Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: cufflinks

https://packages.ecosyste.ms/registries/pypi.org/packages/cufflinks

Productivity Tools for Plotly + Pandas
28 versions
Latest release: over 1 year ago
20 dependent packages
81,167 downloads last month

Papers Mentioning cufflinks 415

10.1186/s13046-018-0916-y
Enhanced efficacy of histone deacetylase inhibitor combined with bromodomain inhibitor in glioblastoma
Cited by: 25
Author(s): Meng Wang, Baocheng Wang, Weiwei Mao, Jiajia Wang, Zhao Yang, Qifeng Li, Chenran Zhang, Yujie Tang, Jie Ma
Software Mentions: 2
Published: about 6 years ago
10.7554/eLife.48916
Siglec1-expressing subcapsular sinus macrophages provide soil for melanoma lymph node metastasis
Cited by: 20
Author(s): Rohit Singh, Beom K. Choi
Software Mentions: 2
Published: almost 5 years ago
10.7554/eLife.20010
Genetic evidence that Nkx2.2 acts primarily downstream of Neurog3 in pancreatic endocrine lineage development
Cited by: 906
Author(s): Angela J. Churchill, Giselle Domínguez Gutiérrez, Ruth A. Singer, David S. Lorberbaum, Kevin A. Fischer, Lori Sussel
Software Mentions: 2
Published: almost 8 years ago
10.7554/eLife.14470
PROP1 triggers epithelial-mesenchymal transition-like process in pituitary stem cells
Cited by: 54
Author(s): María Inés Pérez Millán, Michelle L. Brinkmeier, Amanda H. Mortensen, Sally A. Camper
Software Mentions: 2
Published: over 8 years ago
10.7554/eLife.02811
TAF7L modulates brown adipose tissue formation
Cited by: 24
Author(s): Haiying Zhou, Bo Wan, Ivan Grubisic, Tommy Kaplan, Robert Tjian
Software Mentions: 2
Published: over 10 years ago
10.7554/eLife.08467
Compromising the 19S proteasome complex protects cells from reduced flux through the proteasome
Cited by: 61
Author(s): Peter Tsvetkov, Marc L. Mendillo, Jinghui Zhao, Jan E. Carette, Parker Merrill, Domagoj Cikes, Malini Varadarajan, Ferdy R. van Diemen, Josef Penninger, Alfred L. Goldberg, Thijn R. Brummelkamp, Sandro Santagata, Susan Lindquist
Software Mentions: 2
Published: about 9 years ago
10.7554/eLife.28383
A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis
Cited by: 75
Author(s): Nicolas Altemose, Nudrat Noor, Emmanuelle Bitoun, Afidalina Tumian, Michaël Imbeault, J. Ross Chapman, A. Radu Aricescu, Simon Myers
Software Mentions: 2
Published: about 7 years ago
10.7554/eLife.39030
Targeting MYC dependency in ovarian cancer through inhibition of CDK7 and CDK12/13
Cited by: 101
Author(s): Mei Zeng, Nicholas Kwiatkowski, Tinghu Zhang, Behnam Nabet, Mousheng Xu, Yanke Liang, Chunshan Quan, Jinhua Wang, Mingfeng Hao, Sangeetha Palakurthi, Shan Zhou, Qing Zeng, Paul Kirschmeier, Khyati Meghani, Alan L. Leggett, Jun Qi, Geoffrey I. Shapiro, Joyce F. Liu, Ursula A. Matulonis, Charles Y. Lin, Panagiotis A. Konstantinopoulos, Nathanael S. Gray
Software Mentions: 2
Published: about 6 years ago
10.3390/ijms16034744
Transcriptome Analysis in Rat Kidneys: Importance of Genes Involved in Programmed Hypertension
Cited by: 42
Author(s): You‐Lin Tain, Laura Huang, Julie Y.H. Chan, Chien-Te Lee
Software Mentions: 2
Published: over 9 years ago
10.3390/ijms16047976
RNA Sequencing Identifies Upregulated Kyphoscoliosis Peptidase and Phosphatidic Acid Signaling Pathways in Muscle Hypertrophy Generated by Transgenic Expression of Myostatin Propeptide
Cited by: 16
Author(s): Yuanxin Miao, Jinzeng Yang, Zhong Xu, Jing Lü, Shuhong Zhao, Xinyun Li
Software Mentions: 2
Published: over 9 years ago
10.3390/ijms19082342
Comparative Analysis of Transcriptomes to Identify Genes Associated with Fruit Size in the Early Stage of Fruit Development in Pyrus pyrifolia
Cited by: 18
Author(s): Shuang Jiang, Haishan An, Jun Luo, Xiaoqing Wang, Chunhui Shi, Fanjie Xu
Software Mentions: 2
Published: over 6 years ago
10.3390/ijms19124069
Notched Belly Grain 4, a Novel Allele of Dwarf 11, Regulates Grain Shape and Seed Germination in Rice (Oryza sativa L.)
