pypi: TopHat | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2015.00065

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data
Cited by: 48
Author(s): Sylvie Schulze, Sebastian Henkel, Dominik Driesch, Reinhard Guthke, JÃ¶rg Linde
Software Mentions: 4
Published: almost 10 years ago

10.1186/gb-2012-13-10-r88

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
Cited by: 72
Author(s): Alok K. Tewari, Galip Gürkan Yardımcı, Yoichiro Shibata, Nathan C. Sheffield, Lingyun Song, Barry S. Taylor, Stoyan Georgiev, Gerhard A. Coetzee, Uwe Ohler, Terrence S. Furey, Gregory E. Crawford, Phillip G. Febbo
Software Mentions: 4
Published: almost 13 years ago

10.7554/eLife.41641

IFNγ induces epigenetic programming of human T-bethi B cells and promotes TLR7/8 and IL-21 induced differentiation
Cited by: 104
Author(s): Esther Zumaquero, Sara L Stone, Christopher D. Scharer, Scott A. Jenks, Anoma Nellore, Betty Mousseau, Antonio Rosal-Vela, Davide Botta, John E. Bradley, Wojciech Wojciechowski, Travis Ptacek, Maria I. Danila, Jeffrey C. Edberg, S. Louis Bridges, Robert P. Kimberly, W. Winn Chatham, Trenton R. Schoeb, Alexander F. Rosenberg, Jeremy M. Boss, Igñacio Sanz, Frances E. Lund
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.3976

Brain gene expression analyses in virgin and mated queens of fire ants reveal mating-independent and socially regulated changes
Cited by: 14
Author(s): Travis L. Calkins, Mei Er Chen, Arinder K. Arora, Chloë Hawkings, Cécilia Tamborindeguy, Patricia V. Pietrantonio
Software Mentions: 4
Published: over 6 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

10.1002/ece3.5965

Draft genome of the famous ornamental plant Paeonia suffruticosa
Cited by: 31
Author(s): Shuzuo Lv, Shu Cheng, Zhanying Wang, Shiming Li, Xin Jin, Lei Lan, Bing Yang, Kun Yu, Xiliang Ni, Ning Li, Xiaogai Hou, Gang Huang, Jie Wang, Yang Dong, Erqiang Wang, Jun Huang, Gengyun Zhang, Zhang Can-jun
Software Mentions: 4
Published: over 4 years ago

10.1186/s12915-020-00945-7

Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles
Cited by: 8
Author(s): Hao‐Sen Li, Xiaowen Tang, Yu‐Hao Huang, Zhennan Xu, Meilan Chen, Xue‐Yong Du, Bo-Yuan Qiu, Pei‐Tao Chen, Wei Zhang, Adam Ślipiński, Hermes E. Escalona, Robert M. Waterhouse, Andreas Zwick
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12915-018-0569-5

Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance
Cited by: 16
Author(s): Jessica M Stringer, Samuel C. Forster, Zhibo Qu, Lexie Prokopuk, Moira K O'Bryan, David K. Gardner, Stefan J. White, David L. Adelson, Patrick Western
Software Mentions: 4
Published: about 6 years ago

10.1038/s42003-021-02089-y

Regulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases
Cited by: 10
Author(s): Kei Fukuda, Chikako Shimura, Hisashi Miura, Akie Tanigawa, Takehiro Suzuki, Naoshi Dohmae, Ichiro Hiratani, Yoichi Shinkai
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-019-5428-4

New insights in the control of antioxidants accumulation in tomato by transcriptomic analyses of genotypes exhibiting contrasting levels of fruit metabolites
Cited by: 20
Author(s): Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone, Maria Manuela Rigano
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-14-283

Unscrambling butterfly oogenesis
Cited by: 38
Author(s): Jean-Michel Carter, Susan C. Baker, Ryan C. Pink, David R. F. Carter, Aiden Collins, Jeremie Tomlin, Melanie Gibbs, Casper J. Breuker
Software Mentions: 4
Published: over 11 years ago

10.1093/aobpla/ply013

Patterns of alternative splicing vary between species during heat stress
Cited by: 25
Author(s): Sumetha Kannan, Gillian Halter, Tanya Renner, Elizabeth R. Waters
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.46981

