bioconductor: fgsea | Projects | Ecosyste.ms: Papers

10.1186/s13059-020-02100-5

Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data
Cited by: 56
Author(s): Nikolaus Fortelny, Christoph Bock
Software Mentions: 20
Published: over 4 years ago

10.3390/cancers12040948

Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility
Cited by: 23
Author(s): Henry E. Miller, Aparna Gorthi, Nicklas Bassani, Liesl A. Lawrence, Brian S. Iskra, Alexander J.R. Bishop
Software Mentions: 19
Published: over 4 years ago

10.15252/emmm.202012640

Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor
Cited by: 7
Author(s): Maggie H. Chassé, Benjamin K. Johnson, Elissa A. Boguslawski, Katie M. Sorensen, Jessica E Rosien, Min H. Kang, C. Patrick Reynolds, Lyong Heo, Zachary Madaj, Ian Beddows, Gabrielle E. Foxa, Susan M. Kitchen-Goosen, Bart O. Williams, Timothy J. Triche, Patrick J. Grohar
Software Mentions: 18
Published: almost 4 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

10.7554/eLife.57116

shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data
Cited by: 35
Author(s): Kenichi Shimada, John A. Bachman, Jeremy Muhlich, Timothy J. Mitchison
Software Mentions: 13
Published: almost 4 years ago

10.1038/s42003-021-01842-7

Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer
Cited by: 35
Author(s): Ling Cai, Hongyu Liu, Fang Huang, Junya Fujimoto, Luc Girard, Jun Chen, Yongwen Li, Yu An Zhang, Dhruba Deb, Victor Stastny, Karine Pozo, Christin S. Kuo, Gaoxiang Jia, Chendong Yang, Wei Zou, Adeeb Alomar, Kenneth E. Huffman, Mahboubeh Papari-Zareei, Lin Yang, Benjamin J. Drapkin, Esra A. Akbay, David S. Shames, Ignacio I. Wistuba, Tao Wang, Jane E. Johnson, Guanghua Xiao, Ralph J. DeBerardinis, John D. Minna, Yang Xie, Adi F. Gazdar
Software Mentions: 13
Published: over 3 years ago

10.3390/cancers13174311

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging
Cited by: 15
Author(s): Daria Lazic, Florian Kromp, Fikret Rifatbegovic, Peter Repiščák, Michael Kirr, Filip Mívalt, Florian Halbritter, Marie Bernkopf, Andrea Bileck, Marek Ussowicz, Inge M. Ambros, Peter F. Ambros, Christopher Gerner, Ruth Ladenstein, Christian Ostalecki, Sabine Taschner‐Mandl
Software Mentions: 13
Published: about 3 years ago

10.3390/cancers13163922

Transcriptomic Profiling Reveals Novel Candidate Genes and Signalling Programs in Breast Cancer Quiescence and Dormancy
Cited by: 4
Author(s): Lewis A. Quayle, Amy Spicer, Penelope D. Ottewell, Ingunn Holen
Software Mentions: 13
Published: over 3 years ago

10.3389/fonc.2021.639013

Single-Cell Transcriptome Analysis Identifies Ligand–Receptor Pairs Associated With BCP-ALL Prognosis
Cited by: 3
Author(s): Liang Wu, Mingming Jiang, Ping Yu, Jianfeng Li, Wen Ouyang, Chong Feng, Wei Zhao, Yuting Dai, Jinyan Huang
Software Mentions: 13
Published: over 3 years ago

10.3389/fimmu.2021.647832

Large-Scale Gene Expression Signatures Reveal a Microbicidal Pattern of Activation in Mycobacterium leprae-Infected Monocyte-Derived Macrophages With Low Multiplicity of Infection
Cited by: 9
Author(s): Thyago Leal-Calvo, Bruna Letícia Martins, Daniele Ferreira de Faria Bertoluci, Patrícia Sammarco Rosa, Rodrigo Mendes de Camargo, G. Germano, Vânia Niéto Brito de Souza, Ana Carla Pereira Latini, Milton Ozório Moraes
Software Mentions: 12
Published: over 3 years ago

10.1186/s13059-019-1716-1

A practical guide to methods controlling false discoveries in computational biology
Cited by: 178
Author(s): Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks
Software Mentions: 11
Published: over 5 years ago

10.1172/jci.insight.138970

Hypoxia acts as an environmental cue for the human tissue-resident memory T cell differentiation program
Cited by: 21
Author(s): Farah Hasan, Yulun Chiu, Rebecca Shaw, Junmei Wang, Cassian Yee
Software Mentions: 10
Published: over 3 years ago

10.15252/msb.20209923

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis
Cited by: 122
Author(s): Dénes Türei, Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio-Escat, Michal Klein, Olga Ivanova, Márton Ölbei, Attila Gábor, Fabian J. Theis, Dezső Módos, Tamás Korcsmáros, Julio Sáez-Rodríguez
Software Mentions: 10
Published: over 3 years ago

