bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3390/ijms22115798

Genome-Wide Role of HSF1 in Transcriptional Regulation of Desiccation Tolerance in the Anhydrobiotic Cell Line, Pv11
Cited by: 6
Author(s): Shoko Tokumoto, Yugo Miyata, Ruslan Deviatiiarov, Takahiro Yamada, Yusuke Hiki, О. С. Козлова, Yuki Yoshida, Richard Cornette, Akira Funahashi, Elena Shagimardanova, Oleg Gusev, Takahiro Kikawada
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-66986-8

ssGSEA score-based Ras dependency indexes derived from gene expression data reveal potential Ras addiction mechanisms with possible clinical implications
Cited by: 100
Author(s): Ming Yi, Dwight V. Nissley, Frank McCormick, Robert M. Stephens
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0251868

Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem
Cited by: 3
Author(s): Stephanie Lam, Arun Kommadath, Ó. López-Campos, Nuria Prieto, J. L. Aalhus, M. Juárez, M. E. R. Dugan, Payam Vahmani
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2019.00120

Vaccine-Induced Protection Against Furunculosis Involves Pre-emptive Priming of Humoral Immunity in Arctic Charr
Cited by: 14
Author(s): Laura M. Braden, S. K. Whyte, Alyson Brown, Carter Van Iderstine, Corinne Letendre, David B. Groman, J. Lewis, Sara L. Purcell, Tiago S. Hori, Mark D. Fast
Software Mentions: 3
Published: almost 6 years ago

10.3390/v12111320

Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1
Cited by: 9
Author(s): Maria Kornienko, Gleb Y. Fisunov, Dmitry Bespiatykh, Nikita Kuptsov, Roman Gorodnichev, Ksenia M. Klimina, Eugene E. Kulikov, Elena N. Ilina, Andrey V. Letarov, Egor Shitikov
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-65947-5

De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress
Cited by: 13
Author(s): Elham Younesi-Melerdi, Ghorbanali Nematzadeh, Ali Pakdin Parizi, Mohammad Reza Bakhtiarizadeh, Seyed Abolfazl Motahari
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2019.02016

Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4+ T Cells
Cited by: 10
Author(s): Stephanie D. Byrum, Charity L. Washam, John M. Patterson, Kanan K. Vyas, Kathleen M. Gilbert, Sarah J. Blossom
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-64938-w

Gene expression trajectories during male and female reproductive development in balsam poplar (Populus balsamifera L.)
Cited by: 10
Author(s): Quentin Cronk, Raju Soolanayakanahally, Katharina Bräutigam
Software Mentions: 3
Published: over 4 years ago

10.1186/s12974-021-02191-2

Microglia RAGE exacerbates the progression of neurodegeneration within the SOD1G93A murine model of amyotrophic lateral sclerosis in a sex-dependent manner
Cited by: 13
Author(s): Michael MacLean, Judyta K. Juranek, Swetha Cuddapah, Raquel López‐Díez, Henry H. Ruiz, Jiyuan Hu, Laura Frye, Huilin Li, Paul F. Gugger, Ann Marie Schmidt
Software Mentions: 3
Published: over 3 years ago

10.1186/s13072-017-0158-9

Genome-wide profiling of transcribed enhancers during macrophage activation
Cited by: 21
Author(s): Elena Denisenko, Reto Guler, Musa M. Mhlanga, Harukazu Suzuki, Frank Brombacher, Sebastian Schmeier
Software Mentions: 3
Published: about 7 years ago

10.1186/1746-6148-10-146

Effect of photoperiod on the feline adipose transcriptome as assessed by RNA sequencing
Cited by: 5
Author(s): Akira Mori, Kelly Kappen, A. C. Dilger, Kelly S. Swanson
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0254205

Lapatinib and poziotinib overcome ABCB1-mediated paclitaxel resistance in ovarian cancer
Cited by: 5
Author(s): Joseph R. McCorkle, J Górski, Jinpeng Liu, M.B. Riggs, Anthony McDowell, Nan Lin, Chi Wang, Frederick R. Ueland
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.37182

A selective gut bacterial bile salt hydrolase alters host metabolism
Cited by: 156
Author(s): Lina Yao, Sarah C. Seaton, Sula Ndousse-Fetter, Arijit A. Adhikari, Nicholas DiBenedetto, Amir I. Mina, Alexander S. Banks, Lynn Bry, A. Sloan Devlin
Software Mentions: 3
Published: over 6 years ago

10.1186/s13072-021-00405-8

Altered hypothalamic DNA methylation and stress-induced hyperactivity following early life stress
Cited by: 5
Author(s): Eamon Fitzgerald, Matthew C. Sinton, Sara Wernig-Zorc, Nicholas M. Morton, Megan C. Holmes, James P. Boardman, Amanda J. Drake
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-63040-5

