cran: STAR | Projects | Ecosyste.ms: Papers

10.1093/gigascience/giaa037

The gene-rich genome of the scallop Pecten maximus
Cited by: 46
Author(s): Nathan J. Kenny, Shane McCarthy, Olga Dudchenko, Katherine James, Emma Betteridge, Craig Corton, Jale Dolucan, Daniel Mead, Karen Oliver, Arina D. Omer, Sarah Pelan, Yan Ryan, Ying Sims, Jason Skelton, Michelle Smith, James Torrance, David Weisz, Anil Wipat, E Aiden, Kerstin Howe, Suzanne T. Williams
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-019-6182-3

Characterization of genome-wide variations induced by gamma-ray radiation in barley using RNA-Seq
Cited by: 9
Author(s): Cong Tan, Xiaoqi Zhang, Yin Wang, Dianxin Wu, M. Bellgard, Yonghong Xu, Xiaoli Shu, Gaofeng Zhou, Chengdao Li
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-6341-6

Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco
Cited by: 1
Author(s): Andrian Yang, Abhinav Kishore, Benjamin Phipps, Joshua W. K. Ho
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-020-07136-2

Identification of diverse cell populations in skeletal muscles and biomarkers for intramuscular fat of chicken by single-cell RNA sequencing
Cited by: 18
Author(s): Jinghui Li, Siyuan Xing, Guiping Zhao, Maiqing Zheng, Xinting Yang, Jiahong Sun, Jie Wen, Ranran Liu
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-019-6243-7

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq
Cited by: 44
Author(s): Paulo Rapazote-Flores, Micha Bayer, Linda Milne, Claus Mayer, John Fuller, Wenbin Guo, Pete E. Hedley, Jenny Morris, Claire Halpin, Jason Kam, Sarah M. McKim, Monika Zwirek, M. Cristina Casao, Abdellah Barakate, Miriam Schreiber, Gordon Stephen, Runxuan Zhang, John W. Brown, Robbie Waugh, Craig G. Simpson
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-020-06878-3

Cestode strobilation: prediction of developmental genes and pathways
Cited by: 4
Author(s): Gabriela Prado Paludo, Claudia Elizabeth Thompson, Kendi Nishino Miyamoto, Rafael Lucas Muniz Guedes, Arnaldo Zaha, Ana Tereza Ribeiro de Vasconcelos, Mario Cancela, Henrique Bunselmeyer Ferreira
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-019-6236-6

A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum)
Cited by: 20
Author(s): Xi Chen, Shuo Sun, FangJie Liu, Enhui Shen, Lu Liu, Chu-Yu Ye, Bingguang Xiao, Michael P. Timko, Qian‐Hao Zhu, Longjiang Fan, Peijian Cao
Software Mentions: 2
Published: over 6 years ago

10.1093/gigascience/giab045

StoatyDive: Evaluation and classification of peak profiles for sequencing data
Cited by: 0
Author(s): Florian Heyl, Rolf Backofen
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-020-6462-y

Transcriptome-wide map of m6A circRNAs identified in a rat model of hypoxia mediated pulmonary hypertension
Cited by: 48
Author(s): Hua Su, Guowen Wang, Lingfang Wu, Xiaochun Ma, Kejing Ying, Ruifeng Zhang
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.202658

Insights into epithelial cell senescence from transcriptome and secretome analysis of human oral keratinocytes
Cited by: 10
Author(s): Rachael E Schwartz, Maxim N. Shokhirev, Leonardo R. Andrade, J. Silvio Gutkind, Ramiro Iglesias-Bartolomé, Gerald S. Shadel
Software Mentions: 2
Published: over 5 years ago

10.1080/19490976.2020.1832857

Spermidine improves gut barrier integrity and gut microbiota function in diet-induced obese mice
Cited by: 175
Author(s): Lingyan Ma, Tsuguhito Ota, Zhe Wang, Wenqing Tu, Liyang Ni, Fen Zhuge, Aqian Zheng, Lintao Hu, Yuwu Zhao, Liujie Zheng
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.102922

RNA sequencing analysis of monocrotaline-induced PAH reveals dysregulated chemokine and neuroactive ligand receptor pathways
Cited by: 17
Author(s): Genfa Xiao, Tingjun Wang, Wenxin Zhuang, Chaoyi Ye, Luo Lu, Huajun Wang, Guili Lian, Liangdi Xie
Software Mentions: 2
Published: over 6 years ago

10.1186/s13561-020-00300-0

Practices of decision making in priority setting and resource allocation: a scoping review and narrative synthesis of existing frameworks
Cited by: 9
Author(s): Brayan V. Seixas, François Dionne, Craig Mitton
Software Mentions: 2
Published: over 5 years ago

