10.1186/1471-2105-14-133

How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis
Cited by: 23
Author(s): Robert Lehmann, Rainer Machné, Jens Georg, Manuela Benary, Ilka M. Axmann, Ralf Steuer
Software Mentions: 8
Published: over 12 years ago

10.1038/s41421-021-00279-w

Targeting novel LSD1-dependent ACE2 demethylation domains inhibits SARS-CoV-2 replication
Cited by: 7
Author(s): Wen Juan Tu, Robert McCuaig, Michelle Melino, Daniel J. Rawle, Thuy T. Le, Kexin Yan, Andreas Suhrbier, Rebecca L. Johnston, Lambros T. Koufariotis, Nicola Waddell, E.M. Cross, S. Tsimbalyuk, Amanda L. Bain, Elizabeth Ahern, Natasha Collinson, Simon Phipps, Jade K. Forwood, Nabila Seddiki, Sudha Rao
Software Mentions: 8
Published: about 4 years ago

10.1186/s12935-020-01661-6

Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development
Cited by: 6
Author(s): R. Adam, Sanne M. van Neerven, Cayetano Pleguezuelos-Manzano, Salvatore Simmini, Nicolas Léveillé, Nina E. de Groot, Andrew N Holding, Florian Markowetz, Louis Vermeulen
Software Mentions: 8
Published: over 4 years ago

10.18632/aging.103475

Constructing a global transcriptional regulatory landscape for early non-small cell lung cancer to identify hub genes and key pathways
Cited by: 6
Author(s): Jianlong Bu, Pinyi Zhang, Kaibin Zhu, Yubo Yan, Bowen Shi, Junfeng Wang, Shidong Xu
Software Mentions: 8
Published: almost 5 years ago

10.1038/s41419-021-03525-x

Loss of retinoic acid receptor-related receptor alpha (Rorα) promotes the progression of UV-induced cSCC
Cited by: 6
Author(s): Guolong Zhang, Guorong Yan, Fu Zhuo, Yuhao Wu, Fei Wu, Zhe Zheng, Shiji Fang, Ying Gao, Xiao Bao, Yeqiang Liu, Xiuli Wang, Sibo Zhu
Software Mentions: 8
Published: over 4 years ago

10.1038/s41419-021-03552-8

Transcriptional profiling reveals the transcription factor networks regulating the survival of striatal neurons
Cited by: 12
Author(s): Lin Yang, 智慧 蘇, Zi-Wu Wang, Zhenmeiyu Li, Zicong Shang, Heng Du, Shuai Liu, Dashi Qi, Zhengang Yang, Zhejun Xu, Zhuangzhi Zhang
Software Mentions: 8
Published: over 4 years ago

10.12688/f1000research.13196.2

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Cited by: 42
Author(s): Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Software Mentions: 8
Published: almost 7 years ago

10.1128/mBio.01369-21

HIV-1 Vpr Induces Widespread Transcriptomic Changes in CD4 ⁺ T Cells Early Postinfection
Cited by: 6
Author(s): Hélène Bauby, Christopher Ward, Rupert Hugh-White, Chad M. Swanson, Reiner Schulz, Caroline Goujon, Michael H. Malim
Software Mentions: 8
Published: about 4 years ago

10.3389/fnins.2021.613329

Integrated Transcriptional Profiling Analysis and Immune-Related Risk Model Construction for Intracranial Aneurysm Rupture
Cited by: 4
Author(s): Dezhi Shan, Xing Guo, Guozheng Yang, Zheng He, Rongrong Zhao, Hao Xue, Gang Li
Software Mentions: 8
Published: over 4 years ago

10.3389/fphys.2021.660906

Genome-Wide DNA Methylation Changes Associated With High-Altitude Acclimatization During an Everest Base Camp Trek
Cited by: 6
Author(s): Ainash Childebayeva, Taylor Harman, Julien Weinstein, Trevor A. Day, Tom D. Brutsaert, Abigail W. Bigham
Software Mentions: 8
Published: about 4 years ago

10.1155/2020/2507074

A Network Pharmacology-Based Identification Study on the Mechanism of Xiao-Xu-Ming Decoction for Cerebral Ischemic Stroke
Cited by: 8
Author(s): Dehui Li, Yifan Su, Cheng-Yi Sun, Huanfang Fan, Weijuan Gao
Software Mentions: 8
Published: almost 5 years ago

10.7150/jca.49266

Establishment of the Prognostic Index Reflecting Tumor Immune Microenvironment of Lung Adenocarcinoma Based on Metabolism-Related Genes
Cited by: 13
Author(s): Jianguo Zhang, Jianzhong Zhang, Cheng Yuan, Yuan Luo, Yangyi Li, Panpan Dai, Wenjie Sun, Nannan Zhang, Jiangbo Ren, Mengjie Zhang, Yan Gong, Conghua Xie
Software Mentions: 8
Published: over 5 years ago