Circulating RNA Transcriptome of Pregnant Women with TSH Just Above the Trimester-Specific Reference and its Correlation with the Hypertensive Phenotype
Cited by: 2
Author(s): Andréa Harumy de Lima Hirata, Luiz Antônio de Jesus Rocha, Valdelena Alessandra da Silva, Rafael Fernandes Almeida, Lucas dos Santos Bacigalupo, Patrícia Siqueira Varela, Leonardo Martins Silva, João Bosco Pesquero, Humberto Dellê, Cleber Camacho
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2017.00335

CD103+ CD8 T Cells in the Toxoplasma-Infected Brain Exhibit a Tissue-Resident Memory Transcriptional Profile
Cited by: 45
Author(s): Tyler Landrith, Suhas Sureshchandra, Andrea Rivera, Jessica Jang, Maham Rais, Meera G. Nair, Ilhem Messaoudi, Emma H. Wilson
Software Mentions: 3
Published: over 7 years ago

10.1016/j.isci.2021.102741

Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra syndrome
Cited by: 3
Author(s): Ayumi Yamada, Takae Hirasawa, Kayako Nishimura, Chikako Shimura, Naomi Kogo, Kei Fukuda, Madoka Kato, Masaki Yokomori, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Yoichiro Iwakura, Itoshi Nikaido, Shigeyoshi Itohara, Yoichi Shinkai
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-23858-6

Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element
Cited by: 15
Author(s): Ryo Miyazaki, Hirokazu Yano, Vladimir Sentchilo, van der Peter Meer
Software Mentions: 3
Published: over 6 years ago

10.3390/v11060513

RNASeq Analysis of Aedes albopictus Mosquito Midguts after Chikungunya Virus Infection
Cited by: 20
Author(s): Ravikiran Vedururu, Matthew J. Neave, Mary Tachedjian, Melissa J. Klein, Paul R Gorry, Jean‐Bernard Duchemin, Prasad N. Paradkar
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-23069-z

Enterobacter bugandensis: a novel enterobacterial species associated with severe clinical infection
Cited by: 46
Author(s): Niladri Bhusan Pati, Swapnil Doijad, Tilman Schultze, Gopala Krishna Mannala, Yancheng Yao, Sangeeta Jaiswal, Daniel Ryan, Mrutyunjay Suar, Konrad Gwozdzinski, Boyke Bunk, Mobarak Abu Mraheil, Mohamed A. Marahiel, Julian D. Hegemann, Cathrin Spröer, Alexander Goesmann, Linda Falgenhauer, Torsten Hain, Can Imirzalioglu, Stephen E. Mshana, Jörg Overmann, Trinad Chakraborty
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-22798-5

Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane
Cited by: 14
Author(s): Ratnesh Singh, Tyler Jones, Ching Man Wai, John Jifon, Chifumi Nagai, Ray Ming, Qingyi Yu
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-21560-1

Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources
Cited by: 40
Author(s): Sarika Jaiswal, Tushar J. Antala, M. K. Mandavia, Meenu Chopra, Rahul Singh Jasrotia, R. S. Tomar, Jashminkumar Kheni, U. B. Angadi, Mir Asif Iquebal, B. A. Golakia, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0238594

High accuracy gene expression profiling of sorted cell subpopulations from breast cancer PDX model tissue
Cited by: 1
Author(s): Warren Porter, Eileen Snowden, Friedrich Hahn, Mitchell Ferguson, Frances Tong, W. Shannon Dillmore, Rainer Blaesius
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-19871-4

Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion
Cited by: 29
Author(s): Heather Armstrong, Joanna L. Gillis, I. R. Johnson, Zeyad D. Nassar, Max Moldovan, Claire Levrier, Martin C. Sadowski, Mei Yieng Chin, Emma S. Tomlinson Guns, Gerard A. Tarulli, David J. Lynn, Doug A. Brooks, Luke A. Selth, Margaret M. Centenera, Lisa M. Butler
Software Mentions: 3
Published: almost 7 years ago

10.1515/jib-2020-0031

Differentially methylated CpG sites associated with the high-risk group of prostate cancer
Cited by: 2
Author(s): Anastasiya A. Kobelyatskaya, Elena A. Pudova, Maria Fedorova, K. M. Nyushko, B. Ya. Alekseev, А. Д. Каприн, Д. Ю. Трофимов, Г. Т. Сухих, Anastasiya V. Snezhkina, George S. Krasnov, S. V. Razin, Anna V. Kudryavtseva
Software Mentions: 3
Published: almost 4 years ago

