pypi: TopHat | Projects | Ecosyste.ms: Papers

10.18632/oncotarget.16048

HLA class I loss in metachronous metastases prevents continuous T cell recognition of mutated neoantigens in a human melanoma model
Cited by: 26
Author(s): Barbara Schrörs, Silke Lübcke, Volker Lennerz, Martina Fatho, Anne Bicker, Catherine Wölfel, Patrick Derigs, Thomas Hankeln, Dirk Schadendorf, Annette Paschen, Thomas Wölfel
Software Mentions: 4
Published: over 8 years ago

10.1534/g3.116.028324

Histone H1 Limits DNA Methylation in Neurospora crassa
Cited by: 18
Author(s): Michael Seymour, Lexiang Ji, Alex M. Santos, Masayuki Kamei, Takahiko Sasaki, Evelina Y. Basenko, Robert J. Schmitz, Xiaoyu Zhang, Zachary A. Lewis
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pntd.0001409

A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi
Cited by: 86
Author(s): Young Jun Choi, Elodie Ghedin, Matthew Berriman, Jacqueline A. McQuillan, Nancy Holroyd, George F. Mayhew, Bruce M. Christensen, Michelle L. Michalski
Software Mentions: 4
Published: over 13 years ago

10.3390/insects9040185

Differential Gene Expression in Red Imported Fire Ant (Solenopsis invicta) (Hymenoptera: Formicidae) Larval and Pupal Stages
Cited by: 11
Author(s): Margaret L. Allen, Joshua H. Rhoades, Michael E. Sparks, Michael J. Grodowitz
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2019.00603

Analysis of Key Genes Involved in Potato Anthocyanin Biosynthesis Based on Genomics and Transcriptomics Data
Cited by: 13
Author(s): Nie Tengkun, Dongdong Wang, Xiaoyan Ma, Yue Chen, Qin Chen
Software Mentions: 4
Published: about 6 years ago

10.1186/s12951-020-0576-x

Core–shell nanoparticles suppress metastasis and modify the tumour-supportive activity of cancer-associated fibroblasts
Cited by: 33
Author(s): Dóra Kovács, Nóra Igaz, Annamária Marton, Andrea Rónavári, Péter Bélteky, László Bodai, Gabriella Spengler, László Tiszlavicz, Zsolt Rázga, Péter Hegyi, Csaba Vízler, Imre Boros, Zoltán Kónya, Mónika Kiricsi
Software Mentions: 4
Published: over 5 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: about 6 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: over 12 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: about 4 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: about 4 years ago

10.3389/fonc.2020.573318

PHF20 Promotes Glioblastoma Cell Malignancies Through a WISP1/BGN-Dependent Pathway
Cited by: 6
Author(s): Qianquan Ma, Wenyong Long, Changsheng Xing, Chongming Jiang, Jun Su, Helen Y. Wang, Qing Liu, Rong Fu Wang
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12943-018-0833-x

RNA-Seq profiling of circular RNAs in human laryngeal squamous cell carcinomas
Cited by: 57
Author(s): Cheng Hsien Lu, Xi Su, Amanda Y. Wang, Tao Yuan, Zhenxiao Wang, Chaoping Huang, Yuehua Qiao, Hongyi Hu, Liangfa Liu
Software Mentions: 4
Published: about 7 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0102398

JAGuaR: Junction Alignments to Genome for RNA-Seq Reads
Cited by: 51
Author(s): Yaron S.N. Butterfield, Maayan Kreitzman, Nina Thiessen, Richard Corbett, Yisu Li, Johnson Pang, P. Yussanne, Steven J.M. Jones, İnanç Birol
Software Mentions: 4
Published: about 11 years ago

10.3389/fnmol.2017.00340

Cell Type-Specific mRNA Dysregulation in Hippocampal CA1 Pyramidal Neurons of the Fragile X Syndrome Mouse Model
Cited by: 32
Author(s): Laura Ceolin, Nathalie Bouquier, Jihane Vitre-Boubaker, Stéphanie Rialle, Dany Séverac, Emmanuel Valjent, Julie Perroy, Emma Puighermanal
Software Mentions: 4
Published: almost 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: over 9 years ago