10.3389/fimmu.2021.602539

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways
Cited by: 60
Author(s): Alexander Stewart, Joseph C.F. Ng, Gillian A. Wallis, Vasiliki Tsioligka, Franca Fraternali, Deborah K. Dunn‐Walters
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pbio.3000528

Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity
Cited by: 74
Author(s): Hugo G. Hilton, Nimrod D. Rubinstein, Peter Janki, Andrea Ireland, Nicholas Bernstein, Nicole L. Fong, Kevin M. Wright, Megan Smith, David Finkle, Baby Martin-McNulty, Margaret Roy, Denise M. Imai, Vladimir Jojic, Rochelle Buffenstein
Software Mentions: 10
Published: about 5 years ago

10.7554/eLife.62250

Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells
Cited by: 11
Author(s): Helen M Tauc, Imilce A. Rodriguez‐Fernandez, Jason A. Hackney, Michał Pawlak, Tal Oron, Jerome Korzelius, Hagar F. Moussa, Subhra Chaudhuri, Zora Modrušan, Bruce A Edgar, Heinrich Jasper
Software Mentions: 10
Published: over 3 years ago

10.1186/s12859-020-03866-y

Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline
Cited by: 7
Author(s): Yusuf Khan, Daniel Hammarström, Bent R. Rønnestad, Stian Ellefsen, Rafi Ahmad
Software Mentions: 10
Published: almost 4 years ago

10.1186/s13229-019-0262-8

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

10.1186/s41065-021-00196-8

Dynamic co-expression modular network analysis in nonalcoholic fatty liver disease
Cited by: 4
Author(s): Jing Zheng, WU Hui-zhong, Zhiying Zhang, Songqiang Yao
Software Mentions: 9
Published: over 3 years ago

10.3389/fncel.2020.00065

Single-Cell Analysis of Neuroinflammatory Responses Following Intracranial Injection of G-Deleted Rabies Viruses
Cited by: 29
Author(s): Kee Wui Huang, Bernardo L. Sabatini
Software Mentions: 9
Published: over 4 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: almost 4 years ago

10.1016/j.celrep.2021.109698

Transitions in lineage specification and gene regulatory networks in hematopoietic stem/progenitor cells over human development
Cited by: 33
Author(s): Anindita Roy, Guanlin Wang, Deena Iskander, Sorcha O’Byrne, Natalina E. Elliott, Jennifer O’Sullivan, Gemma Buck, Elisabeth F. Heuston, Wei Wen, Alba Rodríguez-Meira, Peng Hua, Anastasios Karadimitris, Adam J. Mead, David M. Bodine, Irene Roberts, Bethan Psaila, Supat Thongjuea
Software Mentions: 9
Published: about 3 years ago

10.1016/j.celrep.2020.108546

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

10.1186/s12859-020-03910-x

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
Cited by: 48
Author(s): Sebastian Canzler, Jörg Hackermüller
Software Mentions: 9
Published: almost 4 years ago

10.1371/journal.pgen.1009259

Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration
Cited by: 9
Author(s): Passley Hargrove-Grimes, Anupam Mondal, Jessica Gumerson, Jacob Nellissery, Angel Aponte, Linn Gieser, Haohua Qian, Robert N Fariss, Juan S. Bonifacino, Tiansen Li, Anand Swaroop
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12935-020-01230-x

A Gleason score-related outcome model for human prostate cancer: a comprehensive study based on weighted gene co-expression network analysis
Cited by: 19
Author(s): Yongzhi Wang, Zhonghua Yang
Software Mentions: 9
Published: over 4 years ago

10.1186/s12915-018-0518-3

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

10.1186/s13041-020-00681-7

Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer’s disease
Cited by: 22
Author(s): Karissa Barthelson, Stephen Pederson, Morgan Newman, Michael Lardelli
Software Mentions: 9
Published: about 4 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: over 3 years ago

10.3390/ijms22179426

Gravitational Force—Induced 3D Chromosomal Conformational Changes Are Associated with Rapid Transcriptional Response in Human T Cells
Cited by: 14
Author(s): Christian Vahlensieck, Cora S. Thiel, Ye Zhang, Andreas Huge, Oliver Ullrich
Software Mentions: 8
Published: about 3 years ago

10.1038/s41598-021-98966-x

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

10.3390/v13061019

Human Retrotransposons and the Global Shutdown of Homeostatic Innate Immunity by Oncolytic Parvovirus H-1PV in Pancreatic Cancer
Cited by: 2
Author(s): Matthias Neulinger-Muñoz, Dominik Schaack, Svetlana Grekova, Andrea S. Bauer, Thomas Giese, Gabriel Alexander Salg, Elisa Espinet, Barbara Leuchs, Anette Heller, Jürg P. F. Nüesch, Miriam Schenk, Michael Volkmar, Nathalia A. Giese
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pcbi.1006076

