cran: STAR | Projects | Ecosyste.ms: Papers

10.7554/eLife.66063

Distinct skeletal stem cell types orchestrate long bone skeletogenesis
Cited by: 35
Author(s): Thomas H. Ambrosi, Rahul Sinha, Holly Steininger, Malachia Hoover, Matthew P. Murphy, Lauren S. Koepke, Yuting Wang, Wan-Jin Lu, Maurizio Morri, Norma Neff, Irving L. Weissman, Michael T. Longaker, Charles Chan
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms18040747

Metabolic Effect of an Oriental Herbal Medicine on Obesity and Its Comorbidities with Transcriptional Responses in Diet-Induced Obese Mice
Cited by: 4
Author(s): Jiyoung Choi, Ye Jin Kim, Su-Jung Cho, Eun‐Young Kwon, Ri Ryu, Myung‐Sook Choi
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms18081709

Systematic Selection of Reference Genes for the Normalization of Circulating RNA Transcripts in Pregnant Women Based on RNA-Seq Data
Cited by: 20
Author(s): Stephen S.C. Chim, Kwan-Yiu Wong, C.Y. Chung, Stephanie Lam, Jamie Sui-Lam Kwok, Chit-Ying Lai, Yvonne Kwun Yue Cheng, Shuk Yi Annie Hui, Meng Meng, Oi-Ka Chan, Stephen Kwok‐Wing Tsui, Keun-Young Lee, Ting-Fung Chan, Tse Ngong Leung
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13058-020-01275-w

In utero estrogenic endocrine disruption alters the stroma to increase extracellular matrix density and mammary gland stiffness
Cited by: 14
Author(s): Clarissa Wormsbaecher, Andrea R. Hindman, Alex Avendano, Marcos Cortes-Medina, Caitlin E. Jones, Andrew R. Bushman, Lotanna Onua, Claire E Kovalchin, Alina R. Murphy, Hannah L. Helber, Ali Shapiro, Kyle Voytovitch, Xingyan Kuang, Renán Aguilar-Valenzuela, Jennifer L. Leight, Jonathan W. Song, Craig J. Burd
Software Mentions: 3
Published: about 6 years ago

10.1016/j.ccell.2019.05.015

RAC1P29S Induces a Mesenchymal Phenotypic Switch via Serum Response Factor to Promote Melanoma Development and Therapy Resistance
Cited by: 86
Author(s): Daniël A. Lionarons, David C. Hancock, Sareena Rana, Philip East, Christopher Moore, Miguel Murillo, Joana Carvalho, Bradley Spencer–Dene, Eleanor Herbert, Gordon Stamp, Djamil Damry, Dinis Pedro Calado, Ian Rosewell, Ralph Fritsch, Richard R. Neubig, Míriam Molina‐Arcas, Julian Downward
Software Mentions: 3
Published: about 7 years ago

10.1002/cam4.3846

MX2 mediates establishment of interferon response profile, regulates XAF1, and can sensitize melanoma cells to targeted therapy
Cited by: 5
Author(s): Marina Juraleviciute, Jérémie Nsengimana, Julia Newton‐Bishop, Gert J. Hendriks, Ana Slipicevic
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0211978

Testing of library preparation methods for transcriptome sequencing of real life glioblastoma and brain tissue specimens: A comparative study with special focus on long non-coding RNAs
Cited by: 7
Author(s): Marek Večeřa, Jiří Šána, Jan Oppelt, Boris Tichý, Alena Kopková, Radim Lipina, Martin Smrčka, Radim Jančálek, Markéta Hermanová, Leoš Křen, Ondřej Slabý
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0170632

A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples
Cited by: 86
Author(s): Anna Esteve‐Codina, Oriol Arpí, Maria Martinez-García, Estela Pineda, Mar Mallo, Marta Gut, Cristina Carrato, Ana Rovira, Raquel Pérez López, Avelina Tortosa, Marc Dabad, Sonia Del Barco, Simon Heath, Sílvia Bagué, Teresa Ribalta, Francesc Alameda, Núria de la Iglesia, Carmen Balaña
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0232559

Transcriptome analysis indicates dominant effects on ribosome and mitochondrial function of a premature termination codon mutation in the zebrafish gene psen2
Cited by: 9
Author(s): Haowei Jiang, Stephen Pederson, Morgan Newman, Yang Dong, Karissa Barthelson, Michael Lardelli
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0218719

