cran: STAR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0238497

Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC)
Cited by: 2
Author(s): Nabil F. Saba, Ashok R. Dinasarapu, Kelly R. Magliocca, Bhakti Dwivedi, Sandra Seby, Zhaohui S. Qin, Mihir R. Patel, Christopher C. Griffith, Xu Wang, Mark W. El‐Deiry, Conor E. Steuer, Jeanne Kowalski, Dong M. Shin, Michael E. Zwick, Zhuo Georgia Chen
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-021-83110-6

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Cited by: 13
Author(s): Hye Kyung Lee, Ludwig Knabl, Lisa Pipperger, André Volland, Priscilla A. Furth, Keunsoo Kang, Harold E. Smith, Ludwig Knabl, Romuald Bellmann, Christina Bernhard, Norbert Kaiser, Hannes Gänzer, Mathias Ströhle, Andreas Walser, Dorotheé von Laer, Lothar Hennighausen
Software Mentions: 6
Published: over 5 years ago

10.1128/mBio.01714-20

Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium
Cited by: 20
Author(s): Michael Seidl, Holger Kramer, David E. Cook, Gabriel Lorencini Fiorin, Grardy C. M. van den Berg, Luigi Faino, B.P.H.J. Thomma
Software Mentions: 6
Published: almost 6 years ago

10.1101/2020.09.01.20185884

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Cited by: 0
Author(s): Hye Kyung Lee, Ludwig Knabl, Lisa Pipperger, André Volland, Priscilla A. Furth, Keunsoo Kang, Harold E. Smith, Romuald Bellmann, Christina Bernhard, Norbert Kaiser, Hannes Gänzer, Mathias Ströhle, Andreas Walser, Dorothee von Laer, Lothar Hennighausen
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-021-81933-x

Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips
Cited by: 15
Author(s): Heleen H.T. Middelkamp, Anouk H.A. Verboven, Aisen Vivas, Chantal Schoenmaker, Teun Klein Gunnewiek, Robert Passier, Cornelis A. Albers, Peter-Bram A.C. ’t Hoen, Nael Nadif Kasri, Andries D. van der Meer
Software Mentions: 6
Published: over 5 years ago

10.1128/mBio.02683-20

The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral UL4 / UL5 Transcripts
Cited by: 23
Author(s): Ana Cristina Gonzalez-Perez, Markus Stempel, Emanuel Wyler, Christian Urban, Antonio Piras, Thomas Hennig, Sabina Ganskih, Yuanjie Wei, Albert Heim, Markus Landthaler, Andreas Pichlmair, Lars Dölken, Mathias Munschauer, Florian Erhard, Melanie M. Brinkmann
Software Mentions: 6
Published: about 5 years ago

10.7554/eLife.35368

Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila
Cited by: 92
Author(s): Zaijun Ma, Hui Wang, Yuping Cai, Han Wang, Kongyan Niu, Xiaofen Wu, Huanhuan Ma, Yun Yang, Wenhua Tong, Feng Liu, Zhandong Liu, Yaoyang Zhang, Rui Li, Zheng‐Jiang Zhu, Nan Liu
Software Mentions: 6
Published: about 8 years ago

10.1101/2021.05.27.21257952

Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation
Cited by: 3
Author(s): Hye Kyung Lee, Ludwig Knabl, Manuel Wieser, Anna Mur, August Zabernigg, Jana Schumacher, Norbert Kaiser, Priscilla A. Furth, Lothar Hennighausen
Software Mentions: 6
Published: about 5 years ago

10.1186/s13046-021-02034-1

Immuno-genomic classification of colorectal cancer organoids reveals cancer cells with intrinsic immunogenic properties associated with patient survival
Cited by: 14
Author(s): Eun Jeong Cho, Minsuh Kim, Daum Jo, Jihye Kim, Ji-Hye Oh, Hee Chul Chung, Sun-Hye Lee, Deokhoon Kim, Sung Chun, Jihun Kim, Hyeonjin Lee, Tae Won Kim, Chang Sik Yu, Chang‐Keun Sung, Se Jin Jang
Software Mentions: 6
Published: about 5 years ago

10.1101/2021.09.08.21263284

Robust immune response to the BNT162b mRNA vaccine in an elderly population vaccinated 15 months after recovery from COVID-19
Cited by: 12
Author(s): Hye Kyung Lee, Ludwig Knabl, Ludwig Knabl, Sebastian Kapferer, Birgit Pateter, Mary Walter, Priscilla A. Furth, Lothar Hennighausen
Software Mentions: 6
Published: almost 5 years ago

10.1186/s13148-018-0593-x

Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals
Cited by: 19
Author(s): Ilze Elbere, Ivars Silamiķelis, Monta Ustinova, Ineta Kalniņa, Linda Zaharenko, Raitis Pečulis, Ilze Konrāde, Diana M. Ciuculete, Christina Zhukovsky, Dita Gudrā, Ilze Radoviča-Spalviņa, Dāvids Fridmanis, Valdis Pīrāgs, Helgi B. Schiöth, Jānis Kloviņš
Software Mentions: 6
Published: over 7 years ago

