Ecosyste.ms: Papers

10.3389/fmicb.2018.01551

Concerted Metabolic Shifts Give New Insights Into the Syntrophic Mechanism Between Propionate-Fermenting Pelotomaculum thermopropionicum and Hydrogenotrophic Methanocella conradii
Cited by: 22
Author(s): Pengfei Liu, Yahai Lu
Software Mentions: 4
Published: over 6 years ago

10.1038/s42003-021-01661-w

Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction
Cited by: 16
Author(s): Christoph Niemöller, Julius Wehrle, Julian Riba, Rainer Claus, Nathalie Renz, Janika Rhein, Sabine Bleul, Juliane M. Stosch, Justus Duyster, Christoph Plass, Pavlo Lutsik, Daniel B. Lipka, Michael Lübbert, Heiko Becker
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2019.00614

Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines
Cited by: 17
Author(s): Anthony Federico, Tanya T Karagiannis, Kritika Karri, Dileep Kishore, Yusuke Koga, Joshua D. Campbell, Stefano Monti
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.55911

Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice
Cited by: 4
Author(s): Marina Kovalenko, Serkan Erdin, Marissa A Andrew, Jason St. Claire, Melissa Shaughnessey, Leroy Hubert, João Luís Neto, Alexei Stortchevoi, Daniel M. Fass, Ricardo Mouro Pinto, Stephen J. Haggarty, John H. Wilson, Michael E. Talkowski, Vanessa C. Wheeler
Software Mentions: 4
Published: about 4 years ago

10.3389/fimmu.2020.00216

FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells
Cited by: 26
Author(s): Noudjoud Attaf, Iñaki Cervera-Marzal, Chuang Dong, Laurine Gil, Amédée Renand, Lionel Spinelli, Pierre Milpied
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2021.709466

Human Placental Trophoblasts Infected by Listeria monocytogenes Undergo a Pro-Inflammatory Switch Associated With Poor Pregnancy Outcomes
Cited by: 15
Author(s): Lauren J. Johnson, Siavash Azari, Amy Webb, Xiaoli Zhang, Mikhail A. Gavrilin, James L. Marshall, Kara M. Rood, Stéphanie Seveau
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2020.00852

Lnc-ITSN1-2, Derived From RNA Sequencing, Correlates With Increased Disease Risk, Activity and Promotes CD4+ T Cell Activation, Proliferation and Th1/Th17 Cell Differentiation by Serving as a ceRNA for IL-23R via Sponging miR-125a in Inflammatory Bowel Disease
Cited by: 36
Author(s): Jiayan Nie, Qiu Zhao
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.16220

Trisomy 21 consistently activates the interferon response
Cited by: 205
Author(s): Kelly D. Sullivan, Hannah C. Lewis, Amanda A. Hill, Ahwan Pandey, Leisa Jackson, Joseph M Cabral, Keith P Smith, L. Alexander Liggett, Eliana B. Gómez, Matthew D. Galbraith, James DeGregori, Joaquín M. Espinosa
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0232189

Investigating the epithelial barrier and immune signatures in the pathogenesis of equine insect bite hypersensitivity
Cited by: 10
Author(s): Iva Cvitaš, Simone Oberhänsli, Tosso Leeb, Martina Dettwiler, Eliane J. Müller, Rémy Bruggman, Eliane Marti
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.23638

YAP-associated chromosomal instability and cholangiocarcinoma in mice
Cited by: 41
Author(s): Sumera Rizvi, Samantha R. Fischbach, Steven F. Bronk, Petra Hirsova, Anuradha Krishnan, Renumathy Dhanasekaran, James B. Smadbeck, Rory L. Smoot, George Vasmatzis, Gregory J. Gores
Software Mentions: 4
Published: almost 7 years ago

10.1155/2018/2906292

A Simple Guideline to Assess the Characteristics of RNA-Seq Data
Cited by: 21
Author(s): Keun Hong Son, Sungryul Yu, Wonseok Shin, Kyudong Han, Keunsoo Kang
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.60645

Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation
Cited by: 28
Author(s): Christian Brion, Sheila Lutz, Frank W. Albert
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.50895

Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation
Cited by: 23
Author(s): Callison E Alcott, Hari Krishna Yalamanchili, Ping Ji, Meike E van der Heijden, Alexander B. Saltzman, Nathan D. Elrod, Lin Ai, Mei Leng, Bhoomi Bhatt, Shuang Hao, Qi Wang, Afaf Saliba, Jianrong Tang, Anna Malovannaya, Eric J. Wagner, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 4
Published: over 4 years ago