10.7554/eLife.05005

Predicting effective microRNA target sites in mammalian mRNAs
Cited by: 5,158
Author(s): Vikram Agarwal, George W. Bell, Jin Wu Nam, David P. Bartel
Software Mentions: 8
Published: almost 10 years ago

10.1186/s12957-021-02328-w

Identification of novel antioxidant gene signature to predict the prognosis of patients with gastric cancer
Cited by: 10
Author(s): Jianhua Wu, Xuan Wang, Nan Wang, Li Ma, Xin Xie, Hao Zhang, Huafeng Kang, Zhangjian Zhou
Software Mentions: 8
Published: about 4 years ago

10.3389/fgene.2021.647353

Identification of Hub Genes and Their Correlation With Immune Infiltration Cells in Hepatocellular Carcinoma Based on GEO and TCGA Databases
Cited by: 22
Author(s): Rui Huang, Jinying Liu, Hui Li, Lierui Zheng, Haojun Jin, Yaqing Zhang, Wei Ma, Junhong Su, Min Wang, Kun Yang
Software Mentions: 8
Published: about 4 years ago

10.3389/fgene.2019.01331

Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing
Cited by: 50
Author(s): Tian Mou, Wenjiang Deng, Fengyun Gu, Yudi Pawitan, Trung Nghia Vu
Software Mentions: 8
Published: over 5 years ago

10.7717/peerj.11599

A seven-lncRNA signature for predicting Ewing’s sarcoma
Cited by: 8
Author(s): Zhihui Chen, Xinyu Wang, Guozhu Wang, Bin Xiao, Zhe Ma, Hongliang Huo, Weiwei Li
Software Mentions: 8
Published: about 4 years ago

10.1007/s00122-020-03667-0

Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera ‘Pinot Noir’ and Vitis spp. genotypes
Cited by: 6
Author(s): Robert Richter, Susanne Rossmann, Doreen Gabriel, Reinhard Töpfer, Klaus Theres, Eva Zyprian
Software Mentions: 8
Published: almost 5 years ago

10.1186/s12864-016-2848-2

ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
Cited by: 21
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 8
Published: almost 9 years ago

10.1002/cam4.3655

Immune landscape and a promising immune prognostic model associated with TP53 in early‐stage lung adenocarcinoma
Cited by: 17
Author(s): Chia-Chien Wu, Rong Xiang, Lin Wei
Software Mentions: 8
Published: over 4 years ago

10.3389/fonc.2018.00100

Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues
Cited by: 35
Author(s): Erfan Aref‐Eshghi, Laila C. Schenkel, Peter Ainsworth, Hanxin Lin, David I. Rodenhiser, Jean‐Claude Cutz, Bekim Sadiković
Software Mentions: 8
Published: over 7 years ago

10.1186/s13058-021-01445-4

Single cell transcriptome atlas of mouse mammary epithelial cells across development
Cited by: 19
Author(s): Bhupinder Pal, Yunshun Chen, Michael J. G. Milevskiy, François Vaillant, Lexie Prokopuk, Caleb A. Dawson, Bianca D. Capaldo, Xiaoyu Song, Felicity C. Jackling, Paul Timpson, Geoffrey J. Lindeman, Gordon K. Smyth, Jane E. Visvader
Software Mentions: 8
Published: about 4 years ago

10.3389/fonc.2020.01411

Comparison of Stage 4 and Stage 4s Neuroblastoma Identifies Autophagy-Related Gene and LncRNA Signatures Associated With Prognosis
Cited by: 12
Author(s): Xinyao Meng, Honglin Li, Erhu Fang, Jiexiong Feng, Xiaoli Zhao
Software Mentions: 8
Published: almost 5 years ago

10.1042/BSR20204456

A new m6A methylation-related gene signature for prognostic value in patient with urothelial carcinoma of the bladder
Cited by: 9
Author(s): Bin Zheng, Jianwei Wang, Guiting Zhao, Xiaoxu Chen, Zhongshun Yao, Wei He, Wei He
Software Mentions: 8
Published: over 4 years ago

10.1186/s13058-016-0758-5

Patient survival and tumor characteristics associated with CHEK2:p.I157T – findings from the Breast Cancer Association Consortium
Cited by: 37
Author(s): Taru Muranen, Carl Blomqvist, Thilo Dörk, Anna Jakubowska, Päivi Heikkilä, Rainer Fagerholm, Dario Greco, Kristiina Aittomäki, Stig E. Bojesen, Mitul Shah, Alison M. Dunning, Valerie Rhenius, Per Hall, Kamila Czene, Judith S. Brand, Hatef Darabi, Jenny Chang–Claude, Anja Rudolph, Børge G. Nordestgaard, Fergus J. Couch, Steven N. Hart, Jonine D. Figueroa, Montserrat García‐Closas, Peter A. Fasching, Matthias W. Beckmann, Jingmei Li, Jing Liu, Irene L. Andrulis, Robert Winqvist, Katri Pylkäs, Arto Mannermaa, Vesa Kataja, Annika Lindblom, Sara Margolin, Jan Lubiński, Natalia Dubrowinskaja, Manjeet K. Bolla, Joe Dennis, Kyriaki Michailidou, Qin Wang, Douglas F. Easton, Paul D.P. Pharoah, Marjanka K. Schmidt, Heli Nevanlinna
Software Mentions: 8
Published: almost 9 years ago

