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: HTSeq

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

A framework to process and analyze data from high-throughput sequencing (HTS) assays
79 versions
Latest release: over 1 year ago
3 dependent packages
21,995 downloads last month

Papers Mentioning HTSeq 3,071

10.1186/s13059-015-0666-5
Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo
Cited by: 82
Author(s): Masahiko Imashimizu, Hiroki Takahashi, Taku Oshima, Carl McIntosh, Mikhail Bubunenko, Donald L. Court, Mikhail Kashlev
Software Mentions: 2
Published: over 9 years ago
10.1093/dnares/dsaa015
Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale <i>Lotus japonicus</i> Gifu genome sequence
Cited by: 30
Author(s): Nadia Kamal, Terry Mun, Dugald Reid, JL Lin, Turgut Yiğit Akyol, Niels Sandal, Torben Asp, Hideki Hirakawa, Jens Stougaard, Klaus Mayer, Shusei Sato, Stig Uggerhøj Andersen
Software Mentions: 2
Published: over 4 years ago
10.1186/s13059-015-0684-3
Scalable microfluidics for single-cell RNA printing and sequencing
Cited by: 111
Author(s): Sugata Bose, Zhenmao Wan, A. J. H. Carr, Abbas H. Rizvi, G. Vieira, Dana Pe’er, Peter A. Sims
Software Mentions: 2
Published: over 9 years ago
10.1186/s13059-015-0732-z
Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies
Cited by: 31
Author(s): Philip A. Ruzycki, Nicholas M. Tran, Vladimir J. Kefalov, Alexander V. Kolesnikov, Shiming Chen
Software Mentions: 2
Published: about 9 years ago
10.1093/dnares/dsz009
Analysis of an improved Cyanophora paradoxa genome assembly
Cited by: 32
Author(s): Dana C. Price, Ursula Goodenough, Robyn Roth, Jae‐Hyeok Lee, Thamali Kariyawasam, Marek Mutwil, Camilla Ferrari, Fabio Facchinelli, Steven Ball, Ugo Cenci, Cheong Xin Chan, Nicole Wagner, Hwan Su Yoon, Andreas Weber, Debashish Bhattacharya
Software Mentions: 2
Published: over 5 years ago
10.1016/j.dnarep.2019.06.006
The roles of the human SETMAR (Metnase) protein in illegitimate DNA recombination and non-homologous end joining repair
Cited by: 14
Author(s): Michael Tellier, Ronald Chalmers
Software Mentions: 2
Published: over 5 years ago
10.1186/s13059-015-0867-y
Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes
Cited by: 44
Author(s): Dongying Gao, Yupeng Li, Kyung Do Kim, Brian Abernathy, Scott A. Jackson
Software Mentions: 2
Published: almost 9 years ago
10.7554/eLife.18904
Oxytocin improves behavioral and electrophysiological deficits in a novel Shank3-deficient rat
Cited by: 112
Author(s): Hala Harony‐Nicolas, Maya Kay, Johann du Hoffmann, Matthew Klein, Ozlem Bozdagi-Gunal, Mohammed Riad, Nikolaos P. Daskalakis, Sankalp Sonar, Pablo E. Castillo, Patrick R. Hof, Matthew L. Shapiro, Mark G. Baxter, Shlomo Wagner, Joseph D. Buxbaum
Software Mentions: 2
Published: almost 8 years ago
10.1038/s42003-020-01297-2
Redundant type II cadherins define neuroepithelial cell states for cytoarchitectonic robustness
Cited by: 9
Author(s): Kou Hiraga, Yukiko Inoue, Junko Asami, Mayuko Hotta, Yuki Morimoto, Shoji Tatsumoto, Mikio Hoshino, Yasuhiro Go, Tohru Inoue
Software Mentions: 2
Published: about 4 years ago
10.1186/s13059-016-0990-4
Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma
Cited by: 78
Author(s): Bruna Corrêa, Patrícia Rosa de Araújo, Mu Qiao, Suzanne Perea Burns, Chen Chen, Richard Schlegel, Seema Agarwal, Pedro A. F. Galante, Luiz O. F. Penalva
Software Mentions: 2
Published: over 8 years ago
10.1038/s42003-021-01940-6
INPP4B protects from metabolic syndrome and associated disorders
Cited by: 7
Author(s): Manqi Zhang, Yasemin Ceyhan, Elena M. Kaftanovskaya, Judy L. Vasquez, Jean Vacher, Filip K. Knop, Lubov Nathanson, Alexander I. Agoulnik, Michael Ittmann, Irina U. Agoulnik
Software Mentions: 2
Published: over 3 years ago
10.1038/s42003-021-02160-8
Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation
Cited by: 6
Author(s): Taisei Kikuchi, Mehmet Dayı, Vicky L. Hunt, Kenji Ishiwata, Atsushi Toyoda, Asuka Kounosu, Simo Sun, Y. Maeda, Yoko Kondo, Belkisyolé Alarcón de Noya, Óscar Noya, Satoshi Kojima, Toshiaki Kuramochi, Haruhiko Maruyama
Software Mentions: 2
Published: over 3 years ago
10.1186/s13059-016-1092-z
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures
Cited by: 622
