bioconductor: biomaRt | Projects | Ecosyste.ms: Papers

10.18632/aging.203505

Transcriptomic analysis of elderly women with low muscle mass: association with immune system pathway
Cited by: 1
Author(s): Levi H. Jales Neto, Bidossessi Wilfried Hounkpe, Geórgea Hermogenes Fernandes, Liliam Takayama, Valéria F. Caparbo, Neuza Lopes, Alexandre C. Pereira, Rosa Maria Rodrigues Pereira
Software Mentions: 4
Published: about 3 years ago

10.1186/1471-2105-15-S1-S6

CorrelaGenes: a new tool for the interpretation of the human transcriptome
Cited by: 1
Author(s): Paolo Cremaschi, Sergio Rovida, Lucia Sacchi, Antonella Lisa, Francesca Calvi, Alessandra Montecucco, Giuseppe Biamonti, Silvia Bione, Gianni Sacchi
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12915-018-0556-x

Evolutionary stability of topologically associating domains is associated with conserved gene regulation
Cited by: 108
Author(s): Jan Krefting, Miguel A. Andrade‐Navarro, Jonas Ibn-Salem
Software Mentions: 4
Published: over 6 years ago

10.1186/s12885-018-4757-z

Association of tamoxifen resistance and lipid reprogramming in breast cancer
Cited by: 98
Author(s): Susanne Hultsch, Matti Kankainen, Lassi Paavolainen, Ruusu-Maaria Kovanen, Elina Ikonen, Sara Kangaspeska, Vilja Pietiäinen, Olli Kallioniemi
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-017-3566-0

Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development
Cited by: 51
Author(s): Steven Ge
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-020-07009-8

Bivalent genes that undergo transcriptional switching identify networks of key regulators of embryonic stem cell differentiation
Cited by: 6
Author(s): Ah-Jung Jeon, Greg Tucker‐Kellogg
Software Mentions: 4
Published: about 4 years ago

10.1186/1471-2164-11-294

Consistent annotation of gene expression arrays
Cited by: 28
Author(s): Benoît Ballester, Nathan Johnson, G Proctor, Paul Flicek
Software Mentions: 4
Published: over 14 years ago

10.1186/s12864-021-07889-4

Experimental Babesia rossi infection induces hemolytic, metabolic, and viral response pathways in the canine host
Cited by: 6
Author(s): Rachel Smith, Amelia Goddard, Arun K. Boddapati, Steven Brooks, Johan P. Schoeman, Justin Lack, Andrew L. Leisewitz, Hans Ackerman
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-021-07643-w

Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria
Cited by: 7
Author(s): Thomas J. Hall, Michael P. Mullen, Gillian P. McHugo, Kate E. Killick, S.C. Ring, D.P. Berry, Carolina N. Correia, John A. Browne, Stephen V. Gordon, David E. MacHugh
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-11-365

Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury
Cited by: 39
Author(s): Jesper Ryge, Ole Winther, Jacob Wienecke, Albin Sandelin, Ann-Charlotte Westerdahl, Hans Hultborn, Ole Kiehn
Software Mentions: 4
Published: almost 15 years ago

10.1186/1471-2164-13-519

Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression
Cited by: 37
Author(s): Sebastian Müller, Clara Baldin, Marco Groth, Reinhard Guthke, Olaf Kniemeyer, Axel A. Brakhage, Vito Valiante
Software Mentions: 4
Published: about 12 years ago

10.1186/1753-6561-3-S4-S9

Microarray data mining using Bioconductor packages
Cited by: 8
Author(s): Haisheng Nie, Pieter Neerincx, Jan van der Poel, Francesco Ferrari, Silvio Bicciato, Jack A. M. Leunissen, Martien A. M. Groenen
Software Mentions: 4
Published: over 15 years ago

10.1186/1752-0509-8-55

TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level
Cited by: 29
Author(s): Khalid Abnaof, Nikhil Mallela, Gudrun Walenda, Steffen K. Meurer, Kristin Seré, Qiong Lin, Boudewijn J. J. Smeets, Kurt Hoffmann, Wolfgang Wagner, Martin Zenke, Ralf Weiskirchen, Holger Fröhlich
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12917-020-02373-9

Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility
Cited by: 5
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Dag Inge Våge, Teklu Tewoldebrhan Zeremichael, Frøydis Deinboll Myromslien, Eli Grindflek
Software Mentions: 4
Published: over 4 years ago

10.1186/s12935-018-0681-1

Identification of RPL5 and RPL10 as novel diagnostic biomarkers of Atypical teratoid/rhabdoid tumors
Cited by: 6
Author(s): Yanming Ren, Chuanmin Tao, Xiliang Wang, Yan Ju
Software Mentions: 4
Published: about 6 years ago

