Ecosyste.ms: Papers

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: about 4 years ago

10.1186/s13072-016-0095-z

EpiMINE, a computational program for mining epigenomic data
Cited by: 11
Author(s): Sri Ganesh Jammula, Diego Pasini
Software Mentions: 23
Published: over 7 years ago

10.1186/s13059-016-0881-8

A survey of best practices for RNA-seq data analysis
Cited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: over 8 years ago

10.20517/jtgg.2020.51

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq
Cited by: 2
Author(s): Brandon Lieberman, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ning He, Yen‐Yi Ho, Josephine A. Taverna, Tim Hui-Ming Huang, Chun-Liang Chen
Software Mentions: 18
Published: over 4 years ago

10.3389/fimmu.2017.00445

Integration of Immune Cell Populations, mRNA-Seq, and CpG Methylation to Better Predict Humoral Immunity to Influenza Vaccination: Dependence of mRNA-Seq/CpG Methylation on Immune Cell Populations
Cited by: 15
Author(s): Michael T. Zimmermann, Richard B. Kennedy, Diane E. Grill, Ann L. Oberg, Krista M. Goergen, Inna G. Ovsyannikova, Iana H. Haralambieva, Gregory A. Poland
Software Mentions: 16
Published: about 7 years ago

10.3389/fgene.2016.00163

Single-Cell Transcriptomics Bioinformatics and Computational Challenges
Cited by: 101
Author(s): Olivier Poirion, Xun Zhu, Travers Ching, Lana X. Garmire
Software Mentions: 15
Published: over 7 years ago

10.1136/jitc-2020-000705

SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery
Cited by: 17
Author(s): Siwen Hu‐Lieskovan, Srabani Bhaumik, Kavita M. Dhodapkar, Jean‐Charles Grivel, Sumati Gupta, Brent A. Hanks, Sylvia Janetzki, Thomas O. Kleen, Yoshinobu Koguchi, Amanda W. Lund, Cristina Maccalli, Yolanda D. Mahnke, Ruslan D. Novosiadly, Senthamil R. Selvan, Tasha N. Sims, Yingdong Zhao, Holden T. Maecker
Software Mentions: 15
Published: over 3 years ago

10.1186/s12861-018-0163-7

Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells
Cited by: 4
Author(s): Anna Mantsoki, Guillaume Devailly, Anagha Joshi
Software Mentions: 13
Published: about 6 years ago

10.1371/journal.pcbi.1003000

Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
Cited by: 55
Author(s): Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd
Software Mentions: 13
Published: about 11 years ago

10.7554/eLife.54186

Epigenetic inheritance of circadian period in clonal cells
Cited by: 12
Author(s): Yan Li, Yongli Shan, Gokhul Kilaru, Stefano Berto, Guang-Zhong Wang, Kimberly Cox, Seung-Hee Yoo, Shao Nian Yang, Genevieve Konopka, Joseph S. Takahashi
Software Mentions: 13
Published: almost 4 years ago

10.3389/fgene.2018.00278

RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)
Cited by: 11
Author(s): Carolina N. Correia, Kirsten E. McLoughlin, Nicolas C. Nalpas, David A. Magee, John A. Browne, Kévin Rue-Albrecht, Stephen V. Gordon, David E. MacHugh
Software Mentions: 12
Published: over 5 years ago

10.1186/s12920-015-0121-1

Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities
Cited by: 52
Author(s): Eduardo Castro-Nallar, Ying Shen, Robert J. Freishtat, Marcos Pérez‐Losada, Solaiappan Manimaran, Gang Lv, W. Evan Johnson, Keith A. Crandall
Software Mentions: 12
Published: over 8 years ago

10.3389/fcimb.2021.687607

Early Leukocyte Responses in Ex-Vivo Models of Healing and Non-Healing Human Leishmania (Viannia) panamensis Infections
Cited by: 1
Author(s): María Adelaida Gómez, Ashton T. Belew, Adriana Navas, Mariana Rosales-Chilama, Julieth Murillo, Laura A. L. Dillon, Theresa A Alexander, Álvaro José Martínez-Valencia, Najib M. El-Sayed
Software Mentions: 12
Published: over 2 years ago

10.3390/ijms21010167

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism
Cited by: 22
Author(s): Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
Software Mentions: 12
Published: over 4 years ago

10.1371/journal.pone.0190152

RNA-Seq differential expression analysis: An extended review and a software tool
Cited by: 389
Author(s): Juliana Costa-Silva, Douglas Silva Domingues, Fabrício Martins Lopes
Software Mentions: 12
Published: over 6 years ago