Author(s): Yasin Şenbabaoğlu, Ron S. Gejman, Andrew Winer, Ming Liu, Eliezer M. Van Allen, Guillermo Velasco, Diana Miao, Irina Ostrovnaya, Esther Drill, Augustin Luna, Nils Weinhold, William Lee, Brandon Manley, Danny N. Khalil, Samuel D. Kaffenberger, Yingbei Chen, Ludmila Danilova, Martin H. Voss, Jonathan Coleman, Paul Russo, Victor E. Reuter, Timothy A. Chan, Emily H. Cheng, David A. Scheinberg, Toni K. Choueiri, James J. Hsieh, Chris Sander, A. Ari Hakimi
Software Mentions: 2
Published: about 8 years ago
10.1186/s13059-016-1139-1
Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain
Cited by: 245
Author(s): Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xiaoteng Jia, Ronald Micura, Alexandra Lusser
Software Mentions: 2
Published: almost 8 years ago
10.7554/eLife.29702
Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism
Cited by: 62
Author(s): William Putzbach, Quan Gao, Monal Patel, Stijn van Dongen, Ashley Haluck-Kangas, Aishe A. Sarshad, Elizabeth T. Bartom, Kwang Youn Kim, Denise M. Scholtens, Markus Hafner, Jonathan C. Zhao, Andrea E. Murmann, Marcus E. Peter
Software Mentions: 2
Published: about 7 years ago
10.1186/s13059-017-1201-7
Multiple gene movements into and out of haploid sex chromosomes
Cited by: 49
Author(s): Agnieszka P. Lipinska, Nicholas R. T. Toda, Svenja Heesch, Akira F. Peters, J. Mark Cock, Susana M. Coelho
Software Mentions: 2
Published: over 7 years ago
10.1186/s13059-017-1237-8
CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion
Cited by: 136
Author(s): Haiwei Mou, Jordan L. Smith, Lingtao Peng, Hao Yin, Jill E. Moore, Xiao‐Ou Zhang, Chun‐Qing Song, Ankur Sheel, Qiongqiong Wu, Deniz M. Özata, Yingxiang Li, Daniel G. Anderson, Charles P. Emerson, Erik J. Sontheimer, Melissa J. Moore, Zhiping Weng, Wen Xue
Software Mentions: 2
Published: over 7 years ago
10.1038/s42003-019-0284-y
Changes in long-range rDNA-genomic interactions associate with altered RNA polymerase II gene programs during malignant transformation
Cited by: 30
Author(s): Jeannine Diesch, Megan J. Bywater, Elaine Sanij, Donald P. Cameron, William Schierding, Natalie Brajanovski, Jinbae Son, Jirawas Sornkom, Nadine Hein, M. Evers, Richard B. Pearson, Grant A. McArthur, Austen R. D. Ganley, Justin M. O’Sullivan, Ross D. Hannan, Gretchen Poortinga
Software Mentions: 2
Published: almost 6 years ago
10.1038/s42003-021-01907-7
GmBTB/POZ promotes the ubiquitination and degradation of LHP1 to regulate the response of soybean to Phytophthora sojae
Cited by: 26
Author(s): Chuanzhong Zhang, Qun Cheng, Huiyu Wang, Hong Gao, Xin Fang, Xi Chen, Ming Zhao, Wanling Wei, Bo Song, Shanshan Liu, Jianzhong Wu, Shuzhen Zhang, Pengfei Xu
Software Mentions: 2
Published: over 3 years ago
10.1016/j.ymthe.2018.08.023
Recombinant BCG Overexpressing phoP-phoR Confers Enhanced Protection against Tuberculosis
Cited by: 14
Author(s): Sang Kyun Ahn, Vanessa Tran, Andrea S. Leung, Mark Ng, Ming Li, Jun Liu
Software Mentions: 2
Published: almost 6 years ago
10.1038/s42003-021-02541-z
Optimising PHBV biopolymer production in haloarchaea via CRISPRi-mediated redirection of carbon flux
Cited by: 13
Author(s): Lin Lin, Junyu Chen, Ruchira Mitra, Quanxiu Gao, Feiyue Cheng, Tong Xu, Zhenqiang Zuo, Hua Xiang, Jing Han
Software Mentions: 2
Published: about 3 years ago
10.1038/s42003-021-01708-y
Insulin-like 3 affects zebrafish spermatogenic cells directly and via Sertoli cells
Cited by: 8
Author(s): Diego Crespo, Luiz H. C. Assis, Yu Ting Zhang, Diego Safian, Tomasz Furmanek, Kai Ove Skaftnesmo, Birgitta Norberg, Wei Ge, Yung Ching Choi, Marjo J. den Broeder, Juliette Legler, Jan Bogerd, Rüdiger Schulz
Software Mentions: 2
Published: almost 4 years ago
10.1186/s13059-019-1651-1
Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells
Cited by: 49
Author(s): Shraddha Sharma, Jianmin Wang, Emad Alqassim, Scott Portwood, Eduardo Cortes Gomez, Orla Maguire, Per H. Basse, Eunice S. Wang, Brahm H. Segal, Bora E. Baysal
Software Mentions: 2
Published: almost 6 years ago
10.1038/s42003-021-02123-z
Telomere damage promotes vascular smooth muscle cell senescence and immune cell recruitment after vessel injury
Cited by: 27
Author(s): Anna Uryga, Mandy O.J. Grootaert, Abel Martin Garrido, Sebnem Oc, Kirsty Foote, Joel Chappell, Alison Finigan, Francesca Rossiello, Fabrizio d’Adda di Fagagna, Dimitra Aravani, Helle F. Jørgensen, Martin R. Bennett
Software Mentions: 2
Published: over 3 years ago
10.1038/s41380-018-0260-9
