pypi: analysis | Projects | Ecosyste.ms: Papers

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 5 years ago

10.3389/fpls.2017.00413

Identification of Circular RNAs in Kiwifruit and Their Species-Specific Response to Bacterial Canker Pathogen Invasion
Cited by: 54
Author(s): Zupeng Wang, Yifei Liu, Dawei Li, Li Li, Qiong Zhang, Shuaibin Wang, Hongwen Huang
Software Mentions: 7
Published: over 9 years ago

10.1371/journal.pone.0234669

netboxr: Automated discovery of biological process modules by network analysis in R
Cited by: 2
Author(s): Eric Minwei Liu, Augustin Luna, Guanlan Dong, Chris Sander
Software Mentions: 7
Published: almost 6 years ago

10.1111/jcmm.16275

Identification of key candidate biomarkers for severe influenza infection by integrated bioinformatical analysis and initial clinical validation
Cited by: 7
Author(s): Shuai Liu, Zhisheng Huang, Xiaoyan Deng, Xiaohui Zou, Hui Li, Shengrui Mu, Bin Cao
Software Mentions: 7
Published: over 5 years ago

10.1186/1471-2164-15-480

Detection of copy number variations and their effects in Chinese bulls
Cited by: 50
Author(s): Liangzhi Zhang, Shangang Jia, Mingjuan Yang, Yao Xu, Congjun Li, Jiajie Sun, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Yang Zhou, Chunlei Zhang, Xin Zhao, Hong Chen
Software Mentions: 7
Published: about 12 years ago

10.1371/journal.pone.0116508

Large Scale Aggregate Microarray Analysis Reveals Three Distinct Molecular Subclasses of Human Preeclampsia
Cited by: 90
Author(s): Katherine Leavey, Shannon Bainbridge, Brian Cox
Software Mentions: 7
Published: over 11 years ago

10.3390/microorganisms7110492

Genetic and Phenotypic Characterisation of a Saccharomyces cerevisiae Population of ‘Merwah’ White Wine
Cited by: 8
Author(s): Nadine Feghali, Warren Albertin, Edouard Tabet, Ziad Rizk, Angela Bianco, Giacomo Zara, Isabelle Masneuf‐Pomarède, Marilena Budroni
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12859-019-3099-4

DIRECT: RNA contact predictions by integrating structural patterns
Cited by: 14
Author(s): Yiren Jian, Xiaonan Wang, Jaidi Qiu, Huiwen Wang, Zhichao Liu, Yunjie Zhao, Chen Zeng
Software Mentions: 7
Published: almost 7 years ago

10.1042/BSR20200935

WGCNA reveals key gene modules regulated by the combined treatment of colon cancer with PHY906 and CPT11
Cited by: 21
Author(s): Shuqin Xing, Yafei Wang, Kaiwen Hu, Fen Wang, Tao Sun, Quanwang Li
Software Mentions: 7
Published: almost 6 years ago

10.15252/emmm.201809910

Overcoming resistance to anabolic SARM therapy in experimental cancer cachexia with an HDAC inhibitor
Cited by: 16
Author(s): Sophia G. Liva, Yu Chou Tseng, Anees M. Dauki, Michael G. Sovic, Trang Vu, Sally E. Henderson, Yi Chiu Kuo, Jason Benedict, Xiaoli Zhang, Bryan Remaily, Samuel K. Kulp, Moray J. Campbell, Tanios Bekaii‐Saab, Mitch A. Phelps, Ching Shih Chen, Christopher C. Coss
Software Mentions: 7
Published: over 6 years ago

10.1186/s12885-020-07615-5

Genomics and prognosis analysis of epithelial-mesenchymal transition in colorectal cancer patients
Cited by: 15
Author(s): Zizhen Zhang, Shu Zheng, Yaowang Lin, Jiawei Sun, Ning Ding, Jingyu Chen, Jing Zhong, Liuhong Shi, Min Xue
Software Mentions: 7
Published: over 5 years ago

10.1111/jcmm.15805

Identification of purity and prognosis‐related gene signature by network analysis and survival analysis in brain lower grade glioma
Cited by: 15
Author(s): Zujian Xiong, Yi Xiong, Hongwei Liu, L. Chang, Xuejun Li
Software Mentions: 7
Published: almost 6 years ago

10.1155/2021/8323487

LncRNA ELF3-AS1 is a Prognostic Biomarker and Correlated with Immune Infiltrates in Hepatocellular Carcinoma
Cited by: 14
Author(s): Tianming Chen, Changhao Zhu, Xing Wang, Yaozhen Pan
Software Mentions: 7
Published: about 5 years ago

10.18632/aging.103779

Development and validation of an immune and stromal prognostic signature in uveal melanoma to guide clinical therapy
Cited by: 5
Author(s): Qianwen Gong, Qi Wan, Anqi Li, Yubin Yu, Xiangyu Ding, Lin Leng, Xiao-Liang Qi, Liang Hu
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0173115

