cran: COMBAT | Projects | Ecosyste.ms: Papers

10.1084/jem.20210915

Blood transcriptomics reveal the evolution and resolution of the immune response in tuberculosis
Cited by: 27
Author(s): Olivier Tabone, Raman Verma, Akul Singhania, Probir Chakravarty, William J. Branchett, Christine M. Graham, Jo Lee, Trần Thị Huyền Trang, Frédéric Reynier, Philippe Leissner, Karine Kaiser, Marc Rodrigue, Gerrit Woltmann, Pranabashis Haldar, Anne O’Garra
Software Mentions: 27
Published: about 3 years ago

10.1186/s13059-016-0881-8

A survey of best practices for RNA-seq data analysis
Cited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: almost 9 years ago

10.1186/s12920-015-0114-0

Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma
Cited by: 12
Author(s): Vinay Randhawa, Vishal Acharya
Software Mentions: 17
Published: over 9 years ago

10.3390/biom10121606

A Customizable Analysis Flow in Integrative Multi-Omics
Cited by: 14
Author(s): Samuel M. Lancaster, Akshay Sanghi, Si Wu, M Snyder
Software Mentions: 15
Published: almost 4 years ago

10.3389/fgene.2016.00163

Single-Cell Transcriptomics Bioinformatics and Computational Challenges
Cited by: 101
Author(s): Olivier Poirion, Xun Zhu, Travers Ching, Lana X. Garmire
Software Mentions: 15
Published: about 8 years ago

10.7717/peerj.10255

Comprehensive genomic analysis of microenvironment phenotypes in ovarian cancer
Cited by: 4
Author(s): Jingshu Wang, Tingting Zhang, Lina Yang, Gong Yang
Software Mentions: 12
Published: almost 4 years ago

10.3389/fimmu.2018.03017

A Computational Approach Identifies Immunogenic Features of Prognosis in Human Cancers
Cited by: 8
Author(s): Malini Manoharan, Nitin Mandloi, Sushri Priyadarshini, Ashwini Patil, Rohit Gupta, Laxman Iyer, Ravi Gupta, Amitabha Chaudhuri
Software Mentions: 11
Published: almost 6 years ago

10.7717/peerj.10670

Digital Cell Sorter (DCS): a cell type identification, anomaly detection, and Hopfield landscapes toolkit for single-cell transcriptomics
Cited by: 8
Author(s): Sergii Domanskyi, Alex Hakansson, T. J. Bertus, Giovanni Paternostro, Carlo Piermarocchi
Software Mentions: 8
Published: almost 4 years ago

10.1038/s41598-020-78471-3

Cellular correlates of cortical thinning throughout the lifespan
Cited by: 68
Author(s): Didac Vidal‐Piñeiro, Nadine Parker, Jean Shin, Leon French, Håkon Grydeland, Andrea Parolin Jackowski, Athanasia M. Mowinckel, Yash Patel, Zdenka Pausová, Giovanni Abrahão Salum, Øystein Sørensen, Kristine B. Walhovd, Tomáš Paus, Anders M. Fjell, Alzheimer’s Disease Neuroimaging Initiative
Software Mentions: 7
Published: almost 4 years ago

10.3390/ijms22136726

Analysis of the Role of FRMD5 in the Biology of Papillary Thyroid Carcinoma
Cited by: 4
Author(s): Agata M. Gaweł, Maciej Ratajczak, Ewa Gajda, Małgorzata Grzanka, Agnieszka Paziewska, Marta Cieślicka, Maria Kulecka, Małgorzata Oczko-Wojciechowska, Marlena Godlewska
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.49874

Discovery proteomics in aging human skeletal muscle finds change in spliceosome, immunity, proteostasis and mitochondria
Cited by: 114
Author(s): Ceereena Ubaida‐Mohien, Alexey E. Lyashkov, Marta González-Freire, Ravi Tharakan, Michelle Shardell, Ruin Moaddel, Richard D. Semba, Chee W. Chia, Myriam Gorospe, Ranjan Sen, Luigi Ferrucci
Software Mentions: 7
Published: about 5 years ago

10.1186/1471-2105-15-69

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data
Cited by: 15
Author(s): Gan Zhang, Jianwu Wang, Nathan Salomonis, Jennifer Stowe, Gabriel G. Haddad, Andrew D. McCulloch, Ilkay Altıntaş, Alexander C. Zambon
Software Mentions: 7
Published: over 10 years ago

10.1093/gigascience/giaa117

Correcting for experiment-specific variability in expression compendia can remove underlying signals
Cited by: 16
Author(s): Alexandra Lee, YoSon Park, Georgia Doing, Deborah A. Hogan, Casey S. Greene
Software Mentions: 6
Published: about 4 years ago

10.1186/s12885-017-3103-1

Meta-analysis of gene expression in relapsed childhood B-acute lymphoblastic leukemia
Cited by: 21
Author(s): Yock-Ping Chow, Hamidah Alias, Rahman Jamal
Software Mentions: 5
Published: almost 8 years ago

10.18632/oncotarget.14107

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes
Cited by: 59
Author(s): Marta R. Hidalgo, Cankut Çubuk, Alicia Amadoz, Francisco Salavert, José Carbonell-Caballero, Joaquín Dopazo
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pcbi.1008819

Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer
Cited by: 3
Author(s): Héctor Climente-González, Christine Lonjou, Fabienne Lesueur, Dominique Stoppa‐Lyonnet, Nadine Andrieu, Chloé-Agathe Azencott
Software Mentions: 5
Published: over 3 years ago

10.1038/sdata.2018.142

A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research
Cited by: 306
Author(s): Philip L. De Jager, Yiyi Ma, Cristin McCabe, Jishu Xu, Badri N. Vardarajan, Daniel Felsky, Hans‐Ulrich Klein, Charles C. White, Mette A. Peters, Ben Lodgson, Parham Nejad, Ao Tang, Lara M. Mangravite, Lei Yu, Chris Gaiteri, Sara Mostafavi, Julie A. Schneider, David A. Bennett
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-019-48493-7

Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients
Cited by: 13
Author(s): Sunjay Jude Fernandes, Hiromasa Morikawa, Ewoud Ewing, Sabrina Ruhrmann, Rubin Narayan Joshi, Vincenzo Lagani, Nestoras Karathanasis, Mohsen Khademi, Núria Planell, Angelika Schmidt, Ioannis Tsamardinos, Tomas Olsson, Fredrik Piehl, Ingrid Kockum, Maja Jagodic, Jesper Tegnér, David Green
Software Mentions: 5
Published: over 5 years ago

10.3389/fbioe.2017.00084

Meta-Analysis of Aedes aegypti Expression Datasets: Comparing Virus Infection and Blood-Fed Transcriptomes to Identify Markers of Virus Presence
Cited by: 11
Author(s): Kiyoshi F. Fukutani, José Irahe Kasprzykowski, Alexandre Rossi Paschoal, Matheus de Souza Gomes, Aldina Barral, Camila I. de Oliveira, Pablo Ivan Pereira Ramos, Artur T. L. Queiroz
Software Mentions: 5
Published: almost 7 years ago

10.1107/S0907444910045749

Overview of theCCP4 suite and current developments
Cited by: 10,663
Author(s): Martyn Winn, Charles Ballard, Kevin Cowtan, E.J. Dodson, Paul Emsley, Phil Evans, Ronan Keegan, Eugene Krissinel, Andrew G. W. Leslie, Airlie J. McCoy, Stuart McNicholas, Garib N. Murshudov, Navraj S. Pannu, E. A. Potterton, Harold R. Powell, Randy J. Read, A.A. Vagin, K.S. Wilson
Software Mentions: 5
Published: over 13 years ago

10.7554/eLife.44161

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition
Cited by: 30
Author(s): Andrew L. Hong, Yuen-Yi Tseng, Jeremiah A. Wala, Won-Jun Kim, Bryan D. Kynnap, Mihir B. Doshi, Guillaume Kugener, Gabriel J. Sandoval, Thomas P. Howard, Ji Li, Xiaoping Yang, Michelle Tillgren, Mahmhoud Ghandi, Abeer Sayeed, Rebecca Deasy, Abigail Ward, Brian McSteen, Katherine Labella, Paula Keskula, Adam Tracy, Cora Connor, Catherine Clinton, Alanna J. Church, Brian D. Crompton, Katherine A. Janeway, Barbara Van Hare, David Sandak, Ole Gjoerup, Pratiti Bandopadhayay, Paul A. Clemons, Stuart L. Schreiber, David E. Root, Prafulla C. Gokhale, N. Susan, Elizabeth Mullen, Charles W.M. Roberts, Cigall Kadoch, Rameen Beroukhim, Keith L. Ligon, Jesse S. Boehm, William C. Hahn
Software Mentions: 5
Published: over 5 years ago

10.1186/s12920-019-0519-2

A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies
Cited by: 7
Author(s): Joshua Mannheimer, Dawn L. Duval, Ashok Prasad, Daniel L. Gustafson
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cell.2020.10.002

Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics
Cited by: 57
Author(s): Dylan Kotliar, Aaron E. Lin, James Logue, Travis Hughes, Nadine M. Khoury, Siddharth S. Raju, Marc H. Wadsworth, Han Chen, Jonathan R. Kurtz, Bonnie Dighero-Kemp, Zach B. Bjornson, Nilanjan Mukherjee, Brian Sellers, Nancy Tran, Matthew R. Bauer, Gordon Adams, Ricky Adams, John L. Rinn, Marta Melé, Stephen F. Schaffner, Garry P. Nolan, Kayla G. Barnes, Lisa E. Hensley, David R. McIlwain, Alex K. Shalek, Pardis C. Sabeti, Richard S. Bennett
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0110052

Visualization-Aided Classification Ensembles Discriminate Lung Adenocarcinoma and Squamous Cell Carcinoma Samples Using Their Gene Expression Profiles
Cited by: 15
Author(s): Ao Zhang, Chi Wang, Shiji Wang, Liang Li, Zhongmin Liu, Suyan Tian
Software Mentions: 4
Published: about 10 years ago

