bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

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: almost 6 years ago

10.1038/s41598-018-38339-z

Spatial distribution of prokaryotic communities in hypersaline soils
Cited by: 26
Author(s): Blanca Vera-Gargallo, Taniya Roy Chowdhury, Joseph Brown, Sarah Fansler, Ana Durán‐Viseras, Cristina Sánchez‐Porro, Vanessa Bailey, Janet Jansson, António Ventosa
Software Mentions: 9
Published: over 7 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 6 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 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 5 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 7 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: almost 6 years ago

10.7150/jca.56005

Integrated Genomic and Transcriptomic Analysis reveals key genes for predicting dual-phenotype Hepatocellular Carcinoma Prognosis
Cited by: 6
Author(s): Yaobang Wang, Xi Wang, Xiaoliang Huang, Jie Zhang, Jinwen Hu, Yinliang Qi, Bang‐De Xiang, Qiuyan Wang
Software Mentions: 9
Published: over 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: over 7 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: 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: about 5 years ago

10.3389/fmicb.2020.587972

DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil
Cited by: 11
Author(s): Julian Yu, Michael J. Pavia, Lauren M. Deem, Susan E. Crow, Jonathan Deenik, C. Ryan Penton
Software Mentions: 9
Published: almost 6 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 7 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: about 5 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: over 5 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: about 6 years ago

10.1186/s13059-021-02363-6

Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Cited by: 24
Author(s): Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas, Soren Charmsaz, Nicole Groß, Skylar Woolman, Kayla Cruz, Rebecca M Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan, Elizabeth D. Thompson, Elizabeth M. Jaffee, Elana J. Fertig
Software Mentions: 9
Published: over 5 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: almost 6 years ago

10.1371/journal.pone.0241529

Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation
Cited by: 5
Author(s): Anita Silver, Sean Perez, Melanie Gee, Bethany Xu, Shreeya Garg, Kipling Will, Amanjit Gill
Software Mentions: 9
Published: over 5 years ago

10.3390/cancers12030653

Molecular-Clinical Correlation in Pediatric Medulloblastoma: A Cohort Series Study of 52 Cases in Taiwan
Cited by: 6
Author(s): Kuo Sheng Wu, Donald Ming Tak Ho, Shiann-Tarng Jou, Alice L. Yu, Huy Tran, Muh Lii Liang, Hsin Hung Chen, Yi Yen Lee, Yi Wei Chen, Shih Chieh Lin, Feng Chi Chang, Meng‐Li Tsai, Yen‐Lin Liu, Hsin Lun Lee, Kevin Hsieh, Wen Chang Huang, Shian Ying Sung, Che-Chang Chang, Chun A. Changou, Kung‐Hao Liang, Tsung Han Hsieh, Yun Ru Liu, Meng En Chao, Chonghua Wan, Shing Shung Chu, Er Chieh Cho, Tai-Tong Wong
Software Mentions: 9
Published: over 6 years ago

10.3389/fonc.2020.573141

Significance of Tumor Mutation Burden in Immune Infiltration and Prognosis in Cutaneous Melanoma
Cited by: 57
Author(s): Kai Kang, Fucun Xie, Jianshan Mao, Yi Bai, Xiang Wang
Software Mentions: 9
Published: about 6 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 10 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: about 5 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: about 5 years ago

10.3389/fonc.2020.593760

Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue
Cited by: 4
Author(s): Rihards Saksis, Ivars Silamiķelis, Pola Laksa, Kaspars Megnis, Raitis Pečulis, Ilona Mandrika, Olesja Rogoza, Ramona Petrovska, Inga Balcere, Ilze Konrāde, Liva Steina, Jānis Stukēns, Austra Breikša, Jurijs Nazarovs, Jeļizaveta Sokolovska, Valdis Pīrāgs, Jānis Kloviņš, Vita Rovīte
Software Mentions: 9
Published: over 5 years ago

