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/s12870-017-1037-z

Proanthocyanidin accumulation and transcriptional responses in the seed coat of cranberry beans (Phaseolus vulgaris L.) with different susceptibility to postharvest darkening
Cited by: 30
Author(s): José A. Freixas Coutin, Seth Munholland, Anjali Silva, Sanjeena Subedi, Lewis Lukens, William L. Crosby, K. Peter Pauls, Gale G. Bozzo
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

10.1186/1471-2164-14-283

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 12 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

10.1016/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: about 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: over 6 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: over 7 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: over 10 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: over 4 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 11 years ago

10.1080/21505594.2021.1958057

Transcriptional response of <i>Aspergillus fumigatus</i> to copper and the role of the Cu chaperones
Cited by: 6
Author(s): Duaa Anabosi, Zohar Meir, Yana Shadkchan, Mariana Handelman, Ammar Abou-Kandil, Annie Yap, Daniel Urlings, Morgan Gold, Sven Krappmann, Hubertus Haas, Nir Osherov
Software Mentions: 4
Published: almost 4 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

10.18632/oncotarget.23638

YAP-associated chromosomal instability and cholangiocarcinoma in mice
Cited by: 41
Author(s): Sumera Rizvi, Samantha R. Fischbach, Steven F. Bronk, Petra Hirsova, Anuradha Krishnan, Renumathy Dhanasekaran, James B. Smadbeck, Rory L. Smoot, George Vasmatzis, Gregory J. Gores
Software Mentions: 4
Published: over 7 years ago

10.3390/vaccines5040037

Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward
Cited by: 8
Author(s): David J. Lemler, Hayden Brochu, Fang Yang, Erin Harrell, Xinxia Peng
Software Mentions: 4
Published: almost 8 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: about 5 years ago

10.18632/oncotarget.11733

DMBA induced mouse mammary tumors display high incidence of activating <i>Pik3caH1047</i> and loss of function <i>Pten</i> mutations
Cited by: 45
Author(s): Martı́n C. Abba, Yi Zhong, Jae-Ho Lee, Hyunsuk Kil, Yue Lu, Yoko Takata, Melissa S. Simper, Sally Gaddis, Jianjun Shen, C. Marcelo Aldaz
Software Mentions: 4
Published: almost 9 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: about 4 years ago

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

10.18632/oncotarget.8239

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer
Cited by: 13
Author(s): Su‐Jin Baek, Mirang Kim, Donghyuck Bae, Jeong‐Hwan Kim, Hee‐Jin Kim, Myoung‐Eun Han, Sae‐Ock Oh, Yong‐Sung Kim, Seon‐Young Kim
Software Mentions: 4
Published: over 9 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: about 5 years ago

10.18632/oncotarget.7209

Large-scale profiling of signalling pathways reveals an asthma specific signature in bronchial smooth muscle cells
Cited by: 20
Author(s): Elena Alexandrova, Giovanni Nassa, Giacomo Corleone, Anton Buzdin, Alexander Aliper, Nadezhda V. Terekhanova, Denis Shepelin, Alex Zhavoronkov, Michael Tamm, Luciano Milanesi, Nicola Miglino, Alessandro Weisz, Pieter Borger
Software Mentions: 4
Published: over 9 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

10.18632/oncotarget.9093

Collecting duct carcinoma of the kidney is associated with<i>CDKN2A</i>deletion and<i>SLC</i>family gene up-regulation
Cited by: 44
Author(s): Jianmin Wang, Antonios Papanicolau‐Sengos, Sreenivasulu Chintala, Lei Wei, Biao Liu, Qiang Hu, Kiersten Marie Miles, Jeffrey M. Conroy, Sean T. Glenn, Manuela Costantini, Cristina Magi‐Galluzzi, Sabina Signoretti, Toni K. Choueiri, Michele Gallucci, Steno Sentinelli, Vito Michele Fazio, Maria Luana Poeta, Song Liu, Carl Morrison, Роберто Пили
Software Mentions: 4
Published: about 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: 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 5 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: almost 7 years ago

10.3390/ijms221910403

MMP14 Contributes to HDAC Inhibition-Induced Radiosensitization of Glioblastoma
Cited by: 1
Author(s): Yuchuan Zhou, Hongxia Liu, Zheng Wang, Qianping Chen, Songling Hu, Yan Pan, Yang Bai, Jianghong Zhang, Chunlin Shao
Software Mentions: 4
Published: almost 4 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: about 6 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

