10.3389/fmicb.2019.02066

Use of RNA and DNA to Identify Mechanisms of Bacterial Community Homogenization
Cited by: 16
Author(s): Kyle Meyer, Ian A. B. Petersen, Elie Tobi, Lisa Körte, Brendan J. M. Bohannan
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12859-018-2122-5

IntEREst: intron-exon retention estimator
Cited by: 18
Author(s): Ali Oghabian, Dario Greco, Mikko J. Frilander
Software Mentions: 5
Published: over 8 years ago

10.3389/fmicb.2019.02798

The Compositionally Distinct Cyanobacterial Biocrusts From Brazilian Savanna and Their Environmental Drivers of Community Diversity
Cited by: 22
Author(s): Nathali Machado de Lima, Vanessa Moreira Câmara Fernandes, Daniel Roush, Sergio Velasco Ayuso, Janaína Rigonato, Ferrán García-Pichel, Luis Henrique Zanini Branco
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-70206-8

Remote, autonomous real-time monitoring of environmental DNA from commercial fish
Cited by: 28
Author(s): Brian Klitgaard Hansen, Marianne Jacobsen, Anne Lise Middelboe, Christina M. Preston, Roman Marin, Dorte Bekkevold, Steen Wilhelm Knudsen, Peter Rask Møller, Einar Eg Nielsen
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12885-020-06784-7

Right and left-sided colon cancers - specificity of molecular mechanisms in tumorigenesis and progression
Cited by: 45
Author(s): Kavitha Mukund, Natalia Syulyukina, Sonia Ramamoorthy, Shankar Subramaniam
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0156550

Faunal Communities Are Invariant to Fragmentation in Experimental Seagrass Landscapes
Cited by: 31
Author(s): Jonathan S. Lefcheck, Scott R. Marion, Alfonso V. Lombana, Robert J. Orth
Software Mentions: 5
Published: about 10 years ago

10.1590/1678-4685-GMB-2019-0270

Methodological differences can affect sequencing depth with a possible impact on the accuracy of genetic diagnosis
Cited by: 2
Author(s): Murilo Guimarães Borges, Cristiane S. Rocha, Benilton Carvalho, Íscia Lopes‐Cendes
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-020-06911-5

Wild mice with different social network sizes vary in brain gene expression
Cited by: 2
Author(s): Patrícia C. Lopes, Barbara König
Software Mentions: 5
Published: almost 6 years ago

10.1038/srep10670

GPS tracking for mapping seabird mortality induced by light pollution
Cited by: 43
Author(s): Airam Rodríguez, Beneharo Rodríguez, Juan J. Negro
Software Mentions: 5
Published: about 11 years ago

10.3390/ani10071207

Automated Bird Counting with Deep Learning for Regional Bird Distribution Mapping
Cited by: 28
Author(s): Hüseyin Akçay, Bekir Kabasakal, Duygugül Aksu, Nusret Demir, Melih Öz, Ali Erdoğan
Software Mentions: 5
Published: about 6 years ago

10.7150/thno.63416

Mapping the landscape of synthetic lethal interactions in liver cancer
Cited by: 7
Author(s): Chen Yang, Yuchen Guo, Ruolan Qian, Yi‐Wen Huang, Linmeng Zhang, Jun Wang, Xiaowen Huang, Zhicheng Liu, Wenxin Qin, Cun Wang, Huimin Chen, Xuhui Ma, Dayong Zhang
Software Mentions: 5
Published: over 5 years ago

10.1186/s12885-021-08390-7

Identification of prognostic markers for hepatocellular carcinoma based on the epithelial-mesenchymal transition-related gene BIRC5
Cited by: 13
Author(s): Rongzhong Xu, Lin Lei, Bo Zhang, Jian Wang, Fanchen Zhao, Xiaolin Liu, Yiping Li, Yan Li
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0241345

Predicting dive start performance from kinematic variables at water entry in (sub-)elite swimmers
Cited by: 2
Author(s): Marit P. van Dijk, Peter J. Beek, A. J. “Knoek” van Soest
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-015-0685-2

Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells
Cited by: 64
Author(s): Chi Kong Li, Hongzheng Dai, Suzanne N. Martos, Beisi Xu, Yang Gao, Li Teng, Guangjing Zhu, Dustin E. Schones, Zhibin Wang
Software Mentions: 5
Published: about 11 years ago

10.1371/journal.pone.0166283

Relationships between egg-recognition and egg-ejection in a grasp-ejector species
Cited by: 34
Author(s): Manuel Soler, Francisco Ruiz‐Raya, Gianluca Roncalli, Juan Diego Ibáñez‐Álamo
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-020-67871-0

