bioconductor: sva | Projects | Ecosyste.ms: Papers

10.1155/2018/8076397

The Influence of Metabolic Syndrome and Sex on the DNA Methylome in Schizophrenia
Cited by: 12
Author(s): Kyle J. Burghardt, Jaclyn M. Goodrich, Brittany N Lines, Vicki L. Ellingrod
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0255296

Developmental chronodisruption alters placental signaling in mice
Cited by: 2
Author(s): Danielle Clarkson-Townsend, Katie Bales, Karen Hermetz, Amber Burt, Machelle T. Pardue, Carmen J. Marsit
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1006477

Gene Expression Differences in Prostate Cancers between Young and Old Men
Cited by: 26
Author(s): Yuan-Chun Ding, Huiqing Wu, Charles Warden, Linda Steele, Xueli Liu, Maarten van Iterson, Xiwei Wu, Rebecca A. Nelson, Zheng Liu, Yate-Ching Yuan, Susan L. Neuhausen
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1008133

A novel single-cell based method for breast cancer prognosis
Cited by: 14
Author(s): Xiaomei Li, Lin Liu, Gregory J. Goodall, Andreas W. Schreiber, Taosheng Xu, Jiuyong Li, Thuc Duy Le
Software Mentions: 3
Published: about 4 years ago

10.7717/peerj.10171

Identification of key genes and pathways in endometriosis by integrated expression profiles analysis
Cited by: 6
Author(s): Ding Cui, Yang Liu, Junyan Ma, Kejian Lin, Kang Xu, Jizhen Lin
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0142037

Impact of Statins on Gene Expression in Human Lung Tissues
Cited by: 4
Author(s): Jackson Lane, Stephan F. van Eeden, Ma’en Obeidat, Don D. Sin, Scott J. Tebbutt, Wim Timens, Dirkje S. Postma, Michel Laviolette, Peter D. Paré, Yohan Bossé
Software Mentions: 3
Published: about 9 years ago

10.7717/peerj.7873

Identification of crucial genes in abdominal aortic aneurysm by WGCNA
Cited by: 61
Author(s): Siliang Chen, Dan Yang, Chuxiang Lei, Yuan Li, Xiaoning Sun, Mengyin Chen, Xiaoxian Wu, Yuehong Zheng
Software Mentions: 3
Published: about 5 years ago

10.1038/s41419-021-03932-0

An integrative transcriptome study reveals Ddit4/Redd1 as a key regulator of cancer cachexia in rodent models
Cited by: 14
Author(s): Mengyuan Niu, Li Li, Zhonglan Su, Lulu Wei, Wenyuan Pu, Chen Zhao, Yibing Ding, Junaid Wazir, Wangsen Cao, Shiyu Song, Qian Gao, Hongwei Wang
Software Mentions: 3
Published: over 3 years ago

10.18632/aging.202224

Expression profiles revealed potential kidney injury caused by SARS-CoV-2: a systematic analysis of ACE2 and clinical lessons learned from this discovery
Cited by: 2
Author(s): Jukun Song, Jianguo Zhu, Wei-Ming Chen, Guohua Zhu, Wei Wang, Chi Chen, Zhenyu Jia, Yan Zha, Ping Xu, Zheng Wang, Fa Sun, Xiangyan Zhang
Software Mentions: 3
Published: about 4 years ago

10.1126/sciadv.aax0301

Glycosylation of immunoglobulin G is regulated by a large network of genes pleiotropic with inflammatory diseases
Cited by: 84
Author(s): Lucija Klarić, Yakov A. Tsepilov, Chloe Stanton, Massimo Mangino, Timo Tõnis Sikka, Tõnu Esko, Eugene D Pakhomov, Perttu Salo, Joris Deelen, Stuart J. McGurnaghan, Toma Keser, Frano Vučković, Ivo Ugrina, Jasminka Krištić, Ivan Gudelj, Tamara Štambuk, Rosina Plomp, Maja Pučić‐Baković, Tamara Pavić, Marija Vilaj, Irena Trbojević‐Akmačić, Camilla Drake, Paula Dobrinić, Jelena Mlinarec, Barbara Jelušić, Anne Richmond, Maria Timofeeva, Alexander K. Grishchenko, Julia Dmitrieva, Mairead Lesley Bermingham, Sodbo Sharapov, Susan M. Farrington, Evropi Τheodoratou, Hae‐Won Uh, Marian Beekman, Eline Slagboom, Édouard Louis, Michel Georges, Manfred Wuhrer, Helen M. Colhoun, Malcolm G. Dunlop, Markus Perola, Krista Fischer, Ozren Polašek, Harry Campbell, Igor Rudan, James F. Wilson, Vlatka Zoldoš, Véronique Vitart, Tim D. Spector, Yurii S. Aulchenko, Gordan Lauc, Caroline Hayward
Software Mentions: 2
Published: over 4 years ago

10.1097/MD.0000000000025369

Construction of competing endogenous RNA network and identification of novel molecular biomarkers in colon cancer
Cited by: 4
Author(s): Xiaoqing Gu, Zicheng Xu, Yiting Liu, Zonghang Liu, Lei Zheng
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers13092252

