bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s12918-016-0344-6

A method for automated pathogenic content estimation with application to rheumatoid arthritis
Cited by: 9
Author(s): Xiaoyuan Zhou, Christine Nardini
Software Mentions: 4
Published: almost 10 years ago

10.1093/gbe/evy041

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee
Cited by: 19
Author(s): Jason Pizzollo, William Nielsen, Yoichiro Shibata, Alexias Safi, Gregory E. Crawford, Gregory A. Wray, Courtney C. Babbitt
Software Mentions: 4
Published: over 8 years ago

10.1186/s12862-014-0260-6

At the brink of eusociality: transcriptomic correlates of worker behaviour in a small carpenter bee
Cited by: 59
Author(s): Sandra M. Rehan, Ali J. Berens, Amy L. Toth
Software Mentions: 4
Published: almost 12 years ago

10.1093/gbe/evv115

Complete Dosage Compensation inAnopheles stephensiand the Evolution of Sex-Biased Genes in Mosquitoes
Cited by: 40
Author(s): Xiaofang Jiang, James K. Biedler, Yumin Qi, Andrew Brantley Hall, Zhijian Tu
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1007765

Hypomorphic mutation of the mouse Huntington’s disease gene orthologue
Cited by: 12
Author(s): Vidya Murthy, Toma Tebaldi, Toshimi Yoshida, Serkan Erdin, Teresa Calzonetti, Ravi Vijayvargia, Takshashila Tripathi, Emanuela Kerschbamer, Ihn Sik Seong, Alessandro Quattrone, Michael E. Talkowski, James F. Gusella, Katia Georgopoulos, Marcy E. MacDonald, Marta Biagioli
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1005184

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans
Cited by: 111
Author(s): Li Zhao, Janneke Wit, Nicolas Svetec, David J. Begun
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-020-07218-1

Targeted mutagenesis of ∆5 and ∆6 fatty acyl desaturases induce dysregulation of lipid metabolism in Atlantic salmon (Salmo salar)
Cited by: 6
Author(s): Yang Jin, Alex K. Datsomor, Rolf Erik Olsen, Jon Olav Vik, Jacob Torgersen, Rolf B. Edvardsen, Anna Wargelius, Per Winge, Fabian Grammes
Software Mentions: 4
Published: almost 6 years ago

10.15252/embr.201846557

Tamoxifen mechanically reprograms the tumor microenvironment via <scp>HIF</scp> ‐1A and reduces cancer cell survival
Cited by: 55
Author(s): Ernesto Cortés, Dariusz Lachowski, Benjamin Robinson, Müge Sarper, Jaakko Teppo, Stephen D. Thorpe, Tyler J Lieberthal, Kenji Iwamoto, David A. Lee, Mariko Okada‐Hatakeyama, Markku Varjosalo, Armando E. del Río Hernández
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pgen.1008537

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation
Cited by: 33
Author(s): Gregory R. Keele, Bryan C. Quach, Jennifer W. Israel, Grace A. Chappell, Lauren Lewis, Alexias Safi, Jeremy M. Simon, Paul Cotney, Gregory E. Crawford, William Valdar, Ivan Rusyn, Terrence S. Furey
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-020-6541-0

iREAD: a tool for intron retention detection from RNA-seq data
Cited by: 33
Author(s): Hong Dong Li, Cory C. Funk, Nathan D. Price
Software Mentions: 4
Published: over 6 years ago

10.1002/emmm.201201974

Alteration of the micro <scp>RNA</scp> network during the progression of Alzheimer's disease
Cited by: 393
Author(s): Pierre Lau, Koen Bossers, Rekin’s Janky, Evgenia Salta, Carlo Sala Frigerio, Shahar Barbash, Roy Rothman, Annerieke Sierksma, Amantha Thathiah, David Greenberg, Aikaterini S. Papadopoulou, Tilmann Achsel, Torik Ayoubi, Hermona Soreq, Joost Verhaagen, Dick F. Swaab, Stein Aerts, Bart De Strooper
Software Mentions: 4
Published: about 13 years ago

10.1016/j.bbr.2017.04.007

Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis
Cited by: 6
Author(s): Hannah Scott, Mark F. Rogers, Helen L. Scott, Colin Campbell, E. Clea Warburton, James B. Uney
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1006938