10.18632/oncotarget.27693

Differentially expressed full-length, fusion and novel isoforms transcripts-based signature of well-differentiated keratinized oral squamous cell carcinoma
Cited by: 9
Author(s): Neetu Singh, Dinesh Kumar Sahu, Ratnesh Kumar Tripathi, Archana Mishra, Hari Shyam, Pratap Shankar, Mayank Jain, Nawazish Alam, Anil Kumar, Abhishek Mishra, Rebecca Chowdhry, Anjana Singh, Sudeep Gupta, Divya Mehrotra, Preeti Agarwal, Madhu Mati Goel, Arun Chaturvedi, Saurabh Agarwal, Manish Kumar Bajpai, Devendra K. Gupta, Madan Lal Brahma Bhatt, Ravi Kant
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-018-4911-7

Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops
Cited by: 18
Author(s): Karl R. Franke, Skye Schmidt, Sunhee Park, Dong‐Hoon Jeong, Monica Accerbi, Pamela J. Green
Software Mentions: 2
Published: almost 8 years ago

10.1097/HS9.0000000000000522

Performances of Targeted RNA Sequencing for the Analysis of Fusion Transcripts, Gene Mutation, and Expression in Hematological Malignancies
Cited by: 2
Author(s): Sandrine Hayette, Béatrice Grange, Maxime Vallée, Claire Bardel, Sarah Huet, Isabelle Mosnier, Kaddour Chabane, Thomas Simonet, Marie Balsat, Maël Heiblig, Isabelle Tigaud, Franck E. Nicolini, Sylvain Mareschal, Gilles Salles, Pierre Sujobert
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-020-07344-w

Correction for both common and rare cell types in blood is important to identify genes that correlate with age
Cited by: 5
Author(s): Damiano Pellegrino-Coppola, Annique Claringbould, Maartje Stutvoet, Dorret I. Boomsma, M. Arfan Ikram, P. Eline Slagboom, Harm-Jan Westra, Lude Franke
Software Mentions: 2
Published: over 5 years ago

10.1038/s41438-020-0314-4

Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato
Cited by: 34
Author(s): Lei Zhang, Yan Yu, Tianye Shi, Meng Kou, Jian Sun, Tao Xu, Qiang Li, Shaoyuan Wu, Qinghe Cao, Wenqian Hou, Zongyun Li
Software Mentions: 2
Published: about 6 years ago

10.1038/s41438-021-00619-7

DNA methylation affects photoperiodic tuberization in potato (Solanum tuberosum L.) by mediating the expression of genes related to the photoperiod and GA pathways
Cited by: 13
Author(s): Yanjun Ai, Shenglin Jing, Zhengnan Cheng, Botao Song, Conghua Xie, Jun Liu, Jun Zhou
Software Mentions: 2
Published: almost 5 years ago

10.1038/hortres.2017.54

Solar thermotherapy reduces the titer of Candidatus Liberibacter asiaticus and enhances canopy growth by altering gene expression profiles in HLB-affected citrus plants
Cited by: 20
Author(s): Melissa M Doud, Yunsheng Wang, Michelle T Hoffman, Christina L Latza, Wenjian Luo, Cheryl M. Armstrong, T. R. Gottwald, Liangying Dai, Feng Luo, Yongping Duan
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.27906

Characterization of the inflammatory microenvironment and hepatic macrophage subsets in experimental hepatocellular carcinoma models
Cited by: 10
Author(s): Helena Degroote, Sander Lefere, Astrid Vandierendonck, Bart Vanderborght, Tim Meese, Filip Van Nieuwerburgh, Xavier Verhelst, Anja Geerts, Hans Van Vlierberghe, Lindsey Devisscher
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-020-06854-x

Maternal dietary resistant starch does not improve piglet’s gut and liver metabolism when challenged with a high fat diet
Cited by: 2
Author(s): Martine Schroyen, Julie Leblois, Julie Uerlings, Bing Li, Ester Arévalo Sureda, Sébastien Massart, José Wavreille, Jérôme Bindelle, Nadia Everaert
Software Mentions: 2
Published: about 6 years ago

10.18632/oncotarget.27955

Genome wide DNA methylation landscape reveals glioblastoma’s influence on epigenetic changes in tumor infiltrating CD4+ T cells
Cited by: 13
Author(s): Marpe Bam, Sreenivasulu Chintala, Kaleigh Fetcko, Brooke Carmen Williamsen, Seema Siraj, Sheng Liu, Jun Wan, Xiaoling Xuei, Yunlong Liu, Adam Leibold, Mahua Dey
Software Mentions: 2
Published: about 5 years ago

10.1038/s41438-019-0184-9

Multiple quantitative trait loci contribute to resistance to bacterial canker incited by Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis)
Cited by: 20
Author(s): Jibran Tahir, S.M. Hoyte, H. Bassett, Cyril Brendolise, Abhishek Chatterjee, Kerry Templeton, Cecilia Deng, Ross N. Crowhurst, Mirco Montefiori, E.R. Morgan, Andrew Wotton, Keith A. Funnell, Claudia Wiedow, Mareike Knaëbel, Duncan I. Hedderley, J. L. Vanneste, John McCallum, Kirsten Hoeata, Amardeep Nath, David Chagné, L. D. Gea, Susan E. Gardiner
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.immuni.2020.02.014

