bioconductor: Biobase | Projects | Ecosyste.ms: Papers

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

10.1186/1471-2156-15-81

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
Cited by: 16
Author(s): Robert B. Scharpf, Lynn Mireles, Qiong Yang, Anna Köttgen, Ingo Ruczinski, Katalin Suszták, Eitan Halper-Stromberg, Adrienne Tin, Stephen Cristiano, Aravinda Chakravarti, Eric Boerwinkle, Caroline S. Fox, Josef Coresh, W. H. Linda Kao
Software Mentions: 56
Published: almost 11 years ago

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: almost 16 years ago

10.12688/f1000research.9973.2

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Cited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: over 6 years ago

10.3389/fonc.2020.617890

Comparative Proteome Identifies Complement Component 3-Mediated Immune Response as Key Difference of Colon Adenocarcinoma and Rectal Adenocarcinoma
Cited by: 9
Author(s): Jun-Ze Liang, Xiaoling Liang, Liye Zhong, Chutian Wu, Jing Zhang, Yang Wang
Software Mentions: 30
Published: over 3 years ago

10.1186/1751-0473-8-1

MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data
Cited by: 11
Author(s): Guy Brock, Partha Mukhopadhyay, Vasyl Pihur, Cynthia L. Webb, Robert M. Greene, M. Michele Pisano
Software Mentions: 24
Published: almost 12 years ago

10.1371/journal.pcbi.1007792

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
Cited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Software Mentions: 23
Published: over 4 years ago

10.3389/fimmu.2021.701085

A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients
Cited by: 29
Author(s): Florian Bieberich, Rodrigo Vazquez-Lombardi, Alexander Yermanos, Roy Ehling, Derek M Mason, Bastian Wagner, Edo Kapetanovic, Raphaël Brisset Di Roberto, Cédric R. Weber, Miodrag Savic, Fabian Rudolf, Sai T. Reddy
Software Mentions: 23
Published: over 3 years ago

10.1186/s12864-017-4353-7

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism
Cited by: 72
Author(s): Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J. Araúzo-Bravo
Software Mentions: 21
Published: almost 7 years ago

10.1016/j.xcrm.2020.100096

Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV Infection
Cited by: 11
Author(s): Sean M. Hughes, Claire Levy, Fernanda Calienes, Joanne D. Stekler, Urvashi Pandey, Lucia Vojtech, Alicia R. Berard, Kenzie Birse, Laura Noël‐Romas, Brian Richardson, Jackelyn B. Golden, Michael Cartwright, Ann C. Collier, Claire E. Stevens, Marcel E. Curlin, Timothy H. Holtz, Nelly Mugo, Elizabeth Irungu, Elly Katabira, Timothy Muwonge, Javier R. Lama, Jared M. Baeten, Adam Burgener, Jairam R. Lingappa, M. Juliana McElrath, Romel D. Mackelprang, Ian McGowan, Ross D. Cranston, Mark J. Cameron, Florian Hladik
Software Mentions: 21
Published: about 4 years ago

10.1016/j.patter.2021.100322

The role of metadata in reproducible computational research
Cited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: about 3 years ago

10.1002/1878-0261.12960

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago

10.1186/s12864-021-07370-2

GCSscore: an R package for differential gene expression analysis in Affymetrix/Thermo-Fisher whole transcriptome microarrays
Cited by: 3
Author(s): Guy M. Harris, Shahroze Abbas, Michael F. Miles
Software Mentions: 17
Published: almost 4 years ago

10.1186/s12859-015-0719-5

mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics
Cited by: 3
Author(s): Αλέξανδρος Σακελλαρίου, George M. Spyrou
Software Mentions: 15
Published: about 9 years ago

10.1371/journal.pone.0183417

Association of gene expression with biomass content and composition in sugarcane
Cited by: 23
Author(s): Nam V. Hoang, Agnelo Furtado, Angela O'Keeffe, Frederik C. Botha, Robert J. Henry
Software Mentions: 15
Published: about 7 years ago

10.3390/cancers13174348

Histological Grade of Endometrioid Endometrial Cancer and Relapse Risk Can Be Predicted with Machine Learning from Gene Expression Data
Cited by: 4
Author(s): Péter Gargya, Bálint László Bálint
Software Mentions: 14
Published: about 3 years ago

