bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.7554/eLife.39380

Intergenerational epigenetic inheritance of cancer susceptibility in mammals
Cited by: 38
Author(s): Bluma J. Lesch, Zuzana Tóthová, Elizabeth A. Morgan, Zhicong Liao, Roderick T. Bronson, Benjamin L. Ebert, David C. Page
Software Mentions: 9
Published: over 5 years ago

10.7554/eLife.58178

16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural development
Cited by: 24
Author(s): Julien G. Roth, Kristin Muench, Aditya Asokan, Victoria M Mallett, Hongwei Gai, Yogendra Verma, Stephen G. Weber, Carol Charlton, Jonas L. Fowler, Kyle M. Loh, Ricardo E. Dolmetsch, Theo Palmer
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pgen.1008671

PEA15 loss of function and defective cerebral development in the domestic cat
Cited by: 3
Author(s): Emily C. Graff, J. Nicholas Cochran, Christopher B. Kaelin, Kenneth Day, Heather L. Gray‐Edwards, Rie Watanabe, Jey W. Koehler, Rebecca A. Falgoust, Jeremy W. Prokop, R Myers, Nancy R. Cox, Gregory S. Barsh, Douglas R. Martin
Software Mentions: 9
Published: about 4 years ago

10.7554/eLife.58081

IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation
Cited by: 11
Author(s): Pan Li, Madeleine E. Lemieux, Tom Thomas, Julia M. Rogers, Colin H. Lipper, Winston Lee, C. Anderson Johnson, Lynette M. Sholl, Andrew P. South, Jarrod A. Marto, Guillaume Adelmant, Stephen C. Blacklow, Jon C. Aster
Software Mentions: 9
Published: over 4 years ago

10.1002/ece3.7437

Mixing tree species associated with arbuscular or ectotrophic mycorrhizae reveals dual mycorrhization and interactive effects on the fungal partners
Cited by: 14
Author(s): Heike Heklau, Nicole Schindler, François Buscot, Nico Eisenhauer, Olga Ferlian, Luis Daniel Prada-Salcedo, Helge Bruelheide
Software Mentions: 9
Published: over 3 years ago

10.1002/ece3.6221

Effects of captivity, diet, and relocation on the gut bacterial communities of white‐footed mice
Cited by: 18
Author(s): Pauline van Leeuwen, Nadia Mykytczuk, Gabriela F. Mastromonaco, Albrecht I. Schulte‐Hostedde
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.69040

Common virulence gene expression in adult first-time infected malaria patients and severe cases
Cited by: 15
Author(s): Jan Stephan Wichers, Gerry Tonkin‐Hill, Thorsten Thye, Ralf Krumkamp, Benno Kreuels, Jan Strauss, Heidrun von Thien, Jochen Scholz, Helle Hansson, Rasmus Weisel Jensen, Louise Turner, Freia-Raphaella Lorenz, Anna Schöllhorn, Iris Bruchhaus, Egbert Tannich, Rolf Fendel, Thomas D. Otto, Thomas Lavstsen, Tim‐Wolf Gilberger, Michael Duffy, Anna Bachmann
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.65905

Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia
Cited by: 28
Author(s): Sumiko Takao, Lauren Forbes, Masahiro Uni, Shu‐Yuan Cheng, Jose Mario Bello Pineda, Yusuke Tarumoto, Paolo Cifani, Gerard Minuesa, Celine Chen, Michael G. Kharas, Robert K. Bradley, Christopher R. Vakoc, Richard P. Koche, Alex Kentsis
Software Mentions: 9
Published: almost 4 years ago

10.1128/mSystems.00474-21

Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics
Cited by: 12
Author(s): Elizabeth A. McDaniel, Francisco Moya-Flores, Natalie K. Beach, Pamela Y. Camejo, Ben O. Oyserman, Matthew Kizaric, Eng Hoe Khor, Daniel R. Noguera, Katherine D. McMahon
Software Mentions: 9
Published: over 3 years ago

10.1128/mSystems.00493-20

Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses
Cited by: 3
Author(s): John L. Chodkowski, Ashley Shade
Software Mentions: 9
Published: almost 4 years ago

10.1155/2020/4252580

A Novel RNA-Seq-Based Model for Preoperative Prediction of Lymph Node Metastasis in Oral Squamous Cell Carcinoma
Cited by: 7
Author(s): Bo Qiao, Min Zhao, Jing Wu, Huan Wu, Yiming Zhao, Fanhao Meng, Yu Tian, Situo Wang, Jianxin Shi, Haizhong Zhang
Software Mentions: 9
Published: over 4 years ago