10.1016/j.ccell.2017.08.017

Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma
Cited by: 662
Author(s): Alan Mackay, Anna Burford, Diana Carvalho, Elisa Izquierdo, Janat Fazal-Salom, Kathryn R. Taylor, Lynn Bjerke, Matthew Clarke, Maria Vinci, Meera Nandhabalan, Sara Temelso, Sergey Popov, Valeria Molinari, Pichai Raman, Angela J. Waanders, Harry Han, Saumya Gupta, Lynley V. Marshall, Stergios Zacharoulis, Sucheta Vaidya, Henry Mandeville, Leslie Bridges, Andrew Martin, Safa Al‐Sarraj, Christopher Chandler, Ho Keung Ng, Xingang Li, Kun Mu, Saoussen Trabelsi, Dorra H’mida-Ben Brahim, Alexei N. Kisljakov, Д. М. Коновалов, Andrew S. Moore, Ángel M. Carcaboso, Mariona Suñol, Carmen de Torres, Ofelia Cruz, Jaume Mora, Л. И. Шац, João N. Stávale, Lucas Tadeu Bidinotto, Rui Manuel Reis, Natacha Entz‐Werlé, Michael Farrell, Jane Cryan, Darach Crimmins, John Caird, Jane Pears, Michelle Monje, Marie‐Anne Debily, David Castel, Jacques Grill, Cynthia Hawkins, Hamid Nikbakht, Nada Jabado, Suzanne J. Baker, Stefan M. Pfister, David Jones, Maryam Fouladi, André O. von Bueren, Michael Baudis, Adam Resnick, Chris Jones
Software Mentions: 11
Published: over 6 years ago

10.3390/cancers11081104

Differential Expression of DNA Repair Genes in Prognostically-Favorable versus Unfavorable Uveal Melanoma
Cited by: 10
Author(s): Mehmet Doğrusöz, Andrea Ruschel Träsel, Jinfeng Cao, Selҫuk Ҫolak, Sake I. van Pelt, Wilma G. M. Kroes, Amina F.A.S. Teunisse, Samar Alsafadi, Sjoerd G. van Duinen, Gregorius P M Luyten, Pieter A. van der Velden, Adriana Amaro, Ulrich Pfeffer, Aart G. Jochemsen, Martine J. Jager
Software Mentions: 11
Published: almost 5 years ago

10.1371/journal.pone.0188873

A comprehensive analysis of breast cancer microbiota and host gene expression
Cited by: 105
Author(s): Kevin J. Thompson, James N. Ingle, Xiaojia Tang, Nicholas Chia, Patricio Jeraldo, Marina Walther-Antonio, Karunya K. Kandimalla, Stephen Johnson, Jingwen Yao, Sean C. Harrington, Vera J. Suman, Liewei Wang, Richard Weinshilboum, Judy C. Boughey, Jean Pierre A. Kocher, Heidi Nelson, Matthew P. Goetz, Krishna R. Kalari
Software Mentions: 11
Published: over 6 years ago

10.1093/g3journal/jkab104

Strongyloides RNA-seq Browser: a web-based software platform for on-demand bioinformatics analyses of Strongyloides species
Cited by: 2
Author(s): Astra S. Bryant, Stephanie F. DeMarco, Elissa A. Hallem
Software Mentions: 11
Published: about 3 years ago

10.1155/2016/7972351

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments
Cited by: 11
Author(s): Francesco Russo, Dario Righelli, Claudia Angelini
Software Mentions: 11
Published: over 8 years ago

10.1186/s12864-017-3819-y

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
Cited by: 67
Author(s): Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Máximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar, Laurent Vallar
Software Mentions: 11
Published: almost 7 years ago

10.1186/s13073-016-0285-0

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins
Cited by: 55
Author(s): Chan Zhou, Samuel R. York, Jennifer Y. Chen, Joshua V. Pondick, Daniel L. Motola, Raymond T. Chung, Alan C. Mullen
Software Mentions: 11
Published: about 8 years ago

10.1002/embj.201386825

Key regulators control distinct transcriptional programmes in blood progenitor and mast cells
Cited by: 48
Author(s): Fernando J. Calero-Nieto, Felicia Ng, Nicola K. Wilson, Rebecca Hannah, Victoria Moignard, Ana Leal-Cervantes, Isabel Jimenez-Madrid, Evangelia Diamanti, Lorenz Wernisch, Berthold Göttgens
Software Mentions: 10
Published: about 10 years ago

