bioconductor: DSS | Projects | Ecosyste.ms: Papers

10.1186/s13059-014-0550-8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Cited by: 49,504
Author(s): Michael I. Love, Wolfgang Huber, Simon Anders
Software Mentions: 16
Published: almost 10 years ago

10.1038/s41598-018-19655-w

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data
Cited by: 10
Author(s): Benjamin Mayne, Shalem Leemaqz, Sam Buckberry, Carlos M. Rodríguez López, Claire T. Roberts, Tina Bianco‐Miotto, James Breen
Software Mentions: 12
Published: almost 7 years ago

10.1186/s13059-021-02493-x

Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish
Cited by: 7
Author(s): Hyo Sik Jang, Yujie Chen, Jiaxin Ge, Alicia N Wilkening, Yiran Hou, Hyung Joo Lee, You Rim Choi, Rebecca F. Lowdon, Xiaoyun Xing, Daofeng Li, Charles Kaufman, Stephen L. Johnson, Ting Wang
Software Mentions: 12
Published: about 3 years ago

10.1186/s13059-021-02329-8

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution
Cited by: 13
Author(s): Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti, Catalina A. Vallejos
Software Mentions: 11
Published: over 3 years ago

10.1038/s41598-018-28356-3

Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver
Cited by: 34
Author(s): Chris Duncan, Sara A. Grimm, Daniel L. Morgan, Pierre R. Bushel, Brian D. Bennett, John D. Roberts, Frederick L. Tyson, B. Alex Merrick, Paul A. Wade
Software Mentions: 11
Published: over 6 years ago

10.7554/eLife.11613

Epigenomic landscapes of retinal rods and cones
Cited by: 107
Author(s): Alisa Mo, Chongyuan Luo, Fred P. Davis, Eran A. Mukamel, Gilbert L. Henry, Joseph R. Nery, Mark A. Urich, Serge Picard, Ryan Lister, Sean R. Eddy, M Beer, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 11
Published: over 8 years ago

10.15252/msb.20188339

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks
Cited by: 31
Author(s): Jan‐Philipp Mallm, Murat Iskar, Naveed Ishaque, Lara Klett, Sabrina J. Kugler, Jose M. Muiño, Vladimir B. Teif, Alexandra M Poos, Sebastian Großmann, Fabian Erdel, Daniele Tavernari, Sandra D. Koser, Sabrina Schumacher, Benedikt Brors, Rainer König, Daniel Remondini, Martin Vingron, Stephan Stilgenbauer, Peter Lichter, Marc Zapatka, Daniel Mertens, Karsten Rippe
Software Mentions: 10
Published: over 5 years ago

10.1186/gb-2014-15-2-r29

voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Cited by: 4,221
Author(s): Charity W. Law, Yunshun Chen, Wei Shi, Gordon K. Smyth
Software Mentions: 10
Published: almost 11 years ago

10.3389/fgene.2014.00324

Statistical methods for detecting differentially methylated loci and regions
Cited by: 90
Author(s): Mark D. Robinson, Abdullah Kahraman, Charity W. Law, Helen Lindsay, Małgorzata Nowicka, Lukas M. Weber, Xiaobei Zhou
Software Mentions: 9
Published: about 10 years ago

10.26508/lsa.202000794

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
Cited by: 5
Author(s): Elisa Redl, Raheleh Sheibani-Tezerji, Crhistian de Jesus Cardona, Patricia Hamminger, Gerald Timelthaler, Melanie R. Hassler, Maša Zrimšek, Sabine Lagger, Thomas Dillinger, Lorena Hofbauer, Kristina Draganić, Andreas Tiefenbacher, Michael Kothmayer, C. Dietz, Bernard Ramsahoye, Lukas Kenner, Christoph Bock, Christian Seiser, Wilfried Ellmeier, Gabriele Schweikert, Gerda Egger
Software Mentions: 9
Published: almost 4 years ago

10.3389/fcell.2021.643603

Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain
Cited by: 8
Author(s): Samuel E. Ross, Daniel Hesselson, Ozren Bogdanović
Software Mentions: 9
Published: over 3 years ago

