentions: 1
Published: about 4 years ago

10.1186/s12935-017-0394-x

Human basonuclin 2 up-regulates a cascade set of interferon-stimulated genes with anti-cancerous properties in a lung cancer model
Cited by: 5
Author(s): Egon Urgard, Anu Reigo, Eva Reinmaa, Ana Rebane, Andres Metspalu
Software Mentions: 1
Published: over 7 years ago

10.1002/cam4.1275

A blood tumor marker combination assay produces high sensitivity and specificity for cancer according to the natural history
Cited by: 12
Author(s): Tsuneo Kobayashi
Software Mentions: 1
Published: over 6 years ago

10.3390/molecules25173822

In Silico Identification of Potential Natural Product Inhibitors of Human Proteases Key to SARS-CoV-2 Infection
Cited by: 49
Author(s): R.P. Vivek-Ananth, Abhijit Rana, Nithin Rajan, Himansu S. Biswal, Areejit Samal
Software Mentions: 1
Published: about 4 years ago

10.3390/molecules26185698

Molecular Basis of Artemisinin Derivatives Inhibition of Myeloid Differentiation Protein 2 by Combined in Silico and Experimental Study
Cited by: 2
Author(s): Sennan Qiao, Hansi Zhang, Fenyong Sun, Zhenyan Jiang
Software Mentions: 1
Published: almost 3 years ago

10.1002/mgg3.210

A novel approach for next‐generation sequencing of circulating tumor cells
Cited by: 18
Author(s): Stephanie S. Yee, David Lieberman, Tatiana Blanchard, JulieAnn Rader, Jianhua Zhao, Andrea B. Troxel, Daniel DeSloover, Alan Fox, Robert Daber, Bijal Kakrecha, Shrey Sukhadia, George K. Belka, Angela DeMichele, Lewis A. Chodosh, Jennifer J.D. Morrissette, Erica L. Carpenter
Software Mentions: 1
Published: over 8 years ago

10.1111/mmi.14624

Extrachromosomal DNA amplicons in antimalarial‐resistant Plasmodium falciparum
Cited by: 5
Author(s): Jennifer McDaniels, Adam C Huckaby, Sabrina A. Carter, Sabrina Lingeman, Audrey Francis, Molly D. Congdon, Webster L. Santos, Pradipsinh K. Rathod, Jennifer L. Guler
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0054072

OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects
Cited by: 274
Author(s): Quentin Geissmann
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0203203

Software tools for cell culture-related 3D printed structures
Cited by: 24
Author(s): Márton Gulyás, Miklos Csiszer, Előd Méhes, András Czirók
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0011550

Modeling the Ternary Complex TCR-Vβ/CollagenII(261–273)/HLA-DR4 Associated with Rheumatoid Arthritis
Cited by: 33
Author(s): Maria Cristina De Rosa, Bruno Giardina, Cristina Bianchi, Cristiana Carelli Alinovi, Davide Pirolli, Gianfranco Ferraccioli, Maria De Santis, Gabriele Di Sante, Francesco Ria
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0059175

A Single Disulfide Bond Disruption in the β3 Integrin Subunit Promotes Thiol/Disulfide Exchange, a Molecular Dynamics Study
Cited by: 14
Author(s): Lihie Ben-Avraham Levin, Ehud Zelzion, Esther Nachliel, Menachem Gutman, Yossi Tsfadia, Yulia Einav
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0120469

In Silico Screening, Genotyping, Molecular Dynamics Simulation and Activity Studies of SNPs in Pyruvate Kinase M2
Cited by: 18
Author(s): P. Kalaiarasan, Bhupender Kumar, Rupali Chopra, Vibhor Gupta, Naidu Subbarao, R. Bamezai
Software Mentions: 1
Published: over 9 years ago

10.3390/cancers13153798

Human Wnt/β-Catenin Regulates Alloimmune Signaling during Allogeneic Transplantation
Cited by: 4
Author(s): Mahinbanu Mammadli, Robert G. Harris, Sara Mahmudlu, Anjali Verma, Adriana May, Rohan Dhawan, Adam T. Waickman, Jyoti Misra Sen, Avery August, Mobin Karimi
Software Mentions: 1
Published: about 3 years ago

Projects: pypi: g

Papers Mentioning g 130