10.3389/fonc.2021.709210

Single-Cell Transcriptomics Reveals the Complexity of the Tumor Microenvironment of Treatment-Naive Osteosarcoma
Cited by: 45
Author(s): Yun Liu, Wei Feng, Yan Dai, Mengying Bao, Zhenchao Yuan, Mingwei He, Zhaojie Qin, Shijie Liao, Jun He, Qian Huang, Zhenyuan Yu, Yanyu Zeng, Binqian Guo, Rong Huang, Rongliang Yang, Yonghua Jiang, Jinling Liao, Zengming Xiao, Xinli Zhan, Chengsen Lin, Jiake Xu, Yu Ye, Jie Ma, Qingjun Wei, Zengnan Mo
Software Mentions: 9
Published: about 5 years ago

10.3389/fnins.2020.00061

Regionally Distinct Astrocytes Display Unique Transcription Factor Profiles in the Adult Brain
Cited by: 35
Author(s): Brittney Lozzi, Teng-Wei Huang, Debosmita Sardar, Anna Yu-Szu Huang, Benjamin Deneen
Software Mentions: 9
Published: over 6 years ago

10.3389/fonc.2021.695006

Tumor-Infiltrating PD-1hiCD8+-T-Cell Signature as an Effective Biomarker for Immune Checkpoint Inhibitor Therapy Response Across Multiple Cancers
Cited by: 7
Author(s): Zhenyu Yang, Yulan Deng, Jinghui Cheng, Shiyou Wei, Hao Luo, Lunxu Liu
Software Mentions: 9
Published: about 5 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: almost 10 years ago

10.3389/fmicb.2019.01793

The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life
Cited by: 22
Author(s): Wentao Yang, Carola Petersen, Barbara Pees, Johannes Zimmermann, Silvio Waschina, Philipp Dirksen, Philip Rosenstiel, Andreas Tholey, Matthias Leippe, Katja Dierking, Christoph Kaleta, Hinrich Schulenburg
Software Mentions: 9
Published: about 7 years ago

10.3389/fmicb.2020.01398

Microbiome Shifts Associated With the Introduction of Wild Atlantic Horseshoe Crabs (Limulus polyphemus) Into a Touch-Tank Exhibit
Cited by: 9
Author(s): Ariel D. Friel, Sean A. Neiswenter, Cale O. Seymour, Lauren Rose Bali, Ginger McNamara, Fabian Leija, Jack Jewell, Brian P. Hedlund
Software Mentions: 9
Published: about 6 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 6 years ago

10.3389/fmicb.2018.02711

Land-Use Intensity Rather Than Plant Functional Identity Shapes Bacterial and Fungal Rhizosphere Communities
Cited by: 45
Author(s): Ricardo Schöps, Kezia Goldmann, Katharina Herz, Guillaume Lentendu, Ingo Schöning, Helge Bruelheide, Tesfaye Wubet, François Buscot
Software Mentions: 9
Published: almost 8 years ago

10.3389/fphys.2020.624677

Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal
Cited by: 8
Author(s): Rui Fu, Austin E. Gillen, Katharine R. Grabek, Kent Riemondy, L. Elaine Epperson, Carlos D. Bustamante, Jay R. Hesselberth, Sandra L. Martin
Software Mentions: 9
Published: over 5 years ago

10.1186/s40168-019-0745-z

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation
Cited by: 57
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Malene Skovsted Cilieborg, Ole Lund, Susan Holmes, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 9
Published: about 7 years ago

10.1264/jsme2.ME18109

Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields
Cited by: 33
Author(s): Turgut Yiğit Akyol, Rieko Niwa, Hideki Hirakawa, Hayato Maruyama, Takumi Sato, Takae Suzuki, Ayako Fukunaga, Takashi Sato, Shigenobu Yoshida, Keitaro Tawaraya, Masanori Saitô, Tatsuhiro Ezawa, Shusei Sato
Software Mentions: 9
Published: over 7 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: about 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: about 6 years ago

10.1016/j.mad.2021.111437

Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice
Cited by: 6
Author(s): Matías Fuentealba, Daniel K. Fabian, Handan Melike Dönertaş, Janet Thornton, Linda Partridge
Software Mentions: 9
Published: over 5 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 11 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: about 6 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: about 6 years ago