10.1016/j.ajhg.2019.05.010

Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver
Cited by: 33
Author(s): Minal Çalışkan, Elisabetta Manduchi, Harish Rao, Julian A. Segert, Márcia Holsbach Beltrame, Marco Trizzino, YoSon Park, Samuel White Baker, Alessandra Chesi, Matthew E. Johnson, Kenyaita M. Hodge, Michelle E. Leonard, Bao‐Li Loza, Xin Dong, Andrea M. Berrido, Nicholas J. Hand, Robert C. Bauer, Andrew D. Wells, Kim M. Olthoff, Abraham Shaked, Daniel J. Rader, Struan F.A. Grant, Christopher D. Brown
Software Mentions: 6
Published: about 7 years ago

10.1186/s13073-021-00939-2

Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes
Cited by: 17
Author(s): David Z. Pan, Min‐Hua Zong, Caroline Comenho, Sandhya Rajkumar, Amogha Koka, Seung Hyuk Lee, Marcus Alvarez, Dorota Kaminska, Arthur Ko, Janet S. Sinsheimer, Karen L. Mohlke, Nicholas Mancuso, Linda Liliana Muñóz-Hernández, Miguel Francisco Herrera-Hernández, Marı́a Teresa Tusié-Luna, Carlos A. Aguilar-Salinas, Kirsi H. Pietiläinen, Jussi Pihlajamäki, Markku Laakso, Kristina M. Garske, Päivi Pajukanta
Software Mentions: 6
Published: about 5 years ago

10.3389/fimmu.2019.02568

Gene Expression-Based Identification of Antigen-Responsive CD8+ T Cells on a Single-Cell Level
Cited by: 22
Author(s): Yannick F. Fuchs, Virag Sharma, Anne Eugster, Gloria Kraus, Robert Morgenstern, Andreas Dahl, Susanne Reinhardt, A. Petzold, Annett Lindner, Doreen Löbel, Ezio Bonifacio
Software Mentions: 6
Published: almost 7 years ago

10.15252/msb.202110253

Model‐guided development of an evolutionarily stable yeast chassis
Cited by: 5
Author(s): Filipa Pereira, Helena Lopes, Paulo Maia, Britta Meyer, Justyna Nocon, Paula Jouhten, D. Konstantinidis, Eleni Kafkia, Miguel Rocha, Peter Kötter, Isabel Rocha, Kiran R. Patil
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-021-07974-8

SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
Cited by: 8
Author(s): N M Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards, Anélia Horvath
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-020-73376-7

RNA oxidation in chromatin modification and DNA-damage response following exposure to formaldehyde
Cited by: 17
Author(s): Juan C. Gonzalez-Rivera, Mark W. Sherman, Dongyu Wang, Jamie C. L. Chuvalo-Abraham, Lea Hildebrandt Ruiz, Lydia M. Contreras
Software Mentions: 6
Published: almost 6 years ago

10.1242/dev.195883

The BMP antagonist gremlin 1 contributes to the development of cortical excitatory neurons, motor balance and fear responses
Cited by: 4
Author(s): Mari Ichinose, Nobumi Suzuki, Tongtong Wang, Hiroki Kobayashi, Laura Vrbanac, Joseph Kim Fai Ng, Josephine Wright, Tamsin R.M. Lannagan, Krystyna A. Gieniec, Martin Lewis, Ryosuke Ando, Atsushi Enomoto, Simon Koblar, Paul Q. Thomas, Daniel L. Worthley, Susan L. Woods
Software Mentions: 6
Published: about 5 years ago

10.1186/s13148-020-00944-z

Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions
Cited by: 38
Author(s): Qingqin Li, Yu Sun, Tania Wang
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-020-66224-1

Genomic deregulation of PRMT5 supports growth and stress tolerance in chronic lymphocytic leukemia
Cited by: 5
Author(s): Ann-Kathrin Schnormeier, Claudia Pommerenke, Maren Kaufmann, Hans Drexler, Max Koeppel
Software Mentions: 6
Published: about 6 years ago

10.1186/s13059-020-02081-5

The Tug1 lncRNA locus is essential for male fertility
Cited by: 59
Author(s): Jordan P. Lewandowski, Gabrijela Dumbović, Audrey Watson, Tae-Young Hwang, Emily Jacobs-Palmer, Nydia P Chang, Christian Much, Kyle M. Turner, Christopher Kirby, Nimrod D. Rubinstein, Abigail F. Groff, Steve C. Liapis, Chiara Gerhardinger, Assaf C. Bester, Pier Paolo Pandolfi, John G. Clohessy, Hopi E. Hoekstra, Martin Sauvageau, John L. Rinn
Software Mentions: 6
Published: almost 6 years ago

10.3389/fgene.2020.00404

Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization
Cited by: 20
Author(s): Hrant Hovhannisyan, Ester Saus, Ewa Księżopolska, Alex J Hinks Roberts, Edward J. Louis, Toni Gabaldón
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-020-6502-7

Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies
Cited by: 23
Author(s): Xiaohong Li, Nigel G. F. Cooper, Timothy E. O’Toole, Eric C. Rouchka
Software Mentions: 6
Published: over 6 years ago

10.1016/j.cub.2018.09.026

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis
Cited by: 35
Author(s): Ignacio E. Schor, Giovanni Bussotti, Matilda Maleš, Mattia Forneris, Rebecca R. Viales, Anton J. Enright, Eileen E. M. Furlong
Software Mentions: 6
Published: almost 8 years ago