10.3389/fgene.2018.00588

DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data
Cited by: 10
Author(s): Zhihua Gao, Zhiyuan Zhao, Wenqiang Tang
Software Mentions: 8
Published: almost 6 years ago

10.1186/s13059-019-1747-7

Cell type-specific epigenetic links to schizophrenia risk in the brain
Cited by: 65
Author(s): Isabel Mendizabal, Stefano Berto, Noriyoshi Usui, Kazuya Toriumi, Paramita Chatterjee, Connor Douglas, Iksoo Huh, Hyeonsoo Jeong, Thomas S. Layman, Carol A. Tamminga, Todd M. Preuss, Genevieve Konopka, Soojin V. Yi
Software Mentions: 8
Published: over 5 years ago

10.1038/srep44736

Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells
Cited by: 5
Author(s): Jian Yu, Constance Ciaudo
Software Mentions: 8
Published: over 7 years ago

10.12688/f1000research.13196.2

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Cited by: 42
Author(s): Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Software Mentions: 8
Published: about 6 years ago

10.1186/s12859-015-0742-6

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data
Cited by: 60
Author(s): Kamal Kishore, Stefano de Pretis, Ryan Lister, Marco J. Morelli, Valerio Bianchi, Bruno Amati, Joseph R. Ecker, Mattia Pelizzola
Software Mentions: 7
Published: about 9 years ago

10.3390/e21030242

A Method Based on Differential Entropy-Like Function for Detecting Differentially Expressed Genes Across Multiple Conditions in RNA-Seq Studies
Cited by: 1
Author(s): Zhuo Wang, Shuilin Jin, Chiping Zhang
Software Mentions: 7
Published: over 5 years ago

10.3390/bios3030238

A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach
Cited by: 20
Author(s): Sergiusz Wesołowski, Marc R. Birtwistle, Grzegorz A. Rempała
Software Mentions: 7
Published: over 11 years ago

10.1186/s13059-020-1948-0

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility
Cited by: 42
Author(s): Hyung Joo Lee, Yiran Hou, Yujie Chen, Zea Z. Dailey, Aiyana Riddihough, Hyo Sik Jang, Ting Wang, Stephen L. Johnson
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0132866

swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing
Cited by: 43
Author(s): Zhen Wang, Xianfeng Li, Yi Jiang, Qianzhi Shao, Qi Liu, Bingyu Chen, Dongsheng Huang
Software Mentions: 7
Published: over 9 years ago

10.3389/fgene.2019.00774

A Hybrid Ensemble Approach for Identifying Robust Differentially Methylated Loci in Pan-Cancers
Cited by: 3
Author(s): Qi Tian, Jianxiao Zou, Yuan Fang, Zhongli Yu, Jie Tang, Ying Song, Shicai Fan
Software Mentions: 7
Published: about 5 years ago

10.1186/s13072-020-00379-z

DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna
Cited by: 15
Author(s): Jack Hearn, Fiona A. Plenderleith, Tom J. Little
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12859-016-1208-1

NBLDA: negative binomial linear discriminant analysis for RNA-Seq data
Cited by: 34
Author(s): Kai Dong, Hongyu Zhao, Tiejun Tong, Xiang Wan
Software Mentions: 6
Published: about 8 years ago

10.1038/s41598-019-41315-w

Novel Data Transformations for RNA-seq Differential Expression Analysis
Cited by: 23
Author(s): Zeyu Zhang, Danyang Yu, Minseok Seo, Craig P. Hersh, Scott T. Weiss, Weiliang Qiu
Software Mentions: 6
Published: over 5 years ago

10.1534/g3.119.400659

Excess Light Priming in <i>Arabidopsis thaliana</i> Genotypes with Altered DNA Methylomes
Cited by: 7
Author(s): Diep R Ganguly, Bethany A. B. Stone, Andrew F Bowerman, Steven R. Eichten, Barry J. Pogson
Software Mentions: 6
Published: about 5 years ago

10.1534/genetics.116.195008

A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation
Cited by: 12
Author(s): Owen J. L. Rackham, Sarah R. Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K. Srivastava, Jacques Behmoaras, Πέτρος Δελλαπόρτας, Leonardo Bottolo, Enrico Petretto
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pcbi.1005515

Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates
Cited by: 17
Author(s): Andreas Tuerk, Gregor Wiktorin, Serhat Güler
Software Mentions: 6
Published: over 7 years ago

10.1186/s12859-017-1808-4

QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model
Cited by: 36
Author(s): Lian Liu, Shao Wu Zhang, Yufei Huang, Jia Meng
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0181033

Transcriptomic and metabolomic profiles of Chinese citrus fly, Bactrocera minax (Diptera: Tephritidae), along with pupal development provide insight into diapause program
Cited by: 14
Author(s): Jia Wang, Hong-Tao Fan, Ke-Cai Xiong, Ying‐Hong Liu
Software Mentions: 6
Published: over 7 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 3 years ago

10.1186/s13104-020-05012-6

Whole genome bisulfite sequencing of Medicago truncatula A17 wild type and lss mutants
Cited by: 0
Author(s): Nowlan H. Freese, Elise Schnabel, Julia Frugoli
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2020.558036

The Novel Omega-6 Fatty Acid Docosapentaenoic Acid Positively Modulates Brain Innate Immune Response for Resolving Neuroinflammation at Early and Late Stages of Humanized APOE-Based Alzheimer's Disease Models
Cited by: 14
Author(s): Qiu-Lan Ma, Cansheng Zhu, Marco Morselli, Trent Su, Matteo Pelligrini, Zhengqi Lu, Mychica Jones, Paul Denver, Daniel Castro, Xiaohong Gu, Frances Relampagos, Kaitlin Caoili, Bruce Teter, Sally A. Frautschy, Gregory M. Cole
Software Mentions: 5
Published: about 4 years ago

10.1186/s12859-017-1909-0

DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
Cited by: 52
Author(s): John Gaspar, Ronald P. Hart
Software Mentions: 5
Published: almost 7 years ago

10.1038/srep05193

Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies
Cited by: 230
Author(s): Bhagwan Yadav, Tea Pemovska, Agnieszka Szwajda, Evgeny Kulesskiy, Mika Kontro, Reijo Karjalainen, Muntasir Mamun Majumder, Disha Malani, Astrid Murumägi, Jonathan Knowles, Kimmo Porkka, Caroline A. Heckman, Olli Kallioniemi, Krister Wennerberg, Tero Aittokallio
Software Mentions: 5
Published: over 10 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: over 4 years ago

10.1371/journal.pone.0081415

Dispersion Estimation and Its Effect on Test Performance in RNA-seq Data Analysis: A Simulation-Based Comparison of Methods
Cited by: 29
Author(s): Will Landau, Peng Liu
Software Mentions: 5
Published: almost 11 years ago

10.1186/1471-2105-15-S9-S6

BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data
Cited by: 10
Author(s): Jin Gu, Wang Xiao, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Software Mentions: 5
Published: about 10 years ago

10.1186/s12859-019-2845-y

HOME: a histogram based machine learning approach for effective identification of differentially methylated regions
Cited by: 29
Author(s): Akanksha Srivastava, Yuliya V. Karpievitch, Steven R. Eichten, Justin O. Borevitz, Ryan Lister
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-32448-5

The relationship between transgenerational acquired resistance and global DNA methylation in Arabidopsis
Cited by: 51
Author(s): Joost H. M. Stassen, Ana López, Ritushree Jain, David Pascual-Pardo, Estrella Luna, Lisa M. Smith, Jurriaan Ton
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-020-07305-3

Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome
Cited by: 12
Author(s): Xiaodong Tan, Ranran Liu, Yonghong Zhang, Xicai Wang, Jie Wang, Hailong Wang, Guiping Zhao, Maiqing Zheng, Jie Wen
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.39658

Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome
Cited by: 33
Author(s): Srivarsha Rajshekar, Jun Yao, Paige K. Arnold, Sara G. Payne, Yinwen Zhang, Teresa V. Bowman, Robert J. Schmitz, John Edwards, Mary Goll
Software Mentions: 4
Published: almost 6 years ago

