pypi: 0 | Projects | Ecosyste.ms: Papers

10.1186/s12864-021-07542-0

Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn
Cited by: 8
Author(s): Songlin Guo, Shouxiong Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S. Moreno, Genevieve Fairbrother, David A. Hughes, Mark Stoneking, Philipp Khaitovich
Software Mentions: 13
Published: over 3 years ago

10.1186/s12911-017-0500-y

Predicting two-year survival versus non-survival after first myocardial infarction using machine learning and Swedish national register data
Cited by: 53
Author(s): John Wallert, Mattia Tomasoni, Guy Madison, Claes Held
Software Mentions: 12
Published: over 7 years ago

10.1371/journal.pone.0204123

Prediction of early breast cancer patient survival using ensembles of hypoxia signatures
Cited by: 8
Author(s): Inna Y. Gong, Natalie S. Fox, Vincent Huang, Paul C. Boutros
Software Mentions: 12
Published: about 6 years ago

10.1038/s41598-019-48495-5

Latent-period stool proteomic assay of multiple sclerosis model indicates protective capacity of host-expressed protease inhibitors
Cited by: 9
Author(s): Carlos Gutiérrez González, Stephanie Tankou, Laura M. Cox, Ellen P. Casavant, Howard L. Weiner, Joshua E. Elias
Software Mentions: 11
Published: about 5 years ago

10.1186/s12859-018-2105-6

Building protein-protein interaction networks for Leishmania species through protein structural information
Cited by: 17
Author(s): Crhisllane Rafaele dos Santos Vasconcelos, Túlio de Lima Campos, Antônio Mauro Rezende
Software Mentions: 11
Published: over 6 years ago

10.3390/ijms21124217

Transcriptome, Spliceosome and Editome Expression Patterns of the Porcine Endometrium in Response to a Single Subclinical Dose of Salmonella Enteritidis Lipopolysaccharide
Cited by: 6
Author(s): Łukasz Paukszto, Anita Mikołajczyk, J Jastrzebski, Marta Majewska, Kamil Dobrzyń, Marta Kieżun, Tadeusz Kamiński
Software Mentions: 11
Published: over 4 years ago

10.1186/s12859-021-04211-7

RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis
Cited by: 6
Author(s): Alessandro La Ferlita, Salvatore Alaimo, Sebastiano Di Bella, Emanuele Martorana, Georgios I. Laliotis, Francesco Bertoni, Luciano Cascione, Philip N. Tsichlis, Alfredo Ferro, Roberta Bosotti, Alfredo Pulvirenti
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0240895

RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef
Cited by: 9
Author(s): Joel D. Leal-Gutiérrez, Mauricio A. Elzo, Chad Carr, Raluca G. Mateescu
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.ppat.1009933

Trypanosoma brucei triggers a broad immune response in the adipose tissue
Cited by: 11
Author(s): Henrique Machado, Tiago Bizarra-Rebelo, Mariana Sequeira, Sandra Trindade, Tãnia Carvalho, Filipa Rijo‐Ferreira, Barbara Rentroia‐Pacheco, Karine Serre, Luísa M. Figueiredo
Software Mentions: 8
Published: about 3 years ago

10.3389/fgene.2021.647353

Identification of Hub Genes and Their Correlation With Immune Infiltration Cells in Hepatocellular Carcinoma Based on GEO and TCGA Databases
Cited by: 22
Author(s): Rui Huang, Jinying Liu, Hui Li, Lierui Zheng, Haojun Jin, Yaqing Zhang, Wei Ma, Junhong Su, Min Wang, Kun Yang
Software Mentions: 8
Published: over 3 years ago

10.3389/fcell.2021.704242

Two Similar Signatures for Predicting the Prognosis and Immunotherapy Efficacy of Stomach Adenocarcinoma Patients
Cited by: 4
Author(s): Taohua Yue, Shuai Zuo, Jing Zhu, Shuqin Guo, Zhihao Huang, Jichang Li, Xin Wang, Yucun Liu, Shanwen Chen, Pengyuan Wang
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-021-04166-9

PTMViz: a tool for analyzing and visualizing histone post translational modification data
Cited by: 4
Author(s): Kevin Chappell, Stefan Graw, Charity L. Washam, Aaron J. Storey, Chris Bolden, Eric C. Peterson, Stephanie D. Byrum
Software Mentions: 8
Published: over 3 years ago

