bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-017-08239-9

The Candida albicans HIR histone chaperone regulates the yeast-to-hyphae transition by controlling the sensitivity to morphogenesis signals
Cited by: 17
Author(s): Sabrina Jenull, Michael Tscherner, Megha Gulati, Clarissa J. Nobile, Neeraj Chauhan, Karl Kuchler
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-09963-y

Infection with the Makona variant results in a delayed and distinct host immune response compared to previous Ebola virus variants
Cited by: 30
Author(s): Krista Versteeg, Andrea Menicucci, Courtney Woolsey, Chad E. Mire, Joan B. Geisbert, Robert W. Cross, Krystle N. Agans, Daniel R. Jeske, Ilhem Messaoudi, Thomas W. Geisbert
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-10648-9

Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I:C
Cited by: 31
Author(s): Haifei Wang, Jiying Wang, Chao Ning, Xianrui Zheng, Jinlian Fu, Aiguo Wang, Qin Zhang, Jianfeng Liu
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-11237-6

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer
Cited by: 162
Author(s): Rachel Purcell, Tina Visnovska, Patrick J. Biggs, Sebastian Schmeier, Frank Frizelle
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-11379-7

RNA-seq analysis of the kidneys of broiler chickens fed diets containing different concentrations of calcium
Cited by: 12
Author(s): Woncheoul Park, Deivendran Rengaraj, Dong Yong Kil, Heebal Kim, Hak-Kyo Lee, Ki Duk Song
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-13012-z

Global misregulation of genes largely uncoupled to DNA methylome epimutations characterizes a congenital overgrowth syndrome
Cited by: 30
Author(s): Zhiyuan Chen, Darren E. Hagen, Tieming Ji, Christine G. Elsik
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-13176-8

Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans
Cited by: 11
Author(s): Sabrina Simon, Sven Sagasser, Edoardo Saccenti, Mercer R. Brugler, Heike Hadrys, George Amato, Rob DeSalle
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-14083-8

Profiling of miRNAs and target genes related to cystogenesis in ADPKD mouse models
Cited by: 32
Author(s): Yu Mi Woo, Do Yeon Kim, Nam Jin Koo, Yong Min Kim, Sun Young Lee, Je Yeong Ko, Yubin Shin, Bo Hye Kim, Hyowon Mun, Seonju Choi, Eun Ji Lee, Jeong Oh Shin, Eun Young Park, Jinwoong Bok, Jong Hoon Park
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-14418-5

Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis
Cited by: 10
Author(s): Emiko Yoshida, Yasuhisa Terao, Noriko Hayashi, Kaoru Mogushi, Atsushi Arakawa, Yuji Tanaka, Yoshiaki Ito, Hiroko Ohmiya, Yoshihide Hayashizaki, Satoru Takeda, Masayoshi Itoh, Hideya Kawaji
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-14905-9

Sex differentiation in grayling (Salmonidae) goes through an all-male stage and is delayed in genetic males who instead grow faster
Cited by: 13
Author(s): Diane Maitre, Oliver Selmoni, Anshu Uppal, Lucas Marques da Cunha, Laetitia G. E. Wilkins, Julien Roux, Kenyon B. Mobley, Isabelle Castro, Susanne Knörr, Marc Robinson‐Rechavi, Claus Wedekind
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-15061-w

The comprehensive expression analysis of circular RNAs in gastric cancer and its association with field cancerization
Cited by: 28
Author(s): Amanda Ferreira Vidal, Ândrea Ribeiro-dos-Santos, Tatiana Vinasco-Sandoval, Leandro Magalhães, Pablo Pinto, Ana Karyssa Mendes Anaissi, Sâmia Demachki, Paulo Pimentel de Assumpção, Sidney Emanuel Batista dos Santos
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-15420-7

Transcriptomic and epigenetic responses to short-term nutrient-exercise stress in humans
Cited by: 47
Author(s): Rhianna C. Laker, Christian Garde, Donny M. Camera, William J. Smiles, Juleen R. Zierath, John A. Hawley, Romain Barrès
Software Mentions: 3
Published: almost 9 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: almost 9 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: over 8 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: over 8 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: over 8 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: over 8 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: over 8 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: over 8 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 8 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 8 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 6 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 6 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: about 6 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: about 6 years ago