10.12688/wellcomeopenres.15590.1

Evolutionary analysis of the most polymorphic gene family in falciparum malaria
Cited by: 56
Author(s): Thomas D. Otto, Sammy A. Assefa, Ulrike Böhme, Mandy Sanders, Dominic Kwiatkowski, Matthew Berriman, Chris Newbold
Software Mentions: 4
Published: almost 5 years ago

10.18632/aging.202780

circRNA expression profiling of colon tissue from mesalazine-treated mouse of inflammatory bowel disease reveals an important circRNA-miRNA-mRNA pathway
Cited by: 8
Author(s): Wei Zhou, Haiyin Zhang, Y. B. Pan, Yingbin Xu, Yongqing Cao
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1005650

A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data
Cited by: 92
Author(s): Amanda J. Lea, Jenny Tung, Xiang Zhou
Software Mentions: 4
Published: almost 9 years ago

10.3389/fimmu.2021.685237

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

10.3389/fninf.2017.00018

Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework
Cited by: 1
Author(s): Antoine Grigis, David Goyard, Robin Cherbonnier, Thomas Gareau, Dimitri Papadopoulos Orfanos, Nicolas Chauvat, Adrien Di Mascio, Gunter Schümann, Will Spooren, Declan Murphy, Vincent Frouin
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-64514-2

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype
Cited by: 12
Author(s): Sharon A. McGrath‐Morrow, Roland Ndeh, Kathryn A. Helmin, Basil Khuder, Cynthia Rothblum-Oviatt, Joseph M. Collaco, Jonathan H. Wright, Paul A. Reyfman, Howard M. Lederman, Benjamin D. Singer
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2016.00225

Extending the R Library PROPER to Enable Power Calculations for Isoform-Level Analysis with EBSeq
Cited by: 2
Author(s): Amadou Thierno Gaye
Software Mentions: 4
Published: almost 8 years ago

10.1155/2020/3656841

Genetic Profiles Playing Opposite Roles of Pathogenesis in Schizophrenia and Glioma
Cited by: 3
Author(s): Yujie Wen, Zhiwei Xia, Dongjie Li, Quan Cheng, Qing Zhao, Hui Cao
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-018-2086-5

An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data
Cited by: 23
Author(s): W. Garrett Jenkinson, Jordi Abante, Andrew P. Feinberg, John Goutsias
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.61965

Sustained TNF-α stimulation leads to transcriptional memory that greatly enhances signal sensitivity and robustness
Cited by: 15
Author(s): Zuodong Zhao, Zhuqiang Zhang, Jingjing Li, Qiang Dong, Jun Xiong, Yingfeng Li, Mengying Lan, Gang Li, Bing Zhu
Software Mentions: 4
Published: about 4 years ago

10.1186/s12920-020-00780-3

Pan-cancer analysis of differential DNA methylation patterns
Cited by: 7
Author(s): Mai Shi, Stephen Kwok‐Wing Tsui, Hao Wu, Yingying Wei
Software Mentions: 4
Published: about 4 years ago

10.3390/ijerph18157975

Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data
Cited by: 6
Author(s): Yongjun Piao, Wanxue Xu, Kwang Ho Park, Keun Ho Ryu, Rong Xiang
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms20215343

Discrimination of DNA Methylation Signal from Background Variation for Clinical Diagnostics
Cited by: 8
Author(s): Robersy Sánchez, Xiaodong Yang, Thomas A. Maher, Sally A. Mackenzie
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-87457-8

Low biological fluctuation of mitochondrial CpG and non-CpG methylation at the single-molecule level
Cited by: 21
Author(s): Chloe D. Goldsmith, Jesús Rafael Rodríguez‐Aguilera, Ines El-Rifai, Adrien Jarretier-Yuste, Valérie Hervieu, Olivier Raineteau, Pierre Saintigny, Victoria Chagoya de Sánchez, Robert Dante, Gabriel Ichim, Héctor Hernández-Vargas
Software Mentions: 3
Published: over 3 years ago

10.3390/s18020610

An Advanced IoT-based System for Intelligent Energy Management in Buildings
Cited by: 123
Author(s): Vangelis Marinakis, Haris Doukas
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12859-018-2037-1

Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus
Cited by: 25
Author(s): David E. Condon, Phu V. Tran, Yu‐Chin Lien, Jonathan Schug, Michael Georgieff, Rebecca A. Simmons, Kyoung Jae Won
Software Mentions: 3
Published: almost 7 years ago

10.3390/s21113743

A Sensor-Based Decision Support System for Transfemoral Socket Rectification
Cited by: 6
Author(s): Michalis Karamousadakis, Antonis Porichis, Suranjan Ottikkutti, DeJiu Chen, Panagiotis Vartholomeos
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-017-13844-9

Genome-wide discovery of long intergenic noncoding RNAs and their epigenetic signatures in the rat
Cited by: 3
Author(s): Aimin Li, Zhongyin Zhou, Xinhong Hei, Newton O. Otecko, Junying Zhang, Yajun Liu, Huanfu Zhou, Zhiqiang Zhao, Lei Wang
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1008894

AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization
Cited by: 5
Author(s): Nicolas Christophorou, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, Aurélie Chambon, Victor Solier, Daniel Vezon, Mathilde Grelon, Xiaoqi Feng, Nicolas Bouché, Christine Mézard
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1002002

The Free Energy Landscape of Small Molecule Unbinding
Cited by: 94
Author(s): Danzhi Huang, Amedeo Caflisch
Software Mentions: 3
Published: almost 14 years ago

10.1186/s13072-016-0105-1

Targeted bisulfite sequencing of the dynamic DNA methylome
Cited by: 21
Author(s): Michael J. Ziller, Elena K. Stamenova, Hongcang Gu, Andreas Gnirke, Alexander Meissner
Software Mentions: 3
Published: almost 8 years ago

10.3390/nu12020544

Consumption of the Total Western Diet Promotes Colitis and Inflammation-Associated Colorectal Cancer in Mice
Cited by: 29
Author(s): Abby D. Benninghoff, Korry Hintze, Stephany P. Monsanto, Daphne Rodriguez, Ashli Hunter, Sumira Phatak, James J. Pestka, Arnaud J. Van Wettere, Robert E. Ward
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12891-020-03401-3

Physical function and lean body mass as predictors of bone loss after hip fracture: a prospective follow-up study
Cited by: 0
Author(s): Tuuli Suominen, Johanna Edgren, Anu Salpakoski, Mauri Kallinen, Tomas Cervinka, Timo Rantalainen, Timo Törmäkangas, Ari Heinonen, Sarianna Sipilä
Software Mentions: 3
Published: over 4 years ago

10.1155/2020/3158108

Danhong Injection Alleviates Cardiac Fibrosis via Preventing the Hypermethylation of Rasal1 and Rassf1 in TAC Mice
Cited by: 7
Author(s): Sinai Li, Ping Li, Weihong Liu, Juju Shang, Sheng-Lei Qiu, Xiang Li, Wei Liu, Haoyue Shi, Mingxue Zhou, Hongxu Liu
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-018-2229-8

Performance of epistasis detection methods in semi-simulated GWAS
Cited by: 16
Author(s): Clément Chatelain, Guillermo Durand, Vincent Thuillier, Franck Augé
Software Mentions: 3
Published: over 6 years ago

10.1038/s41398-021-01565-7

Intrauterine hyperglycemia impairs memory across two generations
Cited by: 9
Author(s): Kexin Zou, Jun Ren, Shuai Luo, Junyu Zhang, Chuanpeng Zhou, Chengxi Tan, Peng Lv, Xiao Sun, Jian‐Zhong Sheng, Xinmei Liu, He‐Feng Huang, Guo‐Lian Ding
Software Mentions: 3
Published: over 3 years ago

10.1172/jci.insight.141690

Aging imparts cell-autonomous dysfunction to regulatory T cells during recovery from influenza pneumonia
Cited by: 20
Author(s): Luisa Morales‐Nebreda, Kathryn A. Helmin, Manuel A. Torres Acosta, Nikolay S. Markov, Jennifer Yuan Shih Hu, Anthony M. Joudi, Raul Piseaux‐Aillon, Hiam Abdala‐Valencia, Yuliya Politanska, Benjamin D. Singer
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-75889-7