10.1186/s40425-018-0464-1

A novel anti-HER2 anthracycline-based antibody-drug conjugate induces adaptive anti-tumor immunity and potentiates PD-1 blockade in breast cancer
Cited by: 63
Author(s): Lucia D’Amico, Ulrike Menzel, Michael Prummer, Philipp Müller, Mélanie Buchi, Abhishek S. Kashyap, Ulrike Haessler, Alexander Yermanos, Rémy Gébleux, Manfred Briendl, Tamara Hell, Fabian I. Wolter, Roger R. Beerli, Iva Truxová, Radek Špíšek, Tatjana Vlajnic, Ulf Grawunder, Sai T. Reddy, Alfred Zippelius
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13229-021-00432-y

Neuroanatomy and behavior in mice with a haploinsufficiency of AT-rich interactive domain 1B (ARID1B) throughout development
Cited by: 17
Author(s): Jacob Ellegood, Stela P. Petkova, Adrienne Kinman, Lily R. Qiu, Anna Adhikari, A. Ayanna Wade, Darren Fernandes, Zsuzsa Lindenmaier, Amie Creighton, Lauryl M. J. Nutter, Alexander Nord, Jill L. Silverman, Jason P. Lerch
Software Mentions: 4
Published: over 3 years ago

10.18632/oncotarget.9535

Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancer
Cited by: 35
Author(s): Jingwen Zhao, Yu Zhao, Liguo Wang, Jun Zhang, Jeffrey Karnes, Manish Kohli, Guixia Wang, Haojie Huang
Software Mentions: 4
Published: over 8 years ago

10.1038/s41398-017-0050-1

Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study
Cited by: 56
Author(s): Pei‐Fen Kuan, Monika A. Waszczuk, Roman Kotov, Sean Clouston, Xiaohua Yang, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 4
Published: almost 7 years ago

10.3390/cells9112452

Photochemotherapy Induces Interferon Type III Expression via STING Pathway
Cited by: 0
Author(s): Edyta Biskup, Brian D. Larsen, Leonor Rib, Lasse Folkersen, Omid Niazi, Maria R. Kamstrup, Claus Storgaard Sørensen
Software Mentions: 4
Published: about 4 years ago

10.1016/j.celrep.2015.12.082

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells
Cited by: 157
Author(s): Iain C. Macaulay, Valentine Svensson, Charlotte Labalette, Lauren Ferreira, Fiona Hamey, Thierry Voet, Sarah A. Teichmann, Ana Cvejic
Software Mentions: 4
Published: almost 9 years ago

10.3390/ijms21041337

Combined Analysis of the Metabolome and Transcriptome Identified Candidate Genes Involved in Phenolic Acid Biosynthesis in the Leaves of Cyclocarya paliurus
Cited by: 29
Author(s): Weida Lin, Yueling Li, Qiuwei Lu, Hongfei Lü, Junmin Li
Software Mentions: 4
Published: almost 5 years ago

10.3390/molecules21111431

Comparative Transcriptomic Analysis of Grape Berry in Response to Root Restriction during Developmental Stages
Cited by: 20
Author(s): Lu Feng, Qiong Lin, Di Wu, Shiping Wang, Dengliang Wang, Chongde Sun
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-018-5265-x

Corn dried distillers grains with solubles (cDDGS) in the diet of pigs change the expression of adipose genes that are potential therapeutic targets in metabolic and cardiovascular diseases
Cited by: 6
Author(s): Maria Oczkowicz, Tomasz Szmatoła, Małgorzata Świątkiewicz, Klaudia Pawlina-Tyszko, Artur Gurgul, Tomasz Ząbek
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-018-2139-9

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
Cited by: 141
Author(s): MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary T. Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X. Shirley Liu, Henry W. Long
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-15-631

Analysis of stranded information using an automated procedure for strand specific RNA sequencing
Cited by: 29
Author(s): Bárður Sigurgeirsson, Olof Emanuelsson, Joakim Lundeberg
Software Mentions: 4
Published: over 10 years ago

10.1186/s12859-020-03551-0

ARTDeco: automatic readthrough transcription detection
Cited by: 15
Author(s): Samuel J. Roth, Sven Heinz, Christopher Benner
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-019-5570-z

Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica
Cited by: 18
Author(s): Sarah Naiyer, Devinder Kaur, Jamaluddin Ahamad, Sanjai Singh, Yatendra Pratap Singh, Vivek Thakur, Alok Bhattacharya, Sudha Bhattacharya
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pbio.2003648

A direct link between MITF, innate immunity, and hair graying
Cited by: 37
Author(s): Melissa L. Harris, Temesgen Fufa, Joseph W. Palmer, Sandeep S. Joshi, Denise M. Larson, Arturo Incao, Derek Gildea, Niraj Trivedi, Autumne N Lee, Chi-Ping Day, Helen Michael, Thomas J. Hornyak, Glenn Merlino, Nisc Comparative Sequencing Program, William J. Pavan
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-46632-8

TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish
Cited by: 23
Author(s): Sanna Gudmundsson, Maria Wilbe, Beata Filipek-Górniok, Anna-Maja Molin, Sara Ekvall, Josefin Johansson, Amin Allalou, Hans Gylje, Vera M. Kalscheuer, Johan Ledin, Göran Annerén, Marie-Louise Bondeson
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1008361

An osteocalcin-deficient mouse strain without endocrine abnormalities
Cited by: 74
Author(s): Cassandra R. Diegel, Steven Hann, Ugur M. Ayturk, Jennifer C. W. Hu, Kyung-Eun Lim, Casey J. Droscha, Zachary Madaj, Gabrielle E. Foxa, Isaac Izaguirre, Vai Vivarium And Transgenics Core, Noorulain Paracha, Bohdan Pidhaynyy, Terry L. Dowd, Alexander G. Robling, Matthew L. Warman, Bart O. Williams
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pgen.1007891

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
Cited by: 47
Author(s): A. Callegari, Christian Sieben, Alexander Benke, David M. Suter, Beat Fierz, Davide Mazza, Suliana Manley
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1008551

Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance
Cited by: 32
Author(s): Patrícia Alves de Castro, Ana Cristina Colabardini, Adriana Oliveira Manfiolli, Jéssica Chiaratto, Lilian Pereira Silva, Eliciane Cevolani Mattos, Giuseppe Palmisano, Fausto Almeida, Gabriela Félix Persinoti, Laure Nicolas Annick Ries, Laura Mellado, Marina Campos Rocha, Michael Bromley, Roberto Nascimento Silva, Gabriel Scalini de Souza, Flávio Vieira Loures, Iran Malavazi, Neil Andrew Brown, Gustavo H. Goldman
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13073-021-00884-0

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice
Cited by: 14
Author(s): Jessica L Haigh, Anna Adhikari, Nycole A Copping, Tyler W. Stradleigh, A. Ayanna Wade, Rinaldo Catta-Preta, Linda Su-Feher, Iva Zdilar, Sarah Morse, Timothy A. Fenton, Anh B Nguyen, Diana Quintero, Samrawit Agezew, Michael Sramek, Ellie J Kreun, Jasmine Carter, Andrea Gompers, Jason T. Lambert, Cesar P Canales, L Pennacchio, Axel Visel, Diane E. Dickel, Jill L. Silverman, A. Nord
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1006636

TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF
Cited by: 69
Author(s): Hannah Seberg, Eric Van Otterloo, Stacie K. Loftus, Huan Liu, Greg Bonde, Ramakrishna Sompallae, Derek Gildea, Juan Francisco de Paz Santana, J. Robert Manak, William J. Pavan, Trevor Williams, Robert A. Cornell
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-018-5393-3

A comparison between whole transcript and 3’ RNA sequencing methods using Kapa and Lexogen library preparation methods
Cited by: 55
Author(s): Feiyang Ma, Brie K. Fuqua, Yehudit Hasin, Clara Yukhtman, Chris D. Vulpe, Aldons J. Lusis, Matteo Pellegrini
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-43591-y

Apoptotic endothelial cells release small extracellular vesicles loaded with immunostimulatory viral-like RNAs
Cited by: 43
Author(s): Marie-Pierre Hardy, Éric Audemard, Francis Migneault, Albert Feghaly, Sylvie Brochu, Patrick Gendron, Éric Boilard, François Major, Mélanie Dieudé, Marie‐Josée Hébert, Claude Perreault
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-03390-9

Aberrant plasticity of peripheral sensory axons in a painful neuropathy
Cited by: 30
Author(s): Takashi Hirai, Yatendra Mulpuri, Yanbing Cheng, Zheng Xia, Wei Li, Supanigar Ruangsri, Igor Spigelman, Ichiro Nishimura
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0145176

Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy
Cited by: 26
Author(s): Manish Kohli, Liguo Wang, Fang Xie, Hugues Sicotte, Ping Yin, Scott M. Dehm, Steven N. Hart, Peter T. Vedell, Poulami Barman, Rui Qin, Douglas W. Mahoney, Rachel E. Carlson, Jeanette E. Eckel‐Passow, Thomas D. Atwell, Patrick W. Eiken, Brendan P. McMenomy, Eric D. Wieben, Gautam Jha, Rafael E. Jimenez, Richard M. Weinshilboum, Liewei M Wang
Software Mentions: 4
Published: almost 9 years ago

10.3390/cancers12123738

Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients
Cited by: 9
Author(s): Ulf Schmitz, Jaynish S. Shah, Bijay Dhungel, Geoffray Monteuuis, Phuc-Loi Luu, Veronika Petrova, Cynthia Metierre, Shalima S. Nair, Charles G. Bailey, Verity A. Saunders, Ali G. Turhan, Deborah L. White, Susan Branford, Susan J. Clark, Timothy P. Hughes, Justin Wong, John E.J. Rasko
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0151697