Comparative transcriptomes of adenocarcinomas and squamous cell carcinomas reveal molecular similarities that span classical anatomic boundaries
Cited by: 37
Author(s): Eric W. Lin, Tatiana A. Karakasheva, Dong Jin Lee, Ju-Seog Lee, Qi Long, Adam J. Bass, Kwok Kin Wong, Anil K. Rustgi
Software Mentions: 4
Published: about 9 years ago

10.1186/s12862-017-1087-8

Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria
Cited by: 21
Author(s): Melania Abrahamian, Meenakshi S. Kagda, Audrey M. V. Ah‐Fong, Howard S. Judelson
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pgen.1007466

Unique patterns of trimethylation of histone H3 lysine 4 are prone to changes during aging in Caenorhabditis elegans somatic cells
Cited by: 27
Author(s): Mintie Pu, Minghui Wang, Wenke Wang, Velayudhan Satheeja Santhi, Siu Sylvia Lee
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-021-02369-0

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
Cited by: 23
Author(s): Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner, Seth W. Cheetham
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-3390-y

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells
Cited by: 11
Author(s): Alicja Pacholewska, Eliane Marti, Tosso Leeb, Vidhya Jagannathan, Vinzenz Gerber
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pgen.1004924

The Genetic Architecture of the Genome-Wide Transcriptional Response to ER Stress in the Mouse
Cited by: 29
Author(s): Clement Y. Chow, Xiaozhu Wang, David D. Riccardi, Mariana F. Wolfner, Andrew G. Clark
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1005211

Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model
Cited by: 12
Author(s): Ashley P Ng, Yifang Hu, Donald Metcalf, Craig D. Hyland, Helen Ierino, Belinda Phipson, Di Wu, Tracey M. Baldwin, Maria Kauppi, Hiu Kiu, Ladina Di Rago, Douglas J. Hilton, Gordon K. Smyth, Warren S. Alexander
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1004953

Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling
Cited by: 73
Author(s): Kazunari Nozue, An V. Tat, Upendra Kumar Devisetty, Matthew C. Robinson, Maxwell R. Mumbach, Yasunori Ichihashi, Saradadevi Lekkala, Julin N. Maloof
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pgen.1004595

The Groucho Co-repressor Is Primarily Recruited to Local Target Sites in Active Chromatin to Attenuate Transcription
Cited by: 26
Author(s): Aamna K Kaul, Eugene F. Schuster, Barbara Jennings
Software Mentions: 4
Published: about 12 years ago

10.3390/genes11091066

Transcriptome Analysis Reveals a Gene Expression Pattern Associated with Fuzz Fiber Initiation Induced by High Temperature in Gossypium barbadense
Cited by: 6
Author(s): Gongmin Cheng, Longyan Zhang, Hengling Wei, Hantao Wang, Jianhua Lü, Shuxun Yu
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1009097

Diversified regulation of circadian clock gene expression following whole genome duplication
Cited by: 9
Author(s): Alexander C. West, Marianne Iversen, Even H. Jørgensen, Simen Rød Sandve, David G. Hazlerigg, Shona H. Wood
Software Mentions: 4
Published: about 6 years ago

10.31557/APJCP.2020.21.9.2593

Transcriptome Related to Avoiding Immune Destruction in Nasopharyngeal Cancer in Indonesian Patients Using Next-Generation Sequencing
Cited by: 2
Author(s): Risky Hiskia Poluan, Digdo Sudigyo, Gisti Rahmawati, Dicka Wahyu Setiasari, Salsabila Luthfi Sesotyosari, Tirta Wardana, Indwiani Astuti, Didik Setyo Heriyanto, Sagung Rai Indrasari, Cita Herawati, FNU Afiahayati, Sofia Mubarika Haryana
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2164-15-S6-S18

Comparative exomics of Phalariscultivars under salt stress
Cited by: 12
Author(s): Niina Haiminen, Manfred Klaas, Zeyu Zhou, Filippo Utro, Paul Cormican, Thomas Didion, Christian S. Jensen, Christopher E. Mason, Susanne Barth, Laxmi Parida
Software Mentions: 4
Published: about 12 years ago

10.1186/s13059-020-01997-2

Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts
Cited by: 29
Author(s): Benjamin H. Mullin, Jennifer Tickner, Kun Zhu, Jacob Kenny, Shelby Mullin, Suzanne J. Brown, Frank Dudbridge, Nathan J. Pavlos, Edward S. Mocarski, John P. Walsh, Jiake Xu, Scott G. Wilson
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.6946