10.7554/eLife.18683

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development
Cited by: 185
Author(s): Felipe Mora‐Bermúdez, Farhath Badsha, Sabina Kanton, J. Gray Camp, Benjamin Vernot, Kathrin Köhler, Birger Voigt, Keisuke Okita, Tomislav Maričić, Zhisong He, Robert Lachmann, Svante Pääbo, Barbara Treutlein, Wieland B. Huttner
Software Mentions: 10
Published: over 7 years ago

10.7554/eLife.10421

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain
Cited by: 115
Author(s): Claudia Scheckel, Elodie Drapeau, María A. Frías, Christopher Y. Park, John Fak, Ilana Zucker-Scharff, Yan Kou, Vahram Haroutunian, Avi Ma’ayan, Joseph D. Buxbaum, Robert B. Darnell
Software Mentions: 10
Published: about 8 years ago

10.1093/database/bay027

Maser: one-stop platform for NGS big data from analysis to visualization
Cited by: 38
Author(s): Sonoko Kinjo, Norikazu Monma, Sadahiko Misu, Norikazu Kitamura, Junichi Imoto, Kazutoshi Yoshitake, Takashi Gojobori, Kazuho Ikeo
Software Mentions: 10
Published: over 6 years ago

10.1186/s12864-015-2356-9

QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization
Cited by: 33
Author(s): Shanrong Zhao, Li Xi, Jie Quan, Hualin Simon Xi, Ying Zhang, David von Schack, Michael S. Vincent, Baohong Zhang
Software Mentions: 10
Published: over 8 years ago

10.1186/s41065-021-00202-z

RNA-Seq based transcriptome analysis in oral lichen planus
Cited by: 5
Author(s): Haoyu Wang, Yiwen Deng, Siqi Peng, Yán Li, Hui Xu, Qingzhong Wang, Zhenhua Shen
Software Mentions: 10
Published: over 2 years ago

10.1186/s12711-021-00614-5

Influence of genetics and the pre-vaccination blood transcriptome on the variability of antibody levels after vaccination against Mycoplasma hyopneumoniae in pigs
Cited by: 8
Author(s): Fany Blanc, Tatiana Maroilley, Manuel Revilla, Gaëtan Lemonnier, Jean Jacques Leplat, Yvon Billon, Laure Ravon, Olivier Bouchez, Jean Pierre Bidanel, Bertrand Bed’Hom, Marie-Hélène Pinard-van Der Laan, Jordi Estellé, Claire Rogel‐Gaillard
Software Mentions: 10
Published: about 3 years ago

10.7554/eLife.69431

Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2
Cited by: 18
Author(s): Elektra Kantzari Robinson, Pratibha Jagannatha, Sergio Covarrubias, Matthew Cattle, Valeriya Smaliy, Rojin Safavi, Barbara Shapleigh, Robin Abu-Shumays, Miten Jain, Suzanne M. Cloonan, Mark Akeson, Angela N. Brooks
Software Mentions: 9
Published: almost 3 years ago

10.1186/1471-2164-16-S6-S3

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application
Cited by: 54
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Matteo Pallocca, Ernesto Picardi, Anna Maria D’Erchia, Raffaele Calogero, Tiziana Castrignanò, Graziano Pesole
Software Mentions: 9
Published: almost 9 years ago

10.3390/cancers12051122

The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer
Cited by: 11
Author(s): M. Friedrich, Karolin Wiedemann, Kristin Reiche, Sven-Holger Puppel, Gabriele Pfeifer, Ivonne Zipfel, Stefanie Petrou Binder, Ulrike Köhl, G Müller, Kurt Engeland, Achim Aigner, S. Füssel, M. Fröhner, Claudia Peitzsch, Anna Dubrovska, Michael Rade, Sabina Christ, S Schreiber, Jörg Hackermüller, Jörg Lehmann, Marieta Toma, Michael H. Muders, Ulrich Sommer, Gustavo Baretton, Manfred P. Wirth, Friedemann Horn
Software Mentions: 9
Published: about 4 years ago

10.1186/s13040-017-0125-9

Gene set analysis controlling for length bias in RNA-seq experiments
Cited by: 7
Author(s): Xing Ren, Qiang Hu, Song Liu, Jianmin Wang, Jeffrey C. Miecznikowski
Software Mentions: 9
Published: over 7 years ago

10.1038/s41598-017-14576-6

Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi
Cited by: 37
Author(s): Meiser Anjuli, Jürgen Otte, Imke Schmitt, Francesco Dal Grande
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pone.0199274

Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats
Cited by: 25
Author(s): Boris Zybailov, Galina Glazko, Yasir Rahmatallah, Dmitri S. Andreyev, Taylor McElroy, Oleg Karaduta, Stephanie D. Byrum, Lisa Orr, Alan J. Tackett, Samuel G. Mackintosh, Ricky D. Edmondson, Dorothy A. Kieffer, Roy J. Martin, Sean H. Adams, Nosratola D. Vaziri, John M. Arthur
Software Mentions: 9
Published: over 5 years ago

10.3389/fpls.2020.01269

Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and Ripening
Cited by: 27
Author(s): Beatriz Ester García-Gómez, David Ruiz, J. Salazar, M. Rubio, Pedro J. Martínez-García, Pedro Martínez‐Gómez
Software Mentions: 9
Published: over 3 years ago

10.1186/1471-2164-14-892

RNA-Seq optimization with eQTL gold standards
Cited by: 24
Author(s): Shannon Ellis, Saloni Gupta, Foram N. Ashar, Joel S. Bader, Andrew B. West, Dan E. Arking
Software Mentions: 9
Published: over 10 years ago

10.3389/fimmu.2018.02074

Epigenetic Enhancer Marks and Transcription Factor Binding Influence Vκ Gene Rearrangement in Pre-B Cells and Pro-B Cells
Cited by: 13
Author(s): Eden Kleiman, Salvatore Loguercio, Ann J. Feeney
Software Mentions: 9
Published: over 5 years ago

10.1186/s13059-015-0702-5

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
Cited by: 128
Author(s): Alexander Kanitz, Foivos Gypas, Andreas Gruber, Andreas Gruber, Georges Martín, Mihaela Zavolan
Software Mentions: 9
Published: almost 9 years ago

10.1016/j.csbj.2018.01.003

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Cited by: 184
Author(s): Chang Xu
Software Mentions: 9
Published: over 6 years ago

10.1038/s41598-019-55434-x

QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis
Cited by: 28
Author(s): Susan M. Corley, Niamh M. Troy, Anthony Bosco, Marc R. Wilkins
Software Mentions: 9
Published: over 4 years ago

10.3389/fnins.2020.00209

A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer’s Disease
Cited by: 6
Author(s): Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung
Software Mentions: 9
Published: about 4 years ago

10.7554/eLife.65905

Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia
Cited by: 28
Author(s): Sumiko Takao, Lauren Forbes, Masahiro Uni, Shu‐Yuan Cheng, Jose Mario Bello Pineda, Yusuke Tarumoto, Paolo Cifani, Gerard Minuesa, Celine Chen, Michael G. Kharas, Robert K. Bradley, Christopher R. Vakoc, Richard P. Koche, Alex Kentsis
Software Mentions: 9
Published: over 3 years ago

10.1186/s13059-021-02374-3

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle
Cited by: 18
Author(s): Mayra Furlan-Magaril, Masami Ando-Kuri, Rodrigo G. Arzate-Mejía, Jörg Morf, Jonathan Cairns, Abraham Román-Figueroa, Luis Tenorio-Hernández, Augusto César Poot-Hernández, Simon Andrews, Csilla Várnai, Boo Virk, Steven Wingett, Peter Fraser
Software Mentions: 9
Published: almost 3 years ago

10.1186/s13059-018-1435-z

RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellum
Cited by: 152
Author(s): Chunhui Ma, Mengqi Chang, Hongyi Lv, Zhiwei Zhang, Weilong Zhang, Xue He, Gaolang Wu, Shuaiyang Zhao, Yao Zhang, Di Wang, Xufei Teng, Chunying Liu, Qing Li, Arne Klungland, Yamei Niu, Shuhui Song, Wei‐Min Tong
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.pone.0051609

Comparative Transcriptome Profiling of the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice (Oryza sativa L.) Genotypes
Cited by: 129
Author(s): Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Simona Urso, Laura Crispino, Pamela Abbruscato, Pietro Piffanelli, Elisabetta Lupotto, Luigi Cattivelli, Giampiero Valè
Software Mentions: 8
Published: over 11 years ago

10.1186/s13059-015-0862-3

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage
Cited by: 107
Author(s): Charlotte Soneson, Katarina L. Matthes, Małgorzata Nowicka, Charity W. Law, Mark D. Robinson
Software Mentions: 8
Published: over 8 years ago

10.7554/eLife.19545

Splicing repression allows the gradual emergence of new Alu-exons in primate evolution
Cited by: 52
Author(s): Jan Attig, Igor Ruiz de los Mozos, Nejc Haberman, Zhen Wang, Warren Emmett, Kathi Zarnack, Julian König, Jernej Ule
Software Mentions: 8
Published: over 7 years ago