10.1038/s41598-020-67482-9

miRNA–mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome
Cited by: 20
Author(s): Yifan Liu, Ming Zhang, Yanju Shan, Gaige Ji, Xiaojun Ju, Yan Tu, Zhongwei Sheng, Jing Xie, Jianmin Zou, Shu JingTing
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-67513-5

Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM
Cited by: 50
Author(s): Marcus Alvarez, Elior Rahmani, Brandon Jew, Kristina M. Garske, Min‐Hua Zong, Jihane N. Benhammou, Chun Jimmie Ye, Joseph R. Pisegna, Kirsi H. Pietiläinen, Eran Halperin, Päivi Pajukanta
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-68187-9

Prostate cancer-derived holoclones: a novel and effective model for evaluating cancer stemness
Cited by: 9
Author(s): Louise Flynn, Martin P. Barr, Anne‐Marie Baird, Paul Smyth, Órla Casey, Gordon Blackshields, John Greene, Stephen R. Pennington, Emily Hams, Padraic G. Fallon, John O’Leary, Orla Sheils, Stephen Finn
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-67588-0

Glomerular endothelial cell heterogeneity in Alport syndrome
Cited by: 8
Author(s): Hasmik Soloyan, Matthew E. Thornton, Valentina Villani, Patrick Khatchadourian, Paolo Cravedi, Andrea Angeletti, Brendan H. Grubbs, Roger De Filippo, Laura Perin, Sargis Sedrakyan
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-71210-8

Exploring the genetic basis of fatty liver development in geese
Cited by: 3
Author(s): Yu Yang, Huiying Wang, Guangquan Li, Yi Liu, Cui Wang, Daqian He
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-71527-4

A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy
Cited by: 17
Author(s): Mukesh Kumar, Elena Papaleo
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-73694-w

Rewiring of gene expression in circulating white blood cells is associated with pregnancy outcome in heifers (Bos taurus)
Cited by: 14
Author(s): Sarah E. Moorey, Bailey N. Walker, Michelle F Elmore, J. Bradford Elmore, Soren P. Rodning, Fernando H. Biase
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-76688-w

Identification of immune-related genes as prognostic factors in bladder cancer
Cited by: 12
Author(s): Jie Zhu, Han Wang, Ting Ma, Yan He, Meng‐Ru Shen, Wei Song, Jingjing Wang, Jianping Shi, Mengyao Wu, Chao Liu, Wenjie Wang, Yongzhen Huang
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-77105-y

Deep phenotyping of myalgic encephalomyelitis/chronic fatigue syndrome in Japanese population
Cited by: 16
Author(s): Toshimori Kitami, Sanae Fukuda, Tamotsu Kato, Kouzi Yamaguti, Yasuhito Nakatomi, Emi Yamano, Yosky Kataoka, Kei Mizuno, Yuuri Tsuboi, Yasushi Kogo, Harukazu Suzuki, Masayoshi Itoh, M. Morioka, Hideya Kawaji, Haruhiko Koseki, Jun Kikuchi, Yoshihide Hayashizaki, Hiroshi Ohno, Hirohiko Kuratsune, Yasuyoshi Watanabe
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-76762-3

Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203
Cited by: 7
Author(s): Juansheng Ren, Fan Zhang, Fangyuan Gao, Lihua Zeng, Xianjun Lu, Xiuqin Zhao, Jian Lv, Xiangwen Su, Liping Liu, Mingli Dai, Jianlong Xu, Guangjun Ren
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-77402-6

Mycosporine-like amino acid and aromatic amino acid transcriptome response to UV and far-red light in the cyanobacterium Chlorogloeopsis fritschii PCC 6912
Cited by: 16
Author(s): Carole A. Llewellyn, Carolyn Greig, Alla Silkina, Bethan Kultschar, Matthew D. Hitchings, Garry Farnham
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-80065-y

Transcriptomics analysis for the identification of potential age-related genes and cells associated with three major urogenital cancers
Cited by: 3
Author(s): Jinlong Cao, Jianpeng Li, Xin Yang, Pan Li, Zhiqiang Yao, Dali Han, Lijun Ying, Lijie Wang, Junqiang Tian
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-81085-y