10.1016/j.molcel.2019.04.002

Functional Landscape of PCGF Proteins Reveals Both RING1A/B-Dependent-and RING1A/B-Independent-Specific Activities
Cited by: 116
Author(s): Andrea Scelfo, Daniel Fernández-Pérez, Simone Tamburri, Marika Zanotti, Elisa Lavarone, Monica Soldi, Tiziana Bonaldi, Karin Johanna Ferrari, Diego Pasini
Software Mentions: 4
Published: about 6 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: over 6 years ago

10.1371/journal.pone.0175528

The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown
Cited by: 61
Author(s): Shingo Miyauchi, David Navarro, Sacha Grisel, Didier Chevret, Jean‐Guy Berrin, Marie Noelle Rosso
Software Mentions: 4
Published: over 8 years ago

10.3389/fnmol.2017.00419

Ribosomal Protein S6 Phosphorylation Is Involved in Novelty-Induced Locomotion, Synaptic Plasticity and mRNA Translation
Cited by: 27
Author(s): Emma Puighermanal, Anne Biever, Vincent Pascoli, Su Melser, Marine Pratlong, Laura Cutando, Stéphanie Rialle, Dany Séverac, Jihane Boubaker-Vitre, Oded Meyuhas, Giovanni Marsicano, Christian Lüscher, Emmanuel Valjent
Software Mentions: 4
Published: over 7 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: over 7 years ago

10.7554/eLife.63556

Deficient spermiogenesis in mice lacking Rlim
Cited by: 7
Author(s): Feng Wang, María Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Jun Yu, Mary C. Wallingford, Darya A Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando, Pablo E. Visconti, Lara Strittmatter, Ingolf Bach
Software Mentions: 4
Published: over 4 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: over 8 years ago

10.1111/jcmm.15569

LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity
Cited by: 8
Author(s): Amandine Guérin, Delphine Martire, Eva Trenquier, Tom Lesluyes, Sébastien Sagnol, Marine Pratlong, Elise Lefebvre, Frédéric Chibon, Pascal de Santa Barbara, Sandrine Faure
Software Mentions: 4
Published: about 5 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: almost 6 years ago

10.1007/s11105-017-1032-4

Drought-Tolerant Brassica rapa Shows Rapid Expression of Gene Networks for General Stress Responses and Programmed Cell Death Under Simulated Drought Stress
Cited by: 25
Author(s): Yi Guo, Birgit Samans, Sheng Chen, Kidist B. Kibret, Sarah Hatzig, Neil C. Turner, Matthew N. Nelson, Wallace Cowling, Rod J. Snowdon
Software Mentions: 4
Published: about 8 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: about 8 years ago

10.1371/journal.pone.0145257

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation
Cited by: 73
Author(s): Dandan Feng, Qi Li, Hong Yu, Xuelin Zhao, Lingfeng Kong
Software Mentions: 4
Published: over 9 years ago

10.1038/s41438-021-00531-0

Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution
Cited by: 28
Author(s): Chen Hong-guo, Xiangling Zeng, Jie Yang, Xuan Cai, Yumin Shi, Rencheng Zheng, Zhenqi Wang, Junyi Liu, Xiao Su Yi, Siwei Xiao, Qiang Fu, Jingjing Zou, Caiyun Wang
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2021.605095

Improvement of Free Fatty Acid Secretory Productivity in Aspergillus oryzae by Comprehensive Analysis on Time-Series Gene Expression
Cited by: 4
Author(s): Pui Shan Wong, Koichi Tamano, Sachiyo Aburatani
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-95308-9

ACE2 protein expression within isogenic cell lines is heterogeneous and associated with distinct transcriptomes
Cited by: 20
Author(s): Emily Sherman, Brian T. Emmer
Software Mentions: 4
Published: almost 4 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: over 7 years ago

10.1371/journal.pone.0227882

Comparison of the myometrial transcriptome from singleton and twin pregnancies by RNA-Seq
Cited by: 5
Author(s): Sarah Arrowsmith, Yongxiang Fang, Andrew Sharp
Software Mentions: 4
Published: over 5 years ago