10.1186/s12935-020-01707-9

PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer
Cited by: 13
Author(s): Li Zheng, Yaming Li, Xiaolong Wang, Qifeng Yang
Software Mentions: 8
Published: almost 4 years ago

10.1155/2021/8892479

PDZ Binding Kinase/T-LAK Cell-Derived Protein Kinase Plays an Oncogenic Role and Promotes Immune Escape in Human Tumors
Cited by: 4
Author(s): Tingting Feng, Yan Zhang, Sunbin Ling, Chenyang Xu, Yingqi Lyu, Tingting Lu, Xinyuan Liu, Ying Liu, Yiming Wan, Zhong Huang, Dan Su
Software Mentions: 8
Published: about 3 years ago

10.1186/s12864-020-06971-7

Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis
Cited by: 44
Author(s): Asimenia Gavriilidou, Johanna Gutleben, Dennis Versluis, Francesca Forgiarini, Mark W. J. van Passel, Colin J. Ingham, Hauke Smidt, Detmer Sipkema
Software Mentions: 8
Published: over 4 years ago

10.3389/fgene.2020.00634

Construction of a Comprehensive Multiomics Map of Hepatocellular Carcinoma and Screening of Possible Driver Genes
Cited by: 6
Author(s): Ziyu Liu, Yan Lin, Xing Gao, Rongyun Mai, Xuemin Piao, Jiazhou Ye, Rong Liang
Software Mentions: 7
Published: over 4 years ago

10.3390/s20154131

Framework and Methodology for Establishing Port-City Policies Based on Real-Time Composite Indicators and IoT: A Practical Use-Case
Cited by: 8
Author(s): Ignacio Lacalle, Andreu Belsa, Rafael Vaño, Carlos E. Palau
Software Mentions: 7
Published: over 4 years ago

10.3389/fimmu.2021.672158

Analysis of Tumor Microenvironment Characteristics in Bladder Cancer: Implications for Immune Checkpoint Inhibitor Therapy
Cited by: 21
Author(s): Xingyu Chen, Haotian Chen, Dong He, Ying Cheng, Yuxing Zhu, Mengqing Xiao, Hua Lan, Zhanwang Wang, Ke Cao
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0071515

Genomic Investigation into Strain Heterogeneity and Pathogenic Potential of the Emerging Gastrointestinal Pathogen Campylobacter ureolyticus
Cited by: 21
Author(s): Susan Bullman, Alan Lucid, Daniel Corcoran, Roy D. Sleator, Brigid Lucey
Software Mentions: 7
Published: about 11 years ago

10.1371/journal.pgen.1009201

Genomic and transcriptomic landscape of conjunctival melanoma
Cited by: 14
Author(s): Katarina Cisarova, Marc Folcher, Ikram El Zaoui, Rosanna Pescini Gobert, Virginie G. Peter, Béryl Royer‐Bertrand, Léonidas Zografos, Ann Schalenbourg, Michaël Nicolas, Donata Rimoldi, Serge Leyvraz, Nicolò Riggi, Alexandre Moulin, Carlo Rivolta
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12864-021-07544-y

Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam)
Cited by: 14
Author(s): Shizhuo Xiao, Pao Xu, Yitong Deng, Xiaofeng Dai, Lukuan Zhao, Bettina Heider, An Zhang, Zhiguang Zhou, Qinghe Cao
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2164-9-S1-S5

Transcription network construction for large-scale microarray datasets using a high-performance computing approach
Cited by: 14
Author(s): Mengxia Zhu, Qishi Wu
Software Mentions: 7
Published: almost 17 years ago

10.7554/eLife.54655

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation
Cited by: 58
Author(s): Ira Alexandra Iosub, Rob W. van Nues, Stuart McKellar, Karen Jule Nieken, Marta Marchioretto, Brandon Sy, Jai J. Tree, Gabriella Viero, Sander Granneman
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pntd.0008018

Using affinity propagation clustering for identifying bacterial clades and subclades with whole-genome sequences of Francisella tularensis
Cited by: 5
Author(s): Anne Busch, Timo Homeier‐Bachmann, Mostafa Y. Abdel-Glil, Anja Hackbart, Helmut Hotzel, Herbert Tomaso
Software Mentions: 6
Published: about 4 years ago

