10.1371/journal.pone.0077776

Extension of Life Span by Impaired Glucose Metabolism in Caenorhabditis elegans Is Accompanied by Structural Rearrangements of the Transcriptomic Network
Cited by: 20
Author(s): Stefan Priebe, Uwe Menzel, Kim Zarse, Marco Groth, Matthias Platzer, Michael Ristow, Reinhard Guthke
Software Mentions: 6
Published: over 12 years ago

10.1111/febs.15578

Genome‐wide postnatal changes in immunity following fetal inflammatory response
Cited by: 0
Author(s): DC Costa, Núria Bonet, Amanda Solé, José Manuel González de Aledo-Castillo, Eduard Sabidó, Ferrán Casals, Carlota Rovira, Alfons Nadal, J. L. Marı́n, Teresa Cobo, Robert Castelo
Software Mentions: 6
Published: over 5 years ago

10.1038/s41398-021-01561-x

Comparison of mouse models reveals a molecular distinction between psychotic illness in PWS and schizophrenia
Cited by: 5
Author(s): Simona Zahova, Trevor Humby, Jennifer R. Davies, Joanne Morgan, Anthony R Isles
Software Mentions: 6
Published: almost 5 years ago

10.3389/fpls.2021.715309

An Affordable Image-Analysis Platform to Accelerate Stomatal Phenotyping During Microscopic Observation
Cited by: 2
Author(s): Yosuke Toda, Toshiaki Tameshige, Masakazu Tomiyama, Toshinori Kinoshita, Kentaro Shimizu
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-020-66407-w

An understanding of third-party friendships in a tolerant macaque
Cited by: 12
Author(s): Jamie Whitehouse, Hélène Meunier
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0256929

Modelling the effects of the repellent scent marks of pollinators on their foraging efficiency and the plant-pollinator community
Cited by: 0
Author(s): Elise Verrier, Emmanuelle Baudry, Carmen Bessa‐Gomes
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0203361

In silico drug absorption tract: An agent-based biomimetic model for human oral drug absorption
Cited by: 3
Author(s): Jianyuan Deng, Anika Jhandey, Xiao Zhu, Zhibo Yang, Kin Fu Patrick Yik, Zhong Zuo, Tai Ning Lam
Software Mentions: 6
Published: almost 8 years ago

10.3390/genes11040434

Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups
Cited by: 5
Author(s): Daniil S. Wiebe, N. A. Omelyanchuk, Aleksey M. Mukhin, Ivo Große, Sergey A. Lashin, Elena V. Zemlyanskaya, В. В. Миронова
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-018-21161-y

Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
Cited by: 16
Author(s): Yukie Kashima, Ayako Suzuki, Ying Liu, Masahito Hosokawa, Hiroko Matsunaga, Masamitsu Shirai, Kohji Arikawa, Sumio Sugano, Takashi Kohno, Haruko Takeyama, Katsuya Tsuchihara, Yutaka Suzuki
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pgen.1006750

TCF21 and the environmental sensor aryl-hydrocarbon receptor cooperate to activate a pro-inflammatory gene expression program in coronary artery smooth muscle cells
Cited by: 50
Author(s): Juyong Brian Kim, Milos Pjanic, Trieu Nguyen, Clint L. Miller, Dharini Iyer, Boxiang Liu, Ting Wang, Olga V. Sazonova, Iván Cárcamo-Orive, Ljubica Matic, Lars Maegdefessel, Ulf Hedin, Thomas Quertermous
Software Mentions: 6
Published: about 9 years ago

10.1186/s12859-015-0664-3

Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications
Cited by: 5
Author(s): Fang Yu, Ming Hui Chen, Lynn Kuo, Heather Talbott, John S. Davis
Software Mentions: 6
Published: almost 11 years ago

10.3390/pathogens10081063

Gut Microbiota in Military International Travelers with Doxycycline Malaria Prophylaxis: Towards the Risk of a Simpson Paradox in the Human Microbiome Field
Cited by: 1
Author(s): Émilie Javelle, Aurélie Mayet, Matthieu Million, Anthony Levasseur, Rodrigue S. Allodji, Catherine Marimoutou, Chrystel Lavagna, Jérôme Desplans, Pierre-Édouard Fournier, Didier Raoult, Gaëtan Texier
Software Mentions: 6
Published: almost 5 years ago

10.1093/gigascience/giy059

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs
Cited by: 244
Author(s): Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard, Ines Hellmann
Software Mentions: 6
Published: about 8 years ago

10.1128/mSphere.00843-20

Pseudomonas aeruginosa Volatilome Characteristics and Adaptations in Chronic Cystic Fibrosis Lung Infections
Cited by: 10
Author(s): Thomas J. Davis, Ava V. Karanjia, Charity N. Bhebhe, Sarah B. West, Matthew Richardson, Heather D. Bean
Software Mentions: 6
Published: over 5 years ago