Transcriptome variation in response to gastrointestinal nematode infection in goats
Cited by: 6
Author(s): Hadeer M. Aboshady, Nathalie Mandonnet, M. J. Stear, Rémy Arquet, Malia Bederina, Julien Sarry, Gwenola Tosser‐Klopp, Christophe Klopp, Anna M. Johansson, Elisabeth Jonas, Jean-Christophe Bambou
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0236395

The effect of compound kushen injection on cancer cells: Integrated identification of candidate molecular mechanisms
Cited by: 12
Author(s): Jingang Cui, Zhibo Qu, Yuka Harata-Lee, Hao Shen, Thazin Nwe Aung, Wei Wang, R. Daniel Kortschak, David L. Adelson
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0234246

Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia
Cited by: 8
Author(s): Rong Zhang, Jan Gehlen, Amit Kawalia, Maria-Theodora Melissari, Tikam Chand Dakal, Athira M. Menon, Julia Höfele, Korbinian Riedhammer, Lea Waffenschmidt, Júlia Fabian, Katinka Breuer, Jeshurun C Kalanithy, Alina C. Hilger, Ingo G. H. Schmidt‐Wolf, A. Hölscher, Thomas M. Boemers, Markus Pauly, Andreas Leutner, Jörg Fuchs, Guido Seitz, Barbara Ludwikowski, Bárbara Gómez, Jochen Hubertus, Andreas Heydweiller, Ralf Kurz, Johannes Leonhardt, Ferdinand Kosch, Stefan Holland‐Cunz, Oliver Münsterer, B. M. Ure, Eberhard Schmiedeke, Jörg Neser, P. Degenhardt, Stefanie Märzheuser, Katharina Kleine, Mattias Schäfer, Nicole Spychalski, Oliver Johannes Deffaa, Jan‐Hendrik Gosemann, Martin Lacher, Stefanie Heilmann‐Heimbach, Nadine Zwink, Ekkehart Jenetzky, Michael Ludwig, Phillip Grote, Johannes Schumacher, Holger Thiele, Heiko Reutter
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms18091900

Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data
Cited by: 3
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0194518

The influence of transcript assembly on the proteogenomics discovery of microproteins
Cited by: 17
Author(s): Ji Ma, Alan Saghatelian, Maxim N. Shokhirev
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0192606

Maternal high-fat diet associated with altered gene expression, DNA methylation, and obesity risk in mouse offspring
Cited by: 86
Author(s): Madeline Rose Keleher, Syeda Nuzhat Fatima Zaidi, Shyam Shah, MaryAnn Oakley, Cassondra Pavlatos, Samir El Idrissi, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0221634

Comparative multi-omics systems analysis reveal the glycolysis / gluconeogenesis signal pathway play an important role in virulence attenuation in fish-derived GBS YM001
Cited by: 2
Author(s): Yu Liu, Liping Li, Ting Huang, Rui Wang, Weizheng Liang, Qiong Yang, Aiying Lei, Ming Chen
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0232542

Transcriptome analysis identifies genes involved with the development of umbilical hernias in pigs
Cited by: 10
Author(s): Mayla Regina Souza, A. M. G. Ibelli, Igor Ricardo Savoldi, Mauricio Egídio Cantão, J. de O. Peixoto, M. A. Z. Morés, Jader Silva Lopes, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0228590

Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells
Cited by: 8
Author(s): Zhifei Luo, Peggy J. Farnham
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0212513

Lenvatinib plus anti-PD-1 antibody combination treatment activates CD8+ T cells through reduction of tumor-associated macrophage and activation of the interferon pathway
Cited by: 262
Author(s): Yu Kato, Kimiyo Tabata, Takayuki Kimura, Ayako Yachie‐Kinoshita, Yoichi Ozawa, Kazuhiko Yamada, Junichi Ito, Sho Tachino, Yusaku Hori, Masahiro Matsuki, Yoshikazu Matsuoka, Samik Ghosh, Hiroaki Kitano, Ken’ichi Nomoto, Junji Matsui, Yasuhiro Funahashi
Software Mentions: 3
Published: over 7 years ago

10.1002/cti2.1175

Partial absence of PD‐1 expression by tumor‐infiltrating EBV‐specific CD8+ T cells in EBV‐driven lymphoepithelioma‐like carcinoma
Cited by: 7
Author(s): Yannick Simoni, Étienne Becht, Shamin Li, Chiew Yee Loh, Joe Yeong, Tony Kiat Hon Lim, Angela Takano, Daniel S.W. Tan, Evan W. Newell
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms20143457