10.1371/journal.pone.0125000

From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
Cited by: 6
Author(s): Jilong Li, Jie Hou, Sun Liang, Jordan Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin Ryan Merideth, Thomas P. Mawhinney, Valeri V. Mossine, C. Michael Greenlief, John C. Walker, William R. Folk, Mark Hannink, Dennis B. Lubahn, James A. Birchler, Jianlin Cheng
Software Mentions: 8
Published: about 9 years ago

10.1002/1878-0261.12381

A pan‐cancer atlas of cancer hallmark‐associated candidate driver lnc <scp>RNA</scp> s
Cited by: 19
Author(s): Yulan Deng, Shangyi Luo, Xinxin Zhang, Chaoxia Zou, Huating Yuan, Gaoming Liao, Liwen Xu, Chunyu Deng, Yujia Lan, Tingting Zhao, Xu Gao, Yun Xiao, Xia Li
Software Mentions: 8
Published: over 5 years ago

10.1186/s13072-016-0064-6

Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing
Cited by: 59
Author(s): Andrew Keniry, Linden J. Gearing, Natasha Jansz, Joy Liu, Aliaksei Z. Holik, Peter Hickey, Sarah Kinkel, Darcy Moore, Kelsey Breslin, Kelan Chen, Ruijie Liu, Chris Phillips, Miha Pakusch, Christine Biben, Julie Sheridan, Benjamin T. Kile, Catherine Carmichael, Matthew E. Ritchie, Douglas J. Hilton, Marnie E. Blewitt
Software Mentions: 8
Published: almost 8 years ago

10.3390/plants10081536

Variation in Gene Expression between Two Sorghum bicolor Lines Differing in Innate Immunity Response
Cited by: 2
Author(s): Yaya Cui, Dongqin Chen, Yuyong Jiang, Dong Xu, Peter Balint‐Kurti, Gary Stacey
Software Mentions: 8
Published: almost 3 years ago

10.1371/journal.pbio.2002054

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells
Cited by: 76
Author(s): Colin R. Lickwar, J. Gray Camp, Matthew Weiser, Jordan L. Cocchiaro, David M. Kingsley, Terrence S. Furey, Shehzad Z. Sheikh, John F. Rawls
Software Mentions: 8
Published: over 6 years ago

10.1038/s41422-018-0053-3

Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis
Cited by: 162
Author(s): Xiaoying Fan, Ji Dong, Shaobo Zhong, Wei Yuan, Qian Wu, Liying Yan, Jun Yong, Le Sun, Xiaoye Wang, Yangyu Zhao, Wei Wang, Jie Yan, Xiaoqun Wang, Jie Qiao, Fuchou Tang
Software Mentions: 8
Published: almost 6 years ago

10.1186/1471-2164-15-786

A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity
Cited by: 47
Author(s): Matthew Hobbs, Ana Pavasovic, Andrew King, Peter J. Prentis, Mark D. B. Eldridge, Zhiliang Chen, Donald J. Colgan, Adam Polkinghorne, Marc R. Wilkins, Cheyne Flanagan, Amber Gillett, Jon Hanger, Rebecca N. Johnson, Peter Timms
Software Mentions: 8
Published: over 9 years ago

10.7554/eLife.64513

Chondrocytes in the resting zone of the growth plate are maintained in a Wnt-inhibitory environment
Cited by: 25
Author(s): Shawn A Hallett, Yuki Matsushita, Wanida Ono, Naoko Sakagami, Koji Mizuhashi, Nicha Tokavanich, Mizuki Nagata, Annabelle Zhou, Takao Hanabusa, Henry M. Kronenberg, Noriaki Ono
Software Mentions: 8
Published: almost 3 years ago

10.1016/j.cell.2017.04.013

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension
Cited by: 607
Author(s): Judith H.I. Haarhuis, Robin H. van der Weide, Vincent A. Blomen, J. Omar Yáñez-Cuna, Mario Amendola, Marjon S. van Ruiten, Peter H.L. Krijger, Hans Teunissen, René H. Medema, Bas van Steensel, Thijn R. Brummelkamp, Elzo de Wit, Benjamin D. Rowland
Software Mentions: 8
Published: about 7 years ago

10.12688/wellcomeopenres.10501.2

Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection
Cited by: 35
Author(s): Laura Oikkonen, Stefano Lise
Software Mentions: 8
Published: about 7 years ago

10.3390/ijms21103591

Examining Short-Term Responses to a Long-Term Problem: RNA-Seq Analyses of Iron Deficiency Chlorosis Tolerant Soybean
Cited by: 8
Author(s): Adrienne N. Moran Lauter, Lindsay Rutter, Dianne Cook, Jamie A. O’Rourke, Michelle A. Graham
Software Mentions: 8
Published: almost 4 years ago