10.1038/tp.2016.275

A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score
Cited by: 28
Author(s): Diana‐Maria Ciuculete, Adrian Boström, Sarah Voisin, H. Philipps, Olga E. Titova, Marcus Bandstein, Lamia Nikontovic, Michael J. Williams, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 8
Published: over 8 years ago

10.1111/jcmm.15601

Novel gene signatures for prognosis prediction in ovarian cancer
Cited by: 25
Author(s): Mingyang Bao, Lihua Zhang, Yue‐Qing Hu
Software Mentions: 8
Published: about 5 years ago

10.3389/fgene.2021.650554

Exploration of the Role of m6 A RNA Methylation Regulators in Malignant Progression and Clinical Prognosis of Ovarian Cancer
Cited by: 4
Author(s): Qinglv Wei, Dan Yang, Xiaoyi Liu, Hongyan Zhao, Yang Yu, Jing Xu, Tao Liu, Ping Yi
Software Mentions: 8
Published: about 4 years ago

10.3389/fonc.2020.00835

Development and Validation of a 12-Gene Immune Relevant Prognostic Signature for Lung Adenocarcinoma Through Machine Learning Strategies
Cited by: 14
Author(s): Xue Li, Guoshu Bi, Cheng Zhan, Yi Zhang, Yunfeng Yuan, Hong Fan
Software Mentions: 8
Published: about 5 years ago

10.1042/BSR20203676

Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis
Cited by: 7
Author(s): Zhenchao Ma, Jingyu Xu, Lixin Ru, Weihua Zhu
Software Mentions: 8
Published: over 4 years ago

10.1186/s12957-018-1519-y

Identification of hub genes with diagnostic values in pancreatic cancer by bioinformatics analyses and supervised learning methods
Cited by: 23
Author(s): Chunyang Li, Xiaoxi Zeng, Haopeng Yu, Yuanxia Gu, Wei Zhang
Software Mentions: 8
Published: over 6 years ago

10.1097/MD.0000000000027374

Identification and validation of a hypoxia-related prognostic signature in clear cell renal cell carcinoma patients
Cited by: 7
Author(s): Zhengtian Li, Gang Du, Rong Zhao, Weibo Yang, Chan Li, Jun Huang, Zhenpei Wen, Hening Li, Bo Zhang
Software Mentions: 8
Published: almost 4 years ago

10.3389/fonc.2020.590006

AUNIP Expression Is Correlated With Immune Infiltration and Is a Candidate Diagnostic and Prognostic Biomarker for Hepatocellular Carcinoma and Lung Adenocarcinoma
Cited by: 14
Author(s): Chenxi Ma, Wenyan Kang, Lu Yu, Zongcheng Yang, Di Tian
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0143970

A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome
Cited by: 37
Author(s): Katherine James, Shereen Al-Ali, Jessica Tarn, Simon Cockell, Colin S. Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin Pease, Paul Emery, Peter Lanyon, John Hunter, Monica Gupta, Michèle Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert J. Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, Anil Wipat, Julia L. Newton, David Jones, John D. Isaacs, Jennifer Hallinan, Wan‐Fai Ng
Software Mentions: 8
Published: over 9 years ago

10.3389/fonc.2020.574939

Identification of an Immune-Related Gene Signature Based on Immunogenomic Landscape Analysis to Predict the Prognosis of Adult Acute Myeloid Leukemia Patients
Cited by: 19
Author(s): Ruiqi Zhu, Huishan Tao, Wenyi Lin, Liang Tang, Yu Hu
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-017-13731-3

The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation
Cited by: 16
Author(s): Mahdi Golkaram, Jaeshin Jang, Stefan Hellander, Kenneth S. Kosik, Linda R. Petzold
Software Mentions: 8
Published: almost 8 years ago

10.3233/JAD-170011

Analytical Strategy to Prioritize Alzheimer’s Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data
Cited by: 17
Author(s): Shweta Bagewadi Kawalia, Tamara Raschka, Mufassra Naz, Ricardo de Matos Simoes, Philipp Senger, Martin Hofmann-Apitius
Software Mentions: 8
Published: almost 8 years ago