10.1093/bioinformatics/btw777

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
Cited by: 1,059
Author(s): Davis J. McCarthy, Kieran R Campbell, Aaron T. L. Lun, Quin F. Wills
Software Mentions: 14
Published: almost 8 years ago

10.1186/s12859-016-1455-1

MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration
Cited by: 20
Author(s): Carles Hernández-Ferrer, Carlos Ruiz‐Arenas, Alba Beltran-Gomila, Juan R. González
Software Mentions: 14
Published: almost 8 years ago

10.3390/cancers11010091

The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis
Cited by: 5
Author(s): Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu, Liping Qu
Software Mentions: 13
Published: almost 6 years ago

10.1038/s41598-021-82043-4

PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
Cited by: 10
Author(s): Pablo Acera Mateos, Renzo F. Balboa, Simon Easteal, Eduardo Eyras, Hardip R. Patel
Software Mentions: 11
Published: almost 4 years ago

10.1186/1471-2105-15-S1-S11

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again
Cited by: 19
Author(s): Alejandra N. González-Beltrán, Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 11
Published: almost 11 years ago

10.3389/fgene.2020.586602

Multi-Approach Bioinformatics Analysis of Curated Omics Data Provides a Gene Expression Panorama for Multiple Cancer Types
Cited by: 13
Author(s): Bruno César Feltes, Joice de Faria Poloni, Itamar José Guimarães Nunes, Sara Socorro Faria, Márcio Dorn
Software Mentions: 10
Published: almost 4 years ago

10.1186/s12918-015-0169-8

Increased robustness of early embryogenesis through collective decision-making by key transcription factors
Cited by: 8
Author(s): Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi
Software Mentions: 10
Published: over 9 years ago

10.1186/1751-0473-5-3

MADAM - An open source meta-analysis toolbox for R and Bioconductor
Cited by: 20
Author(s): Karl G. Kugler, Laurin A. J. Mueller, Armin Graber
Software Mentions: 10
Published: over 14 years ago

10.1186/s12859-017-1847-x

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Cited by: 42
Author(s): Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes‐Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
Software Mentions: 10
Published: about 7 years ago

10.1371/journal.pone.0041762

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.
Cited by: 7
Author(s): Matthew P Davis, Cei Abreu‐Goodger, Stijn van Dongen, Dong Lu, P. Täte, Nenad Bartoniček, Claudia Kutter, Pentao Liu, William C. Skarnes, Anton J. Enright, Ian Dunham
Software Mentions: 10
Published: almost 13 years ago

10.1186/gb-2004-5-10-r80

Cited by: 10,848
Author(s): Robert Gentleman, Vincent J. Carey, Douglas M. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Maria Iacus, Rafael A. Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony Rossini, Günther Sawitzki, Colin A. Smith, Gordon K. Smyth, Luke Tierney, Jean Yee Hwa Yang, Jianhua Zhang
Software Mentions: 10
Published: almost 21 years ago

10.3389/fimmu.2021.709173

The Role of Hemoglobin Subunit Delta in the Immunopathy of Multiple Sclerosis: Mitochondria Matters
Cited by: 6
Author(s): Afshin Derakhshani, Hossein Safarpour, Behzad Baradaran, Nima Hemmat, Patrizia Leone, Zahra Asadzadeh, Mehrdad Pashazadeh, Behzad Baradaran, Vito Racanelli
Software Mentions: 9
Published: about 3 years ago

10.1038/s41598-019-56829-6

Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues
Cited by: 18
Author(s): Mustafa Sibai, Cüneyd Parlayan, Pelin Tuğlu, Gürkan Öztürk, Turan Demircan
Software Mentions: 9
Published: almost 5 years ago

10.15252/msb.20177862

Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases
Cited by: 53
Author(s): Daniela Michlmayr, Theodore R. Pak, Adeeb Rahman, El ad David Amir, Eun Young Kim, Seunghee Kim‐Schulze, Maria Suprun, Michael G. Stewart, Guajira P. Thomas, Ángel Balmaseda, Li Wang, Jun Zhu, Mayte Suárez‐Fariñas, Steven M. Wolinsky, Andrew Kasarskis, Eva Harris
Software Mentions: 9
Published: over 6 years ago

10.1186/1471-2105-8-221

Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
Cited by: 156
Author(s): Joern Toedling, Oleg Sklyar, Wolfgang Huber
Software Mentions: 9
Published: over 17 years ago

