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/s13059-020-02097-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
10.1186/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
10.1093/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
10.1093/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
10.1093/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
10.1186/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
10.1093/gigascience/giz027
Chromosome-scale genome assembly of kiwifruit <i>Actinidia eriantha</i> with single-molecule sequencing and chromatin interaction mapping
Cited by: 55
Author(s): Wei Tang, Xuepeng Sun, Junyang Yue, Xiaofeng Tang, Chen Jiao, Ying Yang, Xiangli Niu, Min Miao, Danfeng Zhang, Shengxiong Huang, Wei Shi, Mingzhang Li, Congbing Fang, Zhangjun Fei, Yongsheng Liu
Software Mentions: 2
Published: over 5 years ago
10.1002/glia.23717
Gene expression profiling reveals a conserved microglia signature in larval zebrafish
Cited by: 37
Author(s): Julie Mazzolini, Sigrid Le Clerc, Gregoire Morisse, Cédric Coulonges, Laura E. Kuil, Tjakko J. van Ham, Jean‐François Zagury, Dirk Sieger
Software Mentions: 2
Published: about 5 years ago
10.1002/glia.23870
Insights into olfactory ensheathing cell development from a laser‐microdissection and transcriptome‐profiling approach
Cited by: 10
Author(s): Surangi Perera, Ruth M. Williams, Rachel Lyne, O. Oztug D. Stubbs, Dennis P. Buehler, Tatjana Sauka‐Spengler, Masaharu Noda, Gos Micklem, E. Michelle Southard‐Smith, Clare V. H. Baker
Software Mentions: 2
Published: about 4 years ago
10.1186/s41065-016-0021-1
Transcriptome analysis of genes involved in anthocyanins biosynthesis and transport in berries of black and white spine grapes (Vitis davidii)
Cited by: 35
Author(s): Lina Sun, Xiucai Fan, Ying Zhang, Jianfu Jiang, Han Sun, Chonghuai Liu
Software Mentions: 2
Published: almost 8 years ago
10.1038/s41438-019-0168-9
Differential gene expression in non-transgenic and transgenic “M.26” apple overexpressing a peach CBF gene during the transition from eco-dormancy to bud break
Cited by: 15
Author(s): Timothy S. Artlip, Adam McDermaid, Qin Ma, Michael Wisniewski
Software Mentions: 2
Published: over 5 years ago
10.1038/s41438-020-0247-y
Identification and distribution of a single nucleotide polymorphism responsible for the catechin content in tea plants
Cited by: 22
Author(s): Chenkai Jiang, Jianqiang Ma, Yu-Fei Liu, Jie-Dan Chen, Dejiang Ni, Liang Chen
Software Mentions: 2
Published: over 4 years ago
10.1038/s41438-018-0079-1
Transcriptome reprogramming, epigenetic modifications and alternative splicing orchestrate the tomato root response to the beneficial fungus Trichoderma harzianum
Cited by: 80
Author(s): Monica De Palma, Maria Salzano, Clizia Villano, Riccardo Aversano, Matteo Lorito, Michelina Ruocco, Teresa Docimo, Anna Lisa Piccinelli, Nunzio D’Agostino, Marina Tucci
Software Mentions: 2
Published: almost 6 years ago
10.1038/s41438-020-0285-5
CPPU may induce gibberellin-independent parthenocarpy associated with PbRR9 in ‘Dangshansu’ pear
Cited by: 16
Author(s): Liu Cong, Ting Wu, Hanting Liu, Huibin Wang, Haiqi Zhang, Guangping Zhao, Yao Wen, Qianrong Shi, Lingfei Xu, Zhigang Wang
Software Mentions: 2
Published: over 4 years ago
10.1038/s41438-020-00426-6
Melon short internode (CmSi) encodes an ERECTA-like receptor kinase regulating stem elongation through auxin signaling
Cited by: 12
Author(s): Sen Yang, Kaige Zhang, Huayu Zhu, Xiaojing Zhang, Wenkai Yan, Ning Xu, Dongming Liu, Jianbin Hu, Yufeng Wu, Yiqun Weng, Luming Yang
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41438-021-00491-5
PbEIL1 acts upstream of<i>PbCysp1</i>to regulate ovule senescence in seedless pear
Cited by: 10
Author(s): Huibin Wang, Haiqi Zhang, Fangfang Liang, Liu Cong, Linyan Song, Xieyu Li, Rui Zhai, Chengquan Yang, Zhigang Wang, Fengwang Ma, Lingfei Xu
Software Mentions: 2
Published: over 3 years ago
