10.1186/s12866-021-02099-0

The regional diversity of gut microbiome along the GI tract of male C57BL/6 mice
Cited by: 41
Author(s): Enkhchimeg Lkhagva, Hea-Jong Chung, Jinny Hong, W.H. Wilson Tang, Lee S, Seong‐Tshool Hong, Seungkoo Lee
Software Mentions: 5
Published: over 5 years ago

10.1186/s13073-017-0432-2

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes
Cited by: 33
Author(s): Leif Väremo, Tora Ida Henriksen, Camilla Schéele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen, Jens Nielsen
Software Mentions: 5
Published: about 9 years ago

10.1016/j.gpb.2018.04.008

Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake
Cited by: 25
Author(s): Maozhen Han, Melissa Dsouza, Chunyu Zhou, Hongjun Li, Junqian Zhang, Chaoyun Chen, Qi Yao, Chunrong Zhong, Hao Zhou, Jack A. Gilbert, Zhi Wen, Kang Ning
Software Mentions: 5
Published: over 7 years ago

10.1186/s12967-020-02233-y

IRGS: an immune-related gene classifier for lung adenocarcinoma prognosis
Cited by: 22
Author(s): Xiaoshun Shi, Ruidong Li, Xiaoying Dong, Allen M. Chen, Xiguang Liu, Di Lu, Siyang Feng, He Wang, Kaican Cai
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-021-02464-2

Systematic functional interrogation of human pseudogenes using CRISPRi
Cited by: 11
Author(s): Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Xu Han, Yiwen Chen
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-018-21874-0

Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau
Cited by: 40
Author(s): Yunfu Gu, Yan Bai, Quanju Xiang, Xiumei Yu, Ke Zhao, Xiaoping Zhang, Chaonan Li, Songqin Liu, Qiang Chen
Software Mentions: 5
Published: over 8 years ago

10.1186/s13059-021-02334-x

The impact of cell type and context-dependent regulatory variants on human immune traits
Cited by: 27
Author(s): Zepeng Mu, Wei Wei, Benjamin Jung Fair, Jinlin Miao, Ping Zhu, Yang Li
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-020-01960-1

Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons
Cited by: 35
Author(s): Peipei Li, Elizabeth Ensink, Sean Lang, Lee Marshall, Meghan Schilthuis, Jared Lamp, Irving E. Vega, Viviane Labrie
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1009140

Drosophila Caliban preserves intestinal homeostasis and lifespan through regulating mitochondrial dynamics and redox state in enterocytes
Cited by: 12
Author(s): Zhaoxia Dai, Dong Liu, Xiao Du, Ying Ge, Deborah A. Hursh, Xiaolin Bi
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0167570

GWRM: An R Package for Identifying Sources of Variation in Overdispersed Count Data
Cited by: 4
Author(s): Silverio Vílchez-López, A. J. Sáez-Castillo, María José Olmo-Jiménez
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-018-26484-4

Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo
Cited by: 11
Author(s): David W. Waite, Melissa Dsouza, Yuji Sekiguchi, Philip Hugenholtz, Michael W. Taylor
Software Mentions: 5
Published: about 8 years ago

10.1186/s13059-019-1878-x

Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies
Cited by: 24
Author(s): Jeroen van Rooij, Pooja R. Mandaviya, Annique Claringbould, Janine F. Felix, Jenny van Dongen, Rick Jansen, Lude Franke, Peter A.C. ’t Hoen, B.T. Heijmans, Joyce B. J. van Meurs
Software Mentions: 5
Published: over 6 years ago

10.3389/fphar.2020.577150

Screening and Identification of Key Biomarkers in Acquired Lapatinib-Resistant Breast Cancer
Cited by: 4
Author(s): Shengnan Bao, Yi Chen, Fan Yang, Chunxiao Sun, Mingli Yang, Li Wei, Xiang Huang, Jun Li, Hao Wu, Yongmei Yin
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pgen.1009443

Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology
Cited by: 27
Author(s): Eilís Hannon, Georgina Mansell, Emma Walker, Marta F. Nabais, Joe Burrage, Agnieszka Kepa, Janis Best-Lane, Anna Rose, Suzanne Heck, Terrie E. Moffitt, Avshalom Caspi, Louise Arseneault, Jonathan Mill
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0100366

Predator-Prey Interactions between Shell-Boring Beetle Larvae and Rock-Dwelling Land Snails
Cited by: 22
Author(s): Els Baalbergen, Renate A. Helwerda, Rense Schelfhorst, Ruth F. Castillo Cajas, Coline H.M. van Moorsel, Robin Kundrata, Francisco Welter-Schultes, Sinos Giokas, Menno Schilthuizen
Software Mentions: 5
Published: about 12 years ago