10.3389/fendo.2020.554922

Chenodeoxycholic Acid Modulates Bile Acid Synthesis Independent of Fibroblast Growth Factor 19 in Primary Human Hepatocytes
Cited by: 6
Author(s): H Johansson, Jonas Nørskov Søndergaard, Carl Jorns, Claudia Kutter, Ewa Ellis
Software Mentions: 9
Published: over 3 years ago

10.3390/cancers11101606

A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning
Cited by: 12
Author(s): Johannes A Vey, Lorenz A. Kapsner, Maximilian Fuchs, Philipp Unberath, Giulia Veronesi, Meik Kunz
Software Mentions: 8
Published: about 5 years ago

10.1016/j.ebiom.2021.103444

A diagnostic miRNA signature for pulmonary arterial hypertension using a consensus machine learning approach
Cited by: 24
Author(s): Niamh Errington, James Iremonger, Josephine Pickworth, Sokratis Kariotis, Christopher J. Rhodes, Alexander Rothman, Robin Condliffe, Charles Elliot, David G. Kiely, Luke Howard, John Wharton, A. A. Roger Thompson, Nicholas W. Morrell, Martin R. Wilkins, Dennis Wang, Allan Lawrie
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-016-1007-8

readat: An R package for reading and working with SomaLogic ADAT files
Cited by: 11
Author(s): Richard Cotton, Johannes Graumann
Software Mentions: 8
Published: over 8 years ago

10.3390/ijerph18115564

Identification of Hub Genes in Different Stages of Colorectal Cancer through an Integrated Bioinformatics Approach
Cited by: 2
Author(s): Abhijeet R. Patil, Ming-Ying Leung, Sourav Roy
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0127163

Genetic Deletion of the Transcriptional Repressor NFIL3 Enhances Axon Growth In Vitro but Not Axonal Repair In Vivo
Cited by: 2
Author(s): L.R. van der Kallen, Ruben Eggers, Erich Ehlert, Joost Verhaagen, August B. Smit, Ronald E. van Kesteren
Software Mentions: 8
Published: over 9 years ago

10.1186/s12915-017-0379-1

Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors
Cited by: 55
Author(s): Édouard Evangelisti, Anna Gogleva, Thomas Hainaux, Mehdi Doumane, Frej Tulin, Clément Quan, T. S. Yunusov, Kévin Floch, Sebastián Schornack
Software Mentions: 8
Published: over 7 years ago

10.1186/s12864-016-3260-7

DeSigN: connecting gene expression with therapeutics for drug repurposing and development
Cited by: 52
Author(s): Bernard Kok Bang Lee, Kai Hung Tiong, Jit Kang Chang, Chee Sun Liew, Zainal Ariff Abdul Rahman, Aik Choon Tan, Tsung Fei Khang, Sok Ching Cheong
Software Mentions: 7
Published: almost 8 years ago

10.1371/journal.pcbi.1004575

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
Cited by: 292
Author(s): Minzhe Guo, Hui Wang, S. Steven Potter, Jeffrey A. Whitsett, Yan Xu
Software Mentions: 7
Published: almost 9 years ago

10.1016/j.diabres.2019.01.008

Differential methylation of the type 2 diabetes susceptibility locus KCNQ1 is associated with insulin sensitivity and is predicted by CpG site specific genetic variation
Cited by: 14
Author(s): Ushma Jaykamal Shah, Wenting Xie, Allan Flyvbjerg, John J. Nolan, Kurt Højlund, Mark Walker, Caroline L Relton, Hannah R Elliott
Software Mentions: 7
Published: almost 6 years ago

10.3390/cells10092215

Autophagy-Associated IL-15 Production Is Involved in the Pathogenesis of Leprosy Type 1 Reaction
Cited by: 0
Author(s): Bruno Jorge de Andrade Silva, Tamiris Lameira Bittencourt, Thyago Leal-Calvo, Mayara Abud Mendes, Rhana Berto da Silva Prata, Mayara Garcia de Mattos Barbosa, Priscila Ribeiro Andrade, Suzana Côrte-Real, Gilberto Marcelo Sperandio da Silva, Milton Ozório Moraes, Euzenir Nunes Sarno, Roberta Olmo Pinheiro
Software Mentions: 7
Published: about 3 years ago