10.3390/ijms22031399

DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
Cited by: 5
Author(s): Salim Ghannoum, Waldir Leoncio Netto, Damiano Fantini, Benjamin Ragan-Kelley, Amirabbas Parizadeh, Emma Jonasson, Anders Ståhlberg, Hesso Farhan, Alvaro Köhn‐Luque
Software Mentions: 9
Published: over 5 years ago

10.3390/ijms21134763

The Differential Effect of Carbon Dots on Gene Expression and DNA Methylation of Human Embryonic Lung Fibroblasts as a Function of Surface Charge and Dose
Cited by: 15
Author(s): Michal Šíma, Kristýna Vrbová, Táňa Závodná, K. Hoňková, Irena Chvojková, Antonín Ambrož, Jǐŕı Kléma, Andrea Rössnerová, Kateřina Poláková, Tomáš Malina, Jan Belza, Jan Topinka, Pavel Rőssner
Software Mentions: 9
Published: about 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 11 years ago

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 7 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 8 years ago

10.15698/mic2021.08.757

Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes
Cited by: 13
Author(s): Maria Paula Rueda‐Mejia, Lukas Nägeli, Stefanie Lutz, Richard D. Hayes, Adithi R. Varadarajan, Igor V. Grigoriev, Christian H. Ahrens, Florian M. Freimoser
Software Mentions: 9
Published: about 5 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: about 8 years ago

10.7554/eLife.40757

Targets and genomic constraints of ectopic Dnmt3b expression
Cited by: 24
Author(s): Yingying Zhang, Jocelyn Charlton, Rahul Karnik, Isabel Beerman, Zachary D. Smith, Hongcang Gu, Patrick Boyle, Xiaoli Mi, Kendell Clement, Ramona Pop, Andreas Gnirke, Derrick J. Rossi, Alexander Meissner
Software Mentions: 9
Published: almost 8 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 7 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: about 5 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 6 years ago

10.7554/eLife.34058

A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscle
Cited by: 63
Author(s): Maria L. Spletter, Christiane Barz, Assa Yeroslaviz, Xu Zhang, Sandra B. Lemke, Adrien Bonnard, Erich Brunner, Giovanni Cardone, Konrad Basler, Bianca Habermann, Frank Schnorrer
Software Mentions: 9
Published: over 8 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 6 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: over 6 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 5 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 5 years ago

10.1371/journal.pone.0220518

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)
Cited by: 4
Author(s): Albert Fradera-Sola, Ann Thomas, Dagmara Gasior, John A. Harper, Matthew J. Hegarty, Ian Armstead, Narcís Fernández-Fuentes
Software Mentions: 9
Published: about 7 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: almost 9 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 7 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: almost 7 years ago

10.7554/eLife.53278

GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm
Cited by: 25
Author(s): Arun Sharma, Lauren Wasson, Jon A. L. Willcox, Sarah U. Morton, Joshua M. Gorham, Daniel M. DeLaughter, Meraj Neyazi, Manuel Schmid, Radhika Agarwal, Min Young Jang, Christopher N. Toepfer, Tarsha Ward, Yuri Kim, Alexandre C. Pereira, Steven R. DePalma, Angela Tai, Seongwon Kim, David A. Conner, Daniel Bernstein, Bruce D. Gelb, Wendy K. Chung, Elizabeth Goldmuntz, George A. Porter, Martin Tristani‐Firouzi, Deepak Srivastava, Jonathan G. Seidman, Christine E. Seidman
Software Mentions: 9
Published: almost 6 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: almost 9 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: over 5 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: about 7 years ago

10.1038/s41598-019-40503-y

Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions
Cited by: 23
Author(s): Quen J. Cheng, Faraz Behzadi, Supriya Sen, Sho Ohta, Roberto Spreafico, Rosane M. B. Teles, Robert L. Modlin, Alexander Hoffmann
Software Mentions: 8
Published: over 7 years ago