10.1038/s41598-021-95068-6

CENPL, ISG20L2, LSM4, MRPL3 are four novel hub genes and may serve as diagnostic and prognostic markers in breast cancer
Cited by: 17
Author(s): Jun Yin, Chen Lin, Meng Jiang, Xuhai Tang, Danlin Xie, Jingwen Chen, Rongqin Ke
Software Mentions: 8
Published: almost 4 years ago

10.7554/eLife.65508

Seroconversion stages COVID19 into distinct pathophysiological states
Cited by: 36
Author(s): Matthew D. Galbraith, Kohl T Kinning, Kelly D. Sullivan, Ryan M. Baxter, Paula Araya, Kimberly R. Jordan, Seth Russell, Keith P Smith, Ross E Granrath, Jessica Shaw, Monika Dzieciątkowska, Tusharkanti Ghosh, Andrew A. Monte, Angelo D’Alessandro, Kirk C. Hansen, Tellen D Benett, Elena W.Y. Hsieh, Joaquín M. Espinosa
Software Mentions: 8
Published: over 4 years ago

10.1002/cam4.4156

Comprehensive analysis of a new prognosis signature based on histone deacetylases in clear cell renal cell carcinoma
Cited by: 6
Author(s): Fajuan Cheng, Bin Zheng, Jianwei Wang, Guiting Zhao, Zhongshun Yao, Zhihong Niu
Software Mentions: 8
Published: about 4 years ago

10.1016/j.ebiom.2021.103444

A diagnostic miRNA signature for pulmonary arterial hypertension using a consensus machine learning approach
Cited by: 24
Author(s): Niamh Errington, James Iremonger, Josephine Pickworth, Sokratis Kariotis, Christopher J. Rhodes, Alexander Rothman, Robin Condliffe, Charles Elliot, David G. Kiely, Luke Howard, John Wharton, A. A. Roger Thompson, Nicholas W. Morrell, Martin R. Wilkins, Dennis Wang, Allan Lawrie
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0069624

Transcriptomic Analysis of Insulin-Sensitive Tissues from Anti-Diabetic Drug Treated ZDF Rats, a T2DM Animal Model
Cited by: 4
Author(s): Yo Na Kim, Sangok Kim, Il Yong Kim, Jae Hoon Shin, Sooyoung Cho, Sun Shin Yi, Wankyu Kim, Kyung Sub Kim, Sanghyuk Lee, Je Kyung Seong
Software Mentions: 8
Published: about 12 years ago

10.1186/s12864-019-5926-4

lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA
Cited by: 6
Author(s): Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J.C. Slebos, Christine H. Chung, Xuefeng Wang
Software Mentions: 8
Published: about 6 years ago

10.7150/thno.55075

Single-cell transcriptome analysis of the heterogeneous effects of differential expression of tumor PD-L1 on responding TCR-T cells
Cited by: 2
Author(s): Renpeng Ding, Shang Liu, Shanshan Wang, Huanyi Chen, Fei Wang, Qumiao Xu, Linnan Zhu, Xuan Dong, Ying Gu, Xiuqing Zhang, Cheng‐Chi Chao, Qianqian Gao
Software Mentions: 8
Published: over 4 years ago

10.7717/peerj.10682

Identification of the hub genes in gastric cancer through weighted gene co-expression network analysis
Cited by: 7
Author(s): Chunyang Li, Haopeng Yu, Yajing Sun, Xiaoxi Zeng, Wei Zhang
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0255708

Identification of key genes and immune infiltration modulated by CPAP in obstructive sleep apnea by integrated bioinformatics analysis
Cited by: 3
Author(s): Cheng Fan, Sisi Huang, Chunhua Xiang, Tianhui An, Yi Song
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pone.0187722

Plasma microRNA profiling: Exploring better biomarkers for lymphoma surveillance
Cited by: 47
Author(s): Drirh Khare, Neta Goldschmidt, Aya Bardugo, Devorah Gur‐Wahnon, Iddo Z. Ben‐Dov, Batia Avni
Software Mentions: 8
Published: over 7 years ago

10.1038/s41598-021-93034-w

Altered expression of genes controlling metabolism characterizes the tissue response to immune injury in lupus
Cited by: 20
Author(s): Kathryn M. Kingsmore, Prathyusha Bachali, Michelle D. Catalina, Andrea R. Daamen, Sarah Heuer, Robert Robl, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0159921

BEclear: Batch Effect Detection and Adjustment in DNA Methylation Data
Cited by: 19
Author(s): Ruslan Akulenko, Markus Merl, Volkhard Helms
Software Mentions: 8
Published: almost 9 years ago

10.7554/eLife.62800

Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum
Cited by: 18
Author(s): Kathryn H. Milne, Alasdair Ivens, Adam J. Reid, Magda E. Lotkowska, Áine O’Toole, Geetha Sankaranarayanan, Diana Muñoz Sandoval, Wiebke Nahrendorf, Clément Regnault, Nick J. Edwards, Sarah E. Silk, Ruth Payne, Angela M. Minassian, Navin Venkatraman, Mandy Sanders, Adrian V. S. Hill, Michael P. Barrett, Matthew Berriman, Simon J. Draper, J. Alexandra Rowe, Philip J. Spence
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0014524