10.3389/fmicb.2020.00390

Response of Tomato Rhizosphere Bacteria to Root-Knot Nematodes, Fenamiphos and Sampling Time Shows Differential Effects on Low Level Taxa
Cited by: 3
Author(s): Mariantonietta Colagiero, Laura Cristina Rosso, Domenico Catalano, Leonardo Schena, Aurelio Ciancio
Software Mentions: 6
Published: over 4 years ago

10.1128/mBio.02495-18

The Transcriptional Cycle Is Suited to Daytime N 2 Fixation in the Unicellular Cyanobacterium “ Candidatus Atelocyanobacterium thalassa” (UCYN-A)
Cited by: 28
Author(s): María del Carmen Muñoz-Marín, Irina N. Shilova, Tianshu Shi, Hanna Farnelid, Ana María Cabello, Jonathan P. Zehr
Software Mentions: 6
Published: over 5 years ago

10.3390/biomedicines8110455

An Exploratory Pilot Study with Plasma Protein Signatures Associated with Response of Patients with Depression to Antidepressant Treatment for 10 Weeks
Cited by: 9
Author(s): Eun Young Kim, Hee‐Sung Ahn, Min Young Lee, Jeesuk Yu, Jeonghun Yeom, Hee Jong Jeong, Hophil Min, Hyun Jeong Lee, Kyunggon Kim, Yong Min Ahn
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pgen.1004994

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling
Cited by: 147
Author(s): Kristofer Davie, Jelle Jacobs, Mardelle Atkins, Delphine Potier, Valerie Christiaens, Georg Halder, Stein Aerts
Software Mentions: 6
Published: over 9 years ago

10.1038/srep26136

SOX7 co-regulates Wnt/β-catenin signaling with Axin-2: both expressed at low levels in breast cancer
Cited by: 25
Author(s): Huidi Liu, Emilio Mastriani, Zi-Qiao Yan, Shuai Yin, Zheng Zeng, Hong Wang, Qinghai Li, Hongyu Liu, Xiaoyu Wang, Hongchu Bao, Yujie Zhou, Junjie Kou, Dongsheng Li, Ting Li, Jianrui Liu, Yongfang Liu, Lin Yin, Li Qiu, Liling Gong, Shulin Liu
Software Mentions: 6
Published: over 8 years ago

10.1186/1471-2164-14-850

Midgut transcriptome profiling of Anoplophora glabripennis, a lignocellulose degrading cerambycid beetle
Cited by: 62
Author(s): Erin D. Scully, Kelli Hoover, John E. Carlson, Ming Tien, Scott M. Geib
Software Mentions: 5
Published: almost 11 years ago

10.1186/1471-2164-11-723

Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications
Cited by: 66
Author(s): José M. Otero, Wanwipa Vongsangnak, Mohammad Ali Asadollahi, Roberto Olivares-Hernandes, Jérôme Maury, Laurent Farinelli, Loïc Barlocher, Magne Østerås, Michel Schalk, Anthony Clark, Jens Nielsen
Software Mentions: 5
Published: almost 14 years ago

10.1186/s12967-015-0453-9

GLI2 inhibition abrogates human leukemia stem cell dormancy
Cited by: 81
Author(s): Anil Sadarangani, Gabriel Pineda, Kathleen M. Lennon, Hye Jung Chun, Alice Shih, Annelie Schairer, Angela C. Court, Daniel Goff, Sacha Prashad, Ifat Geron, Russell Wall, John Douglas Mcpherson, Richard A. Moore, Minya Pu, Lei Bao, Amy Jackson-Fisher, Michael J. Munchhof, Todd VanArsdale, Tannishtha Reya, Sheldon R. Morris, Mark D. Minden, Karen Messer, Hanna Mikkola, Marco A. Marra, Thomas J. Hudson, Catriona Jamieson
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2105-13-80

Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses
Cited by: 15
Author(s): Wessel N. van Wieringen, Kristian Unger, Gwenaël G. R. Leday, Oscar Krijgsman, Renée X. de Menezes, Bauke Ylstra, Mark A. van de Wiel
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0140885

Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease
Cited by: 18
Author(s): Lela Lackey, Evonne McArthur, Alain Laederach
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0054144

Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory
Cited by: 139
Author(s): José M. Otero, Donatella Cimini, Kiran Raosaheb Patil, Simon Guldberg Poulsen, Lisbeth Olsson, Jens Nielsen
Software Mentions: 4
Published: almost 12 years ago

10.12688/f1000research.9893.2

exprso: an R-package for the rapid implementation of machine learning algorithms
Cited by: 12
Author(s): Thomas P. Quinn, Daniel S. Tylee, Stephen J. Glatt
Software Mentions: 4
Published: almost 7 years ago

10.1186/s40709-020-00118-1

Genome wide meta-analysis of cDNA datasets reveals new target gene signatures of colorectal cancer based on systems biology approach
Cited by: 11
Author(s): Umair Ilyas, Shahiq uz Zaman, Reem Altaf, Humaira Nadeem, Syed Aun Muhammad
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-017-01765-6

Detecting the Molecular System Signatures of Idiopathic Pulmonary Fibrosis through Integrated Genomic Analysis
Cited by: 20
Author(s): Indu Gangwar, Nitesh Kumar Sharma, Ganesh Panzade, Supriya Awasthi, Anurag Agrawal, Ravi Shankar
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-49446-w

De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya
Cited by: 19
Author(s): Nisha Dhiman, Nitesh Kumar Sharma, Pooja Thapa, Isha Sharma, Mohit Kumar Swarnkar, Amit Chawla, Ravi Shankar, Amita Bhattacharya
Software Mentions: 4
Published: about 5 years ago

10.1128/mBio.01157-20

Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection
Cited by: 2
Author(s): Emily Speranza, Ignacio Caballero, Anna N. Honko, Joshua C. Johnson, J. Kyle Bohannon, Lisa Evans DeWald, Dawn M. Gerhardt, Jennifer Sword, Lisa E. Hensley, Richard S. Bennett, John H. Connor
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.46418

Self-sperm induce resistance to the detrimental effects of sexual encounters with males in hermaphroditic nematodes
Cited by: 20
Author(s): Lauren N. Booth, Travis J. Maures, Robin Yeo, Cindy Tantilert, Anne Brunet
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-12-382

Mulcom: a multiple comparison statistical test for microarray data in Bioconductor
Cited by: 5
Author(s): Claudio Isella, Tommaso Renzulli, Davide Corà, Enzo Medico
Software Mentions: 3
Published: about 13 years ago

10.3389/fphar.2018.00583

DeCoST: A New Approach in Drug Repurposing From Control System Theory
Cited by: 15
Author(s): Thanh Nguyen, Syed Aun Muhammad, Sara Ibrahim, Lin Ma, Jinchao Guo, Baogang Bai, Bixin Zeng
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-03133-w

PCDH18 is frequently inactivated by promoter methylation in colorectal cancer
Cited by: 15
Author(s): Dan Zhou, Weiwei Tang, Guoqiang Su, Mingquan Cai, Han‐Xiang An, Yun Zhang
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms22094353

Effects of Whole-Body Adenylyl Cyclase 5 (Adcy5) Deficiency on Systemic Insulin Sensitivity and Adipose Tissue
Cited by: 5
Author(s): Sebastian Dommel, Anne Hoffmann, C Berger, Matthias Kern, Nora Klöting, Aimo Kannt, Matthias Blüher
Software Mentions: 3
Published: over 3 years ago

10.1186/1749-8546-7-19

Effects of alpha-mangostin on the expression of anti-inflammatory genes in U937 cells
Cited by: 39
Author(s): Szu-Hsiu Liu, Lain-Tze Lee, Nai-Yun Hu, Kuo-Kuei Huange, Ying-Chu Shih, Munekazu Iinuma, Jen-Ming Li, Ting-Yu Chou, Wei‐Hsin Wang, Ting-Shou Chen
Software Mentions: 3
Published: about 12 years ago

10.1186/s40709-019-0094-x

A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in alopecia
Cited by: 10
Author(s): Syed Aun Muhammad, Nighat Fatima, Rehan Zafar Paracha, Amjad Ali, Jake Y. Chen
Software Mentions: 3
Published: over 5 years ago