10.1093/gigascience/gix049

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Cited by: 114
Author(s): Sarah S.T. Mak, Shyam Gopalakrishnan, Christian Carøe, Chunyu Geng, Shanlin Liu, Mikkel‐Holger S. Sinding, Lukas F. K. Kuderna, Wenwei Zhang, Shujin Fu, Filipe Garrett Vieira, Mietje Germonpré, Hervé Bocherens, Sergey Fedorov, Bent Petersen, Thomas Sicheritz-Pontén, Tomás Marquès-Bonet, Guojie Zhang, Hui Jiang, M. Thomas P. Gilbert
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0089489

Evidence for an Epistatic Effect between TP53 R72P and MDM2 T309G SNPs in HIV Infection: A Cross-Sectional Study in Women from South Brazil
Cited by: 4
Author(s): Fernando Pires Hartwig, Ludmila Gonçalves Entiauspe, Emily Montosa Nunes, Fernanda Martins Rodrigues, Tiago Collares, Fabiana Kömmling Seixas, Mariângela Freitas da Silveira
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pone.0200390

Molecular marker sequences of cattle Cooperia species identify Cooperia spatulata as a morphotype of Cooperia punctata
Cited by: 18
Author(s): Sabrina Ramünke, Fernando de Almeida Borges, Elke von Son-de Fernex, Georg von Samson‐Himmelstjerna, Jürgen Krücken
Software Mentions: 6
Published: over 6 years ago

10.3390/cancers13143394

Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma
Cited by: 7
Author(s): Fereshteh Izadi, Benjamin Sharpe, Stella P. Breininger, Maria Secrier, Jane Gibson, Robert Walker, S Rahman, Ginny Devonshire, Matthew G. Lloyd, Zoë S. Walters, Rebecca Fitzgerald, Matthew Rose-Zerilli, Tim Underwood
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2017.01379

Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis)
Cited by: 25
Author(s): Obed Hernández‐Gómez, Jason T. Hoverman, Rod N. Williams
Software Mentions: 6
Published: over 7 years ago

10.3389/fgene.2021.625236

Identification of Prognostic Stromal-Immune Score–Based Genes in Hepatocellular Carcinoma Microenvironment
Cited by: 4
Author(s): Shanshan Liu, Guangchuang Yu, Li Liu, Xiaobao Zou, Lang Zhou, Erqiang Hu, Yang Song
Software Mentions: 6
Published: almost 4 years ago

10.18632/aging.202478

Tumor microenvironment characterization in triple-negative breast cancer identifies prognostic gene signature
Cited by: 7
Author(s): Yan Qin, Jiehua Deng, Lihua Zhang, Jiaxing Yuan, Huawei Yang, Qiuyun Li
Software Mentions: 6
Published: almost 4 years ago

10.3390/pathogens9010024

Genome-Wide Analysis of Cyclophilin Proteins in 21 Oomycetes
Cited by: 2
Author(s): Yan Zhang, Kyle Fletcher, Rongkui Han, Richard W. Michelmore, Ruiwu Yang
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0116177

Evolution of p53 Transactivation Specificity through the Lens of a Yeast-Based Functional Assay
Cited by: 12
Author(s): Mattia Lion, Ivan Raimondi, Stefano Donati, Olivier Jousson, Yari Ciribilli, Alberto Inga
Software Mentions: 6
Published: almost 10 years ago

10.1186/s13071-020-04265-1

Molecular analysis of polymorphic species of the genus Marshallagia (Nematoda: Ostertagiinae)
Cited by: 9
Author(s): Abdurakhim Kuchboev, Khanifakhon Sobirova, R. Karimova, Oybek Amirov, Georg von Samson‐Himmelstjerna, Jürgen Krücken
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.34408

The MR-Base platform supports systematic causal inference across the human phenome
Cited by: 2,864
Author(s): Gibran Hemani, Jie Zheng, Benjamin Elsworth, Kaitlin H Wade, Valeriia Haberland, Denis Baird, Charles Laurin, Stephen Burgess, Jack Bowden, Ryan Langdon, Vanessa Tan, James Yarmolinsky, Hashem A. Shihab, Nicholas J. Timpson, David M. Evans, Caroline L Relton, Richard M. Martin, George Davey Smith, Tom R. Gaunt, Philip Haycock
Software Mentions: 6
Published: over 6 years ago