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

10.1371/journal.pone.0239189

Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation
Cited by: 8
Author(s): Hong Dang, Deepika Polineni, Rhonda G. Pace, Jaclyn R. Stonebraker, Harriet Corvol, Garry R. Cutting, Mitchell L. Drumm, Lisa J. Strug, Wanda K. O’Neal, Michael R. Knowles
Software Mentions: 8
Published: almost 4 years ago

10.1038/s41598-020-60998-0

Temporal changes in the gene expression heterogeneity during brain development and aging
Cited by: 28
Author(s): Ulas Işıldak, Mehmet Somel, Janet M. Thornton, Handan Melike Dönertaş
Software Mentions: 8
Published: over 4 years ago

10.1038/s41418-021-00866-0

Fatal cytokine release syndrome by an aberrant FLIP/STAT3 axis
Cited by: 14
Author(s): Chiara Musiu, Simone Caligola, Alessandra Fiore, Alessia Lamolinara, Cristina Frusteri, Francesco Domenico Del Pizzo, Francesco De Sanctis, Stefania Canè, Annalisa Adamo, Francesca Hofer, Roza Maria Barouni, Andrea Grilli, Serena Zilio, Paolo Serafini, Evelina Tacconelli, Katia Donadello, Leonardo Gottin, Enrico Polati, Domenico Girelli, Ildo Polidoro, Piera Amelia Iezzi, Domenico Angelucci, Andrea Capece, Ying Chen, Shi Z, Peter J. Murray, Marco Chilosi, Ido Amit, Silvio Bicciato, Manuela Iezzi, Vincenzo Bronte, Stefano Ugel
Software Mentions: 8
Published: about 3 years ago

10.1242/dmm.040444

Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma
Cited by: 19
Author(s): Parisa Amini, Sina Nassiri, Julia Ettlin, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: almost 6 years ago

10.3389/fcell.2021.642650

A Novel CpG Methylation Risk Indicator for Predicting Prognosis in Bladder Cancer
Cited by: 9
Author(s): Yufeng Guo, Jun Yin, Yuanheng Dai, Yu-Dong Guan, Pinjin Chen, Yongqiang Chen, Chen‐Zheng Huang, Yong‐Jie Lu, Lirong Zhang, Dae‐Kyu Song
Software Mentions: 8
Published: about 3 years ago

10.3389/fcell.2020.00308

Organoid-Transplant Model Systems to Study the Effects of Obesity on the Pancreatic Carcinogenesis in vivo
Cited by: 8
Author(s): Fabio Lupo, Geny Piro, Lorena Torroni, Pietro Delfino, Rosalinda Trovato, Borislav Rusev, Alessandra Fiore, Dea Filippini, Francesco De Sanctis, Marcello Manfredi, Emílio Marengo, Rita T. Lawlor, Maurizio Martini, Giampaolo Tortora, Stefano Ugel, Vincenzo Corbo, Davide Melisi, Carmine Carbone
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.69975

Notch-induced endoplasmic reticulum-associated degradation governs mouse thymocyte β−selection
Cited by: 8
Author(s): Xia Liu, Jingjing Yu, Longyong Xu, Katharine Umphred-Wilson, Fanglue Peng, Yao Ding, Brendan M Barton, Xiangdong Lv, Michael Y Zhao, Shengyi Sun, Yuning Hong, Ling Qi, Stanley Adoro, Xi Chen
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-021-07509-1

Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis
Cited by: 7
Author(s): Yang Dong, Morgan Newman, Stephen Pederson, Karissa Barthelson, Nhi Hin, Michael Lardelli
Software Mentions: 7
Published: over 3 years ago

10.3390/ijms21165923

Oxidant-Induced Alterations in the Adipocyte Transcriptome: Role of the Na,K-ATPase Oxidant Amplification Loop
Cited by: 7
Author(s): Komal Sodhi, James Denvir, Jiang Liu, Juan Sanabria, Yiliang Chen, Roy L. Silverstein, Zijian Xie, Nader G. Abraham, Joseph I. Shapiro
Software Mentions: 7
Published: over 4 years ago

10.3389/fimmu.2021.651475

Novel Insights Into Rheumatoid Arthritis Through Characterization of Concordant Changes in DNA Methylation and Gene Expression in Synovial Biopsies of Patients With Differing Numbers of Swollen Joints
Cited by: 5
Author(s): Andrew Y. Li Yim, Enrico Ferrero, Klio Maratou, Huw D. Lewis, George C. Royal, David F. Tough, Chris Larminie, Marcel M.A.M. Mannens, Peter Henneman, Wouter J. de Jonge, Marleen G H van de Sande, Daniëlle M. Gerlag, Rab K. Prinjha, Paul P. Tak
Software Mentions: 7
Published: over 3 years ago

10.3389/fcell.2021.688798

QSOX2 Is an E2F1 Target Gene and a Novel Serum Biomarker for Monitoring Tumor Growth and Predicting Survival in Advanced NSCLC
Cited by: 3
Author(s): Yaqi Li, Mei Liu, Zhuoxian Zhang, Libin Deng, Zhenyu Zhai, Hua Liu, Yiting Wang, Cheng Zhang, Jianping Xiong, Chao Shi
Software Mentions: 7
Published: over 3 years ago