Early stability and late random tumor progression of a HER2-positive primary breast cancer patient-derived xenograft
Cited by: 6
Author(s): Lorena Landuzzi, Arianna Palladini, Claudio Ceccarelli, Sofia Asioli, Giordano Nicoletti, Veronica Giusti, Francesca Ruzzi, Marianna L. Ianzano, Laura Scalambra, Roberta Laranga, Tania Balboni, Maddalena Arigoni, Martina Olivero, Raffaele Calogero, Carla De Giovanni, Massimiliano Dall’Ora, Enrico Di Oto, Donatella Santini, Maria Pia Foschini, M.C. Cucchi, Simone Zanotti, Mario Taffurelli, Patrizia Nanni, Pier‐Luigi Lollini
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-81639-0

Loss of Parkinson’s susceptibility gene LRRK2 promotes carcinogen-induced lung tumorigenesis
Cited by: 21
Author(s): Chandra B. Lebovitz, Nicole Wretham, Maryam Osooly, Katy Milne, Tia Dash, Shelby Thornton, Basile Tessier‐Cloutier, Paalini Sathiyaseelan, Svetlana Bortnik, Nancy E. Go, Elizabeth C. Halvorsen, Rachel A. Cederberg, Norman S. Chow, Nancy Dos Santos, Kevin L. Bennewith, Brad H. Nelson, Marcel B. Bally, Wan L. Lam, Sharon M. Gorski
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-84080-5

Persistent COUP-TFII expression underlies the myopathy and impaired muscle regeneration observed in resistance to thyroid hormone-alpha
Cited by: 1
Author(s): Paola Aguiari, Yanyun Liu, Astgik Petrosyan, Sheue-yann Cheng, Gregory A. Brent, Laura Perin, Anna Milanesi
Software Mentions: 3
Published: over 5 years ago

10.1038/s41396-020-0693-4

Changes in the transcriptome, ploidy, and optimal light intensity of a cryptomonad upon integration into a kleptoplastic dinoflagellate
Cited by: 10
Author(s): Ryo Onuma, Shunsuke Hirooka, Yu Kanesaki, Takayuki Fujiwara, Hideki Yoshikawa, Shin-ya Miyagishima
Software Mentions: 3
Published: about 6 years ago

10.1038/s41396-017-0039-z

Identifying metabolic pathways for production of extracellular polymeric substances by the diatom Fragilariopsis cylindrus inhabiting sea ice
Cited by: 34
Author(s): Shazia Aslam, Jan Strauss, David N. Thomas, Thomas Möck, Graham J. C. Underwood
Software Mentions: 3
Published: over 8 years ago

10.7150/ijbs.49243

Deciphering the genomic and lncRNA landscapes of aerobic glycolysis identifies potential therapeutic targets in pancreatic cancer
Cited by: 14
Author(s): Lili Zhu, Zheng Wu, Rongkun Li, Xin Xing, Yongsheng Jiang, Jun Li, Yahui Wang, Li-Peng Hu, Xu Wang, Weiting Qin, Yongwei Sun, Zhigang Zhang, Qin Yang, Shu‐Heng Jiang
Software Mentions: 3
Published: over 5 years ago

10.7150/ijbs.57802

Downregulation of ACE2 expression by SARS-CoV-2 worsens the prognosis of KIRC and KIRP patients via metabolism and immunoregulation
Cited by: 14
Author(s): Qian Tang, Yue Wang, Ling Ou, Jieling Li, Kai Zheng, Hui Zhan, Jiayu Gu, Guibao Zhou, Shouqi Xie, Jianping Zhang, Wei Huang, Shaoxiang Wang, Wang Xiao
Software Mentions: 3
Published: over 5 years ago

10.1186/s13046-019-1239-3

RETRACTED ARTICLE: Down-regulated lncRNA DLX6-AS1 inhibits tumorigenesis through STAT3 signaling pathway by suppressing CADM1 promoter methylation in liver cancer stem cells
Cited by: 64
Author(s): Dongmei Wu, Zihui Zheng, Yingbo Zhang, Shao‐Hua Fan, Zi-Feng Zhang, Yongjian Wang, Yuxin Zheng, Jun Lü
Software Mentions: 3
Published: about 7 years ago

10.1002/jev2.12110

Extracellular Vesicle Capture by AnTibody of CHoice and Enzymatic Release (EV‐CATCHER): A customizable purification assay designed for small‐RNA biomarker identification and evaluation of circulating small‐EVs
Cited by: 23
Author(s): Megan I. Mitchell, Iddo Z. Ben‐Dov, Christina Liu, Kenny Ye, Kar Fai Chow, Y.G. Kramer, Anju Gangadharan, Steven Park, Sean Fitzgerald, Andrew Ramnauth, David S. Perlin, Michèle Donato, Emily Bhoy, Ehsan Manouchehri Doulabi, Michael G. Poulos, Masood Kamali‐Moghaddam, Olivier Loudig
Software Mentions: 3
Published: about 5 years ago