Cited by: 15
Author(s): Xiaohong Tong, Yifeng Wang, Aixin Sun, Babatunde Kazeem Bello, Shen Ni, Jian Zhang
Software Mentions: 2
Published: almost 6 years ago
10.3390/ijms20082036
Role of Dusp6 Phosphatase as a Tumor Suppressor in Non-Small Cell Lung Cancer
Cited by: 18
Author(s): Verónica Moncho-Amor, Laura Pintado‐Berninches, Inmaculada Ibáñez de Cáceres, Ester Martín-Villar, Miguel Quintanilla, Probir Chakravarty, María Cortés-Sempere, Beatriz Fernández-Varas, Carlos Rodriguez-Antolín, Javier de Castro, Leandro Sastre, Rosario Perona
Software Mentions: 2
Published: over 5 years ago
10.3390/ijms22137029
Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process
Cited by: 3
Author(s): Caiyun Xiong, Qing-You Gong, Hu Pei, Changjian Liao, Ruichun Yang, Gao-Ke Li, Jiling Huang
Software Mentions: 2
Published: over 3 years ago
10.18632/oncotarget.8927
Potential diagnostic and prognostic marker dimethylglycine dehydrogenase (DMGDH) suppresses hepatocellular carcinoma metastasis <i>in vitro</i> and <i>in vivo</i>
Cited by: 38
Author(s): Gang Liu, Guoqing Hou, Liang Li, Yixue Li, Weiping Zhou, Lei Liu
Software Mentions: 2
Published: over 8 years ago
10.18632/oncotarget.23163
Elucidating mechanisms of sunitinib resistance in renal cancer: an integrated pathological-molecular analysis
Cited by: 22
Author(s): Henriett Butz, Qiang Ding, Roy Nofech‐Mozes, Zsuzsanna Lichner, Heyu Ni, George M. Yousef
Software Mentions: 2
Published: almost 7 years ago
10.3390/jpm4020282
Differential Transcriptome Profile of Peripheral White Cells to Identify Biomarkers Involved in Oxaliplatin Induced Neuropathy
Cited by: 9
Author(s): Manuel Morales, Julio Ávila, Rebeca González-Fernández, Laia Boronat, M L Soriano, Pablo Martín‐Vasallo
Software Mentions: 2
Published: over 10 years ago
10.1098/rsob.190220
Transcriptomic analysis and novel insights into lens fibre cell differentiation regulated by Gata3
Cited by: 9
Author(s): Elena Martynova, Yilin Zhao, Qing Xie, Deyou Zheng, Aleš Cvekl
Software Mentions: 2
Published: almost 5 years ago
10.1038/s41598-017-17356-4
Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei
Cited by: 11
Author(s): Hirzahida Mohd-Padil, Nadzirah Damiri, Suhaila Sulaiman, San Jiun Chai, Sheila Nathan, Mohd Firdaus-Raih
Software Mentions: 1
Published: almost 7 years ago
10.1186/s12864-016-2653-y
Gene and transposable element methylation in great tit (Parus major) brain and blood
Cited by: 47
Author(s): Martijn F.L. Derks, Kyle M. Schachtschneider, Ole Madsen, Elio Schijlen, Koen J. F. Verhoeven, Kees van Oers
Software Mentions: 1
Published: over 8 years ago
10.1038/s41598-018-22384-9
Insights into the ubiquitin-proteasome system of human embryonic stem cells
Cited by: 39
Author(s): Isabel Sáez, Seda Koyuncu, Ricardo Gutiérrez-García, Christoph Dieterich, David Vı́lchez
Software Mentions: 1
Published: over 6 years ago
10.1038/s12276-021-00648-1
Loss of Acot12 contributes to NAFLD independent of lipolysis of adipose tissue
Cited by: 4
Author(s): Sujeong Park, Jinping Song, In-Jeoung Baek, Kyu Yun Jang, Chang Yeob Han, Dae Won Jun, Peter K. Kim, Brian Raught, Eun Hyo Jin
Software Mentions: 1
Published: over 3 years ago
10.18632/oncotarget.16699
Remote reprogramming of hepatic circadian transcriptome by breast cancer
Cited by: 49
Author(s): Hiroaki Hojo, Sora Enya, Miki Arai, Yutaka Suzuki, Takashi Nojiri, Kenji Kangawa, Shinsuke Koyama, Shinpei Kawaoka
Software Mentions: 1
Published: over 7 years ago
10.18632/oncotarget.17359
Lipid catabolism inhibition sensitizes prostate cancer cells to antiandrogen blockade
Cited by: 67
Author(s): Thomas W. Flaig, Maren Salzmann-Sullivan, Lih-Jen Su, Zhiyong Zhang, Molishree Joshi, Miguel A. Gijón, Jihye Kim, John J. Arcaroli, Adrie van Bokhoven, M. Scott Lucia, Francisco G. La Rosa, Isabel R. Schlaepfer
Software Mentions: 1
Published: over 7 years ago
10.3390/diagnostics9030098
Differential Expression Profiles of the Transcriptome and miRNA Interactome in Synovial Fibroblasts of Rheumatoid Arthritis Revealed by Next Generation Sequencing