10.1128/mBio.01468-21

Lung Epithelial Signaling Mediates Early Vaccine-Induced CD4+T Cell Activation andMycobacterium tuberculosisControl
Cited by: 9
Author(s): Shibali Das, Nancy D. Marín, Ekaterina Esaulova, Mushtaq Ahmed, Amanda Swain, Bruce A. Rosa, Makedonka Mitreva, Javier Rangel-Moreno, Mihai G. Netea, Luis B. Barreiro, Maziar Divangahi, Maxim N. Artyomov, Deepak Kaushal, Shabaana A. Khader
Software Mentions: 7
Published: about 3 years ago

10.1002/bit.27209

Comparative genome‐scale analysis of Pichia pastoris variants informs selection of an optimal base strain
Cited by: 31
Author(s): Joseph Brady, Charles A. Whittaker, Melody C. Tan, D. Lee Kristensen, Duanduan Ma, Neil C. Dalvie, Kerry R. Love, J. Christopher Love
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.ppat.1009130

Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles
Cited by: 90
Author(s): Akshamal M Gamage, Kai Sen Tan, Wharton Chan, Jing Liu, Chee Wah Tan, Yew Kwang Ong, Mark Thong, Anand Kumar Andiappan, Danielle E. Anderson, De Yun Wang, Lin‐Fa Wang
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-020-70967-2

Transcriptomics uncovers substantial variability associated with alterations in manufacturing processes of macrophage cell therapy products
Cited by: 14
Author(s): Olga L. Gurvich, Katja A. Puttonen, Aubrey Bailey, Anssi Kailaanmäki, Vita Skirdenko, Minna Sivonen, Sanna Pietikäinen, Nigel R. Parker, Seppo Ylä‐Herttuala, Tuija Kekarainen
Software Mentions: 7
Published: over 4 years ago

10.1038/s41435-020-00118-0

Genomic profiling of T-cell activation suggests increased sensitivity of memory T cells to CD28 costimulation
Cited by: 13
Author(s): Dafni A. Glinos, Blagoje Soskic, Cayman Williams, Alan Kennedy, Luke Jostins, David M. Sansom, Gosia Trynka
Software Mentions: 7
Published: about 4 years ago

10.3389/fcell.2021.624053

“All-In-One” Genetic Tool Assessing Endometrial Receptivity for Personalized Screening of Female Sex Steroid Hormones
Cited by: 7
Author(s): Pavel Deryabin, А. П. Домнина, Inga V. Gorelova, M. V. Rulev, М. А. Petrosyan, Nikolay Nikolsky, Aleksandra Borodkina
Software Mentions: 7
Published: almost 4 years ago

10.7554/eLife.51339

Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature
Cited by: 17
Author(s): Chao Yang, Jason R. Siebert, Robert T. Burns, Yongwei Zheng, Ao Mei, Benedetta Bonacci, Demin Wang, Raúl Urrutia, Matthew J. Riese, Sridhar Rao, Karen-Sue Carlson, Monica S. Thakar, Subramaniam Malarkannan
Software Mentions: 7
Published: over 4 years ago

10.3389/fgene.2018.00052

Gene Expression Meta-Analysis of Seven Candidate Gene Sets for Diabetes Traits Following a GWAS Pathway Study
Cited by: 2
Author(s): Hao Mei, Lianna Li, Michael Griswold, Thomas H. Mosley
Software Mentions: 6
Published: almost 7 years ago

10.3390/brainsci9120381

A Pathway-Based Genomic Approach to Identify Medications: Application to Alcohol Use Disorder
Cited by: 6
Author(s): Laura B. Ferguson, Shruti Patil, Bailey A. Moskowitz, Igor Ponomarev, R. Adron Harris, R. Dayne Mayfield, Robert O. Messing
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-017-14788-w

Smoking induces DNA methylation changes in Multiple Sclerosis patients with exposure-response relationship
Cited by: 50
Author(s): Francesco Marabita, Malin Almgren, Louise K. Sjöholm, Lara Kular, Yun Liu, Tojo James, Nimrod Kiss, Andrew P. Feinberg, Tomas Olsson, Ingrid Kockum, Lars Alfredsson, Tomas J. Ekström, Maja Jagodic
Software Mentions: 6
Published: about 7 years ago

10.1016/j.cell.2021.07.023

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
Cited by: 170
Author(s): Carly G.K. Ziegler, Vincent N. Miao, Anna H. Owings, Andrew W. Navia, Ying Tang, Joshua D. Bromley, Peter Lotfy, Meredith Sloan, Hannah Laird, Hibbard E. Williams, Micayla George, Riley S. Drake, Christian Taube, Adam Parker, Campbell B Sindel, Molly Burger, Yilianys Pride, Mohammad S Hasan, George Abraham, Michal Senitko, Tanya O. Robinson, Alex K. Shalek, Sarah C. Glover, Bruce H. Horwitz, José Ordovás-Montañés
Software Mentions: 6
Published: about 3 years ago