Altered regulation and expression of genes by BET family of proteins in COPD patients
Cited by: 11
Author(s): Rajneesh Malhotra, Nisha Kurian, Xin Zhou, Fang Jiang, Susan J. Monkley, Amy DeMicco, Ib Groth Clausen, Göran Dellgren, Goran Edenro, Miika J. Ahdesmäki, Maryam Clausen, Lisa Öberg, Elisabeth Israelsson, Graham Belfield, Outi Vaarala
Software Mentions: 7
Published: over 9 years ago

10.7554/eLife.66788

An NKX2-1/ERK/WNT feedback loop modulates gastric identity and response to targeted therapy in lung adenocarcinoma
Cited by: 11
Author(s): Rediet Zewdu, Elnaz Mirzaei Mehrabad, Kelley Ingram, Pengshu Fang, Katherine L Gillis, Soledad A. Camolotto, Grace Orstad, Alex Jones, Michelle C. Mendoza, Benjamin T. Spike, Eric L. Snyder
Software Mentions: 7
Published: over 5 years ago

10.1186/s12885-017-3832-1

Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stages
Cited by: 9
Author(s): Daifeng Wang, John D. Haley, Patricia Thompson
Software Mentions: 6
Published: over 8 years ago

10.1155/2020/8537381

Autophagy Regulatory Genes MET and RIPK2 Play a Prognostic Role in Pancreatic Ductal Adenocarcinoma: A Bioinformatic Analysis Based on GEO and TCGA
Cited by: 10
Author(s): Xingyu Li, Zhiqiang Li, Hongwei Zhu, Xiao Yu
Software Mentions: 6
Published: almost 6 years ago

10.18632/aging.202718

TMBIM6, a potential virus target protein identified by integrated multiomics data analysis in SARS-CoV-2-infected host cells
Cited by: 4
Author(s): Qizheng Han, Junhao Wang, Haihua Luo, Lei Li, Xinya Lu, Aihua Liu, Yongqiang Deng, Yong Jiang
Software Mentions: 6
Published: over 5 years ago

10.3389/fnmol.2019.00316

Single Cell and Single Nucleus RNA-Seq Reveal Cellular Heterogeneity and Homeostatic Regulatory Networks in Adult Mouse Stria Vascularis
Cited by: 62
Author(s): Soumya Korrapati, Ian Taukulis, Rafal T. Olszewski, Madeline Pyle, Shoujun Gu, Riya Singh, C. M. Griffiths, Daniel Martin, Erich T. Boger, Robert J. Morell, Michael Hoa
Software Mentions: 6
Published: over 6 years ago

10.1186/s12859-018-2338-4

Data-driven human transcriptomic modules determined by independent component analysis
Cited by: 23
Author(s): Weizhuang Zhou, Russ B. Altman
Software Mentions: 6
Published: almost 8 years ago

10.1186/1471-2156-13-27

EggLib: processing, analysis and simulation tools for population genetics and genomics
Cited by: 139
Author(s): Stéphane De Mita, Mathieu Siol
Software Mentions: 6
Published: over 14 years ago

10.7554/eLife.54695

Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment
Cited by: 168
Author(s): Leilei Zhong, Lutian Yao, Robert J. Tower, Yulong Wei, Zhen Miao, Jihwan Park, Rojesh Shrestha, Luqiang Wang, Wei Yu, Nicholas Holdreith, Xiaobin Huang, Yejia Zhang, Wei Tong, Yanqing Gong, Jaimo Ahn, Katalin Suszták, Nathaniel A. Dyment, Mingyao Li, Fanxin Long, Chider Chen, Patrick Seale, Ling Qin
Software Mentions: 6
Published: over 6 years ago

10.1186/s12859-020-03648-6

A computational framework for modeling and studying pertussis epidemiology and vaccination
Cited by: 4
Author(s): Paolo Castagno, Simone Pernice, Gianni Ghetti, Massimiliano Povero, Lorenzo Pradelli, Daniela Paolotti, Gianfranco Balbo, Matteo Sereno, Marco Beccuti
Software Mentions: 6
Published: almost 6 years ago

10.7554/eLife.50069

Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing pan-neuronal human amyloid beta
Cited by: 49
Author(s): Emelyne Teo, Sudharshan Ravi, Diogo Barardo, Hyung-Seok Kim, Sheng Fong, Amaury Cazenave-Gassiot, Tsze Yin Tan, Jianhong Ching, Jean‐Paul Kovalik, Markus R. Wenk, Rudiyanto Gunawan, Philip K. Moore, Barry Halliwell, Nicholas S. Tolwinski, Jan Gruber
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-016-3199-8

Identification of novel targets of diabetic nephropathy and PEDF peptide treatment using RNA-seq
Cited by: 29
Author(s): Ana Rubín, Anna C. Salzberg, Yuka Imamura, Anzor Grivitishvilli, Joyce Tombran-Tink
Software Mentions: 6
Published: over 9 years ago