Transcriptional landscape of myogenesis from human pluripotent stem cells reveals a key role of TWIST1 in maintenance of skeletal muscle progenitors
Cited by: 27
Author(s): In Young Choi, Hotae Lim, Hyeon Jin Cho, Yohan Oh, Bin Kuan Chou, Hao Bai, Linzhao Cheng, Yong Jun Kim, Sang‐Hwan Hyun, Hyesoo Kim, Joo Heon Shin, Gabsang Lee
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-015-1308-8

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
Cited by: 109
Author(s): Shanrong Zhao, Baohong Zhang
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2164-15-221

From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism
Cited by: 119
Author(s): Inès Zouari, Alessandra Salvioli, Matteo Chialva, Mara Novero, Laura Miozzi, Gian Carlo Tenore, Paolo Bagnaresi, Paola Bonfante
Software Mentions: 4
Published: over 10 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/s13148-019-0690-5

ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells
Cited by: 34
Author(s): Madhobi Sen, Xin Wang, Feda H. Hamdan, Jacobe Rapp, Jessica Eggert, Robyn Laura Kosinsky, Florian Wegwitz, Ana P. Kutschat, Fereshteh Younesi, Jochen Gaedcke, Marian Grade, Elisabeth Heßmann, Argyris Papantonis, Philipp Ströbel, Steven A. Johnsen
Software Mentions: 4
Published: over 5 years ago

10.1016/j.cell.2017.05.029

SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs
Cited by: 162
Author(s): Ryu Suke Nozawa, Lora Boteva, Dinesh C. Soares, Catherine Naughton, Alison R. Dun, Adam Buckle, Bernard Ramsahoye, Peter Christopher Bruton, Rebecca S. Saleeb, María Arnedo, Bill Hill, Rory R. Duncan, Sutherland K. Maciver, Nick Gilbert
Software Mentions: 4
Published: over 7 years ago

10.1016/j.celrep.2018.11.032

Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming
Cited by: 27
Author(s): Andreia Gomes, Ilia Kurochkin, Betty Chang, Michael G. Daniel, Kenneth Law, Namita Satija, Alexander Lachmann, Zichen Wang, Lino Ferreira, Avi Ma’ayan, Benjamin Chen, Dmitri Papatsenko, Ihor R. Lemischka, Kateri Moore, Carlos Filipe Pereira
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.celrep.2019.11.093

Dysregulation of RNA Splicing in Tauopathies
Cited by: 49
Author(s): Daniel J. Apicco, Cheng Zhang, Brandon F. Maziuk, Lulu Jiang, Heather Ballance, Samantha Boudeau, Choong Yong Ung, Hu Li, Benjamin Wolozin
Software Mentions: 4
Published: almost 5 years ago

10.1016/j.stem.2019.09.008

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
Cited by: 71
Author(s): Stephanie Z. Xie, Laura García‐Prat, Véronique Voisin, Raffaele Ferrari, Olga I. Gan, Elvin Wagenblast, Kerstin B. Kaufmann, Andy G.X. Zeng, Shin‐ichiro Takayanagi, Ishita Patel, Esther K. Lee, Joseph Jargstorf, Gareth D. Holmes, Guy Romm, Kristele Pan, Michelle Shoong, Aditi Vedi, Chiara Luberto, Mark D. Minden, Gary D. Bader, Elisa Laurenti, John E. Dick
Software Mentions: 4
Published: about 5 years ago

10.3390/cells9071745

Ribosomal Protein uL11 as a Regulator of Metabolic Circuits Related to Aging and Cell Cycle
Cited by: 7
Author(s): Mateusz Mołoń, Eliza Molestak, Monika Kula-Maximenko, Przemysław Grela, Marek Tchórzewski
Software Mentions: 4
Published: over 4 years ago

10.1038/s41422-018-0066-y

Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta
Cited by: 242
Author(s): Yawei Liu, Xiaoying Fan, Rui Wang, Xiaoyin Lu, Yan-Li Dang, Huiying Wang, Haiyan Lin, Cheng Zhu, Hao Ge, James C. Cross, Hongmei Wang
Software Mentions: 4
Published: over 6 years ago

10.1016/j.stem.2017.03.003

H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos
Cited by: 85
Author(s): Eva Hörmanseder, Angela Simeone, George E. Allen, Charles R. Bradshaw, Magdalena Figlmüller, J. B. Gurdon, Jérôme Jullien
Software Mentions: 4
Published: over 7 years ago

10.3390/antiox9050402

Long Non-Coding RNA and mRNA Profiling in Early-Stage Bovine Embryos Treated with Glutathione
Cited by: 1
Author(s): Qihao Guo, Linlin Cui, Weijun Sun, Li Feng, Hao Huang, Xueming Zhao, Huabin Zhu, Weihua Du
Software Mentions: 4
Published: over 4 years ago