10.1038/s42003-020-01616-7

Gene regulatory networks controlling differentiation, survival, and diversification of hypothalamic Lhx6-expressing GABAergic neurons
Cited by: 24
Author(s): Dong Won Kim, Kai Li, Zoe Qianyi Wang, Yi Stephanie Zhang, Abhijith Bathini, Matthew Brown, Sonia Hao Lin, Parris Whitney Washington, Cuiyun Sun, Susan Lindtner, Bora Lee, Hong Wang, Tomomi Shimogori, John L.R. Rubenstein, Seth Blackshaw
Software Mentions: 6
Published: over 5 years ago

10.15252/msb.20209873

Transcriptionally active enhancers in human cancer cells
Cited by: 20
Author(s): Katja Lidschreiber, Lisa Anna Jung, Henrik von der Emde, Kashyap Dave, Jussi Taipale, Patrick Cramer, Michael Lidschreiber
Software Mentions: 6
Published: over 5 years ago

10.1002/ctm2.253

Multiregion single‐cell sequencing reveals the transcriptional landscape of the immune microenvironment of colorectal cancer
Cited by: 34
Author(s): Wei Wang, Yu Zhong, Zhenkun Zhuang, Junping Xie, Yueer Lu, Chengzhi Huang, Yan Sun, Liang Wu, Jianhua Yin, Hang Yu, Zhiqiang Jiang, Shanshan Wang, Chunqing Wang, Yuanhang Zhang, Yilin Huang, Chongyin Han, Zhenggang Zhong, Jialin Hu, Ying Ouyang, Huisheng Liu, Mengya Yu, Xiaochan Wei, Dandan Chen, Lizhen Huang, Yong Hou, Zhanglin Lin, Shiping Liu, Fei Ling, Xueqing Yao
Software Mentions: 6
Published: over 5 years ago

10.5808/gi.20074

Elucidating molecular mechanisms of acquired resistance to BRAF inhibitors in melanoma using a microfluidic device and deep sequencing
Cited by: 2
Author(s): Jiyeon Han, Yeonjoo Jung, Yukyung Jun, Sungsu Park, Sanghyuk Lee
Software Mentions: 6
Published: over 5 years ago

10.15252/embj.2019102808

HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer
Cited by: 36
Author(s): Jorge Ferrer, Edgar Bernardo, Anthony Beucher, Miguel A. Maestro, Natalia del Pozo, I.R. Hernández Millán, Lena Haeberle, Martin Schlensog, Sami-Alexander Safi, Wolfram Trudo Knoefel, Vanessa Grau, Matías De Vas, Karl B. Shpargel, Eva C. Vaquero, Terry Magnuson, Sagrario Ortega, Irene Espósito, Francisco X. Real, Jorge Ferrer
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-019-50864-z

Circular RNA differential expression in blood cell populations and exploration of circRNA deregulation in pediatric acute lymphoblastic leukemia
Cited by: 62
Author(s): Enrico Gaffo, Elena Boldrin, Anna Dal Molin, Silvia Bresolin, Annagiulia Bonizzato, Luca Trentin, Chiara Frasson, Klaus‐Michael Debatin, Lueder Hinrich Meyer, Geertruy te Kronnie, Stefania Bortoluzzi
Software Mentions: 6
Published: almost 7 years ago

10.3389/fgene.2021.665153

Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species
Cited by: 9
Author(s): Annie Robic, Chloé Cerutti, Christa Kühn, Thomas Faraut
Software Mentions: 6
Published: over 5 years ago

10.1002/JLB.5MA0120-209R

Distinct and shared gene expression for human innate versus adaptive helper lymphoid cells
Cited by: 28
Author(s): Giuseppe Ercolano, Tania Wyss, Bérengère Salomé, Pedro Romero, Sara Trabanelli, Camilla Jandus
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-019-50119-x

Tissue-specific mouse mRNA isoform networks
Cited by: 12
Author(s): Gaurav Kandoi, Julie A. Dickerson
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41598-019-45714-x

Transcriptome Analysis of Long-lived Drosophila melanogaster E(z) Mutants Sheds Light on the Molecular Mechanisms of Longevity
Cited by: 30
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, Nadezhda Zemskaya, Liubov Koval, Eugenia V. Schegoleva, Zulfiya G. Guvatova, George S. Krasnov, Ilya Solovev, Maksim A. Sheptyakov, Alex Zhavoronkov, Anna V. Kudryavtseva
Software Mentions: 6
Published: about 7 years ago

10.7554/eLife.16797

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians
Cited by: 46
Author(s): Jordi Solana, Manuel Irimia, Salah Ayoub, Marta Rodriguez Orejuela, Vera Zywitza, Marvin Jens, Javier Tapial, Debashish Ray, Quaid Morris, Timothy R. Hughes, Benjamin J. Blencowe, Nikolaus Rajewsky
Software Mentions: 6
Published: about 10 years ago

10.1371/journal.pone.0072614

DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster
Cited by: 46
Author(s): Ram Vinay Pandey, Christian Schlötterer
Software Mentions: 6
Published: almost 13 years ago