10.1016/j.mex.2019.01.009

RppH can faithfully replace TAP to allow cloning of 5′-triphosphate carrying small RNAs
Cited by: 18
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, Hanna Lukas, María Méndez-Lago, René F. Ketting
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-018-0404-9

Commensal microbiota modulate gene expression in the skin
Cited by: 126
Author(s): Jacquelyn S. Meisel, Georgia Sfyroera, Casey Bartow‐McKenney, Ciara Gimblet, Julia Bugayev, Joseph Horwinski, Brian Kim, Jonathan R. Brestoff, Amanda S. Tyldsley, Qi Zheng, Brendan P. Hodkinson, David Artis, Elizabeth A. Grice
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13024-021-00462-3

A proteomic network approach resolves stage-specific molecular phenotypes in chronic traumatic encephalopathy
Cited by: 4
Author(s): Laura Gutierrez-Quiceno, Eric B. Dammer, Ashlyn G. Johnson, James Webster, Rhythm Shah, Duc M. Duong, Luming Yin, Nicholas T. Seyfried, Victor E. Alvarez, Thor D. Stein, Ann C. McKee, Chadwick M. Hales
Software Mentions: 4
Published: over 3 years ago

10.1016/j.pain.2013.05.021

HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain
Cited by: 127
Author(s): Franziska Denk, Wenlong Huang, Ben S. Sidders, Angela Bithell, Megan Crow, John Grist, Simone Sharma, Daniel Ziemek, Andrew S.C. Rice, Noel J. Buckley, Stephen B. McMahon
Software Mentions: 4
Published: about 11 years ago

10.7717/peerj.3216

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
Cited by: 9
Author(s): Zhao min Deng, Lizhu Lin, Wen Qiu, Yong qun Zhang, Hong Zhong, Ping Liao, Wu Yun
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pcbi.1008429

Identifying longevity associated genes by integrating gene expression and curated annotations
Cited by: 5
Author(s): F. William Townes, Kareem Carr, Jeffrey W. Miller
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1004604

Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation
Cited by: 77
Author(s): Andrew D. Hoffmann, Xinan Yang, Ozanna Burnicka-Turek, Joshua D. Bosman, Xiaomeng Ren, Jeffrey D. Steimle, Steven A. Vokes, Andrew P. McMahon, Vladimir V. Kalinichenko, Ivan P. Moskowitz
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0117818

mRNA Profiling Reveals Determinants of Trastuzumab Efficiency in HER2-Positive Breast Cancer
Cited by: 33
Author(s): Silvia von der Heyde, Sven Wagner, Czerny Alexander, M. Nietert, Fabian Ludewig, Gabriela Salinas-Riester, Dorit Arlt, Tim Beißbarth
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0244408

Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep
Cited by: 13
Author(s): Seyed Mehdi Esmaeili-Fard, Mohsen Gholizadeh, Seyed Hasan Hafezian, Rostam Abdollahi-Arpanahi
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0246443

Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches
Cited by: 4
Author(s): Shirley Chu, Zachary L. Skidmore, Jason Kunisaki, Jason Walker, Malachi Griffith, Obi L. Griffith, Jeffrey N. Bryan
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0014782

Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA
Cited by: 122
Author(s): Andreia J. Amaral, Luca Ferretti, Hendrik‐Jan Megens, R.P.M.A. Crooijmans, Haisheng Nie, Sebastián E. Ramos-Onsins, Miguel Pérez‐Enciso, Lawrence B. Schook, Martien A. M. Groenen
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0047107

Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos
Cited by: 12
Author(s): Elisa A. Casanova, Michał Okoniewski, Paolo Cinelli
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0233543

A transcriptome-based approach to identify functional modules within and across primary human immune cells
Cited by: 10
Author(s): Saraï Mola, Sylvain Foisy, Gabrielle Boucher, François Major, Claudine Beauchamp, Mohamad Karaky, Philippe Goyette, Sylvie Lesage, John D. Rioux
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0256091

Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data
Cited by: 12
Author(s): María Canive, Óscar González-Recio, Almudena Fernández, Patricia Vázquez, Gerard Badia-Bringué, José Luis Lavín, Joseba M. Garrido, Ramón A. Juste, Marta Alonso‐Hearn
Software Mentions: 4
Published: about 3 years ago

10.3390/cancers7040887

Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics
Cited by: 27
Author(s): Janet Doolittle-Hall, Danielle L. Cunningham Glasspoole, William T. Seaman, Jennifer Webster‐Cyriaque
Software Mentions: 4
Published: about 9 years ago

10.3390/cancers13051126

Transformed Canine and Murine Mesenchymal Stem Cells as a Model for Sarcoma with Complex Genomics
Cited by: 5
Author(s): Natasja Franceschini, Bas Verbruggen, Marianna A. Tryfonidou, Alwine B. Kruisselbrink, Hans J. Baelde, Karin E. de Visser, Károly Szuhai, Anne‐Marie Cleton‐Jansen, Judith V.M.G. Bovée
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers12061618

