bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

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

10.3389/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: almost 8 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

10.1038/s41388-018-0450-6

The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression
Cited by: 40
Author(s): Mark D. Long, Prashant Singh, James R. Russell, Gerard Llimos, Spencer R. Rosario, Abbas Rizvi, Patrick R. van den Berg, Jason Kirk, Lara E. Sucheston‐Campbell, Dominic J. Smiraglia, Moray J. Campbell
Software Mentions: 9
Published: about 8 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: about 6 years ago

10.15252/msb.20209819

Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration
Cited by: 17
Author(s): Nader Morshed, William T. Ralvenius, Alexi Nott, L. Ashley Watson, Felicia H. Rodriguez, Leyla Anne Akay, Brian A. Joughin, Ping‐Chieh Pao, Jay Penney, Lauren M. LaRocque, Diego Mastroeni, Li Huei Tsai, Forest M. White
Software Mentions: 9
Published: almost 6 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

10.1242/dev.158501

Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast
Cited by: 143
Author(s): Giuliano Giuseppe Stirparo, Thorsten Boroviak, Ge Guo, Jennifer Nichols, Austin Smith, Paul Bertone
Software Mentions: 9
Published: almost 9 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

10.1186/s40425-019-0763-1

34th Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2019): part 1
Cited by: 31
Author(s):
Software Mentions: 9
Published: almost 7 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

10.7554/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: over 5 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 6 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: over 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

10.1038/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: over 6 years ago

10.1186/s40425-018-0422-y

33rd Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2018)
Cited by: 36
Author(s):
Software Mentions: 9
Published: almost 8 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: over 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: about 5 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

10.1038/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

10.3389/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

10.1186/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

10.3389/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

10.3389/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

10.7554/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

10.1002/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

10.1111/1462-2920.14870

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

10.1186/s13059-020-02165-2

iMOKA: k-mer based software to analyze large collections of sequencing data
Cited by: 6
Author(s): Claudio Lorenzi, Sylvain Barriere, Jean-Philippe Villemin, Laureline Dejardin Bretones, Alban Mancheron, William Ritchie
Software Mentions: 9
Published: almost 6 years ago

10.1186/s13059-020-1935-5

Opportunities and challenges in long-read sequencing data analysis
Cited by: 1,295
Author(s): Shanika L. Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E. Ritchie, Quentin Gouil
Software Mentions: 9
Published: over 6 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/s13059-018-1414-4

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data
Cited by: 140
Author(s): Kevin C.H. Ha, Benjamin J. Blencowe, Quaid Morris
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

10.1186/s13059-020-02008-0

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Cited by: 24
Author(s): Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan
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 11 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.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

10.3389/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/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

10.1371/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: 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

10.3390/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: over 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 5 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/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 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

10.7150/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: almost 6 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

10.1128/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

10.3389/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

10.1128/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

10.3390/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

10.15698/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

10.1264/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: almost 8 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 8 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

10.1371/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/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

10.1371/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

10.7150/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 6 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

10.1016/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: about 8 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

10.1126/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

10.3389/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: about 5 years ago

10.3389/fcell.2021.651575

An N6-Methyladenosine-Related Gene Set Variation Score as a Prognostic Tool for Lung Adenocarcinoma
Cited by: 8
Author(s): Huijuan Zhang, Jing Hu, Aina Liu, Huajun Qu, Fenge Jiang, Congcong Wang, Steven Mo, Ping Sun
Software Mentions: 8
Published: about 5 years ago

10.1186/s13059-021-02260-y

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Cited by: 31
Author(s): Maša Roller, Ericca L. Stamper, Diego Villar, Osagie Izuogu, Fergal J. Martin, Aisling M. Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T. Odom, Paul Flicek
Software Mentions: 8
Published: over 5 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 6 years ago

10.3389/fmicb.2021.584676

Microbial Community Characteristics Largely Unaffected by X-Ray Computed Tomography of Sediment Cores
Cited by: 0
Author(s): Erica Ewton, Scott Klasek, Erin K. Peck, J. Wiest, Frederick S. Colwell
Software Mentions: 8
Published: over 5 years ago

10.1186/s12864-020-6764-0

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum
Cited by: 15
Author(s): Alice B. Dennis, Gabriel I. Ballesteros, Stéphanie Robin, Lukas Schrader, Jens Bast, Jan Berghöfer, Leo W. Beukeboom, Maya Belghazi, Anthony Bretaudeau, Jan Buellesbach, Elizabeth Cash, Dominique Colinet, Zoé Dumas, Mohammed Errbii, Patrizia Falabella, Jean‐Luc Gatti, Elzemiek Geuverink, Joshua D. Gibson, Corinne Hertaeg, Stefanie Hartmann, Emmanuelle Jacquin‐Joly, Mark Lammers, Blas I. Lavandero, Ina Lindenbaum, Lauriane Massardier-Galatà, Camille Meslin, Nicolas Montagné, Nina Pak, Marylène Poirié, Rosanna Salvia, Chris R. Smith, Denis Tagu, Sophie Tarès, Heiko Vogel, Tanja Schwander, Jean Simon, Christian C. Figueroa, Christoph Vorburger, Fabrice Legeai, Jürgen Gadau
Software Mentions: 8
Published: over 6 years ago