10.3390/plants10040669

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine
Cited by: 4
Author(s): Shuchi Smita, Michael Robben, Anup Deuja, Monica Accerbi, Pamela J. Green, Senthil Subramanian, Anne Fennell
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-82729-9

NLRC5/CITA expression correlates with efficient response to checkpoint blockade immunotherapy
Cited by: 14
Author(s): Sayuri Yoshihama, Steven Cho, Jason Yeung, Xuedong Pan, Gregory Lizee, Kranti Konganti, Valen E. Johnson, Koichi S. Kobayashi
Software Mentions: 4
Published: over 4 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 7 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: about 8 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 9 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: over 6 years ago

10.1371/journal.pone.0225658

Highly multiplexed quantitative PCR-based platform for evaluation of chicken immune responses
Cited by: 15
Author(s): Dominika Borowska, Richard Kuo, Richard Bailey, Kellie Watson, Pete Kaiser, Lonneke Vervelde, Mark P. Stevens
Software Mentions: 4
Published: over 5 years ago

10.1111/pbi.12520

Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Cited by: 89
Author(s): Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Dadakhalandar Doddamani, Lekha T. Pazhamala, Aamir W. Khan, Mahendar Thudi, Suk-Ha Lee, Rajeev K. Varshney
Software Mentions: 4
Published: over 9 years ago

10.1038/srep15041

DDX3Y gene rescue of a Y chromosome AZFa deletion restores germ cell formation and transcriptional programs
Cited by: 57
Author(s): Cyril Ramathal, Benjamin Angulo, Meena Sukhwani, Jun Cui, Jens Durruthy-Durruthy, Fang Fang, Paula Schanes, Paul J. Turek, Kyle E. Orwig, Renee A. Reijo Pera
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41598-020-80635-0

Differentially expressed lncRNAs in liver tissues of TX mice with hepatolenticular degeneration
Cited by: 5
Author(s): Juan Zhang, Ying Ma, Denghui Xie, Bao Yuan-cheng, Weiren Yang, Han Wang, Huaizhou Jiang, Hui Han, Ting Dong
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-27189-4

A Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data
Cited by: 47
Author(s): Gaurav Pandey, O.P. Pandey, Angela Rogers, Mehmet Eren Ahsen, Gabriel E. Hoffman, Benjamin A. Raby, Scott T. Weiss, Eric E. Schadt, Supinda Bunyavanich
Software Mentions: 4
Published: about 7 years ago

10.3389/fcell.2021.675438

Identification of Key Genes With Differential Correlations in Lung Adenocarcinoma
Cited by: 9
Author(s): You Zhou, Bin Xu, Yi Zhou, Jian Liu, Xiao Zheng, Yingting Liu, Hepu Deng, Ming Liu, Xiubao Ren, Jianchuan Xia, Xiangyin Kong, Tao Huang, Jingting Jiang
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-79379-8

Upregulation of 5′-terminal oligopyrimidine mRNA translation upon loss of the ARF tumor suppressor
Cited by: 2
Author(s): Kyle A. Cottrell, Ryan C. Chiou, Jason D. Weber
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-24227-z

A new way of producing pediocin in Pediococcus acidilactici through intracellular stimulation by internalized inulin nanoparticles
Cited by: 19
Author(s): Whee-Soo Kim, Jun-Yeong Lee, Bijay Singh, Sushila Maharjan, Liang Hong, Sang-Mok Lee, Lianhua Cui, Ki-June Lee, Girak Kim, Cheol‐Heui Yun, Seoung-Hun Kang, Yun‐Jaie Choi, Chong‐Su Cho
Software Mentions: 4
Published: over 7 years ago

10.1002/ece3.5965

Draft genome of the famous ornamental plant <i>Paeonia suffruticosa</i>
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: about 5 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: almost 7 years ago

10.1038/s41598-017-17337-7

Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes
Cited by: 2
Author(s): Enrico Capobianco, Camilo Valdes, Samanta Sarti, Zhijie Jiang, Laura Poliseno, Nicolas F. Tsinoremas
Software Mentions: 4
Published: over 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: over 4 years ago

