bioconductor: limma | Projects | Ecosyste.ms: Papers

10.18632/oncotarget.12276

Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers
Cited by: 15
Author(s): Sameer Chopra, Jie Liu, Mehrdad Alemozaffar, Peter W. Nichols, Manju Aron, Daniel J. Weisenberger, Clayton K. Collings, Sumeet Syan, Brian Hu, Mihir Desai, Monish Aron, Vinay Duddalwar, Inderbir S. Gill, Gangning Liang, Kimberly D. Siegmund
Software Mentions: 3
Published: almost 10 years ago

10.3389/fimmu.2018.00821

Acute Zika Virus Infection in an Endemic Area Shows Modest Proinflammatory Systemic Immunoactivation and Cytokine-Symptom Associations
Cited by: 27
Author(s): Jéssica Barletto de Sousa Barros, Paulo Alex Neves da Silva, Rosemary de Carvalho Rocha Koga, Patrícia Gonzalez-Dias, José Rodrigues Carmo Filho, Patrícia Resende Alo Nagib, Verônica Coelho, Hidehiko Nakaya, Simone Gonçalves Fonseca, Irmtraut Araci Hoffmann Pfrimer
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-12-610

Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease
Cited by: 10
Author(s): Rudi Alberts, Hairong Chen, Claudia Pommerenke, August B. Smit, Sabine Spijker, Robert W. Williams, Robert Geffers, Dunja Bruder, Klaus Schughart
Software Mentions: 3
Published: almost 15 years ago

10.1186/s13326-016-0079-8

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease
Cited by: 16
Author(s): Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann‐Apitius, Philipp Senger
Software Mentions: 3
Published: about 10 years ago

10.1186/s12859-017-1467-5

Identifying miRNA sponge modules using biclustering and regulatory scores
Cited by: 21
Author(s): Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-020-67801-0

Novel candidate drugs in anti-tumor necrosis factor refractory Crohn’s diseases: in silico study for drug repositioning
Cited by: 5
Author(s): Min Seob Kwak, Hun Hee Lee, Jae Myung, Hyun Phil Shin, Jung Won Jeon, Jin Young Yoon
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-018-5000-7

Murine host response to Neisseria gonorrhoeae upper genital tract infection reveals a common transcriptional signature, plus distinct inflammatory responses that vary between reproductive cycle phases
Cited by: 11
Author(s): Ian Francis, Epshita A. Islam, Adam C. Gower, Yazdani B. Shaik‐Dasthagirisaheb, Scott D. Gray-Owen, Lee M. Wetzler
Software Mentions: 3
Published: about 8 years ago

10.1186/1471-2105-16-S18-S16

Identification of aberrant gene expression associated with aberrant promoter methylation in primordial germ cells between E13 and E16 rat F3 generation vinclozolin lineage
Cited by: 23
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-15-773

Maize protein phosphatase gene family: identification and molecular characterization
Cited by: 53
Author(s): Kaifa Wei, Si Pan
Software Mentions: 3
Published: over 12 years ago

10.1186/s13036-019-0180-5

Expression profile analysis of long non-coding RNA in skeletal muscle of osteoporosis by microarray and bioinformatics
Cited by: 8
Author(s): Shaojin Liu, Hongxing Huang, Shuang Chai, Hewei Wei, Jiachun Huang, Lei Wan
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-020-68437-w

Injection of seminal fluid into the hemocoel of honey bee queens (Apis mellifera) can stimulate post-mating changes
Cited by: 9
Author(s): W. Cameron Jasper, Laura M. Brutscher, Christina M. Grozinger, Elina L. Niño
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-017-4385-z

Transcriptional effects of a positive feedback circuit in Drosophila melanogaster
Cited by: 5
Author(s): Jarosław Bryk, R. Guy Reeves, Floyd A. Reed, Jai A. Denton
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2164-15-1176

Distinct gene signatures in aortic tissue from ApoE-/-mice exposed to pathogens or Western diet
Cited by: 8
Author(s): Carolyn D. Kramer, Ellen O. Weinberg, Adam C. Gower, Xianbao He, Samrawit Mekasha, Connie Slocum, Lea M. Beaulieu, Lee M. Wetzler, Yuriy O. Alekseyev, Frank C. Gibson, Jane E. Freedman, Robin R. Ingalls, Caroline A. Genco
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-016-2565-x

Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome
Cited by: 14
Author(s): Aimee Benjamin, Benjamin B. Green, B.A. Crooker, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: over 10 years ago

10.18632/aging.203140

A novel ferroptosis-related gene signature for prognostic prediction of patients with lung adenocarcinoma
Cited by: 13
Author(s): Jingjing Jin, Chuan Liu, Shanshan Yu, Lingyi Cai, Andriamifahimanjaka Sitrakiniaina, Ruihong Gu, Wenfeng Li, Fangfang Wu, Xiangyang Xue
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.146098