Genomic analysis of Asian honeybee populations in China reveals evolutionary relationships and adaptation to abiotic stress
Cited by: 6
Author(s): Peng Shi, Jun Zhou, Huali Song, Yujuan Wu, Lan Lan, Xiangyou Tang, Zhengang Ma, Charles R. Vossbrinck, Bettina Vossbrinck, Zeyang Zhou, Jianlong Xu
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1008280

PAX5 is part of a functional transcription factor network targeted in lymphoid leukemia
Cited by: 30
Author(s): Kazuki Okuyama, Tobias Strid, Jacob Kuruvilla, Rajesh Somasundaram, Susana Cristóbal, Emma Smith, Mahadesh A. J. Prasad, Thoas Fioretos, Henrik Lilljebjörn, Shamit Soneji, Stefan Lang, Jonas Ungerbäck, Mikael Sigvardsson
Software Mentions: 4
Published: about 7 years ago

10.1038/s41438-021-00471-9

The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids
Cited by: 27
Author(s): Shanshan Dong, Min Liu, Yang Liu, Fei Chen, Ting Yang, Lu Chen, Xingtan Zhang, Xing Guo, Dongming Fang, Linzhou Li, Tian Deng, Zhen Yao, Xiaoan Lang, Yiqing Gong, Ernest Wu, Yaling Wang, Yamei Shen, Xun Gong, Huan Liu, Shouzhou Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12872-020-01838-x

Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms
Cited by: 4
Author(s): Siwei Bi, Ruiqi Liu, Linfeng He, Jingyi Li, Jun Gu
Software Mentions: 4
Published: almost 6 years ago

10.1242/dmm.042713

Leptin and fractalkine: Novel subcutaneous cytokines in burn injury
Cited by: 4
Author(s): Dominic Friston, Sini Junttila, Júlia Borges Paes Lemes, Helen Laycock, Jose Vicente Torres-Pérez, Elizabeth J. Want, Attila Gyenesei, I. Nagy
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1005755

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer
Cited by: 12
Author(s): Najeeb Halabi, Alejandra Martinez, Halema Al-Farsi, Eliane Mery-Lamarche, Laurence Puydenus, Pascal Pujol, Hanif Khalak, Cameron Mclurcan, Gwénaël Ferron, Denis Querleu, Iman K. Al-Azwani, Eman K. Al-Dous, Yasmin Ali Mohamoud, Joel A. Malek, Arash Rafii
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pgen.1008181

Hepatitis C virus leaves an epigenetic signature post cure of infection by direct-acting antivirals
Cited by: 101
Author(s): Shira Perez, Antony Kaspi, Tom Domovitz, Ateret Davidovich, Anat Lavi-Itzkovitz, Tomer Meirson, Jacinta A Holmes, Chia Yen Dai, Chung Feng Huang, Raymond T. Chung, Nimer Assy, Assam El‐Osta, Gur Yaari, Salomon M. Stemmer, Ming‐Lung Yu, Izhak Haviv, Meital Gal-Tanamy
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1002789

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection
Cited by: 125
Author(s): Yoichiro Shibata, Nathan C. Sheffield, Olivier Fédrigo, Courtney C. Babbitt, Matthew Wortham, Alok K. Tewari, Darin London, Lingyun Song, Bum Kyu Lee, Vishwanath R. Iyer, Stephen C. J. Parker, Elliott H. Margulies, Gregory A. Wray, Terrence S. Furey, Gregory E. Crawford
Software Mentions: 4
Published: over 14 years ago

10.1186/s12862-018-1288-9

Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers
Cited by: 16
Author(s): Bette Hecox-Lea, David B. Mark Welch
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-019-5910-z

Identification and differential expression analysis of anthocyanin biosynthetic genes in leaf color variants of ornamental kale
Cited by: 24
Author(s): Na Guo, Shuo Han, Ming Zong, Guixiang Wang, Shuning Zheng, Fan Liu
Software Mentions: 4
Published: over 7 years ago

10.3390/genes10100745

Differential Gene Expression in Articular Cartilage and Subchondral Bone of Neonatal and Adult Horses
Cited by: 4
Author(s): Ann M. Kemper, Jenny Drnevich, Molly E. McCue, Annette M. McCoy
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pgen.1006295

Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster
Cited by: 35
Author(s): Hangnoh Lee, Dong-Yeon Cho, Cale Whitworth, Robert C. Eisman, Melissa A. S. Phelps, John Roote, Thomas C. Kaufman, Kevin R. Cook, Steven Russell, Teresa M. Przytycka, Brian Oliver
Software Mentions: 4
Published: about 10 years ago

10.31557/APJCP.2020.21.6.1787

Risk Scoring System based on lncRNA Expression for Predicting Survival in Hepatocellular Carcinoma with Cirrhosis
Cited by: 13
Author(s): Jiaxiang Ye, Haixia Li, Jiazhang Wei, Yue Luo, Hongmei Li, Jinyan Zhang, Xi Luo
Software Mentions: 4
Published: over 6 years ago

10.1186/s12885-020-6513-4

Immunogenomic pathways associated with cytotoxic lymphocyte infiltration and survival in colorectal cancer
Cited by: 8
Author(s): Yuanyuan Shen, Yue Guan, Justin Hummel, Chi‐Ren Shyu, Jonathan B. Mitchem
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1005474

Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana
Cited by: 16
Author(s): Christian Kappel, Gerda Trost, Hjördis Czesnick, Anna Ramming, Benjamin Kolbe, Son Lang, Cláudia Bispo, Jörg Becker, Cornelia H. de Moor, Michael Lenhard
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pgen.1009349

Acetyltransferase Enok regulates transposon silencing and piRNA cluster transcription
Cited by: 3
Author(s): Shih-Ying Tsai, Fu Huang
Software Mentions: 4
Published: almost 6 years ago

10.3390/genes10060433

BarkBase: Epigenomic Annotation of Canine Genomes
Cited by: 26
Author(s): Kate Megquier, Diane P. Genereux, Jessica P. Hekman, Ross Swofford, Jason Turner-Maier, Jeremy Johnson, Jacob Alonso, Li Xue, Kathleen M. Morrill, Lynne J. Anguish, Michele Koltookian, Brittney Logan, Claire R. Sharp, Lluís Ferrer, Kerstin Lindblad‐Toh, Vicki N. Meyers-Wallen, Andrew M. Hoffman, Elinor K. Karlsson
Software Mentions: 4
Published: over 7 years ago

10.3390/genes9120579

Integrated Proteomic and Transcriptomic Analysis of Differential Expression of Chicken Lung Tissue in Response to NDV Infection during Heat Stress
Cited by: 19
Author(s): Perot Saelao, Ying Wang, Ganrea Chanthavixay, Vivian M. Yu, Rodrigo A. Gallardo, Jack C. M. Dekkers, Susan J. Lamont, T. Ross Kelly, Huaijun Zhou
Software Mentions: 4
Published: almost 8 years ago

10.3390/genes10020089

A 24 h Age Difference Causes Twice as Much Gene Expression Divergence as 100 Generations of Adaptation to a Novel Environment
Cited by: 12
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Neda Barghi, François Mallard, Kerstin Otte, Christian Schlötterer
Software Mentions: 4
Published: almost 8 years ago

10.3390/genes9090431

Comparative Transcriptomics of Root Development in Wild and Cultivated Carrots
Cited by: 16
Author(s): Gabriela Machaj, Hamed Bostan, Alicja Macko-Podgórni, Massimo Iorizzo, Dariusz Grzebelus
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-020-03888-6

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data
Cited by: 1
Author(s): Noel‐Marie Plonski, Emily Johnson, Madeline Frederick, Heather Mercer, Gail Fraizer, Richard S. Meindl, Gemma Casadesús, Helen Piontkivska
Software Mentions: 4
Published: almost 6 years ago

10.3390/genes9120574

A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women
Cited by: 25
Author(s): Kadri Rekker, Signe Altmäe, Marina Suhorutshenko, Maire Peters, Juan F. Martínez-Blanch, Francisco M. Codoñer, Felipe Vilella, Carlos Simón, Andres Salumets, Agne Velthut-Meikas
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pgen.1003997

Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia
Cited by: 110
Author(s): Zeynep Kalender Atak, Valentina Gianfelici, Gert Hulselmans, Kim De Keersmaecker, Arun George Devasia, Ellen Geerdens, Nele Mentens, Sabina Chiaretti, Kaat Durinck, Anne Uyttebroeck, Peter Vandenberghe, Iwona Włodarska, Jacqueline Cloos, Robin Foà, Franki Speleman, Jan Cools, Stein Aerts
Software Mentions: 4
Published: almost 13 years ago

10.1186/1471-2164-14-862

De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genes
Cited by: 51
Author(s): Peter J.P. Croucher, Michael S. Brewer, Christopher J. Winchell, Geoff Oxford, Rosemary G. Gillespie
Software Mentions: 4
Published: almost 14 years ago

10.18632/aging.102190

Long non-coding RNA CASC19 is associated with the progression and prognosis of advanced gastric cancer
Cited by: 23
Author(s): Wenjie Wang, Changan Guo, Rui Li, Zipeng Xu, Jianping Yu, Ye Yan, Jun Zhao, Jing Wang, Wen-An Wang, An Zhang, Hongtao Li, Chen Wang, Hongbin Liu
Software Mentions: 4
Published: about 7 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 8 years ago

10.1186/s12864-015-2115-y

Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars
Cited by: 36
Author(s): Ryan Ghan, Steven C. Van Sluyter, Uri Hochberg, Asfaw Degu, Daniel Hopper, Richard L. Tillet, Karen Schlauch, Paul A. Haynes, Aaron Fait, Grant R. Cramer
Software Mentions: 4
Published: almost 11 years ago

10.3390/genes8030090

Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics
Cited by: 17
Author(s): Joachim von Wulffen, Andreas Ulmer, Günter Jäger, Oliver Sawodny, Ronny Feuer
Software Mentions: 4
Published: over 9 years ago

10.7717/peerj.3859

How to normalize metatranscriptomic count data for differential expression analysis
Cited by: 31
Author(s): Heiner Klingenberg, Peter Meinicke
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-019-6121-3

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)
Cited by: 22
Author(s): Mingjia Tang, Liang Xu, Yan Wang, Wanwan Cheng, Xiaobo Luo, Yang Xie, Lu Fan, Liwang Liu
Software Mentions: 4
Published: about 7 years ago

10.1093/database/baw052

ToxDB: pathway-level interpretation of drug-treatment data
Cited by: 18
Author(s): Christopher Hardt, Moritz Emanuel Beber, Axel Rasche, Atanas Kamburov, Dennie G. A. J. Hebels, Jos Kleinjans, Ralf Herwig
Software Mentions: 4
Published: almost 11 years ago

10.1093/database/baw168

KTCNlncDB—a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas
Cited by: 13
Author(s): Michał Wojciech Szcześniak, Michał Kabza, Justyna A. Karolak, Małgorzata Rydzanicz, Dorota Nowak, Barbara Ginter-Matuszewska, Piotr Polakowski, Rafał Płoski, Jacek P. Szaflik, Marzena Gajęcka
Software Mentions: 4
Published: almost 10 years ago

10.1016/j.devcel.2021.07.018

Reprogrammed lipid metabolism protects inner nuclear membrane against unsaturated fat
Cited by: 28
Author(s): Anete Romanauska, Alwin Köhler
Software Mentions: 4
Published: about 5 years ago

10.3390/genes9010044

Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma
Cited by: 23
Author(s): Minjia Lu, Xingyu Xu, Baohang Xi, Qi Dai, Chenli Li, Li Su, Xiaobin Zhou, Min Tang, Yanwen Yao, Jialiang Yang
Software Mentions: 4
Published: almost 9 years ago

10.1534/g3.120.401166

DAF-16 and SMK-1 Contribute to Innate Immunity During Adulthood inCaenorhabditis elegans
Cited by: 14
Author(s): Daniel R. McHugh, Elena Koumis, Paul Jacob, Jennifer Goldfarb, Michelle Schlaubitz-Garcia, Safae Bennani, Paul Regan, Prem Patel, Matthew J. Youngman
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.119.400998

A Collection of Pre-mRNA Splicing Mutants in Arabidopsis thaliana
Cited by: 20
Author(s): Tohru Kanno, Peter Venhuizen, Ming‐Tsung Wu, Phebe Chiou, Chia-Liang Chang, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.119.400413

