pypi: webserver | Projects | Ecosyste.ms: Papers

10.3389/fpls.2020.01269

Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and Ripening
Cited by: 27
Author(s): Beatriz Ester García-Gómez, David Ruiz, J. Salazar, M. Rubio, Pedro J. Martínez-García, Pedro Martínez‐Gómez
Software Mentions: 9
Published: over 4 years ago

10.3389/fmicb.2016.00563

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities
Cited by: 21
Author(s): Jeffrey J. Marlow, Connor T. Skennerton, Li Zhou, Karuna Chourey, Robert L. Hettich, Chongle Pan, Victoria J. Orphan
Software Mentions: 6
Published: over 8 years ago

10.3389/fgene.2019.01120

Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets
Cited by: 12
Author(s): Pablo Ivan Pereira Ramos, Luis Willian Pacheco Arge, Nicholas Costa Barroso Lima, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 6
Published: about 5 years ago

10.3390/ijms21197281

SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features
Cited by: 10
Author(s): António Preto, Irina S. Moreira
Software Mentions: 5
Published: about 4 years ago

10.1038/srep13373

Smoking Gun or Circumstantial Evidence? Comparison of Statistical Learning Methods using Functional Annotations for Prioritizing Risk Variants
Cited by: 8
Author(s): Sarah A. Gagliano, Reena Ravji, Michael R. Barnes, Michael E. Weale, Jo Knight
Software Mentions: 4
Published: about 9 years ago

10.15252/embr.201847592

CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes
Cited by: 57
Author(s): Anil Paul Chirackal Manavalan, Květa Pilařová, Michael Kluge, Koen Bartholomeeusen, Michal Rájecký, Jan Oppelt, Prashant Khirsariya, Kamil Paruch, Lumír Krejčí, Caroline C. Friedel, Dalibor Blažek
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-018-2526-2

Constructing a database for the relations between CNV and human genetic diseases via systematic text mining
Cited by: 15
Author(s): Xi Yang, Zhuo Song, Chengkun Wu, Wei Wang, Gen Li, Wei Zhang, Lingqian Wu, Kai Lü
Software Mentions: 4
Published: almost 6 years ago

10.1093/gbe/evab202

Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes
Cited by: 7
Author(s): Kirsten I. Verster, Rebecca L. Tarnopol, Saron M. Akalu, Noah K. Whiteman
Software Mentions: 4
Published: about 3 years ago

10.1002/mbo3.320

Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction
Cited by: 49
Author(s): Yuta Mizuno, Megumi Nagano‐Shoji, Shosei Kubo, Y. Kawamura, Ayako Yoshida, Hisashi Kawasaki, Makoto Nishiyama, Minoru Yoshida, Saori Kosono
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-021-90737-y

Rapid evolution of mammalian APLP1 as a synaptic adhesion molecule
Cited by: 6
Author(s): Wataru Onodera, Toru Asahi, Naoya Sawamura
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-018-4528-x

A systematic approach to RNA-associated motif discovery
Cited by: 14
Author(s): Tian Gao, Jiang Shu, Juan Cui
Software Mentions: 3
Published: almost 7 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: over 3 years ago

10.3389/fmicb.2016.00949

Prediction of Biofilm Inhibiting Peptides: An In silico Approach
Cited by: 38
Author(s): Sudheer Gupta, Ashok Sharma, Shubham K. Jaiswal, Vineet K. Sharma
Software Mentions: 3
Published: over 8 years ago

10.1016/j.heliyon.2021.e06396

Implementation of in silico methods to predict common epitopes for vaccine development against Chikungunya and Mayaro viruses
Cited by: 12
Author(s): Hammadul Hoque, Rahatul Islam, Srijon Ghosh, Md. Mashiur Rahaman, Nurnabi Azad Jewel, M. A. A. Miah
Software Mentions: 3
Published: over 3 years ago

10.1186/s12967-016-1103-6

Prediction of anti-inflammatory proteins/peptides: an insilico approach
Cited by: 77
Author(s): Sudheer Gupta, Ashok Sharma, Vibhuti Shastri, Midhun K. Madhu, Vineet K. Sharma
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-019-3328-x

Improving the organization and interactivity of metabolic pathfinding with precomputed pathways
Cited by: 7
Author(s): Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett, Lydia E. Kavraki
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2164-13-299

PePPER: a webserver for prediction of prokaryote promoter elements and regulons
Cited by: 133
Author(s): Anne de Jong, Hilco Pietersma, Martijn Cordes, Oscar P. Kuipers, Jan Kok
Software Mentions: 2
Published: over 12 years ago