10.3389/fimmu.2021.611656

IL-12p40/IL-23p40 Blockade With Ustekinumab Decreases the Synovial Inflammatory Infiltrate Through Modulation of Multiple Signaling Pathways Including MAPK-ERK and Wnt
Cited by: 16
Author(s): Renée H Fiechter, Henriëtte M. de Jong, Leonieke J J van Mens, Inka A. Fluri, Sander W. Tas, Dominique Baeten, Nataliya Yeremenko, Marleen G H van de Sande
Software Mentions: 3
Published: almost 4 years ago

10.3389/fimmu.2019.02484

Gut Antibody Deficiency in a Mouse Model of CVID Results in Spontaneous Development of a Gluten-Sensitive Enteropathy
Cited by: 18
Author(s): Ahmed Dawood Mohammed, M.A. Wadud Khan, Ioulia Chatzistamou, Douja Chamseddine, Katie N. Kang, Mason Perry, Reilly T. Enos, Angela Murphy, Gregorio Gomez, Ahmed Al-Adhami, Carole A. Oskeritzian, Amy Jolly, Yan Chang, Siying He, Zui Pan, Jason L. Kubinak
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-20057-1

Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency
Cited by: 17
Author(s): Naofumi Ito, K. Katoh, Hiroko Kushige, Yutaka Saitô, Terumasa Umemoto, Yu Matsuzaki, Hiroshi Kanazawa, Daiki Kobayashi, Minami Soga, Takumi Era, Nobuhito Araki, Yasuhide Furuta, Toshio Suda, Yasuyuki S. Kida, Kunimasa Ohta
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13072-019-0281-x

Phosphorylation of TET2 by AMPK is indispensable in myogenic differentiation
Cited by: 23
Author(s): Ting Zhang, Xiangying Guan, Un Lam Choi, Qiang Dong, Melody M. T. Lam, Jianming Zeng, Jun Xiong, Xianju Wang, Terence Chuen Wai Poon, Hongjie Zhang, Xuanjun Zhang, Hailin Wang, Ruiyu Xie, Bing Zhu, Gang Li
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2020.595877

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors
Cited by: 5
Author(s): Vladimir A. Veselovsky, Marina S. Dyachkova, Egor Menyailo, Polina S. Polyaeva, Evgenii I. Olekhnovich, Egor Shitikov, Dmitry Bespiatykh, Tatiana A. Semashko, Artem S. Kasianov, Elena N. Ilina, В Н Даниленко, Ksenia M. Klimina
Software Mentions: 3
Published: about 4 years ago

10.1038/s41389-021-00338-7

USP29-mediated HIF1α stabilization is associated with Sorafenib resistance of hepatocellular carcinoma cells by upregulating glycolysis
Cited by: 29
Author(s): Ruize Gao, David Buechel, Ravi Kiran Reddy Kalathur, Marco Morini, Mairene Coto‐Llerena, Caner Ercan, Salvatore Piscuoglio, Qian Chen, Tanja Blumer, Xueya Wang, Eva Dazert, Markus H. Heim, Michael N. Hall, Fengyuan Tang, Gerhard Christofori
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2018.01344

Common Features of Regulatory T Cell Specialization During Th1 Responses
Cited by: 37
Author(s): Katharina Littringer, Claudia Moresi, Nikolas Rakebrandt, Xiaobei Zhou, Michelle Schorer, Tamas Dolowschiak, Florian Kirchner, Felix Rost, Christian W. Keller, Donal McHugh, Salomé LeibundGut‐Landmann, Mark D. Robinson, Nicole Joller
Software Mentions: 3
Published: over 6 years ago

10.3389/fimmu.2020.01968

Cytoplasmic Citrate Flux Modulates the Immune Stimulatory NKG2D Ligand MICA in Cancer Cells
Cited by: 10
Author(s): Sofie Hedlund Møller, Maiken Mellergaard, Mikkel Madsen, Amaia Vergara Bermejo, Stine Dam Jepsen, Marie Haugsten Hansen, Rikke Illum Høgh, Blanca I. Aldana, Claus Desler, Lene Juel Rasmussen, Elahu G. Sustarsic, Zachary Gerhart-Hines, Evangelia Daskalaki, Craig E. Wheelock, Thomas K. Hiron, Dazhen Lin, Christopher A. O’Callaghan, Hans H. Wandall, Lars Ole Andresen, Søren Skov
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2019.01295

miRNAs Involved in M1/M2 Hyperpolarization Are Clustered and Coordinately Expressed in Alcoholic Hepatitis
Cited by: 18
Author(s): Adam Kim, Paramananda Saikia, Laura E. Nagy
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-017-17386-y

Loss of disease tolerance during Citrobacter rodentium infection is associated with impaired epithelial differentiation and hyperactivation of T cell responses
Cited by: 14
Author(s): Ellen S. Kang, Guohui Zhou, Mitra Yousefi, Romain Cayrol, Jianguo Xia, Samantha Gruenheid
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0188285

DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions
Cited by: 7
Author(s): Yoshimasa Aoto, Tsuyoshi Hachiya, Kazuhiro Okumura, Sumitaka Hase, Kengo Sato, Yuichi Wakabayashi, Yasubumi Sakakibara
Software Mentions: 3
Published: about 7 years ago

10.1186/s12974-020-02011-z

Complement peptide C3a receptor 1 promotes optic nerve degeneration in DBA/2J mice
Cited by: 27
Author(s): Jeffrey M. Harder, Pete A. Williams, Catherine E. Braine, Hongtian Yang, Jocelyn M. Thomas, Nicole E. Foxworth, Simon W. M. John, Gareth R. Howell
Software Mentions: 3
Published: about 4 years ago

10.1155/2017/2421459

Prediction and Validation of Hub Genes Associated with Colorectal Cancer by Integrating PPI Network and Gene Expression Data
Cited by: 19
Author(s): Yong Xiong, Wenxian You, Rong Wang, Linglong Peng, Zhongxue Fu
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0242665

Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice
Cited by: 12
Author(s): Tisha Melia, David J. Waxman
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-017-18128-w

Differential miRNA expression in the three-spined stickleback, response to environmental changes
Cited by: 12
Author(s): С. М. Расторгуев, Artem Nedoluzhko, Natalia Gruzdeva, Eugenia Boulygina, Fedor Sharko, Amina S. Ibragimova, Svetlana Tsygankova, Artemov Av, K. G. Skryabin, Egor Prokhortchouk
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-017-16371-9

Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa
Cited by: 9
Author(s): Jessica K. Jarett, Matthew D. MacManes, Kathleen M. Morrow, M. Sabrina Pankey, Michael P. Lesser
Software Mentions: 3
Published: about 7 years ago

10.1038/s41389-020-0204-5

Transglutaminase-2 facilitates extracellular vesicle-mediated establishment of the metastatic niche
Cited by: 79
Author(s): Aparna Shinde, Juan Sebastian Paez, Sarah Libring, Kelsey Hopkins, Luis Solorio, Michael K. Wendt
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0218858

Transcriptomes of antigen presenting cells in human thymus
Cited by: 13
Author(s): Ingvild Gabrielsen, Hanna Helgeland, Helle Akselsen, Hans Christian Dalsbotten Aass, Arvind Sundaram, Isaac Snowhite, Alberto Pugliese, Siri Tennebø Flåm, Benedicte A. Lie
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0227507

Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease
Cited by: 29
Author(s): Matthew A. Scott, Amelia R. Woolums, Cyprianna E. Swiderski, Andy D. Perkins, Bindu Nanduri, David R. Smith, Brandi B. Karisch, William B. Epperson, J. R. Blanton
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-96150-9

Transcriptomic analysis of the mouse retina after acute and chronic normobaric and hypobaric hypoxia
Cited by: 10
Author(s): Lynn J. A. Ebner, Marijana Samardzija, Federica Storti, Vyara Todorova, Duygu Karademir, Julian Behr, Fraser Simpson, Markus Thiersch, Christian Grimm
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0239938

Severity of bovine tuberculosis is associated with innate immune-biased transcriptional signatures of whole blood in early weeks after experimental Mycobacterium bovis infection
Cited by: 6
Author(s): Jayne E Wiarda, Paola M. Boggiatto, Darrell O. Bayles, W. Ray Waters, Tyler C. Thacker, Mitchell V. Palmer
Software Mentions: 3
Published: about 4 years ago

10.3389/fonc.2020.01029

Abnormal Food Timing Promotes Alcohol-Associated Dysbiosis and Colon Carcinogenesis Pathways
Cited by: 5
Author(s): Faraz Bishehsari, Shirin Moossavi, Phillip A. Engen, Xiaohan Liu, Yue Zhang
Software Mentions: 3
Published: over 4 years ago

10.3390/cells8090986

RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications
Cited by: 19
Author(s): Kai Sen Tan, Anand Kumar Andiappan, Bernett Lee, Yan Yan, Jing Liu, See Aik Tang, Josephine Lum, Ting He, Yew Kwang Ong, Mark Thong, Hui Fang Lim, Hyung-Jin Choi, Olaf Rötzschke, Vincent Chow, De Yun Wang
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2021.659201

Prognostic Prediction of Cytogenetically Normal Acute Myeloid Leukemia Based on a Gene Expression Model
Cited by: 4
Author(s): Yang Liu, Houyu Zhang, Xue Yang, Ting Lu, Shihui Ma, Hui Cheng, Kuangyu Yen, Tao Cheng
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2021.707066

Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/Differentiation Program
Cited by: 3
Author(s): Tiantian Xu, Xiao‐Wen Zeng, Xinhong Wang, Luxi Yang, Gang Luo, Ting Yu
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-36059-y

Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice
Cited by: 22
Author(s): Wayne Xu, Vichithra R. B. Liyanage, Aaron MacAulay, Romina D. Levy, Kyle Curtis, Carl O. Olson, Robby M. Zachariah, Shayan Amiri, Marjorie Buist, Geoffrey Hicks, James R. Davie, Mojgan Rastegar
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-95698-w

PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients
Cited by: 9
Author(s): Kota Fujisawa, Mamoru Shimo, Y-h. Taguchi, Shinya Ikematsu, Ryota Miyata
Software Mentions: 3
Published: over 3 years ago

10.7150/thno.44456

Cartilage Oligomeric Matrix Protein promotes epithelial-mesenchymal transition by interacting with Transgelin in Colorectal Cancer
Cited by: 57
Author(s): Weilong Zhong, Huiqin Hou, Tianyu Li, Shuai Su, Xiaonan Xi, Yusheng Liao, Runxiang Xie, Ge Jin, Xiang Liu, Lanping Zhu, Hongxia Zhang, Xueli Song, Cheng Yang, Tao Sun, Hailong Cao, Bangmao Wang
Software Mentions: 3
Published: almost 5 years ago

10.3390/cells10092376

Transcriptomic Response Dynamics of Human Primary and Immortalized Adrenocortical Cells to Steroidogenic Stimuli
Cited by: 4
Author(s): Kimberly Wellman, Rui Fu, Amber Baldwin, Juilee Rege, Elisabeth Murphy, William E. Rainey, Neelanjan Mukherjee
Software Mentions: 3
Published: over 3 years ago

10.3390/cells10030635

Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana
Cited by: 12
Author(s): Ruchika, Chisato Okudaira, Matomo Sakari, Toshifumi Tsukahara
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-018-33807-y

Characterization of the miRNA regulators of the human ovulatory cascade
Cited by: 23
Author(s): Gil M. Yerushalmi, Mali Salmon‐Divon, Libby Ophir, Yuval Yung, Micha Baum, Giovanni Coticchio, Rubens Fadini, Mario Mignini-Renzini, Mariabeatrice Dal Canto, Ronit Machtinger, Ettie Maman, Ariel Hourvitz
Software Mentions: 3
Published: about 6 years ago

10.3390/cells10092289

Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch
Cited by: 1
Author(s): Julien Alban Nguinkal, Marieke Verleih, Lidia de los Ríos-Pérez, Ronald M. Brunner, Arne Sahm, Saptarshi Bej, Alexander Rebl, Tom Goldammer
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2020.01765

Identification of TYROBP and C1QB as Two Novel Key Genes With Prognostic Value in Gastric Cancer by Network Analysis
Cited by: 26
Author(s): Junjie Jiang, Yongfeng Ding, Mengjie Wu, Xiadong Lyu, Haifeng Wang, Yanyan Chen, Haiyong Wang, Lisong Teng
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.ppat.1008655

Contained Mycobacterium tuberculosis infection induces concomitant and heterologous protection
Cited by: 27
Author(s): Johannes Nemeth, Gregory S. Olson, Alissa C. Rothchild, Ana N. Jahn, Dat Mai, Fergal J. Duffy, Jared L. Delahaye, Sanjay Srivatsan, Courtney R. Plumlee, Kevin B. Urdahl, Elizabeth S. Gold, Alan Aderem, A. Diercks
Software Mentions: 3
Published: over 4 years ago

10.3389/fnins.2019.00297

Regeneration Enhances Metastasis: A Novel Role for Neurovascular Signaling in Promoting Melanoma Brain Metastasis
Cited by: 13
Author(s): Roshini Prakash, Sivan Izraely, Nikita S. Thareja, Rex H. Lee, Maya Rappaport, Riki Kawaguchi, Orit Sagi‐Assif, Shlomit Ben‐Menachem, Tsipi Meshel, Michał Machnicki, Shuichi Ohe, Dave S. B. Hoon, Giovanni Coppola, Isaac P. Witz, S. Thomas Carmichael
Software Mentions: 3
Published: over 5 years ago

10.1002/pld3.240

Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater
Cited by: 10
Author(s): Rejbana Alam, Maureen Hummel, Euson Yeung, Anna M. Locke, John Carlos I. Ignacio, Miriam D. Baltazar, Zhenyu Jia, Ismail Am, Endang M. Septiningsih, Julia Bailey‐Serres
Software Mentions: 3
Published: over 4 years ago

10.1186/s13020-020-00339-5

Identification of drug targets and potential molecular mechanisms for Wantong Jingu Tablet extract in treatment of rheumatoid arthritis: bioinformatics analysis of fibroblast-like synoviocytes
Cited by: 6
Author(s): Zhaodong Li, Fanghua Qi, Fan Li
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms21030861

Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways
Cited by: 21
Author(s): Yingdan Yuan, Bo Zhang, Xinggang Tang, Jinchi Zhang, Jie Lin
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.ppat.1008407

Chemical intervention of influenza virus mRNA nuclear export
Cited by: 10
Author(s): Matthew A. Esparza, Amir Mor, Hanspeter Niederstrasser, Kris M. White, Alexander D. White, Ke Zhang, Shengyan Gao, Juan Wang, Jue Liang, Sei Sho, Ramanavelan Sakthivel, Adwait Amod Sathe, Chao Xing, Raquel Muñoz-Moreno, Jerry W. Shay, Adolfo Garcı́a-Sastre, Joseph M. Ready, Bruce A. Posner, Beatriz M. A. Fontoura
Software Mentions: 3
Published: over 4 years ago

10.1186/s13148-020-00980-9

Developmental programming in human umbilical cord vein endothelial cells following fetal growth restriction
Cited by: 8
Author(s): Fieke Terstappen, Jorg J.A. Calis, Nina D. Paauw, Jaap A. Joles, Bas B. van Rijn, Michal Mokrý, Torsten Plösch, A. Titia Lely
Software Mentions: 3
Published: about 4 years ago

10.1186/s13148-018-0451-x

Integrative analysis of the epigenetic basis of muscle-invasive urothelial carcinoma
Cited by: 20
Author(s): Thomas Sanford, Maxwell V. Meng, Reema Railkar, Piyush K. Agarwal, Sima P. Porten
Software Mentions: 3
Published: almost 7 years ago

10.1155/2018/2465481

RNA Sequencing for Gene Expression Profiles in a Rat Model of Middle Cerebral Artery Occlusion
Cited by: 7
Author(s): Xianchun Duan, Jianghua Gan, Fan Xu, Lili Li, Lei Han, Can Peng, Qiuyu Bao, Ling Xiao, Daiyin Peng
Software Mentions: 3
Published: about 6 years ago

10.1186/s13148-020-00916-3

The fusiform gyrus exhibits an epigenetic signature for Alzheimer’s disease
Cited by: 11
Author(s): Dingailu Ma, Irfete S. Fetahu, Mei Wang, Rui Fang, Jia-hui Li, Huan Liu, Tobin Gramyk, Isabella Iwanicki, Sophie Zhaotao Gu, Winnie Xu, Li Tan, Feizhen Wu, Yujiang Geno Shi
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms17101749

Transcriptome Sequencing and De Novo Assembly of Golden Cuttlefish Sepia esculenta Hoyle
Cited by: 14
Author(s): Changlin Liu, Fazhen Zhao, Jing Yan, Chunsheng Liu, Siwei Liu, Siqing Chen
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.ppat.1008206

Stress keratin 17 enhances papillomavirus infection-induced disease by downregulating T cell recruitment
Cited by: 22
Author(s): Wei Wang, Aayushi Uberoi, Megan E. Spurgeon, Ellery Gronski, Vladimır Majerčiak, Alexei V. Lobanov, Mitchell Hayes, Amanda S. W. Loke, Zhi-Ming Zheng, Paul F. Lambert
Software Mentions: 3
Published: almost 5 years ago

10.3390/plants9111522

Screening of Salt Stress Responsive Genes in Brachypodium distachyon (L.) Beauv. by Transcriptome Analysis
Cited by: 6
Author(s): Xiaocheng Guo, Qingjun Wang, Yuan Liu, Xuejie Zhang, Luoyan Zhang, Shoujin Fan
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.ppat.1007626

A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema
Cited by: 52
Author(s): Dennis Chang, Lorrayne Serra, Dihong Lu, A Mortazavi, Adler R. Dillman
Software Mentions: 3
Published: over 5 years ago

10.1186/s13148-020-00955-w

Morphine leads to global genome changes in H3K27me3 levels via a Polycomb Repressive Complex 2 (PRC2) self-regulatory mechanism in mESCs
Cited by: 4
Author(s): Iraia Muñoa-Hoyos, John Halsall, Manu Araolaza, Carl Ward, Idoia García, Itziar Urizar-Arenaza, Marta Gianzo Citores, Paloma García, Bryan M. Turner, Nerea Subirán
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms21010364

Global Gene Expression Analysis Identifies Age-Related Differences in Knee Joint Transcriptome during the Development of Post-Traumatic Osteoarthritis in Mice
Cited by: 25
Author(s): Aimy Sebastian, Deepa K. Murugesh, Melanie E. Mendez, Nicholas R. Hum, Naiomy Deliz Rios‐Arce, Jillian L. McCool, Blaine A. Christiansen, Gabriela G. Loots
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.ppat.1006033

Resolving host–pathogen interactions by dual RNA-seq
Cited by: 201
Author(s): Alexander J. Westermann, Lars Barquist, Jörg Vogel
Software Mentions: 3
Published: almost 8 years ago