Butyrophilin-2A1 Directly Binds Germline-Encoded Regions of the Vγ9Vδ2 TCR and Is Essential for Phosphoantigen Sensing
Cited by: 144
Author(s): Mohindar Murugesh Karunakaran, Carrie R. Willcox, Mahboob Salim, Daniel Paletta, Alina Suzann Fichtner, Angela Noll, Lisa Starick, Anna Nöhren, Charlotte R Begley, Katie A Berwick, Raphaël A. G. Chaleil, Vincent Pitard, Julie Déchanet‐Merville, Paul A. Bates, Brigitte Kimmel, Timothy J. Knowles, Volker Kunzmann, Lutz Walter, Mark Jeeves, Fiyaz Mohammed, Benjamin E. Willcox, Thomas Herrmann
Software Mentions: 2
Published: over 6 years ago

10.1007/s00401-020-02133-x

Synaptotagmin 13 is neuroprotective across motor neuron diseases
Cited by: 24
Author(s): Monica Nizzardo, Michela Taiana, Federica Rizzo, Julio Aguila Benitez, Jik Nijssen, Ilary Allodi, Valentina Melzi, Nereo Bresolin, Giacomo Pietro Comi, Eva Hedlund, Stefania Corti
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-5676-3

Comprehensive kinome NGS targeted expression profiling by KING-REX
Cited by: 1
Author(s): Giovanni Carapezza, Carlo Cusi, Ettore Rizzo, Laura Raddrizzani, Sebastiano Di Bella, Alessio Somaschini, Antonella Leone, Rosita Lupi, Margherita Mutarelli, Vincenzo Nigro, Diego di Bernardo, Paolo Magni, Antonella Isacchi, Roberta Bosotti
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-020-06952-w

A tentacle for every occasion: comparing the hunting tentacles and sweeper tentacles, used for territorial competition, in the coral Galaxea fascicularis
Cited by: 12
Author(s): Oshra Yosef, Yotam Popovits, Assaf Malik, Maya Ofek-Lalzer, Tali Mass, Daniel Sher
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-019-6292-y

Efficient depletion of ribosomal RNA for RNA sequencing in planarians
Cited by: 22
Author(s): Iana V Kim, E. J. Ross, Sascha Dietrich, Kristina Döring, Alejandro Sánchez Alvarado, Claus-D. Kuhn
Software Mentions: 2
Published: over 6 years ago

10.1111/imcb.12399

GPR43 regulates marginal zone B‐cell responses to foreign and endogenous antigens
Cited by: 9
Author(s): Leona Rohrbeck, Mónika Ádori, Shan Wang, Chenfei He, Christopher Andrew Tibbitt, Mark Chernyshev, Madle Sirel, Ulf Ribacke, Ben Murrell, Mohammad Bohlooly‐Y, Mikael C. I. Karlsson, Gunilla B. Karlsson Hedestam, Jonathan M. Coquet
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-020-6584-2

Sirt2-associated transcriptome modifications in cisplatin-induced neuronal injury
Cited by: 4
Author(s): Xin Zhao, Wei Du, Manchao Zhang, Zainab Atiq, Fang Xia
Software Mentions: 2
Published: over 6 years ago

10.1186/s13012-015-0272-7

What strategies are used to build practitioners’ capacity to implement community-based interventions and are they effective?: a systematic review
Cited by: 124
Author(s): Jennifer Leeman, Larissa Calancie, Marieke A. Hartman, Cam Escoffery, Alison K. Herrmann, Lindsay E. Tague, Alexis Moore, Katherine Wilson, Michelle Schreiner, Carmen D. Samuel‐Hodge
Software Mentions: 2
Published: about 11 years ago

10.1007/s00011-020-01326-0

Novel adipokine associated with OA: retinol binding protein 4 (RBP4) is produced by cartilage and is correlated with MMPs in osteoarthritis patients
Cited by: 17
Author(s): Morena Scotece, Anna Koskinen-Kolasa, Antti Pemmari, Tiina Leppänen, Mari Hämäläinen, Teemu Moilanen, Eeva Moilanen, Katriina Vuolteenaho
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms22137164

Transcriptional Modulation of the Hippo Signaling Pathway by Drugs Used to Treat Bipolar Disorder and Schizophrenia
Cited by: 9
Author(s): Bruna Panizzutti, Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Mark F. Richardson, Trang T. T. Truong, Zoe Liu, Gerwyn Morris, Laura J. Gray, Jee Hyun Kim, Olivia Dean, Michael Berk, Ken Walder
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-017-4354-6

Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis
Cited by: 20
Author(s): Tatiana Maroilley, Gaëtan Lemonnier, Jérôme Lecardonnel, Diane Esquerré, Yuliaxis Ramayo-Caldas, Marie‐José Mercat, Claire Rogel‐Gaillard, Jordi Estellé
Software Mentions: 2
Published: over 8 years ago