SSRIs target prefrontal to raphe circuits during development modulating synaptic connectivity and emotional behavior
Cited by: 52
Author(s): Mariano Soiza-Reilly, Frank J. Meye, Jimmy Olusakin, Ludovic Telley, Emilie Petit, X Chen, Manuel Mameli, Denis Jabaudon, J-Y Sze, Patricia Gaspar
Software Mentions: 2
Published: about 6 years ago
10.1038/s42003-020-01613-w
LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes
Cited by: 12
Author(s): Carl Herdenberg, Pascal M. Mutie, Ola Billing, Ahmad Abdullah, Rona J. Strawbridge, Ingrid Dahlman, Simon Tuck, Camilla Holmlund, Peter Arner, Roger Henriksson, Paul W. Franks, Håkan Hedman
Software Mentions: 2
Published: almost 4 years ago
10.1186/s13059-020-02097-x
Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution
Cited by: 69
Author(s): Catherine L. Peichel, Shaugnessy R. McCann, Joseph A. Ross, Alice F.S. Naftaly, James R. Urton, Jennifer N. Cech, Jane Grimwood, Jeremy Schmutz, R Myers, David M. Kingsley, Michael A. White
Software Mentions: 2
Published: over 4 years ago
10.1038/s42003-019-0334-5
Murine osteoclasts secrete serine protease HtrA1 capable of degrading osteoprotegerin in the bone microenvironment
Cited by: 16
Author(s): Nagahiro Ochiai, Yutaka Nakachi, Tomotaka Yokoo, Takahiro Ichihara, Tore Eriksson, Yuki Yonemoto, Takumi Kato, Hitoshi Ogata, Natsuko Fujimoto, Yasuhiro Kobayashi, Nobuyuki Udagawa, Shinsuke Kaku, Tomokazu Ueki, Yasushi Okazaki, Naoyuki Takahashi, Toshio Suda
Software Mentions: 2
Published: over 5 years ago
10.1002/ctm2.221
Influence of oncogenic mutations and tumor microenvironment alterations on extranodal invasion in diffuse large B‐cell lymphoma
Cited by: 40
Author(s): Rong Shen, Pengpeng Xu, Nan Wang, Hongmei Yi, Lei Dong, Di Fu, Jinyan Huang, Huizhen Huang, Anne Janin, Shu Cheng, Li Wang, Wei‐Li Zhao
Software Mentions: 2
Published: about 4 years ago
10.1186/s13059-021-02384-1
Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells
Cited by: 29
Author(s): Atsushi Onodera, Edahí González-Avalos, Chan-Wang Jerry Lio, Romain O. Georges, Alfonso Bellacosa, Toshinori Nakayama, Anjana Rao
Software Mentions: 2
Published: over 3 years ago
10.1016/j.clim.2015.05.020
Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders
Cited by: 84
Author(s): Pauline A. van Schouwenburg, Emma E Davenport, Anne‐Kathrin Kienzler, Ishita Marwah, Benjamin Wright, Mary Lucas, Tomas Malinauskas, Hilary C. Martin, Helen Lockstone, Jean‐Baptiste Cazier, Helen Chapel, Julian C. Knight, Smita Y. Patel
Software Mentions: 2
Published: about 9 years ago
10.1093/gbe/evv013
Spatial Dynamics of Evolving Dosage Compensation in a Young Sex Chromosome System
Cited by: 32
Author(s): Roland Schultheiß, Heidi M. Viitaniemi, Erica H. Leder
Software Mentions: 2
Published: almost 10 years ago
10.1186/s13148-015-0057-5
Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites
Cited by: 50
Author(s): Sonja Hänzelmann, Fabian Beier, Eduardo Gade Gusmao, Carmen M. Koch, Sebastian Hummel, Iryna Charapitsa, Sylvia Joussen, Vladimı́r Beneš, Tim H. Brümmendorf, George Reid, Ivan G. Costa, Wolfgang Wagner
Software Mentions: 2
Published: over 9 years ago
10.1093/gbe/evw004
Dosage compensation in the African malaria mosquito<i>Anopheles gambiae</i>
Cited by: 26
Author(s): Graham Rose, Elzbieta Krzywińska, Jan Kim, Loic Revuelta, Luca Ferretti, Jaroslaw Krzywinski
Software Mentions: 2
Published: almost 9 years ago
10.1186/s13148-018-0527-7
Vitamin C increases 5-hydroxymethylcytosine level and inhibits the growth of bladder cancer
Cited by: 41
Author(s): Peng Ding, Guangzhe Ge, Yanqing Gong, Yonghao Zhan, Shiming He, Bao Guan, Yifan Li, Ziying Xu, Han Hao, Zhisong He, Gengyan Xiong, Cuijian Zhang, Yue Shi, Yuanyuan Zhou, Weimin Ci, Xuesong Li, Liqun Zhou
Software Mentions: 2
Published: over 6 years ago
10.1093/gbe/evz130
First Estimation of the Spontaneous Mutation Rate in Diatoms
Cited by: 47
Author(s): Marc Krasovec, Sophie Sanchez-Brosseau, Gwenaël Piganeau
Software Mentions: 2
Published: over 5 years ago
10.1186/s13073-014-0111-5
An integrated transcriptome and expressed variant analysis of sepsis survival and death
Cited by: 68
Author(s): Ephraim L. Tsalik, Raymond J. Langley, Darrell L. Dinwiddie, Neil Miller, Byunggil Yoo, Jennifer C. van Velkinburgh, Laurie D. Smith, Isabelle Thiffault, Anja Kathrin Jaehne, Ashlee Valente, Ricardo Henao, Xin Yuan, Seth W. Glickman, Brandon J. Rice, Micah T. McClain, Lawrence Carin, G. Ralph Corey, Geoffrey S. Ginsburg, Charles B. Cairns, Ronny M. Otero, Vance G. Fowler, Emanuel P. Rivers, Christopher W. Woods, Stephen F. Kingsmore