Rare Tumor-Normal Matched Whole Exome Sequencing Identifies Novel Genomic Pathogenic Germline and Somatic Aberrations
Cited by: 1
Author(s): Ryan Sprissler, Bryce Perkins, Laurel Johnstone, Hani M. Babiker, Pavani Chalasani, Branden Lau, Michael F. Hammer, Daruka Mahadevan
Software Mentions: 4
Published: over 4 years ago

10.1016/j.stem.2019.05.013

Engineering Genetic Predisposition in Human Neuroepithelial Stem Cells Recapitulates Medulloblastoma Tumorigenesis
Cited by: 53
Author(s): Miller Huang, Jignesh Tailor, Qiqi Zhen, Aaron H. Gillmor, Matthew Miller, Holger Weishaupt, Justin Chen, Tina Zheng, Emily K. Nash, Lauren McHenry, Zhenyi An, Fubaiyang Ye, Yasuhiro Takashima, James Clarke, Harold Ayetey, Florence M.G. Cavalli, Betty Luu, Branden S. Moriarity, Shirin Ilkhanizadeh, Lukas Chávez, Chunying Yu, Kathreena M. Kurian, Thierry Magnaldo, Nicolas Sévenet, Philipp Koch, Steven M. Pollard, Peter B. Dirks, M Snyder, David A. Largaespada, Yoon Jae Cho, Joanna J. Phillips, Fredrik J. Swartling, A. Sorana Morrissy, Marcel Kool, Stefan M. Pfister, Michael D. Taylor, Austin Smith, William A. Weiss
Software Mentions: 4
Published: about 5 years ago

10.1038/s42003-021-02059-4

Three-dimensional tissue-engineered human skeletal muscle model of Pompe disease
Cited by: 13
Author(s): Jason Wang, Chris J. Zhou, Alastair Khodabukus, Sabrina Tran, Sang-oh Han, Aaron L. Carlson, Lauran Madden, Priya S. Kishnani, Dwight D. Koeberl
Software Mentions: 4
Published: over 3 years ago

10.1530/ERC-19-0448

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

10.1186/s13072-015-0040-6

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships
Cited by: 127
Author(s): Julie Nadel, Rodoniki Athanasiadou, Christophe Lemetre, N. Ari Wijetunga, Pilib Ó Broin, Hanae Sato, Zhengdong Zhang, Jeffrey A. Jeddeloh, Cristina Montagna, Aaron Golden, Cathal Seoighe, John M. Greally
Software Mentions: 4
Published: about 9 years ago

10.3389/fcvm.2018.00186

Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation
Cited by: 15
Author(s): Douglas J. Chapski, Manuel Rosa‐Garrido, Haiyang Nan, Frank Alber, Thomas M. Vondriska
Software Mentions: 4
Published: almost 6 years ago

10.3389/fcell.2021.688855

Transcriptomics Profiling Identifies Cisplatin-Inducible Death Receptor 5 Antisense Long Non-coding RNA as a Modulator of Proliferation and Metastasis in HeLa Cells
Cited by: 7
Author(s): Dilek Cansu Gürer, İpek Erdoğan, Ulvi Ahmadov, Merve Başol, Osama Sweef, Gulcin Cakan-Akdogan, Bünyamin Akgül
Software Mentions: 4
Published: about 3 years ago

10.3389/fcimb.2021.678482

Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells
Cited by: 38
Author(s): Syairah Hanan Shaharuddin, Victoria Wang, Reginaldo da Silva Santos, Andrew Gross, Yizhou Wang, Harneet Jawanda, Yi Zhang, Wohaib Hasan, Gustavo García, Vaithilingaraja Arumugaswami, Dhruv Sareen
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.745277

Chromobox Homolog 8 (CBX8) in Human Tumor Carcinogenesis and Prognosis: A Pancancer Analysis Using Multiple Databases
Cited by: 4
Author(s): Dongjie Shi, Lei Ao, Hua Yu, Yongzhi Xia, Juan Li, Wenjie Zhong, Haijian Xia
Software Mentions: 4
Published: about 3 years ago

10.3389/fgene.2019.00697

Cross-Species Gene Expression Analysis Reveals Gene Modules Implicated in Human Osteosarcoma
Cited by: 12
Author(s): Zheng Jin, Shanshan Liu, Pei‐Wen Zhu, Mengyan Tang, Yuanxin Wang, Yuan Tian, Li Dong, X. D. Zhu, Dongmei Yan, Zhifeng Zhu
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2019.00858

pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks
Cited by: 189
Author(s): Ege Ülgen, Özan Özışık, Uğur Sezerman
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2020.00629