Cited by: 6
Author(s): Chia‐Chun Tseng, Lu Wu, Wen‐Chan Tsai, Tsan‐Teng Ou, Cheng‐Chin Wu, Wan‐Yu Sung, Po‐Lin Kuo, Jeng‐Hsien Yen
Software Mentions: 1
Published: over 5 years ago
10.1038/s42003-021-02405-6
Bromodomain-containing protein BRPF1 is a therapeutic target for liver cancer
Cited by: 15
Author(s): Carol Lai‐Hung Cheng, Felice Hoi-Ching Tsang, Lai Wei, Mengnuo Chen, Don Wai‐Ching Chin, Jialing Shen, Cheuk‐Ting Law, Derek Lee, Carmen Chak‐Lui Wong, Chun‐Ming Wong
Software Mentions: 1
Published: over 3 years ago
10.3390/ani11072142
Fat Deposition in the Muscle of Female and Male Yak and the Correlation of Yak Meat Quality with Fat
Cited by: 6
Author(s): Lin Xiong, Jie Pei, Min Chen, Xiaoyun Wu, Qudratullah Kalwar, Ping Yan, Xian Guo
Software Mentions: 1
Published: over 3 years ago
10.3390/cancers13071672
Targeting Feedforward Loops Formed by Nuclear Receptor RORγ and Kinase PBK in mCRPC with Hyperactive AR Signaling
Cited by: 8
Author(s): Xiong Zhang, Zenghong Huang, Junjian Wang, Zhao Ma, Joy C. Yang, Eva Corey, Christopher P. Evans, Aiming Yu, Hongwu Chen
Software Mentions: 1
Published: over 3 years ago
10.1186/s12864-021-07573-7
Characterization and transcriptomic analysis of a novel yellow-green leaf wucai (Brassica campestris L.) germplasm
Cited by: 9
Author(s): Libing Nie, Zheng Yu-shan, Liting Zhang, Ying Wu, Shidong Zhu, Jinfeng Hou, Guohu Chen, Xiaoyan Tang, Chenggang Wang, Lingyun Yuan
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-018-30088-3
Complementary iTRAQ-based proteomic and RNA sequencing-based transcriptomic analyses reveal a complex network regulating pomegranate (Punica granatum L.) fruit peel colour
Cited by: 27
Author(s): Xiang Luo, Da Cao, Haoxian Li, Dan Zhao, Hui Xue, Juan Niu, Lina Chen, Fuhong Zhang, Shangyin Cao
Software Mentions: 1
Published: over 6 years ago
10.1007/s11357-012-9410-1
Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome
Cited by: 90
Author(s): Shona H. Wood, Thomas Craig, Yang Li, B.J. Merry, João Pedro de Magalhães
Software Mentions: 1
Published: over 12 years ago
10.1038/s41598-018-35892-5
Genome-wide DNA Methylation and RNAseq Analyses Identify Aberrant Signalling Pathways in Focal Cortical Dysplasia (FCD) Type II
Cited by: 22
Author(s): Aparna Banerjee Dixit, Dipika Sharma, Manjari Tripathi, Anupam Srivastava, Debasmita Paul, Parakkal Deepak, Chitra Sarkar, Krishan Kumar, Jyotirmoy Banerjee, P. Sarat Chandra
Software Mentions: 1
Published: almost 6 years ago
10.3390/ijms20051071
Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed (Brassica rapa L.)
Cited by: 48
Author(s): Lan Ma, Jeffrey A. Coulter, Lijun Liu, Yang Zhao, Yu Mei Chang, Yuanyuan Pu, Xiucun Zeng, XU Yao-zhao, Junyan Wu, Yan Fang, Jing Bai, Weizheng Sun
Software Mentions: 1
Published: over 5 years ago
10.1038/s41598-019-41406-8
Integrated transcriptome and in vitro analysis revealed anti-proliferative effect of citral in human stomach cancer through apoptosis
Cited by: 10
Author(s): Sri Renukadevi Balusamy, Sivasubramanian Ramani, Sathishkumar Natarajan, Yeon Ju Kim, Haribalan Perumalsamy
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0156128
Expression Profile and Function Analysis of LncRNAs during Priming Phase of Rat Liver Regeneration
Cited by: 6
Author(s): Jun Li, Wei Jin, Yanli Qin, Weihua Zhao, Cuifang Chang, Chi Xu
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0197272
ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions
Cited by: 20
Author(s): Haythem Latif, Stephen Federowicz, Ali Ebrahim, Janna Tarasova, Richard Szubin, José Utrilla, Karsten Zengler, Jaehyung Kim
Software Mentions: 1
Published: over 6 years ago
10.3390/ijms20071758
Transcriptional and Metabolomic Analyses Indicate that Cell Wall Properties are Associated with Drought Tolerance in Brachypodium distachyon
Cited by: 20
Author(s): Ingo Lenk, Lorraine H. C. Fisher, Martin Vickers, Aderemi Akinyemi, Thomas Didion, Martin Swain, Christian S. Jensen, Luis A. J. Mur, Marina Bosch