Comparative RNA-Seq Analysis Reveals That Regulatory Network of Maize Root Development Controls the Expression of Genes in Response to N Stress
Cited by: 19
Author(s): Xiujing He, Hui Ma, Xing Zhao, Shujun Nie, Yuhua Li, Zhiming Zhang, Yaou Shen, Qi Chen, Yanli Lu, Hai Long, Shufeng Zhou, Shibin Gao, Guangtang Pan, Hung-Ching Lin
Software Mentions: 4
Published: over 8 years ago

10.1038/srep32442

A Multi-Serotype Approach Clarifies the Catabolite Control Protein A Regulon in the Major Human Pathogen Group A Streptococcus
Cited by: 14
Author(s): Sruti DebRoy, Miguel A. Saldaña, Dante Travisany, Andrew Montano, Jessica Galloway-Peña, Nicola Horstmann, Hui Yao, Maurício González, Alejandro Maass, Mauricio Latorre, Samuel A. Shelburne
Software Mentions: 4
Published: about 8 years ago

10.1038/srep29477

Limits of Peripheral Blood Mononuclear Cells for Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis
Cited by: 18
Author(s): Lai-Ping Wong, Kaiyu Jiang, Yanmin Chen, Teresa Hennon, Lucy C Holmes, Carol A. Wallace, James N. Jarvis
Software Mentions: 4
Published: over 8 years ago

10.1038/s41597-020-00719-4

Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells
Cited by: 11
Author(s): Li Chen, Ruirui Yang, Tony Kwan, Chao Tang, Stephen Watt, Yiming Zhang, Guillaume Bourque, Bing Ge, Kate Downes, Mattia Frontini, Willem H. Ouwehand, Jing-wen Lin, Nicole Soranzo, Tomi Pastinen, Ciyong Lu
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0118231

Sugarcane Giant Borer Transcriptome Analysis and Identification of Genes Related to Digestion
Cited by: 12
Author(s): Fernando Campos de Assis Fonseca, Alexandre Augusto Pereira Firmino, Leonardo Lima Pepino Macedo, Roberta Ramos Coelho, José Dijair Antonino de Sousa Júnior, Orzenil B. Silva‐Junior, Roberto Coiti Togawa, George J. Pappas, Luiz Avelar Brandão de Góis, Maria Cristina Mattar da Silva, Maria Fátima Grossi-de-Sá
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.ppat.1009789

Pulmonary mesenchymal stem cells are engaged in distinct steps of host response to respiratory syncytial virus infection
Cited by: 5
Author(s): Melanie Brügger, Thomas Démoulins, G. Tuba Barut, Béatrice Zumkehr, Blandina I. Oliveira Esteves, Kemal Mehinagic, Quentin Haas, Aline Schögler, Marie‐Anne Rameix‐Welti, Jean François Eléouët, Ueli Moehrlen, Thomas Marti, Ralph A. Schmid, Artur Summerfield, Horst Posthaus, Nicolas Ruggli, Sean Hall, Marco P. Alves
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms20225710

The Biological Effects of Complete Gasoline Engine Emissions Exposure in a 3D Human Airway Model (MucilAirTM) and in Human Bronchial Epithelial Cells (BEAS-2B)
Cited by: 13
Author(s): Pavel Rőssner, Tereza Červená, Michal Vojtíšek-Lom, Kristýna Vrbová, Antonín Ambrož, Zuzana Nováková, Fatima Elzeinová, Hasmik Margaryan, V. Beránek, Martin Pechout, David Macoun, Jǐŕı Kléma, Andrea Rössnerová, Miroslav Cigánek, Jan Topinka
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0187150

RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma
Cited by: 13
Author(s): Jennifer K. Grenier, Polly Foureman, Erica A. Sloma, Andrew D. Miller
Software Mentions: 4
Published: about 7 years ago

10.1172/jci.insight.140332

ETV6 germline mutations cause HDAC3/NCOR2 mislocalization and upregulation of interferon response genes
Cited by: 12
Author(s): Marlie H Fisher, Gregory D. Kirkpatrick, Brett M. Stevens, Courtney L. Jones, Michael U. Callaghan, Madhvi Rajpurkar, Joy M. Fulbright, Megan A. Cooper, Jesse W. Rowley, Christopher C. Porter, Arthur Gutierrez‐Hartmann, Kenneth L. Jones, Craig T. Jordan, Eric M. Pietras, Jorge Di Paola
Software Mentions: 4
Published: about 4 years ago

10.1186/s13059-019-1671-x

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing
Cited by: 101
Author(s): Daniel Alpern, Vincent Gardeux, Julie Russeil, Bastien Mangeat, Antonio C. A. Meireles-Filho, Romane Breysse, David L. Hacker, Bart Deplancke
Software Mentions: 4
Published: over 5 years ago