A DNA Repair and Cell Cycle Gene Expression Signature in Pediatric High-Grade Gliomas: Prognostic and Therapeutic Value
Cited by: 2
Author(s): Natacha Entz‐Werlé, Laetitia Poidevin, Petr V. Nazarov, Olivier Poch, Benoît Lhermitte, Marie Pierre Chenard, Hélène Burckel, Éric Guérin, Quentin Fuchs, David Castel, Georges Noël, Laurence Choulier, Monique Dontenwill, Eric Van Dyck
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers13040801

AKT3 Expression in Mesenchymal Colorectal Cancer Cells Drives Growth and Is Associated with Epithelial-Mesenchymal Transition
Cited by: 16
Author(s): Joyce Y. Buikhuisen, Patricia M. Gomez Barila, Arezo Torang, Daniëlle Dekker, J.H. de Jong, Kate Cameron, Sara Vitale, Giorgio Stassi, Sander R. van Hooff, Mauro A. A. Castro, Louis Vermeulen, Jan Paul Medema
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0210371

Long live the queen, the king and the commoner? Transcript expression differences between old and young in the termite Cryptotermes secundus
Cited by: 20
Author(s): José Manuel Monroy Kuhn, Karen Meusemann, Judith Korb
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13229-015-0048-6

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment
Cited by: 120
Author(s): Ping Wang, Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Zheng Zhang, Wenjun Guo, Herbert M. Lachman, Deyou Zheng
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0156624

Sex Differences in Serum Markers of Major Depressive Disorder in the Netherlands Study of Depression and Anxiety (NESDA)
Cited by: 53
Author(s): Jordan M. Ramsey, Jason D. Cooper, Mariska Bot, Paul C. Guest, Femke Lamers, Cynthia Shannon Weickert, Brenda W. J. H. Penninx, Sabine Bahn
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.58376

Lymphangiogenic therapy prevents cardiac dysfunction by ameliorating inflammation and hypertension
Cited by: 31
Author(s): LouJin Song, Xian Chen, Terri A. Swanson, Brianna LaViolette, Jincheng Pang, Teresa Cunio, Michael W. Nagle, Shoh Asano, Katherine Hales, Arun Shipstone, Hanna Sobon, Sabra D Al-Harthy, Youngwook Ahn, Steven Kreuser, Andrew W. Robertson, Casey Ritenour, Frank Voigt, Magalie Boucher, Fu-Rong Sun, William C. Sessa, Rachel J. Roth Flach
Software Mentions: 2
Published: about 4 years ago

10.3389/fcvm.2021.656263

Bioinformatics Analysis Reveals the Potential Diagnostic Biomarkers for Abdominal Aortic Aneurysm
Cited by: 12
Author(s): Xinsheng Xie, En Ci Wang, Dongming Xu, Xiaolong Shu, Yu Zhao, Daqiao Guo, Weiguo Fu, Lixin Wang
Software Mentions: 2
Published: over 3 years ago

10.1074/mcp.TIR119.001906

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients
Cited by: 238
Author(s): Dorte B. Bekker-Jensen, Ana Martínez-Val, Sophia Steigerwald, Patrick Rüther, Kyle L. Fort, Tabiwang N. Arrey, Alexander Harder, Alexander Makarov, Jesper V. Olsen
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0061088

Comparative RNA-Seq and Microarray Analysis of Gene Expression Changes in B-Cell Lymphomas of Canis familiaris
Cited by: 48
Author(s): Marie R. Mooney, Jeff Bond, Noel R. Monks, Emily Eugster, David Cherba, Pamela J. Berlinski, Steve Kamerling, Keith R. Marotti, Heather Simpson, Tony Rusk, Waibhav Tembe, Christophe Legendre, Hollie Benson, Winnie S. Liang, Craig P. Webb
Software Mentions: 2
Published: over 11 years ago

10.3389/fnagi.2021.609679

The Therapeutic Targets of Fingolimod (FTY720) Are Involved in Pathological Processes in the Frontal Cortex of Alzheimer's Disease Patients: A Network Pharmacology Study
Cited by: 14
Author(s): Pengqi Yin, Yang Xue, Tingting Wang, Di Zhong, Guozhong Li
Software Mentions: 2
Published: almost 4 years ago

10.3389/fnagi.2016.00036

microRNA Profiles in Parkinson's Disease Prefrontal Cortex
Cited by: 117
Author(s): Andrew G. Hoss, Adam Labadorf, Thomas G. Beach, Jeanne C. Latourelle, Richard H. Myers
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-15-846

Transcriptome reconstruction and annotation of cynomolgus and African green monkey
Cited by: 12
Author(s): Albert Kim Lee, Hossein Khiabanian, Jeffrey R. Kugelman, Oliver Elliott, Elyse R. Nagle, Guo-Yun Yu, Travis K. Warren, Gustavo Palacios, Raúl Rabadán
Software Mentions: 2
Published: about 10 years ago