10.1038/srep40655

Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae
Cited by: 66
Author(s): Elena Gómez-Díaz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Anna Cohuet, M. Jordan Rowley, Jean-Bosco Ouédraogo, Victor G. Corcés
Software Mentions: 8
Published: over 7 years ago

10.1371/journal.pone.0153782

Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools
Cited by: 11
Author(s): Dena Leshkowitz, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, Shirley Horn‐Saban
Software Mentions: 8
Published: about 8 years ago

10.1186/gb-2013-14-9-r95

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Cited by: 594
Author(s): Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E. Mason, Nicholas D. Socci, Doron Betel
Software Mentions: 8
Published: over 11 years ago

10.3389/fpls.2018.00108

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size
Cited by: 61
Author(s): Sophie Lamarre, Pierre Frasse, Mohamed Zouine, Delphine Labourdette, Elise Sainderichin, Guojian Hu, Véronique Le Berre-Anton, Mondher Bouzayen, Élie Maza
Software Mentions: 8
Published: about 6 years ago

10.1038/s41598-017-06929-y

A systems approach to a spatio-temporal understanding of the drought stress response in maize
Cited by: 64
Author(s): Zhenyan Miao, Zhaoxue Han, Ting Zhang, Siyuan Chen, Chuang Ma
Software Mentions: 8
Published: almost 7 years ago

10.3389/fimmu.2021.617592

Phenotypic and Epigenetic Adaptations of Cord Blood CD4+ T Cells to Maternal Obesity
Cited by: 11
Author(s): Suhas Sureshchandra, Norma Mendoza, Allen Jankeel, Randall M. Wilson, Nicole Marshall, Ilhem Messaoudi
Software Mentions: 8
Published: about 3 years ago

10.7717/peerj.9056

Transcriptional profiling to identify the key genes and pathways of pterygium
Cited by: 11
Author(s): Yihui Chen, Haoyu Wang, Yaping Jiang, Xiaoyan Zhang, Qingzhong Wang
Software Mentions: 8
Published: about 4 years ago

10.1186/1471-2105-15-224

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
Cited by: 275
Author(s): Krishna R. Kalari, Asha Nair, Jaysheel Bhavsar, Daniel R. O’Brien, Jaime Davila, Matthew A. Bockol, Jinfu Nie, Xiaojia Tang, Saurabh Baheti, Jay B. Doughty, Sumit Middha, Hugues Sicotte, E. Aubrey Thompson, Yan W. Asmann, Jean-Pierre A. Kocher
Software Mentions: 8
Published: almost 10 years ago

10.3389/fgene.2018.00588

DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data
Cited by: 10
Author(s): Zhihua Gao, Zhiyuan Zhao, Wenqiang Tang
Software Mentions: 8
Published: over 5 years ago

10.12688/f1000research.17145.2

False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors
Cited by: 35
Author(s): Ashis Saha, Alexis Battle
Software Mentions: 7
Published: about 5 years ago

10.3389/fgene.2019.00185

Myometrial Transcriptional Signatures of Human Parturition
Cited by: 36
Author(s): Zachary Stanfield, Pei F. Lai, Kaiyu Lei, Mark R. Johnson, Andrew M. Blanks, Roberto Romero, Mark R. Chance, Sam Mesiano, Mehmet Koyutürk
Software Mentions: 7
Published: about 5 years ago

10.1186/s13148-020-0821-z

DNA methylation-driven EMT is a common mechanism of resistance to various therapeutic agents in cancer
Cited by: 49
Author(s): Eva Galle, Bernard Thienpont, Sarah Cappuyns, Tom Venken, Pieter Busschaert, Matthias Van Haele, Éric Van Cutsem, Tania Roskams, Jos van Pelt, Chris Verslype, Jeroen Dekervel, Diether Lambrechts
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pbio.3000988

The molecular and metabolic program by which white adipocytes adapt to cool physiologic temperatures
Cited by: 9
Author(s): Hiroyuki Mori, Colleen E. Dugan, Akira Nishii, Ameena Benchamana, Ziru Li, Thomas S. Cadenhead, Arun K. Das, Charles R. Evans, Katherine A. Overmyer, Steven M. Romanelli, Sydney K. Peterson, Devika P. Bagchi, Callie A.S. Corsa, Julie Hardij, Brian S. Learman, Mahmoud El Azzouny, Joshua J. Coon, Ken Inoki, Ormond A. MacDougald
Software Mentions: 7
Published: almost 3 years ago