10.1186/s13024-016-0133-0

Spinal cord injury induces astroglial conversion towards neuronal lineage
Cited by: 36
Author(s): Harun N. Noristani, Jean Charles Sabourin, Hassan Boukhaddaoui, Emilie Chan-Seng, Yannick Nicolas Gerber, Florence E. Perrin
Software Mentions: 3
Published: about 8 years ago

10.18632/aging.103682

Transcriptomic analysis reveals gender differences in gene expression profiling of the hypothalamus of rhesus macaque with aging
Cited by: 1
Author(s): Yong Fan, Congru Li, Wendi Pei, Tao Tan, Rong Li, Jie Qiao, Yang Yu
Software Mentions: 3
Published: about 4 years ago

10.1111/acel.13428

Single‐oocyte transcriptome analysis reveals aging‐associated effects influenced by life stage and calorie restriction
Cited by: 13
Author(s): Tomobumi Mishina, Namine Tabata, Tetsutaro Hayashi, Mika Yoshimura, Mana Umeda, Midori Mori, Yayoi Ikawa, Hiroshi Hamada, Itoshi Nikaido, Tomoya S. Kitajima
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-015-0873-9

TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
Cited by: 34
Author(s): Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stefan Krebs, Gustav Steinhoff, Róbert Dávid, Olaf Wolkenhauer
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12859-018-2107-4

Watchdog – a workflow management system for the distributed analysis of large-scale experimental data
Cited by: 20
Author(s): Michael Kluge, Caroline C. Friedel
Software Mentions: 3
Published: over 6 years ago

10.1186/s12915-019-0693-x

Cold-induced lipid dynamics and transcriptional programs in white adipose tissue
Cited by: 70
Author(s): Zhonglin Xu, Wenjing You, Yanbing Zhou, Wentao Chen, Yizhen Wang, Tizhong Shan
Software Mentions: 3
Published: about 5 years ago

10.1186/s12915-016-0279-9

Global identification of hnRNP A1 binding sites for SSO-based splicing modulation
Cited by: 56
Author(s): Georg M. Bruun, Thomas Koed Doktor, Jonas Borch-Jensen, Akio Matsubara, Adrian R. Krainer, Kinji Ohno, Brage S. Andresen
Software Mentions: 3
Published: over 8 years ago

10.1186/s12885-019-6363-0

The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues
Cited by: 26
Author(s): Michał Marczyk, Chunxiao Fu, Rosanna Lau, Lili Du, Alexander J. Trevarton, Bruno Valentin Sinn, Rebekah E. Gould, Lajos Pusztai, Christos Hatzis, W. Fraser Symmans
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12861-018-0169-1

Dynamic transcriptome landscape of Asian domestic honeybee (Apis cerana) embryonic development revealed by high-quality RNA sequencing
Cited by: 12
Author(s): Xiaofen Hu, Ke Li, Zilong Wang, Zhen Zeng
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-016-3168-2

Novel equine tissue miRNAs and breed-related miRNA expressed in serum
Cited by: 27
Author(s): Alicja Pacholewska, Núria Mach, Xavier Mata, Anne Vaiman, Laurent Schibler, Éric Barrey, V. Gerber
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-018-4627-8

Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse
Cited by: 44
Author(s): Paula Fagundes de Gouvêa, Aline Vianna Bernardi, Luís Eduardo Gerolamo, Emerson de Souza Santos, Diego Mauricio Riaño‐Pachón, Sérgio Akira Uyemura, Taísa Magnani Dinamarco
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-021-07884-9

Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)
Cited by: 7
Author(s): Thu Thi Minh Vo, Tuan V. Nguyen, Gianluca Amoroso, Tomer Ventura, Abigail Elizur
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-15-954

Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples
Cited by: 33
Author(s): Igseo Choi, Hua Bao, Arun Kommadath, Afshin Hosseini, Xinwei Sun, Yan Meng, Paul Stothard, Graham Plastow, Christopher K. Tuggle, James M. Reecy, Eric R. Fritz-Waters, Samuel M. Abrams, Joan K. Lunney, Leluo Guan
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-019-5953-1

Systematic evaluation of RNA-Seq preparation protocol performance
Cited by: 26
Author(s): Hsueh-Ping Chao, Yueping Chen, Yoko Takata, Mary W. Tomida, Kevin Lin, Jason Kirk, Melissa S. Simper, Carol Mikulec, Joyce E. Rundhaug, Susan M. Fischer, Taiping Chen, Dean G. Tang, Yue Lu, Jianjun Shen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-07272-9

Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]
Cited by: 5
Author(s): Zilong Zhao, Dan Liu, Yanjiao Cui, Suying Li, Dan Liang, Daizhen Sun, Jianhe Wang, Zhengli Liu
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-019-6166-3