Genomics of Heat Tolerance in Reproductive Performance Investigated in Four Independent Maternal Lines of Pigs
Cited by: 16
Author(s): Francesco Tiezzi, Luiz F. Brito, Jeremy Howard, Yongjun Huang, Kent Gray, Charles V. Schwab, Justin Fix, Christian Maltecca
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2019.00184

Associations Between Behavioral Effects of Bisphenol A and DNA Methylation in Zebrafish Embryos
Cited by: 38
Author(s): Pål A. Olsvik, Paul Whatmore, Samuel Penglase, Kaja H. Skjærven, Marc Anglès d’Auriac, Ståle Ellingsen
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2017.01221

PI3Kδ Inhibition Enhances the Antitumor Fitness of Adoptively Transferred CD8+ T Cells
Cited by: 56
Author(s): Jacob S. Bowers, Kinga Majchrzak, Michelle H. Nelson, Bülent Arman Aksoy, Megan Wyatt, Aubrey S. Smith, Stefanie R. Bailey, Lillian R. Neal, Jeff Hammerbacher, Chrystal M. Paulos
Software Mentions: 4
Published: about 7 years ago

10.3389/fnins.2017.00112

Antidyskinetic Effects of MEK Inhibitor Are Associated with Multiple Neurochemical Alterations in the Striatum of Hemiparkinsonian Rats
Cited by: 21
Author(s): Guiqin Chen, Shuke Nie, Chao Han, Kai Ma, Xu Yan, Zhentao Zhang, Stella M. Papa, Xin Cao
Software Mentions: 4
Published: over 7 years ago

10.3389/fonc.2021.687629

A Non-Coding RNA Network Involved in KSHV Tumorigenesis
Cited by: 4
Author(s): Julián Naipauer, Martín E García Solá, Daria Salyakina, Santas Rosario, Siôn L. Williams, Omar A. Coso, Martı́n C. Abba, Enrique A. Mesri, Ezequiel Lacunza
Software Mentions: 4
Published: over 3 years ago

10.3390/genes8020068

Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts
Cited by: 34
Author(s): Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, Kumiko Ui-Tei
Software Mentions: 4
Published: almost 8 years ago

10.3390/genes12091363

Meta-Analysis of Brain Gene Expression Data from Mouse Model Studies of Maternal Immune Activation Using Poly(I:C)
Cited by: 4
Author(s): Aodán Laighneach, Lieve Desbonnet, John Kelly, Gary Donohoe, Derek W. Morris
Software Mentions: 4
Published: about 3 years ago

10.1186/s13059-014-0513-0

TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator
Cited by: 120
Author(s): Ya-Ping Tsai, Hsiao-Fan Chen, Sung-Yuan Chen, Wei‐Chung Cheng, Hsei‐Wei Wang, Zih-Jie Shen, Chun-Xiao Song, Shan-Yuan Teng, Chuan He, Kou-Juey Wu
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13059-020-02257-z

Evolutionary conservation and divergence of the human brain transcriptome
Cited by: 22
Author(s): William G Pembroke, Christopher Hartl, Daniel H. Geschwind
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13059-021-02340-z

HDAC4 degradation during senescence unleashes an epigenetic program driven by AP-1/p300 at selected enhancers and super-enhancers
Cited by: 22
Author(s): Eros Di Giorgio, Harikrishnareddy Paluvai, Emiliano Dalla, Liliana Ranzino, Alessandra Renzini, Viviana Moresi, Martina Minisini, Raffaella Picco, Claudio Brancolini
Software Mentions: 4
Published: over 3 years ago

10.1186/s13073-020-00754-1

Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults
Cited by: 20
Author(s): Robert F. Hillary, Daniel Trejo Baños, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, Sven Erik Ojavee, Qian Zhang, David C. Liewald, Craig W. Ritchie, Kathryn Evans, Elliot M. Tucker‐Drob, Naomi R. Wray, Allan F. McRae, Peter M. Visscher, Ian J. Deary, Matthew R. Robinson, Riccardo E. Marioni
Software Mentions: 4
Published: over 4 years ago

10.1038/srep29122

The transcriptomes of novel marmoset monkey embryonic stem cell lines reflect distinct genomic features
Cited by: 16
Author(s): Katharina Debowski, Charis Drummer, Jana Lentes, Maren Cors, Ralf Dressel, Thomas Lingner, Gabriela Salinas-Riester, Sigrid Fuchs, Erika Sasaki, Rüdiger Behr
Software Mentions: 4
Published: over 8 years ago

10.1038/srep29434

Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies
Cited by: 13
Author(s): Dominic Pearce, Laura Arthur, Arran Turnbull, Lorna Renshaw, Victoria Sabine, Jeremy Thomas, John M.S. Bartlett, J. Michael Dixon, Andrew H. Sims
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-018-29329-2