10.1186/s12967-021-03012-z

Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression
Cited by: 18
Author(s): Xu Liu, Li Yao, Jingkun Qu, Lin Liu, Ning Lü, Jiansheng Wang, Zhang Jia
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pbio.1002210

The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster
Cited by: 258
Author(s): Claire L. Webster, Fergal M Waldron, Shaun Robertson, Daisy Crowson, Giada Ferrari, Juan F. Quintana, Jean-Michel Brouqui, Elizabeth H. Bayne, Ben Longdon, Amy H. Buck, Brian P. Lazzaro, Jewelna Akorli, Penelope R. Haddrill, Darren J. Obbard
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0116095

ICan: An Integrated Co-Alteration Network to Identify Ovarian Cancer-Related Genes
Cited by: 9
Author(s): Yuanshuai Zhou, Yongjing Liu, Kening Li, Rui Zhang, Fujun Qiu, Ning Zhao, Yan Xu
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pgen.1008367

Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development
Cited by: 15
Author(s): Robert L. Baker, Wen Fung Leong, Marcus T. Brock, Matthew J. Rubin, R. J. Cody Markelz, Stephen M. Welch, Julin Maloof, Cynthia Weinig
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.0030132

Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes
Cited by: 14
Author(s): Patricia Ryan, Brian W. Kirk, Chad W. Euler, Raymond Schuch, Vincent A. Fischetti
Software Mentions: 5
Published: over 17 years ago

10.1186/1471-2105-14-174

PMTED: a plant microRNA target expression database
Cited by: 46
Author(s): Xiaofan Sun, Boquan Dong, Lingjie Yin, Rongzhi Zhang, Wei Du, Dongfeng Liu, Nan Shi, Aili Li, Yanchun Liang, Long Mao
Software Mentions: 5
Published: over 11 years ago

10.1186/gb-2013-14-6-r66

Separating homeologs by phasing in the tetraploid wheat transcriptome
Cited by: 129
Author(s): Ksenia V. Krasileva, Vince Buffalo, Paul Bailey, Stephen Pearce, Sarah Ayling, Facundo Tabbita, Marcelo Soria, Shichen Wang, Eduard Akhunov, Cristóbal Uauy, Jorge Dubcovsky
Software Mentions: 5
Published: over 11 years ago

10.1007/s13577-021-00492-5

Establishment and characterization of 38 novel patient-derived primary cancer cell lines using multi-region sampling revealing intra-tumor heterogeneity of gallbladder carcinoma
Cited by: 5
Author(s): Feiling Feng, Qiang Cheng, Bin Li, Chen Liu, Huizhen Wang, Xiang Xu, Yang Yu, Zishuo Chen, Xiaobing Wu, Dong Hua, Kai-Jian Chu, Zhenghua Xie, Qingxiang Gao, Lei Xiong, Fugen Li, Bin Yi, Dadong Zhang, Xiaoqing Jiang
Software Mentions: 5
Published: over 3 years ago

10.3389/fpls.2021.620786

On-Farm Trials Reveal Significant but Uncertain Control of Botrytis cinerea by Aureobasidium pullulans and Potassium Bicarbonate in Organic Grapevines
Cited by: 8
Author(s): Anabelle Laurent, David Makowski, Nicolas Aveline, Sévérine Dupin, Fernando E. Miguez
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2105-11-221

GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs
Cited by: 77
Author(s): Alberto Risueño, Celia Fontanillo, Marcel E. Dinger, Javier De Las Rivas
Software Mentions: 5
Published: over 14 years ago

10.1186/s13059-019-1905-y

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
Cited by: 442
Author(s): Shujun Ou, Weija Su, Yi Liao, Kapeel Chougule, Jireh Agda, Adam J. Hellinga, Carlos Santiago Blanco Lugo, Tyler A. Elliott, Doreen Ware, Thomas Peterson, Ning Jiang, Candice N. Hirsch, Matthew B. Hufford
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0119027

Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss Mutant
Cited by: 17
Author(s): Zhiying Li, Jiabin Wang, Xuequan Zhang, Li Xu
Software Mentions: 5
Published: over 9 years ago