10.1002/JLB.5MA0120-209R

Distinct and shared gene expression for human innate versus adaptive helper lymphoid cells
Cited by: 28
Author(s): Giuseppe Ercolano, Tania Wyss, Bérengère Salomé, Pedro Romero, Sara Trabanelli, Camilla Jandus
Software Mentions: 6
Published: over 6 years ago

10.1002/1878-0261.12707

Classification of diffuse lower‐grade glioma based on immunological profiling
Cited by: 40
Author(s): Fan Wu, Zhiliang Wang, Kuan‐Yu Wang, Guanzhang Li, Rui‐Chao Chai, Yuqing Liu, Haiyan Jiang, You Zhai, Yuemei Feng, Zheng Zhao, Wei Zhang
Software Mentions: 6
Published: about 6 years ago

10.7554/eLife.63270

Dissecting phenotypic transitions in metastatic disease via photoconversion-based isolation
Cited by: 4
Author(s): Yogev Sela, Jinyang Li, Paola Kuri, Allyson J. Merrell, Ning Li, Chris Lengner, Pantelis Rompolas, Ben Z. Stanger
Software Mentions: 6
Published: over 5 years ago

10.1093/conphys/coz018

Tracking transcriptomic responses to endogenous and exogenous variation in cetaceans in the Southern California Bight
Cited by: 8
Author(s): Marisa L. Trego, Andrew Whitehead, Nicholas M. Kellar, Morgane Lauf, Rebecca L. Lewison
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pcbi.1007509

Clustering-independent analysis of genomic data using spectral simplicial theory
Cited by: 19
Author(s): Kiya W. Govek, Venkata S. Yamajala, Pablo G. Cámara
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-021-91382-1

RUNX1 and REXO2 are associated with the heterogeneity and prognosis of IDH wild type lower grade glioma
Cited by: 11
Author(s): Haiwei Wang, Xinrui Wang, Liangpu Xu, Ji Zhang, Hua Cao
Software Mentions: 6
Published: about 5 years ago

10.1128/mBio.01037-19

Reprogramming of Small Noncoding RNA Populations in Peripheral Blood Reveals Host Biomarkers for Latent and Active Mycobacterium tuberculosis Infection
Cited by: 24
Author(s): Leonardo Silva de Araujo, Marcelo Ribeiro-Alves, Thyago Leal-Calvo, Janaina Aparecida Medeiros Leung, Verónica Durán, Mohamed Samir, Steven R. Talbot, Aravind Tallam, Fernanda Carvalho de Queiroz Mello, Robert Geffers, Maria Helena Féres Saad, Frank Peßler
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0081458

Stability-Based Comparison of Class Discovery Methods for DNA Copy Number Profiles
Cited by: 1
Author(s): Isabel Martínez Brito, Philippe Hupé, Pierre Neuvial, Emmanuel Barillot
Software Mentions: 6
Published: over 12 years ago

10.18632/aging.102714

ISG20 serves as a potential biomarker and drives tumor progression in clear cell renal cell carcinoma
Cited by: 22
Author(s): Tianbo Xu, Hailong Ruan, Su Gao, Jingchong Liu, Yuenan Liu, Zhengshuai Song, Qi Cao, Keshan Wang, Lin Bao, Di Liu, Junwei Tong, Jian Shi, Huageng Liang, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 6
Published: over 6 years ago

10.1080/21642850.2018.1472602

Scale validation in applied health research: tutorial for a 6-step R-based psychometrics protocol
Cited by: 69
Author(s): Alexandra Dima
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0254368

Identification and validation of a novel ferroptosis-related gene model for predicting the prognosis of gastric cancer patients
Cited by: 6
Author(s): Gang Liu, Jianying Ma, Gang Hu, Huan Jin
Software Mentions: 6
Published: about 5 years ago

10.1186/s13073-021-00861-7

Development of double-positive thymocytes at single-cell resolution
Cited by: 15
Author(s): Young Li, Kun Li, Lianbang Zhu, Bin Li, Dandan Zong, Pengfei Cai, Chen Jiang, Pengcheng Du, Jun Lin, Kun Qu
Software Mentions: 6
Published: over 5 years ago

10.1002/jev2.12022

Microglial derived extracellular vesicles activate autophagy and mediate multi‐target signaling to maintain cellular homeostasis
Cited by: 22
Author(s): Bram Van den Broek, Isabel Pintelon, Ibrahim Hamad, Sofie Kessels, Mansour Haidar, Niels Hellings, Jerome J. A. Hendriks, Markus Kleinewietfeld, Bert Brône, Vincent Timmerman, Jean‐Pierre Timmermans, Veerle Somers, Luc Michiels, Joy Irobi
Software Mentions: 6
Published: almost 6 years ago