10.1002/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

10.15252/msb.20166869

Strand‐specific, high‐resolution mapping of modified RNA polymerase II
Cited by: 46
Author(s): Laura Milligan, Vân Anh Huynh-Thu, Clémentine Delan-Forino, Alex Tuck, Elisabeth Petfalski, Rodrigo Lombraña, Guido Sanguinetti, Grzegorz Kudla, David Tollervey
Software Mentions: 4
Published: about 9 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: about 5 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

10.3390/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: over 6 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: over 5 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: about 7 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 5 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: over 4 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: over 6 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

10.1016/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: over 5 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: about 5 years ago

10.15252/msb.20188591

Widespread inter‐individual gene expression variability in <i>Arabidopsis thaliana</i>
Cited by: 48
Author(s): Sandra Cortijo, Zeynep Gökçe Gayretli Aydın, Sebastian E. Ahnert, James Locke
Software Mentions: 4
Published: over 6 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: almost 7 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: about 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 7 years ago

10.18632/oncotarget.20219

Transcriptional signature of lymphoblastoid cell lines of<i>BRCA1</i>,<i>BRCA2</i>and non-<i>BRCA1/2</i>high risk breast cancer families
Cited by: 8
Author(s): Marie-Christine Pouliot, Charu Kothari, Charles Joly-Beauparlant, Yvan Labrie, Geneviève Ouellette, Jacques Simard, Arnaud Droit, Francine Durocher
Software Mentions: 4
Published: almost 8 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: over 5 years ago

10.1186/s13071-019-3534-4

Eimeria maxima-induced transcriptional changes in the cecal mucosa of broiler chickens
Cited by: 15
Author(s): Charles Li, Xianghe Yan, Hyun S. Lillehoj, Seong-Hwan Oh, Liheng Liu, Zhifeng Sun, Changqin Gu, Youngsub Lee, Zhezi Xianyu, Hongyan Zhao
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

10.7554/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: about 10 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: almost 10 years ago

10.7554/eLife.02104

Mof-associated complexes have overlapping and unique roles in regulating pluripotency in embryonic stem cells and during differentiation
Cited by: 41
Author(s): Sarina Ravens, Marjorie Fournier, Tao Ye, Matthieu Stierlé, Doulaye Dembelé, Virginie Chavant, László Tora
Software Mentions: 4
Published: about 11 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 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: over 7 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: over 9 years ago

10.1186/s12935-019-0953-4

Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes
Cited by: 22
Author(s): Guo Wei, Hui Yu, Lu Zhang, Xiuwei Chen, Yunduo Liu, Yaoxian Wang, Yunyan Zhang
Software Mentions: 4
Published: almost 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: about 9 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 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: over 4 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: almost 7 years ago

10.7717/peerj.7071

Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants
Cited by: 1
Author(s): Jakub Hynšt, Karla Plevová, Lenka Radová, Vojtěch Bystrý, Karol Pál, Šárka Pospı́šilová
Software Mentions: 4
Published: about 6 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 7 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: almost 8 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: over 6 years ago

10.1186/s13068-020-01774-0

Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)
Cited by: 17
Author(s): Tengyue Wang, Lijuan Wei, Jia Wang, Ling Xie, Yang Yang Li, Shuyao Ran, Lanyang Ren, Kun Lu, Jiana Li, Michael P. Timko, Liezhao Liu
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0141225

A catalogue of novel bovine long noncoding RNA across 18 tissues
Cited by: 76
Author(s): Lambros T. Koufariotis, Yi‐Ping Phoebe Chen, Amanda J. Chamberlain, Christy Vander Jagt, Ben J. Hayes
Software Mentions: 4
Published: almost 10 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: over 5 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: almost 8 years ago

10.1371/journal.pone.0243911

The pharmacodynamic and differential gene expression analysis of PPAR α/δ agonist GFT505 in CDAHFD-induced NASH model
Cited by: 12
Author(s): Linfu Liu, Chuang Liu, Menglong Zhao, Qianru Zhang, Ying Lu, Ping Liu, Hua Yang, Jinliang Yang, Xiaoxin Chen, Yuqin Yao
Software Mentions: 4
Published: over 4 years ago