10.1111/1462-2920.14870

Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys
Cited by: 23
Author(s): Laura Weber, Patricia González‐Díaz, Maickel Armenteros, Víctor Manuel Ferrer, Fernando Bretos, Erich Bartels, Alyson E. Santoro, Amy Apprill
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pbio.3001158

Disparate temperature-dependent virus–host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium
Cited by: 66
Author(s): Philip V’kovski, Mitra Gultom, Jenna N. Kelly, Silvio Steiner, Julie Russeil, Bastien Mangeat, Elisa Cora, Joern Pezoldt, Melle Holwerda, Annika Kratzel, Laura Laloli, Manon Wider, Jasmine Portmann, Thao Thi Phuong Tran, Nadine Ebert, Hanspeter Stalder, Rune Hartmann, Vincent Gardeux, Daniel Alpern, Bart Deplancke, Volker Thiel, Ronald Dijkman
Software Mentions: 9
Published: over 3 years ago

10.1128/mSystems.00897-19

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters
Cited by: 26
Author(s): Zachary Liechty, Christian Santos‐Medellín, Joseph Edwards, Bao‐Anh Thi Nguyen, David Mikhail, Shane Eason, Gregory C. Phillips, Venkatesan Sundaresan
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12870-019-1679-0

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon
Cited by: 34
Author(s): Alejandro Sanz-Carbonell, Maria Carmen Marqués, Alexander Bustamante, Mario A. Fares, Guillermo Rodrigo, Gustavo Gómez
Software Mentions: 9
Published: almost 6 years ago

10.18632/aging.203379

Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues
Cited by: 8
Author(s): Margarida Ferreira, Stephany Francisco, Ana Raquel Soares, Ana Nobre, Miguel Pinheiro, Andreia Reis, Sonya Neto, Ana João Rodrigues, Nuno Sousa, Gabriela Moura, Manuel A. S. Santos
Software Mentions: 9
Published: over 3 years ago

10.1177/2515841419835460

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
Cited by: 6
Author(s): Nicholas Owen, Mariya Moosajee
Software Mentions: 9
Published: almost 6 years ago

10.1186/s12890-021-01588-2

A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma
Cited by: 9
Author(s): Fēi Li, Dongcen Ge, Shulan Sun
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-021-92648-4

Transmitting silks of maize have a complex and dynamic microbiome
Cited by: 5
Author(s): Eman M. Khalaf, Anuja Shrestha, Jeffrey Rinne, Michael D. J. Lynch, Charles Shearer, Victor Limay-Rios, L. M. Reid, Manish N. Raizada
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-020-59516-z

Variability in estimated gene expression among commonly used RNA-seq pipelines
Cited by: 37
Author(s): Sonali Arora, Siobhan S. Pattwell, Eric C. Holland, Hamid Bolouri
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41598-020-60336-4

Linagliptin and telmisartan induced effects on renal and urinary exosomal miRNA expression in rats with 5/6 nephrectomy
Cited by: 18
Author(s): Denis Delić, Franziska Wiech, Richard Urquhart, Ogsen Gabrielyan, Kathrin Rieber, Marcel Rolser, Oleg Tsuprykov, Ahmed A. Hasan, Bernhard K. Krämer, Patrick Baum, A Köhler, Florian Gantner, Mark Michael, Berthold Hocher, Thomas Klein
Software Mentions: 9
Published: almost 5 years ago

10.1038/s42003-021-01945-1

Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression
Cited by: 5
Author(s): Andrea Cerase, Alexander N. Young, Nerea Ruiz, Andreas Buneß, Gabrielle M Sant, Mirjam Arnold, Monica Di Giacomo, Michela Ascolani, Manish Kumar, Andreas Hierholzer, Giuseppe Trigiante, Sarah Marzi, Philip Avner
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-020-66998-4

Comparison of differential accessibility analysis strategies for ATAC-seq data
Cited by: 26
Author(s): Paul Gontarz, Shuhua Fu, Xiaoyun Xing, Shaopeng Liu, Benpeng Miao, Viktoriia Bazylianska, Akhil Sharma, Pamela A. F. Madden, K. Lynn Cates, Andrew S. Yoo, Anna Moszczyńska, Ting Wang, Bo Zhang
Software Mentions: 9
Published: over 4 years ago