10.1136/gutjnl-2017-314817

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
Cited by: 110
Author(s): Judith Kraiczy, Komal Nayak, Kate J. Howell, Alex Ross, Jessica L. Forbester, Camilla Salvestrini, Roxana C. Mustata, Sally Perkins, Amanda Andersson-Rolf, Esther Leenen, Anke Liebert, Ludovic Vallier, Philip Rosenstiel, Oliver Stegle, Gordon Dougan, Robert Heuschkel, Bon–Kyoung Koo, Matthias Zilbauer
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2164-15-435

Dynamic imbalance between cancer cell subpopulations induced by Transforming Growth Factor Beta (TGF-β) is associated with a DNA methylome switch
Cited by: 26
Author(s): Marion Martin, Pierre‐Benoit Ancey, Marie-Pierre Cros, G. Durand, Florence Le Calvez-Kelm, Héctor Hernandez-Vargas, Zdenko Herceg
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-019-1700-9

Addressing confounding artifacts in reconstruction of gene co-expression networks
Cited by: 68
Author(s): Princy Parsana, Claire Ruberman, Andrew E. Jaffe, Michael C. Schatz, Alexis Battle, Jeffrey T. Leek
Software Mentions: 2
Published: over 5 years ago

10.18632/oncotarget.25710

TRAF3IP2, a novel therapeutic target in glioblastoma multiforme
Cited by: 13
Author(s): Eckhard Alt, Zahra Barabadi, Andreas Pfnür, Joana E. Ochoa, Fatemeh Daneshimehr, Lea M. Lang, Dong Lin, Stephen E. Braun, Bysani Chandrasekar, Reza Izadpanah
Software Mentions: 2
Published: over 6 years ago

10.1002/2211-5463.12719

Identification of differentially expressed genes and signaling pathways in chronic obstructive pulmonary disease via bioinformatic analysis
Cited by: 14
Author(s): Xinwei Huang, Yunwei Li, Xiaoran Guo, Zongxin Zhu, Xiangyang Kong, Fang Yu, Qiang Wang
Software Mentions: 2
Published: about 5 years ago

10.1186/s12862-020-01633-4

Evolution and transition of expression trajectory during human brain development
Cited by: 9
Author(s): Mingli Li, Hui Tang, Yong Shao, Mingshan Wang, Haibo Xu, Sheng Wang, David M. Irwin, Adeniyi C. Adeola, Tao Zeng, Luonan Chen, Yan Li, Dong‐Dong Wu
Software Mentions: 2
Published: over 4 years ago

10.3389/fpsyt.2018.00743

Childhood Adversity Is Associated With Increased KITLG Methylation in Healthy Individuals but Not in Bipolar Disorder Patients
Cited by: 9
Author(s): Yujie He, Christiaan H. Vinkers, Lotte C Houtepen, Lot de Witte, Marco P. Boks
Software Mentions: 2
Published: almost 6 years ago

10.3389/fpsyt.2018.00081

Circulating MicroRNA Expression Levels Associated With Internet Gaming Disorder
Cited by: 13
Author(s): Minho Lee, Hyeyoung Cho, Seung Hyun Jung, Seon Hee Yim, Sung Min Cho, Ji Won Chun, Soo Hyun Paik, Yae Eun Park, Dong Huey Cheon, Ji Eun Lee, Jung Seok Choi, Daijin Kim, Yeun Jun Chung
Software Mentions: 2
Published: over 6 years ago

10.1186/s13148-017-0362-2

Distinct DNA methylation profiles in subtypes of orofacial cleft
Cited by: 73
Author(s): Gemma C Sharp, Karen Ho, Amy Davies, Evie Stergiakouli, Kerry Humphries, Wendy L. McArdle, Jonathan R Sandy, George Davey Smith, Sarah J. Lewis, Caroline L Relton
Software Mentions: 2
Published: over 7 years ago

10.3389/fpsyt.2021.553305

Weighted Gene Coexpression Network Analysis Reveals Essential Genes and Pathways in Bipolar Disorder
Cited by: 11
Author(s): Zhenqing Zhang, Weiwei Wu, Jindong Chen, Guangyin Zhang, Jinyu Lin, Yankun Wu, Yu Zhang, Yun‐Ai Su, Jitao Li, Tianmei Si
Software Mentions: 2
Published: over 3 years ago

10.3389/fphar.2021.707930

An m6A-Related Prognostic Biomarker Associated With the Hepatocellular Carcinoma Immune Microenvironment
Cited by: 9
Author(s): Yingxi Du, Yarui Ma, Qing Zhu, Tongzheng Liu, Yuchen Jiao, Peng Yuan, Xiaobing Wang
Software Mentions: 2
Published: over 3 years ago

10.3389/fphar.2018.00697

Master Regulators Connectivity Map: A Transcription Factors-Centered Approach to Drug Repositioning
Cited by: 16
Author(s): Marco Antônio De Bastiani, Bianca Pfaffenseller, Fábio Klamt
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1004888

Identifying Network Perturbation in Cancer
Cited by: 34
Author(s): Maxim Grechkin, Benjamin A. Logsdon, Andrew J. Gentles, Su-In Lee
Software Mentions: 2
Published: over 8 years ago