10.1038/s41438-018-0035-0
Investigation of benzylisoquinoline alkaloid biosynthetic pathway and its transcriptional regulation in lotus
Cited by: 39
Author(s): Ximing Deng, Li Zhao, Ting Fang, Yan Xiong, Collins Ogutu, Dong Yang, Sornkanok Vimolmangkang, Yanling Liu, Yuepeng Han
Software Mentions: 2
Published: over 6 years ago
10.1128/IAI.00339-19
Multi-omics Analyses Reveal Synergistic Carbohydrate Metabolism in Streptococcus mutans-Candida albicans Mixed-Species Biofilms
Cited by: 61
Author(s): Kassapa Ellepola, Tin Truong, Yuan Liu, Qifeng Lin, Teck Kwang Lim, Yew Mun Lee, Tong Cao, Hyun Koo, Chaminda Jayampath Seneviratne
Software Mentions: 2
Published: about 5 years ago
10.1172/jci.insight.139179
Reduced left atrial cardiomyocyte PITX2 and elevated circulating BMP10 predict atrial fibrillation after ablation
Cited by: 37
Author(s): Jasmeet S. Reyat, Winnie Chua, Victor Roth Cardoso, Anika Witten, Peter Kastner, S. Nashitha Kabir, Moritz F. Sinner, Robin Wesselink, Andrew P. Holmes, Davor Pavlović, Monika Stoll, Stefan Kääb, Georgios V. Gkoutos, Joris R. de Groot, Paulus Kirchhof, Larissa Fabritz
Software Mentions: 2
Published: over 4 years ago
10.1172/jci.insight.136093
MyD88/CD40 signaling retains CAR T cells in a less differentiated state
Cited by: 33
Author(s): Brooke L. Prinzing, Patrick Schreiner, Matthew Bell, Yiping Fan, Giedre Krenciute, Stephen Gottschalk
Software Mentions: 2
Published: about 4 years ago
10.1172/jci.insight.139445
Smooth muscle–derived progenitor cell myofibroblast differentiation through KLF4 downregulation promotes arterial remodeling and fibrosis
Cited by: 30
Author(s): Sizhao Lu, Austin Jolly, Keith A. Strand, Allison Dubner, Marie Mutryn, Karen S. Moulton, Raphael A. Nemenoff, Mark W. Majesky, Mary C.M. Weiser‐Evans
Software Mentions: 2
Published: almost 4 years ago
10.1172/jci.insight.149381
GADD45A is a protective modifier of neurogenic skeletal muscle atrophy
Cited by: 11
Author(s): Jeffrey T. Ehmsen, Riki Kawaguchi, Damlanur Kaval, Anna E. Johnson, Daniel Nachun, Giovanni Coppola, Ahmet Höke
Software Mentions: 2
Published: over 3 years ago
10.1074/jbc.M117.805051
Effects of chondroitin sulfate proteoglycan 4 (NG2/CSPG4) on soft-tissue sarcoma growth depend on tumor developmental stage
Cited by: 15
Author(s): Shu-Hsuan Claire Hsu, Puviindran Nadesan, Vijitha Puviindran, William B. Stallcup, David G. Kirsch, Benjamin A. Alman
Software Mentions: 2
Published: almost 7 years ago
10.1074/jbc.RA120.015516
Fc γ receptor IIIa/CD16a processing correlates with the expression of glycan-related genes in human natural killer cells
Cited by: 9
Author(s): Kashyap Patel, Maria C. Rodriguez Benavente, W. Walter Lorenz, Emily M. Mace, Adam W. Barb
Software Mentions: 2
Published: almost 4 years ago
10.1007/s00432-018-2631-7
Therapeutic potential of GSK-J4, a histone demethylase KDM6B/JMJD3 inhibitor, for acute myeloid leukemia
Cited by: 68
Author(s): Yunan Li, Mingying Zhang, Mengyao Sheng, Peng Zhang, Zizhen Chen, Wen Xing, Jie Bai, Tao Cheng, Feng Chun Yang, Yuan Zhou
Software Mentions: 2
Published: over 6 years ago
10.1111/jcmm.16419
Circular RNA circANAPC2 mediates the impairment of endochondral ossification by miR‐874‐3p/SMAD3 signalling pathway in idiopathic short stature
Cited by: 12
Author(s): Xijuan Liu, Du Zhi, Xuan Yao, Tianle Sheng, Jinghong Yuan, Jingyu Jia
Software Mentions: 2
Published: over 3 years ago
10.1111/jcmm.16616
Histone deacetylase 9 deficiency exaggerates uterine M2 macrophage polarization
Cited by: 13
Author(s): Yanqin Liu, Meirong Du, Haiyan Lin
Software Mentions: 2
Published: over 3 years ago
10.1242/jcs.167148
<i>Dgcr8</i> and <i>Dicer</i> are essential for sex chromosome integrity during meiosis in males
Cited by: 39
Author(s): A Modzelewski, Stephanie Hilz, Elizabeth A. Crate, Caterina T. H. Schweidenback, Elizabeth A. Fogarty, Jennifer K. Grenier, Raimundo Freire, Paula E. Cohen, Andrew Grimson