10.3390/metabo11060361

Opposing Effects of Ceanothus velutinus Phytochemistry on Herbivore Communities at Multiple Scales
Cited by: 2
Author(s): Casey S. Philbin, M. J. Paulsen, Lora A. Richards
Software Mentions: 6
Published: about 5 years ago

10.1534/genetics.116.195008

A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation
Cited by: 12
Author(s): Owen J. L. Rackham, Sarah R. Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K. Srivastava, Jacques Behmoaras, Πέτρος Δελλαπόρτας, Leonardo Bottolo, Enrico Petretto
Software Mentions: 6
Published: over 9 years ago

10.1186/s12864-021-07812-x

Stage-specific transcriptomic changes in pancreatic α-cells after massive β-cell loss
Cited by: 9
Author(s): Daniel Oropeza, Valentina Cigliola, Agustín Romero, Simona Chera, Santiago A. Rodríguez-Seguí, Pedro Luis Herrera
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0025630

Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for Beginners
Cited by: 284
Author(s): Vincenzo Viscosi, Andrea Cardini
Software Mentions: 6
Published: almost 15 years ago

10.18632/aging.103832

Prognostic model of patients with liver cancer based on tumor stem cell content and immune process
Cited by: 7
Author(s): Jie Zhu, Miaomiao Gao, Yuchen Jin, Weiran Huang, Zhuo Huang, Zhengwei Xie
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12935-020-01552-w

Transcriptomic characterization and innovative molecular classification of clear cell renal cell carcinoma in the Chinese population
Cited by: 7
Author(s): Qiang Zhao, Jian Xue, Bo Hong, Wubin Qian, Tiezhu Liu, Bin Fan, Jie Cai, Yunpeng Ji, Jia Liu, Yong Yang, Qi-Xiang Li, Sheng Guo, Ning Zhang
Software Mentions: 6
Published: almost 6 years ago

10.1002/cam4.3576

Establishment and validation of a prognostic nomogram based on a novel five‐DNA methylation signature for survival in endometrial cancer patients
Cited by: 6
Author(s): Xingchen Li, Fufen Yin, Fan Yuan, Yuan Cheng, Yangyang Dong, Jingyi Zhou, Zhiqi Wang, Jianliu Wang
Software Mentions: 6
Published: over 5 years ago

10.3389/fpsyt.2021.716722

Transcriptomics Analysis Reveals Shared Pathways in Peripheral Blood Mononuclear Cells and Brain Tissues of Patients With Schizophrenia
Cited by: 6
Author(s): Xuemian Song, Yiyun Liu, Juncai Pu, Siwen Gui, Xiaogang Zhong, Xiaopeng Chen, Weiyi Chen, Xiang Chen, Yue Chen, Haiyang Wang, Ke Cheng, Libo Zhao, Peng Xie
Software Mentions: 6
Published: almost 5 years ago

10.18632/aging.202478

Tumor microenvironment characterization in triple-negative breast cancer identifies prognostic gene signature
Cited by: 7
Author(s): Yan Qin, Jiehua Deng, Lihua Zhang, Jiaxing Yuan, Huawei Yang, Qiuyun Li
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-020-02081-5

The Tug1 lncRNA locus is essential for male fertility
Cited by: 59
Author(s): Jordan P. Lewandowski, Gabrijela Dumbović, Audrey Watson, Tae-Young Hwang, Emily Jacobs-Palmer, Nydia P Chang, Christian Much, Kyle M. Turner, Christopher Kirby, Nimrod D. Rubinstein, Abigail F. Groff, Steve C. Liapis, Chiara Gerhardinger, Assaf C. Bester, Pier Paolo Pandolfi, John G. Clohessy, Hopi E. Hoekstra, Martin Sauvageau, John L. Rinn
Software Mentions: 6
Published: almost 6 years ago

10.1038/s42003-021-02397-3

Three-dimensional CRISPR screening reveals epigenetic interaction with anti-angiogenic therapy
Cited by: 4
Author(s): Michael Y. He, Michael M. Halford, Ruofei Liu, James P Roy, Zoe L. Grant, Leigh Coultas, Niko Thio, Omer Gilan, Yih Chih Chan, Mark A. Dawson, Marc G. Achen, Steven A. Stacker
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.1078

Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox
Cited by: 13
Author(s): A. M. R. Ribeiro, Luís Lacerda, Hugo Alexandre Ferreira
Software Mentions: 6
Published: about 11 years ago

10.3389/fonc.2021.632934

RNA N6-Methyladenosine Regulator-Mediated Methylation Modifications Pattern and Immune Infiltration Features in Glioblastoma
Cited by: 19
Author(s): Yimin Pan, Kai Xiao, Yue Li, Yuzhe Li, Qing Liu
Software Mentions: 6
Published: over 5 years ago

10.3389/fonc.2021.652211

Comprehensive Pan-Cancer Analysis Confirmed That ATG5 Promoted the Maintenance of Tumor Metabolism and the Occurrence of Tumor Immune Escape
Cited by: 18
Author(s): Chunxiao Xu, Yusheng Zang, Yuxiang Zhao, Weiqiang Cui, Hong Zhang, Yingcui Zhu, Man Xu
Software Mentions: 6
Published: over 5 years ago

