Ecosyste.ms: Papers

10.1186/s12864-020-07338-8

Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria
Cited by: 10
Author(s): Ilhan Cem Duru, Anne Ylinen, Sergei Belanov, Alan Avila Pulido, Lars Paulín, Petri Auvinen
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12864-018-5266-9

Host microRNA analysis in cyprinid Herpesvirus-3 (CyHV-3) infected common carp
Cited by: 10
Author(s): M. Reichert, Anna Łukasik, Piotr Zielenkiewicz, Marek Matras, Joanna Maj‐Paluch, Magdalena Stachnik, Ewa Borzym
Software Mentions: 6
Published: almost 6 years ago

10.3390/microorganisms8081225

Lactobacillus Mucosae Strain Promoted by a High-Fiber Diet in Genetic Obese Child Alleviates Lipid Metabolism and Modifies Gut Microbiota in ApoE-/- Mice on a Western Diet
Cited by: 19
Author(s): Tianyi Jiang, Huan Wu, Xin Yang, Yue Li, Ziyi Zhang, Feng Chen, Liping Zhao, Chenhong Zhang
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0198632

Allosteric binding sites in Rab11 for potential drug candidates
Cited by: 9
Author(s): Ammu Prasanna Kumar, Suryani Lukman
Software Mentions: 5
Published: over 6 years ago

10.1186/1751-0473-8-8

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies
Cited by: 5
Author(s): Mehdi Pirooznia, Fayaz Seifuddin, Fernando S. Goes, Jeffrey T. Leek, Peter P. Zandi
Software Mentions: 5
Published: over 11 years ago

10.1186/s12862-016-0743-8

Adaptive patterns in the p53 protein sequence of the hypoxia- and cancer-tolerant blind mole rat Spalax
Cited by: 8
Author(s): Vered Domankevich, Yarden Opatowsky, Assaf Malik, Abraham B. Korol, Zeev Frenkel, Irena Manov, Aaron Avivi, Imad Shams
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pcbi.1008988

Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions
Cited by: 10
Author(s): Nikolina Šoštarić, Vera van Noort
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0069666

GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data
Cited by: 21
Author(s): Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Maria Simi, Rita Shaknovich, Fabien Campagne
Software Mentions: 5
Published: over 11 years ago

10.1186/1471-2164-15-946

Conservation analysis of the CydX protein yields insights into small protein identification and evolution
Cited by: 35
Author(s): Rondine J. Allen, Evan P. Brenner, Caitlin E. VanOrsdel, Jessica J. Hobson, David J. Hearn, Matthew R. Hemm
Software Mentions: 5
Published: almost 10 years ago

10.1186/1471-2105-12-184

SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation
Cited by: 19
Author(s): Catherine L. Anderson, Cory L. Strope, Etsuko N. Moriyama
Software Mentions: 4
Published: over 13 years ago

10.1186/1471-2164-14-665

Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation
Cited by: 23
Author(s): Matthias Harbers, Sachi Kato, Michiel de Hoon, Yoshihide Hayashizaki, Piero Carninci, Charles Plessy
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0129422

Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties
Cited by: 45
Author(s): Nagaraja Reddy Rama Reddy, Rucha Harishbhai Mehta, Palak Harendrabhai Soni, Jayanti Makasana, Narendra Gajbhiye, P. Manivel, Jitendra Kumar
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-019-5661-x

Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis
Cited by: 27
Author(s): Yajuan Li, Lingling Zhang, Ruojiao Li, Meiwei Zhang, Yangping Li, Hao Wang, Shi Wang, Zhenmin Bao
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0067129

Preliminary Assessment of Microbiome Changes Following Blood-Feeding and Survivorship in the Amblyomma americanum Nymph-to-Adult Transition using Semiconductor Sequencing
Cited by: 72
Author(s): Arturo C. Menchaca, David K. Visi, Otto F. Strey, Pete D. Teel, Kevin Kalinowski, Michael S. Allen, Phillip Williamson
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-017-4075-x

Analysis of the genome sequence of Phomopsis longicolla: a fungal pathogen causing Phomopsis seed decay in soybean
Cited by: 21
Author(s): Shuxian Li, Omar Darwish, Nadim W. Alkharouf, Bryan Musungu, Benjamin F. Matthews
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0225808

Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering
Cited by: 11
Author(s): Joel D. Klein, Manon Neilen, Marcel van Verk, Bas E. Dutilh, Guido Van den Ackerveken
Software Mentions: 3
Published: over 4 years ago

10.1186/s13062-016-0151-4

modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks
Cited by: 1
Author(s): Neetu Sain, Debasisa Mohanty
Software Mentions: 3
Published: about 8 years ago

10.3390/biology10050371

Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish
Cited by: 5
Author(s): Shital Kumar Mishra, Han Wang
Software Mentions: 3
Published: over 3 years ago

10.3390/biomedicines8020019

A Multi-Omics Analysis of Bone Morphogenetic Protein 5 (BMP5) mRNA Expression and Clinical Prognostic Outcomes in Different Cancers Using Bioinformatics Approaches
Cited by: 23
Author(s): Md. Adnan Karim, Abdus Samad, Utpal Adhikari, Md. Ashraful Kader, Md. Masnoon Kabir, Md. Aminul Islam, Md. Nazmul Hasan
Software Mentions: 3
Published: almost 5 years ago

10.3390/microorganisms8060915

Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum
Cited by: 12
Author(s): Regina Rettenmaier, Martina Schneider, Bernhard Munk, Michael Lebuhn, Sebastian Jünemann, Alexander Sczyrba, Irena Maus, Vladimir V. Zverlov, Wolfgang Liebl
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms8101621

Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis
Cited by: 16
Author(s): Guillaume Dubrulle, Adeline Picot, Stéphanie Madec, Matthieu Le Corre, Audrey Pawtowski, Riccardo Baroncelli, Michel Zivy, Thierry Balliau, Gaétan Le Floch, Flora Pensec
Software Mentions: 3
Published: about 4 years ago

10.1016/j.str.2020.08.004

Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics
Cited by: 14
Author(s): D E. Nicholson, Thomas A. Edwards, Alex J. O’Neill, Neil A. Ranson
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-80868-z

Blood-based protein profiling identifies serum protein c-KIT as a novel biomarker for hypertrophic cardiomyopathy
Cited by: 8
Author(s): Kristina Sonnenschein, Jan Fiedler, David de Gonzalo-Calvo, Xiaoyan Ke, Angelika Pfanne, Annette Just, Carolin Zwadlo, Samira Soltani, Udo Bavendiek, Theresia Kraft, Cristobal dos Remedios, Serghei Cebotari, Johann Bauersachs, Thomas Thum
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2021.639995

Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae
Cited by: 2
Author(s): Rachana Banerjee, Narendrakumar M. Chaudhari, Abhishake Lahiri, Anupam Gautam, Debaleena Bhowmik, Chitra Dutta, Sujay Chattopadhyay, Daniel H. Huson, Sandip Paul
Software Mentions: 3
Published: over 3 years ago

10.1186/s12862-019-1371-x

mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria
Cited by: 2
Author(s): Anastasia A. Kuzminkova, Anastasia D. Sokol, Kristina Ushakova, Konstantin Popadin, Konstantin Gunbin
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2019.02514

Cell-Wall-Degrading Enzymes Required for Virulence in the Host Selective Toxin-Producing Necrotroph Alternaria alternata of Citrus
Cited by: 46
Author(s): Hongshen Ma, Bin Zhang, Yunpeng Gai, Xuepeng Sun, Kuang‐Ren Chung, Hongye Li
Software Mentions: 3
Published: about 5 years ago

10.1099/acmi.0.000166

Identification of a SARS-like bat coronavirus that shares structural features with the spike glycoprotein receptor-binding domain of SARS-CoV-2
Cited by: 6
Author(s): Conchita Fraguas Bringas, David Booth
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2105-7-139

mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code
Cited by: 6
Author(s): Yuliya V. Karpievitch, Jonas S. Almeida
Software Mentions: 2
Published: over 18 years ago

10.1186/1471-2105-10-314

MetaTM - a consensus method for transmembrane protein topology prediction
Cited by: 30
Author(s): Martin Klammer, David N. Messina, Thomas Schmitt, Erik L. L. Sonnhammer
Software Mentions: 2
Published: about 15 years ago