Software Mentions: 2
Published: over 9 years ago
10.1242/jcs.258568
Genetic compensation for cilia defects in <i>cep290</i> mutants by upregulation of cilia-associated small GTPases
Cited by: 13
Author(s): Magdalena Cárdenas-Rodríguez, Christina Austin‐Tse, Judith G.M. Bergboer, Elisa Molinari, Yuya Sugano, Ruxandra Bachmann‐Gagescu, John A. Sayer, Iain A. Drummond
Software Mentions: 2
Published: over 3 years ago
10.1093/jxb/erx157
The Arabidopsis Cys2/His2 zinc finger transcription factor ZAT18 is a positive regulator of plant tolerance to drought stress
Cited by: 86
Author(s): Mingzhu Yin, Yanping Wang, Lihua Zhang, Jinzhu Li, Wenli Quan, Li Yang, Qingfeng Wang, Zhulong Chan
Software Mentions: 2
Published: over 7 years ago
10.1093/jxb/ery132
miR156-SPL modules regulate induction of somatic embryogenesis in citrus callus
Cited by: 72
Author(s): Long Jiang, Chaoyang Liu, Meng-Qi Feng, Yun Liu, Xiaomeng Wu, Wen‐Wu Guo
Software Mentions: 2
Published: over 6 years ago
10.1093/jxb/ery220
ERF72 interacts with ARF6 and BZR1 to regulate hypocotyl elongation in Arabidopsis
Cited by: 56
Author(s): Kun Liu, Yihao Li, Xuena Chen, Lijuan Li, Kai Li, Heping Zhao, Yingdian Wang, Shengcheng Han
Software Mentions: 2
Published: over 6 years ago
10.1093/jxb/eraa489
A small secreted protein from <i>Zymoseptoria tritici</i> interacts with a wheat E3 ubiquitin ligase to promote disease
Cited by: 9
Author(s): Sujit Jung Karki, Aisling Reilly, Binbin Zhou, Maurizio Mascarello, John R. Burke, Fiona M. Doohan, Dimitar Douchkov, Patrick Schweizer, Angela Feechan
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.ppat.1004765
Exome and Transcriptome Sequencing of Aedes aegypti Identifies a Locus That Confers Resistance to Brugia malayi and Alters the Immune Response
Cited by: 35
Author(s): Punita Juneja, Cristina V. Ariani, Yung Shwen Ho, Jewelna Akorli, William J. Palmer, Arnab Pain, Francis M. Jiggins
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.ppat.1005218
The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
Cited by: 48
Author(s): Michael Tscherner, Florian Zwolanek, Sabrina Jenull, Fritz J. Sedlazeck, Andriy Petryshyn, Ingrid E. Frohner, John Mavrianos, Neeraj Chauhan, Arndt von Haeseler, Karl Kuchler
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.ppat.1005356
Type I and Type II Interferon Coordinately Regulate Suppressive Dendritic Cell Fate and Function during Viral Persistence
Cited by: 51
Author(s): Cameron R. Cunningham, Ameya S. Champhekar, Michael V. Tullius, Barbara Jane Dillon, Anjie Zhen, Justin Rafael De la Fuente, Jonathan Herskovitz, Heidi Elsaesser, Laura M. Snell, Elizabeth B. Wilson, Juan Carlos de la Torre, Scott G. Kitchen, Marcus A. Horwitz, Steven J. Bensinger, Stephen T. Smale, David G. Brooks
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.ppat.1005536
Wolbachia Blocks Viral Genome Replication Early in Infection without a Transcriptional Response by the Endosymbiont or Host Small RNA Pathways
Cited by: 75
Author(s): Stephanie M. Rainey, Julien Martinez, Melanie McFarlane, Punita Juneja, Peter Sarkies, Aleksei Lulla, Esther Schnettler, Margus Varjak, Andres Merits, Eric A. Miska, Francis M. Jiggins, Alain Kohl
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.ppat.1005803
The Prostaglandin E2-EP3 Receptor Axis Regulates Anaplasma phagocytophilum-Mediated NLRC4 Inflammasome Activation
Cited by: 26
Author(s): Xiaowei Wang, Dana K. Shaw, Holly Hammond, Fayyaz S. Sutterwala, Manira Rayamajhi, Kari Ann Shirey, Darren J. Perkins, Joseph V. Bonventre, Thangam Sudha Velayutham, Sean M. Evans, Kyle G. Rodino, Lauren VieBrock, Karen M. Scanlon, Nicholas H. Carbonetti, Jason A. Carlyon, Edward A. Miao, Jere W. McBride, Michail Kotsyfakis, Joao H. F. Pedra
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.ppat.1006582
Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing
Cited by: 53