10.7554/eLife.39911

A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of aging yeast
Cited by: 55
Author(s): David G. Hendrickson, Ilya Soifer, Bernd J. Wranik, Griffin Kim, Michael Robles, Patrick A. Gibney, R. Scott McIsaac
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-019-5850-7

Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks
Cited by: 6
Author(s): Kevin B. Walters, Radmir Sarsenov, Wen Siong Too, Roseanna K. Hare, Ian C. Paterson, D Lambert, Stephen Brown, James R. Bradford
Software Mentions: 4
Published: over 5 years ago

10.1186/s12918-017-0412-6

Detection of statistically significant network changes in complex biological networks
Cited by: 27
Author(s): Raghvendra Mall, Luigi Cerulo, Halima Bensmail, Antonio Iavarone, Michele Ceccarelli
Software Mentions: 4
Published: over 7 years ago

10.1002/path.4886

Molecular classification of urothelial carcinoma: global mRNA classification versus tumour-cell phenotype classification
Cited by: 245
Author(s): Gottfrid Sjödahl, Pontus Eriksson, Fredrik Liedberg, Mattias Höglund
Software Mentions: 4
Published: over 7 years ago

10.1093/bib/bbx080

‘Multi-omic’ data analysis using O-miner
Cited by: 13
Author(s): Ajanthah Sangaralingam, Abu Z. Dayem Ullah, Jacek Marzec, Emanuela Gadaleta, A. Nagano, Helen Ross-Adams, Jun Wang, Nick R. Lemoine, Claude Chelala
Software Mentions: 4
Published: over 7 years ago

10.1186/s13024-019-0351-3

Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease
Cited by: 24
Author(s): Ravi S. Pandey, Leah C. Graham, Asli Uyar, Christoph Preuß, Gareth R. Howell, Gregory W. Carter
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pcbi.1008219

A simple, scalable approach to building a cross-platform transcriptome atlas
Cited by: 12
Author(s): Paul W. Angel, Nadia Rajab, Yidi Deng, Chris M. Pacheco, Tyrone Chen, Kim‐Anh Lê Cao, Jarny Choi, Christine A. Wells
Software Mentions: 4
Published: about 4 years ago

10.1186/s13054-020-2788-8

Dynamic LTR retrotransposon transcriptome landscape in septic shock patients
Cited by: 5
Author(s): Marine Mommert, Olivier Tabone, Audrey Guichard, Guy Oriol, Elisabeth Cerrato, Mélanie Denizot, Valérie Cheynet, Alexandre Pachot, Alain Lepape, Guillaume Monneret, Fabienne Venet, Karen Brengel‐Pesce, Julien Textoris, François Mallet
Software Mentions: 4
Published: over 4 years ago

10.1099/jgv.0.001491

Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus
Cited by: 12
Author(s): Arinjay Banerjee, Andrew C. Doxey, Benjamin Tremblay, Michael J. Mansfield, Sonu Subudhi, Jeremy A. Hirota, Matthew S. Miller, Andrew G. McArthur, Samira Mubareka, Karen Mossman
Software Mentions: 3
Published: almost 4 years ago

10.18632/aging.101992

Investigation of bidirectional longitudinal associations between advanced epigenetic age and peripheral biomarkers of inflammation and metabolic syndrome
Cited by: 13
Author(s): Filomene G. Morrison, Mark W. Logue, Dafne Guetta, Hannah Maniates, Annjanette Stone, Steven A. Schichman, Regina E. McGlinchey, William Milberg, Mark W. Miller, Erika J. Wolf
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1007245

The impact of DNA methylation on the cancer proteome
Cited by: 8
Author(s): Majed Mohamed Magzoub, Marcos Prunello, Kevin Brennan, Olivier Gevaert
Software Mentions: 3
Published: over 5 years ago

10.1038/s41416-020-01252-2

Discovery of a biomarker candidate for surgical stratification in high-grade serous ovarian cancer
Cited by: 10
Author(s): Haonan Lu, Paula Cunnea, Katherine Nixon, Natasha Rinne, Eric O. Aboagye, Christina Fotopoulou
Software Mentions: 3
Published: almost 4 years ago

10.1186/bcr3672

A genomic analysis of mouse models of breast cancer reveals molecular features ofmouse models and relationships to human breast cancer
Cited by: 71
Author(s): Daniel P. Hollern, Eran R. Andrechek
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0205968

MetaboClust: Using interactive time-series cluster analysis to relate metabolomic data with perturbed pathways
Cited by: 12
Author(s): Martin Rusilowicz, Mike Dickinson, Adrian J. Charlton, Simon O’Keefe, Julie Wilson
Software Mentions: 3
Published: about 6 years ago

10.1186/s12859-019-2912-4

TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Cited by: 2
Author(s): Salvatore Alaimo, Annalisa Di Maria, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1004735

Genome-Wide Associations between Genetic and Epigenetic Variation Influence mRNA Expression and Insulin Secretion in Human Pancreatic Islets
Cited by: 139
Author(s): Anna Olsson, Petr Volkov, Karl Bacos, Tasnim Dayeh, Elin Hall, Erika Nilsson, Claes Ladenvall, Tina Rönn, Charlotte Ling
Software Mentions: 3
Published: about 10 years ago