A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples
Cited by: 10
Author(s): Xiaojing Lin, Lihong Qiu, Xue Song, Junyan Hou, Weizhi Chen, Jun Zhao
Software Mentions: 3
Published: about 5 years ago

10.1186/s12865-019-0297-9

Comprehensive analyses of long non-coding RNA expression profiles by RNA sequencing and exploration of their potency as biomarkers in psoriatic arthritis patients
Cited by: 12
Author(s): Tao Yue, Mei Ji, Huanru Qu, Mengru Guo, Fengmin Bai, Zhanming Zhang, Weifeng Wang, Xuming Gong, Zhenghua Zhang
Software Mentions: 3
Published: over 5 years ago

10.1093/bioinformatics/btw354

MultiQC: summarize analysis results for multiple tools and samples in a single report
Cited by: 3,836
Author(s): Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller
Software Mentions: 3
Published: over 8 years ago

10.1186/s40659-019-0237-4

Chronic prostatitis alters the prostatic microenvironment and accelerates preneoplastic lesions in C57BL/6 mice
Cited by: 6
Author(s): Yong Gao, Lijuan Wei, Chenbang Wang, Yuanjie Huang, Weidong Li, Tianyu Li, Chao‐Hua Mo, Hua‐Li Qin, Xiaoge Zhong, Yun Wang, Aihua Tan, Zengnan Mo, Yonghua Jiang, Yanling Hu
Software Mentions: 3
Published: over 5 years ago

10.1155/2020/1705387

Ammonia Exposure Induced Cilia Dysfunction of Nasal Mucosa in the Piglets
Cited by: 3
Author(s): Qiankun Wang, Mengyao Wang, Chun Liu, Liurong Huang, Yun Gao, Mei Yu, Zhao Song, Xiaoping Li
Software Mentions: 3
Published: over 4 years ago

10.3390/biomedicines8090292

Anticancer Imidazoacridinone C-1311 is Effective in Androgen-Dependent and Androgen-Independent Prostate Cancer Cells
Cited by: 5
Author(s): Magdalena Niemira, Barbara Borowa-Mazgaj, Samuel B. Bader, Adrianna Moszyńska, Marcin Ratajewski, Kaja Karaś, Mirosław Kwaśniewski, Adam Krętowski, Zofia Mazerska, Ester M. Hammond, Anna Skwarska
Software Mentions: 3
Published: over 4 years ago

10.1038/s41408-020-0320-7

“Direct to Drug” screening as a precision medicine tool in multiple myeloma
Cited by: 18
Author(s): Cecília Bonolo de Campos, Nathalie Meurice, Joachim Petit, Alysia Polito, Yuan Xiao Zhu, Panwen Wang, Laura A. Bruins, Xuewei Wang, Ilsel D Lopez Armenta, Susie A. Darvish, Greg Ahmann, Kimberly J. Henderson, Shulan Tian, Jonas Kruse, William Stewart, Jeremy T. Larsen, Craig B. Reeder, David Dingli, Prashant Kapoor, Shaji Kumar, Rafaël Fonseca, P. Leif Bergsagel, Esteban Braggio, A. Keith Stewart
Software Mentions: 3
Published: over 4 years ago

10.1186/s13229-017-0134-z

Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress
Cited by: 46
Author(s): Dejian Zhao, Ryan Mokhtari, Erika Pedrosa, Rayna Birnbaum, Deyou Zheng, Herbert M. Lachman
Software Mentions: 3
Published: over 7 years ago

10.1186/s13229-019-0311-3

TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling
Cited by: 27
Author(s): Pauline Martín, Vilas Wagh, Surya A. Reis, Serkan Erdin, Roberta L. Beauchamp, Ghalib Shaikh, Michael E. Talkowski, Elizabeth A. Thiele, Steven D. Sheridan, Stephen J. Haggarty, Vijaya Ramesh
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12943-020-01293-4

Long non-coding RNA NEAT1 promotes bone metastasis of prostate cancer through N6-methyladenosine
Cited by: 154
Author(s): Simeng Wen, Yulei Wei, Chong Zen, Wei Xiong, Yuanjie Niu, Yu Zhao
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.molmet.2020.101038

Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting
Cited by: 6
Author(s): Shengshu Huang, Mélanie Makhlouf, Eman H. AbouMoussa, Mayra L. Ruiz Tejada Segura, Lisa S. Mathew, Kun Wang, Man C. Leung, Damien Chaussabel, Darren W. Logan, Antonio Scialdone, Mathieu Garand, Luís R. Saraiva
Software Mentions: 3
Published: about 4 years ago