Chloroplast DNA analysis of the invasive weed, Himalayan balsam (Impatiens glandulifera), in the British Isles
Cited by: 5
Author(s): Daisuke Kurose, Kathryn M. Pollard, C. A. Ellison
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-67690-3

Transcriptomic analysis of the mechanisms of alleviating renal interstitial fibrosis using the traditional Chinese medicine Kangxianling in a rat model
Cited by: 13
Author(s): Yufeng Jiang, Yaohan Zhu, Timing Zhen, Jie Li, Kaichen Xing, Liqun He, Sibo Zhu
Software Mentions: 5
Published: about 6 years ago

10.1186/s12859-019-2728-2

UTAP: User-friendly Transcriptome Analysis Pipeline
Cited by: 88
Author(s): Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran, Dena Leshkowitz
Software Mentions: 5
Published: over 7 years ago

10.3389/fimmu.2021.637832

Dynamic Intracellular Metabolic Cell Signaling Profiles During Ag-Dependent B-Cell Differentiation
Cited by: 3
Author(s): Paula Díez, Martín Pérez‐Andrés, Martin Bøgsted, Mikel Azkargorta, Rodrigo García-Valiente, Rosa Ma Dégano, E Blanco, Sheila Mateos-Gomez, Paloma Bárcena, Santiago Cruz, Rafael Góngora, Félix Elortza, Alicia Landeira-Viñuela, Pablo Juanes-Velasco, Víctor Segura, Raúl Manzano-Román, Júlia Almeida, Karen Dybkær, Alberto Órfão, Manuel Fuentes
Software Mentions: 5
Published: over 5 years ago

10.3390/ijerph18115646

The Influence of Anthropometric Indices and Intermediary Determinants of Hypertension in Bangladesh
Cited by: 2
Author(s): Sally Sonia Simmons, John Elvis Hagan, Thomas Schack
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-021-04046-2

DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks
Cited by: 0
Author(s): Heeju Noh, Hua Ziyi, Panagiotis Chrysinas, Jason E. Shoemaker, Rudiyanto Gunawan
Software Mentions: 5
Published: over 5 years ago

10.3389/fphys.2021.637924

A Subpopulation of Schwann Cell-Like Cells With Nerve Regeneration Signatures Is Identified Through Single-Cell RNA Sequencing
Cited by: 4
Author(s): Zairong Wei, Shenyou Shu, Mingjun Zhang, Sitian Xie, Shijie Tang, Kaiyu Nie, Haihong Li
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-019-1906-x

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation
Cited by: 257
Author(s): Elo Madissoon, Anna Wilbrey-Clark, Ricardo J. Miragaia, Kourosh Saeb‐Parsy, Krishnaa Mahbubani, Nikitas Georgakopoulos, Philippa Harding, Krzysztof Polański, Ni Huang, Karol Nowicki-Osuch, Rebecca C. Fitzgerald, Kevin Loudon, John R. Ferdinand, Menna R. Clatworthy, Anthi Tsingene, Stijn van Dongen, Monika Dąbrowska, Minal Patel, Michael J T Stubbington, Sarah A. Teichmann, Oliver Stegle, Kerstin B. Meyer
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.64940

DIPPER, a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics
Cited by: 32
Author(s): Vivian Tam, Peikai Chen, Anita Yee, Nestor Solis, Théo Klein, Mateusz Kudelko, Rakesh Sharma, Wing‐Lok Chan, Christopher M. Overall, Lisbet Haglund, Pak C. Sham, Kathryn S.E. Cheah, Danny Chan
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.624259

Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy
Cited by: 4
Author(s): Jorge Guerra Pires, Gilberto Ferreira da Silva, Thomas Weyssow, Alessandra Jordano Conforte, Dante Pagnoncelli, Fabrício Silva, Nicolas Carels
Software Mentions: 5
Published: over 5 years ago

10.1093/gbe/evx269

A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry
Cited by: 53
Author(s): Stephen R. Doyle, Roz Laing, David J. Bartley, Collette Britton, Umer Chaudhry, John S. Gilleard, Nancy Holroyd, Barbara K. Mable, Kirsty Maitland, Alison A. Morrison, Andy Tait, Alan S. Tracey, Matthew Berriman, Eileen Devaney, James A. Cotton, Neil Sargison
Software Mentions: 5
Published: over 8 years ago

10.18632/aging.102373

Bioinformatic profiling of prognosis-related genes in the breast cancer immune microenvironment
Cited by: 29
Author(s): Fang Bai, Yu-Chun Jin, Peng Zhang, Hongliang Chen, Yi‐Peng Fu, Mingdi Zhang, Zhen Weng, Kangning Wu
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0098200