10.1186/s12859-019-3028-6

Influence of batch effect correction methods on drug induced differential gene expression profiles
Cited by: 12
Author(s): Wei Zhou, Karel K.M. Koudijs, Stefan Böhringer
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0149475

Diagnosis of Coronary Heart Diseases Using Gene Expression Profiling; Stable Coronary Artery Disease, Cardiac Ischemia with and without Myocardial Necrosis
Cited by: 10
Author(s): Nabila Kazmi, Tom R. Gaunt
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-14-153

Iterative rank-order normalization of gene expression microarray data
Cited by: 106
Author(s): Eric A. Welsh, Steven Eschrich, Anders Berglund, David Fenstermacher
Software Mentions: 3
Published: over 11 years ago

10.12688/f1000research.10960.2

A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification
Cited by: 11
Author(s): Jessica Roelands, Julie Decock, Sabri Boughorbel, Darawan Rinchai, Cristina Maccalli, Michele Ceccarelli, Michael A. Black, Chris Print, Jeff Chou, Scott Presnell, Charlie Quinn, Puthen V. Jithesh, Najeeb Syed, Salha B.J. Al Bader, Shahinaz Bedri, Ena Wang, Francesco M. Marincola, Damien Chaussabel, Peter J.K. Kuppen, Lance D. Miller, Davide Bedognetti, Wouter Hendrickx
Software Mentions: 3
Published: almost 7 years ago

10.15252/msb.20177952

Modeling signaling‐dependent pluripotency with Boolean logic to predict cell fate transitions
Cited by: 42
Author(s): Ayako Yachie‐Kinoshita, Kento Onishi, Joel Östblom, Matthew A Langley, Eszter Pósfai, Janet Rossant, Peter W. Zandstra
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12859-020-3511-0

TS: a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data
Cited by: 1
Author(s): Jianjun Zhang, Xuan Guo, Samantha Gonzales, Jingjing Yang, Xuexia Wang
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0159302

Machine Learning of Protein Interactions in Fungal Secretory Pathways
Cited by: 7
Author(s): Jana Kludas, Mikko Arvas, Sandra Castillo, Tiina Pakula, Merja Oja, Céline Brouard, Jussi Jäntti, Merja Penttilä, Juho Rousu
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pbio.2002690

Common genes associated with antidepressant response in mouse and man identify key role of glucocorticoid receptor sensitivity
Cited by: 26
Author(s): Tania Carrillo-Roa, Christiana Labermaier, Peter Weber, David P. Herzog, Caleb A. Lareau, Sara Santarelli, Klaus V. Wagner, Monika Rex‐Haffner, D. Harbich, Sebastian H. Scharf, Charles B. Nemeroff, Boadie W. Dunlop, W. Edward Craighead, Helen S. Mayberg, Mathias Schmidt, Manfred Uhr, Florian Holsboer, Inge Sillaber, Elisabeth B. Binder, Marianne B. Müller
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0157776

A Genome-Wide mQTL Analysis in Human Adipose Tissue Identifies Genetic Variants Associated with DNA Methylation, Gene Expression and Metabolic Traits
Cited by: 86
Author(s): Petr Volkov, Anna Olsson, Linn Gillberg, Steffen Jørgensen, Charlotte Brøns, Kerstin Eriksson, Leif Groop, Per Anders Jansson, Erika Nilsson, Tina Rönn, Allan Vaag, Charlotte Ling
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1003053

Network Analysis of a Pkd1-Mouse Model of Autosomal Dominant Polycystic Kidney Disease Identifies HNF4α as a Disease Modifier
Cited by: 72
Author(s): Luís F. Menezes, Fang Zhou, Andrew D. Patterson, Klaus Piontek, Kristopher W. Krausz, Frank J. Gonzalez, Gregory G. Germino
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-020-74051-7

Integrative transcriptomic analysis for linking acute stress responses to squamous cell carcinoma development
Cited by: 4
Author(s): Tran Nguyen, Kimal Rajapakshe, Courtney Nicholas, Leticia Tordesillas, Erik A. Ehli, Christel M. Davis, Cristian Coarfa, Elsa R. Flores, Sally E. Dickinson, Clara Curiel‐Lewandrowski, Kenneth Y. Tsai
Software Mentions: 3
Published: about 4 years ago

10.1155/2014/345106

Comparison of Merging and Meta-Analysis as Alternative Approaches for Integrative Gene Expression Analysis
Cited by: 45
Author(s): Jonatan Taminau, Cosmin Lazar, Stijn Meganck, Ann Nowé
Software Mentions: 3
Published: almost 11 years ago

10.1074/jbc.M115.671586

Structure and Function of the Escherichia coli Tol-Pal Stator Protein TolR
Cited by: 30
Author(s): Justyna Aleksandra Wojdyla, Erin E. Cutts, Renata Kaminska, Grigorios Papadakos, Jonathan T. S. Hopper, Phillip J. Stansfeld, David Staunton, Carol V. Robinson, Colin Kleanthous
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0040194

Microarray-Based Sketches of the HERV Transcriptome Landscape
Cited by: 46
Author(s): Philippe Pérot, Nathalie Mugnier, Cécile Montgiraud, Juliette Gimenez, Magali Jaillard, Bertrand Bonnaud, François Mallet
Software Mentions: 3
Published: over 12 years ago

