10.1371/journal.pgen.1008632

Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination
Cited by: 24
Author(s): Wioletta Czaja, Douda Bensasson, Hyo Won Ahn, David Garfinkel, Casey M. Bergman
Software Mentions: 6
Published: over 6 years ago

10.1155/2020/8468303

Investigation of the Potential Mechanism Governing the Effect of the Shen Zhu San on COVID-19 by Network Pharmacology
Cited by: 5
Author(s): Yuxuan Wang, Yuhua Ru, Guowei Zhuo, Maozheng Sheng, Shuangqiu Wang, Jiarui Ma, Guowei Zhou, Xiaohe Sun, Yanqi Zeng, Ya Zhang, Hui Li, Zhigang Lu, Depei Wu, Minghua Wu
Software Mentions: 6
Published: over 5 years ago

10.1186/s40364-021-00292-x

The REASON score: an epigenetic and clinicopathologic score to predict risk of poor survival in patients with early stage oral squamous cell carcinoma
Cited by: 13
Author(s): Chi T. Viet, Gary Yu, Kesava Asam, Carissa M. Thomas, Angela J. Yoon, Yan Chen Wongworawat, Mina Haghighiabyaneh, Courtney A. Kilkuts, Caitlyn M. McGue, Marcus Couey, Nicholas Callahan, Coleen Doan, Paul C. Walker, Khanh K. Nguyen, Stephanie C. Kidd, Steve C. Lee, Anupama Grandhi, Allen Cheng, Ashish Patel, Elizabeth Philipone, Olivia L. Ricks, Clint Allen, Bradley E. Aouizerat
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pbio.3000741

Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei
Cited by: 32
Author(s): Eva Doleželová, Michaela Kunzová, Mario Dejung, Michal Levin, Brian Panicucci, Clément Regnault, Christian J. Janzen, Michael P. Barrett, Falk Butter, Alena Zı́ková
Software Mentions: 6
Published: about 6 years ago

10.3390/tropicalmed6020061

Epidemiology of West Nile Virus Infections in Humans, Italy, 2012–2020: A Summary of Available Evidences
Cited by: 22
Author(s): Matteo Riccò, Simona Peruzzi, Federica Balzarini
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0240010

Framing COVID-19: How we conceptualize and discuss the pandemic on Twitter
Cited by: 135
Author(s): Philipp Wicke, Marianna Bolognesi
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0191557

Modelling human hard palate shape with Bézier curves
Cited by: 9
Author(s): Ruud Janssen, Scott R. Moisik, Dan Dediu
Software Mentions: 6
Published: over 8 years ago

10.1186/s12864-021-07686-z

Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data
Cited by: 6
Author(s): Johannes Smolander, Sofia Khan, Kalaimathy Singaravelu, Leni Kauko, Riikka Lund, Asta Laiho, Laura L. Elo
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.4013

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks
Cited by: 26
Author(s): Jonathan Barnoud, Hubert Santuz, Pierrick Craveur, Agnel Praveen Joseph, Vincent Jallu, Alexandre G. de Brevern, Pierre Poulain
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pgen.1006563

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing
Cited by: 163
Author(s): Rui Zhang, Patricia Deng, Jacobson Dionna, Jin Billy Li
Software Mentions: 6
Published: over 9 years ago

10.3389/fcvm.2020.580573

Comprehensive Identification of Key Genes Involved in Development of Diabetes Mellitus-Related Atherogenesis Using Weighted Gene Correlation Network Analysis
Cited by: 14
Author(s): Qi Huang, Guo-Xiong Deng, Rongguo Wei, Qiaoye Wang, Donghua Zou, Jinru Wei
Software Mentions: 6
Published: over 5 years ago

10.1038/s42003-021-02012-5

High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans
Cited by: 22
Author(s): Alexandra Schoenle, Manon Hohlfeld, Karoline Hermanns, Frédéric Mahé, Colomban de Vargas, Frank Nitsche, Hartmut Arndt
Software Mentions: 6
Published: about 5 years ago

10.3390/tropicalmed6030116

Public Perceptions on Non-Pharmaceutical Interventions for West Nile Virus Infections: A Survey from an Endemic Area in Northern Italy
Cited by: 9
Author(s): Matteo Riccò, Simona Peruzzi, Federica Balzarini
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.484

The mitochondrial genome of<i>Paragonimus westermani</i>(Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda)
Cited by: 29
Author(s): Devendra Kumar Biswal, Anupam Chatterjee, Alok Bhattacharya, Veena Tandon
Software Mentions: 6
Published: almost 12 years ago