Software Mentions: 1
Published: over 5 years ago
10.1186/s40478-021-01130-9
Neuronal hibernation following hippocampal demyelination
Cited by: 4
Author(s): Selva Baltan, Safdar Jawaid, Anthony M. Chomyk, Grahame J. Kidd, Jacqueline Chen, Harsha Battapady, Ricky Chan, Ranjan Dutta, Bruce D. Trapp
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0049144
mRNA-Seq of Single Prostate Cancer Circulating Tumor Cells Reveals Recapitulation of Gene Expression and Pathways Found in Prostate Cancer
Cited by: 118
Author(s): Gordon M. Cann, Zulfiqar Gulzar, Samantha Cooper, Robin Li, Shujun Luo, Mai Tat, Sarah Stuart, Gary P. Schroth, Sandhya Srinivas, Mostafa Ronaghi, James D. Brooks, AmirAli Talasaz
Software Mentions: 1
Published: about 12 years ago
10.1038/s41598-020-66303-3
Selective Induction of Human Autonomic Neurons Enables Precise Control of Cardiomyocyte Beating
Cited by: 16
Author(s): Yoichiro Takayama, Hiroko Kushige, Yuka Akagi, Yutaka Suzuki, Yutaro Kumagai, Yasuyuki S. Kida
Software Mentions: 1
Published: over 4 years ago
10.1186/1471-2164-16-S3-S2
LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data
Cited by: 108
Author(s): Qinghua Jiang, Rui Ma, Jixuan Wang, Xiaoliang Wu, Shuilin Jin, Jiajie Peng, Renjie Tan, Tianjiao Zhang, Li Yu, Yadong Wang
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.pone.0128864
A Genetic Porcine Model of Cancer
Cited by: 116
Author(s): Lawrence B. Schook, Tiago Collares, Wenping Hu, Ying Liang, Fernanda Martins Rodrigues, Laurie A. Rund, Kyle M. Schachtschneider, Fabiana K. Seixas, Kuldeep Singh, Kevin D. Wells, Eric M. Walters, Randall S. Prather, Christopher M. Counter
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0058714
Transcriptome Sequencing of Tumor Subpopulations Reveals a Spectrum of Therapeutic Options for Squamous Cell Lung Cancer
Cited by: 9
Author(s): Christian Barrett, Richard B. Schwab, Hyunchul Jung, Brian Crain, Daniel Goff, Catriona Jamieson, Patricia A. Thistlethwaite, Olivier Harismendy, Dennis A. Carson, Kelly A. Frazer
Software Mentions: 1
Published: over 11 years ago
10.1038/s41598-020-74144-3
Petal abscission in fragrant roses is associated with large scale differential regulation of the abscission zone transcriptome
Cited by: 9
Author(s): Priya Singh, Neeraj Bharti, Amar Pal Singh, Siddharth Tripathi, Saurabh Pandey, Abhishek Chauhan, Abhijeet Kulkarni, Aniruddha P. Sane
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-020-78628-0
Transcriptome analysis of wheat spikes in response to Tilletia controversa Kühn which cause wheat dwarf bunt
Cited by: 10
Author(s): Zhaoyu Ren, Jianjian Liu, Ghulam Muhae Ud Din, Han Zhang, Zhenhui Du, Wanquan Chen, Taiguo Liu, Jianmin Zhang, Shiying Zhao, Li Gao
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pone.0128596
The Peripheral Olfactory Repertoire of the Lightbrown Apple Moth, Epiphyas postvittana
Cited by: 43
Author(s): Jacob A. Corcoran, Melissa D. Jordan, Amali H. Thrimawithana, Ross N. Crowhurst, Richard D. Newcomb
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0170859
Epigenetic Alterations Affecting Transcription Factors and Signaling Pathways in Stromal Cells of Endometriosis
Cited by: 45
Author(s): Iveta Yotova, Emily Hsu, Catherine Do, Aulona Gaba, Matthias Sczabolcs, Sabine Dekan, Lukas Kenner, René Wenzl, Benjamin Tycko
Software Mentions: 1
Published: almost 8 years ago
10.1038/s41598-021-92426-2
Ischemic heart injury leads to HIF1-dependent differential splicing of CaMK2γ
Cited by: 7
Author(s): Allison L Williams, Chad B. Walton, Blake Pinell, Vedbar S. Khadka, Brandyn Dunn, Katie Lee, M. C. Therese Anagaran, Abigail Avelar, Ralph V. Shohet
Software Mentions: 1
Published: over 3 years ago
10.1186/s12864-019-5939-z
The genome-wide impact of cadmium on microRNA and mRNA expression in contrasting Cd responsive wheat genotypes
Cited by: 34
Author(s): Min Zhou, Shigang Zheng, Rong Liu, Lu Lu, Chihong Zhang, Lei Zhang, Levi Yant, Yu Wu
