bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1093/gigascience/giz020

MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs
Cited by: 14
Author(s): Stuart M. Brown, Hao Chen, Yuhan Hao, Bobby Peter Laungani, Thahmina Ali, Changsu Dong, Carlos Lijeron, Baekdoo Kim, Claudia Wultsch, Zhiheng Pei, Konstantinos Krampis
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giaa009

De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas
Cited by: 15
Author(s): Maosheng Chen, Longjian Niu, Miaomiao Zhao, Chuan-Jia Xu, Bang-Zhen Pan, Qi Fu, Yongfu Tao, Hua He, Chaoqi Hou, Zeng-Fu Xu
Software Mentions: 3
Published: almost 5 years ago

10.1002/hed.25537

Association between loss of Y chromosome and poor prognosis in male head and neck squamous cell carcinoma
Cited by: 21
Author(s): Robert Hollows, Wenbin Wei, Jean‐Baptiste Cazier, Hisham Mehanna, Gabriella Parry, Graham Halford, Paul G. Murray
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41438-020-00452-4

Induced defense response in red mango fruit against Colletotrichum gloeosporioides
Cited by: 22
Author(s): Sudheeran Pradeep Kumar, Noa Sela, Mira Carmeli-Weissberg, Rinat Ovadia, Sayantan Panda, Oleg Feygenberg, Dalia Maurer, Michal Oren-Shamir, Asaph Aharoni, Noam Alkan
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41438-018-0020-7

Divergence in the transcriptional landscape between low temperature and freeze shock in cultivated grapevine (Vitis vinifera)
Cited by: 49
Author(s): Jason P. Londo, Alisson P. Kovaleski, Jacquelyn Lillis
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41438-020-0269-5

A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)
Cited by: 9
Author(s): Ting Xue, Xinqing Zheng, Duo Chen, Limin Liang, Nan Chen, Zhen Huang, Wenfang Fan, Jiannan Chen, Chengsong Wan, Shuai Chen, Jinmao Zhu, Binghua Chen, Xingtan Zhang, Youqiang Chen
Software Mentions: 3
Published: over 4 years ago

10.1038/s41438-020-0287-3

Transcriptome analysis and metabolic profiling reveal the key role of carotenoids in the petal coloration of Liriodendron tulipifera
Cited by: 39
Author(s): Zhaodong Hao, Siqin Liu, Lingfeng Hu, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: over 4 years ago

10.1186/s12979-015-0038-8

Hormetic effect of rotenone in primary human fibroblasts
Cited by: 13
Author(s): Shiva Marthandan, Stefan Priebe, Marco Groth, Reinhard Guthke, Matthias Platzer, Peter Hemmerich, Stephan Diekmann
Software Mentions: 3
Published: over 9 years ago

10.1038/sdata.2017.20

Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells
Cited by: 11
Author(s): Stephen J. Pettitt, Dragomir B. Krastev, Helen Pemberton, Yari Fontebasso, Jessica Frankum, Farah L. Rehman, Rachel Brough, Feifei Song, Ilirjana Bajrami, Rumana Rafiq, Fredrik Wållberg, Iwanka Kozarewa, Kerry Fenwick, Javier Armisen-Garrido, Amanda Swain, Aditi Gulati, James Campbell, Alan Ashworth, Christopher J. Lord
Software Mentions: 3
Published: almost 8 years ago

10.1038/sdata.2017.118

A gene expression atlas of adult Schistosoma mansoni and their gonads
Cited by: 44
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: over 7 years ago

10.1038/sdata.2017.163

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
Cited by: 4
Author(s): Margherita Francescatto, Marina Lizio, Ingrid H.C.H.M. Philippens, Luba M. Pardo, Ronald E. Bontrop, Mizuho Sakai, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa, Takeya Kasukawa, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Hideya Kawaji, Patrizia Rizzu, Peter Heutink
Software Mentions: 3
Published: about 7 years ago