10.1186/s12859-015-0574-4

Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease
Cited by: 42
Author(s): Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama
Software Mentions: 5
Published: over 9 years ago

10.1186/s12862-017-1064-2

Rapid turnover of effectors in grass powdery mildew (Blumeria graminis)
Cited by: 45
Author(s): Fabrizio Menardo, Coraline R. Praz, Thomas Wicker, Beat Keller
Software Mentions: 5
Published: about 7 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

10.1371/journal.pone.0191006

A census of P. longum’s phytochemicals and their network pharmacological evaluation for identifying novel drug-like molecules against various diseases, with a special focus on neurological disorders
Cited by: 33
Author(s): Neha Choudhary, Vikram Singh
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12870-021-03193-1

The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn)
Cited by: 7
Author(s): Jingwen Chen, Qian Yan, Jiawei Li, Lei Feng, Yi Zhang, Jing Xu, Rui Xia, Zaohai Zeng, Yuanlong Liu
Software Mentions: 5
Published: about 3 years ago

10.12688/wellcomeopenres.14265.2

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
Cited by: 37
Author(s): John A. Lees, Michaela Kendall, Julian Parkhill, Caroline Colijn, SD Bentley, Rachel Harris
Software Mentions: 5
Published: over 6 years ago

10.2196/25995

Isolating SARS-CoV-2 Strains From Countries in the Same Meridian: Genome Evolutionary Analysis
Cited by: 5
Author(s): Emilio Mastriani, Alexey V. Rakov, Shulin Liu
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmolb.2021.624575

Identification of Radiotherapy-Associated Genes in Lung Adenocarcinoma by an Integrated Bioinformatics Analysis Approach
Cited by: 7
Author(s): Junhao Wang, Qizheng Han, Huizi Liu, Haihua Luo, Lei Li, Aihua Liu, Yong Jiang
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1002415

A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
Cited by: 30
Author(s): Chia Huey Ooi, Hue Kian Oh, H Wang, Angie Lay Keng Tan, Jeanie Wu, Ming‐Hui Lee, Sun Young Rha, Hyun Cheol Chung, David M. Virshup, Patrick Tan
Software Mentions: 4
Published: almost 13 years ago

10.1186/1471-2105-8-273

The utility of MAS5 expression summary and detection call algorithms
Cited by: 144
Author(s): Stuart D Pepper, Emma Saunders, Laura Edwards, Claire Wilson, Crispin Miller
Software Mentions: 4
Published: over 17 years ago

10.1038/srep44171

SEDA: A software package for the Statistical Earthquake Data Analysis
Cited by: 16
Author(s): Anna Maria Lombardi
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-018-2309-9

Predicting overlapping protein complexes based on core-attachment and a local modularity structure
Cited by: 23
Author(s): Rongquan Wang, Caixia Wang, Lingtao Su, Liankun Sun
Software Mentions: 4
Published: over 6 years ago

10.3390/insects11010004

Comparative Transcriptome Analysis of Thitarodes Armoricanus in Response to the Entomopathogenic Fungi Paecilomyces Hepiali and Ophiocordyceps Sinensis
Cited by: 7
Author(s): Zhongchen Rao, Li Cao, Hua Wu, Xuehong Qiu, Guiqing Liu, Richou Han
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1008900

A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata
Cited by: 25
Author(s): Paul J. Seear, Catherine L. Gregory, Darren Heavens, Roswitha Schmickl, Levi Yant, James D. Higgins
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-019-2732-6

The cis-trans binding strength defined by motif frequencies facilitates statistical inference of transcriptional regulation
Cited by: 4
Author(s): Yance Feng, Sheng Zhang, Liang Li, Lei M. Li
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-17298-x

NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma
Cited by: 59
Author(s): Kevin Brennan, June Ho Shin, Joshua K. Tay, Marcos Prunello, Andrew J. Gentles, John B. Sunwoo, Olivier Gevaert
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13073-020-00740-7

Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues
Cited by: 24
Author(s): Jean-David Larouche, Assya Trofimov, Leslie Hesnard, Grégory Ehx, Qingchuan Zhao, Krystel Vincent, Chantal Durette, Patrick Gendron, Jean‐Philippe Laverdure, Éric Bonneil, Caroline Côté, Sébastien Lemieux, Pierre Thibault, Claude Perreault
Software Mentions: 4
Published: over 4 years ago