10.1186/s13040-017-0136-6

Study of Meta-analysis strategies for network inference using information-theoretic approaches
Cited by: 2
Author(s): Ngoc Cam Pham, Benjamin Haibe‐Kains, Pau Bellot, Gianluca Bontempi, Patrick Meyer
Software Mentions: 3
Published: over 7 years ago

10.1093/ibd/izy119

Discovery and Validation of Methylation Biomarkers for Ulcerative Colitis Associated Neoplasia
Cited by: 8
Author(s): Andrew D Beggs, Jonathan James, Germaine Caldwell, Toby Prout, Mark Dilworth, Philippe Taniere, Tariq Iqbal, Dean Morton, Glenn Matthews
Software Mentions: 3
Published: over 6 years ago

10.1038/s41419-018-0896-z

Somatic loss of WWOX is associated with TP53 perturbation in basal-like breast cancer
Cited by: 20
Author(s): Suhaib K. Abdeen, Uri Ben‐David, Aya Shweiki, Bella Maly, Rami I. Aqeilan
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-13-335

Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages
Cited by: 132
Author(s): Jonatan Taminau, Stijn Meganck, Cosmin Lazar, David Steenhoff, Alain Coletta, Colin Molter, Robin Duqué, Virginie de Schaetzen, David Solis, Hugues Bersini, Ann Nowé
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12885-017-3226-4

Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer
Cited by: 27
Author(s): Tyler McInnes, Donghui Zou, Dasari S. Rao, Francesca Maree Munro, Vicky Phillips, John L. McCall, Michael A. Black, Anthony E. Reeve, Parry Guilford
Software Mentions: 2
Published: over 7 years ago

10.1186/s12872-021-02001-w

Genome-wide analysis of DNA methylation and risk of cardiovascular disease in a Chinese population
Cited by: 3
Author(s): Yan Gao, Haiyu Pang, Bowang Chen, Chaoqun Wu, Yanping Wang, Li-Bo Hou, Siming Wang, Dianjianyi Sun, Xin Zheng
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-018-4618-9

DNA Methylation variability among individuals is related to CpGs cluster density and evolutionary signatures
Cited by: 19
Author(s): Domenico Palumbo, Ornella Affinito, Antonella Monticelli, Sérgio Cocozza
Software Mentions: 2
Published: over 6 years ago

10.1038/s41416-021-01455-1

Cancer Grade Model: a multi-gene machine learning-based risk classification for improving prognosis in breast cancer
Cited by: 12
Author(s): Elmira Amiri Souri, Alicia Chenoweth, Anthony Cheung, Sophia N. Karagiannis, Sophia Tsoka
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1003572

A Six Months Exercise Intervention Influences the Genome-wide DNA Methylation Pattern in Human Adipose Tissue
Cited by: 499
Author(s): Tina Rönn, Petr Volkov, Cajsa Davegårdh, Tasnim Dayeh, Elin Hall, Anna Olsson, Erika Nilsson, Åsa Tornberg, Marloes Dekker Nitert, Karl-Fredrik Eriksson, Helena A. Jones, Leif Groop, Charlotte Ling
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0223809

Direct transport vs secondary transfer to level I trauma centers in a French exclusive trauma system: Impact on mortality and determinants of triage on road-traffic victims
Cited by: 15
Author(s): Sophie Hamada, Nathalie Delhaye, Samuel Degoul, Tobias Gauss, Mathieu Raux, Marie-Laure Devaud, Johan Amani, Fabrice Cook, Camille Hego, Jacques Duranteau, Alexandra Rouquette
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0216068

Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach
Cited by: 18
Author(s): Sanchari Sircar, Nita Parekh
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0099716

Prenatal Tobacco Smoke Exposure Is Associated with Childhood DNA CpG Methylation
Cited by: 107
Author(s): Carrie V. Breton, Kimberly D. Siegmund, Bonnie R. Joubert, Xinhui Wang, Weiliang Qui, Vincent J. Carey, Wenche Nystad, Siri Eldevik Håberg, Carole Ober, Dan L. Nicolae, Kathleen C. Barnes, Fernando D. Martínez, Andy Liu, Robert F. Lemanske, Robert C. Strunk, Scott T. Weiss, Stephanie J. London, Frank D. Gilliland, Benjamin A. Raby
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0026542

A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface
Cited by: 73
Author(s): Xiaoxiao Li, James F. LeBlanc, Amy Truong, Ravi Vuthoori, Sharon S. Chen, Jonathan L. Lustgarten, Bennett E. Roth, Jeff Allard, Andrew Ippoliti, Laura L. Presley, James Borneman, William L. Bigbee, Vanathi Gopalakrishnan, Thomas G. Graeber, David Elashoff, Jonathan Braun, Lee Goodglick
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0144316

Multiple Transcriptome Data Analysis Reveals Biologically Relevant Atopic Dermatitis Signature Genes and Pathways
Cited by: 63
Author(s): Debajyoti Ghosh, Lili Ding, Umasundari Sivaprasad, Esmond Geh, Jocelyn M. Biagini Myers, Jonathan A. Bernstein, Gurjit K. Khurana Hershey, Tesfaye B. Mersha
Software Mentions: 2
Published: almost 9 years ago