A decision support framework for prediction of avian influenza
Cited by: 7
Author(s): Samira Yousefinaghani, Rozita Dara, Zvonimir Poljak, Shayan Sharif
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-021-88444-9

Tissue-specific regulatory mechanism of LncRNAs and methylation in sheep adipose and muscle induced by Allium mongolicum Regel extracts
Cited by: 6
Author(s): Jianming Xue, Qi Lv, Khas Erdene, Chenglian Bai, Bingjie Ma, Wangjiao Li, Qina Cao, Fan Zhang, Changjin Ao
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-020-74532-9

Integral correlation for uneven and differently sampled data, and its application to the Law Dome Antarctic climate record
Cited by: 3
Author(s): Jason L. Roberts, Lenneke M. Jong, Felicity McCormack, Mark A. J. Curran, Andrew D. Moy, D. M. Etheridge, Jamin S. Greenbaum, D. A. Young, Steven Phipps, Wujun Xue, T. D. van Ommen, D. D. Blankenship, Martín J. Siegert
Software Mentions: 2
Published: about 4 years ago

10.1002/bit.27493

Random epigenetic modulation of CHO cells by repeated knockdown of DNA methyltransferases increases population diversity and enables sorting of cells with higher production capacities
Cited by: 14
Author(s): Marcus Weinguny, Peter Eisenhut, Gerald Klanert, Nikolaus Virgolini, Nicolas Marx, Andreas Jonsson, Daniel Ivansson, Ann Lövgren, Nicole Borth
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-015-2230-9

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
Cited by: 25
Author(s): Kuei Han Lin, Ben-Yang Liao, Hung-Sheng Chang, Shu‐Mei Huang, Ting Yan Chang, Cheng Yu Yang, Yu Bin Wang, Yu Teh Kirk Lin, Yu Wei Wu, Sen Lin Tang, Hongjun Yu
Software Mentions: 2
Published: almost 9 years ago

10.3390/biom11050642

The ‘Shape-Shifter’ Peptide from the Disulphide Isomerase PmScsC Shows Context-Dependent Conformational Preferences
Cited by: 1
Author(s): Lorna J. Smith, Chloe W. Green, Christina Redfield
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-020-68747-z

Does fertilization with dehydrated sewage sludge affect Terminalia argentea (Combretaceae) and associated arthropods community in a degraded area?
Cited by: 8
Author(s): Jó Cássio Nascimento Carvalho, Farley William Souza Silva, Germano Leão Demolin Leite, Alcinei Místico Azevedo, Gustavo Leal Teixeira, Marcus Alvarenga Soares, José Cola Zanúncio, Jesusa C. Legaspi
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2105-15-S11-S16

XLPM: efficient algorithm for the analysis of protein-protein contacts using chemical cross-linking mass spectrometry
Cited by: 8
Author(s): Mihir Jaiswal, Nathaniel M. Crabtree, Michael Bauer, Roger A. Hall, Kevin D. Raney, Boris Zybailov
Software Mentions: 2
Published: about 10 years ago

10.1038/s41598-018-21211-5

Parental micronutrient deficiency distorts liver DNA methylation and expression of lipid genes associated with a fatty-liver-like phenotype in offspring
Cited by: 40
Author(s): Kaja H. Skjærven, Lars Martin Jakt, Jorge Manuel de Oliveira Fernandes, John Arne Dahl, Anne‐Catrin Adam, Johanna Klughammer, Christoph Bock, Marit Espe
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-019-6146-7

DNA methylomes and transcriptomes analysis reveal implication of host DNA methylation machinery in BmNPV proliferation in Bombyx mori
Cited by: 15
Author(s): Haoling Huang, Ping Wu, Shaolun Zhang, Qi Shang, Haotong Yin, Qirui Hou, Jinbo Zhong, Xijie Guo
Software Mentions: 2
Published: about 5 years ago

10.1120/jacmp.v10i4.3066

Direct machine parameter optimization for intensity modulated radiation therapy (IMRT) of oropharyngeal cancer - a planning study
Cited by: 13
Author(s): Barbara Dobler, Oliver Koelbl, Ludwig Bogner, Fabian Pohl
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0076783