10.1002/ijc.33270

Association between breast cancer risk and disease aggressiveness: Characterizing underlying gene expression patterns
Cited by: 2
Author(s): Emilio Ugalde-Morales, Felix Graßmann, Keith Humphreys, Jingmei Li, Mikael Eriksson, Nicholas P. Tobin, Åke Borg, Johan Vallon‐Christersson, Per Hall, Kamila Czene
Software Mentions: 3
Published: almost 6 years ago

10.3390/jof6040311

Transcriptional Remodeling Patterns in Murine Dendritic Cells Infected with Paracoccidioides brasiliensis: More Is Not Necessarily Better
Cited by: 1
Author(s): Calliandra Maria de-Souza-Silva, Fabián Andrés Hurtado, Aldo Henrique Tavares, Getúlio Pereira de Oliveira Júnior, Tainá Raiol, Christiane Nishibe, Daniel Paiva Agustinho, Nalvo F. Almeida, Maria Tereza Machado Teles Walter, André Moraes Nicola, Anamélia Lorenzetti Bocca, Patrícia Albuquerque, Ildinete Silva-Pereira
Software Mentions: 3
Published: almost 6 years ago

10.1099/jgv.0.000744

Differentially expressed genes during spontaneous lytic switch of Marek's disease virus in lymphoblastoid cell lines determined by global gene expression profiling
Cited by: 9
Author(s): William Mwangi, Deepali Vasoya, Lydia Kgosana, Michael Watson, Venugopal Nair
Software Mentions: 3
Published: over 9 years ago

10.1155/2021/3984463

Identification of Potential lncRNAs and miRNAs as Diagnostic Biomarkers for Papillary Thyroid Carcinoma Based on Machine Learning
Cited by: 14
Author(s): Fei Yang, Jie Zhang, Baokun Li, Zhao Zhi-gang, Yan Liu, Zhen Zhao, Jing Shao, Guiying Wang
Software Mentions: 3
Published: about 5 years ago

10.1155/2017/8027626

Transcriptome Analysis of Two Different Developmental Stages of <i>Paeonia lactiflora</i> Seeds
Cited by: 7
Author(s): Yong-Lei Ma, Jinqiu Cui, Xiujun Lu, Lijie Zhang, Zhijing Chen, Riwen Fei, Xiulan Sun
Software Mentions: 3
Published: over 9 years ago

10.1186/s13045-021-01155-6

Combine and conquer: manganese synergizing anti-TGF-β/PD-L1 bispecific antibody YM101 to overcome immunotherapy resistance in non-inflamed cancers
Cited by: 46
Author(s): Ming Yi, Mengke Niu, Jing Zhang, Shiyu Li, Shuangli Zhu, Yongxiang Yan, Ning Li, Pengfei Zhou, Qian Chu, Kongming Wu
Software Mentions: 3
Published: almost 5 years ago

10.4049/jimmunol.1901072

CXCR3 Identifies Human Naive CD8+ T Cells with Enhanced Effector Differentiation Potential
Cited by: 30
Author(s): Gabriele De Simone, Emilia Maria Cristina Mazza, Antonino Cassotta, Alexey N. Davydov, Mirela Kuka, Veronica Zanon, Fédérica De Paoli, Eloise Scamardella, Maria Metsger, Alessandra Roberto, Karolina Pilipow, Federico Colombo, Elena Tenedini, Enrico Tagliafico, Luca Gattinoni, Domenico Mavilio, Clelia Peano, David A. Price, Satya P. Singh, Joshua M. Farber, Valentina Serra, Francesco Cucca, Francesco Ferrari, Valeria Orrù, Edoardo Fiorillo, Matteo Iannacone, Dmitriy M. Chudakov, Federica Sallusto, Enrico Lugli
Software Mentions: 3
Published: over 6 years ago

10.1038/s41388-019-0845-z

The protein secretion modulator TMED9 drives CNIH4/TGFα/GLI signaling opposing TMED3-WNT-TCF to promote colon cancer metastases
Cited by: 34
Author(s): Sasmita Mishra, Carolina Bernal, Marianna Silvano, Santosh Anand, Ariel Ruiz i Altaba
Software Mentions: 3
Published: about 7 years ago