10.1016/j.celrep.2018.07.026

Fine-Tuning Mybl2 Is Required for Proper Mesenchymal-to-Epithelial Transition during Somatic Reprogramming
Cited by: 16
Author(s): Carl Ward, Giacomo Volpe, Pierre Cauchy, Anetta Ptasińska, Ruba Almaghrabi, Daniel Blakemore, Monica Nafria, Doris Kestner, Jon Frampton, George J. Murphy, Yosef Buganim, Keisuke Kaji, Paloma García
Software Mentions: 4
Published: over 6 years ago

10.1038/s41422-020-0378-6

Comparative analysis of cell lineage differentiation during hepatogenesis in humans and mice at the single-cell transcriptome level
Cited by: 49
Author(s): Xin Wang, Li Yang, Yanchun Wang, Ziran Xu, Yang Feng, Jing Zhang, Yi Wang, Cheng‐Ran Xu
Software Mentions: 4
Published: over 4 years ago

10.1016/j.celrep.2020.107748

Chromatin Priming Renders T Cell Tolerance-Associated Genes Sensitive to Activation below the Signaling Threshold for Immune Response Genes
Cited by: 20
Author(s): Sarah L Bevington, Sky T. H. Ng, Graham J. Britton, Peter Keane, David C. Wraith, Peter N. Cockerill
Software Mentions: 4
Published: over 4 years ago

10.3390/cells9122593

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors
Cited by: 3
Author(s): Silvin Lito, Adama Sidibé, Sten Ilmjärv, Patricie Burda, Matthias R. Baumgartner, Bernhard Wehrle-Haller, Karl‐Heinz Krause, Antoine Marteyn
Software Mentions: 4
Published: almost 4 years ago

10.1111/cmi.12397

The co‐transcriptome of uropathogenic<scp>E</scp>scherichia coli‐infected mouse macrophages reveals new insights into host–pathogen interactions
Cited by: 62
Author(s): Charalampos Harris Mavromatis, Nilesh J. Bokil, Makrina Totsika, Asha Kakkanat, Kolja Schaale, Carlo Vittorio Cannistraci, Tae Woo Ryu, Scott A. Beatson, Glen C. Ulett, Mark A. Schembri, Matthew J. Sweet, Timothy Ravasi
Software Mentions: 4
Published: almost 10 years ago

10.1016/j.cmet.2020.09.001

Bone Marrow Mesenchymal Stem Cells Support Acute Myeloid Leukemia Bioenergetics and Enhance Antioxidant Defense and Escape from Chemotherapy
Cited by: 107
Author(s): Dorian Forte, María García-Fernández, Abel Sánchez-Aguilera, Vaia Stavropoulou, Claire Fielding, Daniel Martín-Pérez, Juan Antonio López, Ana S. H. Costa, Laura Tronci, Efterpi Nikitopoulou, M. Barber, Paolo Gallipoli, Ludovica Marando, Carlos L.F. de Castillejo, Alexandar Tzankov, Sabine Dietmann, Michèle Cavo, Lucia Catani, Antonio Curti, Jesús Vázquez, Christian Frezza, Brian J. P. Huntly, Juerg Schwaller, Simón Méndez-Ferrer
Software Mentions: 4
Published: about 4 years ago

10.3390/jpm9020018

Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research
Cited by: 12
Author(s): Isaac Raplee, Alexei V. Evsikov, Caralina Marín de Evsikova
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-15-636

In depth annotation of the Anopheles gambiae mosquito midgut transcriptome
Cited by: 30
Author(s): Alejandro Padrón, Alvaro Molina-Cruz, Mariam Quiñones, José M. C. Ribeiro, Urvashi N. Ramphul, Janneth Rodrigues, Kui Shen, Ashley Haile, José L. Ramirez, Carolina Barillas‐Mury
Software Mentions: 4
Published: over 10 years ago

10.1038/celldisc.2015.45

Mapping gene regulatory circuitry of Pax6 during neurogenesis
Cited by: 56
Author(s): Sudhir Thakurela, Neha Tiwari, Sandra Schick, Angela Garding, Robert Ivánek, Benedikt Berninger, Vijay Tiwari
Software Mentions: 4
Published: almost 9 years ago