10.1186/s40635-019-0271-0

The peripheral blood transcriptome in septic cardiomyopathy: an observational, pilot study
Cited by: 5
Author(s): Meghan M. Cirulis, Sarah J. Beesley, Emily L. Wilson, Chris Stubben, Troy D. Olsen, Eliotte L. Hirshberg, Lane M. Smith, Michael J. Lanspa, Theodore P. Abraham, Colin K. Grissom, Matthew T. Rondina
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms22136663

Expression Profile of New Marker Genes Involved in Differentiation of Canine Adipose-Derived Stem Cells into Osteoblasts
Cited by: 2
Author(s): Maurycy Jankowski, Mariusz Kaczmarek, Grzegorz Wąsiatycz, Claudia Dompe, Paul Mozdziak, J. M. Jaśkowski, Hanna Piotrowska‐Kempisty, Bartosz Kempisty
Software Mentions: 2
Published: about 5 years ago

10.1016/j.jacbts.2020.09.010

Cardiorenal Tissues Express SARS-CoV-2 Entry Genes and Basigin (BSG/CD147) Increases With Age in Endothelial Cells
Cited by: 30
Author(s): Blerina Ahmetaj‐Shala, Ricky Vaja, Santosh S. Atanur, Peter M. George, Nicholas S. Kirkby, Jane A. Mitchell
Software Mentions: 2
Published: over 5 years ago

10.18632/oncotarget.28056

The antitumoral effects of chemerin are independent from leukocyte recruitment and mediated by inhibition of neoangiogenesis
Cited by: 7
Author(s): Ingrid Dubois-Vedrenne, Diana D.A.D. Al Delbany, Olivier De Henau, Virginie Robert, Maxime Vernimmen, Francina Langa, Anne Lefort, Frédérick Libert, Valérie Wittamer, Marc Parmentier
Software Mentions: 2
Published: almost 5 years ago

10.1172/jci.insight.94716

Molecular characterization of the transition from acute to chronic kidney injury following ischemia/reperfusion
Cited by: 190
Author(s): Jing Liu, Sanjeev Kumar, Egor Dolzhenko, Gregory F. Alvarado, Jinjin Guo, Can Lü, Yibu Chen, Meng Li, Mark C. Dessing, Riana K. Parvez, Pietro E Cippà, A. Michaela Krautzberger, Gohar Saribekyan, Andrew D. Smith, Andrew P. McMahon
Software Mentions: 2
Published: almost 9 years ago

10.1172/jci.insight.120794

Hepatocyte ALOXE3 is induced during adaptive fasting and enhances insulin sensitivity by activating hepatic PPARγ
Cited by: 19
Author(s): Cassandra B. Higgins, Yiming Zhang, Allyson L. Mayer, Hideji Fujiwara, Alicyn I Stothard, Mark Graham, Benjamin M. Swarts, Brian J. DeBosch
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-020-07120-w

Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo
Cited by: 21
Author(s): Jieping Huang, Feng Xue, Ruirui Zhu, Duo Guo, Yutong Wei, Xiaodan Cao, Yun Ma, Deshun Shi
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-016-3161-9

Impact of RNA degradation on fusion detection by RNA-seq
Cited by: 34
Author(s): Jaime Davila, Numrah Fadra, Xiaoke Wang, Amber McDonald, Asha Nair, Barbara R. Crusan, Xia Wu, Joseph H. Blommel, Jin Jen, Kandelaria M. Rumilla, Robert B. Jenkins, Umut Aypar, Eric W. Klee, Benjamin R. Kipp, Kevin C. Halling
Software Mentions: 2
Published: over 9 years ago

10.1172/jci.insight.139043

Epigenetic silencing of CD4 expression in nonpathogenic SIV infection in African green monkeys
Cited by: 8
Author(s): Joseph C. Mudd, Stephen Lai, Sanjana Shah, Andrew R. Rahmberg, Jacob K. Flynn, Carly E. Starke, Molly Perkins, Amy Ransier, Samuel Darko, Daniel C. Douek, Vanessa M. Hirsch, Mark J. Cameron, Jason M. Brenchley
Software Mentions: 2
Published: almost 6 years ago

10.1172/jci.insight.139628

PFKFB3-mediated glycolysis rescues myopathic outcomes in the ischemic limb
Cited by: 20
Author(s): Terence E. Ryan, Cameron A. Schmidt, Michael D. Tarpey, Adam J. Amorese, Dean T. Yamaguchi, Emma J. Goldberg, Melissa Mae R. Inigo, Reema Karnekar, Allison R. O’Rourke, James M. Ervasti, Patricia Brophy, Thomas D. Green, P. Darrell Neufer, Kelsey H. Fisher‐Wellman, Espen E. Spangenburg, Joseph M. McClung
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-018-4591-3

MicroRNA expression profiles of bovine monocyte-derived macrophages infected in vitro with two strains of Streptococcus agalactiae
Cited by: 22
Author(s): Anna Lewandowska-Sabat, Silje Camilla Furre Hansen, T. R. Solberg, Olav Østerås, B. Heringstad, Preben Boysen, I. Olsaker
Software Mentions: 2
Published: over 8 years ago