10.1080/21623945.2021.1910154

Cleavage of the vaspin N-terminus releases cell-penetrating peptides that affect early stages of adipogenesis and inhibit lipolysis in mature adipocytes
Cited by: 4
Author(s): Catherine A Tindall, Estelle Erkner, Jan Stichel, Annette G. Beck‐Sickinger, Anne Hoffmann, Juliane Weiner, John T. Heiker
Software Mentions: 3
Published: almost 4 years ago

10.1186/s40709-021-00136-7

Genome-scale meta-analysis of breast cancer datasets identifies promising targets for drug development
Cited by: 5
Author(s): Reem Altaf, Humaira Nadeem, Mustafeez Mujtaba Babar, Umair Ilyas, Syed Aun Muhammad
Software Mentions: 3
Published: over 3 years ago

10.1186/2043-9113-2-22

mCOPA: analysis of heterogeneous features in cancer expression data
Cited by: 18
Author(s): Chenwei Wang, Alperen Taciroglu, Stefan Maetschke, Colleen C. Nelson, Mark A. Ragan, Melissa J. Davis
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0017118

Distinct Early Molecular Responses to Mutations Causing vLINCL and JNCL Presage ATP Synthase Subunit C Accumulation in Cerebellar Cells
Cited by: 52
Author(s): Yi Cao, John F. Staropoli, Sunita Biswas, Janice A. Espinola, Marcy E. MacDonald, Jongmin Lee, Susan L. Cotman
Software Mentions: 3
Published: over 13 years ago

10.1038/s41598-020-60064-9

Subcellular Compartmentalization of Survivin is Associated with Biological Aggressiveness and Prognosis in Prostate Cancer
Cited by: 15
Author(s): Jan K. Hennigs, Sarah Minner, Pierre Tennstedt, R. Löser, Hartwig Huland, Hans Klose, Markus Graefen, Thorsten Schlomm, Guido Sauter, Carsten Bokemeyer, Friedemann Honecker
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-40762-9

Meta-analysis suggests evidence of novel stress-related pathway components in Orsay virus - Caenorhabditis elegans viral model
Cited by: 3
Author(s): Prachi Mishra, Jessica Ngo, Jahanshah Ashkani, Frédéric Pio
Software Mentions: 3
Published: over 5 years ago

10.1002/cpps.114

Histone Purification Combined with High‐Resolution Mass Spectrometry to Examine Histone Post‐Translational Modifications and Histone Variants in Caenorhabditis elegans
Cited by: 2
Author(s): Lluís Millán-Ariño, Zuo‐Fei Yuan, Marlies E. Oomen, Simone Brandenburg, Alexey Chernobrovkin, Jérôme Salignon, Lioba Körner, Roman A. Zubarev, Benjamin A. Garcia, Christian G. Riedel
Software Mentions: 3
Published: about 4 years ago

10.31557/APJCP.2019.20.11.3399

Repurposing Drugs by In Silico Methods to Target BCR Kinase Domain in Chronic Myeloid Leukemia
Cited by: 1
Author(s): Aparna Natarajan, Thangarajan Rajkumar, K.S. Sabitha
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2018.01757

PARP1 Is Up-Regulated in Non-small Cell Lung Cancer Tissues in the Presence of the Cyanobacterial Toxin Microcystin
Cited by: 63
Author(s): Patrick L. Apopa, Lisa Alley, Rosalind B. Penney, Konstantinos Arnaoutakis, Matthew A. Steliga, Susan Jeffus, Emine Bircan, Banu Gopalan, Jing Jin, Preecha Patumcharoenpol, Piroon Jenjaroenpun, Thidathip Wongsurawat, Nishi Shah, Gunnar Boysen, David W. Ussery, Intawat Nookaew, Pebbles Fagan, Gürkan Bebek, Mohammed S. Orloff
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0081123

ZODET: Software for the Identification, Analysis and Visualisation of Outlier Genes in Microarray Expression Data
Cited by: 5
Author(s): Daniel Roden, Gavin W. Sewell, Anna Lobley, Adam P. Levine, Andrew Smith, Anthony W. Segal
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0167944

Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
Cited by: 11
Author(s): Annereinou Dijkstra, Wynand Alkema, Marjo Starrenburg, Jeroen Hugenholtz, Sacha A. F. T. van Hijum, Peter A. Bron
Software Mentions: 2
Published: almost 8 years ago

10.12688/f1000research.14451.3

Predicting lithium treatment response in bipolar patients using gender-specific gene expression biomarkers and machine learning
Cited by: 13
Author(s): Andy R. Eugene, Jolanta Masiak, Beata Eugene
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1000951