10.1186/s12864-020-6757-z

The whole-transcriptome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak
Cited by: 34
Author(s): Hui Wang, Jincheng Zhong, Chengfu Zhang, Zhixin Chai, Hanwen Cao, Jikun Wang, Jiangjiang Zhu, Jiabo Wang, Qiumei Ji
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-14-54

Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction
Cited by: 72
Author(s): Miguel Redondo‐Nieto, Matthieu Barret, John P. Morrissey, Kieran J. Germaine, Francisco Martínez‐Granero, Emma Barahona, Ana Navazo, María Sánchez-Contreras, Jennifer A. Moynihan, Candela Muriel, David N. Dowling, Fergal O’Gara, Marta Martín, Rafael Rivilla
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12864-019-5536-1

ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation
Cited by: 8
Author(s): Viktor N. Shamanskiy, Valeria N. Timonina, Konstantin Popadin, Konstantin Gunbin
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-15-357

Transcriptomic changes during regeneration of the central nervous system in an echinoderm
Cited by: 68
Author(s): Vladimir Mashanov, Olga Zueva, José E. García‐Arrarás
Software Mentions: 2
Published: almost 11 years ago

10.1186/1472-6807-7-48

Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily
Cited by: 33
Author(s): Elena M. Ibryashkina, Marina Zakharova, Vladimir B. Baskunov, Ekaterina Bogdanova, Maxim Nagornykh, Marat M Den'mukhamedov, Bogdan S. Melnik, Andrzej Koliński, Dominik Gront, Marcin Feder, Alexander S. Solonin, Janusz M. Bujnicki
Software Mentions: 2
Published: over 17 years ago

10.6026/97320630015394

Molecular docking based design of Dengue NS5 methyltransferase inhibitors
Cited by: 4
Author(s): Mohd Adnan Kausar, Abrar Ashraf Ali, Samir Qiblawi, Syed Monowar Alam Shahid, Mohammad Asrar Izhari, Anamika Saral
Software Mentions: 2
Published: over 5 years ago

10.3390/biom11081083

The Right-Handed Parallel β-Helix Topology of Erwinia chrysanthemi Pectin Methylesterase Is Intimately Associated with Both Sequential Folding and Resistance to High Pressure
Cited by: 3
Author(s): Jessica Guillerm, Jean‐Marie Frère, Filip Meersman, André Matagne
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.9572

Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach
Cited by: 100
Author(s): Mohammad Anisur Rahman, M. Nazmul Hoque, M. Rafiul Islam, Salma Akter, Arshad Alam, Mohammad Anwar Siddique, Otun Saha, Munawar Sultana, Keith A. Crandall, M. Anwar Hossain
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0093907

MP3: A Software Tool for the Prediction of Pathogenic Proteins in Genomic and Metagenomic Data
Cited by: 92
Author(s): Ankit Gupta, Rohan Kapil, Darshan B. Dhakan, Vineet K. Sharma
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0179155

Molecular and functional characterization of two isoforms of chalcone synthase and their expression analysis in relation to flavonoid constituents in Grewia asiatica L
Cited by: 24
Author(s): Tareq A. Wani, Shahzad A. Pandith, Ajai Prakash Gupta, Suresh Chandra, Namrata Sharma, Surrinder K. Lattoo
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0203079

Fungicidal action of geraniol against Candida albicans is potentiated by abrogated CaCdr1p drug efflux and fluconazole synergism
Cited by: 53
Author(s): Shweta Singh, Zeeshan Fatima, Kamal Ahmad, Saif Hameed
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0224095

In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach
Cited by: 7
Author(s): Nematollah Gheibi, Mohammad Ghorbani, Hanifeh Shariatifar, Alireza Farasat
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0112341

Analysis of Micro-Rearrangements in 25 Eukaryotic Species Pairs by SyntenyMapper
Cited by: 4
Author(s): Stefanie Kaufmann, Dmitrij Frishman
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0150273

De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq
Cited by: 27
Author(s): Shivanjali Kotwal, Sanjana Kaul, Pooja Sharma, Manik Gupta, Rama Shankar, Mukesh Jain, Manoj K. Dhar
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0118321