10.3390/genes11040434

Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups
Cited by: 5
Author(s): Daniil S. Wiebe, N. A. Omelyanchuk, Aleksey M. Mukhin, Ivo Große, Sergey A. Lashin, Elena V. Zemlyanskaya, В. В. Миронова
Software Mentions: 6
Published: over 4 years ago

10.3389/fgene.2021.639254

Identification and Validation of a Novel Immune-Related Four-lncRNA Signature for Lung Adenocarcinoma
Cited by: 14
Author(s): Jixin Wang, Xiangjun Yin, Yin‐Qiang Zhang, Xuming Ji
Software Mentions: 6
Published: over 3 years ago

10.1038/s42003-021-02000-9

Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures
Cited by: 21
Author(s): Gaia Andreoletti, Cristina Lanata, Laura Trupin, Ishan Paranjpe, Tia S. Jain, Joanne Nititham, Kimberly E. Taylor, Alexis J. Combes, Lenka Maliskova, Chun Jimmie Ye, Patricia P. Katz, Maria Dall’Era, Jinoos Yazdany, Lindsey A. Criswell, Marina Sirota
Software Mentions: 6
Published: over 3 years ago

10.1186/s12920-019-0581-9

The caudate nucleus undergoes dramatic and unique transcriptional changes in human prodromal Huntington’s disease brain
Cited by: 26
Author(s): Filisia Agus, Diego Crespo, Richard H. Myers, Adam Labadorf
Software Mentions: 6
Published: about 5 years ago

10.1002/1878-0261.12709

HPV‐related methylation‐based reclassification and risk stratification of cervical cancer
Cited by: 25
Author(s): Shuanying Yang, Ying Wu, Shuqian Wang, Peng Xu, Yao Deng, Meng Wang, Kang Liu, Tian Tian, Yuyao Zhu, Na Li, Linghui Zhou, Zhijun Dai, Huafeng Kang
Software Mentions: 6
Published: over 4 years ago

10.3390/plants10061033

Metabolic Alterations in Pisum sativum Roots during Plant Growth and Arbuscular Mycorrhiza Development
Cited by: 13
Author(s): O. Y. Shtark, Roman Puzanskiy, G. S. Avdeeva, Vladislav V. Yemelyanov, А. Л. Шаварда, Daria A. Romanyuk, Marina S. Kliukova, А. А. Кирпичникова, И. А. Тихонович, Vladimir A. Zhukov, М. Ф. Шишова
Software Mentions: 6
Published: over 3 years ago

10.3389/fimmu.2021.645446

Antiretroviral Treatment-Induced Decrease in Immune Activation Contributes to Reduced Susceptibility to Tuberculosis in HIV-1/Mtb Co-infected Persons
Cited by: 4
Author(s): Katalin A. Wilkinson, Deborah Schneider-Luftman, Rachel Lai, Christopher Barrington, Nishtha Jhilmeet, David M. Lowe, Gavin Kelly, Robert J. Wilkinson
Software Mentions: 5
Published: over 3 years ago

10.3390/pharmaceutics13040488

A COVID-19 Drug Repurposing Strategy through Quantitative Homological Similarities Using a Topological Data Analysis-Based Framework
Cited by: 11
Author(s): Raúl Pérez-Moraga, Jaume Forés-Martos, Beatriz Suay-García, Jean‐Louis Duval, Antonio Falcó, Joan Climent
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-81538-4

Clinical implications of intrinsic molecular subtypes of breast cancer for sentinel node status
Cited by: 12
Author(s): Maria Rossing, Christina Bligaard Pedersen, Tove Filtenborg Tvedskov, Ilse Vejborg, Maj Lis Møller Talman, Lars Rønn Olsen, Niels Kroman, Finn Cilius Nielsen, Maj Britt Jensen, Bent Ejlertsen
Software Mentions: 5
Published: almost 4 years ago

10.1002/btm2.10198

Transcriptomic response of brain tissue to focused <scp>ultrasound‐mediated blood–brain</scp> barrier disruption depends strongly on anesthesia
Cited by: 12
Author(s): Alexander S. Mathew, Catherine M. Gorick, E. Andrew Thim, William J. Garrison, Alexander L. Klibanov, G. Wilson Miller, Natasha D. Sheybani, Richard J. Price
Software Mentions: 5
Published: almost 4 years ago

10.1172/jci.insight.148694

Natural mucosal barriers and COVID-19 in children
Cited by: 113
Author(s): Carl A. Pierce, Sharlene Sy, Benjamin T. Galen, D. Yitzchak Goldstein, Erika P. Orner, Marla J. Keller, Kevan C. Herold, Betsy C. Herold
Software Mentions: 5
Published: over 3 years ago