10.1371/journal.pone.0193417

Sex- and brain region-specific patterns of gene expression associated with socially-mediated puberty in a eusocial mammal
Cited by: 20
Author(s): Mariela Faykoo-Martinez, D. Ashley Monks, Iva B. Zovkic, Melissa M. Holmes
Software Mentions: 5
Published: over 8 years ago

10.1038/s42003-021-01690-5

Development of a robust protocol for the characterization of the pulmonary microbiota
Cited by: 6
Author(s): Nathan Dumont-Leblond, Marc Veillette, Christine Racine, Philippe Joubert, Caroline Duchaine
Software Mentions: 5
Published: over 5 years ago

10.18632/oncotarget.25330

Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma
Cited by: 14
Author(s): Michael Hamilton, Thomas Girke, Ernest Martinez
Software Mentions: 5
Published: about 8 years ago

10.1186/s13059-015-0840-9

A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63
Cited by: 126
Author(s): Xiaomin Bao, Adam J. Rubin, Kun Qu, Jiajing Zhang, Paul G. Giresi, Howard Y. Chang, Paul A. Khavari
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-018-37679-0

Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level
Cited by: 46
Author(s): Petra Patáková, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Katerina Jureckova, Jan Kolek, Pavlína Koščová, Ivo Provazník
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0195461

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome
Cited by: 80
Author(s): Kris A. Christensen, Jong S. Leong, Dionne Sakhrani, Carlo A. Biagi, David R. Minkley, Ruth E. Withler, Eric B. Rondeau, Ben F. Koop, Robert H. Devlin
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pgen.1008611

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales
Cited by: 17
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Eusebio Navarro, Victoriano Garre
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0230284

Lake-depth related pattern of genetic and morphological diatom diversity in boreal Lake Bolshoe Toko, Eastern Siberia
Cited by: 15
Author(s): Kathleen R. Stoof‐Leichsenring, Katharina Dulias, Boris K. Biskaborn, Ludmila A Pestryakova, Ulrike Herzschuh
Software Mentions: 5
Published: over 6 years ago

10.1111/1755-0998.12694

An integrated framework to identify wildlife populations under threat from climate change
Cited by: 64
Author(s): Orly Razgour, John B. Taggart, Stéphanie Manel, Javier Juste, Carlos Ibáñez, Hugo Rebelo, Antton Alberdi, Gareth Jones, Kirsty Park
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pntd.0004992

Meta-transcriptome Profiling of the Human-Leishmania braziliensis Cutaneous Lesion
Cited by: 54
Author(s): Stephen M Christensen, Laura A. L. Dillon, Lucas P. Carvalho, Sara Passos, Fernanda O. Novais, V. K. Hughitt, Daniel P. Beiting, Edgar M. Carvalho, Phillip Scott, Najib M. El-Sayed, David M. Mosser
Software Mentions: 5
Published: almost 10 years ago

10.1186/s12920-020-00740-x

Integrative analyses of gene expression profile reveal potential crucial roles of mitotic cell cycle and microtubule cytoskeleton in pulmonary artery hypertension
Cited by: 15
Author(s): Jing Luo, Haiyan Li, Zhenwei Liu, Chenlu Li, Ruochen Wang, Jinxia Fang, Saisai Lu, Jing Guo, Xiongzhao Zhu, Xiaobing Wang
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-020-6558-4

Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)
Cited by: 10
Author(s): Fugui Zhang, Xin Xiao, Kun Xu, Xi Cheng, Ting Xie, Jihong Hu, Xiaoming Wu
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.01541

Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida)
Cited by: 15
Author(s): Justyna J. Hampel, Mark J. McCarthy, Sanni L. Aalto, Silvia E. Newell
Software Mentions: 5
Published: about 6 years ago

10.1186/s12967-021-02705-9

Eight-lncRNA signature of cervical cancer were identified by integrating DNA methylation, copy number variation and transcriptome data
Cited by: 23
Author(s): Qihang Zhong, Minzhen Lu, Wei Yuan, Yueyi Cui, Hanqiang Ouyang, Yong Fan, Zhaohui Wang, Congying Wu, Jie Qiao, Jing Hang
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0183906

Flat and complex temperate reefs provide similar support for fish: Evidence for a unimodal species-habitat relationship
Cited by: 39
Author(s): Avery B. Paxton, Emily A. Pickering, Alyssa M. Adler, James C. Taylor, Charles H. Peterson
Software Mentions: 5
Published: almost 9 years ago

10.1038/s41598-019-47087-7

Systems biology and network pharmacology of frailty reveal novel epigenetic targets and mechanisms
Cited by: 6
Author(s): Juan Carlos Gómez-Verján, Ricardo Ramírez‐Aldana, Mario Ulises Pérez‐Zepeda, Ricardo Quiroz‐Baez, Armando Luna–López, Luis Miguel Gutiérrez Robledo
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2017.01574

Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin
Cited by: 25
Author(s): Daniel Medina, Jenifer B. Walke, Zachary Gajewski, Matthew H. Becker, Meredith C. Swartwout, Lisa K. Belden
Software Mentions: 5
Published: almost 9 years ago

10.1038/s41598-021-90654-0

Kernel weighted least square approach for imputing missing values of metabolomics data
Cited by: 7
Author(s): Nishith Kumar, Md. Rakibul Hoque, Masahiro Sugimoto
Software Mentions: 5
Published: about 5 years ago

10.3390/jcm10112524

Evaluation of Intracranial Hypertension in Traumatic Brain Injury Patient: A Noninvasive Approach Based on Cranial Computed Tomography Features
Cited by: 4
Author(s): Yingchi Shan, Yihua Li, Xuxu Xu, Junfeng Feng, Xiang Wu, Guoyi Gao
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-019-48488-4

Predicting Breast Cancer in Breast Imaging Reporting and Data System (BI-RADS) Ultrasound Category 4 or 5 Lesions: A Nomogram Combining Radiomics and BI-RADS
Cited by: 75
Author(s): Weiquan Luo, Qing-xiu Huang, Xiaowen Huang, Hang-Tong Hu, Fuqiang Zeng, Wei Wang
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0085568

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines
Cited by: 58
Author(s): Oliver Rupp, J. Ole Becker, Karina Brinkrolf, Christina Timmermann, Nicole Borth, Alfred Pühler, Thomas Noll, Alexander Goesmann
Software Mentions: 5
Published: over 12 years ago

10.1038/s41598-019-46923-0

The Predominant Oral Microbiota Is Acquired Early in an Organized Pattern
Cited by: 63
Author(s): Rosalyn Sulyanto, Zachary A. Thompson, Clifford J. Beall, Eugene J. Leys, Ann L. Griffen
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.ppat.1009097

Vaginal microbiome-hormonal contraceptive interactions associate with the mucosal proteome and HIV acquisition
Cited by: 17
Author(s): Laura Noël‐Romas, Michelle Perner, Refilwe P. Molatlhegi, Christina Farr Zuend, Amanda Mabhula, Sarah Hoger, Alana Lamont, Kenzie Birse, Alicia R. Berard, Stuart McCorrister, Garett Westmacott, Al Leslie, Vanessa Poliquin, Renee Heffron, Lyle R. McKinnon, Adam Burgener
Software Mentions: 5
Published: over 5 years ago

10.18632/aging.203021

Development of a prognostic model for hepatocellular carcinoma using genes involved in aerobic respiration
Cited by: 1
Author(s): Jiawei Rao, Xukun Wu, Xiaozhuan Zhou, Ronghai Deng, Yu Ma
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-019-45515-2

Open chromatin dynamics in prosensory cells of the embryonic mouse cochlea
Cited by: 13
Author(s): Brent A. Wilkerson, Alex Chitsazan, Leah S. VandenBosch, Matthew S. Wilken, Thomas A. Reh, Olivia Bermingham‐McDonogh
Software Mentions: 5
Published: about 7 years ago

10.1186/s13014-021-01810-9

Impact of feature selection methods and subgroup factors on prognostic analysis with CT-based radiomics in non-small cell lung cancer patients
Cited by: 15
Author(s): Yuto Sugai, Noriyuki Kadoya, Shohei Tanaka, Shunpei Tanabe, Mariko Umeda, Takaya Yamamoto, Kazuya Takeda, Suguru Dobashi, Haruna Ohashi, Ken Takeda, Keiichi Jingu
Software Mentions: 5
Published: about 5 years ago

10.3390/rs11050551

The Influence of Region of Interest Heterogeneity on Classification Accuracy in Wetland Systems
Cited by: 11
Author(s): Tedros M. Berhane, Hugo Costa, Charles R. Lane, Oleg A. Anenkhonov, Victor V. Chepinoga, Bradley C. Autrey
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-019-45368-9

Microbial communities in top- and subsoil of repacked soil columns respond differently to amendments but their diversity is negatively correlated with plant productivity
Cited by: 23
Author(s): Corinne Celestina, Jennifer L. Wood, James B. Manson, Xiaojuan Wang, P. W. G. Sale, Caixian Tang, Ashley E. Franks
Software Mentions: 5
Published: about 7 years ago

10.1002/ece3.4655

Variation in three community features across habitat types and scales within a 15-ha subtropical evergreen-deciduous broadleaved mixed forest dynamics plot in China
Cited by: 1
Author(s): Feng Guo, Junqing Li, Runguo Zang, Xunru Ai, Lan Yao
Software Mentions: 5
Published: over 7 years ago