Deep mRNA Sequencing of the Tritonia diomedea Brain Transcriptome Provides Access to Gene Homologues for Neuronal Excitability, Synaptic Transmission and Peptidergic Signalling
Cited by: 25
Author(s): Adriano Senatore, Neranjan Edirisinghe, Paul S. Katz
Software Mentions: 2
Published: over 9 years ago

10.1002/cmdc.202000237

Structure‐Based Macrocyclization of Substrate Analogue NS2B‐NS3 Protease Inhibitors of Zika, West Nile and Dengue viruses
Cited by: 28
Author(s): Niklas J Braun, Jun-Ping Quek, Simon Huber, Jenny Kouretova, Dorothee Rogge, Heike Lang‐Henkel, Ezekiel Ze Ken Cheong, Bing Liang Alvin Chew, A. Heine, Dahai Luo, Torsten Steinmetzer
Software Mentions: 2
Published: over 4 years ago

10.1002/ece3.6138

Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents
Cited by: 2
Author(s): Beverly J. French, Yan Wei Lim, Brian J. Zgliczynski, Robert A. Edwards, Forest Rohwer, Stuart A. Sandin
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2017.00013

Virome Assembly and Annotation: A Surprise in the Namib Desert
Cited by: 18
Author(s): Uljana Hesse, Peter van Heusden, Bronwyn M. Kirby, Israel Olonade, Leonardo Joaquim van Zyl, Marla Trindade
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2021.724451

Genome of Ganoderma Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for Ganoderma tsugae
Cited by: 12
Author(s): Nan Jiang, Shuang Hu, Bing Peng, Zhenhao Li, Xiaohui Yuan, Shijun Xiao, Yongping Fu
Software Mentions: 2
Published: about 3 years ago

10.3389/fmicb.2016.01817

Finding Potential Therapeutic Targets against Shigella flexneri through Proteome Exploration
Cited by: 19
Author(s): Mohammad Uzzal Hossain, Mukhtar A. Khan, Abu Hashem, Md. Monirul Islam, Mohammad Neaz Morshed, Chaman Ara Keya, Md. Salimullah
Software Mentions: 2
Published: about 8 years ago

10.3390/genes9120609

Towards a Central Role of ISL1 in the Bladder Exstrophy–Epispadias Complex (BEEC): Computational Characterization of Genetic Variants and Structural Modelling
Cited by: 5
Author(s): Ingo G. H. Schmidt‐Wolf, Tikam Chand Dakal, Michael Ludwig, Holger Fröhlich, Riya Mathur, Heiko Reutter
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes12040568

Deciphering the Monilinia fructicola Genome to Discover Effector Genes Possibly Involved in Virulence
Cited by: 19
Author(s): Laura Vilanova, Claudio A. Valero-Jiménez, Jan A.L. van Kan
Software Mentions: 2
Published: over 3 years ago

10.1128/genomeA.00235-16

Draft Genome Sequence of <i>Bacillus clausii</i> UBBC07, a Spore-Forming Probiotic Strain
Cited by: 5
Author(s): Aditya Upadrasta, Swetha Pitta, Ratna Sudha Madempudi
Software Mentions: 2
Published: over 8 years ago

10.1186/s13059-017-1174-6

Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes
Cited by: 64
Author(s): Hongsheng Gui, Duco Schriemer, William Cheng, Rajendra K. Chauhan, Guillermo Antiñolo, Courtney Berrios, Marta Bleda, Alice S. Brooks, Rutger W. W. Brouwer, Alan J. Burns, Stacey S. Cherny, Joaquín Dopazo, Bart J. L. Eggen, Paola Griseri, Binta Jalloh, Thuy Linh Le, Vincent Chi-Hang Lui, Berta Lasa, Ivana Matera, Elly Sau-Wai Ngan, Anna Pelet, Macarena Ruíz-Ferrer, Pak C. Sham, Iain T. Shepherd, Man Ting So, Yunia Sribudiani, Clara S. Tang, Mirjam C G N van den Hout, Herma C. van der Linde, Tjakko J. van Ham, Wilfred F. J. van IJcken, Joanne Verheij, Jeanne Amiel, Salud Borrego, Isabella Ceccherini, Aravinda Chakravarti, Stanislas Lyonnet, Paul K. H. Tam, Maria Mercè García-Barceló, Robert M.W. Hofstra
Software Mentions: 2
Published: over 7 years ago