10.1038/s41598-019-45193-0

Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods
Cited by: 7
Author(s): Polina Drozdova, Daria Bedulina, Ekaterina Madyarova, Lorena Rivarola-Duarte, S Schreiber, Peter F. Stadler, Till Luckenbach, Maxim A. Timofeyev
Software Mentions: 8
Published: over 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: over 9 years ago

10.1093/molbev/msab029

Herbicide Selection Promotes Antibiotic Resistance in Soil Microbiomes
Cited by: 56
Author(s): Hanpeng Liao, Xi Li, Qiue Yang, Yudan Bai, Peng Cui, Chang Wen, Chen Liu, Zhi Chen, Jiahuan Tang, Jiangang Che, Zhen Yu, Stefan Geisen, Shungui Zhou, Ville‐Petri Friman, Yong‐Guan Zhu
Software Mentions: 8
Published: over 5 years ago

10.1038/s41598-018-34019-0

Microbial structure and function in infant and juvenile rhesus macaques are primarily affected by age, not vaccination status
Cited by: 4
Author(s): Yu Hasegawa, Britni Curtis, Vernon Yutuc, Megan Rulien, Kelly Morrisroe, Kristin Watkins, Clayton Ferrier, Chris English, Laura Hewitson, Carolyn M. Slupsky
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: almost 10 years ago

10.1038/s41598-020-68665-0

MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse
Cited by: 15
Author(s): Nicolas Bonhoure, Viviane Praz, Robyn D. Moir, Gilles Willemin, François Mange, Catherine Moret, Ian M. Willis, Nouria Hernandez
Software Mentions: 8
Published: about 6 years ago

10.3390/microorganisms7120662

Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew
Cited by: 17
Author(s): Luca Nerva, Chiara Pagliarani, Massimo Pugliese, M. Monchiero, Solène Gonthier, M. L. Gullino, Giorgio Gambino, Walter Chitarra
Software Mentions: 8
Published: almost 7 years ago

10.1080/19490976.2021.1903289

Translational activity is uncoupled from nucleic acid content in bacterial cells of the human gut microbiota
Cited by: 9
Author(s): Mariia Taguer, Ben Shapiro, Corinne F. Maurice
Software Mentions: 8
Published: over 5 years ago