10.3389/fmicb.2018.01323

Exposure to Arsenic Alters the Microbiome of Larval Zebrafish
Cited by: 37
Author(s): Dylan Dahan, Brooke A. Jude, Regina Lamendella, Felicia Keesing, Gabriel G. Perron
Software Mentions: 9
Published: over 6 years ago

10.3390/jcm10194354

Application of an Exploratory Knowledge-Discovery Pipeline Based on Machine Learning to Multi-Scale OMICS Data to Characterise Myocardial Injury in a Cohort of Patients with Septic Shock: An Observational Study
Cited by: 3
Author(s): Bernardo Bollen Pinto, Vicent Ribas Ripoll, Paula Subías-Beltrán, Antoine Herpain, Cristina Barlassina, Eliandre de Oliveira, Roberta Pastorelli, Daniele Braga, Matteo Barcella, Laia Subirats, Julia Bauzá‐Martinez, Antonia Odena, Manuela Ferrario, Giuseppe Baselli, Federico Aletti, Karim Bendjelid
Software Mentions: 9
Published: about 3 years ago

10.7150/thno.53092

Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy
Cited by: 7
Author(s): Xin Lai, Florian S. Dreyer, Martina Cantone, Martin Eberhardt, Kerstin F. Gerer, Tanushree Jaitly, Steffen Uebe, Christopher Lischer, Arif B. Ekici, Jürgen Wittmann, Hans‐Martin Jäck, Niels Schaft, Jan Dörrie, Julio Vera
Software Mentions: 9
Published: almost 4 years ago

10.3390/microorganisms8010038

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota
Cited by: 13
Author(s): Matteo Chialva, Stefano Ghignone, Mara Novero, Wael N. Hozzein, Luisa Lanfranco, Paola Bonfante
Software Mentions: 9
Published: almost 5 years ago

10.20900/immunometab20210022

Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models
Cited by: 21
Author(s): Austin C. Conklin, Hitoo Nishi, Florencia Schlamp, Tiit Örd, Kadri Õunap, Minna U. Kaikkonen, Edward A. Fisher, Casey E. Romanoski
Software Mentions: 9
Published: over 3 years ago

10.1186/s12915-021-01123-z

The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation
Cited by: 12
Author(s): Jana Sperschneider, Ashley Jones, Jamila Nasim, Bo Xu, Silke Jacques, Chengcheng Zhong, Narayana M. Upadhyaya, Rohit Mago, Yiheng Hu, Melania Figueroa, Karam B. Singh, Eric A. Stone, Ming-Bo Wang, Jennifer Taylor, Peter N. Dodds
Software Mentions: 9
Published: over 3 years ago

10.1007/s00040-018-0624-9

The gut microbiome is associated with behavioural task in honey bees
Cited by: 75
Author(s): Julia C. Jones, Carmelo Fruciano, J. H. Marchant, Falk Hildebrand, Kristoffer Forslund, Peer Bork, Philipp Engel, William O. Hughes
Software Mentions: 9
Published: over 6 years ago

10.1186/s12943-021-01405-8

Uncovering cancer vulnerabilities by machine learning prediction of synthetic lethality
Cited by: 6
Author(s): Salvatore Benfatto, Özdemirhan Serçin, Francesca R. Dejure, Amir Abdollahi, Frank T. Zenke, Balca R. Mardin
Software Mentions: 9
Published: over 3 years ago

10.3390/genes11050532

Sparsity-Penalized Stacked Denoising Autoencoders for Imputing Single-Cell RNA-seq Data
Cited by: 9
Author(s): Weilai Chi, Minghua Deng
Software Mentions: 9
Published: over 4 years ago

10.3389/fpls.2020.01269

Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and Ripening
Cited by: 27
Author(s): Beatriz Ester García-Gómez, David Ruiz, J. Salazar, M. Rubio, Pedro J. Martínez-García, Pedro Martínez‐Gómez
Software Mentions: 9
Published: over 4 years ago

10.1186/s12859-017-1936-x

Software for rapid time dependent ChIP-sequencing analysis (TDCA)
Cited by: 1
Author(s): Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang, David J. Vocadlo
Software Mentions: 9
Published: about 7 years ago

10.1186/s12859-016-0994-9

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
Cited by: 79
Author(s): Ran Bi, Peng Liu
Software Mentions: 9
Published: over 8 years ago

10.1186/s12859-016-1323-z

variancePartition: interpreting drivers of variation in complex gene expression studies
Cited by: 390
Author(s): Gabriel E. Hoffman, Eric E. Schadt
Software Mentions: 9
Published: about 8 years ago