10.3389/fonc.2021.636479

An Immune Cell-Based Signature Associating With EMT Phenotype Predicts Postoperative Overall Survival of ESCC
Cited by: 4
Author(s): Hongliang Yu, Dayong Gu, Chao Yang, Jianhua Xu, Feng Yan, Xu He
Software Mentions: 6
Published: over 5 years ago

10.1186/s13046-019-1372-z

Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer
Cited by: 61
Author(s): Apostolos Zaravinos, Constantinos Roufas, Majdi Nagara, Beatriz de Lucas, Maria Oblovatskaya, Christodoulos Efstathiades, Christos Dimopoulos, Georgios D. Ayiomamitis
Software Mentions: 6
Published: almost 7 years ago

10.3389/fgene.2021.678747

Identification of CXCL10-Relevant Tumor Microenvironment Characterization and Clinical Outcome in Ovarian Cancer
Cited by: 5
Author(s): Jing Jin, Yang Li, Tobias Achu Muluh, Liangke Zhi, Qijie Zhao
Software Mentions: 6
Published: about 5 years ago

10.1186/s13148-018-0582-0

Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes
Cited by: 20
Author(s): Adeline Divoux, Katalin Sandor, Dóra Bojcsuk, Amlan Talukder, Xiaoman Li, Bálint László Bálint, Timothy F. Osborne, Steven R. Smith
Software Mentions: 6
Published: over 7 years ago

10.3389/fgene.2020.00099

A FITM1-Related Methylation Signature Predicts the Prognosis of Patients With Non-Viral Hepatocellular Carcinoma
Cited by: 4
Author(s): J Chen, X Wang, Wei Li, Chao Shang, T Chen, Y Chen
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2021.645839

Multi-Omics Profiling Identifies Risk Hypoxia-Related Signatures for Ovarian Cancer Prognosis
Cited by: 11
Author(s): Xingyu Chen, Hua Lan, Dong He, Runshi Xu, Yao Zhang, Ying Cheng, Haotian Chen, Songshu Xiao, Ke Cao
Software Mentions: 6
Published: about 5 years ago

10.3390/ijms22010078

Alterations in the Genomic Distribution of 5hmC in In Vivo Aged Human Skin Fibroblasts
Cited by: 10
Author(s): Paulina Kołodziej-Wojnar, Joanna Borkowska, Zofia Wicik, Anna Domaszewska-Szostek, Jacek Połosak, Marta Cąkała-Jakimowicz, Olga Bujanowska, Monika Puzianowska-Kuźnicka
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22126307

Transcriptional Profiling Identifies Upregulation of Neuroprotective Pathways in Retinitis Pigmentosa
Cited by: 4
Author(s): Christina B. Bielmeier, Saskia Roth, Sabrina I. Schmitt, Stefaniya Boneva, Anja Schlecht, Mario Vallon, Ernst R. Tamm, Süleyman Ergün, Andreas Neueder, Barbara M. Braunger
Software Mentions: 6
Published: about 5 years ago

10.3390/cancers13081817

USP22 Suppresses SPARC Expression in Acute Colitis and Inflammation-Associated Colorectal Cancer
Cited by: 8
Author(s): Robyn Laura Kosinsky, Dominik Saul, Christoph Ammer‐Herrmenau, William A. Faubion, Albrecht Neeße, Steven A. Johnsen
Software Mentions: 6
Published: over 5 years ago

10.3390/ijms22063028

Characterization of Biological Pathways Regulating Acute Cold Resistance of Zebrafish
Cited by: 19
Author(s): Jing Ren, Yong Long, Ran Liu, Guangliang Song, Qing Li, Zongbin Cui
Software Mentions: 6
Published: over 5 years ago

10.1155/2021/6676537

Machine Learning for Building Immune Genetic Model in Hepatocellular Carcinoma Patients
Cited by: 2
Author(s): Jun Liu, Zheng Chen, Wenli Li
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-018-21161-y

Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
Cited by: 16
Author(s): Yukie Kashima, Ayako Suzuki, Ying Liu, Masahito Hosokawa, Hiroko Matsunaga, Masamitsu Shirai, Kohji Arikawa, Sumio Sugano, Takashi Kohno, Haruko Takeyama, Katsuya Tsuchihara, Yutaka Suzuki
Software Mentions: 6
Published: over 8 years ago

10.1186/s13578-019-0334-7

The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency
Cited by: 6
Author(s): Meisam Yousefi, Sayed-Amir Marashi, Ali Sharifi‐Zarchi, Sara Taleahmad
Software Mentions: 6
Published: almost 7 years ago