10.1002/ece3.3234

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen <i>Pseudogymnoascus destructans</i>
Cited by: 21
Author(s): Christina M. Davy, Michael E. Donaldson, Craig K. R. Willis, Barry J. Saville, L. McGuire, Heather W. Mayberry, Alana Wilcox, Gudrun Wibbelt, Vikram Misra, Trent K. Bollinger, Christopher J. Kyle
Software Mentions: 7
Published: almost 7 years ago

10.1016/j.cmet.2018.04.013

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes
Cited by: 104
Author(s): Tess Tsai-Hsiu Lu, Steffen Heyne, Erez Dror, Eduard Casas, Laura Leonhardt, Thorina Boenke, Ching‐Yao Yang, Sagar, Laura Arrigoni, Kevin Dalgaard, Raffaele Teperino, Lennart Enders, Madhan Selvaraj, Marius Ruf, Sunil Jayaramaiah Raja, Huafeng Xie, Ulrike Boenisch, Stuart H. Orkin, Francis C. Lynn, Brad G. Hoffman, Dominic Grün, Tanya Vavouri, Adelheid Lempradl, J. Andrew Pospisilik
Software Mentions: 7
Published: almost 6 years ago

10.7717/peerj.2888

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
Cited by: 67
Author(s): Xun Zhu, Travers Ching, Xinghua Pan, Sherman M. Weissman, Lana X. Garmire
Software Mentions: 7
Published: over 7 years ago

10.1111/pbi.13205

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass
Cited by: 45
Author(s): Linkai Huang, Guangyan Feng, Haidong Yan, Zhongren Zhang, B. Shaun Bushman, Jianping Wang, Aureliano Bombarely, Mingzhou Li, Zhongfu Yang, Gang Nie, Wengang Xie, Lei Xu, Peilin Chen, Xinxin Zhao, Wenkai Jiang, Xinquan Zhang
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41598-020-73391-8

Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee
Cited by: 36
Author(s): Meaghan L. Pimsler, Kennan Oyen, James D. Herndon, Jason M. Jackson, James P. Strange, Michael E. Dillon, Jeffrey D. Lozier
Software Mentions: 7
Published: over 3 years ago

10.1186/s12859-017-1974-4

CORNAS: coverage-dependent RNA-Seq analysis of gene expression data without biological replicates
Cited by: 14
Author(s): Joel Zi-Bin Low, Tsung Fei Khang, Martti T. Tammi
Software Mentions: 7
Published: over 6 years ago

10.1186/s12864-017-3662-1

Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals
Cited by: 18
Author(s): Masahiro Uesaka, Kiyokazu Agata, Takao Oishi, Kinichi Nakashima, Takuya Imamura
Software Mentions: 7
Published: about 7 years ago

10.7717/peerj.644

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
Cited by: 73
Author(s): Olga Golosova, Ross Henderson, Yuriy Vaskin, Andrei Gabrielian, German Grekhov, Vijayaraj Nagarajan, Andrew J. Oler, Mariam Quiñones, Darrell E. Hurt, Mikhail Fursov, Yentram Huyen
Software Mentions: 7
Published: over 9 years ago

10.1136/jitc-2020-000778

M1^hottumor-associated macrophages boost tissue-resident memory T cells infiltration and survival in human lung cancer
Cited by: 75
Author(s): Eva M. Garrido-Martín, Toby Mellows, James Clarke, Anusha-Preethi Ganesan, Oliver Wood, Angelica Cazaly, Grégory Seumois, Serena Chee, Aiman Alzetani, Emma V. King, Catherine C. Hedrick, Gareth J. Thomas, Peter S. Friedmann, Christian Ottensmeier, Pandurangan Vijayanand, Tilman Sánchez-Elsner
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-020-77727-2

Gene expression in diapausing rotifer eggs in response to divergent environmental predictability regimes
Cited by: 21
Author(s): Eva Tarazona, José Ignacio Lucas-Lledó, Marı́a José Carmona, Eduardo M. García‐Roger
Software Mentions: 7
Published: over 3 years ago

10.1093/bib/bbx143

Bioinformatics for precision oncology
Cited by: 49
Author(s): Jochen Singer, Anja Irmisch, Hans‐Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
Software Mentions: 7
Published: over 6 years ago

10.1186/s13287-020-01823-3

Multiomics global landscape of stemness-related gene clusters in adipose-derived mesenchymal stem cells
Cited by: 8
Author(s): Guan-Ming Lu, Yong-Xian Rong, Zheng Liang, Dong-Lin Hunag, Yuju Ma, Zhizhai Luo, Fengyao Wu, Xinheng Liu, Yu Liu, Steven Mo, Zhongquan Qi, Hong-Mian Li
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13062-016-0169-7