10.1016/j.celrep.2018.03.075

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
Cited by: 432
Author(s): Christopher J. Ricketts, Aguirre A. de Cubas, Huihui Fan, Christof C. Smith, Martin Lang, Ed Reznik, Reanne Bowlby, Ewan A. Gibb, Rehan Akbani, Rameen Beroukhim, Donald P. Bottaro, Toni K. Choueiri, Richard A. Gibbs, Andrew K. Godwin, Scott M. Haake, A. Ari Hakimi, Elizabeth P. Henske, James J. Hsieh, Thai H. Ho, Rupa S. Kanchi, Bhavani Krishnan, David J. Kwiatkowski, Wembin Lui, María J. Merino, Gordon B. Mills, Jerome Myers, Michael L. Nickerson, Victor E. Reuter, Laura S. Schmidt, Carl Simon Shelley, Hui Shen, Brian Shuch, Sabina Signoretti, Ramaprasad Srinivasan, Pheroze Tamboli, George V. Thomas, Benjamin G. Vincent, Cathy D. Vocke, David A. Wheeler, Lixing Yang, William Y. Kim, A. Gordon Robertson, Paul T. Spellman, W. Kimryn Rathmell, W. Marston Linehan, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila M. Reynolds, Ilya Shmulevich, Vésteinn Thórsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Ju Zhang, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin Groß, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah Phillips, Ed Reznik, Francisco Sanchez‐Vega, Chris Sander, Nikolaus Schultz, Robert P. Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul T. Spellman, Christopher C. Benz, Joshua M. Stuart, Christopher Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert A. Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie Kucherlapati, Raju Kucherlapati, Stephen B. Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle R. Covington, Chad J. Creighton, Huyen Dinh, Harshavardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna M. Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Xi Liu, Fengmei Zhao, Julian M. Hess, Elizabeth L. Appelbaum, Matthew H. Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark E. Sherman, Eric M. Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall M. Corcoran, Tony Costello, Christopher M. Hovens, André Lopes Carvalho, Ana Carolina de Carvalho, José Humberto Tavares Guerreiro Fregnani, Adhemar Longatto‐Filho, Rui Manuel Reis, Cristovam Scapulatempo‐Neto, Henrique C. S. Silveira, Daniel Onofre Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia Castro, Michael Ittmann, David G. Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, А. В. Шабунин, М. М. Тавобилов, Christopher McPherson, Ronald E. Warnick, Ross S. Berkowitz, Daniel E. Cramer, Colleen M. Feltmate, Neil S. Horowitz, Adam S. Kibel, Michael G. Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz‐Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino Maria De Rose, Felice Giuliante, Marc T. Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Aleš Vícha, Tomáš Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John A. Chabot, Hanina Hibshoosh, Antonia R. Sepulveda, Tao Su, Yichen Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Román-Román, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell D. Bigner, Eric Lipp, Jeffrey R. Marks, Shannon J. McCall, Roger E. McLendon, Angeles Alvarez Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith A. Delman, Seth D. Force, Fadlo R. Khuri, Kelly R. Magliocca, Shishir K. Maithel, Jeffrey J. Olson, Taofeek K. Owonikoko, Alan Pickens, Suresh S. Ramalingam, Dong Min Shin, Gabriel L. Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad J. M. Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, J. R. Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Täubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Wung Chung, William J. Edenfield, Julie Martin, Éric Baudin, Glenn J. Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven N. Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elı́as Campo, Eva Giné, Armando López Guillermo, Nguyễn Văn Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael J. Birrer, Debra A. Bell, Mitesh J. Borad, Alan H. Bryce, Erik P. Castle, Vishal S. Chandan, John C. Cheville, John A. Copland, Michael B. Farnell, Thomas J. Flotte, Nasra H. Giama, Thai H. Ho, Michael L. Kendrick, Jean-Pierre A. Kocher, Karla Kopp, Catherine D. Moser, David M. Nagorney, Daniel J. O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia G. Que, Michael Rivera, Lewis R. Roberts, Robert C. Smallridge, Thomas C. Smyrk, Melissa L. Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell R. Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey E. Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric‐Bernstam, César A. Moran, Lois M. Ramondetta, David Rice, Anil K. Sood, Pheroze Tamboli, Timothy C. Thompson, Patricia Troncoso, Anne S. Tsao, Ignacio Wistuba, Candace Carter, Lauren E. Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina V. Long, Graham J. Mann, Michael J. Quinn, Robyn P.M. Saw, Richard A. Scolyer, Kerwin F. Shannon, Andrew J. Spillane, onathan Stretch, Maria Synott, John Thompson, James S. Wilmott, Hikmat Al‐Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor E. Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer K. Smith, Howard A. Zaren, Joong-Won Park, Nguyễn Phi Hùng, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacák, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert A. Worrell, Hannah Yang, Marc Moncrieff, Chandra V. Goparaju, Jonathan Melamed, Harvey I. Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John M.S. Bartlett, Jay Engel, Sébastien Gilbert, Jeremy Parfitt, Harman S. Sekhon, George V. Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter J. Urba, Nicholas K. Hayward, H. Th. Marc Timmers, Anna Antenucci, Francesco Facciolo, Gian Luca Grazi, Mirella Marino, Roberta Merola, Ronald R. de Krijger, Anne‐Paule Gimenez‐Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kıvanç Birsoy, Gene H. Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel P. Raymond, Cathy Schilero, Kathy Smolenski, Cecilia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl‐Friedrich Becker, Klaus‐Peter Janssen, Julia Slotta‐Huspenina, Mohamed H. Abdel‐Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James C. Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul E. Wakely, Paul Hansen, Ronald M. Lechan, James F. Powers, Arthur S. Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel M. Henderson, Sima P. Porten, Jens Waldmann, Martin Fassnacht, L. Sylvia, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark A. Nelson, Oliver F. Bathe, Peter R. Carroll, June M. Chan, Philip J. DiSaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry P. Simko, Karen Smith‐McCune, Scott R. VandenBerg, Kevin K. Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis A. Carey, Ian Forgie, Massimo Mannelli, Michael E. Carney, Brenda Hernandez, Benito Campos, Christel Herold‐Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita D. Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David G. Beer, Thomas J. Giordano, Anne‐Marie Mes‐Masson, Fred Saad, Thèrése Bocklage, Lisa M. Landrum, Robert S. Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary E. Zuna, Michael D. Feldman, Federico Valdivieso, Rajiv Dhir, James D. Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, José Sebastião dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Pretti da Cunha Tirapelli, James W.F. Catto, Kathy Agnew, Elizabeth M. Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, S. DiSean Kendall, Cassaundra Shipman, Carol R. Bradford, Thomas E. Carey, Andrea Haddad, Jeffey Moyer, Lisa A. Peterson, Mark E. Prince, Laura S. Rozek, Gregory T. Wolf, Rayleen V. Bowman, Kwun M. Fong, Ian A. Yang, Robert J. Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John F. DiPersio, Bettina F. Drake, Ramaswamy Govindan, Sharon E. Heath, Timothy J. Ley, Brian A. Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália Del Angelo Aredes, Armaz Mariamidze
Software Mentions: 8
Published: over 8 years ago