10.1111/acel.13153

Epigenome signatures landscaped by histone H3K9me3 are associated with the synaptic dysfunction in Alzheimer's disease
Cited by: 44
Author(s): Min Young Lee, Jung‐Hee Lee, Seung Jae Hyeon, Hyesun Cho, Yu Jin Hwang, Jong Yeon Shin, Ann C. McKee, Neil W. Kowall, Jong‐Il Kim, Thor D. Stein, Daehee Hwang, Hoon Ryu
Software Mentions: 6
Published: about 6 years ago

10.3389/fnins.2018.00261

Group Analysis in FieldTrip of Time-Frequency Responses: A Pipeline for Reproducibility at Every Step of Processing, Going From Individual Sensor Space Representations to an Across-Group Source Space Representation
Cited by: 10
Author(s): Lau M. Andersen
Software Mentions: 6
Published: about 8 years ago

10.3389/fonc.2019.00221

Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors
Cited by: 25
Author(s): Swetha Rajasekaran, Lakshmi Dhevi N. Selvan, Kathleen Dotts, Ranjith Kumar, Pukhraj Rishi, Vikas Khetan, Madhoolika Bisht, Karthikeyan Sivaraman, Subrmanian Krishnakumar, Debashis Sahoo, Moray J. Campbell, Sailaja Elchuri, Wayne Miles
Software Mentions: 6
Published: about 7 years ago

10.1038/s41422-020-0374-x

Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma
Cited by: 155
Author(s): Yu-Pei Chen, Jianhua Yin, Wenfei Li, Han-Jie Li, Dongping Chen, Cuijuan Zhang, Jiawei Lv, Yaqin Wang, Xiaomin Li, Junyan Li, Panpan Zhang, Ying‐Qin Li, Qing‐Mei He, Xiaojing Yang, Yuan Liu, Ling‐Long Tang, Guan-Qun Zhou, Yan‐Ping Mao, Wei Chen, Ke Xiong, Hongbo Zhang, Shida Zhu, Yong Hou, Ying Sun, Michael Dean, Ido Amit, Kui Wu, Dong-Ming Kuang, Guibo Li, Na Liu
Software Mentions: 6
Published: almost 6 years ago

10.1002/evl3.148

Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild
Cited by: 28
Author(s): Sónia Pascoal, Judith Risse, Xiao Zhang, Mark Blaxter, Timothée Cézard, Richard Challis, Karim Gharbi, John Hunt, Sujai Kumar, Emma Langan, Xuan Li, Jack G. Rayner, Michael G. Ritchie, L. Basten Snoek, Urmi Trivedi, Nathan W. Bailey
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pcbi.1006701

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Cited by: 271
Author(s): Mohamed Mounir, Marta Lucchetta, Tiago Henrique Da T.C. Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-020-65089-8

Immunorthodontics: in vivo gene expression of orthodontic tooth movement
Cited by: 28
Author(s): Yehuda Klein, Omer Fleissig, David Polak, Yechezkel Barenholz, Ofer Mandelboim, Stella Chaushu
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-020-64516-0

Cyto-Feature Engineering: A Pipeline for Flow Cytometry Analysis to Uncover Immune Populations and Associations with Disease
Cited by: 7
Author(s): Amy Fox, Taru Dutt, Burton Karger, Mauricio Rojas, Andrés Obregón-Henao, G. Brooke Anderson, Marcela Henao-Tamayo
Software Mentions: 6
Published: about 6 years ago

10.1186/s12915-019-0713-x

Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi
Cited by: 31
Author(s): Yuanning Li, Michael G. Tassia, Damien S. Waits, Viktoria E. Bogantes, Kyle T. David, Kenneth M. Halanych
Software Mentions: 6
Published: over 6 years ago

10.3389/fnut.2019.00045

What's Normal? Microbiomes in Human Milk and Infant Feces Are Related to Each Other but Vary Geographically: The INSPIRE Study
Cited by: 135
Author(s): Kimberly A. Lackey, Janet E. Williams, Courtney L. Meehan, Jessica A. Zachek, Elizabeth D. Benda, William J. Price, James A. Foster, Daniel Sellen, Elizabeth Kamau-Mbuthia, Egidioh W. Kamundia, Samwel Mbugua, Sophie E. Moore, Andrew M. Prentice, Debela Gindola K, Linda J. Kvist, Gloria E. Otoo, Cristina García-Carral, Esther Jiménez, Lorena Ruíz, Juan M. Rodríguez, Rossina G. Pareja, Lars Bode, Mark A. McGuire, Michelle K. McGuire
Software Mentions: 6
Published: about 7 years ago

10.1038/s41598-017-01498-6

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
Cited by: 64
Author(s): Juan Salamanca Viloria, Maria Francesca Allega, Matteo Lambrughi, Elena Papaleo
Software Mentions: 6
Published: about 9 years ago

10.3390/diagnostics10060415

Comparison between Statistical Models and Machine Learning Methods on Classification for Highly Imbalanced Multiclass Kidney Data
Cited by: 17
Author(s): Bomi Jeong, Hyun-Jeong Cho, Jieun Kim, Soon Kil Kwon, Suk Bong Hong, ChangSik Lee, TaeYeon Kim, Man Sik Park, Seoksu Hong, Tae‐Young Heo
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pbio.2005710