10.1016/j.omto.2021.04.014

Induction of cell death in ovarian cancer cells by doxorubicin and oncolytic vaccinia virus is associated with CREB3L1 activation
Cited by: 8
Author(s): Anna Mistarz, Matthew A. Graczyk, M. Winkler, Prashant Singh, Eduardo Cortes, Anthony Miliotto, Song Liu, Mark D. Long, Yan Li, Aimee Stablewski, Kieran L. O’Loughlin, Hans Minderman, Kunle Odunsi, Hanna Rokita, AJ Robert McGray, Emese Zsíros, Danuta Kozbor
Software Mentions: 3
Published: almost 3 years ago

10.1007/s12250-021-00370-2

Transcriptome Analyses Implicate Endogenous Retroviruses Involved in the Host Antiviral Immune System through the Interferon Pathway
Cited by: 13
Author(s): Miao Wang, Liying Wang, Haizhou Liu, Jianjun Chen, Di Liu
Software Mentions: 3
Published: over 3 years ago

10.3390/v12060614

The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities
Cited by: 91
Author(s): Elif Damla Arısan, Dafydd Alwyn Dart, Guy H. Grant, Serdar Arısan, Songul Cuhadaroglu, Sigrun Lange, Pinar Uysal-Onganer
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.11615

Transcriptome analysis associated with polysaccharide synthesis and their antioxidant activity in <i>Cyclocarya paliurus</i> leaves of different developmental stages
Cited by: 5
Author(s): Weida Lin, Huanwei Chen, Jianmei Wang, Yongli Zheng, Qiuwei Lu, Ziping Zhu, Na Li, Zexin Jin, Junmin Li, Hongfei Lü
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pbio.3000680

EphrinB1 modulates glutamatergic inputs into POMC-expressing progenitors and controls glucose homeostasis
Cited by: 7
Author(s): M Gervais, Gwenaël Labouèbe, Alexandre Picard, Bernard Thorens, Sophie Croizier
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1008540

MED19 alters AR occupancy and gene expression in prostate cancer cells, driving MAOA expression and growth under low androgen
Cited by: 8
Author(s): Hannah Weber, Rachel Ruoff, Michael J. Garabedian
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pntd.0008105

Dual RNA-Seq characterization of host and pathogen gene expression in liver cells infected with Crimean-Congo Hemorrhagic Fever Virus
Cited by: 16
Author(s): Robert Kozak, Russell S. Fraser, Mia J Biondi, Anna Majer, Sarah J. Medina, Bryan D. Griffin, Darwyn Kobasa, Patrick J. Stapleton, Chantel Urfano, Giorgi Babuadze, Kym Antonation, Lisa Fernando, Stephanie A. Booth, Brandon N. Lillie, Gary P. Kobinger
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0255066

First transcriptome profiling of D. melanogaster after development in a deep underground low radiation background laboratory
Cited by: 8
Author(s): Mikhail Zarubin, A. M. Gangapshev, Yuri Gavriljuk, V. V. Kazalov, Е. В. Кравченко
Software Mentions: 3
Published: over 3 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: almost 8 years ago

10.1371/journal.pone.0242364

Asthma and its relationship to mitochondrial copy number: Results from the Asthma Translational Genomics Collaborative (ATGC) of the Trans-Omics for Precision Medicine (TOPMed) program
Cited by: 12
Author(s): Maxwell P Cocco, E.C. White, Shujie Xiao, Donglei Hu, Angel C. Y. Mak, Patrick Sleiman, Mao Yang, Kevin Bobbitt, Hongsheng Gui, Albert M. Levin, Samantha Hochstadt, Kyle Whitehouse, Dean Rynkowski, Andrea J. Barczak, Gonçalo R. Abecasis, Thomas W. Blackwell, Hyun Min Kang, Deborah A. Nickerson, Søren Germer, Jun Ding, David E. Lanfear, Frank D. Gilliland, W. James Gauderman, Rajesh Kumar, David J. Erle, Fernando D. Martínez, Hákon Hákonarson, Esteban G. Burchard, L. Keoki Williams
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0122011

The Transcriptome of Equine Peripheral Blood Mononuclear Cells
Cited by: 17
Author(s): Alicja Pacholewska, Michaela Drögemüller, Jolanta Klukowska‐Rötzler, Simone Lanz, Eman Hamza, Emmanouil T. Dermitzakis, Eliane Marti, V. Gerber, Tosso Leeb, Vidhya Jagannathan
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0112102

Isolation of Specific Neurons from C. elegans Larvae for Gene Expression Profiling
Cited by: 84
Author(s): W. Clay Spencer, Rebecca McWhirter, Tyne Miller, Pnina Strasbourger, Owen Thompson, LaDeana W. Hillier, Robert H. Waterston, David M. Miller
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0095987

Dissection of Estrogen Receptor Alpha Signaling Pathways in Osteoblasts Using RNA-Sequencing
Cited by: 22
Author(s): Matthew M. Roforth, Elizabeth J. Atkinson, Ellis R. Levin, Sundeep Khosla, David G. Monroe
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0215187

Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans
Cited by: 5
Author(s): Yukio Nomoto, Yukihiko Kubota, Yuto Ohnishi, Kota Kasahara, Aimi Tomita, Takehiro Oshime, Hiroki Yamashita, Muhamad Fahmi, Masahiro Ito
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0232332

Combining signal and sequence to detect RNA polymerase initiation in ATAC-seq data
Cited by: 1
Author(s): Ignacio J. Tripodi, Murad Chowdhury, Margaret Gruca, Robin D. Dowell
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0191096

Thyroid transcriptome analysis reveals different adaptive responses to cold environmental conditions between two chicken breeds
Cited by: 11
Author(s): Shanshan Xie, Xiufen Yang, Dehe Wang, Feng Zhu, Ning Yang, Zhuocheng Hou, Zhonghua Ning
Software Mentions: 3
Published: almost 7 years ago

10.3390/cancers12061696

Molecular Characterization of Astrocytoma Progression Towards Secondary Glioblastomas Utilizing Patient-Matched Tumor Pairs
Cited by: 5
Author(s): Michael Seifert, Gabriele Schackert, Achim Temme, Evelin Schröck, Andreas Deutsch, Barbara Klink
Software Mentions: 3
Published: over 4 years ago

10.1186/s13578-020-00420-4

Temporal transcriptome change of Oncomelania hupensis revealed by Schistosoma japonicum invasion
Cited by: 12
Author(s): Xinyu Feng, Ling-Qian Zhu, Zhiqiang Qin, Xiaojin Mo, Yufan Hao, Ying Jiang, Wei Hu, Shi-Zhu Li
Software Mentions: 3
Published: over 4 years ago

10.1111/cmi.12735

Laser capture microdissection enables transcriptomic analysis of dividing and quiescent liver stages of<i>Plasmodium</i>relapsing species
Cited by: 57
Author(s): Roger Cubí, Shruthi S. Vembar, Anne Biton, Jean‐François Franetich, Mallaury Bordessoulles, Daniel Sossau, Gigliola Zanghì, Henriette Bosson-Vanga, Magalie Bénard, Angel J. Moreno, Nathalie Dereuddre‐Bosquet, Roger Le Grand, Artur Scherf, Dominique Mazier
Software Mentions: 3
Published: over 7 years ago

10.1007/s00018-021-03865-z

Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data
Cited by: 14
Author(s): Robin Herbrechter, Nadine Hube, Raoul Buchholz, Andreas Reiner
Software Mentions: 3
Published: over 3 years ago

10.1016/j.celrep.2020.108108

Malic Enzyme Couples Mitochondria with Aerobic Glycolysis in Osteoblasts
Cited by: 69
Author(s): Wen‐Chih Lee, Xing Ji, Itzhak Nissim, Fanxin Long
Software Mentions: 3
Published: about 4 years ago

10.1002/ctm2.201

Long noncoding RNA lncGALM increases risk of liver metastasis in gallbladder cancer through facilitating N‐cadherin and IL‐1β‐dependent liver arrest and tumor extravasation
Cited by: 8
Author(s): Huaifeng Li, Yunping Hu, Yunpeng Jin, Yi Zhu, Yajuan Hao, Fatao Liu, Yang Yang, Guoqiang Li, Xiaoling Song, Yuanyuan Ye, Sheng Xiang, Yuan Gao, Jinhui Zhu, Yijian Zhang, Lin Jiang, Wen Huang, Jian Zhu, Xiangsong Wu, Yingbin Liu
Software Mentions: 3
Published: about 4 years ago

10.1186/1746-1596-9-142

NF-κB signaling and vesicle transport are correlated with the reactivation of the memory trace of morphine dependence
Cited by: 9
Author(s): Junyi Ye, Zhaoyang Yang, Candong Li, Meimei Cai, Daizhan Zhou, Qin Zhang, Wei Y, Ting Wang, Yun Liu
Software Mentions: 3
Published: over 10 years ago

10.1155/2020/3291853

Transcriptomic Analysis of Fuzi Lizhong Decoction for the Treatment of Stomach Ulcers
Cited by: 2
Author(s): Xin Yang, Haijun Wang, Lei Xu
Software Mentions: 3
Published: almost 5 years ago

10.3389/fcell.2021.685494

Novel Functional Genes Involved in Transdifferentiation of Canine ADMSCs Into Insulin-Producing Cells, as Determined by Absolute Quantitative Transcriptome Sequencing Analysis
Cited by: 2
Author(s): Pengxiu Dai, Jiakai Li, Yijing Chen, Luwen Zhang, Xinke Zhang, Jinglu Wang, Guixiang Qi, Yihua Zhang
Software Mentions: 3
Published: over 3 years ago