Software Mentions: 1
Published: over 5 years ago
10.1038/s41598-021-93363-w
RNA-Seq, physiological, and biochemical analysis of burley tobacco response to nitrogen deficiency
Cited by: 4
Author(s): Yafei Li, Dong Chil Chang, Xiang Zhang, Hongzhi Shi, Huijuan Yang
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0072567
RNA-Seq Characterization of Spinal Cord Injury Transcriptome in Acute/Subacute Phases: A Resource for Understanding the Pathology at the Systems Level
Cited by: 69
Author(s): Kenian Chen, S.Z. Deng, He‐Zuo Lü, Yiyan Zheng, Guodong Yang, Dong H. Kim, Qilin Cao, Jia Qian Wu
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0179391
RNA sequencing demonstrates large-scale temporal dysregulation of gene expression in stimulated macrophages derived from MHC-defined chicken haplotypes
Cited by: 1
Author(s): Kristopher J. L. Irizarry, Eileen Downs, Randall Bryden, Jory Clark, Lisa Griggs, Renee Kopulos, Cynthia M. Boettger, Thomas J. Carr, Calvin L. Keeler, Ellen W. Collisson, Yvonne Drechsler
Software Mentions: 1
Published: about 7 years ago
10.1186/s40064-016-2460-6
Comparative analysis of the terpenoid biosynthesis pathway in Azadirachta indica and Melia azedarach by RNA-seq
Cited by: 10
Author(s): Yuwei Wang, Xiang Chen, Jin Wang, Hang Xun, Sun Jia, Feng Tang
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0217309
RNA-seq reveals differentially expressed genes in rice (Oryza sativa) roots during interactions with plant-growth promoting bacteria, Azospirillum brasilense
Cited by: 37
Author(s): Jacklyn Thomas, Ha Ram Kim, Yasir Rahmatallah, Grant Wiggins, QinQing Yang, Raj Singh, Galina Glazko, Arijit Mukherjee
Software Mentions: 1
Published: over 5 years ago
10.1186/s13287-021-02171-6
Novel live cell fluorescent probe for human-induced pluripotent stem cells highlights early reprogramming population
Cited by: 4
Author(s): Sandhya Sriram, Nam‐Young Kang, Savitha Subramanian, Tannistha Nandi, Sudhagar Selvaraju, Q. Xing, Gerine Tong, Allen Kuan-Liang Chen, Thekkeparambil Chandrabose Srijaya, Patrick Tan, Yuin-Han Loh, Young‐Tae Chang, Shigeki Sugii
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pntd.0005209
Transient In Vivo Resistance Mechanisms of Burkholderia pseudomallei to Ceftazidime and Molecular Markers for Monitoring Treatment Response
Cited by: 13
Author(s): Jason E. Cummings, Richard A. Slayden
Software Mentions: 1
Published: almost 8 years ago
10.1038/tp.2016.204
The DPYSL2 gene connects mTOR and schizophrenia
Cited by: 32
Author(s): Xuan Pham, Guang Song, Shunhua Lao, Loyal A. Goff, Hua Zhu, David Valle, Dimitri Avramopoulos
Software Mentions: 1
Published: about 8 years ago
10.1128/mBio.00723-19
Authentic Modeling of Human Respiratory Virus Infection in Human Pluripotent Stem Cell-Derived Lung Organoids
Cited by: 108
Author(s): Matteo Porotto, Marion Ferren, Chen‐Yong Lin, YT Siu, Negar Makhsous, B. K. Rima, Thomas Briese, Alexander L. Greninger, Hans Willem Snoeck, Anne Moscona
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pgen.1005526
A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis
Cited by: 52
Author(s): Raymond Liang, Genís Campreciós, Yan Kou, Kathleen E. McGrath, Roberta B. Nowak, Seana C. Catherman, Carolina L. Bigarella, Pauline Rimmelé, Xin Zhang, Merlin Nithya Gnanapragasam, James J. Bieker, Dmitri Papatsenko, Avi Ma’ayan, Emery H. Bresnick, Velia M. Fowler, James Palis, Saghi Ghaffari
Software Mentions: 1
Published: about 9 years ago
10.1371/journal.pgen.1007691
Amn1 governs post-mitotic cell separation in Saccharomyces cerevisiae
Cited by: 16
Author(s): Fang Ou, Xiaohua Hu, Lin Wang, Ning Jiang, Jixuan Yang, Bo Li, Zewei Luo
Software Mentions: 1
Published: about 6 years ago
10.1111/pbi.13214
Mutations in <i><scp>MIR</scp>396e</i> and <i><scp>MIR</scp>396f</i> increase grain size and modulate shoot architecture in rice
Cited by: 63
Author(s): Chunbo Miao, Dong Wang, Reqing He, shenkui Liu, Jian‐Kang Zhu
Software Mentions: 1