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria
Cited by: 152
Author(s): Inês S. Pais, Rita S Valente, Marta Sporniak, Luı́s Teixeira
Software Mentions: 6
Published: about 8 years ago

10.1038/s41598-020-63880-1

Global trends in mangrove forest fragmentation
Cited by: 135
Author(s): Dale Bryan-Brown, Rod M. Connolly, Daniel R. Richards, María Fernanda Adame, Daniel A. Friess, Christopher J. Brown
Software Mentions: 6
Published: about 6 years ago

10.1007/s00401-021-02300-8

TERT promoter mutation and chromosome 6 loss define a high-risk subtype of ependymoma evolving from posterior fossa subependymoma
Cited by: 12
Author(s): Christian Thomas, Felix Thierfelder, Malte Träger, Patrick Soschinski, Michael Müther, Dominic Edelmann, Alexandra Förster, Carola Geiler, Hee-Yeong Kim, Katharina Filipski, Patrick N. Harter, Jens Schittenhelm, Franziska Eckert, Georgios Ntoulias, Sven-Axel May, Walter Stummer, Julia Onken, Peter Vajkoczy, Ulrich Schüller, Frank L. Heppner, David Capper, Arend Koch, David Kaul, Werner Paulus, Martin Hasselblatt, Leonille Schweizer
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-020-03818-6

Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans
Cited by: 2
Author(s): Meng Li
Software Mentions: 6
Published: over 5 years ago

10.1186/s12711-019-0453-y

Machine learning applied to transcriptomic data to identify genes associated with feed efficiency in pigs
Cited by: 24
Author(s): M. Piles, Carlos Fernández-Lozano, María Velasco-Galilea, Olga González‐Rodríguez, Juan Pablo Sánchez, D. Torrallardona, María Ballester, Raquel Quintanilla
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-017-17407-w

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation
Cited by: 37
Author(s): Mariana Fontes, Ayşegül Güvenek, Riki Kawaguchi, Dinghai Zheng, Alden Huang, Victoria M. Ho, Patrick B. Chen, Xiaochuan Liu, Thomas J. O’Dell, Giovanni Coppola, Bin Tian, Kelsey C. Martin
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-017-12621-y

Reconstructing human population history from dental phenotypes
Cited by: 44
Author(s): Hannes Rathmann, Hugo Reyes-Centeno, Silvia Ghirotto, Nicole Creanza, Tsunehiko Hanihara, Katerina Harvati
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pbio.2003703

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
Cited by: 164
Author(s): Torsten Günther, Helena Malmström, Emma Svensson, Ayça Omrak, Federico Sánchez-Quinto, Gülşah Merve Kılınç, Maja Krzewińska, Gunilla Eriksson, Magdalena Fraser, Hanna Edlund, Arielle R. Munters, Alexandra Coutinho, Luciana G. Simões, Mário Vicente, Anders Sjölander, Berit J. Sellevold, Roger Jørgensen, Peter Claes, Mark D. Shriver, Cristina Valdiosera, Mihai G. Netea, Jan Apel, Kerstin Lidén, Birgitte Skår, Jan Storå, Anders Götherström, Mattias Jakobsson
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-020-68343-1

Performance prediction of crosses in plant breeding through genotype by environment interactions
Cited by: 13
Author(s): Javad Ansarifar, Faezeh Akhavizadegan, Lizhi Wang
Software Mentions: 6
Published: almost 6 years ago

10.7717/peerj.9697

Phytotoxin synthesis genes and type III effector genes of <i>Pseudomonas syringae</i> pv. <i>actinidiae</i> biovar 6 are regulated by culture conditions
Cited by: 2
Author(s): Karin Hirose, Yasuhiro Ishiga, Takashi Fujikawa
Software Mentions: 6
Published: almost 6 years ago

10.1016/j.ccell.2017.07.004

Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets
Cited by: 212
Author(s): Myron G. Best, Nik Sol, Sjors G J G In ‘t Veld, Adrienne Vancura, Mirte Muller, Anna-Larissa N. Niemeijer, Aniko V. Fejes, Lee Ann Tjon Kon Fat, Anna Egberdina Huis In 't Veld, Cyra E. Leurs, Tessa Y. Le Large, Laura L. Meijer, Irsan Kooi, François Rustenburg, Pepijn Schellen, Heleen Verschueren, Edward P. Post, Laurine E. Wedekind, Jillian Wilhelmina Paulina Bracht, Michelle Esenkbrink, Leon J. Wils, Francesca Favaro, Jilian D. Schoonhoven, Jihane Tannous, Hanne Meijers-Heijboer, Geert Kazemier, Elisa Giovannetti, Jaap C. Reijneveld, Sander Idema, Joep Killestein, Michal Heger, Saskia C.A. de Jager, Rolf T. Urbanus, Imo E. Hoefer, Gérard Pasterkamp, Christine Mannhalter, José Gomez-Arroyo, Harm Jan Bogaard, David P. Noske, W. Peter Vandertop, Daan van den Broek, Bauke Ylstra, R. Jonas A. Nilsson, Jelle Wesseling, Niki Karachaliou, Rafael Rosell, Elizabeth Lee-Lewandrowski, Kent Lewandrowski, Bakhos A. Tannous, Adrianus J. de Langen, Egbert F. Smit, Michel M. van den Heuvel, Thomas Würdinger
Software Mentions: 6
Published: almost 9 years ago