10.1186/1477-5956-6-25

A simple and reliable protocol for mouse serum proteome profiling studies by use of two-dimensional electrophoresis and MALDI TOF/TOF mass spectrometry
Cited by: 10
Author(s): Maria Stella Ritorto, Jürgen Borlak
Software Mentions: 2
Published: almost 17 years ago

10.1038/srep18443

Treating Colon Cancer Cells with FK228 Reveals a Link between Histone Lysine Acetylation and Extensive Changes in the Cellular Proteome
Cited by: 12
Author(s): Tianyun Wang, Yanjie Jia, Xi Zhang, Sun Qilin, Yi-Chun Li, Junhe Zhang, Zhao Chun-hua, Xiaoyin Wang, Li Wang
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-021-96963-8

Revealing the molecular interplay of curcumin as Culex pipiens Acetylcholine esterase 1 (AChE1) inhibitor
Cited by: 16
Author(s): Priyashi Rao, Dweipayan Goswami, Rakesh Rawal
Software Mentions: 2
Published: about 3 years ago

10.4056/sigs.5751047

Genomic analysis of Skermanella stibiiresistens type strain SB22T
Cited by: 13
Author(s): Wentao Zhu, Jing Huang, Mingshun Li, Xiangyang Li, Gejiao Wang
Software Mentions: 2
Published: over 10 years ago

10.3390/ijms22052665

A Genomic Blueprint of Flax Fungal Parasite Fusarium oxysporum f. sp. lini
Cited by: 6
Author(s): Anastasia Samsonova, Alexander Kanapin, Mikhail Bankin, Anton Logachev, Maria Gretsova, Tatiana A. Rozhmina, Maria Samsonova
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22136874

De novo ssRNA Aptamers against the SARS-CoV-2 Main Protease: In Silico Design and Molecular Dynamics Simulation
Cited by: 7
Author(s): Francesco Morena, Chiara Argentati, Ilaria Tortorella, Carla Emiliani, Sabata Martino
Software Mentions: 2
Published: over 3 years ago

10.1007/s10967-016-4864-8

Automation system for neutron activation analysis at the reactor IBR-2, Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
Cited by: 65
Author(s): С. С. Павлов, A. Yu. Dmitriev, M. V. Frontasyeva
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-15-192

Safety in numbers: multiple occurrences of highly similar homologs among Azotobacter vinelandiicarbohydrate metabolism proteins probably confer adaptive benefits
Cited by: 10
Author(s): Mali Mærk, Jostein Johansen, Helga Ertesvåg, Finn Drabløs, Svein Valla
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0040032

CD28 Costimulation Regulates Genome-Wide Effects on Alternative Splicing
Cited by: 38
Author(s): Manish J. Butte, Sun Jung Lee, Jonathan L. Jesneck, Mary E. Keir, W. Nicholas Haining, Arlene H. Sharpe
Software Mentions: 1
Published: over 12 years ago

10.1128/mBio.02473-19

Human <i> V _H 1-69 </i> Gene-Encoded Human Monoclonal Antibodies against Staphylococcus aureus IsdB Use at Least Three Distinct Modes of Binding To Inhibit Bacterial Growth and Pathogenesis
Cited by: 16
Author(s): Monique R. Bennett, Jinhui Dong, Robin Bombardi, Cinque Soto, Helen M Parrington, Rachel S. Nargi, Clara T. Schoeder, Marcus Nagel, Kevin L. Schey, Jens Meiler, Eric P. Skaar, James E. Crowe
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0093768

Novel Identification of Dermacentor variabilis Arp2/3 Complex and Its Role in Rickettsial Infection of the Arthropod Vector
Cited by: 13
Author(s): Natthida Petchampai, Piyanate Sunyakumthorn, Mark L. Guillotte, Victoria I. Verhoeve, Kaikhushroo H. Banajee, Michael T. Kearney, Kevin R. Macaluso
Software Mentions: 1
Published: over 10 years ago

10.1002/pmic.201400614

Metaproteomics and metabolomics analyses of chronically petroleum‐polluted sites reveal the importance of general anaerobic processes uncoupled with degradation
Cited by: 48
Author(s): Rafael Bargiela, Florian‐Alexander Herbst, Mónica Martínez-Martínez, Jana Seifert, David Rojo, Simone Cappello, Maria Inés Genovese, Francesca Crisafi, Renata Denaro, Tatyana N. Chernikova, Coral Barbas, Martin von Bergen, Michail M. Yakimov, Manuel Ferrer, Peter N. Golyshin
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-11-588