Characterization of Oxidative Guanine Damage and Repair in Mammalian Telomeres
Cited by: 157
Author(s): Zhilong Wang, David B. Rhee, Jian Lü, Christina T. Bohr, Fang Zhou, Haritha Vallabhaneni, Nadja C. de Souza-Pinto, Yie Liu
Software Mentions: 2
Published: over 14 years ago

10.3389/fgene.2021.646297

Omics Multi-Layers Networks Provide Novel Mechanistic and Functional Insights Into Fat Storage and Lipid Metabolism in Poultry
Cited by: 8
Author(s): Farzad Ghafouri, Abolfazl Bahrami, Mostafa Sadeghi, S. R. Miraei-Ashtiani, Maryam Bakherad, Herman W. Barkema, Samantha Larose
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.10280

The long non-coding RNA GHSROS reprograms prostate cancer cell lines toward a more aggressive phenotype
Cited by: 4
Author(s): Patrick B. Thomas, Penny L. Jeffery, Manuel D. Gahete, Eliza Whiteside, Carina Walpole, Michelle Maugham, Lidija Jovanovic, Jennifer H. Gunter, Elizabeth D. Williams, Colleen C. Nelson, Adrian C. Herington, Raúl M Luque, Rakesh N. Veedu, Lisa K. Chopin, Inge Seim
Software Mentions: 2
Published: almost 4 years ago

10.1186/1476-4598-5-55

Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
Cited by: 182
Author(s): Adam Ertel, Arun Verghese, Stephen W. Byers, Michael F. Ochs, Aydın Tözeren
Software Mentions: 2
Published: about 18 years ago

10.1186/1471-2229-12-100

Reprogramming of gene expression during compression wood formation in pine: Coordinated modulation of S-adenosylmethionine, lignin and lignan related genes
Cited by: 56
Author(s): David P. Villalobos, Sara M. Díaz-Moreno, El-Sayed S Said, Rafael A. Cañas, Daniel Osuna, Sonia H E Van Kerckhoven, Rocío Bautista, M. Gonzalo Claros, Francisco M. Cánovas, Francisco R. Cantón
Software Mentions: 2
Published: over 12 years ago

10.1186/s41065-020-00119-z

Identification of differentially expressed miRNAs in differentiating benign from malignant pleural effusion
Cited by: 7
Author(s): Qiyu Bao, Yaping Xu, Ming Ding, Ping Chen
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-11-519

Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated
Cited by: 99
Author(s): Mun-Kit Choy, Mehregan Movassagh, Hock Guan Goh, Martin R. Bennett, Thomas A. Down, Roger Foo
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-12-330

MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters
Cited by: 23
Author(s): Bas Jansen, Iziah E. Sama, Dagmar Eleveld-Trancikova, Maaike A. van Hout-Kuijer, Joop H. Jansen, Martijn A. Huynen, Gosse J. Adema
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-11-151

Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements
Cited by: 29
Author(s): Danilo Licastro, Vincenzo A. Gennarino, Francesca Petrera, Remo Sanges, Sandro Banfi, Elia Stupka
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2407-5-95

Folate system correlations in DNA microarray data
Cited by: 8
Author(s): Tomas Radivoyevitch
Software Mentions: 2
Published: over 19 years ago

10.18632/oncotarget.20076

mRNA expression profiles obtained from microdissected pancreatic cancer cells can predict patient survival
Cited by: 4
Author(s): Ana-Bárbara García-García, M. Carmen Gómez-Mateo, Rebeca Hilario, Pilar Rentero-Garrido, Álvaro Martínez‐Doménech, Verónica González-Albert, Andrés Cervantes, Pablo Marín-García, Felipe Javier Chaves, Antonio Ferrández‐Izquierdo, Luís Sabater
Software Mentions: 2
Published: over 7 years ago

10.1093/aob/mcab074

Increased seminal root number associated with domestication improves nitrogen and phosphorus acquisition in maize seedlings
Cited by: 16
Author(s): Alden Perkins, Jonathan P. Lynch
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0026465