SLFN11 captures cancer-immunity interactions associated with platinum sensitivity in high-grade serous ovarian cancer
Cited by: 9
Author(s): C Winkler, Matthew King, Julie Berthe, Domenico Ferraioli, Anna Garuti, Federica Grillo, Jaime Rodriguez‐Canales, Lorenzo Ferrando, Nicolás Chopin, Isabelle Ray‐Coquard, Oona Delpuech, Davide Bedognetti, Alberto Ballestrero, Elisabetta Leo, Gabriele Zoppoli
Software Mentions: 3
Published: almost 5 years ago

10.1016/S1470-2045(17)30243-7

Novel molecular subgroups for clinical classification and outcome prediction in childhood medulloblastoma: a cohort study
Cited by: 359
Author(s): Ed C. Schwalbe, Janet C. Lindsey, Sirintra Nakjang, Stephen Crosier, Amanda Smith, Debbie Hicks, Gholamreza Rafiee, Rebecca Hill, Alice Iliasova, T. J. Stone, Barry Pizer, Antony Michalski, Abhijit Joshi, Stephen B. Wharton, Thomas S. Jacques, Simon Bailey, Daniel Williamson, Steven C. Clifford
Software Mentions: 3
Published: about 9 years ago

10.7554/eLife.24265

Transcription factor TFCP2L1 patterns cells in the mouse kidney collecting ducts
Cited by: 55
Author(s): Max Werth, Kai M. Schmidt‐Ott, Thomas Leete, Andong Qiu, Christian Hinze, Mélanie Viltard, Neal Paragas, Carrie J. Shawber, Wenqiang Yu, Peter Lee, Xia Chen, Abby Sarkar, Weiyi Mu, Alexander Rittenberg, Chyuan Sheng Lin, Jan Kitajewski, Qais Al‐Awqati, Jonathan Barasch
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-020-6589-x

Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments
Cited by: 2
Author(s): Jeffrey Thompson, Devin C. Koestler
Software Mentions: 3
Published: over 6 years ago

10.1172/jci.insight.150483

TNFRSF13B genotypes control immune-mediated pathology by regulating the functions of innate B cells
Cited by: 3
Author(s): Mayara Garcia de Mattos Barbosa, Adam R. Lefferts, Danny Huynh, Hui Liu, Yu Zhang, Beverly Fu, Jenna Barnes, Milagros Samaniego‐Picota, Richard J. Bram, Raif S. Geha, Ariella Shikanov, Eline T. Luning Prak, Evan A. Farkash, Jeffrey L. Platt, Marília Cascalho
Software Mentions: 3
Published: about 5 years ago

10.1038/s41375-020-0762-8

Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing
Cited by: 38
Author(s): Wibowo Arindrarto, Daniel Borràs, Ruben A.L. De Groen, Redmar R van den Berg, Irene J. Locher, Saskia A.M.E. van Diessen, Rosalie van der Holst, Edith D. van der Meijden, M. Willy Honders, Rick H. de Leeuw, Wina Verlaat, Inge Jedema, Wilma G. M. Kroes, Jeroen Knijnenburg, Tom van Wezel, Joost S.P. Vermaat, Peter J.M. Valk, Bart Janssen, Peter de Knijff, Cornelis A.M. van Bergen, Erik B. van den Akker, Peter A C ‘t Hoen, Szymon M. Kiełbasa, Jeroen F. J. Laros, Marieke Griffioen, Hendrik Veelken
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0004839

Expression Analysis of the Theileria parva Subtelomere-Encoded Variable Secreted Protein Gene Family
Cited by: 39
Author(s): Jacqueline Schmuckli‐Maurer, Carlo Casanova, Stéfanie Schmied, Sarah Affentranger, Iana Parvanova, S. Kang'a, Vishvanath Nene, Frank Katzer, Declan J. McKeever, Joachim Müller, Richard P. Bishop, Arnab Pain, Dirk Dobbelaere
Software Mentions: 3
Published: over 17 years ago

10.1371/journal.pone.0140964

Influence of Development and Dietary Phospholipid Content and Composition on Intestinal Transcriptome of Atlantic Salmon (Salmo salar)
Cited by: 30
Author(s): Christian De Santis, John F. Taylor, Laura Martínez-Rubio, Sebastián Boltaña, Douglas R. Tocher
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-021-94360-9

CD276 is an important player in macrophage recruitment into the tumor and an upstream regulator for PAI-1
Cited by: 6
Author(s): Sibel Durlanik, Katrin Fundel‐Clemens, Coralie Viollet, Heinrich J. Huber, Martin Lenter, Kerstin Kitt, Stefan Pflanz
Software Mentions: 3
Published: about 5 years ago