Software Mentions: 2
Published: about 10 years ago
10.1186/s13073-015-0229-0
An integrative systems genetics approach reveals potential causal genes and pathways related to obesity
Cited by: 31
Author(s): Lisette J. A. Kogelman, Daria V. Zhernakova, Harm-Jan Westra, Susanna Cirera, Merete Fredholm, Lude Franke, Haja N. Kadarmideen
Software Mentions: 2
Published: about 9 years ago
10.1161/CIRCULATIONAHA.120.051171
Extracellular Tuning of Mitochondrial Respiration Leads to Aortic Aneurysm
Cited by: 48
Author(s): Jorge Oller, Enrique Gabandé‐Rodríguez, María Jesús Ruiz-Rodríguez, Gabriela Desdín-Micó, Juan Aranda, Raquel Rodrigues‐Díez, C Ballesteros-Martinez, Eva Blanco, Raquel Roldán-Montero, Pedro Acuña, Alberto Gil, Carlos Esteban Martín-López, J. Francisco Nistal, Christian L. Lino Cárdenas, Mark E. Lindsay, José Luis Martı́n-Ventura, Ana M. Briones, Juan Miguel Redondo, Marı́a Mittelbrunn
Software Mentions: 2
Published: over 3 years ago
10.7554/eLife.47791
Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1
Cited by: 59
Author(s): Anna E. Masser, Wenjing Kang, Joydeep Roy, Jayasankar Mohanakrishnan Kaimal, Jany Quintana-Cordero, Marc R. Friedländer, Claes Andréasson
Software Mentions: 2
Published: about 5 years ago
10.1186/s13073-018-0558-x
Disease-specific regulation of gene expression in a comparative analysis of juvenile idiopathic arthritis and inflammatory bowel disease
Cited by: 35
Author(s): Angela Mo, Urko M. Marigorta, Dalia Arafat, Lai Hin Kimi Chan, Lori Ponder, Se Ryeong Jang, Jarod Prince, Subra Kugathasan, Sampath Prahalad, Greg Gibson
Software Mentions: 2
Published: over 6 years ago
10.1186/s13073-019-0620-3
BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma
Cited by: 79
Author(s): Raunak Shrestha, Noushin Nabavi, Yen-Yi Lin, Fan Mo, Shawn Anderson, Stanislav V. Volik, Hans Adomat, Dong Lin, Hui Xue, Xin Dong, Robert Shukin, Robert H. Bell, Brian McConeghy, Anne Haegert, Sonal Brahmbhatt, Estelle Li, Htoo Zarni Oo, Antonio Hurtado-Coll, Ladan Fazli, Joshua Zhou, Yarrow J. McConnell, Andrea McCart, Andrew M. Lowy, Gregg B. Morin, Tianhui Chen, Mads Daugaard, S. Cenk Şahinalp, Faraz Hach, Stéphane Le Bihan, Martin Gleave, Yuzhuo Wang, Andrew Churg, Colin C. Collins
Software Mentions: 2
Published: almost 6 years ago
10.3390/cells7060055
Nanopipettes as Monitoring Probes for the Single Living Cell: State of the Art and Future Directions in Molecular Biology
Cited by: 28
Author(s): Gonca Bülbül, Gepoliano Chaves, Olivier Joseph, Rıfat Emrah Özel, Nader Pourmand
Software Mentions: 2
Published: over 6 years ago
10.3390/cells10040736
Control of Protein and Energy Metabolism in the Pituitary Gland in Response to Three-Week Running Training in Adult Male Mice
Cited by: 3
Author(s): Christina Walz, Julia Brenmoehl, Nares Trakooljul, Antonia Noce, Caroline Caffier, Daniela Ohde, Martina Langhammer, Klaus Wimmers, Siriluck Ponsuksili, Andreas Hoeflich
Software Mentions: 2
Published: over 3 years ago
10.1002/1878-0261.12489
Identification of lnc <scp>RNA</scp> s associated with early‐stage breast cancer and their prognostic implications
Cited by: 39
Author(s): Arunagiri Kuha Deva Magendhra Rao, Krishna Patel, Suneetha Korivi Jyothiraj, Balaiah Meenakumari, Shirley Sundersingh, Velusami Sridevi, Thangarajan Rajkumar, Akhilesh Pandey, Aditi Chatterjee, Harsha Gowda, Samson Mani
Software Mentions: 2
Published: over 5 years ago
10.3390/cells10092403
Analysis of the Reversible Impact of the Chemodrug Busulfan on Mouse Testes
Cited by: 5
Author(s): Laura Thirouard, Hélène Holota, Mélusine Monrose, Manon Garcia, Angélique De Haze, Jean-Paul Saru, Françoise Caira, Claude Beaudoin, David H. Volle
Software Mentions: 2
Published: about 3 years ago
10.3390/cells8020112
Suppression of IgE-Independent Degranulation of Murine Connective Tissue-Type Mast Cells by Dexamethasone
Cited by: 10
Author(s): Keiko Yamada, Hitomi Sato, Kazuma Sakamaki, Mayumi Kamada, Yasushi Okuno, Nobuyuki Fukuishi, Kazuyuki Furuta, Satoshi Tanaka
Software Mentions: 2
Published: almost 6 years ago
10.1016/j.stem.2020.10.018
Membrane Tension Gates ERK-Mediated Regulation of Pluripotent Cell Fate
Cited by: 94
Author(s): Henry De Belly, Aki Stubb, Akira Yanagida, Céline Labouesse, Philip H. Jones, Ewa K. Paluch, Kevin J. Chalut