Published: over 5 years ago
10.1152/physiolgenomics.00004.2014
Protease inhibitor 15, a candidate gene for abdominal aortic internal elastic lamina ruptures in the rat
Cited by: 20
Author(s): Samreen Falak, Sebastian Schäfer, Amelie Baud, Oliver Hummel, Herbert Schulz, Dominique Guyader, Norbert Hübner, Mary Osborne-Pellegrin
Software Mentions: 1
Published: over 10 years ago
10.3390/ijms20205133
Physiological and Transcriptomic Analyses Elucidate That Exogenous Calcium Can Relieve Injuries to Potato Plants (Solanum tuberosum L.) under Weak Light
Cited by: 7
Author(s): Jinfeng Hou, Jie Li, Yang Yang, Zixin Wang, Bowen Chang, Xiaowei Yu, Lingyun Yuan, Chenggang Wang, Guohu Chen, Xiaoyan Tang, Shidong Zhu
Software Mentions: 1
Published: about 5 years ago
10.1155/2017/2790864
<i>Lingguizhugan</i>Decoction Protects against High-Fat-Diet-Induced Nonalcoholic Fatty Liver Disease by Alleviating Oxidative Stress and Activating Cholesterol Secretion
Cited by: 13
Author(s): Lili Yang, Weili Lin, Colleen A. Nugent, Shijun Hao, Haiyan Song, Tao Liu, Peiyong Zheng
Software Mentions: 1
Published: almost 8 years ago
10.1038/s41389-018-0106-y
miR-100 maintains phenotype of tumor-associated macrophages by targeting mTOR to promote tumor metastasis via Stat5a/IL-1ra pathway in mouse breast cancer
Cited by: 48
Author(s): Wei Wang, Yan Liu, Jian Guo, Huiwen He, Xue Mi, Chong Chen, Junling Xie, Shengnan Wang, Peng Wu, Fengqi Cao, Lipeng Bai, Si Qin, Rong Xiang, Yunping Luo
Software Mentions: 1
Published: almost 6 years ago
10.7717/peerj.4461
Identification and characterization of the cytosine-5 DNA methyltransferase gene family in<i>Salvia miltiorrhiza</i>
Cited by: 9
Author(s): Jiang Li, Caili Li, Shanfa Lu
Software Mentions: 1
Published: over 6 years ago
10.1186/s13256-015-0749-7
Translocational renal cell carcinoma (t(6;11)(p21;q12) with transcription factor EB (TFEB) amplification and an integrated precision approach: a case report
Cited by: 12
Author(s): Wolfgang Lilleby, Ljiljana Vlatkovic, Leonardo A. Meza‐Zepeda, Mona-Elisabeth Revheim, Eivind Hovig
Software Mentions: 1
Published: almost 9 years ago
10.1186/s12864-016-2691-5
Transcriptome analysis of Sporisorium scitamineum reveals critical environmental signals for fungal sexual mating and filamentous growth
Cited by: 28
Author(s): Meixin Yan, Weigang Dai, Enping Cai, Yi Zhen Deng, Changqing Chang, Zide Jiang, Lian-Hui Zhang
Software Mentions: 1
Published: over 8 years ago
10.1002/1878-0261.12046
Gene regulatory networking reveals the molecular cue to lysophosphatidic acid-induced metabolic adaptations in ovarian cancer cells
Cited by: 26
Author(s): Upasana Ray, Shreya Roy Chowdhury, Madavan Vasudevan, Kiran Bankar, Susanta Roychoudhury, Sib Sankar Roy
Software Mentions: 1
Published: over 7 years ago
10.3390/ijms21145031
Transcriptome Analysis Provides Insights into Grain Filling in Foxtail Millet (Setaria italica L.)
Cited by: 7
Author(s): Tao Wang, Hui Song, Pengtao Li, Yangyang Wei, Nan Hu, Zhenwen Chen, Weiqi Wang, Jinrong Liu, Baohong Zhang, Renhai Peng
Software Mentions: 1
Published: over 4 years ago
10.1186/s12967-019-1925-0
Reduced eIF3d accelerates HIV disease progression by attenuating CD8+ T cell function
Cited by: 6
Author(s): Yun Pan, Zining Zhang, Lin-Bo Yin, Yajing Fu, Yongjun Jiang, Hong Shang
Software Mentions: 1
Published: over 5 years ago
10.1002/mgg3.740
Gene expression in blood from an individual with β‐thalassemia: An RNA sequence analysis
Cited by: 4
Author(s): Forough Taghavifar, Mohammad Hamid, Gholamreza Shariati
Software Mentions: 1
Published: over 5 years ago
10.1186/s13068-019-1550-4
Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural
Cited by: 13
Author(s): Daria Feldman, David Kowbel, Adi Cohen, N. Louise Glass, Yitzhak Hadar, Oded Yarden
Software Mentions: 1
Published: about 5 years ago
10.18632/oncotarget.27571
Protein phosphatase 1 regulatory subunit 1A regulates cell cycle progression in Ewing sarcoma
Cited by: 5