10.1101/mcs.a002444

Resistance-promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient
Cited by: 15
Author(s): Christopher A. Miller, Sonika Dahiya, Tiandao Li, Robert S. Fulton, Matthew D. Smyth, Gavin P. Dunn, Joshua B. Rubin, Elaine R. Mardis
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms22020574

The Resistance of Narrow-Leafed Lupin to Diaporthe toxica Is Based on the Rapid Activation of Defense Response Genes
Cited by: 7
Author(s): Michał Książkiewicz, Sandra Rychel-Bielska, Piotr Plewiński, Maria Nuc, Witold Irzykowski, M. Jędryczka, Paweł Krajewski
Software Mentions: 4
Published: almost 4 years ago

10.1111/rssc.12213

A Bayesian Model Selection Approach for Identifying Differentially Expressed Transcripts from RNA Sequencing Data
Cited by: 5
Author(s): Panagiotis Papastamoulis, Magnus Rattray
Software Mentions: 4
Published: almost 8 years ago

10.3390/ijms19113687

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities
Cited by: 5
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21061910

NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells
Cited by: 8
Author(s): Edina Erdős, Bálint László Bálint
Software Mentions: 4
Published: over 4 years ago

10.3390/ijms19010031

Transcriptome Analysis of Tomato Leaf Spot Pathogen Fusarium proliferatum: De novo Assembly, Expression Profiling, and Identification of Candidate Effectors
Cited by: 15
Author(s): Meiling Gao, Siyu Yao, Yang Liu, Haining Yu, Pao Xu, Wenhui Sun, Zhongji Pu, Hongman Hou, Yongming Bao
Software Mentions: 4
Published: almost 7 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: about 9 years ago

10.3390/ijms19041140

Aging and Intermittent Fasting Impact on Transcriptional Regulation and Physiological Responses of Adult Drosophila Neuronal and Muscle Tissues
Cited by: 14
Author(s): Sharon Zhang, Eric P. Ratliff, Brandon Molina, Nadja El-Mecharrafie, Jessica Mastroianni, Roxanne W. Kotzebue, Madhulika Achal, Ruth E. Mauntz, Arysa Gonzalez, Ayeh Barekat, William A. Bray, Andrew M Macias, Daniel J. Daugherty, Greg L. Harris, Robert A. Edwards, Kim D. Finley
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21093129

Bisphenol A Exposure in utero Disrupts Hypothalamic Gene Expression Particularly Genes Suspected in Autism Spectrum Disorders and Neuron and Hormone Signaling
Cited by: 18
Author(s): Anne De Piante Henriksen, Alejandro Andrade, Erin P. Harris, Emilie F. Rissman, Jennifer T. Wolstenholme
Software Mentions: 4
Published: over 4 years ago

10.1155/2018/3028290

Stress-Adaptive Responses Associated with High-Level Carbapenem Resistance in KPC-ProducingKlebsiella pneumoniae
Cited by: 4
Author(s): Sheila Adams‐Sapper, Adam Gayoso, Lee W. Riley
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.00170

Dual functions of TAF7L in adipocyte differentiation
Cited by: 39
Author(s): Haiying Zhou, Tommy Kaplan, Yan Li, Ivan Grubisic, Zhengjian Zhang, P. Jeremy Wang, Michael B. Eisen, Robert Tjian
Software Mentions: 4
Published: almost 12 years ago

10.1186/1752-0509-7-S5-S1

Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer
Cited by: 68
Author(s): Akshata R. Udyavar, Megan D. Hoeksema, Jonathan E. Clark, Yong Zou, Zuojian Tang, Zhiguo Li, Ming Li, Heidi Chen, Alexander Statnikov, Yu Shyr, Daniel C. Liebler, John K. Field, Rosana Eisenberg, Lourdes Estrada, Pierre P. Massion, Vito Quaranta
Software Mentions: 4
Published: almost 11 years ago

10.1016/j.cell.2018.07.001

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing
Cited by: 110
Author(s): Jan Attig, Antonella Federico, Clare Gooding, Anob M. Chakrabarti, Aarti Singh, Nejc Haberman, Julian A. Zagalak, Warren Emmett, Christopher W. Smith, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 4
Published: over 6 years ago

10.1093/molbev/msx190

Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome
Cited by: 37
Author(s): Ann Kathrin Huylmans, Ariana Macon, Beatriz Vicoso
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.46566

The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop
Cited by: 29
Author(s): Merve Deniz Abdusselamoglu, Elif Eroğlu, Thomas R Burkard, Juergen A. Knoblich
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.22039

Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq
Cited by: 48
Author(s): Pingzhu Zhou, Fei Gu, Lina Zhang, Brynn N. Akerberg, Qing Ma, Kai Li, Aibin He, Zhiqiang Lin, Sean Stevens, Bin Zhou, William T. Pu
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.02626

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways
Cited by: 80
Author(s): Benoît Ballester, Alejandra Medina-Rivera, Dominic Schmidt, Mar Gonzàlez-Porta, Matthew Carlucci, Marc E. Rothenberg, Kyle Chessman, Aline Faure, Alister P. W. Funnell, Ângela Gonçalves, Claudia Kutter, Margus Lukk, Suraj Menon, William McLaren, Klara Stefflova, Stephen Watt, Matthew T. Weirauch, Merlin Crossley, John C. Marioni, Duncan T. Odom, Paul Flicek, Michael D. Wilson
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0187625

RNA-Seq analysis reveals insight into enhanced rice Xa7-mediated bacterial blight resistance at high temperature
Cited by: 46
Author(s): Stephen P. Cohen, Hongxia Liu, Cristiana T. Argueso, Andy Pereira, Casiana Vera Cruz, Valérie Verdier, Jan E. Leach
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.49501

Single cell analysis reveals immune cell–adipocyte crosstalk regulating the transcription of thermogenic adipocytes
Cited by: 103
Author(s): Prashant Rajbhandari, Douglas Arneson, Sydney K Hart, In Sook Ahn, Graciel Diamante, Leonardo D. Santos, Nima Zaghari, An‐Chieh Feng, Brandon J. Thomas, Laurent Vergnes, Stephen D. Lee, Abha K. Rajbhandari, Karen Reue, Stephen T. Smale, Xia Yang, Peter Tontonoz
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-016-2482-z

Overlapping cell population expression profiling and regulatory inference in C. elegans
Cited by: 6
Author(s): Joshua T. Burdick, Travis Walton, Elicia Preston, Amanda L. Zacharias, Arjun Raj, John I. Murray
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-015-0460-0

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data
Cited by: 20
Author(s): Wuming Gong, Naoko Koyano-Nakagawa, Tongbin Li, Daniel J. Garry
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.08384

Signal transducer and activator of transcription 5 (STAT5) paralog dose governs T cell effector and regulatory functions
Cited by: 69
Author(s): Alejandro V. Villarino, Gertraud W. Robinson, Michael Bonelli, Bárbara Dema, Behdad Afzali, Han-Yu Shih, Hongwei Sun, Stephen R. Brooks, Lothar Hennighausen, Yuka Kanno, John J. O’Shea
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.08851

Maternal LSD1/KDM1A is an essential regulator of chromatin and transcription landscapes during zygotic genome activation
Cited by: 99
Author(s): Katia Ancelin, Laurène Syx, Maud Borensztein, Noémie Ranisavljevic, Ivaylo Vassilev, Luis Briseño-Roa, Tao Liu, Eric Metzger, Nicolas Servant, Emmanuel Barillot, Chongjian Chen, Roland Schüle, Edith Heard
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.39658

Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome
Cited by: 33
Author(s): Srivarsha Rajshekar, Jun Yao, Paige K. Arnold, Sara G. Payne, Yinwen Zhang, Teresa V. Bowman, Robert J. Schmitz, John Edwards, Mary Goll
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-016-2896-7

Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data
Cited by: 8
Author(s): Yongsheng Bai, Jeff Kinne, Brandon Donham, Feng Jiang, Lizhong Ding, Justin Hassler, Randal J. Kaufman
Software Mentions: 4
Published: over 8 years ago

10.1186/s12870-015-0632-0

Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet
Cited by: 10
Author(s): Fei Yi, Jian Chen, Jingjuan Yu
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0144409

The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells
Cited by: 14
Author(s): Thomas Whisenant, Eigen Peralta, Lauren Aarreberg, Nana Gao, Steven R. Head, Phillip Ordoukhanian, James R. Williamson, Daniel R. Salomon
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2164-15-218

Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses
Cited by: 60
Author(s): José F. Sánchez-Sevilla, Eduardo Cruz-Rus, Victoriano Valpuesta, Miguel A. Botella, Iraida Amaya
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.41770