The Genome Sequence of the Eastern Woodchuck (Marmota monax) – A Preclinical Animal Model for Chronic Hepatitis B
Cited by: 13
Author(s): Tyler Alioto, Fernando Cruz, Jèssica Gómez-Garrido, Miriam Triyatni, Marta Gut, Leonor Frías, Anna Esteve‐Codina, Stephan Menne, Anna Kiialainen, Nadine Kumpesa, Fabian Birzele, Roland Schmucki, Ivo Gut, Olivia Spleiss
Software Mentions: 4
Published: almost 7 years ago

10.1534/g3.119.400757

Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize
Cited by: 9
Author(s): Pengfei Qiao, Lin Meng, Miguel Vasquez, Susanne Matschi, James Chamness, Matheus Baseggio, Laurie G. Smith, Mert R. Sabuncu, Michael A. Gore, Michael J. Scanlon
Software Mentions: 4
Published: almost 7 years ago

10.1016/j.dib.2018.11.034

Differential gene expression analysis and SNP/InDel marker discovery in resistant wild Asparagus kiusianus and susceptible A. officinalis in response to Phomopsis asparagi infection
Cited by: 4
Author(s): Mostafa Abdelrahman, Mai Mitoma, Takao Ikeuchi, Motoyuki Mori, Kyoko Murakami, Yukio Ozaki, Masaru Matsumoto, Atsuko Uragami, Akira Kanno
Software Mentions: 4
Published: almost 8 years ago

10.3390/genes11050472

Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
Cited by: 7
Author(s): Mushtaque Ali, Hongyan Cheng, Mahtab Soomro, Shuyan Li, Muhammad Tufail, Mian Faisal Nazir, Feng Xu, Youping Zhang, Dongyun Zuo, Limin Lv, Qiaolian Wang, Guoli Song
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pntd.0007680

Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes
Cited by: 24
Author(s): Luís Miguel González, Karel Estrada, Ricardo Grande, Verónica Jiménez-Jacinto, Leticia Vega‐Alvarado, Elena Sevilla, Jorge de la Barrera, Isabel Cuesta, Ángel Zaballos, José M. Bautista, Cheryl A. Lobo, Alejandro Sánchez-Flores, Estrella Montero
Software Mentions: 4
Published: about 7 years ago

10.1186/s12885-021-07911-8

Construction of the optimization prognostic model based on differentially expressed immune genes of lung adenocarcinoma
Cited by: 6
Author(s): Yuanliang Zhai, Bin Zhao, Yuzhen Wang, Lina Li, Jingjin Li, Li Xu, Linhan Chang, Qian Chen, Zhijun Liao
Software Mentions: 4
Published: over 5 years ago

10.1093/dnares/dsz002

A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants
Cited by: 32
Author(s): Asuka Arimoto, Koki Nishitsuji, Yoshimi Higa, Nana Arakaki, Kanako Hisata, Chuya Shinzato, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 4
Published: over 7 years ago

10.1016/j.ebiom.2019.11.046

Prioritization of novel ADPKD drug candidates from disease-stage specific gene expression profiles
Cited by: 15
Author(s): Tareq B. Malas, Wouter N. Leonhard, Hester Bange, Zoraide Granchi, Kristina Hettne, Gerard J. P. van Westen, Leo Price, Peter A C ‘t Hoen, Dorien J.M. Peters
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-016-2776-1

Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates
Cited by: 28
Author(s): Nathalia Flórez-Zapata, M. Humberto Reyes-Valdés, Octavio Martínez
Software Mentions: 4
Published: over 10 years ago

10.1534/g3.118.200677

Genotype-by-Environment-by-Environment Interactions in the Saccharomyces cerevisiae Transcriptomic Response to Alcohols and Anaerobiosis
Cited by: 5
Author(s): Maria Sardi, Molly Krause, Justin Heilberger, Audrey P. Gasch
Software Mentions: 4
Published: almost 8 years ago

10.1534/g3.118.200516

Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
Cited by: 6
Author(s): Cathy Boscarino, Thomas Nalpathamkalam, Giovanna Pellecchia, Weili Li, Bhooma Thiruvahindrapuram, Daniele Merico
Software Mentions: 4
Published: almost 8 years ago