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
Cited by: 493
Author(s): Fabienne Brenet, Michelle Moh, Patricia Funk, Erika Feierstein, Agnès Viale, Nicholas D. Socci, Joseph M. Scandura
Software Mentions: 7
Published: over 14 years ago

10.1038/s41598-021-94343-w

Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite
Cited by: 7
Author(s): Fernando M. Jabato, José Córdoba-Caballero, Elena Rojano, Carlos Romá‐Mateo, Pascual Sanz, Belén Pérez, Diana Gallego, Pedro Seoane, Juan A. G. Ranea, James R. Perkins
Software Mentions: 7
Published: about 4 years ago

10.7717/peerj.1621

Cross-platform normalization of microarray and RNA-seq data for machine learning applications
Cited by: 71
Author(s): Jeffrey Thompson, Jie Tan, Casey S. Greene
Software Mentions: 7
Published: over 9 years ago

10.7150/jca.50716

Detection of Pancreatic Ductal Adenocarcinoma by A qPCR-based Normalizer-free Circulating Extracellular Vesicles RNA Signature
Cited by: 6
Author(s): Dashan Qin, Yu Zhao, Qingdong Guo, Shoumin Zhu, Shutian Zhang, Li Min
Software Mentions: 7
Published: over 4 years ago

10.7150/jca.53831

Development and Validation of an Immune-Related Long Non-coding RNA Prognostic Model in Glioma
Cited by: 5
Author(s): Xiaowei Qiu, Yuan Tian, Jingnan Xu, Xin Jiang, Zeyu Liu, Xuewei Qi, Xin Chang, Jianxin Zhao, Jinchang Huang
Software Mentions: 7
Published: over 4 years ago

10.1038/s41416-019-0571-x

Prognosis and modulation mechanisms of COMMD6 in human tumours based on expression profiling and comprehensive bioinformatics analysis
Cited by: 24
Author(s): Mi Yang, Weiqiang Huang, Yaling Sun, Huazhen Liang, Min Chen, Xixi Wu, Xiaoqing Wang, Longshan Zhang, Xiaobin Cheng, Yu Fan, Hua Pan, Longhua Chen, Jian Guan
Software Mentions: 7
Published: almost 6 years ago

10.3389/fonc.2021.733595

Identification of Glycolysis-Related lncRNAs and the Novel lncRNA WAC-AS1 Promotes Glycolysis and Tumor Progression in Hepatocellular Carcinoma
Cited by: 22
Author(s): Xigang Xia, Hao Zhang, Peng Xia, Yu Zhu, Jie Liu, Kequan Xu, Yufeng Yuan
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12864-019-6308-7

Human gene expression variability and its dependence on methylation and aging
Cited by: 23
Author(s): Nasser Bashkeel, Theodore J. Perkins, Mads Kærn, Jonathan M. Lee
Software Mentions: 7
Published: over 5 years ago

10.1007/s10549-019-05135-w

A high-risk luminal A dominant breast cancer subtype with increased mobility
Cited by: 21
Author(s): Liping Guo, Guoji Chen, Wen Zhang, Lülin Zhou, Ting Xiao, Di Xia, Yipeng Wang, Feng Li, Kaitai Zhang
Software Mentions: 7
Published: over 6 years ago

10.15252/emmm.202012525

<scp>LSD</scp> 1 inhibition induces differentiation and cell death in Merkel cell carcinoma
Cited by: 36
Author(s): Lukas Leiendecker, Pauline S. Jung, Izabela Krecioch, Tobias Neumann, Alexander Schleiffer, Karl Mechtler, Thomas Wiesner, Anna C. Obenauf
Software Mentions: 7
Published: almost 5 years ago

10.3389/fonc.2021.657094

LINC01977 Promotes Breast Cancer Progression and Chemoresistance to Doxorubicin by Targeting miR-212-3p/GOLM1 Axis
Cited by: 12
Author(s): Zheng Li, Yaming Li, Xiaolong Wang, Yiran Liang, Dan Luo, Dianwen Han, Chen Li, Tong Chen, Hanwen Zhang, Ying Liu, Zekun Wang, Bing Chen, Limin Wang, Wenjing Zhao, Qifeng Yang
Software Mentions: 7
Published: over 4 years ago

10.15252/emmm.202013180

Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1
Cited by: 21
Author(s): George Sflomos, Laura Battista, Patrick Aouad, Fabio De Martino, Valentina Scabia, Athina Stravodimou, Ayyakkannu Ayyanan, Assia Ifticene‐Treboux, Philipp Bücher, Maryse Fiche, Giovanna Ambrosini, Cathrin Brisken, Rls
Software Mentions: 7
Published: over 4 years ago