10.1038/s41598-017-18205-0

Tissue Tropism in Host Transcriptional Response to Members of the Bovine Respiratory Disease Complex
Cited by: 26
Author(s): Susanta K. Behura, P. C. Tizioto, JaeWoo Kim, Natália Vinhal Grupioni, Christopher M. Seabury, Robert D. Schnabel, Laurel J. Gershwin, Alison L. Van Eenennaam, Rachel L. Toaff-Rosenstein, Holly L. Neibergs, Luciana Correia de Almeida Regitano, Jeremy F. Taylor
Software Mentions: 4
Published: over 7 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: over 9 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 5 years ago

10.12688/f1000research.22400.2

Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX
Cited by: 1
Author(s): Aikaterini Alexaki, Jacob Kames, Gaya Hettiarachchi, John C. Athey, Upendra Katneni, Ryan Hunt, Nobuko Hamasaki-Katagiri, David D. Holcomb, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty
Software Mentions: 4
Published: almost 5 years ago

10.1038/srep24375

RNA-seq analysis for detecting quantitative trait-associated genes
Cited by: 33
Author(s): Minseok Seo, Kwondo Kim, Joon Yoon, Jin Young Jeong, Hyun-Jeong Lee, Seoae Cho, Heebal Kim
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-018-25998-1

FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb
Cited by: 8
Author(s): Arun Singh, Cheng-Chi Chang, Hsiao-Yen Ma, Stephen A. Ramsey, Theresa M. Filtz, Chrissa Kioussi
Software Mentions: 4
Published: about 7 years ago

10.3389/fcell.2021.591754

Scaffold-Mediated Developmental Effects on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Are Preserved After External Support Removal
Cited by: 1
Author(s): Jun Li, Jong-Kook Lee, Keiko Miwa, Yuki Kuramoto, Kiyoshi Masuyama, Hideki Yasutake, Satoki Tomoyama, Hiroyuki Nakanishi, Yasushi Sakata
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-31072-7

Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens
Cited by: 12
Author(s): Henry Reyer, Barbara U. Metzler‐Zebeli, Nares Trakooljul, Michael Oster, Eduard Muráni, Siriluck Ponsuksili, Frieder Hadlich, Klaus Wimmers
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-78364-5

Hdac3 deletion in myeloid progenitor cells enhances bone healing in females and limits osteoclast fusion via Pmepa1
Cited by: 7
Author(s): David H. H. Molstad, Elizabeth L. Zars, Andrew Norton, Kim C. Mansky, Jennifer J. Westendorf, Elizabeth W. Bradley
Software Mentions: 4
Published: over 4 years ago

10.1186/s13072-017-0142-4

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure
Cited by: 18
Author(s): Sergey V. Ulianov, Aleksandra A. Galitsyna, Ilya M. Flyamer, Arkadiy K. Golov, Ekaterina E. Khrameeva, Maxim Imakaev, Nezar Abdennur, Mikhail S. Gelfand, А. В. Гаврилов, Sergey V. Razin
Software Mentions: 4
Published: about 8 years ago

10.1186/s13072-016-0070-8

Changes of 5-hydroxymethylcytosine distribution during myeloid and lymphoid differentiation of CD34+ cells
Cited by: 18
Author(s): Xavier Tekpli, Alfonso Urbanucci, Adnan Hashim, Cathrine Broberg Vågbø, Robert Lyle, Marianne Kristiansen Kringen, Anne Cathrine Staff, Ingunn Dybedal, Ian G. Mills, Arne Klungland, Judith Staerk
Software Mentions: 4
Published: about 9 years ago

10.12688/f1000research.9037.2

SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
Cited by: 74
Author(s): Felix Krueger, Simon Andrews
Software Mentions: 4
Published: about 9 years ago

10.1186/s12887-019-1564-x

Study of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation
Cited by: 22
Author(s): Najeeha Talat Iqbal, Sana Syed, Kamran Sadiq, Marium Khan, Junaid Iqbal, Z. Jennie, Fayaz Umrani, Sheraz Ahmed, Elizabeth A. Maier, Lee A. Denson, Yael Haberman, Monica McNeal, Kenneth D.R. Setchell, Xueheng Zhao, Shahida Qureshi, Lanlan Shen, Christopher A. Moskaluk, Ta‐Chiang Liu, Ömer H. Yılmaz, Donald E. Brown, Michael J. Barratt, Vanderlene L. Kung, Jeffrey I. Gordon, Sean R. Moore, Syed Asad Ali
Software Mentions: 4
Published: about 6 years ago