10.15252/embj.2018100882

Life‐long impairment of glucose homeostasis upon prenatal exposure to psychostimulants
Cited by: 11
Author(s): Solomiia Korchynska, Maria Krassnitzer, Katarzyna Maleńczyk, Rashmi B. Prasad, Evgenii Tretiakov, Sabah Rehman, Valentina Cinquina, Victoria Gernedl, Matthias Farlik, Julian Petersen, S Hannes, Julia Schachenhofer, Sonali N. Reisinger, Alice Zambon, Olof Asplund, Isabella Artner, Erik Keimpema, Gert Lübec, Jan Mulder, Christoph Bock, Daniela D. Pollak, Roman A. Romanov, Christian Pifl, Leif Groop, Tomas Hökfelt, Tibor Harkany
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-019-47797-y

Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae
Cited by: 3
Author(s): John P. Lloyd, Megan J. Bowman, Christina B. Azodi, Rosalie P. Sowers, Gaurav D. Moghe, Kevin L. Childs, Shin-Han Shiu
Software Mentions: 6
Published: almost 7 years ago

10.1002/advs.201903200

Size‐Dependent Pulmonary Impact of Thin Graphene Oxide Sheets in Mice: Toward Safe‐by‐Design
Cited by: 34
Author(s): Artur Filipe Rodrigues, Leon Newman, Dhifaf Jasim, Sourav P. Mukherjee, Jun Wang, Isabella Anna Vacchi, Cécilia Ménard‐Moyon, Alberto Bianco, Bengt Fadeel, Kostas Kostarelos, Cyrill Bussy
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-017-3630-9

Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients
Cited by: 42
Author(s): Till Adhikary, Annika Wortmann, Florian Finkernagel, Sonja Lieber, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Sabine Müller‐Brüsselbach, Silke Reinartz, Rolf Müller
Software Mentions: 6
Published: over 9 years ago

10.1016/j.molcel.2021.02.034

POINT technology illuminates the processing of polymerase-associated intact nascent transcripts
Cited by: 44
Author(s): Rui Sousa-Luís, Geneviève Dujardin, Inna Zukher, Hiroshi Kimurâ, Carika Weldon, Maria Carmo‐Fonseca, Nick J. Proudfoot, Takayuki Nojima
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-020-07358-4

Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
Cited by: 33
Author(s): Tracy M. Yamawaki, Daniel Lu, Daniel C. Ellwanger, Dev Bhatt, Paolo Manzanillo, Vanessa Arias, Hong Zhou, Oh Kyu Yoon, Oliver Homann, Songli Wang, Chi-Ming Li
Software Mentions: 6
Published: over 5 years ago

10.1186/s13024-018-0261-9

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model
Cited by: 37
Author(s): Lodewijk J.A. Toonen, Maurice Overzier, Melvin M. Evers, Leticia G. León, Sander A.J. van der Zeeuw, Hailiang Mei, Szymon M. Kiełbasa, Jelle J. Goeman, Kristina Hettne, Ólafur Þ. Magnússon, Marion Poirel, Alexandre Seyer, Peter A.C. ’t Hoen, Willeke M. C. van Roon‐Mom
Software Mentions: 5
Published: about 8 years ago

10.15252/emmm.202013162

The NFIB‐ERO1A axis promotes breast cancer metastatic colonization of disseminated tumour cells
Cited by: 23
Author(s): Federica Zilli, Pedro Marques Ramos, Priska Auf der Maur, Charly Jehanno, Atul Sethi, Marie–May Coissieux, Tobias Eichlisberger, Loïc Sauteur, Adelin Rouchon, Laura Bonapace, Joana Couto, Roland Rad, Michael Rugaard Jensen, Andrea Banfi, Michael Stadler, Mohamed Bentires‐Alj
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-019-40375-2

Transcriptome analysis of rumen epithelium and meta-transcriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis
Cited by: 21
Author(s): Wenli Li, S.L. Gelsinger, Andrea Edwards, Christina Riehle, Daniel C. Koch
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-019-40867-1

Loss of the Polycomb group protein Rnf2 results in derepression of tbx-transcription factors and defects in embryonic and cardiac development
Cited by: 17
Author(s): Naomi D. Chrispijn, Dei M. Elurbe, Michaela Mickoleit, Marco Aben, Dennis E. M. de Bakker, Karolina M. Andralojc, Jan Huisken, Jeroen Bakkers, Leonie M. Kamminga
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-018-38458-7

High-throughput, Efficient, and Unbiased Capture of Small RNAs from Low-input Samples for Sequencing
Cited by: 15
Author(s): Cassandra D. Belair, Hu Tao, Brandon Chu, Jacob W. Freimer, Matthew R. Cooperberg, Robert Blelloch
Software Mentions: 5
Published: over 7 years ago

10.1186/s40168-020-00966-y

Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation
Cited by: 10
Author(s): Rajesh Kaushal, Peng Li, Sunil Kumar Singh, Mengrui Zhang, Xinlian Zhang, Juan Ignacio Vílchez, Zhen Wang, Danxia He, Yu Ye, Suhui Lv, Zhongtian Xu, Rafael J. L. Morcillo, Wei Wang, Wei-Chang Huang, Paul W. Paré, Chun‐Peng Song, Jian‐Kang Zhu, Renyi Liu, Wenxuan Zhong, Ping Ma, Huiming Zhang
Software Mentions: 5
Published: over 5 years ago