10.3390/plants9111612

In-silico Exploration of Channel Type and Efflux Silicon Transporters and Silicification Proteins in 80 Sequenced Viridiplantae Genomes
Cited by: 6
Author(s): Muhammad Amjad Nawaz, Farrukh Azeem, Alexander M. Zakharenko, Xiao Lin, Rana Muhammad Atif, Faheem Shehzad Baloch, Ting‐Fung Chan, Gyuhwa Chung, Junghee Ham, Sangmi Sun, Kirill S. Golokhvast
Software Mentions: 4
Published: about 4 years ago

10.1016/j.gpb.2018.10.006

I3: A Self-organising Learning Workflow for Intuitive Integrative Interpretation of Complex Genetic Data
Cited by: 1
Author(s): Yun Tan, Lulu Jiang, Kankan Wang, Hai Fang
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.1066

Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree
Cited by: 33
Author(s): Nagesh A. Kuravadi, Vijay A. Yenagi, Kannan Rangiah, H. B. Mahesh, Anantharamanan Rajamani, Meghana Deepak Shirke, Heikham Russiachand, Ramya Malarini Loganathan, Chandana Shankara Lingu, S Shilpa, Aishwarya Ramamurthy, B. N. Sathyanarayana, Malali Gowda
Software Mentions: 4
Published: over 9 years ago

10.1186/s13059-020-02240-8

Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer
Cited by: 51
Author(s): Miho Oka, Lai Xu, Toshihiro Suzuki, Toshiaki Yoshikawa, Hiromi Sanada, Hayato Uemura, Akiyasu C. Yoshizawa, Yutaka Suzuki, Tetsuya Nakatsura, Yasushi Ishihama, Ayako Suzuki, Masahide Seki
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2148-8-201

Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis, based on cytochrome b sequences
Cited by: 33
Author(s): Liang Zhao, Jie Zhang, Zhijin Liu, Stephan M. Funk, Fuwen Wei, Muqi Xu, Ming Li
Software Mentions: 4
Published: over 16 years ago

10.7717/peerj.11581

iSUMOK-PseAAC: prediction of lysine sumoylation sites using statistical moments and Chou’s PseAAC
Cited by: 20
Author(s): Yaser Daanial Khan, Nabeel Sabir Khan, Sheraz Naseer, Ahmad Hassan Butt
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-015-0735-9

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population
Cited by: 39
Author(s): Joke Baute, Dorota Herman, Frederik Coppens, Jolien De Block, Bram Slabbinck, Matteo Dell’Acqua, Mario Enrico Pè, Steven Maere, Hilde Nelissen, Dirk Inzé
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-021-02369-0

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
Cited by: 23
Author(s): Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner, Seth W. Cheetham
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-020-07257-8

Intricate genetic variation networks control the adventitious root growth angle in apple
Cited by: 5
Author(s): Caixia Zheng, Fei Shen, Yi Wang, Ting Wu, Xuefeng Xu, Xinzhong Zhang, Zhenhai Han
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmolb.2020.00027

Conformational Changes Induced by S34Y and R98C Variants in the Death Domain of Myd88
Cited by: 2
Author(s): Vijayakumar Gosu, Kyeong-Hye Won, Jae-Don Oh, Donghyun Shin
Software Mentions: 4
Published: over 4 years ago

10.3389/fonc.2021.665080

Bioinformatics, Molecular Docking and Experiments In Vitro Analyze the Prognostic Value of CXC Chemokines in Breast Cancer
Cited by: 14
Author(s): Fei Wang, Chong Yuan, Wu H, Bo Liu, Yong Yang
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-017-3800-9

A comprehensive proteogenomic study of the human Brucella vaccine strain 104 M
Cited by: 12
Author(s): Xiaodong Zai, Qiaoling Yang, Kun Liu, Ruihua Li, Mengying Qian, Taoran Zhao, Yaohui Li, Ying Yin, Dayong Dong, Ling Fu, Shanhu Li, Junjie Xu, Wei Chen
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2021.598778

A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach
Cited by: 14
Author(s): Patricio Oyarzún, Manju Kashyap, Victor Fica, Alexis Salas-Burgos, Faviel F. Gonzalez-Galarza, Antony McCabe, Andrew R. Jones, Derek Middleton, Boštjan Kobe
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2019.01975