Indoor Navigation by People with Visual Impairment Using a Digital Sign System
Cited by: 69
Author(s): Gordon E. Legge, Paul J. Beckmann, Bosco S. Tjan, Gary Havey, K. Kramer, David J. Rolkosky, Rachel Gage, Muzi Chen, Sravan Puchakayala, Aravindhan Rangarajan
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2105-15-215

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments
Cited by: 139
Author(s): Egor Dolzhenko, Andrew D. Smith
Software Mentions: 2
Published: over 10 years ago

10.1186/1742-4690-7-21

Response of a simian immunodeficiency virus (SIVmac251) to raltegravir: a basis for a new treatment for simian AIDS and an animal model for studying lentiviral persistence during antiretroviral therapy
Cited by: 38
Author(s): Mark G. Lewis, Sandro Norelli, Matt Collins, Maria Letizia Barreca, Nunzio Iraci, Barbara Chirullo, Jake Yalley-Ogunro, Jack Greenhouse, Fausto Titti, Enrico Garaci, Andrea Savarino
Software Mentions: 2
Published: over 14 years ago

10.1038/s41598-017-19097-w

A Geodetic Strain Rate Model for the East African Rift System
Cited by: 83
Author(s): D. S. Stamps, E. Saria, C. Kreemer
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41398-017-0047-9

A multi-dimensional characterization of anxiety in monozygotic twin pairs reveals susceptibility loci in humans
Cited by: 18
Author(s): Reid S. Alisch, Carol Van Hulle, Pankaj Chopra, Anita Bhattacharyya, Su‐Chun Zhang, Richard J. Davidson, Ned H. Kalin, H. Hill Goldsmith
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12889-018-6258-z

Study protocol of a 4- parallel arm, superiority, community based cluster randomized controlled trial comparing paper and e-platform based interventions to improve accuracy of recall of last menstrual period (LMP) dates in rural Bangladesh
Cited by: 3
Author(s): Shumona Sharmin Salam, Nazia Binte Ali, Ahmed Ehsanur Rahman, Tazeen Tahsina, Irteja Islam, Asif Iqbal, Dewan Md Emdadul Hoque, Samir K. Saha, Shams El Arifeen
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-017-1383-z

Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha
Cited by: 51
Author(s): Marc W. Schmid, Alejandro Giraldo‐Fonseca, Moritz Rövekamp, Dmitry Smetanin, John L. Bowman, Ueli Grossniklaus
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13059-020-02065-5

Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data
Cited by: 18
Author(s): C. Anthony Scott, Jack D. Duryea, Harry A. Mackay, Maria S. Baker, Eleonora Laritsky, T.D.C.P. Gunasekara, Cristian Coarfa, Robert A. Waterland
Software Mentions: 2
Published: over 4 years ago

10.1016/j.vaccine.2010.06.011

Spatial and socio-demographic predictors of time-to-immunization in a rural area in Kenya: Is equity attainable?
Cited by: 51
Author(s): Jennifer C. Moïsi, Jonathan Kabuka, Dorah Mitingi, Orin S. Levine, J. Anthony G. Scott
Software Mentions: 2
Published: over 14 years ago

10.3389/fphys.2021.697121

Comparative Analysis of Skeletal Muscle DNA Methylation and Transcriptome of the Chicken Embryo at Different Developmental Stages
Cited by: 2
Author(s): Jin-Shan Ran, Jingjing Li, Lingqian Yin, Donghao Zhang, Chunlin Yu, Huarui Du, Xiaosong Jiang, Chaowu Yang, Yiping Liu
Software Mentions: 2
Published: over 3 years ago

10.3389/fonc.2020.586414

A Comprehensive Prognostic and Immune Analysis of SLC41A3 in Pan-Cancer
Cited by: 21
Author(s): Jun Li, Shanqiang Zhang, Wenjie Dai, Chengyu Xie, Jicheng Li
Software Mentions: 2
Published: almost 4 years ago