Author(s): A.T. Shenoy, Terry Brissac, Ryan P. Gilley, Nikhil Kumar, Yong Wang, Norberto González-Juarbe, Whitney S. Hinkle, Sean C. Daugherty, Amol C. Shetty, Sandra Ott, Luke J. Tallon, Jessy Deshane, Hervé Tettelin, Carlos J. Orihuela
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.ppat.1006933
PDZ domain-binding motif of Tax sustains T-cell proliferation in HTLV-1-infected humanized mice
Cited by: 20
Author(s): Éléonore Pérès, Juliana Blin, Emiliano P. Ricci, Maria Artesi, Vincent Hahaut, Anne Van den Broeke, Antoine Corbin, Louis Gazzolo, Lee Ratner, Pierre Jalinot, Madeleine Duc Dodon
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.ppat.1007441
Quantitative RNAseq analysis of Ugandan KS tumors reveals KSHV gene expression dominated by transcription from the LTd downstream latency promoter
Cited by: 22
Author(s): Timothy M. Rose, A. Gregory Bruce, Serge Barcy, Matt Fitzgibbon, Lisa R Matsumoto, Minako Ikoma, Corey Casper, Jackson Orem, Warren Phipps
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.ppat.1007925
Macaque interferon-induced transmembrane proteins limit replication of SHIV strains in an Envelope-dependent manner
Cited by: 11
Author(s): Amit Sharma, Richard N. McLaughlin, Ryan Basom, Caroline Kikawa, Molly OhAinle, Jacob S. Yount, Michael Emerman, Julie Overbaugh
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.ppat.1008063
The male mosquito contribution towards malaria transmission: Mating influences the Anopheles female midgut transcriptome and increases female susceptibility to human malaria parasites
Cited by: 22
Author(s): Farah A. Dahalan, Thomas S. Churcher, Nikolai Windbichler, Mara Lawniczak
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.ppat.1008918
A pathogen branched-chain amino acid catabolic pathway subverts host survival by impairing energy metabolism and the mitochondrial UPR
Cited by: 26
Author(s): Siraje Arif Mahmud, Mohammed A. Qureshi, Madhab Sapkota, Mark W. Pellegrino
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.ppat.1009224
Reliable, scalable functional genetics in bloodstream-form Trypanosoma congolense in vitro and in vivo
Cited by: 13
Author(s): Georgina Awuah‐Mensah, Jennifer McDonald, Pieter C. Steketee, Delphine Autheman, Sarah Whipple, Simon D’Archivio, Cordelia Brandt, Simon Clare, Katherine Harcourt, Gavin J. Wright, Liam J. Morrison, Catarina Gadelha, Bill Wickstead
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-017-07062-6
Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast
Cited by: 2
Author(s): Nadra Al-Husini, Ali Sharifi, Seyed Ahmad Mousavi, Hamidreza Chitsaz, Athar Ansari
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-08763-8
Comparative Transcriptome Analysis of SE initial dedifferentiation in cotton of different SE capability
Cited by: 22
Author(s): Aiping Cao, Yu Zheng, Yu Yu, Xuwen Wang, Dongnan Shao, Jie Sun, Cui Baiming
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-07035-9
Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice
Cited by: 17
Author(s): Shin-Young Lee, Hyobin Jeong, Sichul Lee, Jinwon Lee, Sun-Ji Kim, Ji Won Park, Hye Ryun Woo, Pyung Ok Lim, Gynheung An, Hong Gil Nam, Daehee Hwang
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-06300-1
Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development
Cited by: 72
Author(s): Tom J. Phillips, Hannah Scott, David A. Menassa, Ashleigh L. Bignell, Anubhuti Sood, Jude S. Morton, Takami Akagi, K Azuma, Mark F. Rogers, Catherine E. Gilmore, Gareth J. Inman, Simon Grant, Yealin Chung, Mais M. Aljunaidy, Christy Lynn M. Cooke, Bruno R. Steinkraus, Andrew Pocklington, Angela Logan, Gavin Collett, Helena Kemp, Peter Holmans, Michael P. Murphy, Tudor A. Fulga, Andrew M. Coney, Mitsuru Akashi, Sandra T. Davidge, C. P. Case
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-09471-z
Genetic basis of mycotoxin susceptibility differences between budding yeast isolates
Cited by: 5