10.1038/s41597-019-0117-3

Metagenomics and transcriptomics data from human colorectal cancer
Cited by: 5
Author(s): Tina Visnovska, Patrick J. Biggs, Frank Frizelle, Rachel Purcell
Software Mentions: 3
Published: over 5 years ago

10.1038/s41597-020-00628-6

Consensus transcriptional regulatory networks of coronavirus-infected human cells
Cited by: 23
Author(s): Scott A. Ochsner, Rudolf T. Pillich, Neil J. McKenna
Software Mentions: 3
Published: about 4 years ago

10.1038/srep02898

Soft truncation thresholding for gene set analysis of RNA-seq data: Application to a vaccine study
Cited by: 15
Author(s): Brooke L. Fridley, Gregory D. Jenkins, Diane E. Grill, Richard B. Kennedy, Gregory A. Poland, Ann L. Oberg
Software Mentions: 3
Published: about 11 years ago

10.1038/srep13456

TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability
Cited by: 15
Author(s): Lamiaa Bahnassawy, Thanneer M. Perumal, Laura González-Cano, Anna-Lena Hillje, Leila Taher, Wojciech Makałowski, Yutaka Suzuki, Georg Fuellen, Antonio del Sol, Jens Christian Schwamborn
Software Mentions: 3
Published: over 9 years ago

10.1038/srep18399

Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing
Cited by: 56
Author(s): Aroa Suárez-Vega, Christophe Klopp, Christèle Robert-Granié, Gwenola Tosser‐Klopp, Juan José Arranz
Software Mentions: 3
Published: about 9 years ago

10.1038/srep20837

Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model
Cited by: 15
Author(s): Els Willems, Carlos Guerrero-Bosagna, Eddy Decuypere, Steven Janssens, Johan Buyse, Nadine Buys, Per Jensen, Nadia Everaert
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep24061

Empirical insights into the stochasticity of small RNA sequencing
Cited by: 5
Author(s): Li‐Xuan Qin, Thomas Tuschl, Samuel Singer
Software Mentions: 3
Published: over 8 years ago

10.1038/srep25474

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
Cited by: 41
Author(s): Pamela Milani, Renan Escalante-Chong, Brandon Shelley, Natasha L. Patel-Murray, Xin X, Miriam Adam, Berhan Mandefro, Dhruv Sareen, Clive N. Svendsen, Ernest Fraenkel
Software Mentions: 3
Published: over 8 years ago

10.1038/srep26114

Comparative analysis of the integument transcriptomes of the black dilute mutant and the wild-type silkworm Bombyx mori
Cited by: 17
Author(s): Songyuan Wu, Xiaoling Tong, Chenxing Peng, Xiong Guan, Kunpeng Lu, Hai Hu, Tan D, Chunlin Li, Minjin Han, Cheng Lü, Fangyin Dai
Software Mentions: 3
Published: over 8 years ago

10.1038/srep27043

Differences in DNA Repair Capacity, Cell Death and Transcriptional Response after Irradiation between a Radiosensitive and a Radioresistant Cell Line
Cited by: 33
Author(s): Mireia Borràs-Fresneda, Joan Francesc Barquinero, Maria Gomolka, Sabine Hornhardt, Ute Rößler, Gemma Armengol, Leonardo Barrios
Software Mentions: 3
Published: over 8 years ago

10.1038/srep28702

Global transcriptome changes in perennial ryegrass during early infection by pink snow mould
Cited by: 12
Author(s): Mallikarjuna Rao Kovi, Mohamed Abdelhalim, Anil Kunapareddy, Åshild Ergon, Anne Marte Tronsmo, May Bente Brurberg, Ingerd Skow Hofgaard, Torben Asp, Odd Arne Rognli
Software Mentions: 3
Published: over 8 years ago

10.1038/srep31150

Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay
Cited by: 99
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: over 8 years ago