10.1186/s13059-019-1921-y

Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis
Cited by: 68
Author(s): Rui Yang, Sen Cheng, Nan Luo, Ranran Gao, Kezhuo Yu, Boxi Kang, Li Wang, Qiming Zhang, Fang Qiao, Lei Zhang, Chen Li, Aibin He, Xueda Hu, Jirun Peng, Xianwen Ren, Zemin Zhang
Software Mentions: 8
Published: almost 7 years ago

10.1371/journal.pone.0240996

Biological invasions alter environmental microbiomes: A meta-analysis
Cited by: 11
Author(s): Antonino Malacrinò, Victoria A Sadowski, Tvisha Martin, Nathalia Cavichiolli de Oliveira, Ian J. Brackett, James D. Feller, Kira Harris, ORLANDO COMBITA-HEREDIA, Rosa Vescio, Alison E. Bennett
Software Mentions: 8
Published: almost 6 years ago

10.1186/s13059-021-02261-x

Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer
Cited by: 37
Author(s): Kie Kyon Huang, Jiawen Huang, Jeanie Wu, Ming‐Hui Lee, Su Ting Tay, Vikrant Kumar, R. Kalpana, Nisha Padmanabhan, Chong Xu, Angie Lay Keng Tan, Charlene Chan, Dennis Kappei, Jonathan Göke, Patrick Tan
Software Mentions: 8
Published: over 5 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: about 5 years ago

10.1186/s13059-020-02072-6

HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis
Cited by: 7
Author(s): Guy Karlebach, Peter J. Hansen, Diogo Veiga, Robin Steinhaus, Daniel Daniš, Sheng Li, Olga Anczuków, Peter N. Robinson
Software Mentions: 8
Published: about 6 years ago

10.1186/s13059-020-01998-1

Wheat chromatin architecture is organized in genome territories and transcription factories
Cited by: 89
Author(s): Lorenzo Concia, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Azahara Martin-Ramirez, Ying Huang, Magali Perez, Séverine Domenichini, Natalia Y. Rodriguez Granados, Soon-Kap Kim, Thomas Blein, Susan Duncan, Clement Pichot, Deborah Manza‐Mianza, Caroline Juéry, Etienne Paux, Graham Moore, Heribert Hirt, Catherine Bergounioux, Martín Crespi, Magdy M. Mahfouz, Abdelhafid Bendahmane, Chang Liu, Anthony Hall, Cécile Raynaud, David Latrasse, Moussa Benhamed
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/fcvm.2020.575275

Reactivation of Atrium Genes Is a Primer for Heart Infarction or Regeneration
Cited by: 1
Author(s): Yang Zhen
Software Mentions: 8
Published: almost 6 years ago

10.3389/fmicb.2017.02414

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field
Cited by: 48
Author(s): Bryan D. Emmett, Nicholas D. Youngblut, Daniel H. Buckley, Laurie E. Drinkwater
Software Mentions: 8
Published: almost 9 years ago

10.3389/fcvm.2019.00167

SS-31 Peptide Reverses the Mitochondrial Fragmentation Present in Fibroblasts From Patients With DCMA, a Mitochondrial Cardiomyopathy
Cited by: 21
Author(s): Pranav Machiraju, Xuemei Wang, Rasha Sabouny, Joshua Huang, Tian Zhao, Fatima Iqbal, Melissa A. King, Dimple Prasher, A Lodha, Nerea Jimenez-Tellez, Amir Ravandi, Bob Argiropoulos, David S. Sinasac, Aneal Khan, Timothy E. Shutt, Steven C. Greenway
Software Mentions: 8
Published: almost 7 years ago

10.1186/s12864-016-2848-2

ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
Cited by: 21
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 8
Published: about 10 years ago

10.1186/s13059-018-1567-1

Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders
Cited by: 119
Author(s): Heath O’Brien, Eilís Hannon, Matthew Hill, Carolina Toste, Matthew J. Robertson, Joanne Morgan, Gemma M. McLaughlin, Cathryn M. Lewis, Leonard C Schalkwyk, Lynsey S. Hall, Antonio F. Pardiñas, Michael John Owen, Michael O’Donovan, Jonathan Mill, Nicholas John Bray
Software Mentions: 8
Published: almost 8 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: over 7 years ago

10.1186/s13059-015-0862-3

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage
Cited by: 107
Author(s): Charlotte Soneson, Katarina L. Matthes, Małgorzata Nowicka, Charity W. Law, Mark D. Robinson
Software Mentions: 8
Published: over 10 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 6 years ago

10.1371/journal.pgen.1009435

A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression
Cited by: 14
Author(s): Zachary Carico, Holden C. Stefan, Megan Justice, Askar Yimit, Jill M. Dowen
Software Mentions: 8
Published: over 5 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 5 years ago