10.1016/j.redox.2021.101924

Therapeutic wavelengths of ultraviolet B radiation activate apoptotic, circadian rhythm, redox signalling and key canonical pathways in psoriatic epidermis
Cited by: 9
Author(s): Rachel Addison, Anandika Pawitri, Graham R. Smith, A. Rider, Henry J. Grantham, Simon Cockell, Nick J. Reynolds
Software Mentions: 2
Published: over 3 years ago

10.1186/s12931-016-0346-3

Gene-expression profiles in lung adenocarcinomas related to chronic wood smoke or tobacco exposure
Cited by: 15
Author(s): Alette Ortega-Gómez, Claudia Rangel‐Escareño, Camilo Molina-Romero, Eleazar Omar Macedo-Pérez, Alejandro Avilés‐Salas, Alejandra Lara-García, Gerardo J. Alanis-Funes, Rubén Rodríguez‐Bautista, Alfredo Hidalgo-Miranda, Óscar Arrieta
Software Mentions: 2
Published: over 8 years ago

10.1186/s12931-019-1032-z

RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD
Cited by: 37
Author(s): Jarrett Morrow, Robert Chase, Margaret M. Parker, Kimberly Glass, Minseok Seo, Miguel Divo, Caroline A. Owen, Peter J. Castaldi, Dawn L. DeMeo, Edwin K. Silverman, Craig P. Hersh
Software Mentions: 2
Published: over 5 years ago

10.1186/s12903-020-01266-5

Diagnostic biomarker candidates for pulpitis revealed by bioinformatics analysis of merged microarray gene expression datasets
Cited by: 17
Author(s): Ming Chen, Junkai Zeng, Yeqing Yang, Buling Wu
Software Mentions: 2
Published: about 4 years ago

10.1186/s13072-015-0037-1

Ethnicity-specific epigenetic variation in naïve CD4+ T cells and the susceptibility to autoimmunity
Cited by: 47
Author(s): Patrick Coit, Mikhail Ognenovski, Elizabeth Gensterblum, Kathleen Maksimowicz-McKinnon, Jonathan D. Wren, Amr H. Sawalha
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12888-019-2172-x

Methylation analysis for postpartum depression: a case control study
Cited by: 3
Author(s): Yukako Nakamura, Masahiro Nakatochi, Shohko Kunimoto, Takashi Okada, Branko Aleksić, Miho Toyama, Tomoko Shiino, Mako Morikawa, Aya Yamauchi, Akira Yoshimi, Yoko Furukawa‐Hibi, Taku Nagai, Masako Ohara, Chika Kubota, Kiyofumi Yamada, Masahiko Ando, Norio Ozaki
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.202914

Expression profile, molecular functions, and prognostic significance of miRNAs in primary colorectal cancer stem cells
Cited by: 3
Author(s): Cheng Fan, Ran Lu, Chao Fang, Xueli Zhang, Zhaoying Lv, Yuan Li, Hong Zhang, Zong‐Guang Zhou, Xianming Mo, Xiao‐Feng Sun
Software Mentions: 2
Published: over 3 years ago

10.1038/srep28103

OncoScape: Exploring the cancer aberration landscape by genomic data fusion
Cited by: 9
Author(s): Andreas Schlicker, Magali Michaut, Rubayte Rahman, Lodewyk Wessels
Software Mentions: 2
Published: over 8 years ago

10.3389/fonc.2019.00924

Identification of SPP1 as an Extracellular Matrix Signature for Metastatic Castration-Resistant Prostate Cancer
Cited by: 31
Author(s): Xu Pang, Ran Xie, Zhuo Zhang, Qianxin Liu, Shi-Liang Wu, Yimin Chen
Software Mentions: 2
Published: about 5 years ago

10.1093/eep/dvv007

Prenatal lead exposure is associated with decreased cord blood DNA methylation of the glycoprotein VI gene involved in platelet activation and thrombus formation
Cited by: 28
Author(s): Karin Engström, Filip Rydbeck, Maria Kippler, Tomasz K. Wojdacz, Shams El Arifeen, Marie Vahter, Karin Broberg
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-017-16811-6

Profiling of different pancreatic cancer cells used as models for metastatic behaviour shows large variation in their N-glycosylation
Cited by: 42
Author(s): Stephanie Holst, Ana I. Belo, Elisa Giovannetti, Irma van Die, Manfred Wuhrer
Software Mentions: 2
Published: almost 7 years ago

10.3389/fonc.2020.613102

A Prognostic Model Based on RNA Binding Protein Predicts Clinical Outcomes in Hepatocellular Carcinoma Patients
Cited by: 6
Author(s): Zhongsong Man, Yongqiang Chen, Lu Gao, Guowei Xei, Quanfu Li, Qian Lü, Jun Yan
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12918-015-0250-3

Meta-analysis of sex differences in gene expression in schizophrenia
Cited by: 22
Author(s): Wenyi Qin, Cong Liu, Monsheel S. Sodhi, Hui Lu
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0168680