10.7717/peerj.11860

Expression of cyanobacterial genes enhanced CO2 assimilation and biomass production in transgenic Arabidopsis thaliana
Cited by: 5
Author(s): Anum Zeb Abbasi, Misbah Bilal, Ghazal Khurshid, Charilaos Yiotis, Iftikhar Zeb, Jamshaid Hussain, Ayesha Baig, Mohammad Maroof Shah, Safee Ullah Chaudhary, Bruce Osborne, Raza Ahmad
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0041224

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads
Cited by: 37
Author(s): Colin Davenport, Jens Neugebauer, Nils Beckmann, Benedikt Friedrich, Burim Kameri, Svea Kokott, Malte Paetow, Björn Siekmann, Matthias Wieding-Drewes, Markus Wienhöfer, S. Wolf, Burkhard Tümmler, Volker Ahlers, Frauke Sprengel
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0223993

iCrotoK-PseAAC: Identify lysine crotonylation sites by blending position relative statistical features according to the Chou’s 5-step rule
Cited by: 37
Author(s): Sharaf J. Malebary, Muhammad Safi ur Rehman, Yaser Daanial Khan
Software Mentions: 2
Published: about 5 years ago

10.3389/fonc.2020.599085

Editorial: Bioinformatics Tools (and Web Server) for Cancer Biomarker Development
Cited by: 3
Author(s): Longxiang Xie, Liuyang Wang, Wan Zhu, Jing Zhao, Xiangqian Guo
Software Mentions: 2
Published: about 4 years ago

10.1099/jgv.0.001474

Multiple novel non-canonically transcribed sub-genomic mRNAs produced by avian coronavirus infectious bronchitis virus
Cited by: 12
Author(s): Sarah Keep, Michael S Oade, Filip Lidzbarski-Silvestre, Kirsten Bentley, Phoebe Stevenson-Leggett, Graham Freimanis, Chandana Tennakoon, Nicholas D. Sanderson, John A. Hammond, Richard C. Jones, Paul Britton, Erica Bickerton
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0145648

Prediction of Intra-Species Protein-Protein Interactions in Enteropathogens Facilitating Systems Biology Study
Cited by: 4
Author(s): Ranjan Kumar Barman, Tanmoy Jana, Santasabuj Das, Sudipto Saha
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13072-018-0181-5

Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core
Cited by: 66
Author(s): Andrew T. Fenley, Ramu Anandakrishnan, Yared H. Kidane, Alexey V. Onufriev
Software Mentions: 1
Published: over 6 years ago

10.1002/2211-5463.12495

Structural and interaction analysis of the Rrp5 C‐terminal region
Cited by: 0
Author(s): Natacha Pérébaskine, Stéphane Thore, Sébastien Fribourg
Software Mentions: 1
Published: about 6 years ago

10.3389/fbioe.2021.673005

Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals
Cited by: 10
Author(s): Marc Scherer, Sarel J. Fleishman, Patrik R. Jones, Thomas Dandekar, Elena Bencúrová
Software Mentions: 1
Published: over 3 years ago

10.3897/zookeys.793.28977

Complete mitochondrial genome of Echinophyllia aspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning
Cited by: 4
Author(s): Wentao Niu, Shuangen Yu, Peng Tian, Jiaguang Xiao
Software Mentions: 1
Published: about 6 years ago

10.3390/v9040074

Structure of Ty1 Internally Initiated RNA Influences Restriction Factor Expression
Cited by: 9
Author(s): Leszek Błaszczyk, Marcin Biesiada, Agniva Saha, David Garfinkel, Katarzyna J. Purzycka
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2017.01241

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept
Cited by: 35
Author(s): Melissa B. Duhaime, Natalie Solonenko, Simon Roux, Nathan C. VerBerkmoes, Antje Wichels, Matthew B. Sullivan
Software Mentions: 1
Published: over 7 years ago

10.1080/23802359.2019.1692729

Nearly complete mitochondrial genome of Siobla xizangensis Xiao, Huang & Zhou, 1988 (Hymenoptera: Tenthredinidae) and phylogenetic analysis
Cited by: 4
Author(s): Xi Luo, Meicai Wei, Gengyun Niu
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21218111

Structural Insights into β-arrestin/CB1 Receptor Interaction: NMR and CD Studies on Model Peptides
Cited by: 4
Author(s): Paula Morales, Marta Bruix, María Ángeles Sánchez Jiménez
Software Mentions: 1
Published: about 4 years ago

10.3389/fpls.2020.00263

Nuclear and Chloroplast Sequences Resolve the Enigmatic Origin of the Concord Grape
Cited by: 17
Author(s): Jun Wen, Sterling A. Herron, Xue Yang, Binbin Liu, Yunjuan Zuo, AJ Harris, Yash Kalburgi, Gabriel Johnson, Elizabeth A. Zimmer
Software Mentions: 1
Published: over 4 years ago

10.1186/1745-6150-4-18

Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites
Cited by: 75
Author(s): Sebastian Maurer‐Stroh, Jun Ma, Raphael Tze Chuen Lee, Fernanda L. Sirota, Frank Eisenhaber
Software Mentions: 1
Published: almost 16 years ago