10.1186/s40168-016-0213-y

Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort
Cited by: 361
Author(s): Colin Hill, Denise B. Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B. Jeffery, Carol Anne O’Shea, Claire Watkins, Eugene M. Dempsey, Fulvio Mattivi, Kieran Tuohy, R. Paul Ross, C. Anthony Ryan, Paul W. O’Toole, Catherine Stanton
Software Mentions: 8
Published: over 9 years ago

10.1186/s40168-017-0339-6

Metagenomic characterization of ambulances across the USA
Cited by: 29
Author(s): Niamh B. O’Hara, Harry J. Reed, Ebrahim Afshinnekoo, Donell Harvin, Nora Caplan, Gail Rosen, Brook Frye, Stephen Woloszynek, Rachid Ounit, Shawn Levy, Erin Butler, Christopher E. Mason
Software Mentions: 8
Published: about 9 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 12 years ago

10.1371/journal.pgen.1008515

Dynamic and regulated TAF gene expression during mouse embryonic germ cell development
Cited by: 15
Author(s): Megan A. Gura, Maria M. Mikedis, Kimberly A. Seymour, Dirk G. de Rooij, David C. Page, Richard N. Freiman
Software Mentions: 8
Published: over 6 years ago

10.7554/eLife.62208

A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen
Cited by: 30
Author(s): David E. Cook, Holger Kramer, David E Torres, Michael Seidl, Bart P.H.J. Thomma
Software Mentions: 8
Published: almost 6 years ago

10.1186/s40168-021-01078-x

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
Cited by: 85
Author(s): Fei Xie, Wei Jin, Huazhe Si, Yuan Yuan, Ye Tao, Junhua Liu, Xiaoxu Wang, Chengjian Yang, Qiushuang Li, Xiu-Tian Yan, Limei Lin, Qian Jiang, Lei Zhang, Chang Guo, Chris Greening, Rasmus Heller, Le Luo Guan, Phillip B. Pope, Zhiliang Tan, Weiyun Zhu, Min Wang, Qiang Qiu, Zhipeng Li, Shengyong Mao
Software Mentions: 8
Published: over 5 years ago

10.3389/fpls.2018.01632

Integrated QTL and eQTL Mapping Provides Insights and Candidate Genes for Fatty Acid Composition, Flowering Time, and Growth Traits in a F2 Population of a Novel Synthetic Allopolyploid Brassica napus
Cited by: 22
Author(s): Ruijuan Li, Kwangju Jeong, John Davis, Seungmo Kim, Soonbong Lee, Richard W. Michelmore, Shinje Kim, Julin Maloof
Software Mentions: 8
Published: almost 8 years ago

10.3390/ijms22168742

Inhibition of WHSC1 Allows for Reprogramming of the Immune Compartment in Prostate Cancer
Cited by: 5
Author(s): Muzamil Y. Want, Ellen Karasik, Bryan M. Gillard, AJ Robert McGray, Sebastiano Battaglia
Software Mentions: 8
Published: about 5 years ago

10.3390/ijms22158285

Maize DNA Methylation in Response to Drought Stress Is Involved in Target Gene Expression and Alternative Splicing
Cited by: 14
Author(s): Qi Wang, Jie Xu, Xuemei Pu, Haozhe Lv, Yanjun Liu, Huihui Ma, Fengkai Wu, Qingjun Wang, Xin Feng, Tianhong Liu, Qinghua Tang, Yanli Lu
Software Mentions: 8
Published: about 5 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 6 years ago

10.1186/s13058-019-1123-2

Separation of breast cancer and organ microenvironment transcriptomes in metastases
Cited by: 33
Author(s): Mohammad A. Alzubi, Tia H. Turner, Amy L. Olex, Sahib S. Sohal, Nicholas P. Tobin, Susana Garcia Recio, Jonas Bergh, Thomas Hatschek, Joel S. Parker, Carol A. Sartorius, Charles M. Perou, Mikhail G. Dozmorov, J. Chuck Harrell
Software Mentions: 8
Published: over 7 years ago

10.3389/fmicb.2021.654108

Gut Microbiota of Drosophila subobscura Contributes to Its Heat Tolerance and Is Sensitive to Transient Thermal Stress
Cited by: 22
Author(s): Angélica Jaramillo, Luis E. Castañeda
Software Mentions: 8
Published: over 5 years ago

10.1186/s40168-016-0208-8

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies
Cited by: 124
Author(s): Jonathan Thorsen, Asker Brejnrod, Martin Steen Mortensen, Morten Arendt Rasmussen, Jakob Stokholm, Waleed Abu Al‐Soud, Søren J. Sørensen, Hans Bisgaard, Johannes Waage
Software Mentions: 8
Published: almost 10 years ago

Projects: bioconductor: DESeq2

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Science Score: 100/100

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Papers Mentioning DESeq2 9,583