Dynamics of Two Multi-Stemmed Understory Shrubs in Two Temperate Forests
Cited by: 4
Author(s): Xin Bai, Tania Brenes-Arguedas, Ji Ye, Xugao Wang, Fei Lin, Zuoqiang Yuan, Sheng‐Cai Shi, Dingliang Xing, Zhanqing Hao
Software Mentions: 5
Published: about 12 years ago

10.3389/fphar.2021.616529

Systematic Investigation of DNA Methylation Associated With Platinum Chemotherapy Resistance Across 13 Cancer Types
Cited by: 4
Author(s): Ruizheng Sun, Chao Du, Jiaxin Li, Yanhong Zhou, Xiong Wang, Juanjuan Xiang, Jiheng Liu, Zhifeng Xiao, Fang Li, Li Zheng
Software Mentions: 5
Published: about 5 years ago

10.3389/fnut.2021.658793

Promoting Healthy Eating Behaviors by Incentivizing Exploration of Healthy Alternatives
Cited by: 7
Author(s): Yael Shavit, Yefim Roth, Kinneret Teodorescu
Software Mentions: 5
Published: about 5 years ago

10.18632/aging.203422

Hedgehog dysregulation contributes to tissue-specific inflammaging of resident macrophages
Cited by: 8
Author(s): Mahamat Babagana, Kyu-Seon Oh, Sayantan Chakraborty, Alicja Pacholewska, Mohammad Aqdas, Myong-Hee Sung
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0243105

Machine learning-based e-commerce platform repurchase customer prediction model
Cited by: 14
Author(s): Cheng-Ju Liu, Tienshou Huang, Ping-Tsan Ho, Jui-Chan Huang, Ching-Tang Hsieh
Software Mentions: 5
Published: over 5 years ago

10.1186/s12888-015-0685-5

Distinguishing bipolar and major depressive disorders by brain structural morphometry: a pilot study
Cited by: 66
Author(s): Gabriel Pui Cheong Fung, Yi Deng, Qing Zhao, Zhi Li, Miao Qu, Li Ke, Yonghu Zeng, Jin Zhou, Yantao Ma, Xin Yu, Zhiren Wang, David Shum, Raymond C.K. Chan
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0055635

Functional-Network-Based Gene Set Analysis Using Gene-Ontology
Cited by: 6
Author(s): Billy Chang, Rafal Kustra, Weidong Tian
Software Mentions: 5
Published: over 13 years ago

10.1186/s12864-019-6444-0

The transcriptome of Pinus pinaster under Fusarium circinatum challenge
Cited by: 18
Author(s): Laura Hernandez‐Escribano, Erik A. Visser, Eugenia Iturritxa, Rosa Raposo, Sanushka Naidoo
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1002763

Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance
Cited by: 28
Author(s): Elizabeth K. Engle, Justin C. Fay
Software Mentions: 5
Published: about 14 years ago

10.1371/journal.pone.0205804

Risk taking of educated nematodes
Cited by: 15
Author(s): Denis S. Willett, Hans T. Alborn, Lukasz L. Stelinski, David I. Shapiro‐Ilan
Software Mentions: 5
Published: over 7 years ago

10.18632/aging.103721

Gene expression-based clinical predictions in lung adenocarcinoma
Cited by: 3
Author(s): Yanlu Xiong, Jie Lei, Jinbo Zhao, Yangbo Feng, Tianyun Qiao, Yongsheng Zhou, Tao Jiang, Han Ye
Software Mentions: 5
Published: almost 6 years ago

10.3390/cancers11010053

Prognostic Gene Discovery in Glioblastoma Patients using Deep Learning
Cited by: 34
Author(s): Kelvin Wong, Robert Rostomily, Stephen T.C. Wong
Software Mentions: 5
Published: over 7 years ago

10.3390/cells9061436

Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver
Cited by: 14
Author(s): Qinwei Kim-Wee Zhuang, José Héctor Gálvez, Qian Xiao, Najla AlOgayil, Jeffrey Hyacinthe, Teruko Taketo, Guillaume Bourque, Anna K. Naumova
Software Mentions: 5
Published: about 6 years ago

10.1038/srep46332

Windscapes and olfactory foraging in a large carnivore
Cited by: 40
Author(s): Ron R. Togunov, Andrew E. Derocher, Nicholas J. Lunn
Software Mentions: 5
Published: over 9 years ago

10.1093/aobpla/plz017

Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing
Cited by: 12
Author(s): Benjamin M. Anderson, Kevin R. Thiele, Pauline F. Grierson, Siegfried L. Krauss, Paul Nevill, Ian Small, Xue Zhong, Matthew D. Barrett
Software Mentions: 5
Published: over 7 years ago