10.1038/s41388-020-01435-4

The proapoptotic gene interferon regulatory factor-1 mediates the antiproliferative outcome of paired box 2 gene and tamoxifen
Cited by: 2
Author(s): Shixiong Wang, Venkata S. Somisetty, Baoyan Bai, Igor Chernukhin, Henri Niskanen, Minna U. Kaikkonen, Meritxell Bellet, Jason S. Carroll, Antoni Hurtado
Software Mentions: 3
Published: about 6 years ago

10.1038/s41389-018-0083-1

The FAK inhibitor BI 853520 exerts anti-tumor effects in breast cancer
Cited by: 49
Author(s): Stefanie Tiede, Nathalie Meyer-Schaller, Ravi Kiran Reddy Kalathur, Robert Ivánek, Ernesta Fagiani, Philip Schmassmann, Patrick Stillhard, Simon Häfliger, Norbert Kraut, Norbert Schweifer, Irene C. Waizenegger, Ruben Bill, Gerhard Christofori
Software Mentions: 3
Published: almost 8 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: over 6 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: about 5 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: over 5 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: about 8 years ago

10.3390/ijms21218269

ITGA6+ Human Testicular Cell Populations Acquire a Mesenchymal Rather than Germ Cell Transcriptional Signature during Long-Term Culture
Cited by: 1
Author(s): Robert B. Struijk, Callista L Mulder, Saskia K.M. van Daalen, Cindy M de Winter-Korver, Aldo Jongejan, Sjoerd Repping, Ans M.M. van Pelt
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms21228430

Complementary Transcriptome and Proteome Analyses Provide Insight into the Floral Transition in Bamboo (Dendrocalamus latiflorus Munro)
Cited by: 3
Author(s): Xiaoyan Wang, Yujiao Wang, Guoqian Yang, Lei Zhao, Xuemei Zhang, Li D, Zhenhua Guo
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms21239198

Multi-Omics Analysis Provides Novel Insight into Immuno-Physiological Pathways and Development of Thermal Resistance in Rainbow Trout Exposed to Acute Thermal Stress
Cited by: 18
Author(s): HyeongJin Roh, Ahran Kim, Nameun Kim, Yoonhang Lee, Do-Hyung Kim
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22031252

Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean
Cited by: 7
Author(s): Jamie A. O’Rourke, Michelle A. Graham
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22083982

The MarR-Type Regulator PA3458 Is Involved in Osmoadaptation Control in Pseudomonas aeruginosa
Cited by: 10
Author(s): Karolina Kotecka, Adam Kawałek, Kamil Kobyłecki, Aneta Agnieszka Bartosik
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms22105231

Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge
Cited by: 12
Author(s): Cristina Zamora-Ballesteros, Glória Pinto, Joana Amaral, Luís Valledor, Artur Alves, Julio J. Diez, Jorge Martín‐García
Software Mentions: 3
Published: over 5 years ago

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 5 years ago

10.3390/ijms22126437

BrPP5.2 Overexpression Confers Heat Shock Tolerance in Transgenic Brassica rapa through Inherent Chaperone Activity, Induced Glucosinolate Biosynthesis, and Differential Regulation of Abiotic Stress Response Genes
Cited by: 5
Author(s): Muthusamy Muthusamy, Jong Hee Kim, Suk Hee Kim, So Young Park, Soo In Lee
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22126467

Molecular and Functional Analysis of Sunitinib-Resistance Induction in Human Renal Cell Carcinoma Cells
Cited by: 10
Author(s): Magdalena Rausch, Adriano Rutz, Pierre‐Marie Allard, Céline Delucinge-Vivier, Mylène Docquier, Olivier Dormond, Jean‐Luc Wolfender, Patrycja Nowak-Śliwińska
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22136799

Chrysomycin A Attenuates Neuroinflammation by Down-Regulating NLRP3/Cleaved Caspase-1 Signaling Pathway in LPS-Stimulated Mice and BV2 Cells
Cited by: 16
Author(s): Man Liu, Shanshan Zhang, Dong-Ni Liu, Yinglin Yang, Yue-Hua Wang, Guanhua Du
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22158072

LOXL3 Silencing Affected Cell Adhesion and Invasion in U87MG Glioma Cells
Cited by: 6
Author(s): Talita de Sousa Laurentino, Roseli da Silva Soares, Antônio M. Lerário, Suely Kazue Nagahashi Marie, Sueli Mieko Oba-Shinjo
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22179120