10.1172/jci.insight.148086

High-dimensional mass cytometry identifies T cell and B cell signatures predicting reduced risk of Plasmodium vivax malaria
Cited by: 6
Author(s): Lisa J Ioannidis, Halina M. Pietrzak, Ann Ly, Retno A. S. Utami, Emily M. Eriksson, Stephanie I Studniberg, Waruni Abeysekera, Connie S. N. Li Wai Suen, Dylan Sheerin, Julie Healer, Agatha M. Puspitasari, Dwi Apriyanti, Farah N. Coutrier, Jeanne Rini Poespoprodjo, Enny Kenangalem, Benediktus Andries, Pak Prayoga, Novita Sariyanti, Gordon K. Smyth, Leily Trianty, Alan F. Cowman, Ric N. Price, Rintis Noviyanti, Diana S. Hansen
Software Mentions: 3
Published: about 5 years ago

10.18632/oncotarget.9982

Deregulation of polycomb repressor complex 1 modifier AUTS2 in T-cell leukemia
Cited by: 14
Author(s): Stefan Nagel, Claudia Pommerenke, Corinna Meyer, Maren Kaufmann, Hans G. Drexler, Roderick A.F. MacLeod
Software Mentions: 3
Published: over 10 years ago

10.1172/jci.insight.144913

MMP2 and TLRs modulate immune responses in the tumor microenvironment
Cited by: 21
Author(s): Luciana Rebiero Muniz-Bongers, Christopher B. McClain, Mansi Saxena, Gerold Bongers, Miriam Mérad, Nina Bhardwaj
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-020-03768-z

MADloy: robust detection of mosaic loss of chromosome Y from genotype-array-intensity data
Cited by: 6
Author(s): Juan R. González, Marcos López-Sánchez, Alejandro Cáceres, Pere Puig, Tõnu Esko, Luis A. Pérez‐Jurado
Software Mentions: 3
Published: almost 6 years ago

10.3390/life10090191

The Effect of Tobacco Smoking and Smoking Cessation on Urinal miRNAs in a Pilot Study
Cited by: 2
Author(s): Zdenka Navratilova, Stanislav Losse, Pavla Petrová, Kateřina Sikorová, Alzbeta Chabronova, Martin Petřek
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-021-07977-5

Comparison of the transcriptome in circulating leukocytes in early lactation between primiparous and multiparous cows provides evidence for age-related changes
Cited by: 4
Author(s): Laura Buggiotti, Zhangrui Cheng, Mazdak Salavati, Claire Wathes
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-021-07935-1

A validated generally applicable approach using the systematic assessment of disease modules by GWAS reveals a multi-omic module strongly associated with risk factors in multiple sclerosis
Cited by: 4
Author(s): Tejaswi V. S. Badam, Hendrik A de Weerd, David Martínez-Enguita, Tomas Olsson, Lars Alfredsson, Ingrid Kockum, Maja Jagodic, Zelmina Lubovac-Pilav, Mika Gustafsson
Software Mentions: 3
Published: about 5 years ago

10.1155/2021/9915312

Ferroptosis-Related Gene Signature Promotes Ovarian Cancer by Influencing Immune Infiltration and Invasion
Cited by: 21
Author(s): You Qing Yang, Fan Qi, Jian Huang, Yaoqiu Wu, Haiyan Lin, Qingxue Zhang
Software Mentions: 3
Published: over 5 years ago

10.3389/fmed.2021.667543

m6A RNA Methylation Regulator YTHDF1 Correlated With Immune Microenvironment Predicts Clinical Outcomes and Therapeutic Efficacy in Breast Cancer
Cited by: 10
Author(s): Ying Hu, Qinwen Pan, Minghao Wang, Xiang Ai, Yuzhao Yan, Yuan Tian, Yuting Jing, Peng Tang, Jun Jiang
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-15-879

A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples
Cited by: 13
Author(s): Alberto Risueño, Beatriz Rosón-Burgo, Anna Dolnik, Jesús María Hernández-Rivas, Lars Bullinger, Javier De Las Rivas
Software Mentions: 3
Published: almost 12 years ago

10.26508/lsa.202001000

IL-13 deficiency exacerbates lung damage and impairs epithelial-derived type 2 molecules during nematode infection
Cited by: 11
Author(s): Alistair Chenery, Silvia Rosini, JE Parkinson, Jesuthas Ajendra, Jeremy Herrera, Craig Lawless, Brian H. K. Chan, P’ng Loke, Andrew S. MacDonald, Karl E. Kadler, Tara E. Sutherland, Judith E. Allen
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.147929

Adipocyte-like signature in ovarian cancer minimal residual disease identifies metabolic vulnerabilities of tumor initiating cells
Cited by: 2
Author(s): Mara Artibani, Kenta Masuda, Zhiyuan Hu, Pascal C. Rauher, Garry Mallett, Nina Wietek, Matteo Morotti, Kay Y. Chong, Mohammad KaramiNejadRanjbar, Christos E. Zois, Sunanda Dhar, Salma El-Sahhar, Leticia Campo, Sarah P. Blagden, Stephen Damato, Pubudu Pathiraja, Shibani Nicum, Fergus Gleeson, A Laios, Abdulkhaliq Alsaadi, Laura Santana González, Takeshi Motohara, Ashwag Albukhari, Zhen Lü, Robert C. Bast, Adrian L. Harris, Christer S. Ejsing, Robin W. Klemm, Christopher Yau, Tatjana Sauka‐Spengler, Ashfaq Ahmed
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.103811