10.1172/jci.insight.139163

ROS-producing immature neutrophils in giant cell arteritis are linked to vascular pathologies
Cited by: 42
Author(s): Lihui Wang, Zhichao Ai, Tariq E. Khoyratty, Kristina Zec, Hayley L. Eames, Erinke van Grinsven, Alison Hudak, Susan Morris, David Ahern, Claudia Monaco, Evgeniy Eruslanov, Raashid Luqmani, Irina A. Udalova
Software Mentions: 2
Published: over 5 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: over 5 years ago

10.1063/5.0054639

High shear stress enhances endothelial permeability in the presence of the risk haplotype at 9p21.3
Cited by: 3
Author(s): Evan L. Teng, Evan Masutani, Benjamin Yeoman, Jessica Fung, Rachel Lian, Brenda Ngo, Aditya Kumar, Jesse K. Placone, Valentina Lo Sardo, Adam J. Engler
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-018-5327-0

A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice
Cited by: 31
Author(s): Madeline Rose Keleher, Syeda Nuzhat Fatima Zaidi, Lauren Hicks, Shyam Shah, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-019-5817-8

Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi
Cited by: 16
Author(s): Mari Mäkinen, Jaana Kuuskeri, Pia Laine, Olli‐Pekka Smolander, Andriy Kovalchuk, Zhen Zeng, Fred O. Asiegbu, Lars Paulín, Petri Auvinen, Taina Lundell
Software Mentions: 2
Published: about 7 years ago

10.1172/jci.insight.144955

Modulation of ATXN1 S776 phosphorylation reveals the importance of allele-specific targeting in SCA1
Cited by: 9
Author(s): Larissa Nitschke, Stephanie L. Coffin, Eder Xhako, Dany B. El-Najjar, James P. Orengo, Elizabeth Alcala, Yun Dai, Ying Wan, Zhandong Liu, Harry T. Orr, Huda Y. Zoghbi
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22147583

Comprehensive Genomic and Transcriptomic Analysis of Three Synchronous Primary Tumours and a Recurrence from a Head and Neck Cancer Patient
Cited by: 3
Author(s): Luisa Bresadola, D. F. Weber, Christoph Ritzel, Martin Löwer, Valesca Bukur, Özlem Akilli-Öztürk, Julia Powers Becker, Hisham Mehanna, Barbara Schrörs, Fulvia Vascotto, Uğur Şahin, Anthony Kong
Software Mentions: 2
Published: almost 5 years ago

10.1172/jci.insight.138312

Short-term Western-style diet negatively impacts reproductive outcomes in primates
Cited by: 9
Author(s): Sweta Ravisankar, Alison Y. Ting, Mark K. Murphy, Nash Redmayne, Dorothy Wang, Carrie McArthur, Diana Takahashi, Paul Kievit, Shawn L. Chavez, Jon D. Hennebold
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.143465

Reversible cardiac disease features in an inducible CUG repeat RNA–expressing mouse model of myotonic dystrophy
Cited by: 10
Author(s): Ashish N. Rao, Hannah M. Campbell, Xiangnan Guan, Tarah A. Word, Xander H.T. Wehrens, Zheng Xia, Thomas A. Cooper
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.145857

Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
Cited by: 9
Author(s): Brittany A. Goods, Michael H. Askenase, Erica Markarian, Hannah E. Beatty, Riley S. Drake, Ira Fleming, Jonathan H. DeLong, Naomi H. Philip, Charles Matouk, Issam A. Awad, Mario Zuccarello, Daniel F. Hanley, J. Christopher Love, Alex K. Shalek, Lauren H Sansing
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.101592

Sirtuin 3 attenuates amyloid-β induced neuronal hypometabolism
Cited by: 18
Author(s): Jun Yin, Shiping Li, Megan Nielsen, Tanner Carcione, Winnie S. Liang, Jiong Shi
Software Mentions: 2
Published: over 7 years ago

10.1172/jci.insight.138734

HPV transcript expression affects cervical cancer response to chemoradiation
Cited by: 10
Author(s): Fiona Ruiz, Matthew Inkman, Ramachandran Rashmi, Naoshad Muhammad, Nishanth Gabriel, Christopher A. Miller, Michael D. McLellan, Michael A. Goldstein, Stephanie Markovina, Perry W. Grigsby, Jin Zhang, Julie K. Schwarz
Software Mentions: 2
Published: almost 5 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: about 5 years ago

10.1172/jci.insight.151005

NR4A family members regulate T cell tolerance to preserve immune homeostasis and suppress autoimmunity
Cited by: 13
Author(s): Ryosuke Hiwa, Hailyn V. Nielsen, James L. Mueller, Ravi Mandla, Julie Zikherman
Software Mentions: 2
Published: almost 5 years ago