Functional Genomic Analyses of Exopolysaccharide-Producing Streptococcus thermophilus ASCC 1275 in Response to Milk Fermentation Conditions
Cited by: 8
Author(s): Qinglong Wu, Hung Chu, Aparna Padmanabhan, Nagendra P. Shah
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2020.01023

Integrative Analysis of Membrane Proteome and MicroRNA Reveals Novel Lung Cancer Metastasis Biomarkers
Cited by: 7
Author(s): Yan Kong, Zhi Qiao, Yongyong Ren, Georgi Z. Genchev, Mengyu Ge, Hua Xiao, Hongyu Zhao, Hui Lü
Software Mentions: 4
Published: about 4 years ago

10.3389/fcell.2020.00380

Paternal Resistance Training Modulates Calcaneal Tendon Proteome in the Offspring Exposed to High-Fat Diet
Cited by: 8
Author(s): Ivo Vieira de Sousa Neto, Ramires Alsamir Tibana, Leonardo Gomes de Oliveira da Silva, Eliene Martins de Lira, Gleyce Pires Gonçalves do Prado, Jeeser Alves de Almeida, Octávio Luiz Franco, João Luíz Quagliotti Durigan, Adetola B Adesida, Marcelo Valle de Sousa, Carlos André Ornelas Ricart, Hylane Luiz Damascena, Mariana S. Castro, Wagner Fontes, Jonato Prestes, Rita de Cássia Marqueti
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-021-07932-4

Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots
Cited by: 3
Author(s): Brad S. Coates, Emeline Deleury, Aaron J. Gassmann, Bruce E. Hibbard, Lance J. Meinke, Nicholas J. Miller, Jennifer L. Petzold-Maxwell, B. Wade French, Thomas W. Sappington, Blair D. Siegfried, Thomas Guillemaud
Software Mentions: 4
Published: about 3 years ago

10.3389/fimmu.2021.685237

Key Macrophage Responses to Infection With Mycobacterium tuberculosis Are Co-Regulated by microRNAs and DNA Methylation
Cited by: 11
Author(s): Monika Looney, Rachel Lorenc, Marc K. Halushka, Petros C. Karakousis
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-018-5357-7

A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication
Cited by: 24
Author(s): Yanling Ma, Miao Liu, Jiri Stiller, Chunji Liu
Software Mentions: 4
Published: almost 6 years ago

10.1093/database/baaa115

HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations
Cited by: 4
Author(s): Bohdan B. Khomtchouk, Christopher S. Nelson, Kasra A. Vand, Salvator Palmisano, Robert L. Grossman
Software Mentions: 4
Published: almost 5 years ago

10.1111/eva.12907

<i>Rattus</i>population genomics across the Haida Gwaii archipelago provides a framework for guiding invasive species management
Cited by: 11
Author(s): Bryson M. F. Sjodin, Robyn L. Irvine, Adam T. Ford, Gregg R. Howald, Michael A. Russello
Software Mentions: 4
Published: almost 5 years ago

10.15252/msb.20167233

A method for high‐throughput production of sequence‐verified <scp>DNA</scp> libraries and strain collections
Cited by: 36
Author(s): Justin D. Smith, Ulrich Schlecht, Weihong Xu, Sundari Suresh, Joe Horecka, Michael Proctor, Raeka S. Aiyar, Richard A. O. Bennett, Angela M. Chu, Yong Fuga Li, Kevin Roy, Ronald W. Davis, Lars M. Steinmetz, Richard W. Hyman, Sasha F. Levy, Robert P. St.Onge
Software Mentions: 4
Published: almost 8 years ago

10.1111/mec.14865

Species-complex diversification and host-plant associations in <i>Bemisia tabaci</i> : A plant-defence, detoxification perspective revealed by RNA-Seq analyses
Cited by: 37
Author(s): Osnat Malka, Diego Santos-García, Ester Feldmesser, Elad Sharon, Renate Krause‐Sakate, Hélène Delatte, Sharon van Brunschot, Mitulkumar V. Patel, Paul Visendi, Habibu Mugerwa, Susan Seal, John Colvin, Shai Morin
Software Mentions: 4
Published: about 6 years ago