10.3389/fcell.2020.602731

CircRNA hsa_circ_0008500 Acts as a miR-1301-3p Sponge to Promote Osteoblast Mineralization by Upregulating PADI4
Cited by: 11
Author(s): Qiaoli Zhai, Yi Zhao, Linping Wang, Yan Dai, Peiqing Zhao, Xinxin Xiang, Kui Liu, Wei Du, Wenxiu Tian, Baoye Yang, Tao Li, Lianqing Wang
Software Mentions: 4
Published: over 4 years ago

10.3389/fcell.2021.715762

Probing Synergistic Targets by Natural Compounds for Hepatocellular Carcinoma
Cited by: 2
Author(s): Jian Gao, Zuojing Yin, Zhuanbin Wu, Zhonghua Sheng, Chao Ma, Rui Chen, Xiongwen Zhang, Kailin Tang, Jian Fei, Zhiwei Cao
Software Mentions: 4
Published: about 4 years ago

10.1186/s13072-017-0153-1

Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state
Cited by: 25
Author(s): Rebekka Mauser, Goran Kungulovski, Corinna Keup, Richard Reinhardt, Albert Jeltsch
Software Mentions: 4
Published: almost 8 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 7 years ago

10.1186/s13024-018-0303-3

Inhibition of monocyte-like cell extravasation protects from neurodegeneration in DBA/2J glaucoma
Cited by: 44
Author(s): Pete A. Williams, Catherine E. Braine, Krishnakumar Kizhatil, Nicole E. Foxworth, Nicholas G. Tolman, Jeffrey M. Harder, R. Scott, Gregory L. Sousa, Alyssa Panitch, Gareth R. Howell, Simon W. M. John
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0147221

Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics
Cited by: 36
Author(s): Robert A. Syme, Kar‐Chun Tan, James K. Hane, Kejal N Dodhia, Thomas Stoll, Marcus L. Hastie, Eiko Furuki, Simon R. Ellwood, Angela H. Williams, Yew‐Foon Tan, Alison C. Testa, Jeffrey J. Gorman, Richard P. Oliver
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-020-75060-2

Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal
Cited by: 1
Author(s): Nathalie Charbonnel, Maxime Galan, Caroline Tatard, Anne Loiseau, Christophe Diagne, Ambroise Dalecky, Hugues Parrinello, Stéphanie Rialle, Dany Séverac, Carine Brouat
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-018-32904-2

Transcriptomics and co-expression networks reveal tissue-specific responses and regulatory hubs under mild and severe drought in papaya (Carica papaya L.)
Cited by: 33
Author(s): Samuel David Gamboa-Tuz, Alejandro Pereira-Santana, Jesús Alejandro Zamora‐Briseño, Enrique Castaño, Francisco Espadas-Gil, Jorge Tonatiuh Ayala-Sumuano, Miguel A. Keb-Llanes, Lorenzo Felipe Sánchez Teyer, Luis Carlos Rodríguez-Zapata
Software Mentions: 4
Published: almost 7 years ago

10.1038/srep22398

Gene dysregulation is restored in the Parkinson’s disease MPTP neurotoxic mice model upon treatment of the therapeutic drug CuII(atsm)
Cited by: 12
Author(s): Lesley Cheng, Camelia Quek, Lin W. Hung, Robyn A. Sharples, Nicki A. Sherratt, Kevin J. Barnham, Andrew F. Hill
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-020-79619-x

Identification of loci associated with susceptibility to bovine paratuberculosis and with the dysregulation of the MECOM, eEF1A2, and U1 spliceosomal RNA expression
Cited by: 9
Author(s): María Canive, Nora Fernández-Jiménez, Rosa Casáis, Patricia Vázquez, José L. Lavín, José Ramón Bilbao, Cristina Blanco‐Vázquez, Joseba M. Garrido, Ramón A. Juste, Marta Alonso‐Hearn
Software Mentions: 4
Published: over 4 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: over 11 years ago