Author(s): Xtopher Quispe, Sebastián M. Tapia, Carlos A. Villarroel, Christian I. Oporto, Valentina Abarca, Verónica García, Claudio Martı́nez, Francisco A. Cubillos
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-017-11044-z
Early X chromosome inactivation during human preimplantation development revealed by single-cell RNA-sequencing
Cited by: 77
Author(s): Joana Carvalho Moreira de Mello, Gustavo Ribeiro Fernandes, Maria D. Vibranovski, Lygia V. Pereira
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-017-12550-w
Transcriptomic analysis of the role of RasGEF1B circular RNA in the TLR4/LPS pathway
Cited by: 29
Author(s): Wei Lun Ng, Georgi K. Marinov, Yoon Ming Chin, Yun Mook Lim, Chee Kwee
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-017-13381-5
RNA-Seq transcriptome profiling of mouse oocytes after in vitro maturation and/or vitrification
Cited by: 25
Author(s): Lei Gao, Gong-Xue Jia, Li Ai, Haojia Ma, Zhengyuan Huang, Shi-En Zhu, Yunpeng Hou, Xiangwei Fu
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-017-14800-3
Alterations in the host transcriptome in vitro following Rift Valley fever virus infection
Cited by: 17
Author(s): Chelsea Pinkham, Bibha Dahal, Cynthia L. de la Fuente, Nicole Bracci, Brett Beitzel, Michael E. Lindquist, Aura R. Garrison, Connie S. Schmaljohn, Gustavo Palacios, Aarthi Narayanan, Catherine E. Campbell, Kylene Kehn-Hall
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-017-14967-9
Comparative transcriptome analysis reveals potentially novel roles of Homeobox genes in adipose deposition in fat-tailed sheep
Cited by: 32
Author(s): Dan-Ju Kang, Guangxian Zhou, Shiwei Zhou, Jie Zeng, Xiaolong Wang, Yu Jiang, Yuxin Yang, Yulin Chen
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-017-14275-2
A transcriptomic study of myogenic differentiation under the overexpression of PPARγ by RNA-Seq
Cited by: 8
Author(s): Kan He, Guoying Wu, Wen‐Xing Li, Daogang Guan, Wen Lv, Mengting Gong, Shoudong Ye, Aiping Lu
Software Mentions: 2
Published: about 7 years ago
10.1038/s41598-017-17067-w
Experimental Zika Virus Inoculation in a New World Monkey Model Reproduces Key Features of the Human Infection
Cited by: 53
Author(s): Charles Y. Chiu, Carolyn Martin, Jérôme Bouquet, Tony Li, Shigeo Yagi, Manasi Tamhankar, Vida Hodara, Laura M. Parodi, Sneha Somasekar, Guixia Yu, Luis D. Giavedoni, Suzette D. Tardif, Jean L. Patterson
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-017-17811-2
Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer
Cited by: 34
Author(s): Stéphane Wenric, Sonia ElGuendi, Jean‐Hubert Caberg, Warda Bezzaou, Corinne Fasquelle, Benoît Charloteaux, Latifa Karim, Benoît Hennuy, Pierre Frères, Joëlle Collignon, Meriem Boukerroucha, Hélène Schroeder, Fabrice Olivier, Véronique Jossa, Guy Jérusalem, Claire Josse, Vincent Bours
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-017-17615-4
Genome-Wide Identification of Mitogen-activated Protein Kinase Cascade Genes and Transcriptional Profiling Analysis during Organ Development in Eucommia ulmoides
Cited by: 5
Author(s): Jie Teng, Lin Wang, Huimin Liu, Tana Wuyun, Hongyan Du
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-017-18404-9
RNA-seq identifies a diminished differentiation gene signature in primary monolayer keratinocytes grown from lesional and uninvolved psoriatic skin
Cited by: 33
Author(s): William R. Swindell, Mrinal K. Sarkar, Yun Liang, Xianying Xing, Jaymie Baliwag, James T. Elder, Andrew Johnston, Nicole L. Ward, Jóhann E. Guðjónsson
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-018-19754-8
Transcriptome Analysis in Spleen Reveals Differential Regulation of Response to Newcastle Disease Virus in Two Chicken Lines
Cited by: 39
Author(s): J. Zhang, Michael G. Kaiser, Melissa S. Deist, Rodrigo A. Gallardo, David Bunn, T. Ross Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-018-20266-8