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.ppat.1009475
Paratransgenic manipulation of a tsetse microRNA alters the physiological homeostasis of the fly’s midgut environment
Cited by: 9
Author(s): Yang Liu, Brian L. Weiss, Adeline E Williams, Emre Aksoy, Alessandra de Silva Orfano, Jae Hak Son, Ya Fei Wu, Aurélien Vigneron, Mehmet Karakuş, Serap Aksoy
Software Mentions: 2
Published: over 3 years ago
10.1016/j.postharvbio.2020.111420
New insights into the effects of ethylene on ABA catabolism, sweetening and dormancy in stored potato tubers
Cited by: 18
Author(s): Roberta Tosetti, Amanda J. Waters, Gemma A. Chope, Katherine Cools, M. Carmen Alamar, Simon C. McWilliam, Andrew J. Thompson, Leon A. Terry
Software Mentions: 2
Published: over 3 years ago
10.1186/s13024-017-0212-x
Hexokinases link DJ-1 to the PINK1/parkin pathway
Cited by: 41
Author(s): David N. Hauser, Adamantios Mamais, Mary Anne Conti, Christopher T. Primiani, R. Ileng Kumaran, Allissa Dillman, Rebekah G. Langston, Alexandra Beilina, Joseph H. Garcia, Alberto Díaz‐Ruiz, Michel Bernier, Fabienne C. Fiesel, Xu Hou, Wolfdieter Springer, Yán Li, Rafael de Cabo, Mark Cookson
Software Mentions: 2
Published: about 7 years ago
10.1007/s13238-016-0278-1
Vitamin C alleviates aging defects in a stem cell model for Werner syndrome
Cited by: 52
Author(s): Ying Liu, Weizhou Zhang, Liang Chang, Yan Han, Liang Sun, Xuejun Gong, Hong Tang, Zunpeng Liu, Huichao Deng, Yanxia Ye, Yu Wang, Jian Li, Jie Qiao, Jing Qu, Weiqi Zhang, Guanghui Liu
Software Mentions: 2
Published: over 8 years ago
10.1007/s13238-018-0560-5
CRISPR/Cas9-mediated gene knockout reveals a guardian role of NF-κB/RelA in maintaining the homeostasis of human vascular cells
Cited by: 17
Author(s): Ping Wang, Zunpeng Liu, Xiaoqian Zhang, Jingyi Li, Liang Sun, Zhenyu Ju, Jian Li, Piu Chan, Guanghui Liu, Weiqi Zhang, Moshi Song, Jing Qu
Software Mentions: 2
Published: over 6 years ago
10.1007/s13238-019-0608-1
Modeling CADASIL vascular pathologies with patient-derived induced pluripotent stem cells
Cited by: 38
Author(s): Ling Chen, Zunpeng Liu, Moshi Song, Weiqi Zhang, Si Wang, Xiaoqian Liu, Shuai Ma, Shuhui Sun, Ling Fu, Qun Chu, Juan Carlos Izpisúa Belmonte, Zhaoxia Wang, Jing Qu, Yun Yuan, Guang Hui Liu
Software Mentions: 2
Published: almost 6 years ago
10.1007/s13238-018-0567-y
Chemical screen identifies a geroprotective role of quercetin in premature aging
Cited by: 78
Author(s): Li Geng, Zunpeng Liu, Weiqi Zhang, Wei Li, Zeming Wu, Wei Wang, Rui Ren, Yao Su, Peichang Wang, Liang Sun, Zhenyu Ju, Piu Chan, Moshi Song, Jing Qu, Guanghui Liu
Software Mentions: 2
Published: over 6 years ago
10.1007/s13238-019-0610-7
Telomere-dependent and telomere-independent roles of RAP1 in regulating human stem cell homeostasis
Cited by: 30
Author(s): Xing Zhang, Zunpeng Liu, Xiaoqian Liu, Si Wang, Yiyuan Zhang, Xiaojuan He, Shuhui Sun, Shuai Ma, Ng Shyh‐Chang, Feng Liu, Qiang Wang, Xiaoqun Wang, Lin Liu, Weiqi Zhang, Moshi Song, Guanghui Liu, Jing Qu
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0160970
Whole Transcriptome Profiling Identifies CD93 and Other Plasma Cell Survival Factor Genes Associated with Measles-Specific Antibody Response after Vaccination
Cited by: 17
Author(s): Iana H. Haralambieva, Michael T. Zimmermann, Inna G. Ovsyannikova, Diane E. Grill, Ann L. Oberg, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0143378
Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos
Cited by: 9
Author(s): Rongping Zhang, Hehe Liu, Junying Liu, Jiwei Hu, Xiping Yan, Ding-min-cheng Wang, Liang Li, Jiwen Wang
Software Mentions: 2
Published: almost 9 years ago
10.1007/s13238-020-00740-8
Generation of a Hutchinson–Gilford progeria syndrome monkey model by base editing
Cited by: 44
Author(s): Fang Wang, Weiqi Zhang, Qiong Yang, Yu Kang, Yanling Fan, Jingkuan Wei, Zunpeng Liu, Shao‐Xing Dai, Hao Li, Zifan Li, Lizhu Xu, Chu Chu, Jing Qu, Chenyang Si, Weizhi Ji, Guanghui Liu, Chengzu Long, Yuyu Niu
Software Mentions: 2
Published: over 4 years ago
10.1080/15476286.2018.1532253
RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B
Cited by: 9
Author(s): Laura Broglia, Solange Lise Materne, Anne-Laure Lécrivain, Karin Hahnke, Anaïs Le Rhun, Emmanuelle Charpentier
Software Mentions: 2
Published: about 6 years ago
10.1098/rsos.171718