10.1534/g3.118.200810

Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression
Cited by: 13
Author(s): Stephen J. Bush, Mary E. B. McCulloch, Charity Muriuki, Mazdak Salavati, Gemma M. Davis, Iseabail L. Farquhar, Zofia M. Lisowski, Alan Archibald, David Hume, Emily L. Clark
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-018-4505-4

Transcriptome profiles in peripheral white blood cells at the time of artificial insemination discriminate beef heifers with different fertility potential
Cited by: 28
Author(s): Sarah Dickinson, Brock A. Griffin, Michelle F Elmore, L. A. Kriese-Anderson, J. Bradford Elmore, Paul W. Dyce, Soren P. Rodning, Fernando H. Biase
Software Mentions: 4
Published: over 8 years ago

10.1016/j.heliyon.2021.e06000

Unsupervised subtyping and methylation landscape of pancreatic ductal adenocarcinoma
Cited by: 9
Author(s): Shikha Roy, Amar Singh, Dinesh Gupta
Software Mentions: 4
Published: almost 6 years ago

10.1534/g3.118.200880

Activation of the Bile Acid Pathway and No Observed Antimicrobial Peptide Sequences in the Skin of a Poison Frog
Cited by: 1
Author(s): Megan L. Civitello, Robert D. Denton, Michael Zasloff, John H. Malone
Software Mentions: 4
Published: almost 8 years ago

10.7717/peerj.11995

The modulatory properties of Astragalus membranaceus treatment on endometrial cancer: an integrated pharmacological method
Cited by: 4
Author(s): Qianqian Zhang, Xianghua Huang
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.9307

Succession of bacterial communities on carrion is independent of vertebrate scavengers
Cited by: 8
Author(s): Cody R. Dangerfield, Ethan Frehner, Evan R. Buechley, Çağan H. Şekercioğlu, William J. Brazelton
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.103083

Nudix hydrolase 1 is a prognostic biomarker in hepatocellular carcinoma
Cited by: 6
Author(s): Qifeng Ou, Ning Ma, Zhenzhen Yu, Rongchang Wang, Yucheng Hou, Ziming Wang, Fan Chen, Wen Li, Jiong Bi, Jiachi Ma, Longjuan Zhang, Shan Qiao, Xiaohui Huang
Software Mentions: 4
Published: over 6 years ago

10.1186/s12863-018-0608-9

RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat & rat
Cited by: 21
Author(s): Xiaoxiao Gao, Jing Ye, Chen Yang, Lei Luo, Ya Liu, Jianping Ding, Yunhai Zhang, Yinghui Ling, Weiping Huang, Xiaorong Zhang, Kaifa Zhang, Xiumei Li, Jie Zhou, Fugui Fang, Zubing Cao
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2019.01605

De Novo Transcriptome Analysis of Durum Wheat Flag Leaves Provides New Insights Into the Regulatory Response to Elevated CO2 and High Temperature
Cited by: 26
Author(s): Rubén Vicente, Anthony Bolger, Rafael Martínez‐Carrasco, Pilar Pérez Pérez, Elena Gutiérrez, Björn Usadel, Rosa Morcuende
Software Mentions: 4
Published: almost 7 years ago

10.1038/s42003-019-0391-9

Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation
Cited by: 25
Author(s): Alborz Mazloomian, Shinsuke Araki, Momoko Ohori, Amal M. El-Naggar, Damian Yap, Ali Bashashati, Shigetomi Nakao, Poul H. Sorensen, Atsushi Nakanishi, Sohrab P. Shah, Samuel Aparicio
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.11020

Differential gene expression in a tripartite interaction:Drosophila,Spiroplasmaand parasitic wasps
Cited by: 4
Author(s): Victor Manuel Higareda Alvear, Mariana Mateos, Diego Cortez, Cécilia Tamborindeguy, Esperanza Martínez‐Romero
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-021-02203-0

The chaperonin CCT8 controls proteostasis essential for T cell maturation, selection, and function
Cited by: 5
Author(s): Bergithe E. Oftedal, Stefano Maio, Adam E. Handel, White Mpj., Duncan Howie, Simon Davis, Nicolas Prevot, Ioanna A. Rota, Mary E. Deadman, Benedikt M. Kessler, Román Fischer, Nikolaus S. Trede, Erdinç Sezgin, Rick M. Maizels, G A Holländer
Software Mentions: 4
Published: over 5 years ago