10.1038/srep12615

Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response
Cited by: 27
Author(s): Antonio Fabio Di Narzo, Alexey Kozlenkov, Yongchao Ge, Bin Zhang, Leo Sanelli, Zacnicte May, Yanqing Li, Karim Fouad, Christopher P. Cardozo, Eugene V. Koonin, David J. Bennett, Stella Dracheva
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41598-021-88363-9

Transcriptional signatures in prefrontal cortex confer vulnerability versus resilience to food and cocaine addiction-like behavior
Cited by: 11
Author(s): Mohit Navandar, Elena Martín‐García, Rafaël Maldonado, Beat Lutz, Susanne Gerber, Iñigo Ruı́z de Azúa
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-92385-8

Genome-enabled discovery of evolutionary divergence in brains and behavior
Cited by: 4
Author(s): Chinar Patil, J. B. Sylvester, Kawther Abdilleh, Michael Norsworthy, Karen Pottin, Milan Malinsky, Ryan F. Bloomquist, Zachary V. Johnson, Patrick T. McGrath, J. Todd Streelman
Software Mentions: 4
Published: about 4 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: about 8 years ago

10.1016/j.molmet.2020.101078

Wnt/β-catenin signaling regulates adipose tissue lipogenesis and adipocyte-specific loss is rigorously defended by neighboring stromal-vascular cells
Cited by: 44
Author(s): Devika P. Bagchi, Akira Nishii, Ziru Li, Jennifer B. DelProposto, Callie A.S. Corsa, Hiroyuki Mori, Julie Hardij, Brian S. Learman, Carey N. Lumeng, Ormond A. MacDougald
Software Mentions: 4
Published: over 4 years ago

10.1038/tp.2016.67

Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report
Cited by: 26
Author(s): Michael S. Breen, Anne Uhlmann, Christiane M. Nday, Stephen J. Glatt, Mario Mitt, A. Metsalpu, Dan J. Stein, Nicola Illing
Software Mentions: 4
Published: about 9 years ago

10.1186/s13395-020-00227-4

Transgenic mice expressing tunable levels of DUX4 develop characteristic facioscapulohumeral muscular dystrophy-like pathophysiology ranging in severity
Cited by: 31
Author(s): Takako I. Jones, Guo-Liang Chew, Pamela Barraza‐Flores, Spencer Schreier, Monique Ramirez, Ryan D. Wuebbles, Dean J. Burkin, Robert K. Bradley
Software Mentions: 4
Published: over 5 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: almost 8 years ago

10.3389/fmicb.2018.01061

Profiling of the Transcriptomic Responses of Clonostachys rosea Upon Treatment With Fusarium graminearum Secretome
Cited by: 26
Author(s): Zerihun A. Demissie, Simon J. Foote, Yifang Tan, Michèle C. Loewen
Software Mentions: 4
Published: about 7 years ago

10.1111/tpj.14299

Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat
Cited by: 46
Author(s): Xiaoming Wang, Siyuan Chen, Song Xue, Danni Liu, Peng Zhao, Yunze Lu, Yanbing Cheng, Zhenshan Liu, Xiaojun Nie, Weining Song, Qixin Sun, Shengbao Xu, Chuang Ma
Software Mentions: 4
Published: over 6 years ago

10.1038/sdata.2018.255

Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming
Cited by: 16
Author(s): Zhonghua Du, Lin Jia, Yichen Wang, Cong Wang, Wei Xue, Jingcheng Chen, Yanbo Zhu, Dehai Yu, Lei Zhou, Naifei Chen, Shilin Zhang, Ilkay Celik, Ferhat Ay, Sujun Gao, Songling Zhang, Wei Li, Andrew R. Hoffman, Jiuwei Cui
Software Mentions: 4
Published: over 6 years ago