A newly defined risk signature, consisting of three m6A RNA methylation regulators, predicts the prognosis of ovarian cancer
Cited by: 25
Author(s): Lili Fan, Yu Lin, Lei Han, Guang Shu, Lingyun He, Zhipeng Yan, Rihan Hai, Gang Yin
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-96274-y

Integrated bioinformatics analysis of differentially expressed genes and immune cell infiltration characteristics in Esophageal Squamous cell carcinoma
Cited by: 14
Author(s): Feng Zuo, Jingge Qu, Xiao Liu, Jinghui Liang, Yongmeng Li, Jianhua Jin, Huiying Zhang, Hui Tian
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-14-371

Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor
Cited by: 34
Author(s): Franc Llorens, Manuela Hummel, Lorena Pantano, Xavier Pastor, Ana Vivancos, Ester Castillo, Heidi Mattlin, Anna Ferrer, Matthew Ingham, María Noguera, Robert Kofler, Juliane C. Dohm, Raquel Pluvinet, Mònica Bayés, Heinz Himmelbauer, José Antonio del Río, Eulàlia Martı́, Lauro Sumoy
Software Mentions: 3
Published: over 13 years ago

10.26508/lsa.202000810

DGCR8 deficiency impairs macrophage growth and unleashes the interferon response to mycobacteria
Cited by: 0
Author(s): Barbara Killy, Barbara Bodendorfer, Jörg Mages, Kristina Ritter, Jonathan Schreiber, Christoph Hölscher, Katharina Pracht, Arif B. Ekici, Hans‐Martin Jäck, Roland Lang
Software Mentions: 3
Published: over 5 years ago

10.26508/lsa.201800205

Innate extracellular vesicles from melanoma patients suppress β-catenin in tumor cells by miRNA-34a
Cited by: 22
Author(s): Jung-Hyun Lee, Jochen Dindorf, Martin Eberhardt, Xin Lai, Christian Ostalecki, Nina Koliha, Stefani Gross, Katja Blume, Heiko Bruns, Stefan Wild, Gerold Schuler, Julio Vera, Andreas S. Baur
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-7-126

Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria
Cited by: 97
Author(s): Roland J. Siezen, Jos Boekhorst, Lidia Muscariello, Douwe Molenaar, Bernadet Renckens, Michiel Kleerebezem
Software Mentions: 3
Published: over 20 years ago

10.1186/1471-2164-15-960

Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection
Cited by: 27
Author(s): Ignacio Caballero, Judy Yen, Lisa E. Hensley, Anna N. Honko, Arthur J. Goff, John H. Connor
Software Mentions: 3
Published: over 12 years ago

10.1002/advs.202100363

Calcium–Collagen Coupling is Vital for Biomineralization Schedule
Cited by: 7
Author(s): Jinglun Zhang, Yaoting Ji, Shuting Jiang, Miusi Shi, Wenjin Cai, Richard J. Miron, Yufeng Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12944-019-1032-5

Integrated analysis of gene expression changes associated with coronary artery disease
Cited by: 9
Author(s): Miao Liu, Rui-Xing Yin, Feng Huang, Shuo Yang, Wu-Xian Chen, Jin‐Zhen Wu
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0019322

Generation of a Predictive Melphalan Resistance Index by Drug Screen of B-Cell Cancer Cell Lines
Cited by: 19
Author(s): Martin Boegsted, Johanne Marie Holst, Kirsten Fogd, Steffen Falgreen, Susanne Sørensen, Alexander Schmitz, Anne Bukh, Hans Erik Johnsen, Mette Nyegaard, Karen Dybkær
Software Mentions: 3
Published: over 15 years ago

10.1186/1471-2105-11-553

Algorithm-driven Artifacts in median polish summarization of Microarray data
Cited by: 50
Author(s): Federico M. Giorgi, Anthony Bolger, Marc Lohse, Björn Usadel
Software Mentions: 3
Published: almost 16 years ago

10.1038/s41598-021-96374-9

Integrative genetic, genomic and transcriptomic analysis of heat shock protein and nuclear hormone receptor gene associations with spontaneous preterm birth
Cited by: 10
Author(s): Johanna M. Huusko, Heli Tiensuu, Antti M. Haapalainen, Anu Pasanen, Pinja Tissarinen, Minna K. Karjalainen, Ge Zhang, Kaare Christensen, Kelli K. Ryckman, Bo Jacobsson, Jeffrey C. Murray, Stephen F. Kingsmore, Mikko Hallman, Louis J. Muglia, Mika Rämet
Software Mentions: 3
Published: about 5 years ago