10.1186/1471-2105-8-254

Progressive multiple sequence alignments from triplets
Cited by: 22
Author(s): Matthias Kruspe, Peter F. Stadler
Software Mentions: 5
Published: about 19 years ago

10.1371/journal.pone.0205720

Inhibitory attentional control in anxiety: Manipulating cognitive load in an antisaccade task
Cited by: 14
Author(s): Julian Basanovic, Lies Notebaert, Patrick Clarke, Colin MacLeod, Philippe Jawinski, Nigel T. M. Chen
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pcbi.1006767

The intrinsic dimension of protein sequence evolution
Cited by: 14
Author(s): Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio
Software Mentions: 5
Published: over 7 years ago

10.3758/s13414-019-01674-y

Goal-directed unequal attention allocation during multiple object tracking
Cited by: 12
Author(s): Emily M. Crowe, Christina J. Howard, Angela Attwood, Christopher Kent
Software Mentions: 5
Published: over 7 years ago

10.1002/ece3.6657

Alternative reproductive tactics are associated with sperm performance in invasive round goby from two different salinity environments
Cited by: 6
Author(s): León Green, Jan Niemax, Jens‐Peter Herrmann, Axel Temming, Charlotta Kvarnemo
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0121954

Perinatal Overnutrition Exacerbates Adipose Tissue Inflammation Caused by High-Fat Feeding in C57BL/6J Mice
Cited by: 25
Author(s): Brandon D. Kayser, Michael I. Goran, Sébastien G. Bouret
Software Mentions: 5
Published: over 11 years ago

10.7554/eLife.20937

Enforcement of developmental lineage specificity by transcription factor Oct1
Cited by: 14
Author(s): Zuolian Shen, Jinsuk Kang, Arvind Shakya, Marcin Tabaka, Elke A. Jarboe, Aviv Regev, Dean Tantin
Software Mentions: 5
Published: about 9 years ago

10.1126/sciadv.abh0534

Cell-free DNA TAPS provides multimodal information for early cancer detection
Cited by: 36
Author(s): Paulina Siejka-Zielińska, Jingfei Cheng, Felix Jackson, Yibin Liu, Zahir Soonawalla, Srikanth Reddy, Michael Silva, Luminita Puta, Misti McCain, Emma L. Culver, Noor Bekkali, Benjamin Schuster-Böckler, Pier Francesco Palamara, Derek A. Mann, Helen L. Reeves, Eleanor Barnes, Shivan Sivakumar, Chun-Xiao Song
Software Mentions: 5
Published: almost 5 years ago

10.1002/ece3.5404

Migration distance does not predict blood parasitism in a migratory songbird
Cited by: 7
Author(s): Marjorie C. Sorensen, Tanmay Dixit, Kevin J. Kardynal, Jason Newton, Keith A. Hobson, Staffan Bensch, Susanne Jenni‐Eiermann, Claire N. Spottiswoode
Software Mentions: 5
Published: about 7 years ago

10.18632/aging.102871

Prognostic value of immune-related genes in the tumor microenvironment of lung adenocarcinoma and lung squamous cell carcinoma
Cited by: 52
Author(s): Yan Qu, Bo Cheng, Ningsheng Shao, Yibin Jia, Qingxu Song, Bingxu Tan, Jianbo Wang
Software Mentions: 5
Published: over 6 years ago

10.3389/fpls.2020.00132

Developmental Analysis of Mimulus Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes
Cited by: 9
Author(s): Miguel A. Flores‐Vergara, Elen Oneal, Mário Costa, Gonzalo H. Villarino, Caitlyn Roberts, María Angels de Luis Balaguer, Sı́lvia Coimbra, John H. Willis, Robert G. Franks
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2021.646936

A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data
Cited by: 44
Author(s): Ruizhi Xiang, Wencan Wang, Lei Yang, Shiyuan Wang, Chaohan Xu, Xiaowen Chen
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-27068-y

Climatic niche divergence drives patterns of diversification and richness among mammal families
Cited by: 37
Author(s): Adrián Castro‐Insua, Carola Gómez‐Rodríguez, John J. Wiens, Andrés Baselga
Software Mentions: 5
Published: about 8 years ago

10.3390/cells9091924

Microcurrent Stimulation Triggers MAPK Signaling and TGF-β1 Release in Fibroblast and Osteoblast-Like Cell Lines
Cited by: 14
Author(s): Evangelia Konstantinou, Zoi Zagoriti, Anastasia Pyriochou, Konstantinos Poulas
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2020.00199

Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing
Cited by: 3
Author(s): Christopher Lee, Kai Wang, Tingting Qin, Maureen A. Sartor
Software Mentions: 5
Published: over 6 years ago

10.3389/fpls.2019.01018

Plant Diversity and Fertilizer Management Shape the Belowground Microbiome of Native Grass Bioenergy Feedstocks
Cited by: 17
Author(s): Daniel Revillini, Gail W. T. Wilson, R. M. Miller, Ryan C. Lancione, Nancy Collins Johnson
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12872-021-01961-3

Distinguishing cardiac myxomas from cardiac thrombi by a radiomics signature based on cardiovascular contrast-enhanced computed tomography images
Cited by: 3
Author(s): Wen-Lei Qian, Jiang Yu, Xi Liu, Yingkun Guo, Yuan Li, Xin Tang, Zhigang Yang
Software Mentions: 5
Published: over 5 years ago

10.1186/s13073-020-00760-3

ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer
Cited by: 32
Author(s): Aileen P. Szczepanski, Zibo Zhao, Victoria Sosnowski, Young Ah Goo, Elizabeth T. Bartom, Lu Wang
Software Mentions: 5
Published: about 6 years ago

10.1016/j.gpb.2020.08.001

G9a/GLP-sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments
Cited by: 3
Author(s): Zixiang Yan, Luzhang Ji, Xiangru Huo, Qianfeng Wang, Yuwen Zhang, Bo Wen
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13015-014-0027-z

BicPAM: Pattern-based biclustering for biomedical data analysis
Cited by: 57
Author(s): Rui Henriques, Sara C. Madeira
Software Mentions: 5
Published: over 11 years ago

10.1007/s11357-021-00329-x

Are the 50’s, the transition decade, in choroid plexus aging?
Cited by: 5
Author(s): Ana Carolina Tahira, Fernanda Marques, Bianca Cristina Garcia Lisbôa, Arthur Sant’Anna Feltrin, André Rocha Barbosa, Kátia C. Oliveira, Carlos Alberto de Bragança Pereira, Renata Leite, Lea T. Grinberg, Cláudia Kimie Suemoto, Renata Eloah de Lucena Ferretti‐Rebustini, Carlos Augusto Pasqualucci, Wilson Jacob‐Filho, Helena Brentani, Joana Almeida Palha
Software Mentions: 5
Published: over 5 years ago

10.1128/mSystems.01306-20

Cultivating the Bacterial Microbiota of <i>Populus</i> Roots
Cited by: 12
Author(s): Dana L. Carper, David J. Weston, Aditya Barde, Collin M. Timm, Tse-Yuan S. Lu, Leah H. Burdick, Sara Jawdy, Dawn M. Klingeman, Michael S. Robeson, Allison M. Veach, Melissa Cregger, Udaya C. Kalluri, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-020-66806-z

CD96, a new immune checkpoint, correlates with immune profile and clinical outcome of glioma
Cited by: 26
Author(s): Fangkun Liu, Jing Huang, Fengjiao He, Xiaodong Ma, Fan Fan, Ming Meng, Zhuo Yang, Jintao Zhang
Software Mentions: 5
Published: about 6 years ago

10.1186/s40168-021-01129-3

Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ)
Cited by: 7
Author(s): Wodan Ling, Ni Zhao, Anna Plantinga, Lenore J. Launer, Anthony A. Fodor, Katie A. Meyer, Michael C. Wu
Software Mentions: 5
Published: almost 5 years ago

10.12688/f1000research.15433.1

Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets
Cited by: 5
Author(s): Jayaram Kancherla, Alexander Zhang, Brian Gottfried, Héctor Corrada Bravo
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.ppat.1009349

PD-1 is imprinted on cytomegalovirus-specific CD4+ T cells and attenuates Th1 cytokine production whilst maintaining cytotoxicity
Cited by: 15
Author(s): Helen Parry, Alexander C. Dowell, Jianmin Zuo, Kriti Verma, Francesca Kinsella, Jusnara Begum, Wayne Croft, Archana Sharma-Oates, Guy Pratt, Paul Moss
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2018.00973

A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains
Cited by: 15
Author(s): Xiangchen Li, Wenjun Tong, Lina Wang, Siddiq Ur Rahman, Gehong Wei, Shiheng Tao
Software Mentions: 5
Published: about 8 years ago