10.3389/fonc.2020.597996

Systematic Construction and Validation of an RNA-Binding Protein-Associated Model for Prognosis Prediction in Hepatocellular Carcinoma
Cited by: 4
Author(s): Siyuan Tian, Jingyi Liu, Keshuai Sun, Yansheng Liu, Jiahao Yu, Shuoyi Ma, Miao Zhang, Jia Gui, Xia Zhou, Yulong Shang, Ying Han
Software Mentions: 2
Published: almost 4 years ago

10.3389/fphys.2021.683499

Comparative Transcriptome and DNA Methylation Analysis of Phenotypic Plasticity in the Pacific Abalone (Haliotis discus hannai)
Cited by: 4
Author(s): Zekun Huang, Qizhen Xiao, Feng Yu, Yang Gao, Chengkuan Lu, Wenzhu Peng, Min Han, Xuan Luo, Nan Chen, You Wang, Caihuan Ke
Software Mentions: 2
Published: over 3 years ago

10.3389/fnhum.2018.00418

Brain Network Changes in Fatigued Drivers: A Longitudinal Study in a Real-World Environment Based on the Effective Connectivity Analysis and Actigraphy Data
Cited by: 17
Author(s): André Fonseca, Scott E. Kerick, Jung-Tai King, Chin‐Teng Lin, Tzyy‐Ping Jung
Software Mentions: 2
Published: about 6 years ago

10.3390/metabo10090373

Metabolic Profiling of a Porcine Combat Trauma-Injury Model Using NMR and Multi-Mode LC-MS Metabolomics—A Preliminary Study
Cited by: 4
Author(s): Anna Karen Carrasco Laserna, Yiyang Lai, Guihua Fang, Ganapathy Rajaseger, Mohamed Shirhan Bin Mohamed Atan, Jia Lu, Jian Wu, Mahesh Uttamchandani, Shabbir Moochhala, Sam Fong Yau Li
Software Mentions: 2
Published: about 4 years ago

10.3389/fpsyt.2021.594229

When Depression Breeds Rejection Rather Than Compassion: Disagreeableness, Stigma, and Lack of Empathic Concern Among Support Providers
Cited by: 1
Author(s): Myriam Mongrain, Ariel Shoikhedbrod
Software Mentions: 2
Published: over 3 years ago

10.3389/fnagi.2021.641222

Widespread Decreases in Cerebral Copper Are Common to Parkinson's Disease Dementia and Alzheimer's Disease Dementia
Cited by: 17
Author(s): Melissa Scholefield, Stephanie J. Church, Jiaolong Xu, Stefano Patassini, Federico Roncaroli, Nigel M. Hooper, Richard D. Unwin, Garth J. S. Cooper
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-015-1844-2

Transcriptional analysis of phloem-associated cells of potato
Cited by: 12
Author(s): Tong Lin, Coralie C. Lashbrook, Sung-Ki Cho, Nathaniel M. Butler, Pooja Sharma, Usha Muppirala, Andrew J. Severin, David J. Hannapel
Software Mentions: 2
Published: about 9 years ago

10.3390/ma14185122

Wear Behavior and Machining Performance of TiAlSiN-Coated Tools Obtained by dc MS and HiPIMS: A Comparative Study
Cited by: 9
Author(s): Vítor F. C. Sousa, Francisco Silva, H. Lopes, R. B. Casais, A. Baptista, Gustavo Pinto, Ricardo Alexandre
Software Mentions: 2
Published: about 3 years ago

10.1186/s13148-021-01109-2

Genome‑wide profiling of DNA methylation and gene expression unravel the epigenetic landscape in diabetes-related hypothyroidism
Cited by: 3
Author(s): Jingyi Luo, Xiaoxia Wang, Yuan Li, Lixin Guo
Software Mentions: 2
Published: over 3 years ago

10.15252/embj.2020106174

Selective cross‐linking of coinciding protein assemblies by in‐gel cross‐linking mass spectrometry
Cited by: 24
Author(s): Johannes F. Hevler, Marie V. Lukassen, Alfredo Cabrera‐Orefice, Susanne Arnold, Matti F. Pronker, Vojtěch Franc, Albert J. R. Heck
Software Mentions: 2
Published: almost 4 years ago

Projects: bioconductor: DSS

Papers Mentioning DSS 288