10.1172/jci.insight.135544

PDX-derived organoids model in vivo drug response and secrete biomarkers
Cited by: 55
Author(s): Ling Huang, Bruno Bockorny, Indranil Paul, Dipikaa Akshinthala, Pierre‐Olivier Frappart, Omar Gandarilla, Arindam Bose, Veronica Sanchez‐Gonzalez, Emily E Rouse, Sylvain Lehoux, Nicole Pandell, Christine Lim, John G. Clohessy, Joseph E. Grossman, Raúl González, Sofia Perea Del Pino, George Daaboul, Mandeep S. Sawhney, Steven D. Freedman, Alexander Kleger, Richard D. Cummings, Andrew Emili, Lakshmi Muthuswamy, Manuel Hidalgo, Senthil K. Muthuswamy
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12944-020-01217-7

Genes associated with inflammation may serve as biomarkers for the diagnosis of coronary artery disease and ischaemic stroke
Cited by: 12
Author(s): Peng-Fei Zheng, Fu-Jun Liao, Rui-Xing Yin, Lu-Zhu Chen, Hui Li, Rong-Jun Nie, Yong Wang, Pei-Juan Liao
Software Mentions: 3
Published: over 6 years ago

10.1186/s12944-020-01299-3

Ubiquitin-specific protease as the underlying gene biomarker for aortic stenosis
Cited by: 3
Author(s): Yin Yuan, Lianqun Wang, Bo-Chen Yao, Zhigang Guo
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-9-390

Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays
Cited by: 100
Author(s): Alexandra B. Graf, Brigitte Gasser, Martin Dragosits, Michael Sauer, Germán Leparc, Thomas Tüchler, David P. Kreil, Diethard Mattanovich
Software Mentions: 3
Published: about 18 years ago

10.3389/fmicb.2017.01784

Analyzing the Complex Regulatory Landscape of Hfq – an Integrative, Multi-Omics Approach
Cited by: 14
Author(s): Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V. Galmozzi, Günter Krämer, Jacob G. Malone
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2105-10-288

Exploratory and inferential analysis of gene cluster neighborhood graphs
Cited by: 4
Author(s): Theresa Scharl, Ingo Voglhuber, Friedrich Leisch
Software Mentions: 3
Published: about 17 years ago

10.3389/fimmu.2019.00600

1,25-Dihydroxyvitamin D3 Restrains CD4+ T Cell Priming Ability of CD11c+ Dendritic Cells by Upregulating Expression of CD31
Cited by: 30
Author(s): Louise Saul, Iris Mair, Alasdair Ivens, Pamela Brown, Kay Samuel, John Campbell, Daniel Soong, Nadine Kamenjarin, Richard J. Mellanby
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-15-238

Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models
Cited by: 92
Author(s): Florian Martin, Alain Sewer, Marja Talikka, Yu‐Tao Xiang, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: about 12 years ago

10.1172/jci.insight.137427

Comprehensive plasma proteomic profiling reveals biomarkers for active tuberculosis
Cited by: 31
Author(s): Diana J. Garay‐Baquero, Cory H. White, Naomi F. Walker, Marc Tebruegge, Hannah F. Schiff, César Ugarte-Gil, Stephen Morris-Jones, Ben G. Marshall, Antigoni Manousopoulou, John Adamson, Andrés F. Vallejo, Magdalena K. Bielecka, Robert J. Wilkinson, Liku B. Tezera, Christopher H. Woelk, Spiros D. Garbis, Paul Elkington
Software Mentions: 3
Published: about 6 years ago

10.1172/jci.insight.137029

C5a impairs phagosomal maturation in the neutrophil through phosphoproteomic remodeling
Cited by: 23
Author(s): Alexander Wood, Arlette Vassallo, Marie-Hélène Ruchaud-Sparagano, Jonathan Scott, Carmelo Zinnato, Carmen Gonzalez-Tejedo, Kamal Kishore, Clive S. D’Santos, A. John Simpson, David K. Menon, Charlotte Summers, Edwin R. Chilvers, Klaus Okkenhaug, Andrew Conway Morris
Software Mentions: 3
Published: about 6 years ago

10.3390/md19080429

RKC-B1 Blocks Activation of NF-κB and NLRP3 Signaling Pathways to Suppress Neuroinflammation in LPS-Stimulated Mice
Cited by: 3
Author(s): Man Liu, Yinglin Yang, Shanshan Zhang, Dong-Ni Liu, Lian-Hua Fang, Guanhua Du, Yue-Hua Wang
Software Mentions: 3
Published: about 5 years ago