Unravelling the Role of Trophoblastic-Derived Extracellular Vesicles in Regulatory T Cell Differentiation
Cited by: 25
Author(s): Árpád Ferenc Kovács, Nóra Fekete, Lilla Turiák, András Ács, László Kőhidai, Edit I. Buzás, Éva Pállinger
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2020.572193

Functional Analysis of the teosinte branched 1 Gene in the Tetraploid Switchgrass (Panicum virgatum L.) by CRISPR/Cas9-Directed Mutagenesis
Cited by: 10
Author(s): Yang Liu, Weiling Wang, Bing Yang, Christopher J. Currey, Shui‐zhang Fei
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms21062065

The Beta Subunit of Nascent Polypeptide Associated Complex Plays A Role in Flowers and Siliques Development of Arabidopsis thaliana
Cited by: 2
Author(s): Jan Fíla, Božena Klodová, David Potěšil, Miloslav Juříček, Petr Šesták, Zbyněk Zdráhal, David Honys
Software Mentions: 2
Published: over 6 years ago

10.3389/fpsyt.2018.00778

Dynamic Patterns of Threat-Associated Gene Expression in the Amygdala and Blood
Cited by: 13
Author(s): Adriana Lori, Stephanie A. Maddox, Sumeet K. Sharma, Raül Andero, Kerry J. Ressler, Alicia K. Smith
Software Mentions: 2
Published: over 7 years ago

10.3389/fpsyt.2018.00257

Oxycodone Self-Administration Induces Alterations in Expression of Integrin, Semaphorin and Ephrin Genes in the Mouse Striatum
Cited by: 31
Author(s): Vadim Yuferov, Yong Zhang, Yupu Liang, Connie Zhao, Matthew Randesi, Mary Jeanne Kreek
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.27450

Molecular conservation of marsupial and eutherian placentation and lactation
Cited by: 28
Author(s): Michael W Guernsey, Edward B. Chuong, Guillaume Cornelis, Marilyn B. Renfree, Julie C. Baker
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms19082359

Non-Coding Transcriptome Maps across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye
Cited by: 5
Author(s): Hyosun Hong, Han-Ha Chai, Kyoungwoo Nam, Dajeong Lim, Kyung-Tai Lee, Yoon Jung, Chang-Yeon Cho, Jin‐Wu Nam
Software Mentions: 2
Published: almost 8 years ago

10.3389/fnsyn.2018.00014

CD4+ T Cells Have a Permissive Effect on Enriched Environment-Induced Hippocampus Synaptic Plasticity
Cited by: 11
Author(s): Hadi Zarif, Salma Hosseiny, Agnès Paquet, Kévin Lebrigand, Marie-Jeanne Arguel, Julie Cazareth, Anne Lazzari, Catherine Heurteaux, Nicolas Glaichenhaus, Joëlle Chabry, Alice Guyon, Agnès Petit-Paitel
Software Mentions: 2
Published: about 8 years ago

10.3389/fnsys.2020.571011

Prolonged Targeted Cardiovascular Epidural Stimulation Improves Immunological Molecular Profile: A Case Report in Chronic Severe Spinal Cord Injury
Cited by: 7
Author(s): Ona Bloom, Jill M. Wecht, Bonnie Legg Ditterline, Siqi Wang, Alexander V. Ovechkin, Cláudia A. Angeli, Anthony A. Arcese, Susan J. Harkema
Software Mentions: 2
Published: almost 6 years ago

10.1093/gigascience/giy079

Clinker: visualizing fusion genes detected in RNA-seq data
Cited by: 16
Author(s): Breon Schmidt, N. Davidson, Anthony D. K. Hawkins, Ray C. Bartolo, Ian J. Majewski, Paul G. Ekert, Alicia Oshlack
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.70557

3′HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression
Cited by: 5
Author(s): Pamela Himadewi, Xue Qing David Wang, Fan Feng, Haley Gore, Yushuai Liu, Li Yu, Ryo Kurita, Yukio Nakamura, Gerd P. Pfeifer, Jie Liu, Xiaotian Zhang
Software Mentions: 2
Published: almost 5 years ago