10.1186/s40478-017-0414-z

Serum microRNA miR-501-3p as a potential biomarker related to the progression of Alzheimer’s disease
Cited by: 118
Author(s): Norikazu Hara, Masataka Kikuchi, Akinori Miyashita, Hiroyuki Hatsuta, Yuko Saito, Kensaku Kasuga, Shigeo Murayama, Takeshi Ikeuchi, Ryozo Kuwano
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-018-36768-4

Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets
Cited by: 10
Author(s): Stefan Wyder, Michael T. Raissig, Ueli Grossniklaus
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-021-07912-8

Quantitative analysis of the blood transcriptome of young healthy pigs and its relationship with subsequent disease resilience
Cited by: 8
Author(s): Kyu-Sang Lim, Jian Cheng, Austin M. Putz, Qian Dong, Xue Bai, Hamid Beiki, Christopher K. Tuggle, Michael K. Dyck, Pig Gen Canada, Frédéric Fortin, John C. S. Harding, Graham Plastow, Jack C. M. Dekkers
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-38209-8

Differentially expressed gene networks, biomarkers, long noncoding RNAs, and shared responses with cocaine identified in the midbrains of human opioid abusers
Cited by: 30
Author(s): Manal H. Saad, Matthew Rumschlag, Michael H. Guerra, Candace Savonen, Alaina M Jaster, Philip D. Olson, Adnan Alazizi, Francesca Luca, Roger Piqué-Regi, Carl J. Schmidt, Michael J. Bannon
Software Mentions: 5
Published: over 7 years ago

10.3389/fgene.2020.567812

Integrated Transcriptome and Histone Modification Analysis Reveals NDV Infection Under Heat Stress Affects Bursa Development and Proliferation in Susceptible Chicken Line
Cited by: 13
Author(s): Ganrea Chanthavixay, Colin Kern, Ying Wang, Perot Saelao, Susan J. Lamont, Rodrigo A. Gallardo, Gonzalo Rincón, Huaijun Zhou
Software Mentions: 5
Published: almost 6 years ago

10.1038/s42003-021-02320-w

A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels
Cited by: 13
Author(s): Guste Urbonaite, Jimmy Tsz Hang Lee, Ping Liu, Guillermo E. Parada, Martin Hemberg, Murat Açar
Software Mentions: 5
Published: about 5 years ago

10.18632/aging.101341

Central role of the p53 pathway in the noncoding-RNA response to oxidative stress
Cited by: 45
Author(s): Paola Fuschi, Matteo Carrara, Christine Voellenkle, José Manuel García-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza, Giovanni Nano, Carlo Gaetano, Gaia Spinetti, Annibale Alessandro Puca, Alessandra Magenta, Fabio Martelli
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-017-3817-0

lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets
Cited by: 22
Author(s): Yixiao Gong, Hsin‐Chun Huang, Yu Liang, Thomas Trimarchi, Iannis Aifantis, Aristotelis Tsirigos
Software Mentions: 5
Published: about 9 years ago

10.18632/oncotarget.25329

Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma
Cited by: 13
Author(s): Toshima Z. Parris, Elisabeth Werner Rönnerman, Hanna Engqvist, Jana Biermann, Katarina Truvé, Szilárd Nemes, Eva Forssell-Aronsson, Giovanni Solinas, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 5
Published: over 8 years ago

10.18632/oncotarget.26929

Deregulated expression of NKL homeobox genes in T-cell lymphomas
Cited by: 10
Author(s): Stefan Nagel, Claudia Pommerenke, Roderick A.F. MacLeod, Corinna Meyer, Maren Kaufmann, Silke Fähnrich, Hans Drexler
Software Mentions: 5
Published: over 7 years ago

10.18632/oncotarget.14091

The role of miR-17-92 in the miRegulatory landscape of Ewing sarcoma
Cited by: 13
Author(s): Raphaela Schwentner, David Herrero-Martín, Maximilian Kauer, Cornelia Mutz, Anna M. Katschnig, Grzegorz Sienski, Javier Alonso, Dave N.T. Aryee, Heinrich Kovar
Software Mentions: 5
Published: over 9 years ago

10.1016/j.molcel.2018.09.033

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Cited by: 73
Author(s): Lorea Blázquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, André Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Software Mentions: 5
Published: almost 8 years ago

10.18632/oncotarget.13062

Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Cited by: 29
Author(s): Lei Wei, Sreenivasulu Chintala, Eric Ciamporcero, Swathi Ramakrishnan, May Elbanna, Jianmin Wang, Qiang Hu, Sean T. Glenn, Mitsuko Murakami, Lu Liu, Eduardo Cortes Gomez, Yuchen Sun, Jacob Conroy, Kiersten Marie Miles, Malathi Kullappan, Sudha Ramaiah, Anand Anbarasu, Anna Woloszynska‐Read, Candace S. Johnson, Jeffrey M. Conroy, Song Liu, Carl Morrison, Роберто Пили
Software Mentions: 5
Published: almost 10 years ago

10.1016/j.molcel.2019.11.021

Histone H2AK119 Mono-Ubiquitination Is Essential for Polycomb-Mediated Transcriptional Repression
Cited by: 208
Author(s): Simone Tamburri, Elisa Lavarone, Daniel Fernández-Pérez, E. J. Conway, Marika Zanotti, Daria Manganaro, Diego Pasini
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2018.00026

Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse
Cited by: 26
Author(s): Barbora Kuntová, Romana Stopková, Pavel Stopka
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-018-29472-w

RNA-seq and flow-cytometry of conventional, scalp, and palmoplantar psoriasis reveal shared and distinct molecular pathways
Cited by: 28
Author(s): Richard Ahn, Di Yan, Hsin-Wen Chang, Kristina Lee, Shrishti Bhattarai, Zhiming Huang, Mio Nakamura, Rasnik Singh, Ladan Afifi, Keyon Taravati, Priscila Muñoz-Sandoval, Mariela Pauli, Michael D. Rosenblum, Wilson Liao
Software Mentions: 5
Published: about 8 years ago

10.1155/2018/2439527

RNA-seq Reveals the Overexpression of IGSF9 in Endometrial Cancer
Cited by: 11
Author(s): Zonggao Shi, Chunyan Li, Laura Tarwater, Jun Li, Yang Li, William Kaliney, Darshan S. Chandrashekar, M. Sharon Stack
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-018-29993-4

Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver
Cited by: 10
Author(s): José P. Silva, Derek Van Booven
Software Mentions: 5
Published: about 8 years ago

10.1016/j.isci.2021.102847

High glucose macrophage exosomes enhance atherosclerosis by driving cellular proliferation & hematopoiesis
Cited by: 25
Author(s): Laura Bouchareychas, Phat Duong, Tuan Anh Phu, Eric Alsop, Bessie Meechoovet, Rebecca Reiman, M. Ng, Ryō Yamamoto, Hiromitsu Nakauchi, Warren J. Gasper, Kendall Van Keuren‐Jensen, Robert L. Raffaı̈
Software Mentions: 5
Published: about 5 years ago

10.1186/s12974-019-1500-x

Contribution of LTi and TH17 cells to B cell aggregate formation in the central nervous system in a mouse model of multiple sclerosis
Cited by: 18
Author(s): Verena Schropp, Jörn Rohde, Damiano M. Rovituso, Samir Jabari, Richa Bharti, Stefanie Küerten
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-018-27078-w

Global miRNA expression profile reveals novel molecular players in aneurysmal subarachnoid haemorrhage
Cited by: 19
Author(s): Kátia de Paiva Lopes, Tatiana Vinasco-Sandoval, Ricardo Assunção Vialle, Fernando Mendes Paschoal, Vanessa Albuquerque Paschoal Aviz Bastos, Edson Bor‐Seng‐Shu, Manoel Jacobsen Teixeira, Elizabeth Sumi Yamada, Pablo Diego do Carmo Pinto, Amanda Ferreira Vidal, André M. Ribeiro-dos-Santos, Fabiano Cordeiro Moreira, Sidney Emanuel Batista dos Santos, Eric Homero Albuquerque Paschoal, Ândrea Ribeiro‐dos‐Santos
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-018-27027-7

Immunoprofiles of human Sertoli cells infected with Zika virus reveals unique insights into host-pathogen crosstalk
Cited by: 32
Author(s): Daniel P. Strange, Richard Green, Dietmar W. Siemann, Michael Gale, Saguna Verma
Software Mentions: 5
Published: about 8 years ago

10.1186/s13041-021-00835-1

Altered hippocampal transcriptome dynamics following sleep deprivation
Cited by: 14
Author(s): Marie E. Gaine, Ethan Bahl, Snehajyoti Chatterjee, Jacob J. Michaelson, Ted Abel, Lisa C. Lyons
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-017-4007-9

Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components
Cited by: 28
Author(s): Kenneth Bryan, Beatrice A. McGivney, Gabriella Farries, Paul A. McGettigan, C. L. McGivney, K. F. Gough, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 5
Published: about 9 years ago

10.1186/s13059-021-02505-w

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
Cited by: 23
Author(s): Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Yahan Liang, B Wold, A Mortazavi
Software Mentions: 5
Published: almost 5 years ago

10.1007/s12035-020-01983-6

Transcriptome Analysis of iPSC-Derived Neurons from Rubinstein-Taybi Patients Reveals Deficits in Neuronal Differentiation
Cited by: 15
Author(s): Luciano Calzari, Matteo Barcella, Valentina Alari, Daniele Braga, Rafael Muñoz‐Viana, Cristina Barlassina, Palma Finelli, Cristina Gervasini, Ángel Barco, Silvia Russo, Lidia Larizza
Software Mentions: 5
Published: about 6 years ago

10.3390/ijms21020471

The Influence of Met Receptor Level on HGF-Induced Glycolytic Reprogramming in Head and Neck Squamous Cell Carcinoma
Cited by: 17
Author(s): Verena Boschert, Nicola Klenk, Alexander Abt, Sudha Janaki Raman, Markus Fischer, Roman C. Brands, Axel Seher, Christian Linz, Urs Müller‐Richter, Thorsten Bischler, Stefan Hartmann
Software Mentions: 5
Published: over 6 years ago