10.3390/cells9071579

Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments
Cited by: 6
Author(s): Cankut Çubuk, Fatma Ezgi Can, María Peña‐Chilet, Joaquı́n Dopazo
Software Mentions: 2
Published: over 4 years ago

10.1186/s13148-018-0599-4

Analysis of two birth tissues provides new insights into the epigenetic landscape of neonates born preterm
Cited by: 23
Author(s): Yonghui Wu, Xinyi Lin, Ives Yubin Lim, Li Chen, Ai Ling Teh, Julia L. MacIsaac, Kok Hian Tan, Michæl S. Kobor, Yap Seng Chong, Peter D. Gluckman, Neerja Karnani
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13054-017-1743-9

Transcriptome modulation by hydrocortisone in severe burn shock: ancillary analysis of a prospective randomized trial
Cited by: 10
Author(s): Jonathan Plassais, Fabienne Venet, Marie-Angélique Cazalis, Diane Le Quang, Alexandre Pachot, Guillaume Monneret, S. Tissot, Julien Textoris
Software Mentions: 2
Published: over 7 years ago

10.1186/s13072-016-0108-y

Genome-wide methylation data mirror ancestry information
Cited by: 83
Author(s): Elior Rahmani, Liat Shenhav, Regev Schweiger, Paul Yousefi, Karen Huen, Brenda Eskenazi, Celeste Eng, Scott Huntsman, Donglei Hu, Joshua Galanter, Sam S. Oh, Mélanie Waldenberger, Konstantin Strauch, Harald Grallert, Thomas Meitinger, Christian Gieger, Nina Holland, Esteban G. Burchard, Noah Zaitlen, Eran Halperin
Software Mentions: 2
Published: almost 8 years ago

10.1186/gm534

Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment
Cited by: 28
Author(s): Mika Gustafsson, Måns Edström, Danuta R. Gawel, Colm E. Nestor, Hui Wang, Huan Zhang, Fredrik Barrenäs, James Tod, Ingrid Kockum, Tomas Olsson, Jordi Serra-Musach, Núria Bonifaci, Miguel Ángel Pujana, Jan Ernerudh, Mikael Benson
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13073-020-00752-3

A comparison of epigenetic mitotic-like clocks for cancer risk prediction
Cited by: 42
Author(s): Andrew E. Teschendorff
Software Mentions: 2
Published: over 4 years ago

10.1107/S1600576714008073

A suite of software for processing MicroED data of extremely small protein crystals
Cited by: 15
Author(s): M.G. Iadanza, Tamir Gonen
Software Mentions: 2
Published: over 10 years ago

10.1186/s13287-018-1118-4

Sex influences DNA methylation and gene expression in human skeletal muscle myoblasts and myotubes
Cited by: 47
Author(s): Cajsa Davegårdh, Elin Hall, Christa Broholm, Tora Ida Henriksen, Maria Pedersen, Bente Klarlund Pedersen, Camilla Schéele, Charlotte Ling
Software Mentions: 2
Published: almost 6 years ago

10.1002/JLB.2A0618-228R

Phosphatase inhibitor PPP1R11 modulates resistance of human T cells toward Treg-mediated suppression of cytokine expression
Cited by: 11
Author(s): Rubin Narayan Joshi, Sunjay Jude Fernandes, Mei Shang, Narsis A. Kiani, David Green, Jesper Tegnér, Angelika Schmidt
Software Mentions: 2
Published: over 5 years ago

10.18632/oncotarget.9963

HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status
Cited by: 27
Author(s): Gregory Weitsman, Paul R. Barber, Lan K. Nguyen, Katherine Lawler, Gargi Patel, Natalie Woodman, Muireann Kelleher, Sarah Pinder, Mark Rowley, Paul Ellis, Arnie Purushotham, A. C. C. Coolen, Boris N. Kholodenko, Borivoj Vojnovic, Cheryl Gillett, Tony Ng
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.12672

Early2 factor (E2F) deregulation is a prognostic and predictive biomarker in lung adenocarcinoma
Cited by: 7
Author(s): Lu Chen, Courtney A. Kurtyka, Eric A. Welsh, Jason I. Rivera, Brienne E. Engel, Teresita Muñoz-Antonia, Sean Yoder, Steven Eschrich, Ben Creelan, Alberto Chiappori, Jhanelle E. Gray, José Luis Ramirez, Rafael Rosell, Matthew B. Schabath, Eric B. Haura, Dung-Tsa Chen, W. Douglas Cress
Software Mentions: 2
Published: about 8 years ago

10.18632/oncotarget.14788

Acquired resistance to LY2874455 in FGFR2-amplified gastric cancer through an emergence of novel FGFR2-ACSL5 fusion
Cited by: 40
Author(s): Sun Young Kim, Tae-Jin Ahn, Heejin Bang, Jun Soo Ham, Jusun Kim, Seung Tae Kim, Jiryeon Jang, Moonhee Shim, So Young Kang, Se Hoon Park, Byung Hoon Min, Hyuk Lee, Won Ki Kang, Woong-Yang Park
Software Mentions: 2
Published: almost 8 years ago