Systems Analysis of the Liver Transcriptome in Adult Male Zebrafish Exposed to the Plasticizer (2-Ethylhexyl) Phthalate (DEHP)
Cited by: 44
Author(s): Matthew Huff, Willian A. da Silveira, Oliana Carnevali, Ludivine Renaud, Gary Hardiman
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-018-20727-0
Differential long non-coding RNA expression profiles in human oocytes and cumulus cells
Cited by: 51
Author(s): Julien Bouckenheimer, Patricia Fauque, Charles-Henri Lecellier, Céline Bruno, Thérèse Commes, Jean-Marc Lemaı̂tre, John De Vos, Saïd Assou
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-018-20738-x
Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid
Cited by: 28
Author(s): Niege Silva Mendes, Tamires Aparecida Bitencourt, Pablo Rodrigo Sanches, Rafael Silva‐Rocha, Nilce Maria Martinez-Rossi, Antônio Rossi
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-018-21389-8
STAT3 regulates cytotoxicity of human CD57+ CD4+ T cells in blood and lymphoid follicles
Cited by: 30
Author(s): Jalila Alshekaili, Rochna Chand, Cindy Eunhee Lee, Susan M. Corley, Kristy Kwong, Ilenia Papa, David A. Fulcher, Katrina L. Randall, Jennifer W. Leiding, S. Cindy, Marc R. Wilkins, Gülbû Uzel, Christopher C. Goodnow, Carola G. Vinuesa, Stuart G. Tangye, Matthew C. Cook
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-22021-5
The circadian regulator BMAL1 programmes responses to parasitic worm infection via a dendritic cell clock
Cited by: 57
Author(s): Thomas Hopwood, Sarah Hall, Nicola Begley, Ruth Forman, Sheila Brown, Ryan Vonslow, Ben Saer, Matthew C. Little, Erin A. Murphy, Rebecca Hurst, David Ray, Andrew S. MacDonald, Andy Brass, David A. Bechtold, Julie Gibbs, A. S. I. Loudon, Kathryn J. Else
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-24727-y
Comparative transcriptome analysis to investigate the potential role of miRNAs in milk protein/fat quality
Cited by: 17
Author(s): Xuehui Wang, Li Zhang, Jing Jin, Anting Xia, Chunmei Wang, Yingjun Cui, Bo Qu, LI Qing-zhang, Sheng Chen
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-24811-3
Adaptive response of neonatal sepsis-derived Group B Streptococcus to bilirubin
Cited by: 19
Author(s): Richard Hansen, Sophie Gibson, Eduardo Rodrigues Alves, Mark Goddard, Andrew T. MacLaren, Anne Marie Kärcher, Susan H. Berry, Elaina Susan Renata Collie-Duguid, Emad El-Omar, Mike Munro, Georgina L. Hold
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-25205-1
Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities
Cited by: 58
Author(s): Maxim D. Seferovic, Claudia Sánchez San Martín, Suzette D. Tardif, Julienne N. Rutherford, Eumenia Castro, Tony Li, Vida Hodara, Laura M. Parodi, Luis D. Giavedoni, Donna Layne-Colon, Manasi Tamhankar, Shigeo Yagi, Calla Martyn, Kevin Reyes, Melissa Suter, Kjersti M. Aagaard, Charles Y. Chiu, Jean L. Patterson
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-25530-5
Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis
Cited by: 32
Author(s): Megan E. Forrest, Alina Saiakhova, Lydia Beard, David A. Buchner, Peter C. Scacheri, Thomas LaFramboise, Sanford D. Markowitz, Ahmad M. Khalil
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-25800-2
Genomic alterations of ground-glass nodular lung adenocarcinoma
Cited by: 9
Author(s): Hyun Lee, Je‐Gun Joung, Hyun-Tae Shin, Duk-Hwan Kim, Yujin Kim, Hojoong Kim, O Jung Kwon, Young Mog Shim, Ho Yun Lee, Kyung Soo Lee, Yoon‐La Choi, Woong-Yang Park, D. Neil Hayes, Sang‐Won Um
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-26670-4
Early transcriptional response of human ovarian and fallopian tube surface epithelial cells to norepinephrine
Cited by: 10
Author(s): Anxhela Gjyshi, Sweta Dash, Ling Cen, Chia-Ho Cheng, Chaomei Zhang, Sean Yoder, Jamie K. Teer, Guillermo N. Armaiz-Peña, Alvaro N.A. Monteiro
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-27843-x
Loss of Glis3 causes dysregulation of retrotransposon silencing and germ cell demise in fetal mouse testis