10.1186/gb-2009-10-11-r124

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness
Cited by: 225
Author(s): Ana C. Marques, Chris P. Ponting
Software Mentions: 1
Published: almost 16 years ago

10.1093/gbe/evt185

Unexpected Genomic Variability in Clinical and Environmental Strains of the Pathogenic Yeast Candida parapsilosis
Cited by: 55
Author(s): Leszek P. Pryszcz, Tibor Németh, Attila Gácser, Toni Gabaldón
Software Mentions: 1
Published: about 11 years ago

10.1186/1472-6807-9-45

Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model
Cited by: 60
Author(s): Wenjun Zheng, Mustafa Tekpinar
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12866-016-0680-0

SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli
Cited by: 11
Author(s): Matthew D. Whiteside, Chad R. Laing, Akiff Manji, Peter Kruczkiewicz, Eduardo N. Taboada, Victor P. J. Gannon
Software Mentions: 1
Published: over 8 years ago

10.1186/1755-8794-2-47

Host sequence motifs shared by HIV predict response to antiretroviral therapy
Cited by: 13
Author(s): William Dampier, Perry Evans, Lyle H. Ungar, Aydın Tözeren
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-015-0572-6

DOCKSCORE: a webserver for ranking protein-protein docked poses
Cited by: 28
Author(s): Sony Malhotra, Oommen K. Mathew, Ramanathan Sowdhamini
Software Mentions: 1
Published: over 9 years ago

10.1038/s41398-021-01473-w

Genetic variations influence brain changes in patients with attention-deficit hyperactivity disorder
Cited by: 30
Author(s): Santosh K. Yadav, Ajaz A. Bhat, Sheema Hashem, Sabah Nisar, Madeeha Kamal, Najeeb Syed, Mohamed-Ramzi Temanni, Rakesh Kumar Gupta, Saadat Kamran, Muhammad Waqar Azeem, Amit K. Srivastava, Puneet Bagga, Sanjeev Chawla, Ravinder Reddy, Michael Frenneaux, Khalid Fakhro, Mohammad Haris
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.00469-19

Enrichment and Proteomic Characterization of the Cyst Wall from In Vitro Toxoplasma gondii Cysts
Cited by: 60
Author(s): Vincent Tu, Joshua Mayoral, Tatsuki Sugi, Tadakimi Tomita, Bing Han, Yan Fen, Louis M. Weiss
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2091-11-39

Similarity of molecular phenotype between known epilepsy gene LGI1 and disease candidate gene LGI2
Cited by: 6
Author(s): Vachiranee Limviphuvadh, Ling Ling Chua, Rabi Adawiyah Bte Rahim, Frank Eisenhaber, Sebastian Maurer‐Stroh, Subash Adhikari
Software Mentions: 1
Published: about 14 years ago

10.3390/ijerph17020478

Forest Roles in Particle Removal during Spring Dust Storms on Transport Path
Cited by: 4
Author(s): Wenjun Wu, Bing Wang, Xiang Niu
Software Mentions: 1
Published: almost 5 years ago

10.3892/ol.2014.2165

miR-339-5p inhibits cell migration and invasion in vitro and may be associated with the tumor-node-metastasis staging and lymph node metastasis of non-small cell lung cancer
Cited by: 30
Author(s): Yun Li, Weiguo Zhao, Pengtao Bao, Chunsun Li, Xiu Qing, Yanqing Li, Liangan Chen
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms20194682

Smad7 Binds Differently to Individual and Tandem WW3 and WW4 Domains of WWP2 Ubiquitin Ligase Isoforms
Cited by: 8
Author(s): Lloyd C. Wahl, Jessica E. Watt, Hiu T. T. Yim, Danielle De Bourcier, James Tolchard, Surinder M. Soond, Tharin M. A. Blumenschein, Andrew Chantry
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0131223

Evolution of the tRNALeu (UAA) Intron and Congruence of Genetic Markers in Lichen-Symbiotic Nostoc
Cited by: 10
Author(s): Ulla Kaasalainen, Sanna Olsson, Jouko Rikkinen
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0197053

Genetic diversity and virulence profiles of Listeria monocytogenes recovered from bulk tank milk, milk filters, and milking equipment from dairies in the United States (2002 to 2014)
Cited by: 47
Author(s): Seon Woo Kim, Julie Haendiges, Eric N. Keller, Robert A. Myers, Alexander Kim, Jason E. Lombard, Jeffrey S. Karns, Jo Ann S. Van Kessel, Bradd J. Haley
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-9-429

Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure
Cited by: 1
Author(s): Christopher Bystroff, Bobbie-Jo M. Webb-Robertson
Software Mentions: 1
Published: about 16 years ago

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Papers Mentioning webserver 48