Determination of system level alterations in host transcriptome due to Zika virus (ZIKV) Infection in retinal pigment epithelium
Cited by: 33
Author(s): Pawan Kumar Singh, Indu Khatri, Alokkumar Jha, Carla D. Pretto, Katherine R. Spindler, Vaithilingaraja Arumugaswami, Shailendra Giri, Ashok Kumar, Manoj Bhasin
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-44877-x

A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
Cited by: 55
Author(s): Martin Kuhlwilm, Cédric Boeckx
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-60025-2

Identification of putative biomarkers for Infantile Hemangiomas and Propranolol treatment via data integration
Cited by: 14
Author(s): Horacio Gómez-Acevedo, Yuemeng Dai, Graham M. Strub, Carrie J. Shawber, June K. Wu, Gresham T. Richter
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-75400-2

A systems genomics approach to uncover the molecular properties of cancer genes
Cited by: 0
Author(s): Felix Graßmann, Yudi Pawitan, Kamila Czene
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-021-96149-2

Long noncoding RNA landscapes specific to benign and malignant thyroid neoplasms of distinct histological subtypes
Cited by: 2
Author(s): V. D. Yakushina, В. В. Стрельников, А. С. Танас, А. В. Лавров
Software Mentions: 4
Published: over 3 years ago

10.1186/s40246-018-0170-6

Forward and reverse mutations in stages of cancer development
Cited by: 11
Author(s): Taobo Hu, Yogesh Kumar, Shazia Iram, Si Duan, Yang Li, Lei Chen, Jinfei Chen, Rong Yin, Ava Kwong, Gilberto Ka Kit Leung, Wai Kin Mat, Zhenggang Wu, Xi Long, Colin Chan, Si Chen, Peggy Lee, Siu Kin Ng, Timothy Y. C. Ho, Jianfeng Yang, Xueliang Ding, Suk Ying Tsang, Xinrui Zhou, Danhua Zhang, Enbo Zhou, Lin Xu, Wai-sang Poon, Hongyang Wang, Hong Xue
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.68714

Deep learning detects cardiotoxicity in a high-content screen with induced pluripotent stem cell-derived cardiomyocytes
Cited by: 17
Author(s): Francis Grafton, Jaclyn J. Ho, Sara Ranjbarvaziri, Farshad Farshidfar, Anastasiia Budan, Stephanie Steltzer, Mahnaz Maddah, Kevin E. Loewke, Kristina Green, Snahel Patel, Tim Hoey, Mohammad A. Mandegar
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.60546

Acquisition of innate odor preference depends on spontaneous and experiential activities during critical period
Cited by: 13
Author(s): Qiang Qiu, Yunming Wu, Limei Ma, Wenjing Xu, Max Hills, Vivekanandan Ramalingam, Chong Yu
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms17091426

Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs
Cited by: 26
Author(s): Julia Welzenbach, Christiane Neuhoff, Hanna Heidt, Mehmet Ulaş Çınar, Christian Looft, K. Schellander, Ernst Tholen, Christine Große‐Brinkhaus
Software Mentions: 4
Published: about 8 years ago

10.3390/ijms21238898

MicroRNA Profiling in Oesophageal Adenocarcinoma Cell Lines and Patient Serum Samples Reveals a Role for miR-451a in Radiation Resistance
Cited by: 8
Author(s): Frederike Butz, Ann-Kathrin Eichelmann, George C. Mayne, Tingting Wang, Isabell Bastian, Karen Chiam, Shashikanth Marri, Pamela J. Sykes, Bas P. L. Wijnhoven, Eelke Toxopeus, Michael Michael, Christos S. Karapetis, Richard Hummel, David I. Watson, Damian J. Hussey
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms22031208

Transcriptomic Signatures and Upstream Regulation in Human Skeletal Muscle Adapted to Disuse and Aerobic Exercise
Cited by: 14
Author(s): Pavel A. Makhnovskii, Roman O. Bokov, Fedor A. Kolpakov, D. V. Popov
Software Mentions: 4
Published: almost 4 years ago

10.18632/oncotarget.12204

Human PDE4D isoform composition is deregulated in primary prostate cancer and indicative for disease progression and development of distant metastases
Cited by: 21
Author(s): René Böttcher, Kalyan Dulla, Dianne van Strijp, Natasja F. Dits, Esther I. Verhoef, George S. Baillie, Geert J.L.H. van Leenders, Miles D. Houslay, Guido Jenster, Ralf Hoffmann
Software Mentions: 4
Published: about 8 years ago

10.1186/s12967-020-02400-1

Collapsing the list of myocardial infarction-related differentially expressed genes into a diagnostic signature
Cited by: 11
Author(s): German Osmak, Natalia Baulina, Philipp Koshkin, О. О. Фаворова
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-66791-3

Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters
Cited by: 43
Author(s): Matteo Bergamaschi, Christian Maltecca, Constantino Schillebeeckx, Nathan P. McNulty, Charles V. Schwab, Caleb M Shull, Justin Fix, Francesco Tiezzi
Software Mentions: 3
Published: over 4 years ago

10.3389/fonc.2020.00845

Multi-Omic Regulation of the PAM50 Gene Signature in Breast Cancer Molecular Subtypes
Cited by: 14
Author(s): Soledad Ochoa, Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 3
Published: over 4 years ago

10.1038/s41421-021-00266-1

Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture
Cited by: 25
Author(s): Yanfang Lu, Miao Liu, Jennifer Yang, Sherman M. Weissman, Xinghua Pan, Samuel G. Katz, Siyuan Wang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1002565

Tcf7 Is an Important Regulator of the Switch of Self-Renewal and Differentiation in a Multipotential Hematopoietic Cell Line
Cited by: 92
Author(s): Jia Qian Wu, Montrell Seay, Vincent P. Schulz, Manoj Hariharan, David Tuck, Lian Jin, Jie Du, Minyi Shi, Zhijia Ye, Mark Gerstein, M Snyder, Sherman M. Weissman
Software Mentions: 3
Published: over 12 years ago

10.3389/fcell.2021.700061

DeepGP: An Integrated Deep Learning Method for Endocrine Disease Gene Prediction Using Omics Data
Cited by: 1
Author(s): Ningyi Zhang, Haoyan Wang, Xu Chen, Liyuan Zhang, Tianyi Zang
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-56590-w

A systems biology approach reveals neuronal and muscle developmental defects after chronic exposure to ionising radiation in zebrafish
Cited by: 8
Author(s): Sophia Murat El Houdigui, Christelle Adam-Guillermin, Giovanna Loro, Caroline Arcanjo, Sandrine Frelon, Magali Floriani, Nicolas Dubourg, Emilie Baudelet, Stéphane Audebert, Luc Camoin, Olivier Armant
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms21218269

ITGA6+ Human Testicular Cell Populations Acquire a Mesenchymal Rather than Germ Cell Transcriptional Signature during Long-Term Culture
Cited by: 1
Author(s): Robert B. Struijk, Callista L Mulder, Saskia K.M. van Daalen, Cindy M de Winter-Korver, Aldo Jongejan, Sjoerd Repping, Ans M.M. van Pelt
Software Mentions: 3
Published: about 4 years ago

10.1038/sdata.2015.68

Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes
Cited by: 40
Author(s): Wasco Wruck, Karl Kashofer, Samrina Rehman, Andriani Daskalaki, Daniela Berg, Ewa Gralka, Justyna Józefczuk, Katharina Drews, Vikash Pandey, Christian Regenbrecht, Christoph Wierling, Paola Turano, Ulrike Korf, Kurt Zatloukal, Hans Lehrach, Hans V. Westerhoff, James Adjaye
Software Mentions: 3
Published: almost 9 years ago

10.1038/sdata.2019.11

Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins
Cited by: 38
Author(s): Peter Blattmann, Vivienne Stutz, Giulia Lizzo, J. Wall Richard, Philipp Gut, Ruedi Aebersold
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-51141-9

Divergence in Transcriptional and Regulatory Responses to Mating in Male and Female Fruitflies
Cited by: 21
Author(s): Emily K. Fowler, Thomas Bradley, Simon Moxon, Tracey Chapman
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-49031-1

Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering
Cited by: 10
Author(s): Takahide Mori, Haruka Takaoka, Junko Yamane, Cantas Alev, Wataru Fujibuchi
Software Mentions: 3
Published: about 5 years ago

10.3389/fendo.2021.690387

L-Cell Expression of Melanocortin-4-Receptor Is Marginal in Most of the Small Intestine in Mice and Humans and Direct Stimulation of Small Intestinal Melanocortin-4-Receptors in Mice and Rats Does Not Affect GLP-1 Secretion
Cited by: 1
Author(s): Rune Ehrenreich Kuhre, Ida M. Modvig, Sara L. Jepsen, Hüsün Sheyma Kizilkaya, Cecilie Bæch-Laursen, Christopher A. Smith, Frank Reimann, Fiona M. Gribble, Mette M. Rosenkilde, Jens J. Holst
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-020-3371-7

PANEV: an R package for a pathway-based network visualization
Cited by: 15
Author(s): Valentino Palombo, Marco Milanesi, Gabriella Sferra, Stefano Capomaccio, Sandy Sgorlon, Mariasilvia D’Andrea
Software Mentions: 3
Published: almost 5 years ago