10.3389/fonc.2021.674394

Comprehensive Analysis of Cyclin Family Gene Expression in Colon Cancer
Cited by: 12
Author(s): Jieling Li, Liyuan Zhou, Ying Liu, Lingzhi Yang, Dayi Jiang, Kuan Li, Shouqi Xie, Wang Xiao, Shaoxiang Wang
Software Mentions: 7
Published: over 4 years ago

10.1186/s12967-020-02697-y

A novel immune classification reveals distinct immune escape mechanism and genomic alterations: implications for immunotherapy in hepatocellular carcinoma
Cited by: 58
Author(s): Zaoqu Liu, Yuyuan Zhang, Chengcheng Shi, Xueliang Zhou, Kaihao Xu, Dechao Jiao, Zhenqiang Sun, Xinwei Han
Software Mentions: 7
Published: over 4 years ago

10.1042/BSR20200492

Profiles of overall survival-related gene expression-based risk signature and their prognostic implications in clear cell renal cell carcinoma
Cited by: 3
Author(s): Zihao He, Tuo Deng, Xiaolu Duan, Guohua Zeng
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0196117

Identification of a neutrophil-related gene expression signature that is enriched in adult systemic lupus erythematosus patients with active nephritis: Clinical/pathologic associations and etiologic mechanisms
Cited by: 37
Author(s): Joan E. Wither, Stephenie D. Prokopec, Babak Noamani, Nan-Hua Chang, Dennisse Bonilla, Zahi Touma, Carmen Ávila-Casado, Heather N. Reich, James W. Scholey, Paul R. Fortin, Paul C. Boutros, Carolina Landolt-Marticorena
Software Mentions: 7
Published: about 7 years ago

10.7150/jca.47557

Identification of a prognostic 4-mRNA signature in laryngeal squamous cell carcinoma
Cited by: 1
Author(s): Cheng Zhang, Bin Shen, Xinwei Chen, Shang Gao, Xiaohua Ying, Pin Dong
Software Mentions: 7
Published: over 4 years ago

10.3389/fonc.2021.654185

Overexpression of GINS4 Is Associated With Tumor Progression and Poor Survival in Hepatocellular Carcinoma
Cited by: 6
Author(s): Ziying Zhang, Peng Chen, Hui Xie, Peiguo Cao
Software Mentions: 7
Published: over 4 years ago

10.1038/srep29042

Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana
Cited by: 35
Author(s): Frédéric Bouché, Maria D’Aloia, Pierre Tocquin, Guillaume Lobet, Nathalie Detry, Claire Périlleux
Software Mentions: 7
Published: about 9 years ago

10.3389/fonc.2020.00033

PLXNC1 Enhances Carcinogenesis Through Transcriptional Activation of IL6ST in Gastric Cancer
Cited by: 9
Author(s): Jie Chen, Haining Liu, Jinggui Chen, Bo Sun, Jianghong Wu, Chunyan Du
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.57843

Increased longevity due to sexual activity in mole-rats is associated with transcriptional changes in the HPA stress axis
Cited by: 17
Author(s): Arne Sahm, Matthias Platzer, Philipp Koch, Yoshiyuki Henning, Martin Bens, Marco Groth, Hynek Burda, Sabine Begall, Saskia Ting, Moritz Goetz, Paul Van Daele, Magdalena Staniszewska, Jasmin Klose, Pedro Fragoso Costa, Steve Hoffmann, Karol Szafranski, Philip Dammann
Software Mentions: 7
Published: over 4 years ago

10.3389/fonc.2020.01409

Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma
Cited by: 43
Author(s): Yin Wu, Xingjun Jiang, Jun Tan, Zhaoqi Xin, Quanwei Zhou, Chaohong Zhan, Xianyong Fu, Zhaoping Wu, Youwei Guo, Zhipeng Jiang, Chao Ren, Guihua Tang
Software Mentions: 7
Published: almost 5 years ago

10.15252/emmm.201910606

Novel Alzheimer risk genes determine the microglia response to amyloid‐β but not to TAU pathology
Cited by: 149
Author(s): Annerieke Sierksma, Ashley Lu, Renzo Mancuso, Nicola Fattorelli, Nicola Thrupp, Evgenia Salta, Jesus Zoco, David Blum, Luc Buée, Bart De Strooper, Mark Fiers
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2020.00895

Identification of Hub Genes Associated With Hepatocellular Carcinoma Using Robust Rank Aggregation Combined With Weighted Gene Co-expression Network Analysis
Cited by: 10
Author(s): Hongjiang Song, Na Ding, Shang Li, Jianlong Liao, Aimin Xie, Youtao Yu, Chunlong Zhang, Caifang Ni
Software Mentions: 7
Published: almost 5 years ago