Differential gene expression is not required for facultative sex allocation: a transcriptome analysis of brain tissue in the parasitoid wasp <i>Nasonia vitripennis</i>
Cited by: 6
Author(s): Nicola Cook, Rebecca A. Boulton, Jade Green, Urmi Trivedi, Eran Tauber, Bart Pannebakker, Michael G. Ritchie, David M. Shuker
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pone.0165953
Genome-Wide Identification, Characterization, and Stress-Responsive Expression Profiling of Genes Encoding LEA (Late Embryogenesis Abundant) Proteins in Moso Bamboo (Phyllostachys edulis)
Cited by: 32
Author(s): Zhuo Huang, Xiaojuan Zhong, Jun He, Si-Han Jin, Han-Du Guo, Xiaofang Yu, Yujue Zhou, Xi Li, Min Ma, Qibing Chen, Hai Long
Software Mentions: 2
Published: about 8 years ago
10.1016/j.redox.2020.101434
Redox activation of excitatory pathways in auditory neurons as mechanism of age-related hearing loss
Cited by: 28
Author(s): Francis Rousset, German Nacher-Soler, Marta Coelho, Sten Ilmjärv, Vivianne Beatrix Christina Kokje, Antoine Marteyn, Yves Cambet, Michael Perny, Marta Roccio, Vincent Jaquet, Pascal Senn, Karl Heinz Krause
Software Mentions: 2
Published: almost 5 years ago
10.1016/j.redox.2021.102030
Compensatory expression of NRF2-dependent antioxidant genes is required to overcome the lethal effects of Kv11.1 activation in breast cancer cells and PDOs
Cited by: 5
Author(s): Vitalyi Senyuk, Najmeh Eskandari, Ying Jiang, Rebeca García-Varela, Rachel Sundstrom, Luigi Leanza, Roberta Peruzzo, Mark E. Burkard, Richard D. Minshall, Sandro Gentile
Software Mentions: 2
Published: about 3 years ago
10.7554/eLife.39823
A virus-packageable CRISPR screen identifies host factors mediating interferon inhibition of HIV
Cited by: 94
Author(s): Molly OhAinle, Louisa Helms, Jolien Vermeíre, Ferdinand Roesch, Daryl Humes, Ryan Basom, Jeffrey J. Delrow, Julie Overbaugh, Michael Emerman
Software Mentions: 2
Published: almost 6 years ago
10.1186/s12958-021-00702-7
Irisin deletion induces a decrease in growth and fertility in mice
Cited by: 12
Author(s): Yunjing Luo, Xiaoyong Qiao, Yaxian Ma, Hongxia Deng, Charles C. Xu, Liangzhi Xu
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0241966
Transcripts of wheat at a target locus on chromosome 6B associated with increased yield, leaf mass and chlorophyll index under combined drought and heat stress
Cited by: 3
Author(s): Jessica Schmidt, Melissa Garcia, Chris Brien, Priyanka Kalambettu, Trevor Garnett, Delphine Fleury, Penny J. Tricker
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0217343
Identification of two molecular subtypes in canine mast cell tumours through gene expression profiling
Cited by: 6
Author(s): Lidia Hildebrand Pulz, Camila Neri Barra, Pâmela Almeida Alexandre, Greice Cestari Huete, Karine Germano Cadrobbi, Adriana Tomoko Nishiya, Sílvio Henrique de Freitas, Heidge Fukumasu, Ricardo de Francisco Strefezzi
Software Mentions: 2
Published: over 5 years ago
10.1186/s12931-019-1038-6
AGER expression and alternative splicing in bronchial biopsies of smokers and never smokers
Cited by: 20
Author(s): Alen Faiz, Maarten van den Berge, Cornelis J Vermeulen, Nick H. T. ten Hacken, Victor Guryev, Simon D. Pouwels
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0156045
Transcriptome Analysis and Gene Identification in the Pulmonary Artery of Broilers with Ascites Syndrome
Cited by: 21
Author(s): Fei Yang, Cao H, Qingyang Xiao, Xiaomin Guo, Zhuang Yu, Caiying Zhang, Tiancheng Wang, Huayuan Lin, Yan-Chun Song, Guoliang Hu, Ping Liu
Software Mentions: 2
Published: over 8 years ago
10.1186/s12284-021-00474-z
RETRACTED ARTICLE: Light Harvesting-like Protein 3 Interacts with Phytoene Synthase and Is Necessary for Carotenoid and Chlorophyll Biosynthesis in Rice
Cited by: 0
Author(s): Yun Feng, Debatosh Das, Tao Song, Jianhua Zhang
Software Mentions: 2
Published: over 3 years ago
10.1126/sciadv.aaw6710
The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction to control tumor progression
Cited by: 34
Author(s): Yingjuan Qian, Lei Zhang, Mingyang Cai, Hongxia Li, Heming Xu, Huan Yang, Zhongfang Zhao, Suhn Kyong Rhie, Peggy J. Farnham, Jiandang Shi, Wange Lu
Software Mentions: 2
Published: over 5 years ago
10.1126/sciadv.aaw4717
Neuronal GPCR NPR-8 regulates <i>C. elegans</i> defense against pathogen infection
Cited by: 34