10.3389/fmicb.2020.01536

Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations
Cited by: 13
Author(s): Elias Broman, Xiaole Sun, Christian Stranne, Marco Salgado, Stefano Bonaglia, M. C. Geibel, Martin Jakobsson, Alf Norkko, Christoph Humborg, Francisco J. A. Nascimento
Software Mentions: 9
Published: over 4 years ago

10.1038/s41396-019-0458-0

Virome heterogeneity and connectivity in waterfowl and shorebird communities
Cited by: 53
Author(s): Michelle Wille, Mǎng Shī, Marcel Klaassen, Aeron C. Hurt, Edward C. Holmes
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0209656

A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn’s disease patients
Cited by: 14
Author(s): Andrew Y. Li Yim, Jessica R. de Bruyn, Nicolette W. Duijvis, Catriona Sharp, Enrico Ferrero, Wouter J. de Jonge, Manon E. Wildenberg, Marcel M.A.M. Mannens, Christianne J. Buskens, Geert R. D’Haens, Peter Henneman, Anje A. te Velde
Software Mentions: 9
Published: almost 6 years ago

10.1016/j.molcel.2018.08.004

Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development
Cited by: 226
Author(s): Mateusz Mendel, Kuan-Ming Chen, David Homolka, Pascal Gos, Radha Raman Pandey, A.A. McCarthy, Ramesh S. Pillai
Software Mentions: 9
Published: over 6 years ago

10.1186/s42523-021-00118-z

Microbial composition differs between production systems and is associated with growth performance and carcass quality in pigs
Cited by: 5
Author(s): Christian Maltecca, Robert R. Dunn, Yuqing He, Nathan P. McNulty, Constantino Schillebeeckx, Charles V. Schwab, Caleb M Shull, Justin Fix, Francesco Tiezzi
Software Mentions: 9
Published: over 3 years ago

10.3389/fmicb.2020.00175

Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients
Cited by: 10
Author(s): Johanna Gutleben, Catarina Loureiro, Laura Adriana Ramírez Romero, Sudarshan A. Shetty, René H. Wijffels, Hauke Smidt, Detmer Sipkema
Software Mentions: 9
Published: almost 5 years ago

10.1007/s00401-020-02187-x

Interleukin-1 promotes autoimmune neuroinflammation by suppressing endothelial heme oxygenase-1 at the blood–brain barrier
Cited by: 44
Author(s): Judith Hauptmann, Lisa Johann, Fédérico Marini, Maja Kitic, E. Colombo, Ilgiz A. Mufazalov, Martin W. Krueger, Khalad Karram, Sonja Moos, Florian Wanke, Florian C. Kurschus, Matthias Klein, Sílvia Cardoso, Johannes Strauß, Subhashini Bolisetty, Fred Lühder, Markus Schwaninger, Harald Binder, Ingo Bechman, Tobias Bopp, Anupam Agarwal, Miguel P. Soares, Tommy Regen, Ari Waisman
Software Mentions: 9
Published: over 4 years ago

10.1038/s41437-018-0059-0

Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral
Cited by: 46
Author(s): Kate M. Quigley, Patricia A. Warner, Line K. Bay, Bette L. Willis
Software Mentions: 9
Published: almost 7 years ago

10.1186/s12859-020-03703-2

SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o
Cited by: 25
Author(s): Fernando Puente-Sánchez, Natalia García-García, Javier Tamames
Software Mentions: 9
Published: over 4 years ago

10.3389/fmicb.2018.02452

Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter
Cited by: 52
Author(s): Umer Zeeshan Ijaz, Lojika Sivaloganathan, Aaron McKenna, Anne Richmond, Carmel Kelly, Mark Linton, Alexandros Ch. Stratakos, Ursula Lavery, Abdi Elmi, Brendan W. Wren, Nick Dorrell, Nicolae Corcionivoschi, Ozan Gundogdu
Software Mentions: 9
Published: about 6 years ago

10.1186/s13229-019-0262-8

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer
Cited by: 25
Author(s): Jaume Forés-Martos, Ferrán Catalá-López, Jon Sánchez-Valle, Kristina Ibáñez, Héctor Tejero, Helena Palma-Gudiel, Joan Climent, Véra Pancaldi, Lourdes Fañanás, Celso Arango, Mara Parellada, Anaı̈s Baudot, Daniel Vogt, John L.R. Rubenstein, Alfonso Valencia, Rafael Tabarés‐Seisdedos
Software Mentions: 9
Published: over 5 years ago