10.1172/jci.insight.149149

Endothelium-protective, histone-neutralizing properties of the polyanionic agent defibrotide
Cited by: 20
Author(s): Hui Shi, Alex A. Gandhi, Stephanie A. Smith, Qiuyu Wang, Diane Chiang, Srilakshmi Yalavarthi, Ramadan A. Ali, Chao Liu, Gautam Sule, Pei‐Suen Tsou, Yu Zuo, Yogendra Kanthi, Evan A. Farkash, Jiandie D. Lin, James H. Morrissey, Jason S. Knight
Software Mentions: 2
Published: almost 5 years ago

10.1038/srep18429

Single-target high-throughput transcription analyses reveal high levels of alternative splicing present in the FPPS/GGPPS from Plasmodium falciparum
Cited by: 14
Author(s): Heloisa B. Gabriel, Mauro Ferreira de Azevedo, Giuseppe Palmisano, Gerhard Wunderlich, Emı́lia A. Kimura, Alejandro M. Katzin, João M. P. Alves
Software Mentions: 2
Published: over 10 years ago

10.1038/srep18475

Transcriptome analysis reveals mucin 4 to be highly associated with periodontitis and identifies pleckstrin as a link to systemic diseases
Cited by: 42
Author(s): Anna Lundmark, Haleh Davanian, Tove Båge, Gunnar Johannsen, Catalin Koro, Joakim Lundeberg, Tülay Yucel‐Lindberg
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-018-4962-9

Dietary supplementation with olive mill wastewaters induces modifications on chicken jejunum epithelial cell transcriptome and modulates jejunum morphology
Cited by: 18
Author(s): Marcella Sabino, Katia Cappelli, Stefano Capomaccio, Luisa Pascucci, Ilaria Biasato, Andrea Verini-Supplizi, Andrea Valiani, Massimo Trabalza‐Marinucci
Software Mentions: 2
Published: almost 8 years ago

10.18632/aging.103236

Long noncoding RNA LINC00963 induces NOP2 expression by sponging tumor suppressor miR-542-3p to promote metastasis in prostate cancer
Cited by: 23
Author(s): Sun Feng, Ke Wu, Zhixian Yao, Xingyu Mu, Zhong Zheng, Menghao Sun, Yong Wang, Zhihong Liu, Yi-yong Zhu
Software Mentions: 2
Published: about 6 years ago

10.1038/srep26164

Therapeutic Blockade of Immune Complex-Mediated Glomerulonephritis by Highly Selective Inhibition of Bruton’s Tyrosine Kinase
Cited by: 31
Author(s): Samantha A. Chalmers, Jessica Doerner, Todd Bosanac, Sara Khalil, Dustin M. Smith, Christian Harcken, Janice Dimock, Evan Der, Leal Herlitz, Deborah Webb, Elise Seccareccia, Di Feng, Jay S. Fine, Meera Ramanujam, Elliott S. Klein, Chaim Putterman
Software Mentions: 2
Published: about 10 years ago

10.1186/s12864-020-6484-5

Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants
Cited by: 28
Author(s): Raphaël Leman, Hélène Tubeuf, Sabine Raad, Isabelle Tournier, Céline Derambure, Raphaël Lanos, Pascaline Gaildrat, G Castelain, Julie Hauchard, Audrey Killian, Stéphanie Baert‐Desurmont, Angélina Legros, Nicolas Goardon, Céline Quesnelle, Agathe Ricou, Laurent Castéra, Dominique Vaur, Gérald Le Gac, Chandran Ka, Yann Fichou, Françoise Bonnet‐Dorion, Nicolas Sévenet, Marine Guillaud‐Bataille, Nadia Boutry‐Kryza, Inès Schultz, Virginie Caux‐Moncoutier, Maria Rossing, Logan C. Walker, Amanda B. Spurdle, Claude Houdayer, Alexandra Martins, Sophie Krieger
Software Mentions: 2
Published: over 6 years ago

10.1038/srep31313

CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs
Cited by: 119
Author(s): Tim Schneider, Lee-Hsueh Hung, Silke Schreiner, Stefan Starke, Heinrich Eckhof, Oliver Roßbach, Stefan Reich, Jan Medenbach, Albrecht Bindereif
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep34420

Single-cell SNP analyses and interpretations based on RNA-Seq data for colon cancer research
Cited by: 13
Author(s): Jiahuan Chen, Qian Zhou, Yangfan Wang, Kang Ning
Software Mentions: 2
Published: almost 10 years ago

10.18632/aging.102614

CircNF1-419 improves the gut microbiome structure and function in AD-like mice
Cited by: 19
Author(s): Diling Chen, Longkai Qi, Yuna Guo, Yadi Liu, Xiaocui Tang, Xiangxiang Zhu, Miao Zhang, Li Ran, Ou Shuai, Dongdong Wang, Yizhen Xie, Xiaohong Yuan, Burton B. Yang, Qingping Wu
Software Mentions: 2
Published: over 6 years ago