Gene duplications in prokaryotes can be associated with environmental adaptation
Cited by: 75
Author(s): Marit S Bratlie, Jostein Johansen, Brad T. Sherman, Dawei Huang, Richard A. Lempicki, Finn Drabløs
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2164-14-462

Cytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes
Cited by: 36
Author(s): Kathrin K. Geyer, Iain W. Chalmers, Neil Mackintosh, Julie Elizabeth Hirst, Rory Geoghegan, Mathieu Badets, Peter M. Brophy, Klaus Brehm, Karl F. Hoffmann
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0020133

From SNPs to Genes: Disease Association at the Gene Level
Cited by: 62
Author(s): Benjamin Lehne, Cathryn M. Lewis, Thomas Schlitt
Software Mentions: 1
Published: over 13 years ago

10.1186/s12931-021-01698-9

Adhatoda Vasica attenuates inflammatory and hypoxic responses in preclinical mouse models: potential for repurposing in COVID-19-like conditions
Cited by: 19
Author(s): Atish Gheware, Dhwani Dholakia, Soundarapandian Kannan, Lipsa Panda, Ritu Rani, Bijay Pattnaik, Veena Jain, Yash Parekh, M. Ghalib Enayathullah, Kiran Kumar Bokara, V. Subramanian, Mitali Mukerji, Anurag Agrawal, Bhavana Prasher
Software Mentions: 1
Published: over 3 years ago

10.1038/srep14187

‘Obesity’ is healthy for cetaceans? Evidence from pervasive positive selection in genes related to triacylglycerol metabolism
Cited by: 32
Author(s): Zhengfei Wang, Zhuo Chen, Shixia Xu, Wenhua Ren, Kaiya Zhou, Guang Yang
Software Mentions: 1
Published: about 9 years ago

10.1128/mSphere.00269-18

<i>Fusobacterium</i> Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction
Cited by: 21
Author(s): S. Michelle Todd, Robert E. Settlage, Kevin K. Lahmers, Daniel J. Slade
Software Mentions: 1
Published: about 6 years ago

10.5005/jp-journals-10018-1232

Intrahepatic Cholestasis of Pregnancy: Spontaneous vs in vitro Fertilization
Cited by: 8
Author(s): Füsun F. Bölükbaş, Cengiz Bölükbaş, Hatice Balaban, Cem Aygün, Seyda İgnak, Emine Ergul, Mehtap Yazıcıoğlu, Suat Süphan Erşahin
Software Mentions: 1
Published: almost 7 years ago

10.3389/fimmu.2021.669812

Development of a Novel Multi-Epitope Vaccine Against Crimean-Congo Hemorrhagic Fever Virus: An Integrated Reverse Vaccinology, Vaccine Informatics and Biophysics Approach
Cited by: 31
Author(s): Muhammad Tahir ul Qamar, Saba Ismail, Sajjad Ahmad, Muhammad Usman Mirza, Sumra Wajid Abbasi, Usman Ali Ashfaq, Lingling Chen
Software Mentions: 1
Published: over 3 years ago

10.3389/fimmu.2017.00513

Comparative Analysis of Immune Checkpoint Molecules and Their Potential Role in the Transmissible Tasmanian Devil Facial Tumor Disease
Cited by: 19
Author(s): Andrew S. Flies, Nicholas B. Blackburn, A. Bruce Lyons, John D. Hayball, Gregory M. Woods
Software Mentions: 1
Published: over 7 years ago

10.3389/fmed.2020.594439

Structural Comparison of the SARS CoV 2 Spike Protein Relative to Other Human-Infecting Coronaviruses
Cited by: 34
Author(s): Marni E. Cueno, Kenichi Imai
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-016-2445-4

Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity
Cited by: 31
Author(s): Morteza Shojaei Moghadam, Andreas Albersmeier, Anderson M. Winkler, Lorenzo Cimmino, Kjersti Rise, Martin F. Hohmann‐Marriott, Jörn Kalinowski, Christian Rückert, Alexander Wentzel, Rahmi Lale
Software Mentions: 1
Published: almost 9 years ago