10.1038/s42003-019-0606-0

Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites
Cited by: 49
Author(s): Maéva Angélique Techer, Rahul Rane, Miguel L. Grau, John M. K. Roberts, Shawn Sullivan, Ivan Liachko, Anna K. Childers, Jay D. Evans, Alexander S. Mikheyev
Software Mentions: 4
Published: about 5 years ago

10.3390/genes10100823

Dissecting the Genome-Wide Evolution and Function of R2R3-MYB Transcription Factor Family in Rosa chinensis
Cited by: 13
Author(s): Yu Han, Jiayao Yu, Tao Zhao, Tangren Cheng, Jia Wang, Weiru Yang, Huitang Pan, Qixiang Zhang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-016-2695-1

Improving microRNA target prediction with gene expression profiles
Cited by: 22
Author(s): Cesaré Ovando-Vázquez, Daniel Lepe-Soltero, Cei Abreu‐Goodger
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-019-3220-8

Modeling aspects of the language of life through transfer-learning protein sequences
Cited by: 292
Author(s): Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes, Burkhard Rost
Software Mentions: 4
Published: almost 5 years ago

10.1093/molbev/msw004

Environmental Correlation Analysis for Genes Associated with Protection against Malaria
Cited by: 20
Author(s): Margaret J. Mackinnon, Carolyne Ndila, Sophie Uyoga, Alex Macharia, Robert W. Snow, Gavin Band, Anna Rautanen, Kirk A. Rockett, Dominic P. Kwiatkowski, Thomas N. Williams
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-015-1660-8

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus
Cited by: 59
Author(s): Michael H. Perlin, Joëlle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan M. Goldberg, Sébastien Duplessis, Bernard Henrissat, Sarah Young, Qiandong Zeng, Gabriela Aguileta, Elsa Petit, Hélène Badouin, Jared Andrews, Dominique Razeeq, Toni Gabaldón, Hadi Quesneville, Tatiana Giraud, Michael E. Hood, David J. Schultz, Christina A. Cuomo
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2105-12-275

AlignHUSH: Alignment of HMMs using structure and hydrophobicity information
Cited by: 11
Author(s): Krishnadev Oruganty, Narayanaswamy Srinivasan
Software Mentions: 4
Published: over 13 years ago

10.1186/s12915-020-00802-7

A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity
Cited by: 25
Author(s): Timothy Driscoll, Victoria I. Verhoeve, Joseph J. Gillespie, J. Spencer Johnston, Mark L. Guillotte, Kristen E. Rennoll-Bankert, M. Sayeedur Rahman, Darren E. Hagen, Christine G. Elsik, Kevin R. Macaluso, Abdu F. Azad
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0255971

TCF21 regulates miR-10a-5p/LIN28B signaling to block the proliferation and invasion of melanoma cells
Cited by: 5
Author(s): Hongxia Zhu, Mengshi Kang, Xinping Bai
Software Mentions: 4
Published: about 3 years ago

10.3390/cells9020387

Separated Siamese Twins: Intronic Small Nucleolar RNAs and Matched Host Genes May be Altered in Conjunction or Separately in Multiple Cancer Types
Cited by: 7
Author(s): Marianna Penzo, Rosanna Clima, Davide Treré, Lorenzo Montanaro
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12888-018-1741-8

Prevalence of depression or depressive symptoms among people living with HIV/AIDS in China: a systematic review and meta-analysis
Cited by: 68
Author(s): Tingting Wang, Hanlin Fu, Atipatsa Chiwanda Kaminga, Zhanzhan Li, Gangqiang Guo, Lizhang Chen, Qiongxuan Li
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0256471

Radiology- and gene-based risk stratification in small renal cell carcinoma: A preliminary study
Cited by: 0
Author(s): Takao Sugiyama, Yasuhiro Ushijima, Yuki Motomura, Katsumi Sakamoto, Masakazu Hirakawa, Akihiro Nishie, Koshi Mimori, Yasuo Yamashita, Takashi Tsutsumi, Kousei Ishigami
Software Mentions: 4
Published: about 3 years ago

10.1186/s12859-017-1820-8

An effective approach to detecting both small and large complexes from protein-protein interaction networks
Cited by: 18
Author(s): Bin Xu, Yan Wang, Zewei Wang, Jiaogen Zhou, Shuigeng Zhou, Jihong Guan
Software Mentions: 4
Published: about 7 years ago

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