10.3390/biology10050405

Human Endogenous Retroviruses (HERVs) and Mammalian Apparent LTRs Retrotransposons (MaLRs) Are Dynamically Modulated in Different Stages of Immunity
Cited by: 6
Author(s): Maria Paola Pisano, Nicole Grandi
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2020.550769

HDAC3 Mediates the Inflammatory Response and LPS Tolerance in Human Monocytes and Macrophages
Cited by: 26
Author(s): Mohammed Ghiboub, Jing Zhao, Andrew Y. Li Yim, Ronald Schilderink, Caroline Verseijden, Patricia H. P. van Hamersveld, José Duarte, Theodorus B. M. Hakvoort, Iris Admiraal, Nicola Harker, David F. Tough, Peter Henneman, Menno P.J. de Winther, Wouter J. de Jonge
Software Mentions: 5
Published: about 4 years ago

10.18632/aging.103296

High mutation load, immune-activated microenvironment, favorable outcome, and better immunotherapeutic efficacy in melanoma patients harboring MUC16/CA125 mutations
Cited by: 14
Author(s): Qinghua Wang, Yichen Yang, Meng Yang, Xiangchun Li, Kexin Chen
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-77777-6

Comparative analysis of transcriptomic profile, histology, and IDH mutation for classification of gliomas
Cited by: 6
Author(s): Paul Tran, Lynn Tran, John Nechtman, Bruno dos Santos, Sharad Purohit, Khaled Bin Satter, Boying Dun, Ravindra Kolhe, Suash Sharma, Roni J. Bollag, Jin Xiong She
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-019-45515-2

Open chromatin dynamics in prosensory cells of the embryonic mouse cochlea
Cited by: 13
Author(s): Brent A. Wilkerson, Alex Chitsazan, Leah S. VandenBosch, Matthew S. Wilken, Thomas A. Reh, Olivia Bermingham‐McDonogh
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-90797-0

Targeting of the CD80/86 proinflammatory axis as a therapeutic strategy to prevent severe COVID-19
Cited by: 9
Author(s): Antonio Julià, Irene Bonafonte-Pardàs, Antonio Gómez, María López-Lasanta, Mireia López-Corbeto, Sergio H Martínez-Mateu, Jordi Lladós, Iván Rodríguez-Nunez, R Myers, Sara Marsal
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-021-02263-9

Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs
Cited by: 62
Author(s): Yang Zhang, Tuan M. Nguyen, Xiao‐Ou Zhang, Limei Wang, Tin Phan, John G. Clohessy, Pier Paolo Pandolfi
Software Mentions: 5
Published: almost 4 years ago

10.3390/cancers13092115

Chromatin-Directed Proteomics Identifies ZNF84 as a p53-Independent Regulator of p21 in Genotoxic Stress Response
Cited by: 8
Author(s): Anna Strzeszewska-Potyrała, Karolina Staniak, Joanna Czarnecka‐Herok, Mahmoud-Reza Rafiee, Marcin Herok, Grażyna Mosieniak, Jeroen Krijgsveld, Ewa Sikora
Software Mentions: 5
Published: over 3 years ago

10.1038/s41389-020-0224-1

Desmoplastic small round cell tumor is dependent on the EWS-WT1 transcription factor
Cited by: 24
Author(s): Jenna M. Gedminas, Maggie H. Chassé, Mitchell McBrairty, Ian Beddows, Susan M. Kitchen-Goosen, Patrick J. Grohar
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-019-1674-7

Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list
Cited by: 38
Author(s): Paul F. Harrison, Andrew Pattison, David Powell, Traude H. Beilharz
Software Mentions: 5
Published: over 5 years ago

10.1128/mSystems.00200-18

Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors
Cited by: 59
Author(s): Ashkaan K. Fahimipour, Sarah Ben Maamar, Alexander McFarland, Ryan A. Blaustein, Jing Chen, A. Glawe, Jeff Kline, Jessica L. Green, Rolf U. Halden, Kevin Van Den Wymelenberg, Curtis Huttenhower, Erica M. Hartmann
Software Mentions: 4
Published: about 6 years ago

10.3390/antiox10091380

NRF2 Mediates Therapeutic Resistance to Chemoradiation in Colorectal Cancer through a Metabolic Switch
Cited by: 7
Author(s): Séan M. O’Cathail, Chieh‐Hsi Wu, Russell J. Thomas, M. Hawkins, Tim Maughan, Annabelle Lewis
Software Mentions: 4
Published: about 3 years ago

10.1186/s12920-019-0518-3

Integrative genomic and transcriptomic analysis of genetic markers in Dupuytren’s disease
Cited by: 9
Author(s): Junghyun Jung, Go Woon Kim, Byungjo Lee, Jong Wha J. Joo, Wonhee Jang
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/6057948

Identification and Verification of a 17 Immune-Related Gene Pair Prognostic Signature for Colon Cancer
Cited by: 3
Author(s): Qianshi Zhang, Zhen Feng, Yongnian Zhang, Shasha Shi, Yu Zhang, Shuo Ren
Software Mentions: 4
Published: over 3 years ago