10.15252/embr.201642378

Linear ubiquitination by <scp>LUBEL</scp> has a role in <i>Drosophila</i> heat stress response
Cited by: 31
Author(s): Tomoko Asaoka, Jorge Almagro, Christine Ehrhardt, Yi-Chun Isabella Tsai, Alexander Schleiffer, Luiza Deszcz, Sini Junttila, Leonie Ringrose, Karl Mechtler, Anoop Kavirayani, Attila Gyenesei, Kay Hofmann, Peter Duchek, Katrin Rittinger, Fumiyo Ikeda
Software Mentions: 7
Published: almost 9 years ago

10.1042/BSR20203336

Comprehensive analysis of tumor mutation burden and immune microenvironment in gastric cancer
Cited by: 17
Author(s): Jie Yu, QianYun Zhang, Mengchuan Wang, Shi-Dong Liang, Hongyun Huang, Lang Xie, Chunhui Cui
Software Mentions: 7
Published: over 4 years ago

10.26508/lsa.201800085

Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells
Cited by: 29
Author(s): Constantine Mylonas, Peter Tessarz
Software Mentions: 7
Published: about 7 years ago

10.1186/s12864-021-07593-3

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response
Cited by: 23
Author(s): Florencia Schlamp, Sofie Y. N. Delbare, Angela M. Early, Martin T. Wells, Sumanta Basu, Andrew G. Clark
Software Mentions: 7
Published: over 4 years ago

10.3390/bios3030238

A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach
Cited by: 20
Author(s): Sergiusz Wesołowski, Marc R. Birtwistle, Grzegorz A. Rempała
Software Mentions: 7
Published: about 12 years ago

10.1186/1756-8935-8-6

De novo identification of differentially methylated regions in the human genome
Cited by: 639
Author(s): Timothy J. Peters, Michael Buckley, Aaron L. Statham, Ruth Pidsley, Katherine Samaras, Reginald V. Lord, Susan J. Clark, Peter L. Molloy
Software Mentions: 7
Published: over 10 years ago

10.3390/e21030242

A Method Based on Differential Entropy-Like Function for Detecting Differentially Expressed Genes Across Multiple Conditions in RNA-Seq Studies
Cited by: 1
Author(s): Zhuo Wang, Shuilin Jin, Chiping Zhang
Software Mentions: 7
Published: over 6 years ago

10.3390/ijms19061808

Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation
Cited by: 8
Author(s): Mahmoud Ahmed, Jin Seok Hwang, Trang Huyen Lai, Sahib Zada, Huynh Quoc Nguyen, Trang Min Pham, Miyong Yun, Deok Ryong Kim
Software Mentions: 7
Published: about 7 years ago

10.1371/journal.pone.0196836

Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series
Cited by: 17
Author(s): Juan Manuel Gálvez, Daniel Castillo, José Benavente Herrera, Belén San Román, Olga Valenzuela, Francisco M. Ortuño Guzman, Ignacio Rojas
Software Mentions: 7
Published: about 7 years ago

10.3389/fonc.2020.00061

The Prognostic Significance of Metabolic Syndrome and a Related Six-lncRNA Signature in Esophageal Squamous Cell Carcinoma
Cited by: 18
Author(s): Yu Liu, Li-Yu Wang, Hengchang Liu, Chunxiang Li, Jie He
Software Mentions: 7
Published: over 5 years ago

10.3389/fonc.2021.584884

Tumor Microenvironmental Competitive Endogenous RNA Network and Immune Cells Act as Robust Prognostic Predictor of Acute Myeloid Leukemia
Cited by: 16
Author(s): Yuanrong Cheng, Xiaoran Wang, Peiyan Qi, Chengxiu Liu, Shoubi Wang, Qi Wan, Yurun Liu, Yangfeng Su, Lin Jin, Ying Liu, Chaoyang Li, Xuan Sang, Yang Liu, Chang Liu, Hucheng Duan, Zhichong Wang
Software Mentions: 7
Published: over 4 years ago

10.1002/ece3.4756

Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral <i>Montipora capitata</i>
Cited by: 9
Author(s): Martin Helmkampf, M. Renee Bellinger, Monika Frazier, Misaki Takabayashi
Software Mentions: 7
Published: over 6 years ago

10.7717/peerj.11219

Construction and validation of an RNA-binding protein-associated prognostic model for colorectal cancer
Cited by: 8
Author(s): Yifei Miao, Hongling Zhang, Bai-Horng Su, Jiangtao Wang, Wuxia Quan, Qiutian Li, Denghai Mi
Software Mentions: 7
Published: over 4 years ago