Identifying the Main Functional Pathways Associated with Cognitive Resilience to Alzheimer’s Disease
Cited by: 11
Author(s): Marta Pérez-González, Sara Badesso, Elena Lorenzo, Elizabeth Guruceaga, Alberto Pérez-Mediavilla, Ana Garcı́a-Osta, Mar Cuadrado‐Tejedor
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22189799

Identification of miR-199a-5p, miR-214-3p and miR-99b-5p as Fibrosis-Specific Extracellular Biomarkers and Promoters of HSC Activation
Cited by: 7
Author(s): Catherine Jane Messner, Saskia Schmidt, Dilek Özkul, Carine Gaiser, Luigi Terracciano, Stephan Krähenbühl, Laura Suter‐Dick
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms22189693

Fetal Brain Elicits Sexually Conflicting Transcriptional Response to the Ablation of Uterine Forkhead Box A2 (Foxa2) in Mice
Cited by: 5
Author(s): Pramod Dhakal, Monica Strawn, Ananya Samal, Susanta K. Behura
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms22189719

Genome-Wide Analysis of LncRNA in Bovine Mammary Epithelial Cell Injuries Induced by Escherichia Coli and Staphylococcus Aureus
Cited by: 11
Author(s): Changjie Lin, Yifan Zhu, Zhiyu Hao, Haojun Xu, Ting Li, Jinghan Yang, Xi Chen, Yingyu Chen, Aizhen Guo, Changmin Hu
Software Mentions: 3
Published: almost 5 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: almost 6 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: about 5 years ago

10.1186/s12974-020-01900-7

A1 reactive astrocytes and a loss of TREM2 are associated with an early stage of pathology in a mouse model of cerebral amyloid angiopathy
Cited by: 30
Author(s): Xavier Taylor, Pablo Cisternas, Yanwen You, Yingjian You, Shunian Xiang, Yamil Marambio, Jie Zhang, Rubén Vidal, Cristian A. Lasagna‐Reeves
Software Mentions: 3
Published: about 6 years ago

10.1186/s12974-019-1628-8

Midbrain microglia mediate a specific immunosuppressive response under inflammatory conditions
Cited by: 28
Author(s): Miguel A. Abellanas, Marta Zamarbide, Leyre Basurco, Esther Luquin, Marta Garcı́a-Granero, Pedro Clavero, Patxi San Martín-Úriz, Amaia Vilas, Elisa Mengual, Sandra Hervás-Stubbs, Marta Aymerich
Software Mentions: 3
Published: almost 7 years ago

10.1523/JNEUROSCI.1163-18.2018

A Multicomponent Neuronal Response Encodes the Larval Decision to Pupariate upon Amino Acid Starvation
Cited by: 19
Author(s): Siddharth Jayakumar, Shlesha Richhariya, Bipan Kumar Deb, Gaiti Hasan
Software Mentions: 3
Published: almost 8 years ago

10.1155/2020/9235101

Identification of Key Differentially Expressed Transcription Factors in Glioblastoma
Cited by: 8
Author(s): Gang Qin, Beiquan Hu, Xianfeng Li, Rongjie Li, Youshi Meng, Yimei Wang, Donghua Zou, Feng Wang
Software Mentions: 3
Published: about 6 years ago

10.1155/2020/8841622

Cancer Stem Cell Characteristics by Network Analysis of Transcriptome Data Stemness Indices in Breast Carcinoma
Cited by: 2
Author(s): Zeng-Hong Wu, Youjing Zhang, Changli Jia
Software Mentions: 3
Published: almost 6 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: about 5 years ago

10.1186/s13048-020-00712-w

A novel signature of two long non-coding RNAs in BRCA mutant ovarian cancer to predict prognosis and efficiency of chemotherapy
Cited by: 4
Author(s): Yinglian Pan, Jia Li, Yuzhu Liu, Yiyu Han, Qian Li, Qin Zou, Zhongpei Zhang, Jin Long Huang, Qingchun Deng
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12885-015-1955-9

The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy
Cited by: 51
Author(s): Katayoon Kasaian, Sam M. Wiseman, Blair Walker, Jacqueline E. Schein, Yongjun Zhao, Martin Hirst, Richard A. Moore, Andrew J. Mungall, Marco A. Marra, Steven J.M. Jones
Software Mentions: 3
Published: over 10 years ago