Altered Epithelial Gene Expression in Peripheral Airways of Severe Asthma
Cited by: 47
Author(s): Akul Singhania, Hitasha Rupani, Nivenka Jayasekera, Simon Lumb, Paul Hales, Neil Gozzard, Donna E. Davies, Christopher H. Woelk, Peter H. Howarth
Software Mentions: 2
Published: almost 8 years ago

10.3389/fonc.2020.577229

CXCL1 Regulated by miR-302e Is Involved in Cell Viability and Motility of Colorectal Cancer via Inhibiting JAK-STAT Signaling Pathway
Cited by: 9
Author(s): Biyin Chen, Li Song, Xiuzhen Nie, Fangfeng Lin, Zhen Yu, Wencui Kong, Xiaoyan Qi, Wenwu Wang
Software Mentions: 2
Published: over 3 years ago

10.1186/s13148-019-0788-9

Comprehensive longitudinal study of epigenetic mutations in aging
Cited by: 20
Author(s): Yunzhang Wang, Robert Karlsson, Juulia Jylhävä, Åsa K. Hedman, Catarina Almqvist, Ida Karlsson, Nancy L. Pedersen, Malin Almgren, Sara Hägg
Software Mentions: 2
Published: almost 5 years ago

10.3389/fonc.2020.572919

Identification of a Transcriptional Prognostic Signature From Five Metabolic Pathways in Oral Squamous Cell Carcinoma
Cited by: 9
Author(s): Xiang Wu, Yuan Yao, Zhongwu Li, Huan Ge, Dongmiao Wang, Yanling Wang
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-019-41110-7

Genomewide Study of Epigenetic Biomarkers of Opioid Dependence in European- American Women
Cited by: 25
Author(s): Janitza L. Montalvo-Ortiz, Zhongshan Cheng, Henry R. Kranzler, Huiping Zhang, Joel Gelernter
Software Mentions: 2
Published: over 5 years ago

10.1093/bioinformatics/btu029

Reference-free cell mixture adjustments in analysis of DNA methylation data
Cited by: 393
Author(s): E. Andrés Houseman, John Molitor, Carmen J. Marsit
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pcbi.1008631

Modeling drug response using network-based personalized treatment prediction (NetPTP) with applications to inflammatory bowel disease
Cited by: 5
Author(s): Lei Han, Zahra N. Sayyid, Russ B. Altman
Software Mentions: 2
Published: almost 4 years ago

10.1155/2020/6353814

Identification of a Transcription Factor-microRNA-Gene Coregulation Network in Meningioma through a Bioinformatic Analysis
Cited by: 2
Author(s): Juan Wang, Yan Liang, Hui Yang, Jianhuang Wu
Software Mentions: 2
Published: over 4 years ago

10.3389/fnmol.2018.00039

Species-Specific 5 mC and 5 hmC Genomic Landscapes Indicate Epigenetic Contribution to Human Brain Evolution
Cited by: 14
Author(s): Andy Madrid, Pankaj Chopra, Reid S. Alisch
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2105-15-S5-S4

Use of Attribute Driven Incremental Discretization and Logic Learning Machine to build a prognostic classifier for neuroblastoma patients
Cited by: 20
Author(s): Davide Cangelosi, Marco Muselli, Stefano Parodi, Fabiola Blengio, Pamela Becherini, Rogier Versteeg, Massimo Conte, Luigi Varesio
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0226555

Association of cord blood methylation with neonatal leptin: An epigenome wide association study
Cited by: 10
Author(s): Rachel Kadakia, Yinan Zheng, Zhou Zhang, Wei Zhang, Jami L. Josefson, Lifang Hou
Software Mentions: 2
Published: almost 5 years ago

10.3389/fimmu.2021.693074

Plasma Metabolomics Reveals Dysregulated Metabolic Signatures in HIV-Associated Immune Reconstitution Inflammatory Syndrome
Cited by: 9
Author(s): Luxin Pei, Kiyoshi F. Fukutani, Rafael Tibúrcio, Adam Rupert, Eric Dahlstrom, Frances Galindo, Elizabeth Laidlaw, Andrea Lisco, Maura Manion, Bruno B. Andrade, Irini Sereti
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-019-2855-9

Batch correction evaluation framework using a-priori gene-gene associations: applied to the GTEx dataset
Cited by: 21
Author(s): Judith Somekh, Shai S. Shen-Orr, Isaac S. Kohane
Software Mentions: 2
Published: over 5 years ago

10.1186/s13058-018-0978-y

Identification and validation of single-sample breast cancer radiosensitivity gene expression predictors
Cited by: 35
Author(s): Martin Sjöström, Johan Staaf, Patrik Edén, Fredrik Wärnberg, Jonas Bergh, Per Malmström, Mårten Fernö, Emma Niméus, Irma Fredriksson
Software Mentions: 2
Published: over 6 years ago