10.1111/1755-0998.13022

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring
Cited by: 64
Author(s): Jérôme Morinière, Michael Balke, Dieter Doczkal, Matthias F. Geiger, Laura A. Hardulak, Gerhard Haszprunar, Axel Hausmann, Lars Hendrich, Ledis Regalado, Björn Rulik, Stefan Schmidt, Johann‐Wolfgang Wägele, Paul D. N. Hebert
Software Mentions: 6
Published: about 7 years ago

10.1002/cam4.3133

Charactering tumor microenvironment reveals stromal‐related transcription factors promote tumor carcinogenesis in gastric cancer
Cited by: 14
Author(s): Haining Liu, Shujuan Ni, Hanbo Wang, Qiongyan Zhang, Wei-Hung Weng
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pcbi.1007939

Iterative point set registration for aligning scRNA-seq data
Cited by: 3
Author(s): Amir Alavi, Ziv Bar‐Joseph
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-016-2381-3

Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida
Cited by: 40
Author(s): Antony T. Vincent, Mélanie V. Trudel, Luca Freschi, Vandan Nagar, Cynthia Gagné-Thivierge, Roger C. Levesque, Steve J. Charette
Software Mentions: 6
Published: over 10 years ago

10.1186/s13059-020-02042-y

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations
Cited by: 60
Author(s): Nicolai Karcher, Edoardo Pasolli, Francesco Asnicar, Kun Huang, Adrian Tett, Serena Manara, Federica Armanini, D. J. G. Bain, Sylvia H. Duncan, Petra Louis, Moreno Zolfo, Paolo Manghi, Mireia Vallès-Colomer, Roberta Raffaetà, Omar Rota‐Stabelli, María Carmen Collado, Georg Zeller, Daniel Falush, Frank Maixner, Alan W. Walker, Curtis Huttenhower, Nicola Segata
Software Mentions: 6
Published: about 6 years ago

10.1186/1471-2105-7-467

Goulphar: rapid access and expertise for standard two-color microarray normalization methods
Cited by: 55
Author(s): Sophie Lemoine, Florence Combes, Nicolas Servant, Stéphane Le Crom
Software Mentions: 6
Published: over 19 years ago

10.1186/s12864-019-6034-1

De novo profiling of RNA viruses in Anopheles malaria vector mosquitoes from forest ecological zones in Senegal and Cambodia
Cited by: 19
Author(s): Eugeni Belda, Ferdinand Nanfack-Minkeu, Karin Eiglmeier, Guillaume Carissimo, Inge Holm, Mawlouth Diallo, Diawo Diallo, Amélie Vantaux, Saorin Kim, Igor V. Sharakhov, Kenneth D. Vernick
Software Mentions: 6
Published: almost 7 years ago

10.3389/fpls.2021.613059

Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato (Solanum lycopersicum L. Mill)
Cited by: 24
Author(s): Vicent Arbona, Miguel González-Guzmán, Zara Pitarch, José Tomás Matus, Héctor Candela, José L. Rambla, Antonio Granell, Aurelio Gómez‐Cadenas
Software Mentions: 6
Published: over 5 years ago

10.7717/peerj.9621

Identification and validation of prognostic signature for breast cancer based on genes potentially involved in autophagy
Cited by: 11
Author(s): Shanliang Zhong, Huanwen Chen, Su-Jin Yang, Jifeng Feng, Siying Zhou
Software Mentions: 6
Published: almost 6 years ago

10.3389/fcell.2021.644220

Prognostic Signatures of Metabolic Genes and Metabolism-Related Long Non-coding RNAs Accurately Predict Overall Survival for Osteosarcoma Patients
Cited by: 8
Author(s): Chang Gong, Rong Tang, Yawei Shi, Liu Tai-cong, Kaisheng Zhou, Nan Wu, Haihong Zhang
Software Mentions: 6
Published: over 5 years ago

10.1186/s12915-019-0731-8

The round goby genome provides insights into mechanisms that may facilitate biological invasions
Cited by: 28
Author(s): Irene Adrian‐Kalchhauser, Anders Blomberg, Tomas Larsson, Zuzana Musilová, Claire R. Peart, Martin Pippel, Monica Hongrø Solbakken, Jaanus Suurväli, Jean‐Claude Walser, Joanna Y. Wilson, Magnus Alm Rosenblad, Demián Burguera, Silvia Gutnik, Nico K. Michiels, Mats Töpel, Kirill Pankov, Siegfried Schloissnig, Sylke Winkler
Software Mentions: 6
Published: over 6 years ago

10.1186/s12917-020-02332-4

Dietary supplementation of micro-encapsulated sodium butyrate in healthy horses: effect on gut histology and immunohistochemistry parameters
Cited by: 7
Author(s): Wendy Wambacq, D.A. van Doorn, Pauline Rovers-Paap, Richard Ducatelle, Lieven Vlaminck, Marta Ribeiro Alves Lourenço, Myriam Hesta
Software Mentions: 6
Published: about 6 years ago