10.1186/s12885-021-07928-z

Integrated bioinformatic analysis identifies UBE2Q1 as a potential prognostic marker for high grade serous ovarian cancer
Cited by: 8
Author(s): Rachel Topno, I.K. Singh, Manoj Kumar, Pallavi Agarwal
Software Mentions: 5
Published: over 5 years ago

10.1186/s13148-020-00888-4

Alternative methylation of intron motifs is associated with cancer-related gene expression in both canine mammary tumor and human breast cancer
Cited by: 13
Author(s): A-Reum Nam, Kanghoon Lee, Hyeon-Ji Hwang, Johannes J. Schabort, Jaehoon An, Sungho Won, Je‐Yoel Cho
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-019-43091-z

A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model
Cited by: 10
Author(s): Tatjana Sajic, Rodolfo Ciuffa, Vera Lemos, Pan Xu, Valentina Leone, Chen Li, Evan G. Williams, Georgios Makris, Amir Banaei‐Esfahani, Mathias Heikenwälder, Kristina Schoonjans, Ruedi Aebersold
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0044736

Brain Transcriptional and Epigenetic Associations with Autism
Cited by: 131
Author(s): Matthew R. Ginsberg, Robert A. Rubin, Tatiana Falcone, Angela H. Ting, Marvin R. Natowicz
Software Mentions: 5
Published: almost 14 years ago

10.18632/aging.103861

Development of a susceptibility gene based novel predictive model for the diagnosis of ulcerative colitis using random forest and artificial neural network
Cited by: 20
Author(s): Hanyang Li, Lijie Lai, Jun Shen
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0171689

Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock
Cited by: 10
Author(s): Samanwoy Mukhopadhyay, Pravat Kumar Thatoi, AK Pandey, B. K. Das, Balachandran Ravindran, Samsiddhi Bhattacharjee, Saroj Kant Mohapatra
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0238304

Investigation of gene-gene interactions in cardiac traits and serum fatty acid levels in the LURIC Health Study
Cited by: 5
Author(s): Jiayan Zhou, Kristin Passero, Nicole Palmiero, Bertram Müller‐Myhsok, Marcus E. Kleber, Winfried Maerz, Molly A. Hall
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-019-41452-2

Using Bacterial Transcriptomics to Investigate Targets of Host-Bacterial Interactions in Caenorhabditis elegans
Cited by: 21
Author(s): Jason P. Chan, Justin Wright, Hoi Tong Wong, Anastasia Ardasheva, Jamey T. Brumbaugh, Christopher J. McLimans, Regina Lamendella
Software Mentions: 5
Published: over 7 years ago

10.1038/srep40803

Dynamics of Bemisia tabaci biotypes and insecticide resistance in Fujian province in China during 2005–2014
Cited by: 43
Author(s): Feng-Luan Yao, Yu Zheng, Xiaoyan Huang, Xue-Ling Ding, Jiuran Zhao, Nicolas Desneux, Yumei He, Qiyong Weng
Software Mentions: 5
Published: over 9 years ago

10.3389/fonc.2021.633950

Identification of a Novel Glycolysis-Related Gene Signature Correlates With the Prognosis and Therapeutic Responses in Patients With Clear Cell Renal Cell Carcinoma
Cited by: 13
Author(s): Zhengtong Lv, Qi Lin, Xiheng Hu, Miao Mo, Huichuan Jiang, Yuan Li
Software Mentions: 5
Published: over 5 years ago

10.18632/aging.103977

Identification of immune landscape signatures associated with clinical and prognostic features of hepatocellular carcinoma
Cited by: 2
Author(s): Hongmei Yan, Yu-Chuan Chen, Kai Wang, Yu Lu, Xixin Huang, Qianyu Li, Yuwen Xie, Jiayu Lin, Yueyun He, Xinyu Yi, Yanzhi Wang, Longhua Chen, Yi Ding, Yiyi Li
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-017-06355-0

Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
Cited by: 5
Author(s): Prashanna Balaji Venkatasubramanian, Gamze Toydemir, Nicole de Wit, Edoardo Saccenti, Vítor A. P. Martins dos Santos, Peter van Baarlen, Jerry M. Wells, María Suárez-Diez, Jurriaan J. Mes
Software Mentions: 5
Published: almost 9 years ago

10.3389/fonc.2021.670927

Influence of Different Age Cutoff Points on the Prediction of Prognosis of Cancer Patients Receiving ICIs and Potential Mechanistic Exploration
Cited by: 5
Author(s): Rui Guan, Qiong Lyu, Anqi Lin, Junyi Liang, Weimin Ding, Manming Cao, Peng Luo, Jian Zhang
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-27027-7