10.1186/s12989-014-0048-2

Inhalation of rod-like carbon nanotubes causes unconventional allergic airway inflammation
Cited by: 81
Author(s): Elina Rydman, Marit Ilves, Antti Joonas Koivisto, Pia Anneli Sofia Kinaret, Vittorio Fortino, Terhi Savinko, Maili Lehto, Ville Pulkkinen, Minnamari Vippola, Kaarle Hämeri, Sampsa Matikainen, Henrik Wolff, Kai Savolainen, Dario Greco, Harri Alenius
Software Mentions: 2
Published: about 10 years ago

10.1016/j.ebiom.2016.03.036

Molecular signatures define alopecia areata subtypes and transcriptional biomarkers
Cited by: 66
Author(s): Ali Jabbari, Jane E. Cerise, James C. Chen, Julian Mackay‐Wiggan, Madeleine Duvic, Vera H. Price, Maria Hordinsky, David A. Norris, Raphael Clynes, Angela M. Christiano
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2021.615655

Macrophage M2 Co-expression Factors Correlate With the Immune Microenvironment and Predict Outcome of Renal Clear Cell Carcinoma
Cited by: 26
Author(s): Yutao Wang, Kexin Yan, Jiaxing Lin, Jun Li, Jianbin Bi
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers13102316

Validation of the Combined Biomarker for Prediction of Response to Checkpoint Inhibitor in Patients with Advanced Cancer
Cited by: 4
Author(s): Jin‐Chul Kim, You-Jeong Heo, Soyoung Kang, Jeeyun Lee, Kyoung‐Mee Kim
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-86494-7

DNA methylation architecture of the ACE2 gene in nasal cells of children
Cited by: 20
Author(s): Andrés Cárdenas, Sheryl L. Rifas–Shiman, Joanne E. Sordillo, Dawn L. DeMeo, Andrea A. Baccarelli, Marie‐France Hivert, Diane R. Gold, Emily Oken
Software Mentions: 2
Published: over 3 years ago

10.1002/ctm2.221

Influence of oncogenic mutations and tumor microenvironment alterations on extranodal invasion in diffuse large B‐cell lymphoma
Cited by: 40
Author(s): Rong Shen, Pengpeng Xu, Nan Wang, Hongmei Yi, Lei Dong, Di Fu, Jinyan Huang, Huizhen Huang, Anne Janin, Shu Cheng, Li Wang, Wei‐Li Zhao
Software Mentions: 2
Published: about 4 years ago

10.1186/s12935-021-02130-4

LPCAT1 overexpression promotes the progression of hepatocellular carcinoma
Cited by: 20
Author(s): Rong‐Quan He, Jian‐Di Li, Xiu‐Fang Du, Yi‐Wu Dang, Linjie Yang, Zhi‐Guang Huang, Limin Liu, Lin Liao, Hong Yang, Gang Chen
Software Mentions: 2
Published: over 3 years ago

10.3389/fendo.2019.00472

Identification of Seven Aberrantly Methylated and Expressed Genes in Adrenocortical Carcinoma
Cited by: 5
Author(s): He Xiao, Weixiang He, Ping Chen, Dongmei Xu, Guang Zeng, Zhuo Li, Mingliu Huang, Xinghuan Wang, Michael E. DiSanto, Xinhua Zhang
Software Mentions: 2
Published: over 5 years ago

10.1186/s13148-019-0722-1

Novel age-associated DNA methylation changes and epigenetic age acceleration in middle-aged African Americans and whites
Cited by: 59
Author(s): Salman M. Tajuddin, Dena G. Hernandez, Brian H. Chen, Nicole Noren Hooten, Nicolle A. Mode, Mike A. Nalls, Andrew B. Singleton, Ngozi Ejiogu, Kumaraswamy Naidu Chitrala, Alan B. Zonderman, Michele K. Evans
Software Mentions: 2
Published: over 5 years ago

10.1002/cam4.3284

Gene signature‐based prediction of triple‐negative breast cancer patient response to Neoadjuvant chemotherapy
Cited by: 17
Author(s): Yanding Zhao, Evelien Schaafsma, Chao Cheng
Software Mentions: 2
Published: over 4 years ago

10.1038/s41398-019-0373-1

Stress dynamically regulates co-expression networks of glucocorticoid receptor-dependent MDD and SCZ risk genes
Cited by: 9
Author(s): Corinna Zimmermann, Janine Arloth, Sara Santarelli, Anne Löschner, Peter Weber, Mathias Schmidt, Dietmar Spengler, Elisabeth B. Binder
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41398-020-01147-z

Combined effects of genotype and childhood adversity shape variability of DNA methylation across age
Cited by: 23
Author(s): Darina Czamara, Elleke Tissink, Johanna Tuhkanen, Jade Martins, Yvonne Awaloff, Amanda J. Drake, Batbayar Khulan, Aarno Palotie, Sibylle Winter, Charles B. Nemeroff, W. Edward Craighead, Boadie W. Dunlop, Helen S. Mayberg, Becky Kinkead, Sanjay J. Mathew, Dan V. Iosifescu, Thomas C. Neylan, Christine Heim, Jari Lahti, Johan G. Eriksson, Katri Räikkönen, Kerry J. Ressler, Nadine Provençal, Elisabeth B. Binder
Software Mentions: 2
Published: almost 4 years ago