10.1186/s12920-019-0513-8

Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine
Cited by: 7
Author(s): Samir Rachid Zaim, Colleen Kenost, Joanne Berghout, Francesca Vitali, Helen Hao Zhang, Yves A. Lussier
Software Mentions: 6
Published: about 7 years ago

10.3389/fcell.2021.646774

CRISPR-cas9 Screening Identified Lethal Genes Enriched in Cell Cycle Pathway and of Prognosis Significance in Breast Cancer
Cited by: 6
Author(s): Xi Sun, Zheng Wang, Xiaosong Chen, Kunwei Shen
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-019-6073-7

GENAVi: a shiny web application for gene expression normalization, analysis and visualization
Cited by: 36
Author(s): Alberto Luiz P Reyes, Tiago C. Silva, Simon Coetzee, Jasmine T Plummer, Brian D. Davis, Stephanie Chen, Dennis J. Hazelett, Kate Lawrenson, Benjamin P. Berman, Simon A. Gayther, Michelle R. Jones
Software Mentions: 6
Published: over 6 years ago

10.1186/s12859-016-1204-5

LMAP: Lightweight Multigene Analyses in PAML
Cited by: 12
Author(s): Emanuel Maldonado, Daniela Almeida, Tibisay Escalona, Imran Khan, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 6
Published: almost 10 years ago

10.1038/s41598-021-90538-3

Identification of prognostic biomarkers related to the tumor microenvironment in thyroid carcinoma
Cited by: 6
Author(s): Junwei Du, Guoquan Li, Yang-sen Li, Xinguang Qiu
Software Mentions: 6
Published: almost 5 years ago

10.3389/fcell.2021.724837

Integrative Analysis of m6A Regulator-Mediated RNA Methylation Modification Patterns and Immune Characteristics in Lupus Nephritis
Cited by: 14
Author(s): Huanhuan Zhao, Shaokang Pan, Jiayu Duan, Fengxun Liu, Guangpu Li, Dongwei Li, Zhangsuo Liu
Software Mentions: 6
Published: almost 5 years ago

10.1080/21655979.2020.1840731

Bioinformatics analysis to screen key prognostic genes in the breast cancer tumor microenvironment
Cited by: 9
Author(s): Qian Ye, Xiaofei Han, Zhengsheng Wu
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-021-07720-0

Comparative neurotranscriptomics reveal widespread species differences associated with bonding
Cited by: 5
Author(s): Joel A. Tripp, Alejandro Berrío, Lisa A. McGraw, Mikhail V. Matz, Jamie K. Davis, Kiyoshi Inoue, James W. Thomas, Larry J. Young, Steve Phelps
Software Mentions: 6
Published: about 5 years ago

10.1186/s13040-021-00261-y

A prognostic model based on seven immune-related genes predicts the overall survival of patients with hepatocellular carcinoma
Cited by: 6
Author(s): Qian Yan, Wenjiang Zheng, Boqing Wang, Baoqian Ye, Huiyan Luo, Xinqian Yang, Ping Zhang, Xiongwen Wang
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0243360

DSAVE: Detection of misclassified cells in single-cell RNA-Seq data
Cited by: 2
Author(s): Johan Gustafsson, Jonathan L. Robinson, Juan Salvador Inda-Díaz, Elias Björnson, Rebecka Jörnsten, Jens Nielsen
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-017-09834-6

Opposite trends in the genus Monsonia (Geraniaceae): specialization in the African deserts and range expansions throughout eastern Africa
Cited by: 10
Author(s): Sara García-Aloy, Isabel Sanmartín, Gudrun Kadereit, Daniel Vitales, Ana M. Millanes, Cristina Roquet, Pablo Vargas, María Luisa Alarcón, Juan José Aldasoro
Software Mentions: 6
Published: almost 9 years ago

10.7554/eLife.35368

Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila
Cited by: 92
Author(s): Zaijun Ma, Hui Wang, Yuping Cai, Han Wang, Kongyan Niu, Xiaofen Wu, Huanhuan Ma, Yun Yang, Wenhua Tong, Feng Liu, Zhandong Liu, Yaoyang Zhang, Rui Li, Zheng‐Jiang Zhu, Nan Liu
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pone.0243694

Impact of social isolation due to COVID-19 on the seasonality of pediatric respiratory diseases
Cited by: 50
Author(s): Milena Siciliano Nascimento, Diana Milena Baggio, Linus Pauling Fascina, Cristiane do Prado
Software Mentions: 6
Published: over 5 years ago