Immunoprofiles of human Sertoli cells infected with Zika virus reveals unique insights into host-pathogen crosstalk
Cited by: 32
Author(s): Daniel P. Strange, Richard Green, Dietmar W. Siemann, Michael Gale, Saguna Verma
Software Mentions: 5
Published: about 8 years ago

10.2196/24656

An Automatic Ontology-Based Approach to Support Logical Representation of Observable and Measurable Data for Healthy Lifestyle Management: Proof-of-Concept Study
Cited by: 25
Author(s): Ayan Chatterjee, Andreas Prinz, Martin Gerdes, Santiago Martínez
Software Mentions: 5
Published: over 5 years ago

10.1186/s12862-019-1570-5

Adaptive divergence in shell morphology in an ongoing gastropod radiation from Lake Malawi
Cited by: 6
Author(s): Bert Van Bocxlaer, Claudia M Ortiz-Sepulveda, Pieter Gurdebeke, Xavier Vekemans
Software Mentions: 5
Published: over 6 years ago

10.18632/oncotarget.14091

The role of miR-17-92 in the miRegulatory landscape of Ewing sarcoma
Cited by: 13
Author(s): Raphaela Schwentner, David Herrero-Martín, Maximilian Kauer, Cornelia Mutz, Anna M. Katschnig, Grzegorz Sienski, Javier Alonso, Dave N.T. Aryee, Heinrich Kovar
Software Mentions: 5
Published: over 9 years ago

10.1186/s13059-019-1764-6

BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
Cited by: 94
Author(s): Tongxin Wang, Travis Johnson, Wei Shao, Zixiao Lu, Bryan R. Helm, Jie Zhang, Kun Huang
Software Mentions: 5
Published: almost 7 years ago

10.3389/fcell.2021.595744

A Highly Conserved Shh Enhancer Coordinates Hypothalamic and Craniofacial Development
Cited by: 2
Author(s): Zoe Crane-Smith, Jeffrey J. Schoenebeck, Katy A. Graham, Paul S. Devenney, Lorraine Rose, Mark Ditzell, E. S. Anderson, Joseph I. Thomson, Natalia Klenin, Deborah M. Kurrasch, Laura A. Lettice, Robert E. Hill
Software Mentions: 5
Published: over 5 years ago

10.3390/nu12082280

How Does Time Use Differ between Individuals Who Do More versus Less Foodwork? A Compositional Data Analysis of Time Use in the United Kingdom Time Use Survey 2014–2015
Cited by: 8
Author(s): Chloe Clifford Astbury, Louise Foley, Tarra L. Penney, Jean Adams
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-019-53298-9

A pilot study of peripheral blood DNA methylation models as predictors of knee osteoarthritis radiographic progression: data from the Osteoarthritis Initiative (OAI)
Cited by: 10
Author(s): Christopher M. Dunn, Michael C. Nevitt, J.A. Lynch, Matlock A. Jeffries
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2016.02079

Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea
Cited by: 49
Author(s): Timo Kohn, Anja Heuer, Mareike Jogler, John Vollmers, Christian Boedeker, Boyke Bunk, Patrick Rast, Daniela Borchert, Ines Glöckner, Heike M. Freese, Hans‐Peter Klenk, Jörg Overmann, Anne‐Kristin Kaster, Manfred Rohde, Sandra Wiegand, Christian Jogler
Software Mentions: 5
Published: over 9 years ago

10.3390/cancers13040610

Comprehensive Epstein-Barr Virus Transcriptome by RNA-Sequencing in Angioimmunoblastic T Cell Lymphoma (AITL) and Other Lymphomas
Cited by: 17
Author(s): Nader Bayda, Valentin Tilloy, Alain Chaunavel, Racha Bahri, Mohamad Adnan Halabi, Jean Feuillard, Arnaud Jaccard, Sylvie Ranger-Rogez
Software Mentions: 5
Published: over 5 years ago

10.3389/fonc.2021.613696

The Prognostic Impact of Tumor Architecture for Upper Urinary Tract Urothelial Carcinoma: A Propensity Score-Weighted Analysis
Cited by: 5
Author(s): Huiying Liu, Yen Ta Chen, Shun‐Chen Huang, Hung‐Jen Wang, Yufang Cheng, Chih Hsiung Kang, Wei Ching Lee, Yu-Li Su, Chun‐Chieh Huang, Yeong‐Hwa Chang, Yao‐Chi Chuang, Hao Luo, Po‐Hui Chiang
Software Mentions: 5
Published: over 5 years ago

10.1038/srep23490

Combinatorial microenvironmental regulation of liver progenitor differentiation by Notch ligands, TGFβ and extracellular matrix
Cited by: 33
Author(s): Kerim B. Kaylan, Viktoriya Ermilova, Ravi Chandra Yada, Gregory H. Underhill
Software Mentions: 5
Published: over 10 years ago