10.1002/cam4.2223

Comprehensive characterization of cancer‐testis genes in testicular germ cell tumor
Cited by: 18
Author(s): Yu-Ting Chang, Xuewei Wang, Yide Xu, Yang Liu, Qufei Qian, Sihan Ju, Chen Yao, Shuaizhou Chen, Na Qin, Zijuan Ma, Juncheng Dai, Hongxia Ma, Guangfu Jin, Erbao Zhang, Cheng Wang
Software Mentions: 2
Published: over 5 years ago

10.1016/S2213-2600(19)30469-2

Blood transcriptional biomarkers for active pulmonary tuberculosis in a high-burden setting: a prospective, observational, diagnostic accuracy study
Cited by: 74
Author(s): Chris Turner, Gupta Rk, Evdokia Tsaliki, Jennifer Roe, Prasenjit Mondal, Georgina Nyawo, Zaida Palmer, R F Miller, Byron W P Reeve, Grant Theron, Mahdad Noursadeghi
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.00836-16

The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility
Cited by: 102
Author(s): Mary E. Kable, Yanin Srisengfa, Miles Laird, José J. Zaragoza, J. W. McLeod, J. Heidenreich, Maria L. Marco
Software Mentions: 2
Published: about 8 years ago

10.18632/aging.202725

The networks of m6A-SARS-CoV-2 related genes and immune infiltration patterns in idiopathic pulmonary fibrosis
Cited by: 4
Author(s): Xinyu Li, Cheng Pan, Zijue Zhu, Haozheng Cai, Quan Zhuang
Software Mentions: 2
Published: over 3 years ago

10.1097/MD.0000000000022815

Identification of therapeutic targets and mechanisms of tumorigenesis in non-small cell lung cancer using multiple-microarray analysis
Cited by: 3
Author(s): Dan Zhao, MU Hai-jun, Hai Bing Shi, Hong Xia Bi, Yun Jiang, Guo Hua Liu, Hong Zheng, Bo Liu
Software Mentions: 2
Published: about 4 years ago

10.2217/epi-2018-0091

Evidence for DNA methylation mediating genetic liability to non-syndromic cleft lip/palate
Cited by: 22
Author(s): Laurence J Howe, Tom G Richardson, Ryan Arathimos, Lucas Alvizi, Maria Rita Passos‐Bueno, Philip Stanier, Ellen Aagaard Nøhr, Kerstin U. Ludwig, Elisabeth Mangold, Michael Knapp, Evie Stergiakouli, Beaté St Pourcain, George Davey Smith, Jonathan R Sandy, Caroline L Relton, Sarah J. Lewis, Gibran Hemani, Gemma C Sharp
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12885-015-1492-6

Anticancer drug sensitivity prediction in cell lines from baseline gene expression through recursive feature selection
Cited by: 105
Author(s): Zuoli Dong, Naiqian Zhang, Chun Li, Haiyun Wang, Yun Fang, Jun Wang, Xiaoqi Zheng
Software Mentions: 1
Published: over 9 years ago

10.1186/s13321-019-0359-2

An integrated quantitative structure and mechanism of action-activity relationship model of human serum albumin binding
Cited by: 17
Author(s): Angela Serra, Serli Önlü, Pietro Coretto, Dario Greco
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-73214-w

A methodology for predicting tissue-specific metabolic roles of receptors applied to subcutaneous adipose
Cited by: 1
Author(s): Judith Somekh
Software Mentions: 1
Published: about 4 years ago

10.3389/fimmu.2021.687975

IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures
Cited by: 262
Author(s): Dongqiang Zeng, Zilan Ye, Rongfang Shen, Guangchuang Yu, Jiani Wu, Yi Xiong, Rui Zhou, Wenjun Qiu, Na Huang, Li Sun, Xuejun Li, Jianping Bin, Yulin Liao, Min Shi, Wangjun Liao
Software Mentions: 1
Published: over 3 years ago

10.1186/s13148-018-0471-6

Identifying and correcting epigenetics measurements for systematic sources of variation
Cited by: 28
Author(s): Flavie Perrier, Alexei Novoloaca, Srikant Ambatipudi, Laura Baglietto, Akram Ghantous, Vittorio Perduca, Myrto Barrdahl, Sophia Harlid, Ken K. Ong, Alexia Cardona, Silvia Polidoro, Therese Haugdahl Nøst, Kim Overvad, Hanane Omichessan, Martijn E.T. Dollé, Christina Bamia, José María Huerta, Paolo Víneis, Zdenko Herceg, Isabelle Romieu, Pietro Ferrari
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2019.00599

Cancer as a Tissue Anomaly: Classifying Tumor Transcriptomes Based Only on Healthy Data
Cited by: 11
Author(s): Thomas P. Quinn, Thin Nguyen, Samuel C. Lee, Svetha Venkatesh
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-00195-8