10.1038/sdata.2018.305

The sequence and de novo assembly of hog deer genome
Cited by: 7
Author(s): Wei Wang, Yan Huang, Shiyi Chen, Zhenzhen Li, Jun Yi, Lili Niu, Jia-Po Deng, Weigang Chen, Yunfeng Pu, Xianbo Jia, Yu Qu, Ang Chen, Yan Zhong, Xiaoxi Yu, Shuai Pang, Wanlong Huang, Yue Han, Guangjian Liu, Jianqiu Yu
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: over 8 years ago

10.1371/journal.pone.0166104

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes
Cited by: 249
Author(s): Shoko Iwai, Thomas Weinmaier, Brian L. Schmidt, Donna G. Albertson, Neil J. Poloso, Karim Dabbagh, Todd Z. DeSantis
Software Mentions: 4
Published: over 8 years ago

10.1038/s41398-020-01096-7

Gestational diabetes induces behavioral and brain gene transcription dysregulation in adult offspring
Cited by: 11
Author(s): Keren Aviel-Shekler, Yara Hamshawi, Worood Sirhan, Dmitriy Getselter, Kannan Srikanth, Assaf Malka, Ron Piran, Evan Elliott
Software Mentions: 4
Published: over 4 years ago

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: over 10 years ago

10.3389/fcimb.2016.00193

Genome-Wide Transcriptional and Post-transcriptional Regulation of Innate Immune and Defense Responses of Bovine Mammary Gland to Staphylococcus aureus
Cited by: 41
Author(s): Lingzhao Fang, Yali Hou, Jinpeng An, Bingjie Li, Mengyuan Song, Xiao Wang, Peter Sørensen, Yichun Dong, Chao Liu, Yachun Wang, Huabin Zhu, Shengli Zhang, Ying Yu
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0148039

Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks
Cited by: 27
Author(s): Rebecca A. Nebel, Dejian Zhao, Erika Pedrosa, Jill Kirschen, Herbert M. Lachman, Deyou Zheng, Brett S. Abrahams
Software Mentions: 3
Published: over 9 years ago

10.1126/sciadv.abe5357

S100A8/S100A9 cytokine acts as a transcriptional coactivator during breast cellular transformation
Cited by: 24
Author(s): Ruisheng Song, Kevin Struhl
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0142221

Large-Scale Transcriptome Analysis of Cucumber and Botrytis cinerea during Infection
Cited by: 51
Author(s): Weiwen Kong, Nan Chen, Tingting Liu, Jing Zhu, Jingqi Wang, Xiaoqing He, Yi Jin
Software Mentions: 3
Published: over 9 years ago

10.1186/s13104-018-3864-x

Transcriptomic evidence for distinct mechanisms underlying abscission deficiency in the Arabidopsis mutants haesa/haesa-like 2 and nevershed
Cited by: 6
Author(s): Isaiah Taylor, John C. Walker
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0079118

Discovering Transcription and Splicing Networks in Myelodysplastic Syndromes
Cited by: 11
Author(s): Hongyan Wang, Jianguo Wen, Chung‐Che Chang, Xiaobo Zhou
Software Mentions: 3
Published: over 11 years ago

10.1186/s12284-021-00515-7

A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling
Cited by: 5
Author(s): Chao Zhou, Xiaoyun Liu, Xinglei Li, Hanlin Zhou, Sijia Wang, Yanfei Zhu, Yonghong Zhang, Sanhe Li, Aiqing You, Lei Zhou, Zhengquan He
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.49808

Extracellular matrix-inducing Sox9 promotes both basal progenitor proliferation and gliogenesis in developing neocortex
Cited by: 26
Author(s): Ayse Güven, Nereo Kalebic, Katherine R. Long, Marta Florio, Samir Vaid, Holger Brandl, Denise Stenzel, Wieland B. Huttner
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0077396

The Pituitary Gland of the European Eel Reveals Massive Expression of Genes Involved in the Melanocortin System
Cited by: 15
Author(s): Eirill Ager-Wick, Ron P. Dirks, Erik Burgerhout, Rasoul Nourizadeh-Lillabadi, Daniëlle L. de Wijze, Herman P. Spaink, Guido E.E.J.M. van den Thillart, Katsumi Tsukamoto, Sylvie Dufour, Finn‐Arne Weltzien, Christiaan V. Henkel
Software Mentions: 3
Published: almost 12 years ago

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