10.1242/bio.028548

Transcriptome sequencing of the naked mole rat (Heterocephalus glaber) and identification of hypoxia tolerance genes
Cited by: 9
Author(s): Bao Xiao, Li Li, Chang Xu, Shihua Zhao, Lei Lin, Jishuai Cheng, Wenjing Yang, Cong Wang, Guanghan Kan, Shufang Cui
Software Mentions: 2
Published: over 9 years ago

10.1093/gigascience/giy131

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
Cited by: 87
Author(s): Daniel Mapleson, Luca Venturini, Gemy Kaithakottil, David Swarbreck
Software Mentions: 2
Published: over 7 years ago

10.1186/s13058-021-01468-x

Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer
Cited by: 9
Author(s): Anastasia A. Ionkina, Gabriela Balderrama-Gutierrez, Krystian J Ibanez, Steve Huy D. Phan, Angelique Cortez, A Mortazavi, Jennifer A. Prescher
Software Mentions: 2
Published: almost 5 years ago

10.1093/gigascience/giz027

Chromosome-scale genome assembly of kiwifruit Actinidia eriantha 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 7 years ago

10.1093/gigascience/giz044

SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
Cited by: 22
Author(s): Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
Software Mentions: 2
Published: about 7 years ago

10.3390/biomedicines9070705

Multiplex Patient-Based Drug Response Assay in Pancreatic Ductal Adenocarcinoma
Cited by: 8
Author(s): Andrew Armstrong, Muhammad R. Haque, Sina Mirbagheri, Usman Barlass, Douglas Gilbert, Jaimin Amin, Ajaypal Singh, Ankur Naqib, Faraz Bishehsari
Software Mentions: 2
Published: about 5 years ago

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

10.7554/eLife.50561

MicroRNA-934 is a novel primate-specific small non-coding RNA with neurogenic function during early development
Cited by: 11
Author(s): Kanella Prodromidou, Ioannis S. Vlachos, Maria Gaitanou, Georgia Kouroupi, Artemis G. Hatzigeorgiou, Rebecca Matsas
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.54603

Coverage-dependent bias creates the appearance of binary splicing in single cells
Cited by: 32
Author(s): Carlos Fernando Buen Abad Najar, Nir Yosef, Liana F. Lareau
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.54659

Osterix-Cre marks distinct subsets of CD45- and CD45+ stromal populations in extra-skeletal tumors with pro-tumorigenic characteristics
Cited by: 9
Author(s): Biancamaria Ricci, Eric Tycksen, Hamza Celik, Jad I. Belle, Francesca Fontana, Roberto Civitelli, Roberta Faccio
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0246615

Deciphering the transcriptomic regulation of heat stress responses in Nothofagus pumilio
Cited by: 4
Author(s): Maximiliano Estravis-Barcalá, Katrin Heer, Paula Marchelli, Birgit Ziegenhagen, María Verónica Arana, Nicolás Bellora
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.30919

ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2
Cited by: 118
Author(s): Devanshi Jain, M. Rhyan Puno, Cem Meydan, Nathalie Lailler, Christopher E. Mason, Christopher D. Lima, Kathryn V. Anderson, Scott Keeney
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0255085

Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive
Cited by: 0
Author(s): J. L. Webb, Simon M. Moe, Andrew Bolstad, Elizabeth McNeill
Software Mentions: 2
Published: almost 5 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

10.1371/journal.pone.0249658

Koala cathelicidin PhciCath5 has antimicrobial activity, including against Chlamydia pecorum
Cited by: 5
Author(s): Emma Peel, Yuanyuan Cheng, Julianne T. Djordjevic, Denis O’Meally, Mark S. Thomas, Michael Kuhn, Tania C. Sorrell, Wilhelmina M. Huston, Katherine Belov
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.30094

Dissection of affinity captured LINE-1 macromolecular complexes
Cited by: 59
Author(s): Martin S. Taylor, Ilya Altukhov, Kelly R. Molloy, Paolo Mita, Hua Jiang, Emily M. Adney, Aleksandra Wudzinska, Sana Badri, Dimitry D Ischenko, George Eng, Kathleen H. Burns, David Fenyö, Brian T. Chait, Dmitry Alexeev, Michael P. Rout, Jef D. Boeke, John LaCava
Software Mentions: 2
Published: over 8 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

10.1186/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

10.1371/journal.pone.0176768

Induction of endogenous retroelements as a potential mechanism for mouse-specific drug-induced carcinogenicity
Cited by: 3
Author(s): Timothy Coskran, Zhijie Jiang, James E. Klaunig, Dixie L. Mager, Leslie Obert, Andrew W. Robertson, Nicholas F. Tsinoremas, Zemin Wang, Mark Gosink
Software Mentions: 2
Published: about 9 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