10.3389/fmicb.2021.602812

Comparative Transcriptomics and RNA-Seq-Based Bulked Segregant Analysis Reveals Genomic Basis Underlying Cronartium ribicola vcr2 Virulence
Cited by: 4
Author(s): Junjun Liu, Richard A. Sniezko, Arezoo Zamany, Holly Williams, Kangakola Omendja, Angelia Kegley, Douglas P. Savin
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-019-39299-8

Designing a multi-epitope based vaccine to combat Kaposi Sarcoma utilizing immunoinformatics approach
Cited by: 110
Author(s): Ved Chauhan, Tripti Rungta, Kapil Goyal, Mini P. Singh
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-14-94

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria
Cited by: 33
Author(s): Dmitry A. Ravcheev, Aaron A. Best, Natalia V. Sernova, Marat D. Kazanov, Pavel S. Novichkov, Dmitry A. Rodionov
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-019-42511-4

Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation
Cited by: 15
Author(s): Esther Camacho, Sandra González-de la Fuente, Alberto Rastrojo, Ramón Peiró‐Pastor, José Carlos Solana, Laura Tabera, Francisco Gamarro, Fernando Carrasco-Ramiro, José Marı́a Requena, Begoña Aguado
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2017.00086

Comparative Genomic Analysis of Two Vibrio toranzoniae Strains with Different Virulence Capacity Reveals Clues on Its Pathogenicity for Fish
Cited by: 5
Author(s): Aide Lasa, Cynthia Gibas, Jesús L. Romalde
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-6-181

Sal-Site: Integrating new and existing ambystomatid salamander research and informational resources
Cited by: 75
Author(s): Jeramiah J. Smith, Srikrishna Putta, John Walker, D. Kevin Kump, Amy Samuels, James R. Monaghan, David W. Weisrock, Chuck Stäben, S. Randal Voss
Software Mentions: 1
Published: almost 19 years ago

10.3389/fpls.2017.00096

Small RNAs Derived from the T-DNA of Agrobacterium rhizogenes in Hairy Roots of Phaseolus vulgaris
Cited by: 5
Author(s): Pablo Peláez, Alejandrina Hernández-López, Georgina Estrada-Navarrete, Federico Sánchez
Software Mentions: 1
Published: almost 8 years ago

10.3389/fpls.2017.01409

Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Cited by: 25
Author(s): Dandan Guo, Yongbiao Xue, Dongqiao Li, Bei-Bei He, Xin‐Lei Jia, Xin Dong, Meili Guo
Software Mentions: 1
Published: over 7 years ago

10.3390/genes9100477

Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics
Cited by: 14
Author(s): Vikas Sharma, Fauzul Mobeen, Tulika Prakash
Software Mentions: 1
Published: about 6 years ago

10.5402/2012/630861

Study on Genetic Variance of miR-541 in Type 1 Diabetes
Cited by: 4
Author(s): Bong-Ho Han, Xing Ming Shi, Peng Quan, Wentao Gao
Software Mentions: 1
Published: almost 12 years ago

10.3390/genes10060417

Genome Analysis of Hypomyces perniciosus, the Causal Agent of Wet Bubble Disease of Button Mushroom (Agaricus bisporus)
Cited by: 15
Author(s): Dan Li, Frederick Leo Sossah, Lei Sun, Yongping Fu, Li Yu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12862-017-0994-z

Evolution of the vertebrate insulin receptor substrate (Irs) gene family
Cited by: 21
Author(s): Ahmad Al-Salam, David M. Irwin
Software Mentions: 1
Published: over 7 years ago

10.1128/genomeA.00109-15

Draft Genome Sequence of a Highly Virulent Strain of the Plant Pathogen Dickeya solani, IFB0099
Cited by: 17
Author(s): Małgorzata Golanowska, Marco Galardini, Marco Bazzicalupo, Nicole Hugouvieux‐Cotte‐Pattat, Alessio Mengoni, Marta Potrykus, M. Sławiak, Ewa Łojkowska
Software Mentions: 1
Published: over 9 years ago