10.1172/jci.insight.133393

Histone deacetylases 1 and 2 restrain CD4+ cytotoxic T lymphocyte differentiation
Cited by: 20
Author(s): Teresa Preglej, Patricia Hamminger, Maik Luu, Tanja Bulat, Liisa Andersen, Lisa Göschl, Valentina Stolz, Ramona Rica, Lisa Sandner, Darina Waltenberger, Roland Tschismarov, Thomas Faux, Thorina Boenke, Asta Laiho, Laura L. Elo, Shoji Sakaguchi, Günter Steiner, Thomas Decker, Barbara Bohle, Alexander Visekruna, Christoph Bock, Birgit Strobl, Christian Seiser, Nicole Boucheron, Wilfried Ellmeier
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-852

Transcriptional response to cardiac injury in the zebrafish: systematic identification of genes with highly concordant activity across in vivo models
Cited by: 10
Author(s): Sophie Rodius, Petr V. Nazarov, Isabel A. Nepomuceno-Chamorro, Céline Jeanty, Juan Manuel González‐Rosa, Mark Ibberson, Ricardo Costa, Ioannis Xénarios, Nadia Mercader, Francisco Azuaje
Software Mentions: 3
Published: almost 12 years ago

10.18632/oncotarget.8713

Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung adenocarcinoma
Cited by: 43
Author(s): Naiara da Costa Cinegaglia, Sónia C. S. Andrade, Tomáš Tokár, Maísa Pinheiro, Fabio Severino, Rogério Antônio de Oliveira, Érica Nishida Hasimoto, Daniele Cristina Catâneo, Antônio José Maria Catâneo, Júlio Defaveri, Cleonilson Protásio de Souza, Márcia Maria Chiquitelli Marques, Robson Francisco Carvalho, Luiz Lehmann Coutinho, Jefferson Luiz Gross, Sílvia Regina Rogatto, Wan L. Lam, Igor Jurišica, Patrícia P. Reis
Software Mentions: 3
Published: over 10 years ago

10.1155/2021/3170261

lncRNA PAPPA-AS1 Induces the Development of Hypertrophic Scar by Upregulating TLR4 through Interacting with TAF15
Cited by: 5
Author(s): Pengju Fan, Yongjie Wang, Jingjing Li, Man Fang
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-019-5900-1

Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data
Cited by: 5
Author(s): Fernando Carazo, Marian Gimeno, Juan A Ferrer-Bonsoms, Ángel Rubio
Software Mentions: 3
Published: about 7 years ago

10.3389/fimmu.2019.00708

Immunological Molecular Responses of Human Retinal Pigment Epithelial Cells to Infection With Toxoplasma gondii
Cited by: 15
Author(s): Shervi Lie, E Rochet, Erik Segerdell, Yuefang Ma, Liam M. Ashander, Audra Shadforth, Timothy A. Blenkinsop, Michael Michael, Binoy Appukuttan, Beth Wilmot, Justine R. Smith
Software Mentions: 3
Published: over 7 years ago

10.1155/2020/5310793

Identification of a 5-Gene Metabolic Signature for Predicting Prognosis Based on an Integrated Analysis of Tumor Microenvironment in Lung Adenocarcinoma
Cited by: 14
Author(s): Xiaolin Yu, Xiaomei Zhang, Yanxia Zhang
Software Mentions: 3
Published: about 6 years ago

10.18632/aging.202997

Identification of potential autophagy-associated lncRNA in prostate cancer
Cited by: 6
Author(s): Jun Li, Hong Du, Wenqiang Chen, Mingxing Qiu, Peng He, Zhiwei Ma
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-96995-0

The human type 2 diabetes-specific visceral adipose tissue proteome and transcriptome in obesity
Cited by: 26
Author(s): Nicholas J. Carruthers, Clarissa Strieder‐Barboza, Joseph A. Caruso, Carmen G. Flesher, Nicki A. Baker, Samuel A. Kerk, Alexander Ky, Anne P. Ehlers, Oliver A. Varban, Costas A. Lyssiotis, Carey N. Lumeng, Paul M. Stemmer, Robert W. O’Rourke
Software Mentions: 3
Published: about 5 years ago

10.1534/g3.120.401477

Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana
Cited by: 5
Author(s): Margi Hartanto, Ronny V.L. Joosen, L. Basten Snoek, Leo A.J. Willems, Mark G. Sterken, Dick de Ridder, Henk W. M. Hilhorst, Wilco Ligterink, Harm Nijveen
Software Mentions: 3
Published: almost 6 years ago

10.3390/medicina57090861

Gene Expression Analysis in Patients with Cocaine-Induced Midline Destructive Lesions
Cited by: 3
Author(s): Matteo Trimarchi, Giacomo Bertazzoni, Alessandro Vinciguerra, Celia Pardini, Fabio Simeoni, Davide Cittaro, Mario Bussi, Dejan Lazarevic
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-021-04288-0

MUREN: a robust and multi-reference approach of RNA-seq transcript normalization
Cited by: 4
Author(s): Yance Feng, Lei M. Li
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-021-07423-6