The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders
Cited by: 51
Author(s): Cheen Euong Ang, Qing Ma, Orly L. Wapinski, Sheng Hua Fan, Ryan A. Flynn, Qian Yi Lee, Bradley P. Coe, Masahiro Onoguchi, Victor Hipolito Olmos, T. Brian, Lynn Dukes-Rimsky, Jin Xu, Koji Tanabe, Liang Jiang Wang, Ulrich Elling, Josef Penninger, Yang Zhao, Kun Qu, Evan E. Eichler, Anand Srivastava, Marius Wernig, Howard Y. Chang
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12870-020-2268-y

Modulation of volatile compound metabolome and transcriptome in grape berries exposed to sunlight under dry-hot climate
Cited by: 24
Author(s): Lei He, Xiaoqing Xu, Yu Wang, Wei-Kai Chen, Ruonan Sun, Guodong Cheng, Bin Liu, Changyong Wu, Chang‐Qing Duan, Jun Wang, Qiu-Hong Pan
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.21697

Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ
Cited by: 43
Author(s): Lorenzo Rinaldi, Alexandra Avgustinova, Mercé Martı́n, Debayan Datta, Guiomar Solanas, Neus Prats, Salvador Aznar Benitah
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0145176

Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy
Cited by: 26
Author(s): Manish Kohli, Liguo Wang, Fang Xie, Hugues Sicotte, Ping Yin, Scott M. Dehm, Steven N. Hart, Peter T. Vedell, Poulami Barman, Rui Qin, Douglas W. Mahoney, Rachel E. Carlson, Jeanette E. Eckel‐Passow, Thomas D. Atwell, Patrick W. Eiken, Brendan P. McMenomy, Eric D. Wieben, Gautam Jha, Rafael E. Jimenez, Richard M. Weinshilboum, Liewei M Wang
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0210672

Identification of new regulators through transcriptome analysis that regulate anthocyanin biosynthesis in apple leaves at low temperatures
Cited by: 28
Author(s): Tingting Song, Keting Li, Ting Wu, Yi Wang, Xinzhong Zhang, Xuefeng Xu, Yuncong Yao, Zhenhai Han
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13072-018-0186-0

Transient reduction of DNA methylation at the onset of meiosis in male mice
Cited by: 36
Author(s): Valeriya Gaysinskaya, Brendan Miller, Chiara De Luca, Godfried W. van der Heijden, Kasper D. Hansen, Alex Bortvin
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0244038

Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation
Cited by: 9
Author(s): Manuel Peter, Dominik F. Aschauer, Renata Rose, Anne Sinning, Florian Grössl, Dominic Kargl, Klaus Kraitsy, Thomas R Burkard, Heiko J. Luhmann, Wulf Haubensak, Simon Rumpel
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.27786

Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response
Cited by: 29
Author(s): Xu Zhang, Xiaoli Chen, Qiuying Liu, Shaojie Zhang, Wenqian Hu
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.36998

Downregulation of ribosome biogenesis during early forebrain development
Cited by: 63
Author(s): Kevin F. Chau, Morgan L. Shannon, Ryann M. Fame, Erin Fonseca, Hillary Mullan, Matthew B. Johnson, Anoop K. Sendamarai, Mark W. Springel, Laurent Beaugerie, Maria K. Lehtinen
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.08007

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome
Cited by: 129
Author(s): Yoong Wearn Lim, Lionel A. Sanz, Xiaoqin Xu, Stella R. Hartono, Frédéric Chédin
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-021-07679-y

Global investigation of estrogen-responsive genes regulating lipid metabolism in the liver of laying hens
Cited by: 14
Author(s): Jingyao Ren, Weihua Tian, Keren Jiang, Zhang Wang, Dandan Wang, Zhuanjian Li, Fengbin Yan, Yanbin Wang, Yadong Tian, Kepeng Ou, Hongjun Wang, Xiangtao Kang, Hong Li, Xiaojun Liu
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0192383

Adaptability of the Saccharomyces cerevisiae yeasts to wine fermentation conditions relies on their strong ability to consume nitrogen
Cited by: 40
Author(s): Claire Brice, Francisco A. Cubillos, Sylvie Dequin, Carole Camarasa, Claudio Martı́nez
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-019-5895-7

Comparative physiology and transcriptome analysis allows for identification of lncRNAs imparting tolerance to drought stress in autotetraploid cassava
Cited by: 21
Author(s): Xiao Liang, Xianwen Shang, Sheng Cao, Xuewen Xie, Wendan Zeng, Lingyun Lu, Songbi Chen, Huabing Yan
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.35551