10.1093/molbev/msz099

Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae)
Cited by: 72
Author(s): Marc Tollis, Jooke Robbins, Andrew E. Webb, Lukas F. K. Kuderna, Aleah F. Caulin, Jacinda D Garcia, Martine Bérubé, Nader Pourmand, Tomàs Marquès-Bonet, Mary J. O’Connell, Per Palsbøll, Carlo C. Maley
Software Mentions: 5
Published: over 7 years ago

10.3390/ijms21051720

Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana
Cited by: 27
Author(s): Stephanie Schaarschmidt, Axel Fischer, Ellen Zuther, Dirk K. Hincha
Software Mentions: 5
Published: over 6 years ago

10.1002/advs.202001402

TRADES: Targeted RNA Demethylation by SunTag System
Cited by: 25
Author(s): Jing Mo, Zonggui Chen, Shanshan Qin, Shu Li, Chuangang Liu, Lu Zhang, Ruoxi Ran, Ying Kong, Fang Wang, Song-Mei Liu, Yu Zhou, Xiaolian Zhang, Xiaocheng Weng, Xiang Zhou
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2019.00689

Transcription Profiling of Monocyte-Derived Macrophages Infected In Vitro With Two Strains of Streptococcus agalactiae Reveals Candidate Pathways Affecting Subclinical Mastitis in Cattle
Cited by: 6
Author(s): Anna Lewandowska-Sabat, Е. В. Кирсанова, Christophe Klopp, T. R. Solberg, B. Heringstad, Olav Østerås, Preben Boysen, I. Olsaker
Software Mentions: 5
Published: about 7 years ago

10.1093/molbev/msy198

Phylotranscriptomic Insights into the Diversification of EndothermicThunnusTunas
Cited by: 13
Author(s): Adam Ciezarek, Owen G. Osborne, Oliver N. Shipley, Edward J. Brooks, S Tracey, Jaime D. McAllister, Luke D. Gardner, Michael J.E. Sternberg, Barbara A. Block, Vincent Savolainen
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13073-021-00952-5

Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes
Cited by: 39
Author(s): Bethany Barnes, Louisa Nelson, Anthony Tighe, George J. Burghel, I‐Hsuan Lin, Sudha Desai, Joanne C. McGrail, Robert D. Morgan, Stephen S. Taylor
Software Mentions: 5
Published: almost 5 years ago

10.15252/msb.20209888

Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine
Cited by: 6
Author(s): Daniel O’Connor, Marta Pinto, Dylan Sheerin, Adriana Tomić, Ruth Drury, Samuel Channon‐Wells, Ushma Galal, Christina Dold, Hannah Robinson, Simon Kerridge, Emma Plested, Henry J. Hughes, Lisa Stockdale, Manish Sadarangani, Matthew D. Snape, Christine S. Rollier, Michael Levin, Andrew J. Pollard
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13073-021-00924-9

The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches
Cited by: 8
Author(s): Julie M. Steinbrink, Rachel A. Myers, Kaiyuan Hua, Melissa D. Johnson, Jessica Seidelman, Ephraim L. Tsalik, Ricardo Henao, Geoffrey S. Ginsburg, Christopher W. Woods, Barbara D. Alexander, Micah T. McClain
Software Mentions: 5
Published: about 5 years ago

10.1093/molbev/msaa110

Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum
Cited by: 10
Author(s): Rosa Fernández, Marina Marcet‐Houben, Fabrice Legeai, Gautier Richard, Stéphanie Robin, Valentin Wucher, Cinta Pegueroles, Toni Gabaldón, Denis Tagu
Software Mentions: 5
Published: over 6 years ago

10.1016/j.ajhg.2021.04.024

Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder
Cited by: 6
Author(s): Holger Hengel, Shabab B. Hannan, Sarah Dyack, Sara MacKay, Ulrich Schatz, Martin Fleger, Andreas Kurringer, Ghassan Balousha, Zaïd Ghanim, Fowzan S. Alkuraya, Hamad Alzaidan, Hessa S. Alsaif, Tadahiro Mitani, Sevcan Tuğ Bozdoğan, Davut Pehlivan, James R. Lupski, Joseph J Gleeson, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Elliott H. Sherr, Kendall C. Parks, Emanuela Argilli, Amber Begtrup, Hamid Galehdari, Osama Balousha, Gholamreza Shariati, Neda Mazaheri, Reza Azizi Malamiri, Alistair T. Pagnamenta, Helen Kingston, Siddharth Banka, Adam Jackson, Mathew Osmond, Angelika Rieß, Tobias B. Haack, Thomas Nägele, Stefanie Schuster, Stefan Hauser, Jakob Admard, Nicolas Casadei, Ana Velić, Boris Maček, Stephan Ossowski, Henry Houlden, Reza Maroofian, Lüdger Schöls
Software Mentions: 5
Published: about 5 years ago

10.3390/ijms20133315

Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts
Cited by: 10
Author(s): Simona Cantarella, Davide Carnevali, Marco Morselli, Anastasia Conti, Matteo Pellegrini, Barbara Montanini, Giorgio Dieci
Software Mentions: 5
Published: about 7 years ago