10.3389/fmicb.2017.01563

Role of Age-Related Shifts in Rumen Bacteria and Methanogens in Methane Production in Cattle
Cited by: 28
Author(s): Chong Liu, Qinghui Meng, Yongxing Chen, Mengsi Xu, Min Shen, Rui Gao, Shangquan Gan
Software Mentions: 6
Published: almost 9 years ago

10.3389/fneur.2020.00729

Googling the Lifetime Risk of Stroke Around the World
Cited by: 3
Author(s): Thanh G. Phan, Anisha Haseeb, Richard Beare, Velandai Srikanth, Amanda G Thrift, Henry Ma
Software Mentions: 6
Published: almost 6 years ago

10.1002/ece3.6418

Genomic signals found using RNA sequencing show signatures of selection and subtle population differentiation in walleye (<i>Sander vitreus</i>) in a large freshwater ecosystem
Cited by: 12
Author(s): Matt J. Thorstensen, Jennifer D. Jeffrey, Jason R. Treberg, Douglas A. Watkinson, Eva C. Enders, Ken M. Jeffries
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0106397

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
Cited by: 138
Author(s): Mehmet K. Samur
Software Mentions: 6
Published: almost 12 years ago

10.1038/s41598-020-61164-2

Hurricane-Induced Rainfall is a Stronger Predictor of Tropical Forest Damage in Puerto Rico Than Maximum Wind Speeds
Cited by: 43
Author(s): Jazlynn Hall, Robert Muscarella, Andrew W. Quebbeman, Gabriel Arellano, Jill Thompson, Jess K. Zimmerman, María Uríarte
Software Mentions: 6
Published: over 6 years ago

10.3389/fninf.2021.678403

FlywheelTools: Data Curation and Manipulation on the Flywheel Platform
Cited by: 5
Author(s): Tinashe M. Tapera, Matthew Cieslak, Max Bertolero, Azeez Adebimpe, Geoffrey K. Aguirre, Ellyn R. Butler, Philip A. Cook, Diego Davila, Mark A. Elliott, Sophia Linguiti, Kristin Murtha, William Tackett, John A. Detre, Theodore D. Satterthwaite
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0101581

Analysis of the Transcriptome in Hyperoxic Lung Injury and Sex-Specific Alterations in Gene Expression
Cited by: 25
Author(s): Krithika Lingappan, Chandramouleeswaran Srinivasan, Weiwu Jiang, Lihua Wang, Xanthi I. Couroucli, Bhagavatula Moorthy
Software Mentions: 6
Published: about 12 years ago

10.7554/eLife.46464

Molecular and anatomical organization of the dorsal raphe nucleus
Cited by: 120
Author(s): Kee Wui Huang, Nicole Ochandarena, Adrienne C. Philson, Minsuk Hyun, Jaclyn E Birnbaum, Marcelo Cicconet, Bernardo L. Sabatini
Software Mentions: 6
Published: almost 7 years ago

10.1111/eva.12047

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals
Cited by: 14
Author(s): John D. Kirwan, Michaël Bekaert, Jennifer M. Commins, Kalina T. J. Davies, Stephen J. Rossiter, Emma C. Teeling
Software Mentions: 6
Published: over 13 years ago

10.1186/s13148-015-0123-z

High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases
Cited by: 32
Author(s): Daniel Nätt, I. Johansson, Tomas Faresjö, Johnny Ludvigsson, Annika Thorsell
Software Mentions: 6
Published: almost 11 years ago

10.7554/eLife.52648

Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
Cited by: 34
Author(s): Anneke Dixie Kakebeen, Alexander Daniel Chitsazan, Madison Corinne Williams, Lauren Saunders, Andrea E. Wills
Software Mentions: 6
Published: about 6 years ago

10.1002/ctm2.253

Multiregion single‐cell sequencing reveals the transcriptional landscape of the immune microenvironment of colorectal cancer
Cited by: 34
Author(s): Wei Wang, Yu Zhong, Zhenkun Zhuang, Junping Xie, Yueer Lu, Chengzhi Huang, Yan Sun, Liang Wu, Jianhua Yin, Hang Yu, Zhiqiang Jiang, Shanshan Wang, Chunqing Wang, Yuanhang Zhang, Yilin Huang, Chongyin Han, Zhenggang Zhong, Jialin Hu, Ying Ouyang, Huisheng Liu, Mengya Yu, Xiaochan Wei, Dandan Chen, Lizhen Huang, Yong Hou, Zhanglin Lin, Shiping Liu, Fei Ling, Xueqing Yao
Software Mentions: 6
Published: over 5 years ago