Cited by: 3
Author(s): Erica Ungewitter, Emmi Rotgers, Hong Soon Kang, Kristin Lichti-Kaiser, Leping Li, Sara A. Grimm, Anton M. Jetten, Hisayuki Yao
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-27940-x
Transcriptome analysis of two contrasting rice cultivars during alkaline stress
Cited by: 34
Author(s): Ning Li, Hualong Liu, Jian Sun, Hongliang Zheng, Jingguo Wang, Liuqing Yang, Hongwei Zhao, Detang Zou
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-28158-7
Recognition of candidate transcription factors related to bilberry fruit ripening by de novo transcriptome and qRT-PCR analyses
Cited by: 15
Author(s): Nga Nguyen, Marko Suokas, Katja Karppinen, Jaana Vuosku, Laura Jaakola, Hely Häggman
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-29093-3
Gene expression profiles of germ-free and conventional piglets from the same litter
Cited by: 19
Author(s): Jing Sun, Huan Zhong, Lei Du, Xiaolei Li, Yuchun Ding, Haoran Cao, Zuohua Liu, Liangpeng Ge
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-30621-4
TNFR2 ligation in human T regulatory cells enhances IL2-induced cell proliferation through the non-canonical NF-κB pathway
Cited by: 31
Author(s): Jun Wang, Ricardo C. Ferreira, Wenyu Lü, Samatha Farrow, Kate Downes, Lutz Jermutus, Ralph Minter, Rafia S. Al‐Lamki, Jordan S. Pober, John R. Bradley
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-30466-x
A cancer vaccine approach for personalized treatment of Lynch Syndrome
Cited by: 15
Author(s): Snigdha Majumder, Rakshit Shah, Jisha Elias, Malini Manoharan, Priyanka Shah, Anjali Kumari, Papia Chakraborty, Vasumathi Kode, Yogesh Mistry, Karunakaran Coral, Bharti Mittal, Sakthivel Murugan Sm, Lakshmi Mahadevan, Ravi Gupta, Amitabha Chaudhuri, Arati Khanna-Gupta
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-30882-z
Expression profiling in a mammalian host reveals the strong induction of genes encoding LysM domain-containing proteins in Enterococcus faecium
Cited by: 8
Author(s): Margherita Cacaci, Caroline Giraud, L Léger, Riccardo Torelli, Cécilia Martini, Brunella Posteraro, Valentina Palmieri, Maurizio Sanguinetti, Francesca Bugli, Axel Hartke
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-30602-7
Cigarette smoke exposure decreases CFLAR expression in the bronchial epithelium, augmenting susceptibility for lung epithelial cell death and DAMP release
Cited by: 30
Author(s): Alen Faiz, Irene H. Heijink, Cornelis J Vermeulen, Victor Guryev, Maarten van den Berge, Martijn C. Nawijn, Simon D. Pouwels
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-30754-6
An Adult Zebrafish Model Reveals that Mucormycosis Induces Apoptosis of Infected Macrophages
Cited by: 29
Author(s): Azucena López-Muñoz, Francisco E. Nicolás, Diana García‐Moreno, Ana B. Pérez-Oliva, María Isabel Navarro-Mendoza, Miguel Ángel Hernández‐Oñate, Alfredo Herrera-Estrella, Santiago Torres-Martı́nez, Rosa M. Ruiz‐Vázquez, Victoriano Mulero
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-018-31420-7
Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses
Cited by: 16
Author(s): Matthew Chung, Laura Teigen, Hong Liu, Silvia Libro, Amol C. Shetty, Nikhil Kumar, Xüna Zhao, Robin E. Bromley, Luke J. Tallon, Lisa Sadzewicz, Claire M. Fraser, David A. Rasko, Scott G. Filler, Jeremy M. Foster, Michelle L. Michalski, Vincent M. Bruno, Julie C. Dunning Hotopp
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-018-32154-2
Regional Differences in mRNA and lncRNA Expression Profiles in Non-Failing Human Atria and Ventricles
Cited by: 28
Author(s): Eric K. Johnson, Scot J. Matkovich, Jeanne M. Nerbonne
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-018-32266-9
Transcriptional profiling of Zygosaccharomyces bailii early response to acetic acid or copper stress mediated by ZbHaa1
Cited by: 13
Author(s): Miguel Antunes, Margarida Palma, Isabel Sá‐Correia
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-018-32519-7