Ssd1 and Gcn2 suppress global translation efficiency in replicatively aged yeast while their activation extends lifespan
Cited by: 54
Author(s): Zheng Hu, Bo Xia, Spike D. L. Postnikoff, Zih Jie Shen, Alin Tomoiaga, Troy A. A. Harkness, Ja Hwan Seol, Wei Li, Kaifu Chen, Jessica K. Tyler
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.64283

Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs
Cited by: 19
Author(s): Swati Gaikwad, Fardin Ghobakhlou, David J. Young, Jyothsna Visweswaraiah, Hongen Zhang, Alan G. Hinnebusch
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.19893

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status
Cited by: 16
Author(s): Dongming Li, Ana Marie S. Palanca, So Youn Won, Lei Gao, Ying Feng, Ajay A. Vashisht, Li Liu, Yuanyuan Zhao, Xigang Liu, Xiuyun Wu, Shaofang Li, Brandon H. Le, Yun Ju Kim, Guodong Yang, Shengben Li, Jinyuan Liu, James A. Wohlschlegel, Hongwei Guo, Beixin Mo, Xuemei Chen, Julie A. Law
Software Mentions: 4
Published: over 7 years ago

10.1186/s12870-020-02336-0

Morpho-physiological integrators, transcriptome and coexpression network analyses signify the novel molecular signatures associated with axillary bud in chrysanthemum
Cited by: 10
Author(s): Sagheer Ahmad, Cunquan Yuan, Qingqing Yang, Yujie Yang, Tangren Cheng, Jia Wang, Huitang Pan, Qixiang Zhang
Software Mentions: 4
Published: over 4 years ago

10.12688/f1000research.15604.1

Androgen-dependent alternative mRNA isoform expression in prostate cancer cells
Cited by: 14
Author(s): Jennifer Munkley, Teresa Maia, Jesús Ibarluzea, Karen E. Livermore, Daniel Vodák, Ingrid Ehrmann, Katherine James, Prabhakar Rajan, Nuno L. Barbosa‐Morais, David Elliott
Software Mentions: 4
Published: over 6 years ago

10.1186/s40303-016-0017-9

αT-catenin in restricted brain cell types and its potential connection to autism
Cited by: 20
Author(s): Stephen Sai Folmsbee, Douglas R. Wilcox, Koen Tyberghein, Pieter De Bleser, Warren G. Tourtellotte, Jolanda van Hengel, Frans van Roy, Cara J. Gottardi
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-020-6613-1

Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals
Cited by: 11
Author(s): Yali Hou, Furong Qi, Xue Bai, Tong Ren, Xu Shen, Qing Chu, Xiquan Zhang, Xuemei Lu
Software Mentions: 4
Published: over 4 years ago

10.1186/s12870-015-0661-8

A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit
Cited by: 51
Author(s): Noam Chayut, Hui Yuan, Shachar Ohali, Ayala Meir, Yelena Yeselson, Vitaly Portnoy, Yi Zheng, Zhangjun Fei, Efraim Lewinsohn, Nurit Katzir, Arthur A. Schaffer, Shimon Gepstein, Joseph Burger, L i Li, Yaakov Tadmor
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0191564

Study of formation of green eggshell color in ducks through global gene expression
Cited by: 4
Author(s): Fa Xu, Ang Li, Jing Lan, Yue Ming Wang, Mengmeng Yan, Sen Lian, Xu Wu
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41388-019-1005-1

Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines
Cited by: 12
Author(s): Li Wang, Hongying Zhao, Jing Li, Yingqi Xu, Yujia Lan, Wenkang Yin, Xiaoqin Liu, Lei Yu, Shan Lin, Michael Yifei Du, Xia Li, Yun Xiao, Yunpeng Zhang
Software Mentions: 4
Published: about 5 years ago

10.1016/j.ijpara.2018.01.004

Transcriptomic profiling of nematode parasites surviving vaccine exposure
Cited by: 19
Author(s): Guillaume Sallé, Roz Laing, James A. Cotton, Kirsty Maitland, Axel Martinelli, Nancy Holroyd, Alan S. Tracey, Matthew Berriman, William D. Smith, G. F. J. Newlands, Eve Hanks, Eileen Devaney, Collette Britton
Software Mentions: 4
Published: over 6 years ago

10.1186/s12870-017-0996-4

Stress-responsive pathways and small RNA changes distinguish variable developmental phenotypes caused by MSH1 loss
Cited by: 24
Author(s): Mon Ray Shao, Sunil Kumar Kenchanmane Raju, John D. Laurie, Robersy Sánchez, Sally A. Mackenzie
Software Mentions: 4
Published: almost 8 years ago