10.1186/s12879-018-3066-0

Machine learning methods reveal the temporal pattern of dengue incidence using meteorological factors in metropolitan Manila, Philippines
Cited by: 79
Author(s): Thaddeus M. Carvajal, Katherine M. Viacrusis, Lara Fides T. Hernandez, Howell T. Ho, Divina Amalin, Kozo Watanabe
Software Mentions: 6
Published: about 8 years ago

10.3390/cancers12041028

Changes in the Expression of Pre-Replicative Complex Genes in hTERT and ALT Pediatric Brain Tumors
Cited by: 8
Author(s): Aurora Idilli, Francesca Pagani, Emanuela Kerschbamer, Francesco Berardinelli, Manuel Bernabé, María L. Cayuela, Silvano Piazza, Pietro Luigi Poliani, Emilio Cusanelli, Marina Mione
Software Mentions: 6
Published: about 6 years ago

10.1186/s12920-021-00989-w

Identification of key genes in calcific aortic valve disease via weighted gene co-expression network analysis
Cited by: 7
Author(s): Jin-Yu Sun, Hua Yang, Hui Shen, Qiang Qu, Junyan Kan, Xiangqing Kong, Wei Sun, Yue-Yun Shen
Software Mentions: 6
Published: about 5 years ago

10.1186/s12920-021-01003-z

Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia
Cited by: 5
Author(s): Megumi Onishi-Seebacher, Galina Erikson, Zoe Sawitzki, Devon P. Ryan, Gabriele Greve, Michael Lübbert, Thomas Jenuwein
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2021.657658

Weighted Gene Co-expression Network Analysis Identified a Novel Thirteen-Gene Signature Associated With Progression, Prognosis, and Immune Microenvironment of Colon Adenocarcinoma Patients
Cited by: 2
Author(s): Cangang Zhang, Zhe Zhao, Haibo Li, Shukun Yao, Dongyan Zhao
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12864-019-6375-9

Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristics
Cited by: 27
Author(s): Yanchao Xu, Richard Odongo Magwanga, Xiaomin Yang, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Yangyang Wei, Kunbo Wang, Fang Liu
Software Mentions: 6
Published: over 6 years ago

10.3390/cancers12113311

Role of miRNAs in Sigmoid Colon Cancer: A Search for Potential Biomarkers
Cited by: 2
Author(s): Denílson Bezerra Marques, Layse Raynara Ferreira-Costa, Lorenna Larissa Ferreira-Costa, Ana Beatriz Bezerra-Oliveira, Romualdo da Silva Corrêa, Carlos César de Oliveira Ramos, Tatiana Vinasco-Sandoval, Kátia de Paiva Lopes, Ricardo Assunção Vialle, Amanda Ferreira Vidal, Vivian Nogueira Silbiger, Ândrea Ribeiro-dos-Santos
Software Mentions: 6
Published: over 5 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: almost 5 years ago

10.18632/aging.103695

Glioblastoma cell differentiation trajectory predicts the immunotherapy response and overall survival of patients
Cited by: 26
Author(s): Zihao Wang, Xiaopeng Guo, Lu Gao, Yu Wang, Wenbin Ma, Bing Xing
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12864-019-6076-4

Transcriptome analysis of the effect of C-C chemokine receptor 5 deficiency on cell response to Toxoplasma gondii in brain cells
Cited by: 7
Author(s): Kaoru Kobayashi, Kousuke Umeda, Fumie Ihara, Sadao Tanaka, Junya Yamagishi, Yutaka Suzuki, Yoshifumi Nishikawa
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41426-018-0069-2

Neurotropism and behavioral changes associated with Zika infection in the vector <i>Aedes aegypti</i>
Cited by: 26
Author(s): Julie Gaburro, Asim Bhatti, Jenni Harper, Isabelle Jeanne, Megan Dearnley, Diane Green, Saeid Nahavandi, Prasad N. Paradkar, Jean‐Bernard Duchemin
Software Mentions: 6
Published: about 8 years ago

10.1016/j.cell.2021.07.018

TDP-43 condensation properties specify its RNA-binding and regulatory repertoire
Cited by: 99
Author(s): Martina Hallegger, Anob M. Chakrabarti, Flora Lee, Bo Lim Lee, Aram Gustav Amalietti, Hana M. Odeh, Katie E. Copley, Jack D. Rubien, Bede Portz, Klara Kuret, Ina Huppertz, Frédérique Rau, Rickie Patani, Nicolas L. Fawzi, James Shorter, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0251354

Altering mammalian transcription networking with ADAADi: An inhibitor of ATP-dependent chromatin remodeling
Cited by: 3
Author(s): Ramalingam Radhakrishnan, Upasana Bedi Chanana, Saddam Hussain, Soni Sharma, Kaveri Goel, Deepa Bisht, Ketki Patne, Pynskhem Bok Swer, Joel W. Hockensmith, Rohini Muthuswami
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-019-42988-z

Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms
Cited by: 6
Author(s): Bo‐Hye Nam, DongAhn Yoo, Young‐Ok Kim, Jung Youn Park, Younhee Shin, Ga-Hee Shin, Chan-Il Park, Heebal Kim, Woori Kwak
Software Mentions: 6
Published: about 7 years ago

10.1186/s12870-014-0315-2

The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes
Cited by: 8
Author(s): Gopal Misra, Piyush Priya, Nitesh Bandhiwal, Neha Bareja, Mukesh Jain, Sabhyata Bhatia, Debasis Chattopadhyay, Akhilesh K. Tyagi, Gitanjali Yadav
Software Mentions: 6
Published: over 11 years ago

10.18632/oncotarget.22636

3D-cultivation of NSCLC cell lines induce gene expression alterations of key cancer-associated pathways and mimic<i>in-vivo</i>conditions
Cited by: 11
Author(s): Gabriele Gamerith, Johannes Michael Rainer, Julia Huber, Hubert Hackl, Zlatko Trajanoski, Stefan Koeck, Edith Lorenz, Johann Kern, Reinhard Kofler, Jens M. Kelm, Heinz Zwierzina, Arno Amann
Software Mentions: 6
Published: over 8 years ago

10.1080/21642850.2018.1472602

Scale validation in applied health research: tutorial for a 6-step R-based psychometrics protocol
Cited by: 69
Author(s): Alexandra Dima
Software Mentions: 6
Published: over 8 years ago

10.3390/ijerph18094543

A Study of the Effects of the COVID-19 Pandemic on the Experience of Back Pain Reported on Twitter® in the United States: A Natural Language Processing Approach
Cited by: 13
Author(s): Krzysztof Fiok, Waldemar Karwowski, Edgar Gutiérrez, Maham Saeidi, Awad M. Aljuaid, Mohammad Reza Davahli, Redha Taı̈ar, Tadeusz Marek, Ben D. Sawyer
Software Mentions: 6
Published: about 5 years ago

10.3390/cells8080921

Genes Controlled by DNA Methylation Are Involved in Wilms Tumor Progression
Cited by: 12
Author(s): João Victor da Silva Guerra, Bruna Maria de Sá Pereira, Jéssica Gonçalves Vieira da Cruz, Nicole de Miranda Scherer, Carolina Furtado, Rafaela Montalvão de Azevedo, Paulo Sérgio Lopes de Oliveira, Paulo Faria, Mariana Boroni, Beatriz de Camargo, Mariana Maschietto
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0180322

Affected pathways and transcriptional regulators in gene expression response to an ultra-marathon trail: Global and independent activity approaches
Cited by: 6
Author(s): María Maqueda, Emma Roca, Daniel Brotons, José Manuel Nieto Soria, Alexandre Perera
Software Mentions: 6
Published: over 8 years ago

10.3934/publichealth.2021034

On the relationship between COVID-19 reported fatalities early in the pandemic and national socio-economic status predating the pandemic
Cited by: 2
Author(s): Kathleen L. Foster, Alessandro Selvitella
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-019-5933-5

Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana
Cited by: 13
Author(s): Sony Kumari, Sneha Yadav, Debadutta Patra, Sharmila Singh, Ananda K. Sarkar, Kishore C. S. Panigrahi
Software Mentions: 6
Published: almost 7 years ago

10.3390/cells8060517

Fecal Microbiota Transplantation Controls Murine Chronic Intestinal Inflammation by Modulating Immune Cell Functions and Gut Microbiota Composition
Cited by: 46
Author(s): Claudia Burrello, Maria Rita Giuffrè, Angeli Dominique Macandog, Angélica Díaz‐Basabe, Fulvia Milena Cribiù, Gianluca Lopez, Francesca Borgo, Luigi Nezi, Flavio Caprioli, Maurizio Vecchi, Federica Facciotti
Software Mentions: 6
Published: about 7 years ago

10.3389/fgene.2021.701065

Identification of Tumor Antigens and Immune Landscape in Glioblastoma for mRNA Vaccine Development
Cited by: 12
Author(s): Liguo Ye, Long Wang, Jian Yang, Ping Hu, Chunyu Zhang, Shiao Tong, Zhennan Liu, Daofeng Tian
Software Mentions: 6
Published: almost 5 years ago

10.3389/fvets.2019.00389

Simulation Based Evaluation of Time Series for Syndromic Surveillance of Cattle in Switzerland
Cited by: 1
Author(s): Céline Faverjon, Sara Schärrer, D. Hadorn, John Berezowski
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2020.00099

A FITM1-Related Methylation Signature Predicts the Prognosis of Patients With Non-Viral Hepatocellular Carcinoma
Cited by: 4
Author(s): J Chen, X Wang, Wei Li, Chao Shang, T Chen, Y Chen
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2021.675260