10.1016/j.celrep.2020.108546

RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions
Cited by: 33
Author(s): Panagiotis Kotsantis, Sandra Segura-Bayona, Pol Margalef, Paulina Marzec, Phil Ruis, Graeme Hewitt, Roberto Bellelli, Harshil Patel, Robert Goldstone, Anna R. Poetsch, Simon J. Boulton
Software Mentions: 9
Published: about 4 years ago

10.1038/s41421-021-00274-1

Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19
Cited by: 21
Author(s): Yun Tan, Wei Zhang, Zhaoqin Zhu, Na Qiao, Yun Ling, Mingquan Guo, Tong Yin, Hai Fang, Xiaoguang Xu, Gang Lu, Peipei Zhang, Shuangshuang Yang, Ziyu Fu, Dongguo Liang, Yinyin Xie, Ruihong Zhang, Lu Jiang, Shuting Yu, Jing Lu, Fang-Ying Jiang, Jian Chen, Chenlu Xiao, Shengyue Wang, Shuo Chen, Xiu‐Wu Bian, Hongzhou Lu, Feng Liu, Sai‐Juan Chen
Software Mentions: 9
Published: over 3 years ago

10.1186/s12864-015-1676-0

deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies
Cited by: 14
Author(s): Chengcai Chu, Zhiming Fang, Xing Hua, Yaning Yang, Enguo Chen, Allen W. Cowley, Mingyu Liang, Pengyuan Liu, Yan Lu
Software Mentions: 9
Published: over 9 years ago

10.1016/j.celrep.2020.108308

Developmental Gene Expression Differences between Humans and Mammalian Models
Cited by: 34
Author(s): Margarida Cardoso-Moreira, Ioannis Sarropoulos, Britta Velten, Matthew Mort, David Neil Cooper, Wolfgang Huber, Henrik Kaessmann
Software Mentions: 9
Published: about 4 years ago

10.1186/s12867-018-0111-x

Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis
Cited by: 4
Author(s): Paola M. Boggiatto, Daniel Fitzsimmons, Darrell O. Bayles, David P. Alt, Catherine E. Vrentas, Steven C. Olsen
Software Mentions: 9
Published: over 6 years ago

10.1186/1471-2164-16-S7-S14

Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads
Cited by: 12
Author(s): Hung I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang, Yidong Chen
Software Mentions: 9
Published: over 9 years ago

10.1126/sciadv.abc8492

Persistent epigenetic reprogramming of sweet taste by diet
Cited by: 29
Author(s): Anoumid Vaziri, Morteza Khabiri, Brendan T. Genaw, Christina E. May, Peter L. Freddolino, Monica Dus
Software Mentions: 9
Published: about 4 years ago

10.1186/s12915-018-0518-3

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
Cited by: 21
Author(s): Angelika Schmidt, Francesco Marabita, Narsis A. Kiani, Catharina C. Groß, Henrik J. Johansson, Szabolcs Éliás, Sini Rautio, Matilda Eriksson, Sunjay Jude Fernandes, Gilad Silberberg, Ubaid Ullah, Urvashi Bhatia, Harri Lähdesmäki, Janne Lehtiö, David Gomez-Cabrero, Heinz Wiendl, Riitta Lahesmaa, Jesper Tegnér
Software Mentions: 9
Published: over 6 years ago

10.1186/s40168-020-00977-9

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas
Cited by: 84
Author(s): Alice Baniel, Katherine R. Amato, Jacinta C. Beehner, Thore J. Bergman, Arianne Mercer, Rachel F. Perlman, Lauren Petrullo, Laurie J Reitsema, Sierra Sams, Amy Lu, Noah Snyder‐Mackler
Software Mentions: 9
Published: almost 4 years ago

10.1093/bioinformatics/btaa838

<i>MicrobiomeExplorer</i>: an R package for the analysis and visualization of microbial communities
Cited by: 16
Author(s): Janina Reeder, Mo Huang, Joshua S. Kaminker, Joseph N. Paulson
Software Mentions: 9
Published: about 4 years ago

10.7554/eLife.42675

The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila
Cited by: 20
Author(s): Katrin Domsch, Julie Carnesecchi, Vanessa Disela, Jana Friedrich, Nils Trost, Olga Ermakova, Maria Polychronidou, Ingrid Lohmann
Software Mentions: 9
Published: over 5 years ago