10.1186/s13073-021-00885-z

Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis
Cited by: 24
Author(s): Sunny Z. Wu, Daniel Roden, Ghamdan Al-Eryani, Nenad Bartoniček, Kate Harvey, Aurélie Cazet, Chia-Ling Chan, Simon Junankar, Mun Hui, Ewan A. Millar, Julia Beretov, Lisa Kristina Horvath, Anthony M. Joshua, Phillip D. Stricker, James S. Wilmott, Camelia Quek, Georgina V. Long, Richard A. Scolyer, Bertrand Z. Yeung, Davendra Segara, Cindy Mak, Sanjay Warrier, Joseph E. Powell, Sandra A. O’Toole, Elgene Lim, Alexander Swarbrick
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0205427

Identification of gene expression predictors of occupational benzene exposure
Cited by: 11
Author(s): Courtney Schiffman, Cliona M. McHale, Alan Hubbard, Luoping Zhang, Reuben Thomas, Roel Vermeulen, Guilan Li, Min Shen, Stephen M. Rappaport, Shu Yin, Qing Lan, Martyn T. Smith, Nathaniel Rothman
Software Mentions: 5
Published: almost 8 years ago

10.1186/s12974-019-1418-3

Correlation of alteration of HLA-F expression and clinical characterization in 593 brain glioma samples
Cited by: 36
Author(s): Enshan Feng, Tingyu Liang, Xiaoyong Wang, Juan Du, Kai Tang, Xiaoxuan Wang, Fang Wang, Guoxiang You
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0004481

Age and Diet Affect Gene Expression Profile in Canine Skeletal Muscle
Cited by: 17
Author(s): Ingmar S. Middelbos, Brittany M. Vester, Lisa K. Karr-Lilienthal, Lawrence B. Schook, Kelly S. Swanson
Software Mentions: 5
Published: over 17 years ago

10.1186/s13073-020-00747-0

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale
Cited by: 37
Author(s): Soumaya Zlitni, Alex Bishara, Eli L. Moss, Е. И. Ткаченко, Joyce B. Kang, Rebecca Culver, Tessa M. Andermann, Ziming Weng, Christina M. Wood, Christine Handy, Hanlee P. Ji, Serafim Batzoglou, Ami S. Bhatt
Software Mentions: 5
Published: about 6 years ago

10.1038/srep22932

Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in the horse
Cited by: 44
Author(s): Núria Mach, Sandra Plancade, Alicja Pacholewska, Jérôme Lecardonnel, Julie Rivière, Marco Moroldo, Anne Vaiman, Caroline Morgenthaler, Marine Beinat, Alizée Nevot, Céline Robert, Éric Barrey
Software Mentions: 5
Published: over 10 years ago

10.3389/fpls.2020.00948

Systematic Review of Plant Ribosome Heterogeneity and Specialization
Cited by: 49
Author(s): Federico Martinez‐Seidel, Olga Beine-Golovchuk, Yin-Chen Hsieh, Joachim Kopka
Software Mentions: 5
Published: about 6 years ago

10.1111/pbi.12615

A comprehensive draft genome sequence for lupin (<i>Lupinus angustifolius</i>), an emerging health food: insights into plant–microbe interactions and legume evolution
Cited by: 149
Author(s): James K. Hane, Ming Yao, Lars G. Kamphuis, Matthew N. Nelson, Gagan Garg, Craig A. Atkins, Philipp E. Bayer, Armando Bravo, Scott Bringans, Steven B. Cannon, David Edwards, Rhonda C. Foley, Ling Gao, Maria J. Harrison, Wei Huang, Bhavna Hurgobin, Sean Li, Cheng-Wu Liu, Annette McGrath, Grant Morahan, Jeremy D. Murray, James L. Weller, Jianbo Jian, Karam B. Singh
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0125009

Incidence and Risk Factors of Childhood Pneumonia-Like Episodes in Biliran Island, Philippines—A Community-Based Study
Cited by: 28
Author(s): Hisato Kosai, Raita Tamaki, Mayuko Saito, Kentaro Tohma, Portia Alday, Alvin G. Tan, Marianette T. Inobaya, Akira Suzuki, Taro Kamigaki, Soccoro Lupisan, Veronica Tallo, Hitoshi Oshitani
Software Mentions: 5
Published: about 11 years ago

10.1371/journal.ppat.1009441

Viral infection of human neurons triggers strain-specific differences in host neuronal and viral transcriptomes
Cited by: 8
Author(s): Colleen A. Mangold, Molly M. Rathbun, Daniel W. Renner, Chad V. Kuny, Moriah L. Szpara
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0054469

Does Domestication Cause Changes in Growth Reaction Norms? A Study of Farmed, Wild and Hybrid Atlantic Salmon Families Exposed to Environmental Stress
Cited by: 100
Author(s): Monica Favnebøe Solberg, Øystein Skaala, Frank Nilsen, Kevin A. Glover
Software Mentions: 5
Published: over 13 years ago