10.3389/fgene.2020.566159

Identifying 8-mRNAsi Based Signature for Predicting Survival in Patients With Head and Neck Squamous Cell Carcinoma via Machine Learning
Cited by: 10
Author(s): Yanhua Tian, Juncheng Wang, Chao Qin, Guanghao Zhu, Xuan Chen, Zhixiang Chen, Yuexiang Qin, Ming Wei, Zhexuan Li, Xin Zhang, Yunxia Lv, Gengming Cai
Software Mentions: 6
Published: almost 6 years ago

10.1016/j.cell.2021.07.023

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
Cited by: 170
Author(s): Carly G.K. Ziegler, Vincent N. Miao, Anna H. Owings, Andrew W. Navia, Ying Tang, Joshua D. Bromley, Peter Lotfy, Meredith Sloan, Hannah Laird, Hibbard E. Williams, Micayla George, Riley S. Drake, Christian Taube, Adam Parker, Campbell B Sindel, Molly Burger, Yilianys Pride, Mohammad S Hasan, George Abraham, Michal Senitko, Tanya O. Robinson, Alex K. Shalek, Sarah C. Glover, Bruce H. Horwitz, José Ordovás-Montañés
Software Mentions: 6
Published: almost 5 years ago

10.1016/j.celrep.2019.06.046

Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry
Cited by: 68
Author(s): Pavel Bouchal, Olga T. Schubert, Jakub Faktor, Lenka Čápková, Hana Imrichová, Karolína Zoufalová, Vendula Páralová, Roman Hrstka, Yansheng Liu, H. Alexander Ebhardt, Eva Budínská, Rudolf Nenutil, Ruedi Aebersold
Software Mentions: 6
Published: about 7 years ago

10.1098/rsos.191480

Mid and hindgut transcriptome profiling analysis of Atlantic salmon ( Salmon salar ) under unpredictable chronic stress
Cited by: 2
Author(s): Signe Dille Løvmo, Angelico Madaro, Paul Whatmore, Tora Bardal, Mari‐Ann Östensen, Simen Rød Sandve, Rolf Erik Olsen
Software Mentions: 6
Published: over 6 years ago

10.1016/j.celrep.2021.109362

Nutritional regulation of oligodendrocyte differentiation regulates perineuronal net remodeling in the median eminence
Cited by: 29
Author(s): Sara Kohnke, Sophie Buller, Danaé Nuzzaci, Katherine Ridley, Brian Lam, Helena Pivoňková, Marie A. Bentsen, Kimberly M. Alonge, Chao Zhao, John Tadross, Staffan Holmqvist, Takahiro Shimizu, Hannah A. Hathaway, Hui‐Liang Li, Wendy B. Macklin, Michael W. Schwartz, William D. Richardson, Giles S.H. Yeo, R. J. M. Franklin, Ragnhildur Thóra Káradóttir, David H. Rowitch, Clémence Blouet
Software Mentions: 6
Published: about 5 years ago

10.3389/fimmu.2021.632798

Comprehensive Transcriptomic Analysis Identifies Novel Antiviral Factors Against Influenza A Virus Infection
Cited by: 11
Author(s): Ao Zhou, Dong Xia, Mengyun Liu, Bin Tang
Software Mentions: 6
Published: about 5 years ago

10.1155/2021/9943465

Construction and Validation of an Autophagy-Related Prognostic Model for Osteosarcoma Patients
Cited by: 2
Author(s): Qian-Nan Hu, Ting Lei, Pengfei Lei, Yihe Hu
Software Mentions: 6
Published: about 5 years ago

10.3389/fgene.2020.00011

Novel Combined Tissue Transcriptome Analysis After Lentogenic Newcastle Disease Virus Challenge in Inbred Chicken Lines of Differential Resistance
Cited by: 6
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2021.705646

On Deep Landscape Exploration of COVID-19 Patients Cells and Severity Markers
Cited by: 9
Author(s): Aarón Vázquez-Jiménez, Ugo Enrique Avila-Ponce De León, Meztli Matadamas-Guzmán, Erick Andrés Muciño-Olmos, Yoscelina Estrella Martínez-López, Thelma Escobedo-Tapia, Osbaldo Reséndis-Antonio
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41419-021-03738-0

A KDM4A-PAF1-mediated epigenomic network is essential for acute myeloid leukemia cell self-renewal and survival
Cited by: 18
Author(s): Matthew E. Massett, Laura Monaghan, Shaun Patterson, Niamh Mannion, Roderick P Bunschoten, Alex Hoose, Sandra Marmiroli, Rob M. J. Liskamp, Heather G. Jørgensen, David Vetrie, Alison M. Michie, Xu Huang
Software Mentions: 6
Published: about 5 years ago

10.3390/ijms22094598

Combined Transcriptomic and Proteomic Analysis of Perk Toxicity Pathways
Cited by: 6
Author(s): Rebeka Popovic, Ivana Celardo, Yao Yu, Ana Carolina Oliveira Costa, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 6
Published: over 5 years ago