Aluminum or Low pH – Which Is the Bigger Enemy of Barley? Transcriptome Analysis of Barley Root Meristem Under Al and Low pH Stress
Cited by: 16
Author(s): Miriam Szurman-Zubrzycka, Karolina Chwiałkowska, Magdalena Niemira, Mirosław Kwaśniewski, M. Nawrot, Monika Gajecka, Paul B. Larsen, Iwona Szarejko
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0185797

A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia
Cited by: 21
Author(s): Fernando Palluzzi, Raffaele Ferrari, Francesca Graziano, Valeria Novelli, Giacomina Rossi, Daniela Galimberti, Innocenzo Rainero, Luisa Benussi, Benedetta Nacmias, Amalia C. Bruni, Daniele Cusi, Erika Salvi, Barbara Borroni, Mario Grassi
Software Mentions: 6
Published: over 8 years ago

10.1038/s42003-020-01616-7

Gene regulatory networks controlling differentiation, survival, and diversification of hypothalamic Lhx6-expressing GABAergic neurons
Cited by: 24
Author(s): Dong Won Kim, Kai Li, Zoe Qianyi Wang, Yi Stephanie Zhang, Abhijith Bathini, Matthew Brown, Sonia Hao Lin, Parris Whitney Washington, Cuiyun Sun, Susan Lindtner, Bora Lee, Hong Wang, Tomomi Shimogori, John L.R. Rubenstein, Seth Blackshaw
Software Mentions: 6
Published: over 5 years ago

10.3389/fimmu.2021.632667

PD-1 Blockade Modulates Functional Activities of Exhausted-Like T Cell in Patients With Cutaneous Leishmaniasis
Cited by: 16
Author(s): Renan Garcia de Moura, Luciana Polaco Covre, Carlos Henrique Fantecelle, Vitor Alejandro Torres Gajardo, Carla Baroni Cunha, Lorenzzo Lyrio Stringari, Ashton T. Belew, Camila Batista Daniel, Sandra Ventorin von Zeidler, Carlos E. Tadokoro, Herbert Leonel de Matos Guedes, Raphael Lubiana Zanotti, David M. Mosser, Aloísio Falqueto, Arne N. Akbar, Daniel Cláudio Oliveira Gomes
Software Mentions: 6
Published: over 5 years ago

10.1186/s13068-021-01948-4

Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids
Cited by: 6
Author(s): Jose J De Vega, Ned Peel, Sarah Purdy, Sarah Hawkins, Iain S. Donnison, Sarah Dyer, Kerrie Farrar
Software Mentions: 6
Published: about 5 years ago

10.3389/fimmu.2020.00715

Hepatic Transcriptome Analysis Identifies Divergent Pathogen-Specific Targeting-Strategies to Modulate the Innate Immune System in Response to Intramammary Infection
Cited by: 15
Author(s): A. Heimes, J. Brodhagen, Rosemarie Weikard, Hans‐Martin Seyfert, Doreen Becker, M. Meyerholz, Wolfram Petzl, Holm Zerbe, Martina Hoedemaker, L. Rohmeier, Hans‐Joachim Schuberth, Marion Schmicke, Susanne Engelmann, Christa Kühn
Software Mentions: 6
Published: about 6 years ago

10.3389/fimmu.2021.634741

Activation of the DDR Pathway Leads to the Down-Regulation of the TGFβ Pathway and a Better Response to ICIs in Patients With Metastatic Urothelial Carcinoma
Cited by: 18
Author(s): Chaozheng Zhou, Anqi Lin, Manming Cao, Weimin Ding, Weiming Mou, Ningyi Guo, Zhenyu Chen, Jian Zhang, Peng Luo
Software Mentions: 6
Published: about 5 years ago

10.1038/s41396-019-0549-y

Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion
Cited by: 16
Author(s): Colin Miller, Henry C Holm, Lara Horstmann, J. C. George, Helen F. Fredricks, Benjamin A. S. Van Mooy, Amy Apprill
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0148016

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria
Cited by: 99
Author(s): Christina Bienhold, Lucie Zinger, Antje Boetius, Alban Ramette
Software Mentions: 6
Published: over 10 years ago

10.1038/s41598-019-41336-5

Female novelty and male status dynamically modulate ejaculate expenditure and seminal fluid proteome over successive matings in red junglefowl
Cited by: 9
Author(s): Aitor Álvarez-Fernández, Kirill Borziak, Grant C. McDonald, Steve Dorus, Tommaso Pizzari
Software Mentions: 6
Published: about 7 years ago