10.3390/biomedicines9070829

Biphasic Effects of Blue Light Irradiation on Human Umbilical Vein Endothelial Cells
Cited by: 4
Author(s): Kejia Kan, Yi-Fei Mu, Marielle Bouschbacher, Carsten Sticht, Natalia Kuch, Martin Sigl, Nuh N. Rahbari, Norbert Gretz, Prama Pallavi, Michael Keese
Software Mentions: 4
Published: over 3 years ago

10.3390/biom10040524

Uncovering Prognosis-Related Genes and Pathways by Multi-Omics Analysis in Lung Cancer
Cited by: 30
Author(s): Ken Asada, Kazuma Kobayashi, Samuel Joutard, Masashi Tubaki, Satoshi Takahashi, Ken Takasawa, Masaaki Komatsu, Syuzo Kaneko, Jun Sese, Ryuji Hamamoto
Software Mentions: 4
Published: over 4 years ago

10.1186/s12934-021-01583-6

Molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine candidate for rotavirus
Cited by: 6
Author(s): Neil C. Dalvie, Joseph Brady, Laura E. Crowell, Mary Kate Tracey, Andrew M. Biedermann, Kawaljit Kaur, John M. Hickey, D. Lee Kristensen, Alexandra Bonnyman, Sergio A. Rodriguez-Aponte, Charles A. Whittaker, Marina Bok, Celina G. Vega, Tarit Mukhopadhyay, Sangeeta B. Joshi, David B. Volkin, Viviana Parreño, Kerry R. Love, J. Christopher Love
Software Mentions: 4
Published: over 3 years ago

10.3390/plants10050919

Transcriptomic Analysis of Radish (Raphanus sativus L.) Spontaneous Tumor
Cited by: 2
Author(s): А.А. Ткаченко, И. Е. Додуева, Varvara E. Tvorogova, Alexander V. Predeus, Olga Pravdina, Ksenia Kuznetsova, Л. А. Лутова
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0251396

Fullerenol changes metabolite responses differently depending on the iron status of cucumber plants
Cited by: 5
Author(s): Nikolai P. Bityutskii, Kirill L. Yakkonen, Roman Puzanskiy, Kseniia A. Lukina, А. Л. Шаварда, Konstantin N. Semenov
Software Mentions: 4
Published: over 3 years ago

10.1038/s41419-021-03727-3

Interrogation of gender disparity uncovers androgen receptor as the transcriptional activator for oncogenic miR-125b in gastric cancer
Cited by: 14
Author(s): Ben Liu, Meng Zhou, Xiangchun Li, Xining Zhang, Qinghua Wang, Luyang Liu, Meng Yang, Da Yang, Yan Guo, Qiang Zhang, Hong Zheng, Qiong Wang, Lian Li, Xinlei Chu, Wei Wang, Haixin Li, Fengju Song, Yuan Pan, Wei Zhang, Kexin Chen
Software Mentions: 4
Published: over 3 years ago

10.1016/j.celrep.2021.109105

Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins
Cited by: 24
Author(s): Joseph Hiatt, Devin A. Cavero, Michael McGregor, Weihao Zheng, Jonathan M. Budzik, Theodore L. Roth, Kelsey M. Haas, David Wu, Ujjwal Rathore, Anke Meyer-Franke, Mohamed S. Bouzidi, Eric Shifrut, Youjin Lee, Vigneshwari Easwar Kumar, Eric V. Dang, David E. Gordon, Jason A. Wojcechowskyj, Judd F. Hultquist, Krystal A. Fontaine, Satish K. Pillai, Jeffery S. Cox, Joel D. Ernst, Nevan J. Krogan, Alexander Marson
Software Mentions: 4
Published: over 3 years ago

10.1016/j.crtox.2021.07.003

Reproducibility and robustness of high-throughput S1500+ transcriptomics on primary rat hepatocytes for chemical-induced hepatotoxicity assessment
Cited by: 3
Author(s): Fan Lee, Imran Shah, Yun Ting Soong, Jiangwa Xing, Inn Chuan Ng, Farah Tasnim, Hanry Yu
Software Mentions: 4
Published: almost 4 years ago

10.1530/ERC-19-0448

Effects of epigenetic pathway inhibitors on corticotroph tumour AtT20 cells
Cited by: 5
Author(s): Kate E Lines, P. Filippakopoulos, Mark Stevenson, Susanne Müller, Helen Lockstone, Benjamin Wright, Stefan Knapp, David Buck, C. Bountra, R V Thakker
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2021.654657

Discovery and Verification of an Immune-Related Gene Pairs Signature for Predicting Prognosis in Head and Neck Squamous Cell Carcinoma
Cited by: 0
Author(s): Jiarong He, Xinqi Fang, Mingming Han
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.716606