10.1002/ctm2.156

A three‐lncRNA signature of pretreatment biopsies predicts pathological response and outcome in esophageal squamous cell carcinoma with neoadjuvant chemoradiotherapy
Cited by: 17
Author(s): Chaoqi Zhang, Zhihui Zhang, Guochao Zhang, Liyan Xue, Haijun Yang, Yuejun Luo, Xiaoli Zheng, Yonglei Zhang, Yufen Yuan, Ruixue Lei, Zhaoyang Yang, Bo Zheng, Zhen Zhang, Le Wang, Yun Cao, Sihui Wang, Feng Wang, Lingling Fang, Qingpeng Zeng, Jiagen Li, Shugeng Gao, Qi Xue, Nan Sun, Jie He
Software Mentions: 6
Published: almost 6 years ago

10.3390/microorganisms7120595

Dynamic Succession of Microbiota during Ensiling of Whole Plant Corn Following Inoculation with Lactobacillus buchneri and Lactobacillus hilgardii Alone or in Combination
Cited by: 40
Author(s): Pascal Drouin, Julien Tremblay, Frédérique Chaucheyras‐Durand
Software Mentions: 6
Published: over 6 years ago

10.1038/s41396-021-00987-x

Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria
Cited by: 14
Author(s): François Thomas, Nolwen Le Duff, Ting-Di Wu, Aurélie Cébron, Stéphane Uroz, Pascal Riera, Cédric Leroux, Gwenn Tanguy, Erwan Legeay, Jean‐Luc Guerquin‐Kern
Software Mentions: 6
Published: about 5 years ago

10.7150/thno.55946

Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome
Cited by: 28
Author(s): Xiaomin Hu, Hanyu Li, Xinyue Zhao, Ronggang Zhou, Honghong Liu, Yiting Sun, Yue Fan, Yanan Shi, Shushan Qiao, Shuang‐Jiang Liu, Hongwei Liu, Shuyang Zhang
Software Mentions: 6
Published: over 5 years ago

10.3390/plants10061039

Comparative Analysis of Re-Annotated Genes Provides Insight into Evolutionary Divergence and Expressions of Aquaporin Family in Pepper
Cited by: 2
Author(s): Yeon Mi Lee, Geun Young Chae, Min Kyung Kim, Seungill Kim
Software Mentions: 6
Published: about 5 years ago

10.3390/microorganisms9020208

Aquatic Bacterial Diversity, Community Composition and Assembly in the Semi-Arid Inner Mongolia Plateau: Combined Effects of Salinity and Nutrient Levels
Cited by: 29
Author(s): Xiangming Tang, Guobo Xie, Kwang‐Tsao Shao, Wei Tian, Guang Gao, Boqiang Qin
Software Mentions: 6
Published: over 5 years ago

10.1002/acm2.13107

Clinical and radiological predictors of epidermal growth factor receptor mutation in nonsmall cell lung cancer
Cited by: 12
Author(s): Yutao Dang, Ruotian Wang, Kun Qian, Jie Lu, Haixiang Zhang, Yi Zhang
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-87829-0

GWAS analysis reveals distinct pathogenicity profiles of Australian Parastagonospora nodorum isolates and identification of marker-trait-associations to septoria nodorum blotch
Cited by: 7
Author(s): H. Phan, Eiko Furuki, Lukas Hunziker, Kasia Rybak, Kar‐Chun Tan
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2021.623799

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management
Cited by: 11
Author(s): Ahmad Nuruddin Khoiri, Supapon Cheevadhanarak, Jiraporn Jirakkakul, Sudarat Dulsawat, Peerada Prommeenate, Anuwat Tachaleat, Kanthida Kusonmano, Songsak Wattanachaisaereekul, Sawannee Sutheeworapong
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2021.701186

Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines
Cited by: 9
Author(s): Josephine Z. Rapp, Matthew B. Sullivan, Jody W. Deming
Software Mentions: 6
Published: almost 5 years ago

10.3390/ijms22010078

Alterations in the Genomic Distribution of 5hmC in In Vivo Aged Human Skin Fibroblasts
Cited by: 10
Author(s): Paulina Kołodziej-Wojnar, Joanna Borkowska, Zofia Wicik, Anna Domaszewska-Szostek, Jacek Połosak, Marta Cąkała-Jakimowicz, Olga Bujanowska, Monika Puzianowska-Kuźnicka
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2017.02102

Functionality of Root-Associated Bacteria along a Salt Marsh Primary Succession
Cited by: 17
Author(s): Miao Wang, Erqin Li, Chen Liu, Alexandre Jousset, Joana Falcão Salles
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pntd.0008780

Genomic and transcriptional analysis of genes containing fibrinogen and IgSF domains in the schistosome vector Biomphalaria glabrata, with emphasis on the differential responses of snails susceptible or resistant to Schistosoma mansoni
Cited by: 8
Author(s): Lijun Lu, Eric S. Loker, Coen M. Adema, Si-Ming Zhang, Lijing Bu
Software Mentions: 6
Published: over 5 years ago