10.7554/eLife.50960

Comprehensive annotations of human herpesvirus 6A and 6B genomes reveal novel and conserved genomic features
Cited by: 30
Author(s): Yaara Finkel, Dominik Schmiedel, Julie Tai-Schmiedel, Aharon Nachshon, Roni Winkler, Martina Dobešová, Michal Schwartz, Ofer Mandelboim, Noam Stern-Ginossar
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms20225539

Changes in Calcium Homeostasis and Gene Expression Implicated in Epilepsy in Hippocampi of Mice Overexpressing ORAI1
Cited by: 12
Author(s): Łukasz Majewski, Bartosz Wojtaś, Filip Maciąg, Jacek Kuźnicki
Software Mentions: 2
Published: over 6 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

10.1371/journal.pone.0174575

Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce
Cited by: 15
Author(s): Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms20225706

CRISPR/Cas9-Mediated Knock-Out of KrasG12D Mutated Pancreatic Cancer Cell Lines
Cited by: 22
Author(s): Eva Lentsch, Lifei Li, Susanne Pfeffer, Arif B. Ekici, Leila Taher, Christian Pilarsky, Robert Grützmann
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.36865

Pdgfra marks a cellular lineage with distinct contributions to myofibroblasts in lung maturation and injury response
Cited by: 119
Author(s): Rongbo Li, Ksenija Bernau, Nathan Sandbo, Jing Gu, Sebastian Preißl, Xin Sun
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0171221

PI3Kδ inhibitor idelalisib in combination with BTK inhibitor ONO/GS-4059 in diffuse large B cell lymphoma with acquired resistance to PI3Kδ and BTK inhibitors
Cited by: 43
Author(s): Anella Yahiaoui, Sarah Meadows, Rick Sorensen, Zhi-Hua Cui, Kathleen Keegan, Robert Brockett, Guang Chen, Christophe Quéva, Li Li, Stacey Tannheimer
Software Mentions: 2
Published: over 9 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

10.3390/ijms19051485

PIMT/NCOA6IP Deletion in the Mouse Heart Causes Delayed Cardiomyopathy Attributable to Perturbation in Energy Metabolism
Cited by: 8
Author(s): Yuzhi Jia, Ning Liu, Navin Viswakarma, Ruya Sun, Mathew J. Schipma, Shu Meng, Edward B. Thorp, Yashpal S. Kanwar, Bayar Thimmapaya, Janardan K. Reddy
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0194485

Expression profiling of disease progression in canine model of Duchenne muscular dystrophy
Cited by: 16
Author(s): Candice Brinkmeyer-Langford, Candice P. Chu, Cynthia Balog-Alvarez, Xue Yu, James J. Cai, Mary B. Nabity, Joe N. Kornegay
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0224835

Metformin strongly affects transcriptome of peripheral blood cells in healthy individuals
Cited by: 19
Author(s): Monta Ustinova, Ivars Silamiķelis, Ineta Kalniņa, Laura Ansone, Vita Rovīte, Ilze Elbere, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Ekaterina Aladyeva, Ilze Konrāde, Valdis Pīrāgs, Jānis Kloviņš
Software Mentions: 2
Published: over 6 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

10.1371/journal.pone.0195893

A20 regulates canonical wnt-signaling through an interaction with RIPK4
Cited by: 8
Author(s): Brooke N. Nakamura, Alison Glazier, Michael G. Kattah, Bao Duong, Yulin Jia, Daniel Campo, Ling Shao
Software Mentions: 2
Published: about 8 years ago

10.1155/2015/831352

Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing DataIn Silico
Cited by: 6
Author(s): Mei Feng, Sumei Wang, Li Zhang
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.63972

HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics
Cited by: 57
Author(s): Amy R. Strom, Ronald Biggs, Edward J. Banigan, Xiaotao Wang, Katherine Chiu, Cameron Herman, Jimena Collado, Feng Yue, Joan C. Ritland Politz, Leah J. Tait, David Scalzo, Agnes Telling, Mark Groudine, Clifford P. Brangwynne, John F. Marko, Andrew D. Stephens
Software Mentions: 2
Published: about 5 years ago