Identification of Hypoxia-Induced Genes in Human SGBS Adipocytes by Microarray Analysis
Cited by: 50
Author(s): Kathrin Geiger, Andreas Leiherer, Axel Muendlein, Nicole M. Stark, Simone Geller-Rhomberg, Christoph H. Saely, Martin Wabitsch, Peter Fraunberger
Software Mentions: 2
Published: about 13 years ago

10.3390/cancers11101598

Diagnostic and Prognostic Value of B4GALT1 Hypermethylation and Its Clinical Significance as a Novel Circulating Cell-Free DNA Biomarker in Colorectal Cancer
Cited by: 25
Author(s): Francesco Picardo, Antonella Romanelli, Laura Muinelo‐Romay, Tommaso Mazza, Caterina Fusilli, Paola Parrella, Jorge Barbazán, Rafael López‐López, Raffaela Barbano, Mariangela De Robertis, Chiara Taffon, Veronica Bordoni, Chiara Agrati, Manuela Costantini, Francesca Ricci, Paolo Graziano, Evaristo Maiello, Lucia Anna Muscarella, Vito Michele Fazio, Maria Luana Poeta
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1003203

Positional Cloning Reveals Strain-Dependent Expression of Trim16 to Alter Susceptibility to Bleomycin-Induced Pulmonary Fibrosis in Mice
Cited by: 12
Author(s): Anguel N. Stefanov, Jessica K. Fox, François Depault, Christina K. Haston
Software Mentions: 1
Published: almost 12 years ago

10.7554/eLife.08638

Hypocretin neuron-specific transcriptome profiling identifies the sleep modulator Kcnh4a
Cited by: 53
Author(s): Laura Yelin-Bekerman, Idan Elbaz, Alex Diber, Dvir Dahary, Liron Gibbs-Bar, Shahar Alon, Tali Lerer-Goldshtein, Lior Appelbaum
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1003513

Integrated Transcriptomic and Epigenomic Analysis of Primary Human Lung Epithelial Cell Differentiation
Cited by: 48
Author(s): Crystal N. Marconett, Baosen Zhou, Megan E. Rieger, Suhaida A. Selamat, Mickael Dubourd, Xiaohui Fang, Sean K. Lynch, Theresa Ryan Stueve, Kimberly D. Siegmund, Benjamin P. Berman, Zea Borok, Ite A. Laird-Offringa
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0103851

SNP@lincTFBS: An Integrated Database of Polymorphisms in Human LincRNA Transcription Factor Binding Sites
Cited by: 15
Author(s): Shangwei Ning, Zhenqun Zhao, Jingrun Ye, Peng Wang, Hui Zhi, Ronghong Li, Tingting Wang, Jianjian Wang, Lihua Wang, Xia Li
Software Mentions: 1
Published: over 10 years ago

10.2196/12227

Use of a Biofeedback Breathing App to Augment Poststress Physiological Recovery: Randomized Pilot Study
Cited by: 9
Author(s): David Plans, Davide Morelli, Stefan Sütterlin, Lucie Ollis, Georgia Derbyshire, Mark Cropley
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2199-10-68

Expression of HNF4alpha in the human and rat choroid plexus – Implications for drug transport across the blood-cerebrospinal-fluid (CSF) barrier
Cited by: 25
Author(s): Monika Niehof, Jürgen Borlak
Software Mentions: 1
Published: almost 16 years ago

10.3390/genes9060295

C/EBPβ Promotes STAT3 Expression and Affects Cell Apoptosis and Proliferation in Porcine Ovarian Granulosa Cells
Cited by: 8
Author(s): Xiaolong Yuan, Xiaofeng Zhou, Yingting He, Yuyi Zhong, Ailing Zhang, Zhe Zhang, Hao Zhang, Jiaqi Li
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pbio.1001280

Combinatorial Activation and Repression by Seven Transcription Factors Specify Drosophila Odorant Receptor Expression
Cited by: 77
Author(s): Shadi Jafari, Liza Alkhori, Alexander Schleiffer, Anna Brochtrup, Thomas Hummel, Mattias Alenius
Software Mentions: 1
Published: over 12 years ago

10.18632/oncotarget.10234

CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter
Cited by: 242
Author(s): Samrat Roy Choudhury, Yi Cui, Katarzyna Lubecka, Barbara Stefańska, Joseph Irudayaraj
Software Mentions: 1
Published: over 8 years ago

Projects: bioconductor: Biobase

Papers Mentioning Biobase 104