10.3390/ijms22063200

Identification of Transcriptomic Differences between Lower Extremities Arterial Disease, Abdominal Aortic Aneurysm and Chronic Venous Disease in Peripheral Blood Mononuclear Cells Specimens
Cited by: 4
Author(s): Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Przemysław Kołodziej, Jolanta Szymańska, Bartosz J. Płachno, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki, Anna Bogucka‐Kocka
Software Mentions: 9
Published: almost 4 years ago

10.3389/fgene.2020.00817

Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure
Cited by: 17
Author(s): Júber Herrera-Uribe, Haibo Li, Kristen A Byrne, Zahra F Bond, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.55862

Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants
Cited by: 16
Author(s): Carlos Martínez-Ruiz, Rodrigo Pracana, Eckart Stolle, Carolina Ivon Paris, Richard A. Nichols, Yannick Wurm
Software Mentions: 9
Published: over 4 years ago

10.1186/s12885-017-3726-2

Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer
Cited by: 26
Author(s): Melissa Quintero, Douglas Adamóski, Larissa Menezes dos Reis, Carolline Fernanda Rodrigues Ascenção, Krishina Ratna Sousa de Oliveira, Kaliandra de Almeida Gonçalves, Milton Dias, Marcelo Falsarella Carazzolle, Sandra Martha Gomes Dias
Software Mentions: 9
Published: about 7 years ago

10.1186/s12864-019-5870-3

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods
Cited by: 56
Author(s): Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado‐Torres, Martha Kimos, Nicholas J. Brandon, A.J. Cross, Daniel R. Weinberger, Joo Heon Shin
Software Mentions: 9
Published: over 5 years ago

10.7554/eLife.69431

Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2
Cited by: 18
Author(s): Elektra Kantzari Robinson, Pratibha Jagannatha, Sergio Covarrubias, Matthew Cattle, Valeriya Smaliy, Rojin Safavi, Barbara Shapleigh, Robin Abu-Shumays, Miten Jain, Suzanne M. Cloonan, Mark Akeson, Angela N. Brooks
Software Mentions: 9
Published: over 3 years ago

10.3389/fcell.2021.704242

Two Similar Signatures for Predicting the Prognosis and Immunotherapy Efficacy of Stomach Adenocarcinoma Patients
Cited by: 4
Author(s): Taohua Yue, Shuai Zuo, Jing Zhu, Shuqin Guo, Zhihao Huang, Jichang Li, Xin Wang, Yucun Liu, Shanwen Chen, Pengyuan Wang
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pcbi.1006076

Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data
Cited by: 211
Author(s): Travers Ching, Xun Zhu, Lana X. Garmire
Software Mentions: 8
Published: over 6 years ago

10.3390/e23080945

Statistical Approach of Gene Set Analysis with Quantitative Trait Loci for Crop Gene Expression Studies
Cited by: 1
Author(s): Das S, N. Shesh
Software Mentions: 8
Published: over 3 years ago

10.1002/ece3.4894

Contrasting patterns of divergence at the regulatory and sequence level in European <i>Daphnia galeata</i> natural populations
Cited by: 8
Author(s): Suda Parimala Ravindran, Maike Herrmann, Mathilde Cordellier
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.pcbi.1008488

On the NF-Y regulome as in ENCODE (2019)
Cited by: 4
Author(s): Mirko Ronzio, Andrea Bernardini, Giulio Pavesi, Roberto Mantovani, Diletta Dolfini
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pcbi.1008748

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Cited by: 6
Author(s): Martín Garrido‐Rodriguez, Daniel López-López, Francisco Ortuño, María Peña‐Chilet, Eduardo Muñóz, Marco A. Calzado, Joaquı́n Dopazo
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12864-019-5926-4

lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA
Cited by: 6
Author(s): Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J.C. Slebos, Christine H. Chung, Xuefeng Wang
Software Mentions: 8
Published: over 5 years ago

10.1128/mSystems.00917-20

FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses
Cited by: 7
Author(s): Matthew Chung, Ricky S. Adkins, John Mattick, Katie R. Bradwell, Amol Shetty, Lisa Sadzewicz, Luke J. Tallon, Claire M. Fraser, David A. Rasko, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pgen.1008658

Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish
Cited by: 63
Author(s): Arne Jacobs, Madeleine Carruthers, Andrey A. Yurchenko, Н. В. Гордеева, S. S. Alekseyev, Oliver E. Hooker, Jong S. Leong, David R. Minkley, Eric B. Rondeau, Ben F. Koop, Colin E. Adams, Kathryn R. Elmer
Software Mentions: 8
Published: over 4 years ago