10.1038/srep22851

An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder
Cited by: 17
Author(s): Leandro Lima, Ana Cecília Feio-dos-Santos, Síntia Belangero, Ary Gadelha, Rodrigo A. Bressan, Giovanni Abrahão Salum, Pedro Mário Pan, Tais Moriyama, Ana Soledade Graeff‐Martins, Ana Carina Tamanaha, Pedro Gomes de Alvarenga, Fernanda Valle Krieger, Bacy Fleitlich-Bilyk, Andrea Parolin Jackowski, Elisa Brietzke, João Ricardo Sato, Guilherme Polanczyk, Jair de Jesus Mari, Gisele Gus Manfro, Maria Conceição do Rosário, Eurípedes Constantino Miguel, Renato Puga, Ana Carolina Tahira, Viviane Neri Souza, Thais Chile, Gisele Rodrigues Gouveia, Sérgio Nery Simões, Xiao Chang, Renata Pellegrino, Lifeng Tian, Joseph T. Glessner, Ronaldo Fumio Hashimoto, Luís Augusto Rohde, Patrick Sleiman, Hákon Hákonarson, Helena Brentani
Software Mentions: 3
Published: over 8 years ago

10.1038/s42003-020-01118-6

Post-transcriptional air pollution oxidation to the cholesterol biosynthesis pathway promotes pulmonary stress phenotypes
Cited by: 17
Author(s): Juan C. Gonzalez-Rivera, Kevin C. Baldridge, Dongyu Wang, Kanan Patel, Jamie C. L. Chuvalo-Abraham, Lea Hildebrandt Ruiz, Lydia M. Contreras
Software Mentions: 3
Published: over 4 years ago

10.1038/s41419-018-0671-1

Transcriptome analysis of the adult human Klinefelter testis and cellularity-matched controls reveals disturbed differentiation of Sertoli- and Leydig cells
Cited by: 30
Author(s): Sofia B. Winge, Marlene Danner Dalgaard, Kirstine Belling, James C. Jensen, John Nielsen, Lise Aksglæde, Mikkel Heide Schierup, Søren Brunak, Niels E. Skakkebæk, Anders Juul, Ewa Rajpert‐De Meyts, Kristian Almstrup
Software Mentions: 3
Published: over 6 years ago

10.1038/srep28998

The RNA binding protein HuR determines the differential translation of autism-associated FoxP subfamily members in the developing neocortex
Cited by: 33
Author(s): Tatiana Popovitchenko, Kevin J. Thompson, Barbara Viljetić, Xuan Jiao, D. L. Kontonyiannis, Megerditch Kiledjian, Ronald P. Hart, Mladen-Roko Rašin
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2021.617512

An Information Theoretical Multilayer Network Approach to Breast Cancer Transcriptional Regulation
Cited by: 5
Author(s): Soledad Ochoa, Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 3
Published: over 3 years ago

10.1523/ENEURO.0287-18.2018

Overweight Mice Show Coordinated Homeostatic and Hedonic Transcriptional Response across Brain
Cited by: 0
Author(s): Ilario De Toma, Ilona Grabowicz, Marta Fructuoso, Daniel Trujillano, Bartek Wilczyński, Mara Dierssen
Software Mentions: 3
Published: about 6 years ago

10.1534/g3.120.401240

Genomic Prediction Informed by Biological Processes Expands Our Understanding of the Genetic Architecture Underlying Free Amino Acid Traits in Dry <i>Arabidopsis</i> Seeds
Cited by: 8
Author(s): Sarah D. Turner, Kevin A. Bird, Alexander E. Lipka, Elizabeth G. King, Timothy Beissinger, Ruthie Angelovici
Software Mentions: 3
Published: about 4 years ago

10.1038/srep37622

HMGA1P7-pseudogene regulates H19 and Igf2 expression by a competitive endogenous RNA mechanism
Cited by: 33
Author(s): Marco De Martino, Floriana Forzati, Marianna Marfella, Simona Pellecchia, Claudio Arra, Luigi Terracciano, Alfredo Fusco, Francesco Esposito
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-43409-x

TGFβ-induced cytoskeletal remodeling mediates elevation of cell stiffness and invasiveness in NSCLC
Cited by: 22
Author(s): Evgeny Gladilin, Sebastian Ohse, Melanie Boerries, Hauke Busch, Cong Xu, Martin Schneider, Michael Meister, Roland Eils
Software Mentions: 3
Published: over 5 years ago

10.1038/srep46695

Pathways and Genes Associated with Immune Dysfunction in Sheep Paratuberculosis
Cited by: 16
Author(s): Anton Gossner, Craig Watkins, Francesca Chianini
Software Mentions: 3
Published: over 7 years ago