10.1155/2020/8537381

Autophagy Regulatory Genes MET and RIPK2 Play a Prognostic Role in Pancreatic Ductal Adenocarcinoma: A Bioinformatic Analysis Based on GEO and TCGA
Cited by: 10
Author(s): Xingyu Li, Zhiqiang Li, Hongwei Zhu, Xiao Yu
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2020.588778

Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription
Cited by: 21
Author(s): Benjamin Pontiller, Sandra Martínez‐García, Daniel Lundin, Jarone Pinhassi
Software Mentions: 6
Published: almost 6 years ago

10.3389/fspor.2020.518148

A Systematic Review and Meta-Analysis on the Longitudinal Effects of Unilateral Knee Extension Exercise on Muscle Strength
Cited by: 1
Author(s): Ekin Altan, Svenja Elizabeth Seide, Ismail Bayram, Leonardo Gizzi, Hayri Ertan, Oliver Röhrle
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.55159

Condensin I subunit Cap-G is essential for proper gene expression during the maturation of post-mitotic neurons
Cited by: 9
Author(s): Amira Hassan, Pablo Araguas Rodriguez, Stefan Heidmann, Emma L Walmsley, Gabriel Aughey, Tony D. Southall
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-020-60476-7

EPDR1 up-regulation in human colorectal cancer is related to staging and favours cell proliferation and invasiveness
Cited by: 11
Author(s): Francisco Gimeno-Valiente, Ángela L. Riffo‐Campos, Guillermo Ayala, Noelia Tarazona, Fernanda Mariel Rodríguez, Marisol Huerta, J. Montón-Bueno, Susana Roselló, Luís Franco, Gerardo López-Rodas, Josefa Castillo
Software Mentions: 6
Published: over 6 years ago

10.1186/s40168-017-0389-9

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming
Cited by: 340
Author(s): Kyle Hartman, Marcel G. A. van der Heijden, Raphaël Wittwer, Samiran Banerjee, Jean Claude Walser, Klaus Schlaeppi
Software Mentions: 6
Published: over 8 years ago

10.1038/s41396-020-00783-z

Root pathogen diversity and composition varies with climate in undisturbed grasslands, but less so in anthropogenically disturbed grasslands
Cited by: 16
Author(s): Camille S. Delavaux, Josh L. Schemanski, Geoffrey L. House, Alice G. Tipton, Benjamin A. Sikes, James D. Bever
Software Mentions: 6
Published: almost 6 years ago

10.1126/sciadv.abj1132

Plasma lipids and growth faltering: A longitudinal cohort study in rural Gambian children
Cited by: 2
Author(s): Gerard Bryan Gonzales, Daniëlla Brals, Bakary Sonko, Fatou Sosseh, Andrew M. Prentice, Sophie E. Moore, Albert Koulman
Software Mentions: 6
Published: almost 5 years ago

10.18632/oncotarget.15749

Gene regulatory pattern analysis reveals essential role of core transcriptional factors’ activation in triple-negative breast cancer
Cited by: 15
Author(s): Li Min, Cheng Zhang, Like Qu, Jialiang Huang, Lan Jiang, Jiafei Liu, Luca Pinello, Guo‐Cheng Yuan, Chengchao Shou
Software Mentions: 6
Published: over 9 years ago

10.1038/s41598-021-86032-5

A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes
Cited by: 18
Author(s): Timothy Warwick, Marcel H. Schulz, Stefan Günther, Ralf Gilsbach, Antonio Neme, Carsten Carlberg, Ralf P. Brandes, Sabine Seuter
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-016-1420-z

T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes
Cited by: 9
Author(s): Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos, Grigoris D. Amoutzias
Software Mentions: 6
Published: over 9 years ago

10.1002/1878-0261.12351

GeneExpressScore Signature: a robust prognostic and predictive classifier in gastric cancer
Cited by: 18
Author(s): Xiaoqiang Zhu, Xianglong Tian, Tiantian Sun, Chuangqi Yu, Yingying Cao, Tingting Yan, Chaoqin Shen, Yanwei Lin, Jing–Yuan Fang, Jie Hong, Haoyan Chen
Software Mentions: 6
Published: almost 8 years ago

10.3389/fgene.2021.674783

Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions
Cited by: 8
Author(s): Victoria A. Scobeyeva, Ilya V. Artyushin, A.A. Krinitsina, Nikitin Pavel, Antipin Mi, Sergei V. Kuptsov, Maxim S. Belenikin, Denis O. Omelchenko, Maria D. Logacheva, Е. А. Коноров, Andrei E. Samoilov, Anna S. Speranskaya
Software Mentions: 6
Published: about 5 years ago

10.1534/g3.113.006742

The Developmental Transcriptome of the Mosquito <i>Aedes aegypti</i>, an Invasive Species and Major Arbovirus Vector
Cited by: 184
Author(s): Omar S. Akbari, Igor Antoshechkin, Henry Amrhein, Brian A. Williams, Rose DiLoreto, Jeremy E. Sandler, Bruce A. Hay
Software Mentions: 6
Published: almost 13 years ago