10.1186/s12935-021-02049-w

Multi-omics analysis reveals prognostic value of tumor mutation burden in hepatocellular carcinoma
Cited by: 19
Author(s): Qianhui Xu, Hao Xu, Ruilong Deng, Zijie Wang, Nanjun Li, Zhixuan Qi, Jiaxin Zhao, Wen Huang
Software Mentions: 6
Published: almost 5 years ago

10.3389/fgene.2020.00307

Alternative Quantifications of Landscape Complementation to Model Gene Flow in Banded Longhorn Beetles [Typocerus v. velutinus (Olivier)]
Cited by: 2
Author(s): Richard Borthwick, Alida de Flamingh, Maximillian H.K. Hesselbarth, Anjana Parandhaman, Helene H. Wagner, Hossam Eldien M. Abdel Moniem
Software Mentions: 6
Published: over 6 years ago

10.1002/cam4.3984

Signature based on metabolic‐related gene pairs can predict overall survival of osteosarcoma patients
Cited by: 8
Author(s): Long‐Qing Li, Liang‐Hao Zhang, Yongjie Yuan, Xin Lu, Yi Zhang, Yong‐Kui Liu, Wen Jiang, Manhas Abdul Khader, Tao Liu, Jiazhen Li, Yan Zhang
Software Mentions: 6
Published: about 5 years ago

10.1242/dev.199604

The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotency
Cited by: 16
Author(s): Nicola Festuccia, Nick Owens, Almira Chervova, Agnès Dubois, Pablo Navarro
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12885-021-08341-2

Identification of the prognostic value of ferroptosis-related gene signature in breast cancer patients
Cited by: 55
Author(s): Ding Wang, Guodong Wei, Jiangwei Ma, Shuai Cheng, Longyuan Jia, Xinyue Song, Ming Zhang, Mingyi Ju, Lin Wang, Lin Zhao, Shijie Xin
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2021.739975

Prognostic Role of ceRNA Network in Immune Infiltration of Hepatocellular Carcinoma
Cited by: 7
Author(s): Qianhui Xu, Shaohuai Chen, Yuanbo Hu, Wen Huang
Software Mentions: 6
Published: almost 5 years ago

10.3390/biology10060502

Characterization of Tumor-Associated Macrophages and the Immune Microenvironment in Limited-Stage Neuroendocrine-High and -Low Small Cell Lung Cancer
Cited by: 22
Author(s): Dávid Dóra, Christopher J. Rivard, Hui Yu, Shivaun Lueke Pickard, Viktória László, Tünde Harkó, Zsolt Megyesfalvi, Elek Dinya, Csongor Gerdán, Gábor Szegvári, Fred R. Hirsch, Balázs Döme, Zoltán Lohinai
Software Mentions: 6
Published: about 5 years ago

10.1242/dmm.049012

Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol
Cited by: 16
Author(s): Karen E. Boschen, Travis Ptacek, Matthew E. Berginski, Jeremy M. Simon, Scott E. Parnell
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-018-5066-2

A comparative analysis of library prep approaches for sequencing low input translatome samples
Cited by: 52
Author(s): Yang Song, Béatrice Milon, Sandra Ott, Xüna Zhao, Lisa Sadzewicz, Amol C. Shetty, Erich T. Boger, Luke J. Tallon, Robert J. Morell, Anup Mahurkar, Ronna Hertzano
Software Mentions: 6
Published: almost 8 years ago

10.1186/s12885-021-08520-1

Computational analysis for identification of early diagnostic biomarkers and prognostic biomarkers of liver cancer based on GEO and TCGA databases and studies on pathways and biological functions affecting the survival time of liver cancer
Cited by: 21
Author(s): Shuangquan Gao, Jian Gang, Man Yu, Guiliang Xin, Huixin Tan
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12885-018-4848-x

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
Cited by: 53
Author(s): Kasey Jividen, Katarzyna Kedzierska, Chunsong Yang, Karol Szlachta, Aakrosh Ratan, Bryce M. Paschal
Software Mentions: 6
Published: over 7 years ago

10.1534/g3.118.200017

Environmental and Evolutionary Drivers of the Modular Gene Regulatory Network Underlying Phenotypic Plasticity for Stress Resistance in the Nematode <i>Caenorhabditis remanei</i>
Cited by: 20
Author(s): Kristin L. Sikkink, Rose M. Reynolds, Catherine M. Ituarte, William A. Cresko, Patrick C. Phillips
Software Mentions: 6
Published: over 7 years ago

10.3389/fonc.2020.572708

Hematopoietic Gene Expression Regulation Through m6A Methylation Predicts Prognosis in Stage III Colorectal Cancer
Cited by: 1
Author(s): Zheng Zhou, Shaobo Mo, Ruiqi Gu, Weixing Dai, Xinhui Zou, Lingyu Han, Long Zhang, Renjie Wang, Guoxiang Cai
Software Mentions: 6
Published: almost 6 years ago