10.1186/s13229-020-00407-5

Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank
Cited by: 9
Author(s): Chloe X. Yap, Gail A. Alvares, Anjali K. Henders, Lin Tian, Leanne Wallace, Alaina Farrelly, Tiana McLaren, Jolene Berry, Anna A. E. Vinkhuyzen, Maciej Trzaskowski, Jian Zeng, Yuanhao Yang, Dominique Cleary, Rachel Grove, Claire Hafekost, Alexis Harun, Helen Holdsworth, Rachel Jellett, Feroza Khan, Lauren P. Lawson, Jodie Leslie, Mira Levis Frenk, Anne Masi, Nisha E. Mathew, Melanie Muniandy, Michaela Nothard, Peter M. Visscher, Paul A. Dawson, Cheryl Dissanayake, Valsamma Eapen, Helen Heussler, Andrew J. O. Whitehouse, Naomi R. Wray, Jacob Gratten
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-018-27912-1

Expression ratio of the TGFβ-inducible gene MYO10 is prognostic for overall survival of squamous cell lung cancer patients and predicts chemotherapy response
Cited by: 11
Author(s): Dmytro Dvornikov, Marc A. Schneider, Sebastian Ohse, Magdalena Szczygieł, I. Titkova, Marcus Rosenblatt, Thomas Muley, Arne Warth, Felix Herth, Hendrik Dienemann, Michael Thomas, Jens Timmer, Marcel Schilling, Hauke Busch, Melanie Boerries, Michael Meister, Ursula Klingmüller
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-020-0873-9

Pan-cancer molecular analysis of the RB tumor suppressor pathway
Cited by: 47
Author(s): Erik S. Knudsen, Ram Nambiar, Spencer R. Rosario, Dominic J. Smiraglia, David W. Goodrich, Agnieszka K. Witkiewicz
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2020.00265

Modulator-Dependent RBPs Changes Alternative Splicing Outcomes in Kidney Cancer
Cited by: 12
Author(s): Yan Wang, Steven Chen, Xi Rao, Yunlong Liu
Software Mentions: 3
Published: over 4 years ago

10.1186/s12967-020-02405-w

COVID-19: viral–host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection
Cited by: 76
Author(s): Francesco Messina, Emanuela Giombini, Chiara Agrati, Francesco Vairo, Tommaso Ascoli Bartoli, Samir Al Moghazi, Mauro Piacentini, Franco Locatelli, Gary P. Kobinger, Markus Maeurer, Alimuddin Zumla, Maria Rosaria Capobianchi, F. Lauria, Giuseppe Ippolito, Isabella Abbate, Chiara Agrati, Samir Al Moghazi, Tommaso Ascoli Bartoli, Barbara Bartolini, Maria Rosaria Capobianchi, Alessandro Capone, Delia Goletti, Gabriella Rozera, Carla Nisii, Roberta Gagliardini, Fabiola Ciccosanti, Gian María Fimia, Emanuele Nicastri, Emanuela Giombini, Simone Lanini, Alessandra D’Abramo, Gabriele Rinonapoli, Enrico Gottardi, Chiara Montaldo, Raffaella Marconi, Antonio Addis, Bradley A. Maron, Ginestra Bianconi, Bertrand De Meulder, Jason Kennedy, Shabaana A. Khader, Francesca Luca, Markus Maeurer, Mauro Piacentini, Stefano Merler, Giuseppe Pantaleo, Rafick‐Pierre Sékaly, Serena Sanna, Nicola Segata, Alimuddin Zumla, Francesco Messina, Francesco Vairo, F. Lauria, Giuseppe Ippolito
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2021.689897

Polycystic Ovary Syndrome and Risk of Five Common Psychiatric Disorders Among European Women: A Two-Sample Mendelian Randomization Study
Cited by: 3
Author(s): Long-Fei Jin, Jia-En Yu, Yuxiao Chen, Haijun Pang, Jian‐Zhong Sheng, He‐Feng Huang
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2015.00174

Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations
Cited by: 44
Author(s): Ovidiu D. Iancu, Alexandre M. Colville, Denesa Oberbeck, Priscila Darakjian, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 3
Published: over 9 years ago

10.1523/ENEURO.0234-20.2020

Effects of L-DOPA on Gene Expression in the Frontal Cortex of Rats with Unilateral Lesions of Midbrain Dopaminergic Neurons
Cited by: 0
Author(s): Anna Radlicka, Kinga Kamińska, Małgorzata Borczyk, Marcin Piechota, Michał Korostyński, Joanna Pera, Elżbieta Lorenc‐Koci, Jan Rodriguez Parkitna
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2021.637322

Leveraging Single-Cell RNA-seq Data to Uncover the Association Between Cell Type and Chronic Liver Diseases
Cited by: 4
Author(s): Xiangyu Ye, Jian Wei, Ming Yue, Yan Wang, Hongbo Chen, Yongfeng Zhang, Yifan Wang, Meiling Zhang, Peng Huang, Rongbin Yu
Software Mentions: 3
Published: over 3 years ago

Projects: bioconductor: biomaRt

Papers Mentioning biomaRt 446