10.3389/fonc.2020.00215

A Novel Long Non-coding RNA, MSTRG.51053.2 Regulates Cisplatin Resistance by Sponging the miR-432-5p in Non-small Cell Lung Cancer Cells
Cited by: 24
Author(s): Jie Zhang, Chuanqin Xu, Y Gao, Yi Wang, Zongli Ding, Yueming Zhang, Wenyi Shen, Yulong Zheng, Yufeng Wan
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-98420-y

Short-term transcriptomic response to plasma membrane injury
Cited by: 3
Author(s): Swantje Christin Häger, Catarina Dias, Stine Lauritzen Sønder, André Vidas Olsen, Isabelle da Piedade, Anne Sofie Busk Heitmann, Elena Papaleo, Jesper Nylandsted
Software Mentions: 3
Published: about 3 years ago

10.7150/thno.46642

Precise and efficient silencing of mutant KrasG12D by CRISPR-CasRx controls pancreatic cancer progression
Cited by: 26
Author(s): Wang Jiang, Hao Li, Xiyu Liu, Jianping Zhang, Wuhu Zhang, Tianjiao Li, Liang Liu, Xianjun Yu
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13148-021-01043-3

Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations
Cited by: 14
Author(s): Jiayi Pei, Maike Schuldt, Emília Nagyová, Zhujie Gu, Said el Bouhaddani, Loukia Yiangou, Manon A. A. Jansen, Jorg J.A. Calis, Larissa M. Dorsch, Christian Snijders Blok, Noortje A.M. van den Dungen, Nico Lansu, Bastiaan J. Boukens, Igor R. Efimov, Michelle Michels, Marianne C. Verhaar, Roel de Weger, Aryan Vink, Frank G. van Steenbeek, Annette F. Baas, Richard P. Davis, Hae‐Won Uh, Diederik W.D. Kuster, Caroline Cheng, Michal Mokrý, Jolanda van der Velden, Folkert W. Asselbergs, Magdaléna Harakaľová
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2017.01784

Analyzing the Complex Regulatory Landscape of Hfq – an Integrative, Multi-Omics Approach
Cited by: 14
Author(s): Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V. Galmozzi, Günter Krämer, Jacob G. Malone
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.ppat.1005841

The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing
Cited by: 144
Author(s): Federico A. De Maio, Guillermo Risso, Néstor Gabriel Iglesias, Priya S. Shah, Berta Pozzi, Leopoldo Germán Gebhard, Pablo Mammi, Estefanía Mancini, Marcelo J. Yanovsky, Raul Andino, Nevan J. Krogan, Anabella Srebrow, Andrea V. Gamarnik
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms20236090

Disclosure of the Molecular Mechanism of Wheat Leaf Spot Disease Caused by Bipolaris sorokiniana through Comparative Transcriptome and Metabolomics Analysis
Cited by: 21
Author(s): Wei Ye, Taomei Liu, Weiyang Zhang, Saini Li, Muzi Zhu, Haohua Li, Yali Kong, Luoshan Xu
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.ppat.1005211

Fundamental Roles of the Golgi-Associated Toxoplasma Aspartyl Protease, ASP5, at the Host-Parasite Interface
Cited by: 101
Author(s): Pierre‐Mehdi Hammoudi, Damien Jacot, Christina Mueller, Manlio Di Cristina, Sunil Kumar Dogga, Jean Baptiste Marq, Julia D. Romano, Nicolò Tosetti, Juan Dubrot, Yalin Emre, Matteo Lunghi, Isabelle Coppens, Masahiro Yamamoto, Daniel Sojka, Paco Pino, Dominique Soldati‐Favre
Software Mentions: 3
Published: about 9 years ago

10.1186/s13148-018-0508-x

H3K27 acetylation and gene expression analysis reveals differences in placental chromatin activity in fetal growth restriction
Cited by: 39
Author(s): Nina D. Paauw, A. Titia Lely, Jaap A. Joles, Arie Franx, Floris Groenendaal, Michal Mokrý, Bas B. van Rijn
Software Mentions: 3
Published: over 6 years ago

10.1042/BSR20202463

Explore prognostic biomarker of bladder cancer based on competing endogenous network
Cited by: 6
Author(s): Faping Li, Hui Guo, Bin Liu, Nian Liu, Zhixiang Xu, Yishu Wang, Honglan Zhou
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0083504

RNA Sequencing of the Exercise Transcriptome in Equine Athletes
Cited by: 43
Author(s): Stefano Capomaccio, Nicola Vitulo, Andrea Verini-Supplizi, Gianni Barcaccia, Alessandro Albiero, Michela D’Angelo, Davide Campagna, Giorgio Valle, Michela Felicetti, Maurizio Silvestrelli, Katia Cappelli
Software Mentions: 3
Published: almost 11 years ago