10.17179/excli2015-168

Data- and knowledge-based modeling of gene regulatory networks: an update.
Cited by: 24
Author(s): Jörg Linde, Sylvie Schulze, Sebastian Henkel, Reinhard Guthke
Software Mentions: 8
Published: almost 10 years ago

10.1371/journal.pgen.1009324

Virus-derived variation in diverse human genomes
Cited by: 0
Author(s): Shohei Kojima, Anselmo Jiro Kamada, Nicholas F. Parrish
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pcbi.1006907

Ten quick tips for effective dimensionality reduction
Cited by: 164
Author(s): Linh P. Nguyen, Susan Holmes
Software Mentions: 8
Published: over 5 years ago

10.7554/eLife.64513

Chondrocytes in the resting zone of the growth plate are maintained in a Wnt-inhibitory environment
Cited by: 25
Author(s): Shawn A Hallett, Yuki Matsushita, Wanida Ono, Naoko Sakagami, Koji Mizuhashi, Nicha Tokavanich, Mizuki Nagata, Annabelle Zhou, Takao Hanabusa, Henry M. Kronenberg, Noriaki Ono
Software Mentions: 8
Published: over 3 years ago

10.1038/tp.2015.169

Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain
Cited by: 56
Author(s): Aslihan Dincer, David P. Gavin, Ke Xu, B Zhang, Joel T. Dudley, Eric E. Schadt, Schahram Akbarian
Software Mentions: 8
Published: about 9 years ago

10.1371/journal.pcbi.1007666

Methods detecting rhythmic gene expression are biologically relevant only for strong signal
Cited by: 22
Author(s): David Laloum, Marc Robinson‐Rechavi
Software Mentions: 8
Published: almost 5 years ago

10.1038/s41598-021-98966-x

Identification of immune-related subtypes of colorectal cancer to improve antitumor immunotherapy
Cited by: 4
Author(s): Xiangkuo Zheng, Yong Gao, Chunhua Yu, Guiquan Fan, Pengwu Li, Ming Zhang, Jian Yu, Mingqing Xu
Software Mentions: 8
Published: about 3 years ago

10.1016/j.csbj.2021.05.024

Machine learning applied to serum and cerebrospinal fluid metabolomes revealed altered arginine metabolism in neonatal sepsis with meningoencephalitis
Cited by: 12
Author(s): Peng Zhang, Zhangxing Wang, Huixian Qiu, Wenhao Zhou, Mingbang Wang, Guoqiang Cheng
Software Mentions: 8
Published: almost 4 years ago

10.7717/peerj.9056

Transcriptional profiling to identify the key genes and pathways of pterygium
Cited by: 11
Author(s): Yihui Chen, Haoyu Wang, Yaping Jiang, Xiaoyan Zhang, Qingzhong Wang
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-021-93570-5

Three dimensional modeling of biologically relevant fluid shear stress in human renal tubule cells mimics in vivo transcriptional profiles
Cited by: 18
Author(s): Emily J. Ross, Emily R. Gordon, Hanna Sothers, Roshan Darji, Oakley Baron, Dustin W. Haithcock, Balabhaskar Prabhakarpandian, Kapil Pant, R Myers, Sara J. Cooper, Nancy J. Cox
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-017-1803-9

XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation
Cited by: 11
Author(s): Yuanhang Liu, Ping Wu, Jingqi Zhou, Teresa L. Johnson‐Pais, Zhao Lai, Wasim H. Chowdhury, Ronald Rodríguez, Yidong Chen
Software Mentions: 8
Published: about 7 years ago

10.1038/srep40655

Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae
Cited by: 66
Author(s): Elena Gómez-Díaz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Anna Cohuet, M. Jordan Rowley, Jean-Bosco Ouédraogo, Victor G. Corcés
Software Mentions: 8
Published: almost 8 years ago

10.1038/srep35903

Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia
Cited by: 59
Author(s): Zi Yi Wan, Jun Xia, Grace Lin, Le Wang, Valerie Chun Ling Lin, Gen Hua Yue
Software Mentions: 8
Published: about 8 years ago

10.1186/s12864-021-07918-2

CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis
Cited by: 10
Author(s): Carlos Alberto Oliveira de Biagi, Ricardo Perecin Nociti, Danielle Barbosa Brotto, Breno Osvaldo Funicheli, Patrícia de Cássia Ruy, João Paulo Bianchi Ximenez, David Livingstone Alves Figueiredo, Wilson A. Silva
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-020-62354-8

Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal components
Cited by: 18
Author(s): Parisa Amini, Sina Nassiri, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: over 4 years ago

10.3390/microorganisms8040485

Characterization of the Duodenal Mucosal Microbiome in Obese Adult Subjects by 16S rRNA Sequencing
Cited by: 33
Author(s): Carmela Nardelli, Ilaria Granata, Valeria D’Argenio, Salvatore Tramontano, Debora Compare, Mario Rosario Guarracino, Gerardo Nardone, Vincenzo Pilone, Lucia Sacchetti
Software Mentions: 8
Published: over 4 years ago

10.1186/s12864-018-4649-2

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation
Cited by: 15
Author(s): Zhisong He, Qianhui Yu
Software Mentions: 8
Published: over 6 years ago

10.1016/j.immuni.2019.02.006

Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis
Cited by: 121
Author(s): Tomas Castro‐Dopico, Thomas W. Dennison, John R. Ferdinand, Rebeccah J. Mathews, Aaron Fleming, Dean Clift, Benjamin J Stewart, Chenzhi Jing, Konstantina Strongili, Larisa I. Labzin, Edward J M Monk, Kourosh Saeb‐Parsy, Clare E. Bryant, Simon Clare, Miles Parkes, Menna R. Clatworthy
Software Mentions: 8
Published: over 5 years ago

10.1016/j.heliyon.2019.e01558

Factor Analysis for Bicluster Acquisition (FABIA) revealed vincristine-sensitive transcript pattern of canine transmissible venereal tumors
Cited by: 5
Author(s): Kaj Chokeshaiusaha, Denis Puthier, Cong Tu Nguyen, Pansawut Sudjaidee, Thanida Sananmuang
Software Mentions: 8
Published: over 5 years ago

10.3390/genes11040435

Identification of Potential Biomarkers for Anti-PD-1 Therapy in Melanoma by Weighted Correlation Network Analysis
Cited by: 14
Author(s): Xuanyi Wang, Zixuan Chai, Yinghong Li, Fei Long, Youjin Hao, Guizhi Pan, Mingwei Liu, Bo Li
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0187722

Plasma microRNA profiling: Exploring better biomarkers for lymphoma surveillance
Cited by: 47
Author(s): Drirh Khare, Neta Goldschmidt, Aya Bardugo, Devorah Gur‐Wahnon, Iddo Z. Ben‐Dov, Batia Avni
Software Mentions: 8
Published: about 7 years ago

10.1186/s12864-021-07659-2

Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite
Cited by: 15
Author(s): Océane Cassan, Sophie Lèbre, Antoine Martin
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0249691

Profiling DNA break sites and transcriptional changes in response to contextual fear learning
Cited by: 25
Author(s): Ryan Stott, Oleg Kritsky, Li‐Huei Tsai
Software Mentions: 8
Published: over 3 years ago

10.3389/fpls.2021.675760

Genotype-Specific Expression and NLR Repertoire Contribute to Phenotypic Resistance Diversity in Plantago lanceolata
Cited by: 4
Author(s): Pezhman Safdari, Layla Höckerstedt, Mikael Brosché, Jarkko Salojärvi, Anna‐Liisa Laine
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0249148

Ethnically biased microsatellites contribute to differential gene expression and glutathione metabolism in Africans and Europeans
Cited by: 5
Author(s): Nicholas A. Kinney, Lin Kang, Harpal Bains, Elizabeth Lawson, Mesam Husain, Kumayl Husain, Inderjit Sandhu, Yongdeok Shin, Javan K. Carter, Ramu Anandakrishnan, Pawel Michalak, Harold R. Garner
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0232271

Benchmarking RNA-seq differential expression analysis methods using spike-in and simulation data
Cited by: 20
Author(s): Bukyung Baik, Susan A. Yoon, Dougu Nam
Software Mentions: 8
Published: over 4 years ago

10.3389/fmolb.2021.613359

Identification of a Hypoxia-Related Signature for Predicting Prognosis and the Immune Microenvironment in Bladder Cancer
Cited by: 10
Author(s): Minxiao Jiang, Ren Lang, Yuanlei Chen, Huan Wang, Haiyang Wu, Sheng Cheng, Gonghui Li, Shicheng Yu
Software Mentions: 8
Published: over 3 years ago

Projects: bioconductor: DESeq2

Papers Mentioning DESeq2 9,583