10.1038/s41598-021-84860-z

Characterisation, identification, clustering, and classification of disease
Cited by: 17
Author(s): Anthony J Webster, Kezia Gaitskell, Iain Turnbull, B J Cairns, Robert Clarke
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms21020471

The Influence of Met Receptor Level on HGF-Induced Glycolytic Reprogramming in Head and Neck Squamous Cell Carcinoma
Cited by: 17
Author(s): Verena Boschert, Nicola Klenk, Alexander Abt, Sudha Janaki Raman, Markus Fischer, Roman C. Brands, Axel Seher, Christian Linz, Urs Müller‐Richter, Thorsten Bischler, Stefan Hartmann
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2018.02253

A Unique Saccharomyces cerevisiae × Saccharomyces uvarum Hybrid Isolated From Norwegian Farmhouse Beer: Characterization and Reconstruction
Cited by: 38
Author(s): Kristoffer Krogerus, Richard Preiss, Brian Gibson
Software Mentions: 5
Published: almost 8 years ago

10.3389/fendo.2021.679582

Transcriptomic Profiling of Human Placenta in Gestational Diabetes Mellitus at the Single-Cell Level
Cited by: 31
Author(s): Yuqi Yang, Fang Guo, Yue Peng, Rong Chen, Wenbo Zhou, Huihui Wang, Jun Ouyang, Bin Yu, Zhengfeng Xu
Software Mentions: 5
Published: about 5 years ago

10.1093/gigascience/giab067

Association of female reproductive tract microbiota with egg production in layer chickens
Cited by: 5
Author(s): Yuan Su, Shilin Tian, Diyan Li, Wei Zhu, Tao Wang, Suchismita Mishra, Ranlei Wei, Zhongxian Xu, Mengnan He, Xiaoling Zhao, Huadong Yin, Xiaolan Fan, Bo Zeng, Mingyao Yang, Deying Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Qing Zhu, Mingzhou Li
Software Mentions: 5
Published: almost 5 years ago

10.3390/genes11121512

You Had Me at “MAGIC”!: Four Barley MAGIC Populations Reveal Novel Resistance QTL for Powdery Mildew
Cited by: 13
Author(s): Fluturë Novakazi, Lene Krusell, J. Jensen, Jihad Orabi, A. Jahoor, Tommy Bengtsson
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2021.652408

Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver
Cited by: 21
Author(s): Xianliang Hou, Yane Yang, Ping Li, Zhipeng Zeng, Wenlong Hu, Ruilian Zhe, Xinqiong Liu, Donge Tang, Minglin Ou, Yong Dai
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.36967

Topography of cancer-associated immune cells in human solid tumors
Cited by: 187
Author(s): Jakob Nikolas Kather, Meggy Suarez-Carmona, Pornpimol Charoentong, Cleo–Aron Weis, Daniela Hirsch, Peter Bankhead, Marcel Horning, Dyke Ferber, Ivan Kel, Esther Herpel, Sarah Schott, Inka Zörnig, Jochen Utikal, Alexander Marx, Timo Gaiser, Hermann Brenner, Jenny Chang‐Claude, Michael Hoffmeister, Dirk Jäger, Niels Halama
Software Mentions: 5
Published: almost 8 years ago

10.1038/s42003-020-01477-0

Differential longitudinal establishment of human fecal bacterial communities in germ-free porcine and murine models
Cited by: 9
Author(s): Nirosh D. Aluthge, Wesley A Tom, Alison Bartenslager, Thomas E. Burkey, Phillip S. Miller, Kelly D. Heath, Craig Kreikemeier-Bower, Hatem Kittana, Robert Schmaltz, Amanda E. Ramer‐Tait, Samodha C. Fernando
Software Mentions: 5
Published: over 5 years ago

10.1186/s13062-015-0088-z

The human disease network in terms of dysfunctional regulatory mechanisms
Cited by: 22
Author(s): Jing Yang, Sujuan Wu, Wentao Dai, Yixue Li, Yuanyuan Li
Software Mentions: 5
Published: almost 11 years ago

10.3389/fmed.2021.674338

Role of Immune Cell-Specific Hypermethylation Signatures in Classification and Risk Stratification of Breast Cancer
Cited by: 0
Author(s): Yong Chen, Fada Xia, Bo Jiang, Wenlong Wang, Xinying Li
Software Mentions: 5
Published: almost 5 years ago

10.3389/fimmu.2021.590742

High Throughput Multi-Omics Approaches for Clinical Trial Evaluation and Drug Discovery
Cited by: 30
Author(s): Jessica Zielinski, Jason J. Luke, Silvia Guglietta, Carsten Krieg
Software Mentions: 5
Published: over 5 years ago