Consensus module analysis of abdominal fat deposition across multiple broiler lines
Cited by: 7
Author(s): Hui Yuan, Jun Lü
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.7262

miR-451a is underexpressed and targets AKT/mTOR pathway in papillary thyroid carcinoma
Cited by: 72
Author(s): Emanuela Minna, Paola Romeo, Matteo Dugo, Loris De Cecco, Katia Todoerti, Silvana Pilotti, Francesco Perrone, Ettore Seregni, Luca Agnelli, Antonino Neri, Angela Greco, Maria Grazia Borrello
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-021-97059-z

Gelatin methacrylate hydrogels culture model for glioblastoma cells enriches for mesenchymal-like state and models interactions with immune cells
Cited by: 6
Author(s): Nameeta Shah, Pavan M. Hallur, Raksha A. Ganesh, Pranali Sonpatki, Divya Naik, Komal Prasad Chandrachari, Ralph B. Puchalski, Aditya Chaubey
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0216898

Epstein-Barr virus (EBV) activates NKL homeobox gene HLX in DLBCL
Cited by: 14
Author(s): Stefan Nagel, Cord C. Uphoff, Wilhelm G. Dirks, Claudia Pommerenke, Corinna Meyer, Hans G. Drexler
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-017-4389-8

Time-course transcriptome analysis of human cellular reprogramming from multiple cell types reveals the drastic change occurs between the mid phase and the late phase
Cited by: 9
Author(s): Akihiro Kuno, Ken Nishimura, Satoru Takahashi
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0054398

miRNA Gene Promoters Are Frequent Targets of Aberrant DNA Methylation in Human Breast Cancer
Cited by: 114
Author(s): Lukáš Vrba, J. Muñoz-Rodríguez, Martha R. Stampfer, Bernard W. Futscher
Software Mentions: 3
Published: over 13 years ago

10.1186/1471-2164-11-344

Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays
Cited by: 18
Author(s): Cyril Dégletagne, Céline Keime, Benjamin Rey, Marc de Dinechin, Fabien Forcheron, Paul Chuchana, Pierre Jouventin, Christian Gautier, Claude Duchamp
Software Mentions: 3
Published: over 16 years ago

10.1097/MD.0000000000012679

Comprehensive assessment gene signatures for clear cell renal cell carcinoma prognosis
Cited by: 11
Author(s): Po-Ya Chang, Zhitong Bing, Jinhui Tian, Jingyun Zhang, Xiuxia Li, Long Ge, Juan Ling, Kun Yang, Yumin Li
Software Mentions: 3
Published: almost 8 years ago

10.3389/fimmu.2019.02736

Exacerbation of Chikungunya Virus Rheumatic Immunopathology by a High Fiber Diet and Butyrate
Cited by: 28
Author(s): Natalie A. Prow, Thiago Dominguez Crespo Hirata, Bing Tang, Thibaut Larcher, Pamela Mukhopadhyay, Tiago Lubiana Alves, Thuy T. Le, Joy Gardner, Yee Suan Poo, Eri Nakayama, Viviana P. Lutzky, Helder I. Nakaya, Andreas Suhrbier
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-017-3495-y

Active module identification in intracellular networks using a memetic algorithm with a new binary decoding scheme
Cited by: 4
Author(s): Dong Li, Zhisong Pan, Guyu Hu, Zexuan Zhu, Shan He
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-021-97319-y

An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis
Cited by: 11
Author(s): Negin Sheybani, Mohammad Reza Bakhtiarizadeh, Abdolreza Salehi
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.50135

Duodenum Intestine-Chip for preclinical drug assessment in a human relevant model
Cited by: 127
Author(s): Magdalena Kasendra, Raymond Luc, Jianyi Yin, Dimitris V. Manatakis, Gauri Kulkarni, Carolina Lucchesi, Josiah Sliz, Αθανασία Αποστόλου, Laxmi Sunuwar, Jenifer Obrigewitch, Kyung Jin Jang, Mark Donowitz, Katia Karalis
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-595

Gene network-based analysis identifies two potential subtypes of small intestinal neuroendocrine tumors
Cited by: 34
Author(s): Mark Kidd, Irvin M. Modlin, Ignat Drozdov
Software Mentions: 3
Published: over 12 years ago

10.1186/s12859-019-3107-8

Topology Consistency of Disease-specific Differential Co-regulatory Networks
Cited by: 4
Author(s): Maryam Nazarieh, Hema Sekhar Reddy Rajula, Volkhard Helms
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-021-98067-9

DNA methylation changes following narrative exposure therapy in a randomized controlled trial with female former child soldiers
Cited by: 6
Author(s): Samuel Carleial, Daniel Nätt, Eva Unternährer, Thomas Elbert, Katy Robjant, Sarah Wilker, Vanja Vukojević, Iris‐Tatjana Kolassa, Anja C. Zeller, Anke Koebach
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-021-07953-z

Integrative lncRNA landscape reveals lncRNA-coding gene networks in the secondary cell wall biosynthesis pathway of moso bamboo (Phyllostachys edulis)
Cited by: 9
Author(s): Jiongliang Wang, Yinguang Hou, Yu Wang, Hansheng Zhao
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-9-85