10.1038/srep33151

De novo Transcriptome Analysis Reveals Distinct Defense Mechanisms by Young and Mature Leaves of Hevea brasiliensis (Para Rubber Tree)
Cited by: 37
Author(s): Yuxiao Fang, Hailiang Mei, Binhui Zhou, Xiaohu Xiao, Meng Yang, Yacheng Huang, Xiangyu Long, Songnian Hu, Chaorong Tang
Software Mentions: 3
Published: over 8 years ago

10.1038/srep33296

Global analysis of differential gene expression related to long-term sperm storage in oviduct of Chinese Soft-Shelled Turtle Pelodiscus sinensis
Cited by: 23
Author(s): Tengfei Liu, Ping Yang, Hong Chen, Yufei Huang, Yi Liu, Yasir Waqas, Nisar Ahmed, Xia Chu, Qiusheng Chen
Software Mentions: 3
Published: over 8 years ago

10.1038/srep37536

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle
Cited by: 24
Author(s): Alejandra Rougon‐Cardoso, Mitzi Flores-Ponce, Hilda E. Ramos-Aboites, Christian E. Martínez-Guerrero, Youjin Hao, Luís Cunha, Jonathan Alejandro Rodríguez-Martínez, Cesaré Ovando-Vázquez, José Roberto Bermúdez-Barrientos, Cei Abreu‐Goodger, Noelina Hernández, Nélson Simões, Rafaél Montiel
Software Mentions: 3
Published: about 8 years ago

10.1038/srep40049

The molecular sensory machinery of a Chagas disease vector: expression changes through imaginal moult and sexually dimorphic features
Cited by: 41
Author(s): José Manuel Latorre-Estivalis, Hugh M. Robertson, Kimberly K. O. Walden, Jerônimo C. Ruiz, Leilane Oliveira Gonçalves, Alessandra A. Guarneri, Marcelo G. Lorenzo
Software Mentions: 3
Published: almost 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 4 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

10.1038/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

10.1038/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

10.1038/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: over 4 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: over 4 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: over 4 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: over 4 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: over 4 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: over 4 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: about 4 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: about 4 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: about 4 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: about 4 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: about 4 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: almost 4 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: almost 4 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: almost 4 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: almost 4 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: over 4 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: almost 7 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: almost 4 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: almost 4 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: over 5 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: over 3 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: over 4 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: about 4 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 7 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: over 3 years ago

10.1155/2017/8027626

Transcriptome Analysis of Two Different Developmental Stages of Paeonia lactiflora 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: almost 8 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: over 3 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: about 5 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: over 5 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: over 4 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: over 6 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

10.1038/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

10.1515/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

10.7554/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

10.18632/oncotarget.11309

Proteolysis-a characteristic of tumor-initiating cells in murine metastatic breast cancer
Cited by: 8
Author(s): Larissa E. Hillebrand, Fee Bengsch, Jochen Hochrein, Jan Hülsdünker, Julia Lynne Glade Bender, Marie Follo, Hauke Busch, Melanie Boerries, Thomas Reinheckel
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.14050

Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer
Cited by: 12
Author(s): Yanxiao Zhang, Jie Yu, Vladimir Grachtchouk, Tingting Qin, Carey N. Lumeng, Maureen A. Sartor, Ronald J. Koenig
Software Mentions: 3
Published: about 8 years ago

10.18632/oncotarget.13346

Differentiated regulation of immune-response related genes between LUAD and LUSC subtypes of lung cancers
Cited by: 51
Author(s): Mengzhu Chen, Xiu Ying Liu, Jie Du, Xiu‐Jie Wang, Xia Lei
Software Mentions: 3
Published: about 8 years ago

10.18632/oncotarget.15829

Re-expression of miR-200c suppresses proliferation, colony formation andin vivotumor growth of murine claudin-low mammary tumor cells
Cited by: 18
Author(s): Robert A. Jones, Katrina L. Watson, Anthony Bruce, Sarah Nersesian, Jenna Kitz, Roger A. Moorehead
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.16252