Author(s): Wen Luo, Changxin Xu, Sarah Phillips, Aliza Gardenswartz, Jeremy Rosenblum, Janet Ayello, Stephen L. Lessnick, Huai-Xiang Hao, Mitchell S. Cairo
Software Mentions: 1
Published: over 4 years ago
10.1186/s12863-017-0488-4
Deciphering alternative splicing and nonsense-mediated decay modulate expression in primary lymphoid tissues of birds infected with avian pathogenic E. coli (APEC)
Cited by: 7
Author(s): Hongyan Sun
Software Mentions: 1
Published: over 7 years ago
10.14440/jbm.2018.211
Analysis of gene expression in filamentous cells of Candida albicans grown on agar plates
Cited by: 5
Author(s): Paul E. Creger, Jill R. Blankenship
Software Mentions: 1
Published: almost 7 years ago
10.1111/jcmm.13200
RPA3 is a potential marker of prognosis and radioresistance for nasopharyngeal carcinoma
Cited by: 34
Author(s): Chen Qu, Yiying Zhao, Guo‐Kai Feng, Chen Chen, Yijing Tao, Shu Zhou, Songran Liu, Hui Chang, Mu‐Sheng Zeng, Yunfei Xia
Software Mentions: 1
Published: over 7 years ago
10.1186/s41065-021-00195-9
Regulation of DNA methylation on key parasitism genes of Cysticercus cellulosae revealed by integrative epigenomic-transcriptomic analyses
Cited by: 2
Author(s): Xinrui Wang, Weiyi Song, Guanyu Ji, Yining Song, Xiaolei Liu, Xin Luo, Mingyuan Liu, Shicheng Sun
Software Mentions: 1
Published: over 3 years ago
10.3390/biomedicines9080934
Anti-Toxoplasma gondii Effects of a Novel Spider Peptide XYP1 In Vitro and In Vivo
Cited by: 10
Author(s): Yuan Liu, Yaqin Tang, Tao Xing, Mengqi Wu, Shengjie Hou, Xiaohua Liu, Jing Li, Mei Deng, Shuaiqin Huang, Liping Jiang
Software Mentions: 1
Published: over 3 years ago
10.1186/s12862-014-0250-8
Temporal genomic evolution of bird sex chromosomes
Cited by: 39
Author(s): Zongji Wang, Jilin Zhang, Wei Yang, Na An, Pei Zhang, Guojie Zhang, Qi Zhou
Software Mentions: 1
Published: almost 10 years ago
10.1155/2020/6354183
3D Culture System for Liver Tissue Mimicking Hepatic Plates for Improvement of Human Hepatocyte (C3A) Function and Polarity
Cited by: 18
Author(s): Zhidong Jia, Yuan Cheng, Xinghua Jiang, Chengyan Zhang, Gaoshang Wang, Jiangang Xu, Li Yang, Qing Peng, Yi Gao
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.ppat.1007289
Circulating HLA-DR+CD4+ effector memory T cells resistant to CCR5 and PD-L1 mediated suppression compromise regulatory T cell function in tuberculosis
Cited by: 24
Author(s): Asma Ahmed, Vasista Adiga, Suraja Kumar Nayak, Jitendra Kumar, Chirag Dhar, Pravat Nalini Sahoo, Bharath K. Sundararaj, George D. Souza, Annapurna Vyakarnam
Software Mentions: 1
Published: about 6 years ago
10.1093/gigascience/giy146
Whole-genome sequence of the oriental lung fluke<i>Paragonimus westermani</i>
Cited by: 29
Author(s): Harald Oey, Martha Zakrzewski, Kanwar Narain, Kangjam Rekha Devi, Takeshi Agatsuma, Sujeevi Nawaratna, Geoffrey N. Gobert, Malcolm K. Jones, Mark A. Ragan, Donald P. McManus, Lutz Krause
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.ppat.1009113
Rhabditophanes diutinus a parthenogenetic clade IV nematode with dauer larvae
Cited by: 2
Author(s): Alex Dulovic, Tess Renahan, Waltraud Röseler, Christian Rödelsperger, Ann M. Rose, Adrian Streit
Software Mentions: 1
Published: almost 4 years ago
10.1186/s13742-016-0151-4
Draft genome of the leopard gecko, Eublepharis macularius
Cited by: 49
Author(s): Zijun Xiong, Fang Li, Qiye Li, Long Zhang, Tony Gamble, Jiao Zheng, Ling Kui, Cai Li, Shengbin Li, Huanming Yang, Guojie Zhang
Software Mentions: 1
Published: about 8 years ago
10.1186/s12918-018-0571-0
Functional enrichment analysis based on long noncoding RNA associations
Cited by: 10
Author(s): Kuo‐Sheng Hung, Chung-Chi Hsiao, Tun‐Wen Pai, Chin-Hwa Hu, Wen-Shyong Tzou, Wen-Der Wang, Yet-Ran Chen
Software Mentions: 1
Published: over 6 years ago
10.1186/s12870-019-2223-y
Receptor kinase FERONIA regulates flowering time in Arabidopsis
Cited by: 23
Author(s): Long Wang, Tao Yang, Qinlu Lin, Bingqian Wang, Li Xu, Sheng Luan
Software Mentions: 1
Published: almost 5 years ago