10.3389/fonc.2021.660242

Identification and Validation of a Five-Gene Signature Associated With Overall Survival in Breast Cancer Patients
Cited by: 6
Author(s): Xiaolong Wang, Chen Li, Tong Chen, Wenhao Li, Hanwen Zhang, Dong Zhang, Ying Liu, Dianwen Han, Yaming Li, Zheng Li, Dan Luo, Ning Zhang, Qifeng Yang
Software Mentions: 7
Published: almost 4 years ago

10.1002/ece3.7901

Linking ecology, morphology, and metabolism: Niche differentiation in sympatric populations of closely related species of the genus <i>Littorina</i> (<i>Neritrema</i>)
Cited by: 7
Author(s): Arina L. Maltseva, Marina A. Varfolomeeva, Roman V. Ayanka, Elizaveta R. Gafarova, Egor A. Repkin, Polina Pavlova, Alexei L. Shavarda, Natalia A. Mikhailova, Andrei I. Granovitch
Software Mentions: 7
Published: about 4 years ago

10.3389/fgene.2019.01372

4See: A Flexible Browser to Explore 4C Data
Cited by: 12
Author(s): Yousra Ben Zouari, Angeliki Platania, Anne Molitor, Tom Sexton
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.678436

Development of an Immune-Related LncRNA Prognostic Signature for Glioma
Cited by: 8
Author(s): Yudong Cao, Hecheng Zhu, Jun Tan, Yin Wu, Quanwei Zhou, Zhaoqi Xin, Zhaoping Wu, Zhipeng Jiang, Youwei Guo, Yirui Kuang, Can Li, Ming Zhao, Xingjun Jiang, Jian Peng, Chao Ren
Software Mentions: 7
Published: about 4 years ago

10.3390/medicina55060269

A Robust Approach for Identification of Cancer Biomarkers and Candidate Drugs
Cited by: 10
Author(s): Shahjaman, Rezanur Rahman, S. M. Shahinul Islam, Md. Nurul Haque Mollah
Software Mentions: 7
Published: about 6 years ago

10.1042/BSR20204340

TIGIT-related transcriptome profile and its association with tumor immune microenvironment in breast cancer
Cited by: 8
Author(s): Qin Zhang, Chaowei Gao, Jianqiang Shao, Zunyi Wang
Software Mentions: 7
Published: over 4 years ago

10.1155/2021/5555634

Downregulation of ATP6V1A Involved in Alzheimer’s Disease via Synaptic Vesicle Cycle, Phagosome, and Oxidative Phosphorylation
Cited by: 15
Author(s): Zhike Zhou, Jun Bai, Shanshan Zhong, Rongwei Zhang, Kexin Kang, Xiaoqian Zhang, Ying Xu, Chuansheng Zhao, Mei Zhao
Software Mentions: 7
Published: over 4 years ago

10.3389/fgene.2021.639642

Immune-Related Genes Are Prognostic Markers for Prostate Cancer Recurrence
Cited by: 10
Author(s): Min Fu, Qiang Wang, Hanbo Wang, Ying Dai, Jin Wang, Weiting Kang, Zilian Cui, Xunbo Jin
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-021-93509-w

Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation
Cited by: 9
Author(s): Muhammad Munir Iqbal, Michael Serralha, Parwinder Kaur, David Martino
Software Mentions: 7
Published: about 4 years ago

10.3389/fonc.2021.729340

Tumor Mutation Burden-Associated LINC00638/miR-4732-3p/ULBP1 Axis Promotes Immune Escape via PD-L1 in Hepatocellular Carcinoma
Cited by: 15
Author(s): Qi Feng, Xiaojing Du, Zhiying Zhao, Ding Zhang, Mengli Huang, Yuezong Bai, Biwei Yang, Wenxing Qin, Jinglin Xia
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0201830

Exposure to a firefighting overhaul environment without respiratory protection increases immune dysregulation and lung disease risk
Cited by: 14
Author(s): Stephen J. Gainey, Gavin P. Horn, Albert E. Towers, Maci L. Oelschlager, Vincent L. Tir, Jenny Drnevich, Kenneth W. Fent, Stephen Kerber, Denise L. Smith, Gregory G. Freund
Software Mentions: 7
Published: almost 7 years ago

10.1038/s41598-017-13397-x

The effect of insecticide synergist treatment on genome-wide gene expression in a polyphagous pest
Cited by: 28
Author(s): Simon Snoeck, Robert Greenhalgh, Luc Tirry, Richard M. Clark, Thomas Van Leeuwen, Wannes Dermauw
Software Mentions: 7
Published: almost 8 years ago

10.3389/fgene.2020.595757

Periostin Contributes to Immunoglobulin a Nephropathy by Promoting the Proliferation of Mesangial Cells: A Weighted Gene Correlation Network Analysis
Cited by: 4
Author(s): Jinlong Wu, Qisheng Lin, Shu Li, Xinghua Shao, Xuying Zhu, Minfang Zhang, Wenyan Zhou, Zhaohui Ni
Software Mentions: 7
Published: over 4 years ago