10.3390/nu9070752

Fruit and Juice Epigenetic Signatures Are Associated with Independent Immunoregulatory Pathways
Cited by: 10
Author(s): Jessie Nicodemus‐Johnson, Robert Sinnott
Software Mentions: 2
Published: over 7 years ago

10.1186/s40169-015-0080-3

Targeting polo‐like kinase 1, a regulator of p53, in the treatment of adrenocortical carcinoma
Cited by: 19
Author(s): Kimberly J. Bussey, Aditi Bapat, Claire Linnehan, Melissa Wandoloski, Erica Dastrup, Erik Rogers, Paul Gonzales, Michael J. Demeure
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13031-021-00343-y

Assessing exposure to war-related traumatic events in older Vietnamese war survivors
Cited by: 6
Author(s): Yvette Young, Kim Korinek, Zachary Zimmer, Trần Khánh Toàn
Software Mentions: 1
Published: over 3 years ago

10.1186/s13054-019-2524-4

Pre-hospital plasma transfusion: a valuable coagulation support or an expensive fluid therapy?
Cited by: 15
Author(s): Christian Fenger-Eriksen, Dietmar Fries, Jean-Stéphane David, Pierre Bouzat, Marcus D. Lancé, Oliver Grottke, Donat R. Spahn, Herbert Schöechl, Marc Maegele
Software Mentions: 1
Published: over 5 years ago

10.1007/s11060-016-2202-1

Relapse patterns and outcome after relapse in standard risk medulloblastoma: a report from the HIT-SIOP-PNET4 study
Cited by: 89
Author(s): Magnus Sabel, Gudrun Fleischhack, Stephan Tippelt, Göran Gustafsson, François Doz, Rolf Dieter Kortmann, Maura Massimino, Aurora Navajas, Katja von Hoff, Stefan Rutkowski, Monika Warmuth‐Metz, Steven C. Clifford, Torsten Pietsch, Barry Pizer, Birgitta Lannering
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1008106

Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones
Cited by: 11
Author(s): Fabrizio Clarelli, Adam C. Palmer, Bhupender Singh, Merete Storflor, Silje Lauksund, Ted Cohen, Sören Abel, Pia Abel zur Wiesch
Software Mentions: 1
Published: over 4 years ago

10.1093/database/bav025

SCAN database: facilitating integrative analyses of cytosine modification and expression QTL
Cited by: 19
Author(s): Wei Zhang, Eric R. Gamazon, Xu Zhang, Anuar Konkashbaev, Chun Yu Liu, Keely L. Szilágyi, M. Eileen Dolan, Nancy J. Cox
Software Mentions: 1
Published: over 9 years ago

10.1016/j.ebiom.2014.10.012

Prediction of Clinical Outcome for All Stages and Multiple Cell Types of Non-small Cell Lung Cancer in Five Countries Using Lung Cancer Prognostic Index
Cited by: 8
Author(s): Tiehua Chen, Luming Chen
Software Mentions: 1
Published: almost 10 years ago

10.3332/ecancer.2016.689

Next generation metronomic chemotherapy—report from the Fifth Biennial International Metronomic and Anti-angiogenic Therapy Meeting, 6–8 May 2016, Mumbai
Cited by: 9
Author(s): Pan Pantziarka, Lisa Hutchinson, Nicolas André, Sébastien Benzekry, Francesco Bertolini, Atanu Bhattacharjee, Shubhada Chiplunkar, Dan G. Duda, Vikram Gota, Sudeep Gupta, Amit Joshi, Sadhana Kannan, Robert S. Kerbel, Mark W. Kieran, Antonella Palazzo, Aparna R. Parikh, Eddy Pasquier, Vijay Patil, Kumar Prabhash, Yuval Shaked, Giselle L. Saulnier Sholler, Jaroslav Štěrba, David J. Waxman, Shripad Banavali
Software Mentions: 1
Published: about 8 years ago

10.3332/ecancer.2014.463

ecancermedicalscience
Cited by: 15
Author(s): Gauthier Bouche, Nicolas André, Shripad Banavali, Frank Berthold, Alfredo Berruti, Guido Bocci, Giovanni Brandi, Ugo Cavallaro, Saverio Cinieri, Marco Colleoni, Giuseppe Curigliano, Teresa Di Desidero, Alexandru Eniu, Nicola Fazio, Robert S. Kerbel, Lisa Hutchinson, Urszula Ledzewicz, Elisabetta Munzone, Eddy Pasquier, O. Graciela Scharovsky, Yuval Shaked, Jaroslav Štěrba, Martín Villalba, Francesco Bertolini
Software Mentions: 1
Published: almost 8 years ago

10.1186/1476-069X-12-58

Association between In Utero arsenic exposure, placental gene expression, and infant birth weight: a US birth cohort study
Cited by: 66
Author(s): Dennisliang Fei, Devin C. Koestler, Zhigang Li, Camilla Giambelli, Avencia Sánchez-Mejías, Julie A. Gosse, Carmen J. Marsit, Margaret R. Karagas, David J. Robbins
Software Mentions: 1
Published: over 11 years ago