10.1172/jci.insight.144294

The MUC5B-associated variant rs35705950 resides within an enhancer subject to lineage- and disease-dependent epigenetic remodeling
Cited by: 20
Author(s): Fabienne Gally, Sarah K. Sasse, Jonathan S. Kurche, Margaret Gruca, Jonathan Cardwell, Tsukasa Okamoto, Hong Wei Chu, Xiaomeng Hou, Olivier Poirion, Justin Buchanan, Sebastian Preißl, Bing Ren, Sean P. Colgan, Robin D. Dowell, Ivana V. Yang, David A. Schwartz, Anthony N. Gerber
Software Mentions: 5
Published: over 5 years ago

10.1172/jci.insight.146196

Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis
Cited by: 9
Author(s): Carolin Czauderna, Alicia Poplawski, Colm J. O’Rourke, Darko Castven, Benjamín Pérez-Aguilar, Diana Becker, Markus M. Nöthen, Margarete Odenthal, W Amer, M Schmiel, Uta Drebber, Harald Binder, Dirk A. Ridder, Mario Schindeldecker, Beate K. Straub, Peter R. Galle, Jesper B. Andersen, Snorri S. Thorgeirsson, Young Nyun Park, Jens U. Marquardt
Software Mentions: 5
Published: almost 5 years ago

10.1038/s42003-021-01799-7

Genomic insights into the host specific adaptation of the Pneumocystis genus
Cited by: 16
Author(s): Ousmane Cissé, Liang Ma, John P. Dekker, Pavel P. Khil, Jung Ho Youn, Jason M. Brenchley, Robert V Blair, Bapi Pahar, Magali Chabé, Koen K. A. Van Rompay, Rebekah I. Keesler, Antti Sukura, Vanessa M. Hirsch, Geetha Kutty, Yueqin Liu, Peng Li, Jie Chen, Jun Song, Christiane Weissenbacher‐Lang, Jie Xu, Nathan S. Upham, Jason E. Stajich, Christina A. Cuomo, Melanie T. Cushion, Joseph A. Kovacs
Software Mentions: 5
Published: over 5 years ago

10.1111/acel.13280

Modeling the human aging transcriptome across tissues, health status, and sex
Cited by: 23
Author(s): Maxim N. Shokhirev, Adiv A. Johnson
Software Mentions: 5
Published: over 5 years ago

10.3390/cells8080919

The Combination of IFN β and TNF Induces an Antiviral and Immunoregulatory Program via Non-Canonical Pathways Involving STAT2 and IRF9
Cited by: 11
Author(s): Mélissa K. Mariani, Pouria Dasmeh, Audray Fortin, Élise Caron, Mario Kalamujic, Alexander N. Harrison, Diana Ioana Hotea, Dacquin M. Kasumba, Sandra Cervantes-Ortiz, Espérance Mukawera, Adrian W.R. Serohijos, Nathalie Grandvaux
Software Mentions: 5
Published: almost 7 years ago

10.3389/fnut.2019.00058

Integrated Analysis of Human Milk Microbiota With Oligosaccharides and Fatty Acids in the CHILD Cohort
Cited by: 66
Author(s): Shirin Moossavi, Faisal Atakora, Kozeta Miliku, Shadi Sepehri, Bianca Robertson, Qing Duan, Allan B. Becker, Piushkumar J. Mandhane, Stuart E. Turvey, Theo J. Moraes, Diana L. Lefebvre, Malcolm R. Sears, Padmaja Subbarao, Catherine J. Field, Lars Bode, Ehsan Khafipour, Meghan B. Azad
Software Mentions: 5
Published: about 7 years ago

10.1186/s13071-016-1843-4

Evaluation of three enzyme-linked immunosorbent assays for sarcoptic mange diagnosis and assessment in the Iberian ibex, Capra pyrenaica
Cited by: 24
Author(s): Arián Ráez‐Bravo, José E. Granados, Emmanuel Serrano, Debora Dellamaria, Rosa Casáis, Luca Rossi, Anna Puigdemont, Francisco Javier Cano-Manuel, Paulino Fandós, Jesús M. Pérez, J. Alberto Espinosa, Ramón C. Soriguer, Carlo Vittorio Citterio, Jorge Ramón López‐Olvera
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0233266

Automatic hoof-on and -off detection in horses using hoof-mounted inertial measurement unit sensors
Cited by: 6
Author(s): Marij Tijssen, Elin Hernlund, Marie Rhodin, Stephan Bosch, J. P. Voskamp, M. Nielen, F. M. Serra Braganςa
Software Mentions: 5
Published: about 6 years ago