Comparative in depth RNA sequencing of P. tricornutum’s morphotypes reveals specific features of the oval morphotype
Cited by: 16
Author(s): Clément Ovide, Marie‐Christine Kiefer‐Meyer, Caroline Bérard, Nicolas Vergne, Thierry Lecroq, Carole Plasson, Carole Burel, Sophie Bernard, Azeddine Driouich, Patrice Lerouge, Isabelle Tournier, Hélène Dauchel, Muriel Bardor
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-018-32818-z
Meta-analysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial “spaceflight response”
Cited by: 15
Author(s): Michael D. Morrison, Wayne L. Nicholson
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-018-32400-7
Differentiation enhances Zika virus infection of neuronal brain cells
Cited by: 21
Author(s): Carolyn Martin, Tony Li, Jérôme Bouquet, Jessica Streithorst, Guixia Yu, Aditi Paranjpe, Charles Y. Chiu
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-018-33140-4
Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere
Cited by: 10
Author(s): Patricia Fajardo-Cavazos, Michael D. Morrison, Kathleen M. Miller, Andrew C. Schuerger, Wayne L. Nicholson
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-018-33629-y
LncRNA BLAT1 is Upregulated in Basal-like Breast Cancer through Epigenetic Modifications
Cited by: 25
Author(s): Yoo Jane Han, Sonja Boatman, Jing Zhang, Xinxin Du, Albert C. Yeh, Yonglan Zheng, Jeffrey Mueller, Olufunmilayo I. Olopade
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-018-35516-y
Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
Cited by: 17
Author(s): Eleonora Zorzan, Ramy Elgendy, Mery Giantin, Mauro Dacasto, Claudia Sissi
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-018-37804-z
The Effect of Micro- and Nanoscale Surface Topographies on Silk on Human Corneal Limbal Epithelial Cell Differentiation
Cited by: 15
Author(s): Kai Kang, Brian D. Lawrence, Xiaoyi Gao, Victor H. Guaiquil, Aihong Liu, Mark I. Rosenblatt
Software Mentions: 2
Published: almost 6 years ago
10.1038/s41598-018-38379-5
Transcriptome profiling of zebrafish optic fissure fusion
Cited by: 20
Author(s): Rose Richardson, Nicholas Owen, Maria Toms, Rodrigo Young, Dhani Tracey‐White, Mariya Moosajee
Software Mentions: 2
Published: almost 6 years ago
10.1038/s41598-019-39873-0
Age-related gene and miRNA expression changes in airways of healthy individuals
Cited by: 29
Author(s): Jennie Ong, Roy R Woldhuis, Ilse M. Boudewijn, Anke van den Berg, Joost Kluiver, Klaas Kok, Martijn Terpstra, Victor Guryev, Maaike de Vries, Cornelis J Vermeulen, Wim Timens, C. A. Brandsma
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-40518-5
Maintenance of MYC expression promotes de novo resistance to BET bromodomain inhibition in castration-resistant prostate cancer
Cited by: 32
Author(s): Daniel J. Coleman, Lina Gao, Jacob Schwartzman, James E. Korkola, David A. Sampson, Daniel S. Derrick, Joshua A. Urrutia, Ariel Balter, Julja Burchard, Carly J. King, Kami Chiotti, Laura M. Heiser, Joshi J. Alumkal
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-42731-8
Abiotic and biotic stresses induce a core transcriptome response in rice
Cited by: 112
Author(s): Stephen P. Cohen, Jan E. Leach
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-43426-w
Human gut derived-organoids provide model to study gluten response and effects of microbiota-derived molecules in celiac disease
Cited by: 67
Author(s): Rachel Freire, Laura Ingano, Gloria Serena, Murat Çetinbaş, Anthony Anselmo, Anna Sapone, Ruslan I. Sadreyev, Alessio Fasano, Stefania Senger
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-44637-x
Transcriptomic analysis of resistant and susceptible banana corms in response to infection by Fusarium oxysporum f. sp. cubense tropical race 4
Cited by: 35
Author(s): Lei Zhang, Alberto Cenci, Mathieu Rouard, Dong Zhang, Yunyue Wang, Weihua Tang, Si-Jun Zheng
Software Mentions: 2
Published: over 5 years ago