10.1186/s12940-017-0267-8

The aquaglyceroporin AQP9 contributes to the sex-specific effects of in utero arsenic exposure on placental gene expression
Cited by: 16
Author(s): Emily F. Winterbottom, Devin C. Koestler, Dennis Liang Fei, Eric Wika, Anthony J. Capobianco, Carmen J. Marsit, Margaret R. Karagas, David J. Robbins
Software Mentions: 1
Published: over 7 years ago

10.1080/15592294.2015.1111504

DNA methylation profiling to assess pathogenicity of BRCA1 unclassified variants in breast cancer
Cited by: 12
Author(s): Kirsty Flower, Natalie Shenker, Mona El‐Bahrawy, David E. Goldgar, Michael T. Parsons, Amanda B. Spurdle, Joanna R. Morris, Robert E. Brown, James M. Flanagan
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13722-021-00225-x

Integrating a brief alcohol intervention with tobacco addiction treatment in primary care: qualitative study of health care practitioner perceptions
Cited by: 7
Author(s): Nadia Minian, Aliya Noormohamed, M. Shankar Lingam, Laurie Zawertailo, Bernard Le Foll, Jürgen Rehm, Norman Giesbrecht, Andriy V. Samokhvalov, Dolly Baliunas, Peter Selby
Software Mentions: 1
Published: over 3 years ago

10.1038/s41380-019-0450-0

Altered white matter microstructure in 22q11.2 deletion syndrome: a multisite diffusion tensor imaging study
Cited by: 46
Author(s): Julio E. Villalon‐Reina, Kenia Martínez, Xiaoping Qu, Christopher R. K. Ching, Talia M. Nir, Deydeep Kothapalli, Conor K. Corbin, Daqiang Sun, Amy Lin, Jennifer K. Forsyth, Leila Kushan, Ariana Vajdi, Maria Jalbrzikowski, Laura Hansen, Rachel K. Jonas, Thérèse van Amelsvoort, Geor Bakker, Wendy R. Kates, Kevin M. Antshel, Wanda Fremont, Linda E. Campbell, Kathryn McCabe, Eileen Daly, Maria Gudbrandsen, Clodagh Murphy, Declan Murphy, Michael C. Craig, Beverly S. Emanuel, Donna M. McDonald‐McGinn, Jacob Vorstman, Ania Fiksinski, Sanne Koops, Kosha Ruparel, David R. Roalf, Raquel E. Gur, J. Eric Schmitt, Tony J. Simon, Naomi J. Goodrich-Hunsaker, Courtney A. Durdle, Joanne L. Doherty, Adam Cunningham, Marianne van den Bree, David Linden, Michael John Owen, Hayley Moss, Sinéad Kelly, Gary Donohoe, Kieran C. Murphy, Celso Arango, Neda Jahanshad, Paul M. Thompson, Carrie E. Bearden
Software Mentions: 1
Published: over 5 years ago

10.3390/molecules26010184

Macrophage Migration Inhibitory Factor (MIF) and Its Homologue D-Dopachrome Tautomerase (DDT) Inversely Correlate with Inflammation in Discoid Lupus Erythematosus
Cited by: 10
Author(s): Rosario Caltabiano, Rocco De Pasquale, Eliana Piombino, Giorgia Campo, Ferdinando Nicoletti, Eugenio Cavalli, Katia Mangano, Paolo Fagone
Software Mentions: 1
Published: almost 4 years ago

10.3390/membranes11080549

Protein Crystallization in a Microfluidic Contactor with Nafion®117 Membranes
Cited by: 2
Author(s): Mariella Polino, Hoon Suk Rho, M.P. Pina, Reyes Mallada, Ana Luı́sa Carvalho, Maria João Romão, Isabel M. Coelhoso, Han Gardeniers, João G. Crespo, Carla A. M. Portugal
Software Mentions: 1
Published: over 3 years ago

10.1007/s10549-018-5061-y

A mouse model featuring tissue-specific deletion of p53 and Brca1 gives rise to mammary tumors with genomic and transcriptomic similarities to human basal-like breast cancer
Cited by: 16
Author(s): Daniel P. Hollern, Cristina M. Contreras, Stephanie T. Dance-Barnes, Grace O. Silva, Adam D. Pfefferle, Jessie Xiong, David B. Darr, Jerry Usary, Kevin R. Mott, Charles M. Perou
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmed.2018.00091

The Role of Plasma Transfusion in Massive Bleeding: Protecting the Endothelial Glycocalyx?
Cited by: 39
Author(s): Stefano Barelli, Lorenzo Alberio
Software Mentions: 1
Published: over 6 years ago

10.3389/fninf.2018.00021

Better Diffusion Segmentation in Acute Ischemic Stroke Through Automatic Tree Learning Anomaly Segmentation
Cited by: 32
Author(s): Jens Kjærgaard Boldsen, Thorbjørn S Engedal, Salvador Pedraza, Tae-Hee Cho, Götz Thomalla, Norbert Nighoghossian, Jean‐Claude Baron, Jens Fiehler, Leif Østergaard, Kim Mouridsen
Software Mentions: 1
Published: over 6 years ago

Projects: cran: COMBAT

Papers Mentioning COMBAT 157