10.1038/srep21557

Metabolic/Proteomic Signature Defines Two Glioblastoma Subtypes With Different Clinical Outcome
Cited by: 73
Author(s): Giovanna Marziali, Michele Signore, Mariachiara Buccarelli, Sveva Grande, Alessandra Palma, Mauro Biffoni, Antonella Rosi, Quintino Giorgio D’Alessandris, Maurizio Martini, Luigi Maria Larocca, Ruggero De Maria, Roberto Pallini, Lucia Ricci‐Vitiani
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0251800

Comparison of machine-learning methodologies for accurate diagnosis of sepsis using microarray gene expression data
Cited by: 5
Author(s): Dominik Schaack, Markus A. Weigand, Florian Uhle
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-020-71309-y

Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil
Cited by: 25
Author(s): Tomás Gomes Reis Veloso, Marliane de Cássia Soares da Silva, Wilton Soares Cardoso, Rogério Carvalho Guarçoni, Maria Catarina Megumi Kasuya, Lucas Louzada Pereira
Software Mentions: 5
Published: almost 6 years ago

10.1186/1471-2164-14-293

A data-driven approach to preprocessing Illumina 450K methylation array data
Cited by: 805
Author(s): Ruth Pidsley, Chloe Wong, Manuela Volta, Katie Lunnon, Jonathan Mill, Leonard C. Schalkwyk
Software Mentions: 5
Published: about 13 years ago

10.1186/s13041-021-00835-1

Altered hippocampal transcriptome dynamics following sleep deprivation
Cited by: 14
Author(s): Marie E. Gaine, Ethan Bahl, Snehajyoti Chatterjee, Jacob J. Michaelson, Ted Abel, Lisa C. Lyons
Software Mentions: 5
Published: almost 5 years ago

10.1186/1471-2164-15-704

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda
Cited by: 26
Author(s): Fabrice Legeai, Sylvie Gimenez, Bernard Duvic, Jean-Michel Escoubas, Anne-Sophie Gosselin-Grenet, Florence Blanc, Clément François, Imène Séninet, Anthony Bretaudeau, Doriane Mutuel, Pierre-Alain Girard, Christelle Monsempès, Ghislaine Magdelenat, Frédérique Hilliou, René Feyereisen, Mylène Ogliastro, Anne-Nathalie Volkoff, Emmanuelle Jacquin‐Joly, Emmanuelle d’Alençon, Nicolas Nègre, Philippe Fournier
Software Mentions: 5
Published: almost 12 years ago

10.1016/j.schres.2020.04.017

Modeling perception and behavior in individuals at clinical high risk for psychosis: Support for the predictive processing framework
Cited by: 17
Author(s): Eren Kafadar, Vijay A. Mittal, Gregory P. Strauss, Hannah C. Chapman, Lauren M. Ellman, Sonia Bansal, James M. Gold, Ben Alderson-Day, Samuel Evans, Jamie Moffatt, Steven M. Silverstein, Elaine F. Walker, Scott W. Woods, Philip R. Corlett, Albert R. Powers
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-80453-4

Prognostic signature of lung adenocarcinoma based on stem cell-related genes
Cited by: 7
Author(s): Zhanghao Huang, Muqi Shi, Hao Zhou, Jinjie Wang, Haijian Zhang, Jia Hai Shi
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-019-5511-x

RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions
Cited by: 35
Author(s): Kirti Shekhawat, Hugh-G. Patterton, Florian F. Bauer, Mathabatha Evodia Setati
Software Mentions: 5
Published: over 7 years ago

10.3389/fimmu.2019.00330

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression
Cited by: 37
Author(s): Florian Kirchner, Katharina Littringer, Simon Altmeier, Van Du T. Tran, Franziska Annett Schönherr, Christina Braunsdorf, Marco Pagni, Dominique Sanglard, Nicole Joller, Salomé LeibundGut‐Landmann
Software Mentions: 5
Published: over 7 years ago

10.3390/cancers12082261

MiR-302b as a Combinatorial Therapeutic Approach to Improve Cisplatin Chemotherapy Efficacy in Human Triple-Negative Breast Cancer
Cited by: 12
Author(s): Alessandra Cataldo, Sandra Romero-Córdoba, Ilaria Plantamura, Giulia Cosentino, Alfredo Hidalgo‐Miranda, Elda Tagliabue, Marilena V. Iorio
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13321-019-0399-7

HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
Cited by: 3
Author(s): Julien Wist
Software Mentions: 5
Published: over 6 years ago