10.4049/jimmunol.1602033

Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells
Cited by: 45
Author(s): Ruth Brignall, Pierre Cauchy, Sarah L Bevington, Bethany Gorman, Angela Oliveira Pisco, James Bagnall, Christopher Boddington, William Rowe, Hazel England, Kevin Rich, Lorraine Schmidt, Nigel P. Dyer, Mark A. Travis, Sascha Ott, Dean A. Jackson, Peter N. Cockerill, Pawel Paszek
Software Mentions: 4
Published: about 7 years ago

10.1186/s12870-017-1108-1

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription
Cited by: 17
Author(s): Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
Software Mentions: 4
Published: about 7 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

10.1186/s13046-018-0957-2

miR-296-5p suppresses EMT of hepatocellular carcinoma via attenuating NRG1/ERBB2/ERBB3 signaling
Cited by: 64
Author(s): Dongmin Shi, Lixin Li, Xinyu Bian, Xuejiang Shi, Lili Lü, Hongxin Zhou, Ting-Jia Pan, Jian Zhou, Jia Fan, Wei–Zhong Wu
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0151697

Comparative RNA-Seq Analysis Reveals That Regulatory Network of Maize Root Development Controls the Expression of Genes in Response to N Stress
Cited by: 19
Author(s): Xiujing He, Hui Ma, Xing Zhao, Shujun Nie, Yuhua Li, Zhiming Zhang, Yaou Shen, Qi Chen, Yanli Lu, Hai Long, Shufeng Zhou, Shibin Gao, Guangtang Pan, Hung-Ching Lin
Software Mentions: 4
Published: over 8 years ago

10.1084/jem.20150907

Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells
Cited by: 76
Author(s): Alejandro V. Villarino, Giuseppe Sciumè, Fred P. Davis, S. Iwata, Beatrice Zitti, Gertraud W. Robinson, Lothar Hennighausen, Yuka Kanno, John J. O’Shea
Software Mentions: 4
Published: about 7 years ago

10.1186/1471-2164-15-845

Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data
Cited by: 66
Author(s): Kunshan Zhang, Kefei Huang, Yuan Luo, Siguang Li
Software Mentions: 4
Published: about 10 years ago

10.1128/mSphere.00479-21

Rhinovirus Reduces the Severity of Subsequent Respiratory Viral Infections by Interferon-Dependent and -Independent Mechanisms
Cited by: 12
Author(s): James T. Van Leuven, Andrés González, Emmanuel C. Ijezie, Alexander Q. Wixom, John L. Clary, Maricris N. Naranjo, Benjamin J. Ridenhour, Craig R. Miller, Tanya A. Miura
Software Mentions: 4
Published: over 3 years ago

10.1128/mSphere.00528-19

Antibody-Dependent Dengue Virus Entry Modulates Cell Intrinsic Responses for Enhanced Infection
Cited by: 19
Author(s): Chee-Yong Chan, John Z.H. Low, Esther S. Gan, Eugenia Z. Ong, Summer L. Zhang, Hwee Cheng Tan, Xiaoran Chai, Sujoy Ghosh, Eng Eong Ooi, Kap Luk Chan
Software Mentions: 4
Published: about 5 years ago

10.1128/mSystems.00596-19

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics
Cited by: 7
Author(s): Matthew Chung, Laura Teigen, Silvia Libro, Robin E. Bromley, Dustin Olley, Nikhil Kumar, Lisa Sadzewicz, Luke J. Tallon, Anup Mahurkar, Jeremy M. Foster, Michelle L. Michalski, Julie C. Dunning Hotopp
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-019-49817-3

An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo
Cited by: 35
Author(s): Steffen Israel, Markus Ernst, Olympia E. Psathaki, Hannes C.A. Drexler, Ellen Casser, Yutaka Suzuki, Wojciech Makałowski, Michele Boiani, Georg Fuellen, Leila Taher
Software Mentions: 4
Published: about 5 years ago

10.3389/fcimb.2017.00227

Transcriptomic Profiling of High-Density Giardia Foci Encysting in the Murine Proximal Intestine
Cited by: 32
Author(s): Jonathan K Pham, Christopher Nosala, Elaine P. Scott, Kristofer Nguyen, Kari D. Hagen, Hannah Starcevich, Scott C. Dawson
Software Mentions: 4
Published: over 7 years ago

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