10.3390/ijms20225724

A Comparative Analysis of Edwardsiella tarda-Induced Transcriptome Profiles in RAW264.7 Cells Reveals New Insights into the Strategy of Bacterial Immune Evasion
Cited by: 16
Author(s): Huili Li, Bo Sun, Xianhui Ning, Shuai Jiang, Li Sun
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-32579-9

ADIPOR1 is essential for vision and its RPE expression is lost in the Mfrprd6 mouse
Cited by: 32
Author(s): Valentin M. Sluch, Angela Banks, Hui Li, Maura Crowley, Vanessa Davis, Chuanxi Xiang, Junzheng Yang, John Demirs, Joanna Vrouvlianis, Barrett Leehy, Shawn Hanks, Alexandra M. Hyman, Jorge Aranda, Bo Chang, Chad E. Bigelow, Dennis S. Rice
Software Mentions: 3
Published: about 6 years ago

10.1155/2021/6633289

A Robust Circular RNA-Associated Three-Gene Prognostic Signature for Patients with Gastric Cancer
Cited by: 2
Author(s): Li Yang, Rui Li, Xiuli Wang, Yuan Yuan, Yangmei Zhang
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2019.01914

Soil Metatranscriptomes Under Long-Term Experimental Warming and Drying: Fungi Allocate Resources to Cell Metabolic Maintenance Rather Than Decay
Cited by: 28
Author(s): Adriana L. Romero‐Olivares, Germán Meléndrez-Carballo, Asunción Lago‐Lestón, Kathleen K. Treseder
Software Mentions: 3
Published: over 5 years ago

10.1186/s13068-021-01880-7

CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate
Cited by: 14
Author(s): Friederike Gutmann, Cosimo Jann, Filipa Pereira, Anders Johansson, Lars M. Steinmetz, Kiran Raosaheb Patil
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.ppat.1003341

Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy
Cited by: 132
Author(s): Michael J. Strong, Guiyin Xu, Joseph Coco, Carl Baribault, Dass S. Vinay, Michelle Lacey, Amy L. Strong, Teresa A. Lehman, Michael Seddon, Zhen Lin, Monica Concha, Melody Baddoo, MaryBeth Ferris, Kenneth F. Swan, Deborah E. Sullivan, Matthew E. Burow, Christopher M. Taylor, Erik K. Flemington
Software Mentions: 3
Published: over 11 years ago

10.3389/fmicb.2018.00445

Comparative mRNA-Seq Analysis Reveals the Improved EPS Production Machinery in Streptococcus thermophilus ASCC 1275 During Optimized Milk Fermentation
Cited by: 25
Author(s): Qinglong Wu, Nagendra P. Shah
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0135143

Large-Scale Transcriptome Analysis in Faba Bean (Vicia faba L.) under Ascochyta fabae Infection
Cited by: 39
Author(s): Sara Ocaña, Pedro Seoane, Rocío Bautista, Carmen Palomino, M. Gonzalo Claros, A. M. Torres, Eva Madrid
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0074912

Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Gba1 Mutant Mouse Model Treated with Velaglucerase alfa or Imiglucerase
Cited by: 17
Author(s): Nupur Dasgupta, You-Hai Xu, Sangwon Oh, Ying Sun, Jia Li, Mehdi Keddache, Gregory A. Grabowski
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0256319

Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening
Cited by: 4
Author(s): Fernando G. Razo-Mendivil, Fernando Hernández-Godínez, Corina Hayano-Kanashiro, Octavio Martínez
Software Mentions: 3
Published: over 3 years ago

10.1155/2020/3040839

The Oncogenic Role of CENPA in Hepatocellular Carcinoma Development: Evidence from Bioinformatic Analysis
Cited by: 17
Author(s): Yuan Zhang, Lei Yang, Jia Shi, Yao Lu, Xiaorong Chen, Zongguo Yang
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-88029-6

Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn & Fayoumi)
Cited by: 4
Author(s): Venkata Krishna Vanamamalai, Priyanka Garg, Gautham Kolluri, Ravi Kumar Gandham, Itishree Jali, Shailesh Sharma
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-87955-9

Induced pluripotent stem cells from subjects with Lesch-Nyhan disease
Cited by: 5
Author(s): Diane Sutcliffe, Ashok R. Dinasarapu, Jasper E. Visser, Joery den Hoed, Fatemeh Seifar, Piyush Joshi, Irène Ceballos-Picot, Tejas Sardar, Ellen J. Hess, Yan V. Sun, Zhexing Wen, Michael E. Zwick, Hyder A. Jinnah
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1002968

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State
Cited by: 199
Author(s): Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, J Stamatoyannopoulos, Jason Ernst, M Kellis, Bing Ren
Software Mentions: 3
Published: almost 12 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568