Niclosamide is a potential therapeutic for familial adenomatosis polyposis by disrupting Axin-GSK3 interaction
Cited by: 26
Author(s): Ahn Sk, Nam Hee Kim, Kyungro Lee, Yong Hoon, Ji Hye Yang, So Young, Eunae Sandra Cho, Yoonmi Lee, Jeong Ho Seok, Hyun Soo Cho, Yongseok Jeon, Young Su Yuk, Suebean Cho, Kyoung Tai No, Hyun Sil Kim, Ho Lee, Jiwon Choi, Jong In Yook
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.16518

Novel RNA biomarkers of prostate cancer revealed by RNA-seq analysis of formalin-fixed samples obtained from Russian patients
Cited by: 29
Author(s): Anastasia S. Nikitina, Е. И. Шарова, S. A. Danilenko, Т. Б. Бутусова, A.O. Vasiliev, А. В. Говоров, Elena A. Prilepskaya, Dmitry Pushkar, Elena S. Kostryukova
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.16051

Identification of molecular targets for esophageal carcinoma diagnosis using miRNA-seq and RNA-seq data from The Cancer Genome Atlas: a study of 187 cases
Cited by: 29
Author(s): Jiang‐Hui Zeng, Dandan Xiong, Yu‐Yan Pang, Yu Zhang, Rongjiang Tang, Dan Luo, Gang Chen
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.16451

RNA sequencing analyses reveal novel differentially expressed genes and pathways in pancreatic cancer
Cited by: 43
Author(s): Yiming Mao, Jianjun Shen, Yue Lu, Kevin Lin, Huamin Wang, Yanan Li, Ping Chang, Mary G. Walker, Donghui Li
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.18162

Upregulation of long noncoding RNA HOXA-AS3 promotes tumor progression and predicts poor prognosis in glioma
Cited by: 53
Author(s): Fan Wu, Chuanbao Zhang, Jinquan Cai, Fan Yang, Tingyu Liang, Xiaoyan Yan, Haoyuan Wang, Wen Wang, Jing Chen, Tao Jiang
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.19483

Identification of hub genes involved in the development of hepatocellular carcinoma by transcriptome sequencing
Cited by: 8
Author(s): Yongchang Zheng, Junyu Long, Liangcai Wu, Haohai Zhang, Lin Li, Ying Zheng, Anqiang Wang, Jianzhen Lin, Xiaobo Yang, Xinting Sang, Ke Hu, Jie Pan, Haitao Zhao
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.20013

An integrated lncRNA, microRNA and mRNA signature to improve prognosis prediction of colorectal cancer
Cited by: 31
Author(s): Yong Xiong, Rong Wang, Linglong Peng, Wenxian You, Jinlai Wei, Shouru Zhang, Xingye Wu, Jun Guo, Jiaman Xu, Zhenbing Lv, Zhongxue Fu
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.19557

cFLIP critically modulates apoptotic resistance in epithelial-to-mesenchymal transition
Cited by: 6
Author(s): Chandrasekhar Padmanabhan, Eric J. Rellinger, Jing Zhu, Hanbing An, Luke Woodbury, Dai H. Chung, Alex G. Waterson, Craig W. Lindsley, Anna L. Means, R. Daniel Beauchamp
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.25552

ERα-mediated cell cycle progression is an important requisite for CDK4/6 inhibitor response in HR+ breast cancer
Cited by: 9
Author(s): Karineh Petrossian, Noriko Kanaya, Chiao Lo, Pei-Yin Hsu, Duc T. Nguyen, Lixin Yang, Lu Yang, Charles Warden, Xiwei Wu, Raju Pillai, Lauren Bernal, Chiun‐Sheng Huang, Laura Kruper, Yuan Yuan, George Somlo, Joanne Mortimer, Shiuan Chen
Software Mentions: 3
Published: over 6 years ago

10.18632/oncotarget.25998

Bladder cancer detection by urinary extracellular vesicle mRNA analysis
Cited by: 21
Author(s): Taku Murakami, Cindy M. Yamamoto, Tomoshige Akino, Hiroshi Tanaka, Nobuyuki Fukuzawa, Hiroyoshi Suzuki, Takahiro Osawa, Takeshi Tsuji, Toshimori Seki, Hiroshi Harada
Software Mentions: 3
Published: over 6 years ago