10.1186/s12862-016-0743-8

Adaptive patterns in the p53 protein sequence of the hypoxia- and cancer-tolerant blind mole rat Spalax
Cited by: 8
Author(s): Vered Domankevich, Yarden Opatowsky, Assaf Malik, Abraham B. Korol, Zeev Frenkel, Irena Manov, Aaron Avivi, Imad Shams
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0229183

Divorce and adolescent academic achievement: Heterogeneity in the associations by parental education
Cited by: 9
Author(s): Sondre Aasen Nilsen, Kyrre Breivik, Bente Wold, Kristin Gärtner Askeland, Børge Sivertsen, Mari Hysing, Tormod Bøe
Software Mentions: 5
Published: over 6 years ago

10.1093/hmg/ddv203

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans
Cited by: 65
Author(s): Ali Amin Al Olama, Tokhir Dadaev, Dennis J. Hazelett, Qiuyan Li, Daniel Leongamornlert, Ed Saunders, Sarah H. Stephens, Clara Cieza-Borrella, Ian Whitmore, Sara Benlloch Garcia, Graham G. Giles, Melissa C. Southey, Liesel M. FitzGerald, Henrik Grönberg, Fredrik Wiklund, Markus Aly, Brian E. Henderson, Fredrick Schumacher, Christopher A. Haiman, Johanna Schleutker, Tiina Wahlfors, Teuvo L.J. Tammela, Børge G. Nordestgaard, Tim Key, Ruth C. Travis, David E. Neal, Jenny Donovan, Freddie C. Hamdy, Paul D.P. Pharoah, Nora Pashayan, Kay‐Tee Khaw, Janet L. Stanford, Stephen N. Thibodeau, Shannon K. McDonnell, Daniel J. Schaid, Christiane Maier, Walther Vogel, Manuel Luedeke, Kathleen Herkommer, Adam S. Kibel, Cezary Cybulski, Dominika Wokołorczyk, Wojciech Kluźniak, Lisa A. Cannon‐Albright, Hermann Brenner, Katja Butterbach, Volker Arndt, Jong Y. Park, Thomas A. Sellers, Hui‐Yi Lin, Chavdar Slavov, Radka Kaneva, Vanio Mitev, Jyotsna Batra, Judith A. Clements, Amanda B. Spurdle, Manuel R. Teixeira, Paula Paulo, Sofia Maia, Hardev Pandha, Agnieszka Michael, Andrzej M. Kierzek, Koveela Govindasami, Michelle Guy, Artitaya Lophatonanon, Kenneth Muir, Ana Viñuela, Andrew Anand Brown, Cogs-Cruk Gwas-Ellipse Initiative, Mathew Freedman, David V. Conti, Douglas F. Easton, Gerhard A. Coetzee, Rosalind Eeles, Zsofia Kote‐Jarai
Software Mentions: 5
Published: about 11 years ago

10.1186/s13059-015-0863-2

IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation
Cited by: 89
Author(s): Roser Vento‐Tormo, Carlos Company, Javier Rodríguez-Ubreva, Lorenzo de la Rica, José Urquiza, Biola M. Javierre, Radhakrishnan Sabarinathan, Ana Luque, Manel Esteller, Josep M. Aran, Damiana Álvarez-Errico, Esteban Ballestar
Software Mentions: 5
Published: over 10 years ago

10.3389/fmolb.2021.624575

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

10.1016/j.celrep.2019.07.039

Activation and In Vivo Evolution of the MAIT Cell Transcriptome in Mice and Humans Reveals Tissue Repair Functionality
Cited by: 130
Author(s): Timothy S C Hinks, Emanuele Marchi, Maisha Jabeen, Moshe Olshansky, Ayako Kurioka, Troi Pediongco, Bronwyn S. Meehan, Lyudmila Kostenko, Stephen J. Turner, Alexandra J. Corbett, Zhenjun Chen, Paul Klenerman, James McCluskey
Software Mentions: 5
Published: almost 7 years ago

10.1016/j.celrep.2021.109101

Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation
Cited by: 18
Author(s): Nicholas T. Crump, Andreas V. Hadjinicolaou, Meng Xia, John Walsby-Tickle, Uzi Gileadi, Ji‐Li Chen, Mashiko Setshedi, Lars Rønn Olsen, I-Jun Lau, Laura Godfrey, Lynn Quek, Zhanru Yu, Erica Ballabio, Mike Bogetofte Barnkob, Giorgio Napolitani, Mariolina Salio, Hashem Koohy, Benedikt M. Kessler, Stephen Taylor, Paresh Vyas, James McCullagh, Thomas A. Milne, Vincenzo Cerundolo
Software Mentions: 5
Published: about 5 years ago

10.7150/jca.46721

Complement sC5b-9 and CH50 increase the risk of cancer-related mortality in patients with non-small cell lung cancer
Cited by: 1
Author(s): Jing Li, Zhijun Cao, Lijie Mi, Zhihua Xu, Xiangmei Wu
Software Mentions: 5
Published: over 6 years ago