10.1038/srep37137

An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Cited by: 51
Author(s): Anders Jemt, Fredrik Salmén, Anna Lundmark, Annelie Mollbrink, José Fernández Navarro, Patrik L. Ståhl, Tülay Yucel‐Lindberg, Joakim Lundeberg
Software Mentions: 2
Published: over 9 years ago

10.1038/srep40121

Diversity, distribution, and significance of transposable elements in the genome of the only selfing hermaphroditic vertebrate Kryptolebias marmoratus
Cited by: 28
Author(s): Jae-Sung Rhee, Beom-Soon Choi, Jaebum Kim, Bomi Kim, Young-Mi Lee, Il-Chan Kim, Akira Kanamori, Ik‐Young Choi, Manfred Schartl, Jae‐Seong Lee
Software Mentions: 2
Published: over 9 years ago

10.18632/aging.202759

Transcriptome and lipidome profile of human mesenchymal stem cells with reduced senescence and increased trilineage differentiation ability upon drug treatment
Cited by: 7
Author(s): Yue Chen, Xinglan An, Zengmiao Wang, Shan Guan, Hongyu An, Qingyuan Huang, Haobo Zhang, Lin Li, Bo Huang, Huiyu Wang, Min Lü, Huan Nie, Jun Wang, Xiangpeng Dai, Xin Lü
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22168607

Transcriptome Analysis in a Primary Human Muscle Cell Differentiation Model for Myotonic Dystrophy Type 1
Cited by: 7
Author(s): Vanessa Todorow, Stefan Hintze, Alastair Kerr, Andreas Hehr, Benedikt Schöser, Peter Meinke
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-020-6657-2

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data
Cited by: 8
Author(s): Vasanthan Jayakumar, Hiromi Ishii, Misato Seki, Wakako Kumita, Takashi Inoue, Sumitaka Hase, Kengo Sato, Hideyuki Okano, Erika Sasaki, Yasubumi Sakakibara
Software Mentions: 2
Published: over 6 years ago

10.1038/srep43782

Elevated Fibroblast growth factor 21 (FGF21) in obese, insulin resistant states is normalised by the synthetic retinoid Fenretinide in mice
Cited by: 26
Author(s): Nicola Morrice, George D. Mcilroy, Sheshu R. Tammireddy, Jennifer Reekie, Kirsty Shearer, Mary K. Doherty, Mirela Delibegović, Phillip D. Whitfield, Nimesh Mody
Software Mentions: 2
Published: over 9 years ago

10.1038/srep43184

Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors
Cited by: 65
Author(s): Andrew Hughes, Jennifer M. Enright, Connie A. Myers, Susan Q. Shen, Joseph C. Corbo
Software Mentions: 2
Published: over 9 years ago

10.1038/srep44383

De novo and reference transcriptome assembly of transcripts expressed during flowering provide insight into seed setting in tetraploid red clover
Cited by: 17
Author(s): Mallikarjuna Rao Kovi, Helga Amdahl, Muath Alsheikh, Odd Arne Rognli
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-020-6673-2

Comparison of RNA isolation methods on RNA-Seq: implications for differential expression and meta-analyses
Cited by: 30
Author(s): Amanda N. Scholes, Jeffrey A. Lewis
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms22168634

Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin
Cited by: 2
Author(s): Raymond L. Konger, Ethel Derr‐Yellin, Teresa A. Zimmers, Terrence M. Katona, Xiaoling Xuei, Yunlong Liu, Hongming Zhou, Edward Simpson, Matthew J. Turner
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms22169086

Programmed Cell Death in Developing Brachypodium distachyon Grain
Cited by: 1
Author(s): Safia Saada, Charles U. Solomon, Sinéad Drea
Software Mentions: 2
Published: almost 5 years ago

10.18632/aging.202749

Functional genomics study of protein inhibitor of activated STAT1 in mouse hippocampal neuronal cells revealed by RNA sequencing
Cited by: 7
Author(s): Kan He, Jian Zhang, Justin Liu, Yandi Cui, Leyna G. Liu, Shoudong Ye, Qian Ban, Ruolan Pan, Dahai Liu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-017-00403-5

Differential expression of chemosensory-protein genes in midguts in response to diet of Spodoptera litura
Cited by: 23
Author(s): Xin Yi, Jiangwei Qi, Xiaofan Zhou, Hu Mei, Zhenbang Guo
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-00629-3

Bone marrow-derived mesenchymal stem cells (BMSCs) repair acute necrotized pancreatitis by secreting microRNA-9 to target the NF-κB1/p50 gene in rats
Cited by: 42
Author(s): Daohai Qian, Wei Ge, Chenglei Xu, Zhigang He, Jie Hua, Jian Li, Qili Hu, Shengping Lin, Jian Gong, Hui Meng, Bo Zhou, Hong‐Fei Teng, Song Zhang
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms22179578

Canady Helios Cold Plasma Induces Breast Cancer Cell Death by Oxidation of Histone mRNA
Cited by: 11
Author(s): Xiaoqian Cheng, Saravana R. K. Murthy, Taisen Zhuang, Lawan Ly, Olivia Jones, Giacomo Basadonna, Michael Keidar, Yasmine Kanaan, Jerome Canady
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-020-07301-7

RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge
Cited by: 8
Author(s): Taylor W Bailey, Andrea Pires dos Santos, Naíla Cannes do Nascimento, Shaojun Xie, Jyothi Thimmapuram, M. Preeti Sivasankar, Abigail Cox
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22179463

Chondrocytes from Osteoarthritis Patients Adopt Distinct Phenotypes in Response to Central TH1/TH2/TH17 Cytokines
Cited by: 7
Author(s): Antti Pemmari, Tiina Leppänen, Mari Hämäläinen, Teemu Moilanen, Eeva Moilanen
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-015-1876-7

Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap
Cited by: 77
Author(s): Shanrong Zhao, Ying Zhang, William Gordon, Jie Quan, Hualin Simon Xi, Sarah Du, David von Schack, Baohong Zhang
Software Mentions: 2
Published: almost 11 years ago

10.3390/ijms22179218

Sodium Iodate-Induced Degeneration Results in Local Complement Changes and Inflammatory Processes in Murine Retina
Cited by: 19
Author(s): Anne Enzbrenner, Rahel Zulliger, Josef Biber, Ana Maria Quintela Pousa, Nicole Schäfer, Corinne Stucki, Nicolas Giroud, Marco Berrera, Elöd Körtvely, Roland Schmucki, Laura Badi, Antje Grosche, Diana Pauly, Volker Enzmann
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-020-6587-z

RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection
Cited by: 13
Author(s): Carlos Trujillo-Moya, Andrea Ganthaler, Wolfgang Stöggl, Ilse Kranner, Silvio Schüler, Reinhard Ertl, Sarah Schlosser, Jan-Peter George, Stefan Mayr
Software Mentions: 2
Published: about 6 years ago

10.18632/aging.102529

Circular RNA NF1-419 enhances autophagy to ameliorate senile dementia by binding Dynamin-1 and Adaptor protein 2 B1 in AD-like mice
Cited by: 52
Author(s): Diling Chen, Yuna Guo, Longkai Qi, Xiaocui Tang, Yadi Liu, Xuefei Yang, Guoping Hu, Ou Shuai, Tianqiao Yong, Dongdong Wang, Yizhen Xie, Burton B. Yang, Qingping Wu
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-018-4719-5

Transcriptional profiling of swine mammary gland during the transition from colostrogenesis to lactogenesis using RNA sequencing
Cited by: 29
Author(s): Valentino Palombo, Juan J. Loor, Mariasilvia D’Andrea, Mario Vailati-Riboni, Khuram Shahzad, Uffe Krogh, Peter Kappel Theil
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-019-5608-2

Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes
Cited by: 4
Author(s): Siebe Loontiens, Lisa Depestel, Suzanne Vanhauwaert, Givani Dewyn, Charlotte Gistelinck, Karen Verboom, Wouter Van Loocke, Filip Matthijssens, Andy Willaert, Jo Vandesompele, Franki Speleman, Kaat Durinck
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms22189840

Anaesthesia-Induced Transcriptomic Changes in the Context of Renal Ischemia Uncovered by the Use of a Novel Clamping Device
Cited by: 1
Author(s): Charles Verney, David Legouis, Sandrine Placier, Tiffany Migeon, Philippe Bonnin, David Buob, Juliette Hadchouel, Pierre Galichon
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms22189842

Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing
Cited by: 6
Author(s): Zheng-Shan He, Andan Zhu, Jun‐Bo Yang, Weishu Fan, Li D
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms221810112

Tissue-Specific Metabolic Reprogramming during Wound-Induced Organ Formation in Tomato Hypocotyl Explants
Cited by: 6
Author(s): Eduardo Larriba, Ana Belén Sánchez-García, Cristina Martínez‐Andújar, Alfonso Albacete, José Manuel Pérez-Pérez
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-017-07514-z

Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
Cited by: 7
Author(s): Trees‐Juen Chuang, Yu-Hsiang Tseng, Chia-Ying Chen, Yi-Da Wang
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-018-4486-3

FuSpot: a web-based tool for visual evaluation of fusion candidates
Cited by: 1
Author(s): Jackson A. Killian, Taha M. Topiwala, Alex R. Pelletier, David Frankhouser, Pearlly S. Yan, Ralf Bundschuh
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-018-4619-8

The performance of coalescent-based species tree estimation methods under models of missing data
Cited by: 63
Author(s): Michael Nute, Jed Chou, Erin K. Molloy, Tandy Warnow
Software Mentions: 2
Published: about 8 years ago

10.18632/aging.103602

Depletion of exosomal circLDLR in follicle fluid derepresses miR-1294 function and inhibits estradiol production via CYP19A1 in polycystic ovary syndrome
Cited by: 51
Author(s): Xin Huang, Bi Wu, Miaoxin Chen, Hong Li, Pengcheng Kong, Zhiyun Wei
Software Mentions: 2
Published: about 6 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759