Augmented Expansion of Treg Cells From Healthy and Autoimmune Subjects via Adult Progenitor Cell Co-Culture
Cited by: 5
Author(s): James L. Reading, Valerie D. Roobrouck, Caroline Hull, Pablo D. Becker, Jelle Beyens, Alice Valentin-Torres, Dominic A. Boardman, Estefania Nova Lamperti, Samantha R. Stubblefield, Giovanna Lombardi, Robert Deans, Anthony E. Ting, Timothy Tree
Software Mentions: 4
Published: about 3 years ago

10.3389/fimmu.2021.666163

Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients
Cited by: 22
Author(s): Stéphanie Bibert, Nicolas Guex, João Lourenço, Thomas Brahier, Matthaios Papadimitriou-Olivgeris, Lauro Damonti, Oriol Manuel, Robin Liechti, Lou Götz, Jonathan Tschopp, Mathieu Quinodoz, Péter Vollenweider, Jean‐Luc Pagani, Mauro Oddo, Olivier Hügli, Frédéric Lamoth, Véronique Erard, Cathy Voide, Mauro Delorenzi, Nathalie Rufer, Fabio Candotti, Carlo Rivolta, Noémie Boillat‐Blanco, Pierre‐Yves Bochud
Software Mentions: 4
Published: over 3 years ago

10.3389/fneur.2021.691631

Hippocampal Transcriptome Changes After Subarachnoid Hemorrhage in Mice
Cited by: 4
Author(s): Angelique Regnier-Golanov, Friederike Dündar, Paul Zumbo, Doron Betel, Magda S Hernandez, Leif E. Peterson, Eng H. Lo, Eugene V. Golanov, Gavin W. Britz
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-018-1406-4

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
Cited by: 159
Author(s): Koen Van den Berge, Fanny Perraudeau, Charlotte Soneson, Michael I. Love, Davide Risso, Jean-Philippe Vert, Mark D. Robinson, Sandrine Dudoit
Software Mentions: 4
Published: over 6 years ago

10.1016/j.immuni.2019.12.007

Regulatory T Cells Restrain Interleukin-2- and Blimp-1-Dependent Acquisition of Cytotoxic Function by CD4+ T Cells
Cited by: 112
Author(s): Anna Śledzińska, Maria Vila de Mucha, Katharina Bergerhoff, Alastair Hotblack, Dafne Franz Demane, Ehsan Ghorani, Ayse U. Akarca, Maria A V Marzolini, Isabelle Solomon, Frederick Arce Vargas, Martin Pulé, Masahiro Ono, Benedict Seddon, George Kassiotis, Charlotte E. Ariyan, Thomas Korn, Teresa Marafioti, Graham M. Lord, Hans J. Stauss, Richard G. Jenner, Karl S. Peggs, Sergio A. Quezada
Software Mentions: 4
Published: almost 5 years ago

10.3390/jcm8101535

Connecting Histopathology Imaging and Proteomics in Kidney Cancer through Machine Learning
Cited by: 30
Author(s): Francisco Azuaje, Sang Yoon Kim, Daniel Hernández, Gunnar Dittmar
Software Mentions: 4
Published: about 5 years ago

10.1016/j.redox.2019.101321

Cannabidiol induces antioxidant pathways in keratinocytes by targeting BACH1
Cited by: 94
Author(s): Laura Casares, Víctor García, Martín Garrido‐Rodriguez, Estrella Millán, Juan A. Collado, Adela García‐Martín, Jon Peñarando, Marco A. Calzado, Laureano de la Vega, Eduardo Muñóz
Software Mentions: 4
Published: almost 5 years ago

10.21203/rs.3.rs-333578/v1

Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19
Cited by: 2
Author(s): Brian Le, Gaia Andreoletti, Tomiko Oskotsky, Albert Vallejo-Gracia, Romel Rosales, Katharine Yu, Idit Kosti, Kristoffer E. Leon, Daniel Bunis, Christine Li, G. Renuka Kumar, Kris M. White, Adolfo Garcı́a-Sastre, Mélanie Ott, Marina Sirota
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-61273-y

Comprehensive transcriptome profiling of Taiwanese colorectal cancer implicates an ethnic basis for pathogenesis
Cited by: 8
Author(s): Shao‐Min Wu, Wen‐Sy Tsai, Sum-Fu Chiang, Yi-Hsuan Lai, Chung‐Pei Ma, Jianhua Wang, Jeng-Feng Lin, Pei-Shan Lu, Chao-Ping Yang, Bertrand Chin‐Ming Tan, Hsuan Liu
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-91625-1

Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19
Cited by: 24
Author(s): Brian Le, Gaia Andreoletti, Tomiko Oskotsky, Albert Vallejo-Gracia, Romel Rosales, Katharine Yu, Idit Kosti, Kristoffer E. Leon, Daniel Bunis, Christine Li, G. Renuka Kumar, Kris M. White, Adolfo Garcı́a-Sastre, Mélanie Ott, Marina Sirota
Software Mentions: 4
Published: over 3 years ago

Projects: bioconductor: fgsea

Papers Mentioning fgsea 150