10.1186/s13048-017-0345-0

R-spondin2, a novel target of NOBOX: identification of variants in a cohort of women with primary ovarian insufficiency
Cited by: 9
Author(s): Justine Bouilly, Isabelle Beau, Sara Barraud, Valérie Bernard, Brigitte Delemer, Jacques Young, Nadine Binart
Software Mentions: 1
Published: over 7 years ago

10.1128/genomeA.01072-16

Genome Sequences of Malonate-Positive Cronobacter sakazakii Serogroup O:2, Sequence Type 64 Strains CDC 1121-73 and GK1025, Isolated from Human Bronchial Wash and a Powdered Infant Formula Manufacturing Plant
Cited by: 5
Author(s): Hannah R. Chase, Gopal Gopinath, Jayanthi Gangiredla, Isha R. Patel, Mahendra H. Kothary, L. Carter, Venugopal Sathyamoorthy, B. Lee, E. Park, YeonJoo Yoo, Taejung Chung, Hyerim Choi, So-Young Jun, J. Park, Seungeun Jeong, M. Kim, Felix Reich, Günter Klein, Ben D. Tall
Software Mentions: 1
Published: almost 8 years ago

10.1128/genomeA.00032-17

Genome Sequence of <i>Arcobacter</i> sp. Strain LA11, Isolated from the Abalone <i>Haliotis discus</i>
Cited by: 3
Author(s): Yukino Mizutani, Reiji Tanaka
Software Mentions: 1
Published: over 7 years ago

10.1128/genomeA.00335-17

Draft Genome Sequence of Staphylococcus fleurettii Strain MBTS-1 Isolated from Cucumber
Cited by: 1
Author(s): Bo Li, Erik Brinks, Charles M. A. P. Franz, Gyu-Sung Cho
Software Mentions: 1
Published: over 7 years ago

10.1128/genomeA.00967-17

Draft Genome Sequence of Zoonotic Streptococcus canis Isolate G361
Cited by: 10
Author(s): Inga Eichhorn, Mark van der Linden, Michael Jarek, Marcus Fulde
Software Mentions: 1
Published: about 7 years ago

10.1128/genomeA.00104-18

Genome Sequences of 15 Klebsiella sp. Isolates from Sugarcane Fields in Colombia’s Cauca Valley
Cited by: 2
Author(s): Luz K. Medina-Cordoba, Aroon T. Chande, Lavanya Rishishwar, Leonard W. Mayer, Leonardo Mariño-Ramírez, Lina C. Valderrama-Aguirre, Augusto Valderrama-Aguirre, Joel E. Kostka, I. King Jordan
Software Mentions: 1
Published: over 6 years ago

10.1264/jsme2.ME3201rh

Genomics and Metagenomics in Microbial Ecology: Recent Advances and Challenges
Cited by: 16
Author(s): Takashi Narihiro, Yoichi Kamagata
Software Mentions: 1
Published: almost 8 years ago

10.1128/MRA.01429-20

Draft Genome Sequence of Streptococcus agalactiae TA B490, a Multidrug-Resistant Strain Isolated from Bovine Mastitis in Argentina
Cited by: 1
Author(s): Jimena Soledad Cadona, Luciana Belén Hernandez, Ramiro Lorenzo, Enriqueta Bottini, Ana Victoria Bustamante, Andrea Mariel Sanso
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.00165-19

Genome Sequence of Marine-Derived <i>Streptomyces</i> sp. Strain F001, a Producer of Akashin A and Diazaquinomycins
Cited by: 3
Author(s): Jana Braesel, Chase M. Clark, Kevin Kunstman, Stefan J. Green, Mark Maienschein‐Cline, Brian T. Murphy, Alessandra S. Eustáquio
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms7100421

Genomic Insights into the Fungal Lignocellulolytic Machinery of Flammulina rossica
Cited by: 5
Author(s): Young-Jin Park, Chang‐Soo Lee, Won-Sik Kong
Software Mentions: 1
Published: about 5 years ago

10.3390/md12063516

Emerging Strategies and Integrated Systems Microbiology Technologies for Biodiscovery of Marine Bioactive Compounds
Cited by: 57
Author(s): Javier Rocha-Martín, Catriona Harrington, Alan D. W. Dobson, Fergal O’Gara
Software Mentions: 1
Published: over 10 years ago