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
Cited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: over 7 years ago

10.1186/s12859-018-2353-5

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data
Cited by: 81
Author(s): Roelof J.C. Kluin, Kristel Kemper, Thomas Kuilman, Julian R. de Ruiter, Vivek Iyer, Josep V. Forment, Paulien Cornelissen-Steijger, Iris de Rink, Petra ter Brugge, Ji‐Ying Song, Sjoerd Klarenbeek, Ultan McDermott, Jos Jonkers, Arno Velds, David J. Adams, Daniel S. Peeper, Oscar Krijgsman
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-018-4934-0

Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola
Cited by: 30
Author(s): Xiaofei Liang, Shengping Shang, Qiuyue Dong, Bo Wang, Rong Zhang, Mark L. Gleason, Guangyu Sun
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-018-24863-5

Long non-coding RNAs involved in the regulatory network during porcine pre-implantation embryonic development and iPSC induction
Cited by: 15
Author(s): Zhong Liu, Haiyuan Mu, Bingqiang Wen, Wei Zhang, Qingqing Wei, Ge Gao, Jianyong Han, Suying Cao
Software Mentions: 7
Published: about 6 years ago

10.3390/jof7090700

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi
Cited by: 3
Author(s): Grace N. Ijoma, Sylvie M Heri, Tonderayi Matambo, Memory Tekere
Software Mentions: 7
Published: over 2 years ago

10.1371/journal.ppat.1005438

Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression
Cited by: 42
Author(s): Jason Lamontagne, Joshua Chang Mell, Michael J. Bouchard
Software Mentions: 7
Published: about 8 years ago

10.1186/gb-2013-14-2-r18

The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila
Cited by: 29
Author(s): Tobias Kockmann, Moritz Gerstung, Tommy Beat Schlumpf, Zhu Xhinzhou, Daniel Heß, Niko Beerenwinkel, Christian Beisel, Renato Paro
Software Mentions: 7
Published: over 11 years ago

10.1186/s13040-016-0099-z

SePIA: RNA and small RNA sequence processing, integration, and analysis
Cited by: 22
Author(s): Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 7
Published: almost 8 years ago

10.1186/s12915-020-0752-3

Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells
Cited by: 33
Author(s): Donnchadh S. Dunican, Heidi K. Mjoseng, Leanne Duthie, Ilya M. Flyamer, Wendy A. Bickmore, Richard R. Meehan
Software Mentions: 7
Published: about 4 years ago

10.1186/1471-2105-16-S13-S7

Enhancing cancer clonality analysis with integrative genomics
Cited by: 6
Author(s): Erich A. Peterson, Michael Bauer, Shweta S. Chavan, Cody Ashby, Niels Weinhold, Christoph Heuck, Gareth J. Morgan, Donald J. Johann
Software Mentions: 7
Published: over 8 years ago

10.1186/1471-2164-14-204

RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome
Cited by: 63
Author(s): Yvan Wenger, Brigitte Galliot
Software Mentions: 7
Published: over 11 years ago

10.1371/journal.pone.0083984

Characterizing the Infection-Induced Transcriptome of Nasonia vitripennis Reveals a Preponderance of Taxonomically-Restricted Immune Genes
Cited by: 34
Author(s): Timothy B. Sackton, John H. Werren, Andrew G. Clark
Software Mentions: 7
Published: over 10 years ago

10.1186/1471-2229-13-213

Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17
Cited by: 12
Author(s): Claude Urbany, Andreas Benke, Johanna Marsian, Bruno Huettel, Richard Reinhardt, Benjamin Stich
Software Mentions: 7
Published: over 10 years ago

10.1038/srep41531

Transcriptomic analysis of common carp anterior kidney during Cyprinid herpesvirus 3 infection: Immunoglobulin repertoire and homologue functional divergence
Cited by: 23
Author(s): Matthew J. Neave, Agus Sunarto, Kenneth A. McColl
Software Mentions: 7
Published: over 7 years ago

10.1186/s12859-019-2684-x

From trash to treasure: detecting unexpected contamination in unmapped NGS data
Cited by: 42
Author(s): Mara Sangiovanni, Ilaria Granata, Amarinder Singh Thind, Mario Rosario Guarracino
Software Mentions: 7
Published: about 5 years ago

10.1186/1471-2164-15-702

Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves
Cited by: 58
Author(s): Adrienne N. Moran Lauter, Gregory A. Peiffer, Tao Yin, Steven A. Whitham, Dianne Cook, Randy C. Shoemaker, Michelle A. Graham
Software Mentions: 7
Published: over 9 years ago