Author(s): Durai Sellegounder, Yiyong Liu, Phillip Wibisono, Chia-Hui Chen, David J. Leap, Jesse Sun
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pone.0179762
Tumor Necrosis Factor dynamically regulates the mRNA stabilome in rheumatoid arthritis fibroblast-like synoviocytes
Cited by: 20
Author(s): Konstantinos Loupasakis, David Kuo, Upneet K. Sokhi, Cheol Ho Sohn, Bethany Syracuse, Ευγενία Γιαννοπούλου, Sung Ho Park, Hee‐Ju Kang, Gunnar Rätsch, Lionel B. Ivashkiv, George D. Kalliolias
Software Mentions: 2
Published: over 7 years ago
10.1016/j.molmet.2018.11.010
Deletion of myeloid IRS2 enhances adipose tissue sympathetic nerve function and limits obesity
Cited by: 16
Author(s): Marie-Therese Rached, Steven Millership, Silvia Pedroni, Agharul I. Choudhury, Ana S.H. Costa, Darran G. Hardy, Justyna Glegola, Elaine E. Irvine, Colin Selman, Megan Woodberry, Vijay K. Yadav, Sanjay Khadayate, António Vidal-Puig, Samuel Virtue, Christian Frezza, Dominic J. Withers
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0179922
Transcriptomic analysis to uncover genes affecting cold resistance in the Chinese honey bee (Apis cerana cerana)
Cited by: 21
Author(s): Kai Xu, Qingsheng Niu, Huiting Zhao, Yali Du, Yusuo Jiang
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0128350
Putative Regulatory Factors Associated with Intramuscular Fat Content
Cited by: 66
Author(s): A. S. M. César, Luciana Correia de Almeida Regitano, James E. Koltes, Eric R. Fritz-Waters, Dante Pazzanese Duarte Lanna, G. Gasparin, Gerson Barreto Mourão, P. S. N. Oliveira, James M. Reecy, Luiz Lehmann Coutinho
Software Mentions: 2
Published: over 9 years ago
10.1016/j.ymgmr.2019.100531
Effectiveness of integrated interpretation of exome and corresponding transcriptome data for detecting splicing variants of genes associated with autosomal recessive disorders
Cited by: 9
Author(s): Mamiko Yamada, Hisato Suzuki, Yuichi Shiraishi, Kenjiro Kosaki
Software Mentions: 2
Published: almost 5 years ago
10.1126/sciadv.abi8787
Optogenetic modeling of human neuromuscular circuits in Duchenne muscular dystrophy with CRISPR and pharmacological corrections
Cited by: 14
Author(s): Amaia Paredes‐Redondo, Peter Harley, Eleni Maniati, David Ryan, Sandra Louzada, Jinhong Meng, Anna Kowala, Beiyuan Fu, Fengtang Yang, Pengtao Liu, Silvia Marino, Olivier Pourquié, Francesco Muntoni, Jun Wang, Ivo Lieberam, Yung‐Yao Lin
Software Mentions: 2
Published: about 3 years ago
10.7554/eLife.43101
Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae
Cited by: 39
Author(s): Alok Arun, Susana M. Coelho, Akira F. Peters, Simon Bourdareau, Laurent Pérès, Delphine Scornet, Martina Strittmatter, Agnieszka P. Lipinska, Haiqin Yao, Olivier Godfroy, Gabriel J Montecinos, Komlan Avia, Nicolas Macaisne, Christelle Troadec, Abdelhafid Bendahmane, J. Mark Cock
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0184974
Effects of salinity on the cellular physiological responses of Natrinema sp. J7-2
Cited by: 10
Author(s): Yadong Mei, Huan Liu, Shunxi Zhang, Ming Yang, Chun Hu, Jian Zhang, Ping Shen, Xiangdong Chen
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.pone.0244648
Transcriptomic analysis of the honey bee (Apis mellifera) queen spermathecae reveals genes that may be involved in sperm storage after mating
Cited by: 11
Author(s): Juliana Rangel, Tonya F. Shepherd, Alejandra González, Andrew Hillhouse, Kranti Konganti, Nancy H. Ing
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0215472
UV-C treatment promotes quality of early ripening apple fruit by regulating malate metabolizing genes during postharvest storage
Cited by: 19
Author(s): Jakaria Chowdhury Onik, Yajing Xie, Yuquan Duan, Xiaojia Hu, Zhidong Wang, Qiong Lin
Software Mentions: 2
Published: over 5 years ago
10.1038/s41597-019-0087-5
Activity/exercise-induced changes in the liver transcriptome after chronic spinal cord injury
Cited by: 8
Author(s): Julia H. Chariker, Sujata Saraswat Ohri, Cynthia Gomes, Fiona Brabazon, Kathryn A. Harman, Kathryn M. DeVeau, David S.K. Magnuson, Michał Hetman, Jeffrey C. Petruska, Scott R. Whittemore, Eric C. Rouchka
Software Mentions: 2
Published: over 5 years ago
10.1002/mgg3.270
Gene-centric analysis implicates nuclear encoded mitochondrial protein gene variants in migraine susceptibility
Cited by: 7
Author(s): Shani Stuart, Miles C. Benton, David Eccles, Heidi G. Sutherland, Larisa M. Haupt, Rodney Arthur Lea, Lyn R. Griffiths