10.18632/oncotarget.26300

Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
Cited by: 52
Author(s): Oliver Mrowczynski, A. Madhankumar, Jeffrey M. Sundstrom, Yuanjun Zhao, Yuka Imamura Kawasawa, Becky Slagle‐Webb, Christine Mau, Russell Payne, Elias Rizk, Brad E. Zacharia, James R. Connor
Software Mentions: 3
Published: about 6 years ago

10.18632/oncotarget.27112

Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells
Cited by: 2
Author(s): Piyush More, Ute Goedtel-Armbrust, Viral Shah, Marianne Mathaes, Thomas Kindler, Miguel A. Andrade‐Navarro, Leszek Wojnowski
Software Mentions: 3
Published: over 5 years ago

10.1186/s13018-020-01994-y

Differential gene expression in skin RNA of horses affected with degenerative suspensory ligament desmitis
Cited by: 7
Author(s): Abigail Haythorn, M.F. Young, James B. Stanton, Jian Zhang, P. O. E. Mueller, Jaroslava Halper
Software Mentions: 3
Published: about 4 years ago

10.1186/s13018-021-02604-1

Identification and comparison of novel circular RNAs with associated co-expression and competing endogenous RNA networks in postmenopausal osteoporosis
Cited by: 4
Author(s): Weiyi Diao, Yongguang Wang, Jun Zhang, Haiyu Shao, Yanlei Huang, Mengran Jin
Software Mentions: 3
Published: over 3 years ago

10.3390/jpm11020062

Modified Significance Analysis of Microarrays in Heterogeneous Diseases
Cited by: 2
Author(s): I‐Shiang Tzeng
Software Mentions: 3
Published: almost 4 years ago

10.1098/rsob.160330

Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress
Cited by: 10
Author(s): Erica Acton, Ahwon Lee, Pei Zhao, Stéphane Flibotte, Mauricio Neira, Sunita Sinha, Jennifer Chiang, Patrick Flaherty, Corey Nislow, Guri Giaever
Software Mentions: 3
Published: over 7 years ago

10.1098/rsob.190141

Identification of a novel regulatory pathway for PPARα by RNA-seq characterization of the endothelial cell lipid peroxidative injury transcriptome
Cited by: 4
Author(s): Fangfang Dou, Beiling Wu, Sun Liang, Jiulin Chen, Te Liu, Zhihua Yu, Chuan Chen
Software Mentions: 3
Published: about 5 years ago

10.1128/JVI.02394-20

CAGE-Seq Reveals that HIV-1 Latent Infection Does Not Trigger Unique Cellular Responses in a Jurkat T Cell Model
Cited by: 1
Author(s): Hiroyuki Matsui, Kotaro Shirakawa, Yoshinobu Konishi, Shigeki Hirabayashi, Anamaria Daniela Sarca, Hirofumi Fukuda, Ryosuke Nomura, Emani Stanford, Yoshihito Horisawa, Yasuhiro Kazuma, Tadahiko Matsumoto, Hiroyuki Yamazaki, Yuji Murakawa, Emilie Battivelli, Eric Verdin, Yoshio Koyanagi, Akifumi Takaori‐Kondo
Software Mentions: 3
Published: over 3 years ago

10.1128/JVI.01010-21

Kinetic Multi-omic Analysis of Responses to SARS-CoV-2 Infection in a Model of Severe COVID-19
Cited by: 19
Author(s): Angelene M. Cantwell, Harinder Singh, Maryann P. Platt, Yonghao Yu, Yi‐Han Lin, Yuji Ikeno, Gene B. Hubbard, Yan Xiang, Norberto González-Juarbe, Peter H. Dube
Software Mentions: 3
Published: about 3 years ago