10.1093/gigascience/giz147

Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa
Cited by: 16
Author(s): Miriam Payá‐Milans, Laura Poza‐Viejo, Patxi San Martín-Úriz, David Lara‐Astiaso, Mark D. Wilkinson, Pedro Crevillén
Software Mentions: 8
Published: almost 7 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 6 years ago

10.1093/gigascience/giz004

The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches
Cited by: 103
Author(s): Darshan B. Dhakan, Abhijit Maji, Ashok Sharma, Rituja Saxena, Joby Pulikkan, Tony Grace, Andrés Gómez, Joy Scaria, Katherine R. Amato, Vineet K. Sharma
Software Mentions: 8
Published: over 7 years ago

10.1080/19490976.2021.1966263

Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen <i>Citrobacter rodentium</i>
Cited by: 28
Author(s): Mareike Neumann, Alex Steimle, Erica T. Grant, Mathis Wolter, Amy Parrish, Stéphanie Willième, Dirk Brenner, Eric C. Martens, Mahesh S. Desai
Software Mentions: 8
Published: over 5 years ago

10.1016/j.celrep.2021.109118

Resident memory T cells in tumor-distant tissues fortify against metastasis formation
Cited by: 14
Author(s): Laura S. Christian, Liuyang Wang, Bryan Jian Wei Lim, Dachuan Deng, Haiyang Wu, Xiaofan Wang, Qi-Jing Li
Software Mentions: 8
Published: over 5 years ago

10.1186/s13073-021-00866-2

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium
Cited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: over 5 years ago

10.1186/s13073-020-00812-8

Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression
Cited by: 89
Author(s): Trine Line Hauge Okholm, Shashank Sathe, Samuel S. Park, Andreas Bjerregaard Kamstrup, Asta Mannstaedt Rasmussen, Archana Shankar, Zong Ming Chua, Niels Fristrup, Morten Muhlig Nielsen, Søren Vang, Lars Dyrskjøt, Stefan Aigner, Christian Kroun Damgaard, G Yeo, Jakob Skou Pedersen
Software Mentions: 8
Published: almost 6 years ago

10.1016/j.gpb.2019.09.007

Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota Are Attributable to Its Key Ingredient Berberine
Cited by: 59
Author(s): Xizhan Xu, Zezheng Gao, Fuchao Yang, Yingying Yang, Liang Chen, Han Chieh Lin, Na Zhao, Jiayue Xu, Xinmiao Wang, Yue Ma, Lian Shu, Xueyou Hu, Na Lyu, Yuanlong Pan, Baoli Zhu, Linhua Zhao, Xiaolin Tong, Jun Wang
Software Mentions: 8
Published: almost 6 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: about 5 years ago