Software Mentions: 2
Published: almost 8 years ago
10.7554/eLife.03189
The transcriptional response to tumorigenic polarity loss in Drosophila
Cited by: 100
Author(s): Brandon D. Bunker, Tittu Thomas Nellimoottil, Ryan M. Boileau, Anne-Kathrin Classen, David Bilder
Software Mentions: 2
Published: over 9 years ago
10.7554/eLife.19942
Genome-wide identification of neuronal activity-regulated genes in Drosophila
Cited by: 67
Author(s): Chen Xiao, Reazur Rahman, Fang Guo, Michael Rosbash
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0116309
Gene Expression Dosage Regulation in an Allopolyploid Fish
Cited by: 14
Author(s): Isa Matos, Miguel P. Machado, Manfred Schartl, M. M. Coelho
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0156453
Comprehensive RNA-Seq Analysis on the Regulation of Tomato Ripening by Exogenous Auxin
Cited by: 41
Author(s): Jiayin Li, Xiaoya Tao, Li Li, Linchun Mao, Zisheng Luo, Zia Ullah Khan, Tiejin Ying
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0098578
Digital Gene-Expression Profiling Analysis of the Cholesterol-Lowering Effects of Alfalfa Saponin Extract on Laying Hens
Cited by: 14
Author(s): Lu Zhou, Shi Ya, Rui Guo, Minggen Liang, Xiaoyan Zhu, Chengzhang Wang
Software Mentions: 2
Published: over 10 years ago
10.1038/srep14617
mirPRo–a novel standalone program for differential expression and variation analysis of miRNAs
Cited by: 34
Author(s): Jieming Shi, Min Dong, Lei Li, Lin Liu, Agustín Luz-Madrigal, Panagiotis A. Tsonis, Katia Del Rio‐Tsonis, Chun Liang
Software Mentions: 2
Published: about 9 years ago
10.1002/mgg3.1115
Identification of novel differentially expressed genes in retinas of STZ‐induced long‐term diabetic rats through RNA sequencing
Cited by: 5
Author(s): Xindan Xing, Yan Jiang, Hanying Wang, Yuan Zhang, Tian Niu, Qing Yuan, Ching‐Yi Wang, Haiyan Wang, Kun Liu
Software Mentions: 2
Published: almost 5 years ago
10.1038/srep18794
MicroRNAs in Honey Bee Caste Determination
Cited by: 93
Author(s): Regan Ashby, Sylvain Forêt, Iain Searle, Ryszard Maleszka
Software Mentions: 2
Published: almost 9 years ago
10.1038/srep21124
Comparative transcriptome analysis among parental inbred and crosses reveals the role of dominance gene expression in heterosis in Drosophila melanogaster
Cited by: 11
Author(s): Xianwen Wu, Rongni Li, Qianqian Li, Haigang Bao, Changxin Wu
Software Mentions: 2
Published: over 8 years ago
10.1038/srep24985
Characterization of key triacylglycerol biosynthesis processes in rhodococci
Cited by: 63
Author(s): Sawsan Amara, Nicolas Seghezzi, Hiroshi Otani, Carlos Díaz-Salazar, Jie Liu, Lindsay D. Eltis
Software Mentions: 2
Published: over 8 years ago
10.1038/srep25493
Large-scale rewiring of innate immunity circuitry and microRNA regulation during initial rice blast infection
Cited by: 26
Author(s): Ze-Yuan Li, Jing Xia, Zheng Chen, Yang Yu, Quanfeng Li, Yuchan Zhang, Jinping Zhang, Congying Wang, Xiaoyuan Zhu, Weixiong Zhang, Yue‐Qin Chen
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0091353
Natural Antisense Transcripts and Long Non-Coding RNA in Neurospora crassa
Cited by: 41
Author(s): Yamini Arthanari, Christian Heintzen, Sam Griffiths-Jones, Susan K. Crosthwaite
Software Mentions: 2
Published: over 10 years ago
10.1038/srep26657
The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation
Cited by: 25
Author(s): Charles C. Bell, Paulo Amaral, Anton M.F. Kalsbeek, Graham Magor, Kevin R. Gillinder, Pierre Tangermann, Lorena Di Lisio, Seth W. Cheetham, Franziska Gruhl, Jessica E. Frith, Michael R. Tallack, Ke Lin Ru, Joanna Crawford, John S. Mattick, Marcel E. Dinger, Andrew C. Perkins
Software Mentions: 2
Published: over 8 years ago
10.3390/molecules24173046
Next Generation Sequencing-Based Transcriptome Predicts Bevacizumab Efficacy in Combination with Temozolomide in Glioblastoma
Cited by: 5
Author(s): Alimu Adilijiang, Masaki Hashimoto, Yusuke Okuno, Kosuke Aoki, Fumiharu Ohka, Sachi Maeda, Kuniaki Tanahashi, Kazuya Motomura, Hiroyuki Shimizu, Junya Yamaguchi, Toshihiko Wakabayashi, Atsushi Natsume
Software Mentions: 2
Published: over 5 years ago
10.1038/srep27507
Genome-wide DNA methylation profiles changes associated with constant heat stress in pigs as measured by bisulfite sequencing
Cited by: 60
Author(s): Ya Hao, Yanjun Cui, Xianhong Gu
Software Mentions: 2
Published: over 8 years ago