10.1007/s00404-019-05336-0

Changes in intestinal microflora in digestive tract diseases during pregnancy
Cited by: 20
Author(s): Min Jin, Dong Li, Rui Ji, Wen Li, Xiaofei Xu, Yanqing Li
Software Mentions: 4
Published: almost 7 years ago

10.3389/fpls.2021.727302

Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses
Cited by: 4
Author(s): Minsu Park, Wookap Choi, Sang Yoon Shin, Hongman Moon, Dowhan Lee, Yun Shil Gho, Ki Hong Jung, Jong Seong Jeon, Chanseok Shin
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0192947

Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men
Cited by: 26
Author(s): Kathryn Burton, Grégory Pimentel, Nadine Zangger, Nathalie Vionnet, Jocelyne Drai, P. G. McTernan, François P. Pralong, Mauro Delorenzi, Guy Vergères
Software Mentions: 4
Published: over 8 years ago

10.1186/s13072-018-0246-5

Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus
Cited by: 54
Author(s): Adam J. Bewick, Zachary Sanchez, Elizabeth C. McKinney, Allen J. Moore, Patricia J. Moore, Robert J. Schmitz
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-017-3675-9

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress
Cited by: 23
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0204038

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period
Cited by: 3
Author(s): Ramona Krauss, Belinda Phipson, Alicia Oshlack, Nikita Prasad-Gupta, Michael Cheung, Joseph J. Smolich, Salvatore Pepe
Software Mentions: 4
Published: about 8 years ago

10.1002/2211-5463.12983

Identification of modules and novel prognostic biomarkers in liver cancer through integrated bioinformatics analysis
Cited by: 5
Author(s): Bo Shen, Kun Li, Yuting Zhang
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0168573

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil
Cited by: 33
Author(s): Seung‐Yoon Oh, Jonathan J. Fong, Myung Soo Park, Young Woon Lim
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41438-020-00432-8

Transcriptional regulation of bark freezing tolerance in apple (Malus domestica Borkh.)
Cited by: 9
Author(s): Yin Liang, Shanshan Wang, Chang Zhao, Xinwei Ma, Yiyong Zhao, Jing Shao, Yuebo Li, Honglian Li, Song Hong‐wei, Hong Mā, Hao Li, Bingbing Zhang, Liangsheng Zhang
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12863-019-0790-4

Transcriptome, physiological and biochemical analysis of Triarrhena sacchariflora in response to flooding stress
Cited by: 17
Author(s): Jia Wang, Hao Sun, Jiajin Sheng, Surong Jin, Fangjian Zhou, Zhongli Hu, Youxiang Diao
Software Mentions: 4
Published: almost 7 years ago

10.1093/jxb/erw006

Evidence for maternal control of seed size in maize from phenotypic and transcriptional analysis
Cited by: 32
Author(s): Xia Zhang, Candice N. Hirsch, Rajandeep S. Sekhon, Natalia de León, Shawn M. Kaeppler
Software Mentions: 4
Published: almost 11 years ago

10.7717/peerj.4600

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data
Cited by: 146
Author(s): Li Chen, James Reeve, Lujun Zhang, Shengbing Huang, Xuefeng Wang, Jun Chen
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2016.01431

Quantitative Resistance to Verticillium Wilt in Medicago truncatula Involves Eradication of the Fungus from Roots and Is Associated with Transcriptional Responses Related to Innate Immunity
Cited by: 13
Author(s): Maoulida Toueni, Cécile Ben, Aurélie Le Ru, Laurent Gentzbittel, Martina Rickauer
Software Mentions: 4
Published: about 10 years ago

10.1186/1471-2164-15-676

De novo transcriptome sequencing and digital gene expression analysis predict biosynthetic pathway of rhynchophylline and isorhynchophylline from Uncaria rhynchophylla, a non-model plant with potent anti-alzheimer’s properties
Cited by: 58
Author(s): Qianqian Guo, Xiaojun Ma, Shugen Wei, Deyou Qiu, Iain W. Wilson, Ping Wu, Qi Tang, Lijun Liu, Shoukun Dong, Zimin Wei
Software Mentions: 4
Published: about 12 years ago

10.1186/1471-2164-15-155

Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses
Cited by: 36
Author(s): Xin Luo, Minho Chae, Raga Krishnakumar, Charles G. Danko, W. Lee Kraus
Software Mentions: 4
Published: over 12 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568