10.1186/s40168-017-0235-0

Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens
Cited by: 30
Author(s): Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R. Babik, Molly C. Reid, Eoghan M. Smyth, Lauren E. Hittle, Joseph N. Paulson, Raul Cruz‐Cano, Mihai Pop, Stephanie Buehler, Pamela I. Clark, Amy R. Sapkota, Emmanuel F. Mongodin
Software Mentions: 8
Published: over 9 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 8 years ago

10.1016/j.stem.2020.03.005

GATA3 Mediates a Fast, Irreversible Commitment to BMP4-Driven Differentiation in Human Embryonic Stem Cells
Cited by: 42
Author(s): Alexandra Gunne-Braden, Adrienne E. Sullivan, Borzo Gharibi, Rahuman S. Malik Sheriff, Alok Kumar Maity, Yi Fang Wang, A. Edwards, Ming Jiang, Michael Howell, Robert Goldstone, Roy Wollman, Philip East, Silvia Santos
Software Mentions: 8
Published: over 6 years ago

10.3390/microorganisms9061326

Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer
Cited by: 5
Author(s): Thijs Van Gerrewey, Christophe El‐Nakhel, Stefania De Pascale, Jolien De Paepe, Peter Clauwaert, Frederiek‐Maarten Kerckhof, Nico Boon, Danny Geelen
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 6 years ago

10.3389/fonc.2020.574939

Identification of an Immune-Related Gene Signature Based on Immunogenomic Landscape Analysis to Predict the Prognosis of Adult Acute Myeloid Leukemia Patients
Cited by: 19
Author(s): Ruiqi Zhu, Huishan Tao, Wenyi Lin, Liang Tang, Yu Hu
Software Mentions: 8
Published: almost 6 years ago

10.3389/fonc.2021.640881

Exploration of an Integrative Prognostic Model of Radiogenomics Features With Underlying Gene Expression Patterns in Clear Cell Renal Cell Carcinoma
Cited by: 10
Author(s): Yeqian Huang, Hao Zeng, Linyan Chen, Yuling Luo, Xuelei Ma, Ye Zhao
Software Mentions: 8
Published: over 5 years ago

10.3389/fphys.2021.662132

Liver Transcriptome Dynamics During Hibernation Are Shaped by a Shifting Balance Between Transcription and RNA Stability
Cited by: 10
Author(s): Austin E. Gillen, Rui Fu, Kent Riemondy, Jennifer Jager, Bin Fang, Mitchell A. Lazar, Sandra L. Martin
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0200925

PNPase knockout results in mtDNA loss and an altered metabolic gene expression program
Cited by: 12
Author(s): Eriko Shimada, Fasih M. Ahsan, Mahta Nili, Dian Huang, Sean Atamdede, Tara TeSlaa, Dana Case, Xiang Yu, Brian D. Gregory, Benjamin J. Perrin, Carla M. Koehler, Michael A. Teitell
Software Mentions: 8
Published: about 8 years ago

10.1371/journal.pone.0153782

Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools
Cited by: 11
Author(s): Dena Leshkowitz, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, Shirley Horn‐Saban
Software Mentions: 8
Published: over 10 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 5 years ago

10.3389/fnins.2018.00031

Exploring the Complexity of Cortical Development Using Single-Cell Transcriptomics
Cited by: 12
Author(s): Hyobin Jeong, Vijay Tiwari
Software Mentions: 8
Published: over 8 years ago

10.1371/journal.pone.0209200

Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus
Cited by: 61
Author(s): Matthew Fuirst, Richard R. Veit, Megan Hahn, Nolwenn M. Dheilly, Lesley H. Thorne
Software Mentions: 8
Published: almost 8 years ago

10.1371/journal.pone.0251032

Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivation
Cited by: 2
Author(s): Y-h. Taguchi, Turki Turki
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pgen.1006995

Environmental perturbations lead to extensive directional shifts in RNA processing
Cited by: 24
Author(s): Allison L. Richards, Donovan Watza, Anthony Findley, Adnan Alazizi, Xiaoquan Wen, Athma A. Pai, Roger Piqué-Regi, Francesca Luca
Software Mentions: 8
Published: almost 9 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning DESeq2 9,583