10.1186/s12931-016-0459-8

Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations
Cited by: 47
Author(s): Robert S. Busch, Weiliang Qiu, Jessica Lasky‐Su, Jarrett Morrow, Gerard J. Criner, Dawn L. DeMeo
Software Mentions: 6
Published: almost 10 years ago

10.1371/journal.pone.0116177

Evolution of p53 Transactivation Specificity through the Lens of a Yeast-Based Functional Assay
Cited by: 12
Author(s): Mattia Lion, Ivan Raimondi, Stefano Donati, Olivier Jousson, Yari Ciribilli, Alberto Inga
Software Mentions: 6
Published: over 11 years ago

10.1371/journal.pone.0073938

A Toxicogenomic Approach for the Prediction of Murine Hepatocarcinogenesis Using Ensemble Feature Selection
Cited by: 16
Author(s): Johannes Eichner, Nadine Kossler, Clemens Wrzodek, Arno Kalkuhl, Dorthe Bach Toft, Nina Ostenfeldt, V. Espley Richard, Andreas Zell
Software Mentions: 6
Published: almost 13 years ago

10.3389/fgene.2020.00663

Gastric Cancer Tumor Microenvironment Characterization Reveals Stromal-Related Gene Signatures Associated With Macrophage Infiltration
Cited by: 29
Author(s): Shenyu Wei, Jiahua Lu, Jianying Lou, Connie R. Shi, Shaowei Mo, Yaojian Shao, Junjie Ni, Wu Zhang, Xiangdong Cheng
Software Mentions: 5
Published: about 6 years ago

10.1155/2021/6648093

Integrated Analysis to Identify a Redox-Related Prognostic Signature for Clear Cell Renal Cell Carcinoma
Cited by: 16
Author(s): Yue Wu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Jihong Liu, Tao Wang
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.658323

Discovery and Validation of Key Biomarkers Based on Immune Infiltrates in Alzheimer’s Disease
Cited by: 22
Author(s): Zhuohang Liu, Hang Li, Shuyi Pan
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.721873

Screening of DNA Damage Repair Genes Involved in the Prognosis of Triple-Negative Breast Cancer Patients Based on Bioinformatics
Cited by: 4
Author(s): Nan Wang, Yuanting Gu, Jiangrui Chi, Xinwei Li, Youyi Xiong, Chaochao Zhong, Fang Wang, Xinxing Wang, Lin Li
Software Mentions: 5
Published: about 5 years ago

10.1186/s12967-018-1707-0

Evaluation of the prognostic value of paraoxonase 1 in the recurrence and metastasis of hepatocellular carcinoma and establishment of a liver-specific predictive model of survival
Cited by: 18
Author(s): Zhenzhen Yu, Qifeng Ou, Chongxi Fan, Jiong Bi, Wen Li, Jiachi Ma, Rongchang Wang, Xiaohui Huang
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.ppat.1008477

Immunosuppressive FK506 treatment leads to more frequent EBV-associated lymphoproliferative disease in humanized mice
Cited by: 15
Author(s): Nicole Caduff, Donal McHugh, Anita Murer, Patrick C. Rämer, Ana Raykova, Vanessa Landtwing, Lisa Rieble, Christian W. Keller, Michael Prummer, Laurent Hoffmann, Janice K. P. Lam, Aks Chiang, Friedrich Raulf, Tarik Azzi, Christoph Berger, Tina Rubic-Schneider, Elisabetta Traggiai, Jan D. Lünemann, Michael Kammüller, Christian Münz
Software Mentions: 5
Published: over 6 years ago

10.3389/fcell.2021.662707

PLXNC1: A Novel Potential Immune-Related Target for Stomach Adenocarcinoma
Cited by: 12
Author(s): Zhizhan Ni, Chenshen Huang, Hongmei Zhao, Jinzhe Zhou, Muren Hu, Qing Chen, Bujun Ge, Qi Huang
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0070433

Genome-Wide Expression of Transcriptomes and Their Co-Expression Pattern in Subtropical Maize (Zea mays L.) under Waterlogging Stress
Cited by: 54
Author(s): Nepolean Thirunavukkarasu, Firoz Hossain, Sweta Mohan, Kaliyugam Shiriga, Swati Mittal, R.C. Sharma, Rita Singh, H. S. Gupta
Software Mentions: 5
Published: about 13 years ago

10.1038/s41419-021-03450-z

ECT2 overexpression promotes the polarization of tumor-associated macrophages in hepatocellular carcinoma via the ECT2/PLK1/PTEN pathway
Cited by: 26
Author(s): Dafeng Xu, Yu Wang, Junzhen Wu, Zhensheng Zhang, Jiacheng Chen, Mingwei Xie, Rong Tang, Cheng Chen, Liang Chen, Shaomin Lin, Xiangxiang Luo, Jinfang Zheng
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0208917

The hindgut microbiota of praying mantids is highly variable and includes both prey-associated and host-specific microbes
Cited by: 6
Author(s): Kara Tinker, Elizabeth A. Ottesen
Software Mentions: 5
Published: over 7 years ago