10.1155/2021/9922185

The Silence of PSMC6 Inhibits Cell Growth and Metastasis in Lung Adenocarcinoma
Cited by: 11
Author(s): Jianyu Zhang, Kezhi Shi, Xi Liao, Shijun Li, Dan Bao, Ying Qian, Daojun Li
Software Mentions: 2
Published: about 5 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

10.1155/2021/1978434

RNA-seq-Based Screening in Coal Dust-Treated Cells Identified PHLDB2 as a Novel Lung Cancer-Related Molecular Marker
Cited by: 1
Author(s): Deyong Ge, Yuhan Shao, Mengjie Wang, Huihui Tao, Min Mu, Xinrong Tao
Software Mentions: 2
Published: about 5 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

10.7554/eLife.58172

Irisin directly stimulates osteoclastogenesis and bone resorption in vitro and in vivo
Cited by: 61
Author(s): Eben G. Estell, Phuong Le, Yosta Vegting, Hyeonwoo Kim, Christiane D. Wrann, Mary L. Bouxsein, Kenichi Nagano, Roland Baron, Bruce M. Spiegelman, Clifford J. Rosen
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms20236083

Dual RNA Sequencing of Vitis vinifera during Lasiodiplodia theobromae Infection Unveils Host–Pathogen Interactions
Cited by: 22
Author(s): Micael F. M. Gonçalves, R. Nunes, Laurentijn Tilleman, Yves Van de Peer, Dieter Deforce, Filip Van Nieuwerburgh, Ana Cristina Esteves, Artur Alves
Software Mentions: 2
Published: over 6 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

10.1371/journal.pone.0191033

Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology
Cited by: 0
Author(s): Bruce H. Howard, Tazuko H. Hirai, Valya R. Russanova
Software Mentions: 2
Published: over 8 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

10.1371/journal.pone.0218133

Sex differences in sympathetic gene expression and cardiac neurochemistry in Wistar Kyoto rats
Cited by: 6
Author(s): Richard Bayles, Joanne Tran, Antoinette Olivas, William R. Woodward, Suzanne S. Fei, Lina Gao, Beth A. Habecker
Software Mentions: 2
Published: about 7 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

10.1371/journal.pone.0229170

CD20 is dispensable for B-cell receptor signaling but is required for proper actin polymerization, adhesion and migration of malignant B cells
Cited by: 13
Author(s): Veronika Kozlová, Aneta Ledererová, Adriana Ladungová, Helena Peschelová, Pavlína Janovská, Aleksander Ślusarczyk, J Domagała, Pavel Kopcil, Viera Vakulová, Jan Oppelt, Vı́tězslav Bryja, Michael Doubek, Jiřı́ Mayer, Šárka Pospı́šilová, Michal Šmída
Software Mentions: 2
Published: over 6 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

10.1172/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: almost 6 years ago

10.7554/eLife.54501

Semiochemical responsive olfactory sensory neurons are sexually dimorphic and plastic
Cited by: 18
Author(s): Aashutosh Vihani, Xiaoyang Serene Hu, Sivaji Gundala, Sachiko Koyama, Eric Block, Hiroaki Matsunami
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

10.1371/journal.pone.0108095

High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing
Cited by: 42
Author(s): Hyunghoon Cho, Joe R. Davis, Xin Li, Kevin S. Smith, Alexis Battle, Stephen B. Montgomery
Software Mentions: 2
Published: almost 12 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

10.1371/journal.pone.0201822

RNA variant identification discrepancy among splice-aware alignment algorithms
Cited by: 7
Author(s): Ji Hyung Hong, Yoon Ho Ko, Keunsoo Kang
Software Mentions: 2
Published: almost 8 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

10.1155/2019/8427042

Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery
Cited by: 37
Author(s): Nagarajan Nagasundaram, Edward Kien Yee Yapp, Nguyen Quoc Khanh Le, Balu Kamaraj, Abeer Mohammed Al‐Subaie, Hui‐Yuan Yeh
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0210404

Screening human cell lines for viral infections applying RNA-Seq data analysis
Cited by: 13
Author(s): Cord C. Uphoff, Claudia Pommerenke, Sabine A. Denkmann, Hans G. Drexler
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0054848

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing
Cited by: 290
Author(s): John E. McCormack, Michael Harvey, Brant C. Faircloth, Nicholas G. Crawford, Travis C. Glenn, Robb T. Brumfield
Software Mentions: 2
Published: over 13 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

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759