10.1128/mBio.01157-20

Previremic Identification of Ebola or Marburg Virus Infection Using Integrated Host-Transcriptome and Viral Genome Detection
Cited by: 2
Author(s): Emily Speranza, Ignacio Caballero, Anna N. Honko, Joshua C. Johnson, J. Kyle Bohannon, Lisa Evans DeWald, Dawn M. Gerhardt, Jennifer Sword, Lisa E. Hensley, Richard S. Bennett, John H. Connor
Software Mentions: 4
Published: about 5 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: over 5 years ago

10.1186/s12985-016-0659-3

Derivation of chicken induced pluripotent stem cells tolerant to Newcastle disease virus-induced lysis through multiple rounds of infection
Cited by: 7
Author(s): Leonardo Susta, Ying He, Jessica M. Hutcheson, Yangqing Lu, Franklin D. West, Steven L. Stice, Ping Yu, Zaid Abdo, Claudio L. Afonso
Software Mentions: 4
Published: over 8 years ago

10.1186/s13068-018-1060-9

Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analyses
Cited by: 33
Author(s): Xing Qin, Xiaoyun Su, Huiying Luo, Rui Ma, Bin Yao, Fuying Ma
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: over 6 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

10.1128/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: about 4 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 7 years ago

10.18632/oncotarget.20977

Selecting lncRNAs in gastric cancer cells for directed therapy with bioactive peptides and chemotherapy drugs
Cited by: 7
Author(s): Wenyan Han, Rui Xiao, Chuanling Zhang, Qimuge Suyila, Xian Li, Xiulan Su
Software Mentions: 4
Published: almost 8 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/s41598-020-79619-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

10.1038/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/s41598-020-78364-5

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

10.1371/journal.pone.0244593

Comparative RNA-Seq analysis unfolds a complex regulatory network imparting yellow mosaic disease resistance in mungbean [Vigna radiata (L.) R. Wilczek]
Cited by: 24
Author(s): Uttarayan Dasgupta, Gyan P. Mishra, Harsh Kumar Dikshit, Dwijesh Chandra Mishra, Tejas C. Bosamia, Anirban Roy, Jyotika Bhati, Priti, Muraleedhar S. Aski, Ranjeet Kumar, Amit Kumar Singh, Atul Kumar, S. K. Sinha, Sundeep Chaurasia, Shelly Praveen, Ramakrishnan M. Nair
Software Mentions: 4
Published: over 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

10.1186/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

10.1038/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

10.1371/journal.pone.0216679

Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel
Cited by: 8
Author(s): Fatma Zohra Djazouli Alim, Elena V. Romanova, Yea Ling Tay, Ahmad Yamin bin Abdul Rahman, Kok‐Gan Chan, Kar‐Wai Hong, Mark F. Rogers, Bruce R. Southey, Michael Greenwood, André Souza Mecawi, Mohammad Rais Mustafa, Nicole Mahy, Colin Campbell, José Antunes‐Rodrigues, Jonathan V. Sweedler, David Murphy, Charles C.T. Hindmarch
Software Mentions: 4
Published: about 6 years ago

10.1155/2013/340620

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity
Cited by: 79
Author(s): Matteo Carrara, Marco Beccuti, Fulvio Lazzarato, Federica Cavallo, Francesca Cordero, Susanna Donatelli, Raffaele Calogero
Software Mentions: 4
Published: over 12 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/s41598-020-75060-2

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/s41598-021-92385-8

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

10.1038/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

10.1371/journal.pone.0098404

Deep Sequencing Reveals New Aspects of Progesterone Receptor Signaling in Breast Cancer Cells
Cited by: 12
Author(s): Anastasia Kougioumtzi, Panayiotis Tsaparas, Angeliki Magklara
Software Mentions: 4
Published: about 11 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

10.1371/journal.pone.0115842

Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis
Cited by: 14
Author(s): Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo J. Komotar, Jennifer Clarke, Ming Zhang, Nagi G. Ayad
Software Mentions: 4
Published: over 10 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

10.1186/s12864-021-07699-8

Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome
Cited by: 8
Author(s): Stefania Bertazzoni, Darcy A. B. Jones, H. Phan, Kar‐Chun Tan, James K. Hane
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0081809

Next Generation Sequencing Analysis of Human Platelet PolyA+ mRNAs and rRNA-Depleted Total RNA
Cited by: 55
Author(s): Antheia Kissopoulou, Jon Jonasson, Tomas Lindahl, Abdimajid Osman
Software Mentions: 4
Published: over 11 years ago