Statistical issues in the analysis of Illumina data
Cited by: 91
Author(s): Mark J. Dunning, Nuno L. Barbosa‐Morais, Andy G. Lynch, Simon Tavaré, Matthew E. Ritchie
Software Mentions: 3
Published: over 18 years ago

10.1371/journal.pone.0239061

In silico transcriptional analysis of mRNA and miRNA reveals unique biosignatures that characterizes different types of diabetes
Cited by: 4
Author(s): J Carlos Angulo, Caian L. Vinhaes, Eduardo R. Fukutani, Victor V. S. Albuquerque, Artur T. L. Queiroz, Bruno B. Andrade, Kiyoshi F. Fukutani
Software Mentions: 3
Published: almost 6 years ago

10.1186/2044-5040-2-7

miR-206 integrates multiple components of differentiation pathways to control the transition from growth to differentiation in rhabdomyosarcoma cells
Cited by: 36
Author(s): Kyle L. MacQuarrie, Zizhen Yao, Janet M. Young, Yi Cao, Stephen J. Tapscott
Software Mentions: 3
Published: over 14 years ago

10.1186/s13395-015-0059-1

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging
Cited by: 72
Author(s): Jing Su, Carl Johan Ekman, Nikolay Oskolkov, Leo Lahti, Kristoffer Ström, Alvis Brāzma, Leif Groop, Johan Rung, Ola Hansson
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-13-105

Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures
Cited by: 41
Author(s): Ana I. Manzano, Jack J. W. A. van Loon, Peter C. M. Christianen, Juana María González-Rubio, F. Javier Medina, Raúl Herranz
Software Mentions: 3
Published: over 14 years ago

10.3389/fmed.2020.00556

Expression Pattern and Prognostic Value of Key Regulators for m6A RNA Modification in Hepatocellular Carcinoma
Cited by: 12
Author(s): Lele Zhang, Yiting Qiao, Jiacheng Huang, Dalong Wan, Lin Zhou, Shigang Lin, Shusen Zheng
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0080099

Assessing Differential Expression in Two-Color Microarrays: A Resampling-Based Empirical Bayes Approach
Cited by: 4
Author(s): Dongmei Li, Marc A. Le Pape, Nisha I. Parikh, Will X. Chen, Timothy D. Dye
Software Mentions: 3
Published: almost 13 years ago

10.1080/21623945.2020.1776082

The common pathophysiologic threads between Asian Indian diabetic’s ‘Thin Fat Phenotype’ and partial lipodystrophy: the peripheral adipose tissue transcriptomic evidences
Cited by: 3
Author(s): Aditya Saxena, Prabhat Tiwari, Nitin Wahi, Anshul Kumar, Sandeep Kumar Mathur
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-015-1972-8

Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Cited by: 14
Author(s): Rossana Sussarellu, Arnaud Huvet, Sylvie Lapègue, Virgile Quillen, Christophe Lelong, Florence Cornette, Lasse Fast Jensen, Nicolas Bierne, Pierre Boudry
Software Mentions: 3
Published: almost 11 years ago

10.3389/fimmu.2019.02762

Hypoxia Inducible Factor 1α Inhibits the Expression of Immunosuppressive Tryptophan-2,3-Dioxygenase in Glioblastoma
Cited by: 21
Author(s): Soumya R. Mohapatra, Ahmed Sadik, Lars-Oliver Tykocinski, Jörn Dietze, Gernot Poschet, Ines Heiland, Christiane A. Opitz
Software Mentions: 3
Published: almost 7 years ago

10.1080/21623945.2020.1789283

Identification of differentially expressed mRNA and the Hub mRNAs modulated by lncRNA Meg3 as a competing endogenous RNA in brown adipose tissue of mice on a high-fat diet
Cited by: 5
Author(s): Yemin Zhang, Yalin Fu, Yuyang Zheng, Zhongyuan Wen, Changhua Wang
Software Mentions: 3
Published: over 6 years ago

10.1534/g3.112.004127

Natural Variation in the Yeast Glucose-Signaling Network Reveals a New Role for the Mig3p Transcription Factor
Cited by: 19
Author(s): Jeffrey A. Lewis, Audrey P. Gasch
Software Mentions: 3
Published: almost 14 years ago

10.3389/fimmu.2021.704557

Identification and Validation of Immune-Related Methylation Clusters for Predicting Immune Activity and Prognosis in Breast Cancer
Cited by: 1
Author(s): Anli Yang, Ying Zhou, Yanan Kong, Xiaoli Wei, Feng Ye, Lijuan Zhang, Xian Zhong, Mingyue Li, Shilin Lu, Xin An, Weikai Xiao
Software Mentions: 3
Published: about 5 years ago

Projects: bioconductor: limma

Science Score: 78/100

Bonuses:

Penalties:

Papers Mentioning limma 7,776