Discovery of circulating proteins associated to knee radiographic osteoarthritis
Cited by: 27
Author(s): L. Lourido, Burcu Ayoglu, Juan Fernández‐Tajes, N. Oreiro, Frauke Henjes, Cecilia Hellström, Jochen M. Schwenk, Cristina Ruiz-Romero, Peter Nilsson, Francisco J. Blanco
Software Mentions: 1
Published: over 7 years ago

10.1186/s13073-016-0374-0

High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis
Cited by: 26
Author(s): David Gomez-Cabrero, Malin Almgren, Louise K. Sjöholm, Aase Hensvold, Mikael V. Ringh, Rakel Tryggvadóttir, Juha Kere, Annika Scheynius, Nathalie Acevedo, Lovisa E. Reinius, Margaret A. Taub, Carolina Montaño, Martin J. Aryee, Jason I. Feinberg, Andrew P. Feinberg, Jesper Tegnér, Lars Klareskog, Anca I. Catrina, Tomas J. Ekström
Software Mentions: 1
Published: almost 8 years ago

10.1016/j.celrep.2019.08.050

TCR and Inflammatory Signals Tune Human MAIT Cells to Exert Specific Tissue Repair and Effector Functions
Cited by: 164
Author(s): Tianqi Leng, Hossain Delowar Akther, Carl-Philipp Hackstein, Kate Powell, T. P. King, Matthias Friedrich, Z Christoforidou, Sarah McCuaig, Mastura Neyazi, Carolina V. Arancibia‐Cárcamo, Joachim Hagel, Fiona Powrie, Raphael Sanches Peres, Val Millar, Daniel Ebner, Rajesh Lamichhane, James E. Ussher, Tsc Hinks, Emanuele Marchi, C Willberg, Paul Klenerman
Software Mentions: 1
Published: about 5 years ago

10.1186/s12920-018-0340-3

Impaired type I interferon regulation in the blood transcriptome of recurrent asthma exacerbations
Cited by: 9
Author(s): José L. Gómez, María Paula Díaz, Gustavo Niño, Clemente J. Britto
Software Mentions: 1
Published: over 6 years ago

10.1186/gb-2014-15-2-r37

The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts
Cited by: 376
Author(s): James Wagner, Stephan Busche, Bing Ge, Tony Kwan, Tomi Pastinen, Mathieu Blanchette
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12859-015-0478-3

Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat
Cited by: 69
Author(s): Caleb K. Stein, Pingping Qu, Joshua Epstein, Amy Buros, Adam Rosenthal, John Crowley, Gareth J. Morgan, Bart Barlogie
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-26640-w

Stability and reproducibility of proteomic profiles measured with an aptamer-based platform
Cited by: 91
Author(s): Claire H. Kim, Shelley S. Tworoger, Meir J. Stampfer, Simon T. Dillon, Xuesong Gu, Sherilyn Sawyer, Andrew T. Chan, Towia A. Libermann, A. Heather Eliassen
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-020-06908-0

The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution
Cited by: 9
Author(s): Andrey Höglund, Katharina Strempfl, Jesper Fogelholm, Dominic Wright, Rie Henriksen
Software Mentions: 1
Published: over 4 years ago

10.1186/s13059-016-0964-6

Exploiting single-cell expression to characterize co-expression replicability
Cited by: 66
Author(s): Megan Crow, Anirban Paul, Sara Ballouz, Zheng Huang, Jesse Gillis
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-32090-1

DNA methylation in adolescents with anxiety disorder: a longitudinal study
Cited by: 11
Author(s): Andressa Bortoluzzi, Giovanni Abrahão Salum, Eduarda Dias da Rosa, Vinícius de Saraiva Chagas, Mauro A. A. Castro, Gisele Gus Manfro
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.15133

Low PCA3 expression is a marker of poor differentiation in localized prostate tumors: exploratory analysis from 12,076 patients
Cited by: 29
Author(s): Mohammed Alshalalfa, Gerald W. Verhaegh, Ewan A. Gibb, María Santiago-Jiménez, Nicholas Erho, Jennifer Jordan, Kasra Yousefi, Lucia L.C. Lam, Tyler Kolisnik, Jijumon Chelissery, Roland Seiler, Ashley E. Ross, R. Jeffrey Karnes, Edward M. Schaeffer, Tamara Lotan, Robert B. Den, Stephen J. Freedland, Elai Davicioni, Eric A. Klein, Jack A. Schalken
Software Mentions: 1
Published: almost 8 years ago

10.3390/s21072436

Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis
Cited by: 1
Author(s): Yiming Huang, William Thomas Lingwood Smith, Colin R. Harwood, Anil Wipat, Jaume Bacardit
Software Mentions: 1
Published: over 3 years ago

10.1186/s12935-019-0817-y

Construction and comprehensive analysis of a ceRNA network to reveal potential prognostic biomarkers for hepatocellular carcinoma
Cited by: 88
Author(s): Junyu Long, Yi Bai, Xiaobo Yang, Jianzhen Lin, Xu Yang, Dongxu Wang, Li He, Yongchang Zheng, Hong Zhao
Software Mentions: 1
Published: over 5 years ago

Projects: bioconductor: sva

Papers Mentioning sva 511