10.1007/s00401-013-1168-8

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy
Cited by: 162
Author(s): Katja Kobow, Antony Kaspi, K N Harikrishnan, K. Kiese, Mark Ziemann, Ishant Khurana, Ina Fritzsche, Jan Hauke, Eric Hahnen, Roland Coras, Angelika Mühlebner, Assam El‐Osta, Ingmar Blümcke
Software Mentions: 3
Published: almost 13 years ago

10.1186/s40478-018-0569-2

ABCA1 haplodeficiency affects the brain transcriptome following traumatic brain injury in mice expressing human APOE isoforms
Cited by: 16
Author(s): Emilie L. Castranio, Cody M. Wolfe, Kyong Nyon Nam, Florent Letronne, Nicholas F. Fitz, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 3
Published: about 8 years ago

10.1002/advs.201902040

Deubiquitylase OTUD6B Governs pVHL Stability in an Enzyme‐Independent Manner and Suppresses Hepatocellular Carcinoma Metastasis
Cited by: 27
Author(s): Xinxin Liu, Xiaoli Zhang, Zhiqiang Peng, Chunnan Li, Ze Wang, Chanjuan Wang, Zhikang Deng, Bo Wu, Yu Cui, Zhanxin Wang, Chun-Ping Chu, Ming‐Hua Zheng, Lingqiang Zhang
Software Mentions: 3
Published: over 6 years ago

10.18632/aging.101578

High expression of the breast cancer susceptibility gene BRCA1 in long-lived termite kings
Cited by: 9
Author(s): Eisuke Tasaki, Yuki Mitaka, Tomonari Nozaki, Keiko Kobayashi, Kenji Matsuura, Yoshihito Iuchi
Software Mentions: 3
Published: almost 8 years ago

10.18632/aging.203425

ADAM15 correlates with prognosis, immune infiltration and apoptosis in hepatocellular carcinoma
Cited by: 9
Author(s): Jun Xu, Yong Guan, Yi Chao Zhang, Zhendong Qiu, Yu Zhou, Chen Chen, Jie-Ping Yu, Weixing Wang
Software Mentions: 3
Published: about 5 years ago

10.18632/aging.104004

Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer
Cited by: 9
Author(s): Hongjing Shang, Jianfeng Zheng, Jinyi Tong
Software Mentions: 3
Published: almost 6 years ago

10.18632/aging.102652

Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson’s disease
Cited by: 8
Author(s): Chunlei Han, Yunpeng Liu, Yun‐Peng Sui, Ning Chen, Tingting Du, Ying Jiang, Chenjia Guo, Kailiang Wang, Qiao Wang, Shiying Fan, Michio Shimabukuro, Fangang Meng, Yuan Fang, Jianguo Zhang
Software Mentions: 3
Published: over 6 years ago

10.18632/aging.202410

Systems pharmacology dissection of Epimedium targeting tumor microenvironment to enhance cytotoxic T lymphocyte responses in lung cancer
Cited by: 11
Author(s): Chao Huang, Zhihua Li, Jinglin Zhu, Xuetong Chen, Yuanyuan Hao, Ruijie Yang, Ruifei Huang, Jun Zhou, Zhenzhong Wang, Wei Xiao, Chunli Zheng, Yonghua Wang
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.103698

A two-gene-based prognostic signature for pancreatic cancer
Cited by: 8
Author(s): Shengqian Zhou, Yuanliang Yan, Xi Chen, Shuangshuang Zeng, Jie Wei, Xiang Wang, Zhicheng Gong, Zhijie Xu
Software Mentions: 3
Published: almost 6 years ago

10.18632/aging.202714

High expression of CD52 in adipocytes: a potential therapeutic target for obesity with type 2 diabetes
Cited by: 3
Author(s): Rui Mao, Fan Yang, Yu Zhang, Hongtao Liu, Pengsen Guo, Yanjun Liu, Tongtong Zhang
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.101541

Comprehensive analysis of circRNA expression pattern and circRNA-miRNA-mRNA network in the pathogenesis of atherosclerosis in rabbits
Cited by: 129
Author(s): Feng Zhang, Ruyou Zhang, Xiaoyu Zhang, Yingnan Wu, Xiaoying Li, Shuang Zhang, Wen-ying Hou, Yu Ding, Jiawei Tian, Lei Sun, Xiangdong Kong
Software Mentions: 3
Published: almost 8 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568