10.1111/mpp.12964

A complex network of additive and epistatic quantitative trait loci underlies natural variation of <i>Arabidopsis thaliana</i> quantitative disease resistance to <i>Ralstonia solanacearum</i> under heat stress
Cited by: 22
Author(s): Nathalie Aoun, Henri Desaint, Léa Boyrie, Maxime Bonhomme, Laurent Deslandes, Richard Berthomé, Fabrice Roux
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-020-73376-7

RNA oxidation in chromatin modification and DNA-damage response following exposure to formaldehyde
Cited by: 17
Author(s): Juan C. Gonzalez-Rivera, Mark W. Sherman, Dongyu Wang, Jamie C. L. Chuvalo-Abraham, Lea Hildebrandt Ruiz, Lydia M. Contreras
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-021-92042-0

Socioeconomic position links circulatory microbiota differences with biological age
Cited by: 12
Author(s): Hannah Craven, Dagmara McGuinness, Sarah Buchanan, Norman Galbraith, David McGuinness, Brian Jones, Emilie Combet, Denise Mafra, Peter Bergman, Anne Ellaway, Peter Stenvinkel, Umer Zeeshan Ijaz, Paul G. Shiels
Software Mentions: 6
Published: about 5 years ago

10.1002/ece3.4501

Giant coral reef fishes display markedly different susceptibility to night spearfishing
Cited by: 5
Author(s): Alan R. Pearse, Richard Hamilton, J. Howard Choat, John Pita, Glenn R. Almany, Nate Peterson, Grant Hamilton, Erin E. Peterson
Software Mentions: 6
Published: almost 8 years ago

10.1038/s41420-021-00547-4

Impairment of neuronal mitochondrial function by l-DOPA in the absence of oxygen-dependent auto-oxidation and oxidative cell damage
Cited by: 5
Author(s): Philipp Hörmann, Sylvie Delcambre, Jasmin E. Hanke, Robert Geffers, Marcel Leist, Karsten Hiller
Software Mentions: 6
Published: about 5 years ago

10.1038/sdata.2017.44

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
Cited by: 119
Author(s): Sebastian Beier, Axel Himmelbach, Christian Colmsee, Xiao Qi Zhang, Roberto A. Barrero, Qisen Zhang, Lin Li, Micha Bayer, Dan Bolser, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz‐Amatriaín, Rachid Ounit, Steve Wanamaker, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Dharanya Sampath, Darren Heavens, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K. McCooke, Cong Tan, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse Poland, M. Bellgard, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Peter Langridge, Gary J. Muehlbauer, Paul J. Kersey, Matthew D. Clark, Mario Cáccamo, Alan H. Schulman, Matthias Platzer, Timothy J. Close, Mats Hansson, Guoping Zhang, Ilka Braumann, Chengdao Li, Robbie Waugh, Uwe Scholz, Nils Stein, Martin Mascher
Software Mentions: 6
Published: about 9 years ago

10.18632/aging.103350

A novel molecular-clinicopathologic nomogram to improve prognosis prediction of hepatocellular carcinoma
Cited by: 3
Author(s): Zhongjing Zhang, Wanqing Weng, Weiguo Huang, Boda Wu, Yi Zhou, Jie Zhang, Tuo Deng, Yan Wen, Jiecheng Zhang, Jian‐Yang Ao, Qiyu Zhang, Ke‐Qing Shi
Software Mentions: 6
Published: about 6 years ago

10.3390/ijms21249622

Novel Liver X Receptor Ligand GAC0001E5 Disrupts Glutamine Metabolism and Induces Oxidative Stress in Pancreatic Cancer Cells
Cited by: 7
Author(s): Shivangi Srivastava, Scott Widmann, Charles Ho, Donovan Nguyen, Alexis Nguyen, Asitha Premaratne, Jan‐Åke Gustafsson, Chin-Yo Lin
Software Mentions: 6
Published: over 5 years ago

10.3389/fpsyg.2020.00372

Community Characteristics, Victimization, and Psychological Adjustment Among School-Aged Adopted Children With Lesbian, Gay, and Heterosexual Parents
Cited by: 7
Author(s): Abbie E. Goldberg, Randi L. Garcia
Software Mentions: 6
Published: over 6 years ago

10.7150/jca.50413

Construction of a Glycolysis-related long noncoding RNA signature for predicting survival in endometrial cancer
Cited by: 27
Author(s): Yuan Jiang, Jie Chen, Jiwei Ling, Xiaonian Zhu, Pinping Jiang, Xiaohu Tang, Huaqiang Zhou, Rong Li
Software Mentions: 6
Published: over 5 years ago

10.18632/oncotarget.22942

S-adenosyl-methionine (SAM) alters the transcriptome and methylome and specifically blocks growth and invasiveness of liver cancer cells
Cited by: 33
Author(s): Yan Wang, Zhong Sheng Sun, Moshe Szyf
Software Mentions: 6
Published: over 8 years ago