10.1186/s12870-017-1065-8
Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses
Cited by: 88
Author(s): Zhaoen Yang, Qian Gong, Wenqiang Qin, Zuoren Yang, Yuan Cheng, Lili Lu, Xianping Ge, Chaojun Zhang, Zhipeng Wu
Software Mentions: 1
Published: over 7 years ago
10.3390/genes10120993
Identification of Key Genes Involved in Embryo Development and Differential Oil Accumulation in Two Contrasting Maize Genotypes
Cited by: 11
Author(s): Xiangxiang Zhang, Meiyan Hong, Hongping Wan, Lixia Luo, Zeen Yu, Ruixing Guo
Software Mentions: 1
Published: almost 5 years ago
10.1534/g3.114.013532
Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the <i>Drosophila melanogaster</i> Group
Cited by: 15
Author(s): Rebekah L. Rogers, Ling Shao, Jaleal Sanjak, Peter Andolfatto, Kevin R. Thornton
Software Mentions: 1
Published: almost 10 years ago
10.3389/fpls.2019.01536
QTL and Transcriptomic Analyses Implicate Cuticle Transcription Factor SHINE as a Source of Natural Variation for Epidermal Traits in Cucumber Fruit
Cited by: 11
Author(s): Stephanie Rett-Cadman, Marivi Colle, Ben N. Mansfeld, Cornelius S. Barry, Yuhui Wang, Yiqun Weng, Lei Gao, Zhangjun Fei, Rebecca Grumet
Software Mentions: 1
Published: almost 5 years ago
10.1038/srep10314
Integrated Genomics Identifies Convergence of Ankylosing Spondylitis with Global Immune Mediated Disease Pathways
Cited by: 20
Author(s): Mohammed Uddin, D. Codner, S M Mahmud Hasan, Stephen W. Scherer, Darren D. O’Rielly, Proton Rahman
Software Mentions: 1
Published: over 9 years ago
10.1186/s12870-019-1960-2
Transcriptome analysis revealed expression of genes related to anthocyanin biosynthesis in eggplant (Solanum melongena L.) under high-temperature stress
Cited by: 46
Author(s): Shengmei Zhang, Aidong Zhang, Xuexia Wu, Zongwen Zhu, Zuofen Yang, Yuelin Zhu, Dingshi Zha
Software Mentions: 1
Published: about 5 years ago
10.3389/fpls.2020.584167
The Ankyrin-Repeat Gene GmANK114 Confers Drought and Salt Tolerance in Arabidopsis and Soybean
Cited by: 23
Author(s): Juan-Ying Zhao, Zhiwei Lü, Yi Sun, Zhengwu Fang, Jun Chen, Yongbin Zhou, Ming Chen, You-Zhi Ma, Zhao-Shi Xu, Donghong Min
Software Mentions: 1
Published: about 4 years ago
10.1038/srep18019
Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome
Cited by: 12
Author(s): Meili Chen, Yibo Hu, Jingxing Liu, Qi Wu, Chenglin Zhang, Jun Yu, Jingfa Xiao, Fuwen Wei, Jiayan Wu
Software Mentions: 1
Published: almost 9 years ago
10.3389/fphys.2015.00377
Maternal Melatonin Therapy Rescues Prenatal Dexamethasone and Postnatal High-Fat Diet Induced Programmed Hypertension in Male Rat Offspring
Cited by: 38
Author(s): You‐Lin Tain, Jiunn‐Ming Sheen, Hong‐Ren Yu, Chih‐Cheng Chen, Mao‐Meng Tiao, Chien‐Ning Hsu, Yu‐Ju Lin, Kuang-Che Kuo, Laura Huang
Software Mentions: 1
Published: almost 9 years ago
10.3389/fonc.2020.00576
Transducin-Like Enhancer of Split-1 Inhibits Malignant Behaviors in vitro and Predicts a Better Prognosis in Pancreatic Ductal Adenocarcinoma
Cited by: 5
Author(s): Yizhi Wang, Deshan Yuan, Li Zhou, Liang Zeng, Weixun Zhou, Jun Lü, Bolun Jiang, Lei You, Junchao Guo, Yupei Zhao
Software Mentions: 1
Published: over 4 years ago
10.1186/1471-2105-15-188
An integrative method to normalize RNA-Seq data
Cited by: 18
Author(s): Cyril Filloux, Cédric Meersseman, Romain Philippe, Lionel Forestier, Christophe Klopp, Dominique Rocha, Abderrahman Maftah, P. Teufel Daniel
Software Mentions: 1
Published: over 10 years ago
10.1038/srep24507
A Network of Splice Isoforms for the Mouse
Cited by: 18
Author(s): Hong Dong Li, Rajasree Menon, Ridvan Eksi, Aysam Guerler, Yang Zhang, Gilbert S. Omenn, Yuanfang Guan
Software Mentions: 1
Published: over 8 years ago
10.3389/fmicb.2020.01808
Transcriptomic Analysis of Rhodococcus opacus R7 Grown on o-Xylene by RNA-Seq
Cited by: 9
Author(s): Jessica Zampolli, Alessandra Di Canito, Andrea Manconi, Luciano Milanesi, Patrizia Di Gennaro, Alessandro Orro
Software Mentions: 1
Published: over 4 years ago