10.1002/evl3.166

Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation
Cited by: 6
Author(s): Joel L. Pick, Masaomi Hatakeyama, Kate E. Ihle, Julien Gasparini, Claudy Haussy, Satoshi Ishishita, Yoichi Matsuda, Takashi Yoshimura, Masahiro M. Kanaoka, Rie Shimizu‐Inatsugi, Kentaro Shimizu, Barbara Tschirren
Software Mentions: 5
Published: about 6 years ago

10.1186/gm500

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy
Cited by: 105
Author(s): Mark N Cruickshank, Alicia Oshlack, Christiane Theda, Peter G Davis, David Martino, Penelope M. Sheehan, Yun Dai, Richard Saffery, Lex W. Doyle, Jeffrey M Craig
Software Mentions: 5
Published: over 13 years ago

10.1098/rstb.2014.0240

Assigning and visualizing germline genes in antibody repertoires
Cited by: 19
Author(s): Simon D. W. Frost, Ben Murrell, Alamgir Hossain, Gregg J. Silverman, Sergei L. Kosakovsky Pond
Software Mentions: 5
Published: almost 11 years ago

10.1186/s13072-020-00359-3

UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells
Cited by: 5
Author(s): Beisi Xu, Brett B. Mulvey, Muneeb Salie, Xiaoyang Yang, Yurika Matsui, Anjana Nityanandam, Yiping Fan, Jamy C. Peng
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13072-021-00417-4

Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C
Cited by: 2
Author(s): Ning Liu, Wai Yee Low, Hamid Alinejad‐Rokny, Stephen Pederson, Timothy Sadlon, Simon C. Barry, James Breen
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13059-017-1304-1

Abundant expression of somatic transposon-derived piRNAs throughout Tribolium castaneum embryogenesis
Cited by: 16
Author(s): Maria Ninova, Sam Griffiths-Jones, Matthew Ronshaugen
Software Mentions: 5
Published: almost 9 years ago

10.3390/cancers12082322

Comparison of NGS and MFC Methods: Key Metrics in Multiple Myeloma MRD Assessment
Cited by: 14
Author(s): Katharina Kriegsmann, Michael Hundemer, Nicole Hofmeister-Mielke, Philipp Reichert, Calin-Petru Manta, Mohamed H.S. Awwad, Sandra Sauer, Uta Bertsch, Britta Besemer, Roland Fenk, Mathias Hänel, Markus Munder, Katja Weisel, Igor W Blau, Andreas Neubauer, Carsten Müller‐Tidow, Marc S. Raab, Hartmut Goldschmidt, Stefanie Huhn
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12900-016-0063-7

3D QSAR, pharmacophore and molecular docking studies of known inhibitors and designing of novel inhibitors for M18 aspartyl aminopeptidase of Plasmodium falciparum
Cited by: 22
Author(s): Madhuri Kumari, Subhash Chandra, Neeraj Tiwari, Naidu Subbarao
Software Mentions: 5
Published: almost 10 years ago

10.1172/jci.insight.143058

Targeted DNA methylation profiling reveals epigenetic signatures in peanut allergy
Cited by: 26
Author(s): Xiaoying Zhou, Xiaorui Han, Shu‐Chen Lyu, Bryan Bunning, Laurie Kost, Iris Chang, Shu Cao, Vanitha Sampath, Kari Nadeau
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-017-1285-0

Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Cited by: 66
Author(s): Oliver S. Burren, Arcadio Rubio Garćıa, Biola M. Javierre, Daniel B. Rainbow, Jonathan Cairns, Nicholas Cooper, John Lambourne, Ellen Schofield, Xaquín Castro Dopico, Ricardo C. Ferreira, Richard M. R. Coulson, Frances Burden, Sophia Rowlston, Kate Downes, Steven W. Wingett, Mattia Frontini, Willem H. Ouwehand, Peter Fraser, Mikhail Spivakov, John A. Todd, Linda S. Wicker, Antony J. Cutler, Chris Wallace
Software Mentions: 5
Published: almost 9 years ago

10.1002/ece3.7434

Tree diversity and functional leaf traits drive herbivore‐associated microbiomes in subtropical China
Cited by: 1
Author(s): Yang Li, Douglas Chesters, Ming‐Qiang Wang, Tesfaye Wubet, Andreas Schuldt, Perttu Anttonen, Pengfei Guo, Jing‐Ting Chen, Qianxiong Zhou, Nai‐Li Zhang, Keping Ma, Helge Bruelheide, Chunsheng Wu, Chao‐Dong Zhu
Software Mentions: 5
Published: over 5 years ago