10.1186/s13073-015-0237-0

Identification of global regulators of T-helper cell lineage specification
Cited by: 36
Author(s): Kartiek Kanduri, Subhash Tripathi, Antti Larjo, Henrik Mannerström, Ubaid Ullah, Riikka Lund, R. David Hawkins, Bing Ren, Harri Lähdesmäki, Riitta Lahesmaa
Software Mentions: 6
Published: over 10 years ago

10.3389/fnagi.2021.602781

Exploring the Key Genes and Identification of Potential Diagnosis Biomarkers in Alzheimer’s Disease Using Bioinformatics Analysis
Cited by: 20
Author(s): Wuhan Yu, Weihua Yu, Yan Yang, Yang Lü
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-017-4386-y

Global accumulation of circRNAs during aging in Caenorhabditis elegans
Cited by: 127
Author(s): Mariela Cortés-López, Matthew Gruner, Daphne A. Cooper, Hannah N. Gruner, Alexandru-Ioan Voda, Alexander M. van der Linden, Pedro Miura
Software Mentions: 6
Published: over 8 years ago

10.1038/srep21518

Activation of the TGFβ pathway impairs endothelial to haematopoietic transition
Cited by: 32
Author(s): Özge Vargel, Yang Zhang, Kinga Kosim, Kerstin Ganter, Sophia Föehr, Yannicka Mardenborough, Maya Shvartsman, Anton J. Enright, Jeroen Krijgsveld, Christophe Lancrin
Software Mentions: 6
Published: over 10 years ago

10.3389/fgene.2021.665153

Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species
Cited by: 9
Author(s): Annie Robic, Chloé Cerutti, Christa Kühn, Thomas Faraut
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.12035

To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere
Cited by: 4
Author(s): Ankit T. Hinsu, Ashvin Dumadiya, Anjali Joshi, Rohitkumar Kotadiya, Kavan N. Andharia, Prakash G. Koringa, Ramesh Kothari
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmicb.2019.03077

A High-Throughput Interbacterial Competition Screen Identifies ClpAP in Enhancing Recipient Susceptibility to Type VI Secretion System-Mediated Attack by Agrobacterium tumefaciens
Cited by: 12
Author(s): Hsiao‐Han Lin, Manda Yu, Manoj Kumar Sriramoju, Shang-Te Danny Hsu, Chi-Te Liu, Erh‐Min Lai
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2020.610009

Evidence That Microorganisms at the Animal-Water Interface Drive Sea Star Wasting Disease
Cited by: 28
Author(s): Citlalli A Aquino, Ryan M Besemer, Christopher M. DeRito, Jan Kocian, Ian Porter, Peter T. Raimondi, Jordan E Rede, Lauren M. Schiebelhut, Jed P. Sparks, John P. Wares, Ian Hewson
Software Mentions: 6
Published: over 5 years ago

10.1073/pnas.2104315118

Global range expansion history of pepper (<i>Capsicum</i>spp.) revealed by over 10,000 genebank accessions
Cited by: 39
Author(s): Pasquale Tripodi, M. Timothy Rabanus‐Wallace, Lorenzo Barchi, Sandip M. Kale, Salvatore Esposito, Alberto Acquadro, Roland Schafleitner, Maarten van Zonneveld, Jaime Prohens, María José Díez, Andreas Börner, Jérémy Salinier, Bernard Caromel, Arnaud Bovy, Filiz Boyaci, Gancho Pasev, Ronny Brandt, Axel Himmelbach, Ezio Portis, Richard Finkers, Sergio Lanteri, Ilan Paran, Véronique Lefebvre, Giovanni Giuliano, Nils Stein
Software Mentions: 6
Published: almost 5 years ago

10.3390/microorganisms9020252

Relationships among Fecal, Air, Oral, and Tracheal Microbial Communities in Pigs in a Respiratory Infection Disease Model
Cited by: 7
Author(s): Robert Valeris-Chacín, Amanda Sponheim, Eduardo Fano, Richard E. Isaacson, Randall S. Singer, Joel Nerem, Fernando Leite, Maria Pieters
Software Mentions: 6
Published: over 5 years ago

10.3390/ani11030625

RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats
Cited by: 6
Author(s): Dongdong Bo, Xunping Jiang, Guiqiong Liu, Ronggui Hu, Yuqing Chong
Software Mentions: 6
Published: over 5 years ago

10.1186/s42523-020-0022-2

Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome
Cited by: 15
Author(s): Younjung Kim, Marcus H. Y. Leung, Wendy Kwok, Guillaume Fournié, Jun Li, Patrick K. H. Lee, Dirk U. Pfeiffer
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pgen.1008156

Transcriptomic basis and evolution of the ant nurse-larval social interactome
Cited by: 14
Author(s): Michael Warner, Alexander S. Mikheyev, Timothy A. Linksvayer
Software Mentions: 5
Published: about 7 years ago