10.1128/JVI.00969-19

Differentiation into an Effector Memory Phenotype Potentiates HIV-1 Latency Reversal in CD4+T Cells
Cited by: 67
Author(s): Deanna A. Kulpa, Aarthi Talla, Jessica H. Brehm, Susan Pereira Ribeiro, Sally Yuan, Anne-Gaelle Bebin-Blackwell, Michael D. Miller, Richard Barnard, Steven G. Deeks, Daria J. Hazuda, Nicolas Chomont, Rafick‐Pierre Sékaly
Software Mentions: 3
Published: about 5 years ago

10.1186/s12967-021-02865-8

Metabolic classification of bladder cancer based on multi-omics integrated analysis to predict patient prognosis and treatment response
Cited by: 11
Author(s): Chaozhi Tang, Meng Yu, Jiakang Ma, Yuyan Zhu
Software Mentions: 3
Published: over 3 years ago

10.1186/s12967-020-02497-4

Identification and validation of stemness-related lncRNA prognostic signature for breast cancer
Cited by: 59
Author(s): Xiaoying Li, Yang Li, Xinmiao Yu, Feng Jin
Software Mentions: 3
Published: over 4 years ago

10.1186/s12967-018-1706-1

Crosstalk in competing endogenous RNA networks reveals new circular RNAs involved in the pathogenesis of early HIV infection
Cited by: 41
Author(s): Yue Zhang, Hui Zhang, Minghui An, Bin Zhao, Haibo Ding, Zining Zhang, Ying He, Hong Shang, Xiaoxu Han
Software Mentions: 3
Published: about 6 years ago

10.1186/s12967-018-1535-2

In silico identification of drug target pathways in breast cancer subtypes using pathway cross-talk inhibition
Cited by: 22
Author(s): Claudia Cava, Gloria Bertoli, Isabella Castiglioni
Software Mentions: 3
Published: over 6 years ago

10.1186/s12967-020-02550-2

Classification models using circulating neutrophil transcripts can detect unruptured intracranial aneurysm
Cited by: 13
Author(s): Kerry E. Poppenberg, Vincent M. Tutino, Li Lü, Muhammad Waqas, Armond June, Lee Chaves, Kaiyu Jiang, James N. Jarvis, Yijun Sun, Kenneth V. Snyder, Elad I. Levy, Adnan H. Siddiqui, John Kolega, Hui Meng
Software Mentions: 3
Published: about 4 years ago

10.1186/s12967-018-1732-z

Integrated analysis of dysregulated long non-coding RNAs/microRNAs/mRNAs in metastasis of lung adenocarcinoma
Cited by: 49
Author(s): Lifeng Li, Mengle Peng, Wenhua Xue, Zhirui Fan, Tian Wang, Jingyao Lian, Yunkai Zhai, Wenping Lian, Dongchun Qin, Jie Zhao
Software Mentions: 3
Published: about 6 years ago

10.1186/s12967-018-1593-5

A circRNA–miRNA–mRNA network identification for exploring underlying pathogenesis and therapy strategy of hepatocellular carcinoma
Cited by: 199
Author(s): Dandan Xiong, Yi‐Wu Dang, Peng Lin, Dong‐Yue Wen, Rong‐Quan He, Dan Luo, Zhaoyong Feng, Gang Chen
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0218292

Proteome of normal human perilymph and perilymph from people with disabling vertigo
Cited by: 28
Author(s): Huai-San Lin, Yin Ren, Andrew C. Lysaght, Shyan‐Yuan Kao, Konstantina M. Stanković
Software Mentions: 3
Published: over 5 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: about 4 years ago

10.1186/s12864-018-5303-8

Higher plane of nutrition pre-weaning enhances Holstein calf mammary gland development through alterations in the parenchyma and fat pad transcriptome
Cited by: 13
Author(s): Mario Vailati-Riboni, Ryan Bucktrout, Siyuan Zhan, Ashley Geiger, Joshua C McCann, R.M. Akers, Juan J. Loor
Software Mentions: 3
Published: about 6 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568