10.3390/jcm9092930

Proteomic Profiles of Exosomes of Septic Patients Presenting to the Emergency Department Compared to Healthy Controls
Cited by: 8
Author(s): Daniel C. Morris, Anja Kathrin Jaehne, Michael Chopp, Zhanggang Zhang, Laila Poisson, Yalei Chen, Indrani Datta, Emanuel P. Rivers
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2019.00772

Polycystic Ovary Syndrome: Novel and Hub lncRNAs in the Insulin Resistance-Associated lncRNA–mRNA Network
Cited by: 22
Author(s): Jun Zhao, Jiayu Huang, Xue Geng, Weiwei Chu, Shang Li, Zi‐Jiang Chen, Yanzhi Du
Software Mentions: 5
Published: almost 7 years ago

10.3389/fgene.2020.610704

Investigation on Potential Correlation Between Small Nuclear Ribonucleoprotein Polypeptide A and Lung Cancer
Cited by: 6
Author(s): Maoxi Yuan, Chunxiao Yu, Xin Chen, Yubing Wu
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cell.2019.05.047

Neutrophils Driving Unconventional T Cells Mediate Resistance against Murine Sarcomas and Selected Human Tumors
Cited by: 147
Author(s): Andrea Ponzetta, Roberta Carriero, Silvia Carnevale, Marialuisa Barbagallo, Martina Molgora, Chiara Perucchini, Elena Magrini, Francesca Gianni, Paolo Kunderfranco, Nadia Polentarutti, Fabio Pasqualini, Sabrina Di Marco, Domenico Supino, Clelia Peano, Ferdinando Carlo Maria Cananzi, Piergiuseppe Colombo, Silvana Pilotti, Suliman Yousef Alomar, Eduardo Bonavita, Maria Rosaria Galdiero, Cecília Garlanda, Alberto Mantovani, Sébastien Jaillon
Software Mentions: 5
Published: about 7 years ago

10.3389/fimmu.2021.643298

Immunomodulation of T Helper Cells by Tumor Microenvironment in Oral Cancer Is Associated With CCR8 Expression and Rapid Membrane Vitamin D Signaling Pathway
Cited by: 14
Author(s): Marco Fraga, Milly Yáñez, Macarena Sherman, Faryd Llerena, Mauricio Hernández, Guillermo Nourdin, Francisco Álvarez, Joaquín Urrizola, César Rivera, Liliana Lamperti, Lorena Nova, S Rojas Castro, Olga Zambrano, Alejandro Cifuentes, León Campos, Sergio Moya, J. Pastor, Marcelo Nuñez, Jorge Gatica, Jorge Figueroa, Felipe Zúñiga, Carlos Salomón, Gustavo Cerda, Ricardo Puentes, Gonzalo Labarca, Mabel Vidal, Reuben McGregor, Estefanía Nova-Lamperti
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.649270

Elevated GAS2L3 Expression Correlates With Poor Prognosis in Patients With Glioma: A Study Based on Bioinformatics and Immunohistochemical Analysis
Cited by: 3
Author(s): Yan Zhou, Limin Zhang, Sirong Song, Lixia Xu, Yan Yan, Haiyang Wu, Xiaoguang Tong, Hua Yan
Software Mentions: 5
Published: over 5 years ago

10.1111/jcmm.16615

Transcriptome and DNA methylation analysis reveals molecular mechanisms underlying intrahepatic cholangiocarcinoma progression
Cited by: 4
Author(s): Yunyan Peng, Guohao Meng, Xinyi Sheng, Hongqiang Gao
Software Mentions: 5
Published: about 5 years ago

10.3390/cancers12061487

Only Hematopoietic Stem and Progenitor Cells from Cord Blood Are Susceptible to Malignant Transformation by MLL-AF4 Translocations
Cited by: 12
Author(s): Kathy-Ann Secker, Lukas Bruns, Hildegard Keppeler, Johan Jeong, Thomas Hentrich, Julia M. Schulze‐Hentrich, Barbara Mankel, Falko Fend, Dominik Schneidawind, Corina Schneidawind
Software Mentions: 5
Published: about 6 years ago

10.1016/j.celrep.2020.107691

Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells
Cited by: 17
Author(s): Monica Nafria, Peter Keane, Elizabeth Ng, Edouard G. Stanley, Andrew G. Elefanty, Constanze Bonifer
Software Mentions: 5
Published: over 6 years ago

10.1038/srep46156

Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens
Cited by: 18
Author(s): Xi Lan, Yan Wang, Kai Tian, Fei Ye, Huadong Yin, Xiaoling Zhao, Hengyong Xu, Yong Huang, Haibo Li, John Hsieh, Susan J. Lamont, Qing Zhu
Software Mentions: 5
Published: over 9 years ago

Projects: pypi: analysis

Science Score: 90/100

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Papers Mentioning analysis 2,036