10.3390/ijms20143543

Sex-Dimorphic Behavioral Alterations and Altered Neurogenesis in U12 Intron Splicing-Defective Zrsr1 Mutant Mice
Cited by: 9
Author(s): Francisco Alén, Isabel Gómez-Redondo, Patricia Rivera, Juan Suárez, Priscila Ramos‐Ibeas, Eva Pericuesta, Raúl Fernández‐González, Serafín Pérez‐Cerezales, Keiko Horiuchi, Laura Orío, Fernando Rodríguez de Fonseca, Alfonso Gutiérrez‐Adán
Software Mentions: 5
Published: about 7 years ago

10.1186/s13195-020-00716-0

Prognosis prediction model for conversion from mild cognitive impairment to Alzheimer’s disease created by integrative analysis of multi-omics data
Cited by: 27
Author(s): Daichi Shigemizu, Shintaro Akiyama, Sayuri Higaki, Toshiyuki Sugimoto, Takashi Sakurai, Keith A. Boroevich, Alok Sharma, Tatsuhiko Tsunoda, Takahiro Ochiya, Shumpei Niida, Kouichi Ozaki
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13229-020-00369-8

Chd8 haploinsufficiency impairs early brain development and protein homeostasis later in life
Cited by: 18
Author(s): Jessica A. Jiménez, Travis Ptacek, Alex H. Tuttle, Ralf S. Schmid, Sheryl S. Moy, Jeremy M. Simon, Mark J. Zylka
Software Mentions: 5
Published: almost 6 years ago

10.3390/ijms21113770

Transcriptional Activity and Stability of CD39+CD103+CD8+ T Cells in Human High-Grade Endometrial Cancer
Cited by: 13
Author(s): Hagma H. Workel, Nienke van Rooij, Annechien Plat, Diana C.J. Spierings, Rudolf S.N. Fehrmann, Hans W. Nijman, Marco de Bruyn
Software Mentions: 5
Published: about 6 years ago

10.1186/s13100-018-0138-z

Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis
Cited by: 33
Author(s): Gavin Pereira, Laura Sánchez, Paul Schaughency, Alejandro Rubio-Roldán, Justin Choi, Evarist Planet, Ranjan Batra, Priscilla Turelli, Didier Trono, Lyle W. Ostrow, John Ravits, Haig H. Kazazian, Sarah J. Wheelan, Sara R. Heras, Jens Mayer, José L. García‐Pérez, John Goodier
Software Mentions: 5
Published: over 7 years ago

10.1186/s13073-020-00747-0

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale
Cited by: 37
Author(s): Soumaya Zlitni, Alex Bishara, Eli L. Moss, Е. И. Ткаченко, Joyce B. Kang, Rebecca Culver, Tessa M. Andermann, Ziming Weng, Christina M. Wood, Christine Handy, Hanlee P. Ji, Serafim Batzoglou, Ami S. Bhatt
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-021-07937-z

The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments
Cited by: 13
Author(s): Stephanie De Vos, Stéphane Rombauts, Louis Coussement, Wannes Dermauw, Marnik Vuylsteke, Patrick Sorgeloos, James S. Clegg, Ziro Nambu, Filip Van Nieuwerburgh, Parisa Norouzitallab, Thomas Van Leeuwen, Tim De Meyer, Gilbert Van Stappen, Yves Van de Peer, Peter Bossier
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13073-020-00783-w

The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
Cited by: 50
Author(s): Florent Petitprez, Sacha Lévy, Chengming Sun, Maxime Meylan, Christophe Linhard, Étienne Becht, Nabila Elarouci, David Tavel, Lubka T. Roumenina, Mira Ayadi, Catheriné Sautès-Fridman, Aurélien de Reyniès
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-017-3673-y

Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos
Cited by: 95
Author(s): Jenna Kropp Schmidt, José A. Carrillo, Hadjer Namous, Daniels Alyssa, Sana M. Salih, Jiuzhou Song, Hasan Khatib
Software Mentions: 5
Published: over 9 years ago

10.1186/s13073-017-0432-2

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes
Cited by: 33
Author(s): Leif Väremo, Tora Ida Henriksen, Camilla Schéele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen, Jens Nielsen
Software Mentions: 5
Published: about 9 years ago

10.1186/s13073-016-0348-2

Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring
Cited by: 9
Author(s): José P. Silva, Guerline Lambert, Derek Van Booven, Claes Wahlestedt
Software Mentions: 5
Published: almost 10 years ago

10.7554/eLife.68967

Spatially patterned excitatory neuron subtypes and projections of the claustrum
Cited by: 17
Author(s): Sarah R. Erwin, Brianna N. Bristow, Kaitlin E Sullivan, Rennie M Kendrick, Brian A. Marriott, Lihua Wang, Jody Clements, Andrew L. Lemire, Jesse Jackson, Mark S. Cembrowski
Software Mentions: 5
Published: about 5 years ago

10.1186/s40168-020-00980-0

The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut
Cited by: 33
Author(s): Jason W. Arnold, Jeffery Roach, Salvador Fabela, Emily Moorfield, Shengli Ding, R. Eric Blue, Sue F. Dagher, Scott T. Magness, Rita Tamayo, José M. Bruno-Bárcena, M. Andrea Azcárate-Peril
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.48216

Cis-regulatory basis of sister cell type divergence in the vertebrate retina
Cited by: 28
Author(s): Daniel P. Murphy, Andrew Hughes, Karen A. Lawrence, Connie A. Myers, Joseph C. Corbo
Software Mentions: 5
Published: almost 7 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759