10.3389/fgene.2020.00311

Weighted Gene Coexpression Network Analysis of Features That Control Cancer Stem Cells Reveals Prognostic Biomarkers in Lung Adenocarcinoma
Cited by: 57
Author(s): Yi Liao, Yulei Wang, Mengqing Cheng, Chengliang Huang, Xiaoxuan Fan
Software Mentions: 6
Published: about 6 years ago

10.1186/s12863-021-00991-2

The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells
Cited by: 4
Author(s): Ritu Mann-Nüttel, Shafaqat Ali, Patrick Petzsch, Karl Köhrer, Judith Alferink, Stefanie Scheu
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12885-017-3832-1

Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stages
Cited by: 9
Author(s): Daifeng Wang, John D. Haley, Patricia Thompson
Software Mentions: 6
Published: over 8 years ago

10.1186/s40168-019-0766-7

Discordant transmission of bacteria and viruses from mothers to babies at birth
Cited by: 61
Author(s): Rabia Maqsood, Rachel Rodgers, Cynthia Rodríguez, Scott A. Handley, I. Malick Ndao, Phillip I. Tarr, Barbara Warner, Efrem S. Lim, Lori R. Holtz
Software Mentions: 6
Published: over 6 years ago

10.1242/bio.058222

RNA-Seq reveals changes in human placental metabolism, transport and endocrinology across the first–second trimester transition
Cited by: 15
Author(s): Malwina Prater, Russell S. Hamilton, Hong Wa Yung, Andrew Sharkey, Paul Robson, N. Erlyani Abd Hamid, Eric Jauniaux, D. Stephen Charnock-Jones, Graham J. Burton, Tereza Cindrová‐Davies
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2014.00541

Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland
Cited by: 71
Author(s): Antje Gittel, Jiří Bárta, Iva Kohoutová, Jörg Schnecker, Birgit Wild, Petr Čapek, Christina Kaiser, Vigdis Torsvik, Andreas Richter, Christa Schleper, Tim Urich
Software Mentions: 6
Published: over 11 years ago

10.1186/s13620-017-0103-z

Month-wise variation and prediction of bulk tank somatic cell count in Brazilian dairy herds and its impact on payment based on milk quality
Cited by: 10
Author(s): Marcos Busanello, Larissa Nazareth de Freitas, João Pedro Pereira Winckler, Hiron Pereira Farias, Carlos Tadeu dos Santos Dias, Laerte Dagher Cassoli, Paulo Fernando Machado
Software Mentions: 6
Published: almost 9 years ago

10.15252/emmm.201708587

Reinstating plasticity and memory in a tauopathy mouse model with an acetyltransferase activator
Cited by: 54
Author(s): Snehajyoti Chatterjee, Raphaelle Cassel, Anne Schneider‐Anthony, Karine Mérienne, Brigitte Cosquer, Laura Tzeplaeff, Sarmistha Sinha, Manoj Kumar, Piyush Chaturbedy, M. Eswaramoorthy, Stéphanie Le Gras, Céline Keime, Olivier Bousiges, P. Dutar, Petnoï Petsophonsakul, Claire Rampon, Jean‐Christophe Cassel, Luc Buée, David Blum, Tapas K. Kundu, Anne‐Laurence Boutillier
Software Mentions: 6
Published: almost 8 years ago

10.15252/emmm.202013412

The immune suppressive microenvironment affects efficacy of radio‐immunotherapy in brain metastasis
Cited by: 23
Author(s): Katja Niesel, Marcel H. Schulz, Julian Anthes, Tijna Alekseeva, Jadranka Macas, Anna Salamero-Boix, Aylin Möckl, T. Oberwahrenbrock, Marco Lolies, Stefan Stein, Karl H. Plate, Yvonne Reiss, Franz Rödel, Lisa Sevenich
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2021.642608

Significance of Tumor Mutation Burden Combined With Immune Infiltrates in the Progression and Prognosis of Advanced Gastric Cancer
Cited by: 18
Author(s): Xiong Guo, Xiaolong Liang, Yujun Wang, Anqi Cheng, Han Zhang, Chuan Qin, Ziwei Wang
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12885-020-6702-1

Identification of immune cells and mRNA associated with prognosis of gastric cancer
Cited by: 35
Author(s): Mingming Wang, Zedong Li, Pei Yu, Jianyu Fang, Tao Fang, Jiajia Wu, Jun Zhou
Software Mentions: 6
Published: over 6 years ago

10.3389/fdata.2021.725095

NPARS—A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science
Cited by: 2
Author(s): Li Ma, Erich A. Peterson, Ik Jae Shin, Jason Muesse, Katy Marino, Matthew A. Steliga, Donald J. Johann
Software Mentions: 6
Published: almost 5 years ago