bioconductor: GenomicFeatures | Projects

10.1007/s00401-019-02109-6

Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases
Cited by: 37
Author(s): Elena Perenthaler, Anita Nikoncuk, Soheil Yousefi, Woutje M. Berdowski, Maysoon Alsagob, Ivan Čapo, Herma C. van der Linde, Paul van den Berg, Edwin H. Jacobs, Darija Putar, Mehrnaz Ghazvini, Eleonora Aronica, Wilfred F. J. van IJcken, Walter G. de Valk, Evita Medici-van den Herik, Marjon van Slegtenhorst, Lauren Brick, Mariya Kozenko, Jennefer N. Kohler, Jonathan A. Bernstein, Kristin G. Monaghan, Amber Begtrup, Rebecca Torene, Amna Al Futaisi, Fathiya Al Murshedi, Renjith Mani, Faisal Al Azri, Erik‐Jan Kamsteeg, Majid Mojarrad, Atieh Eslahi, Zaynab Khazaei, Fateme Massinaei Darmiyan, Mohammad Doosti, Ehsan Ghayoor Karimiani, Jana Vandrovcová, Faisal Zafar, Nuzhat Rana, Krishna Kumar Kandaswamy, Jozef Hertecant, Péter Bauer, Mohammed A. AlMuhaizea, Mustafa A. Salih, Mazhor Aldosary, Rawan Almass, Laila AlQuait, Wafa Qubbaj, Serdar Coşkun, Khaled O. Alahmadi, Muddathir H. Hamad, Salem Alwadaee, Khalid Awartani, Anas Dababo, Futwan Al‐Mohanna, Dilek Çolak, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Murat Günel, A. Gülhan Ercan-Şençiçek, Gouri Rao Passi, Huma Arshad Cheema, Stéphanie Efthymiou, Henry Houlden, Aida M. Bertoli‐Avella, Alice S. Brooks, Kyle Retterer, Reza Maroofian, Namik Kaya, Tjakko J. van Ham, Tahsin Stefan Barakat
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-021-07627-w

Draft genome of a biparental beetle species, Lethrus apterus
Cited by: 0
Author(s): Nikolett Nagy, R. Rácz, Oliver Rimington, Szilárd Póliska, Pablo Orozco‐terWengel, Michael William Bruford, Zoltán Barta
Software Mentions: 4
Published: over 3 years ago

10.1155/2018/1351964

Topological Characterization of Human and Mouse m5C Epitranscriptome Revealed by Bisulfite Sequencing
Cited by: 16
Author(s): Zhen Wei, Panneerdoss Subbarayalu, Santosh Timilsina, Jingting Zhu, Tabrez A. Mohammad, Zhi-Liang Lu, João Pedro de Magalhães, Yidong Chen, Rong Rong, Yufei Huang, Manjeet K. Rao, Jia Meng
Software Mentions: 4
Published: over 6 years ago

10.1007/s00253-019-09904-x

Effect of ethanol supplementation on the transcriptional landscape of bionanocellulose producer Komagataeibacter xylinus E25
Cited by: 30
Author(s): Małgorzata Ryngajłło, Paulina Jacek, Izabela Cielecka, Halina Kalinowska, Stanisław Bielecki
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-015-0620-2

AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing
Cited by: 13
Author(s): Jesper R. Gådin, Ferdinand M. van’t Hooft, Per Eriksson, Lasse Folkersen
Software Mentions: 4
Published: over 9 years ago

10.18632/oncotarget.11733

DMBA induced mouse mammary tumors display high incidence of activating Pik3caH1047 and loss of function Pten mutations
Cited by: 45
Author(s): Martı́n C. Abba, Yi Zhong, Jae-Ho Lee, Hyunsuk Kil, Yue Lu, Yoko Takata, Melissa S. Simper, Sally Gaddis, Jianjun Shen, C. Marcelo Aldaz
Software Mentions: 4
Published: about 8 years ago

10.3390/ijms19082285

Effect of ACTH and hCG on the Expression of Gonadotropin-Inducible Ovarian Transcription Factor 1 (Giot1) Gene in the Rat Adrenal Gland
Cited by: 6
Author(s): Karol Jopek, Marianna Tyczewska, Manjunath Ramanjaneya, Marta Szyszka, Piotr Celichowski, Paulina Milecka, Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.02929

Transcriptional Landscape of a blaKPC-2 Plasmid and Response to Imipenem Exposure in Escherichia coli TOP10
Cited by: 11
Author(s): Agnès B Jousset, Isabelle Rosinski‐Chupin, Julie Takissian, Philippe Glaser, Rémy A. Bonnin, Thierry Naas
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2021.652901

Comparative Transcriptome Analyses Reveal a Transcriptional Landscape of Human Silicosis Lungs and Provide Potential Strategies for Silicosis Treatment
Cited by: 15
Author(s): Junling Pang, Yunbo Luo, Wei Dong, Zhujie Cao, Xianmei Qi, Meiyue Song, Ying Liu, Zhaoguo Li, Jin Zhang, Baicun Li, Jingyu Chen, Jing Wang, Chen Wang
Software Mentions: 4
Published: over 3 years ago

10.3390/plants9070864

Exploring Mechanisms of Quantitative Resistance to Leptosphaeria maculans (Blackleg) in the Cotyledons of Canola (Brassica napus) Based on Transcriptomic and Microscopic Analyses
Cited by: 6
Author(s): Michelle Hubbard, Chun Zhai, Gary Peng
Software Mentions: 3
Published: over 4 years ago

10.1038/srep37536

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle
Cited by: 24
Author(s): Alejandra Rougon‐Cardoso, Mitzi Flores-Ponce, Hilda E. Ramos-Aboites, Christian E. Martínez-Guerrero, Youjin Hao, Luís Cunha, Jonathan Alejandro Rodríguez-Martínez, Cesaré Ovando-Vázquez, José Roberto Bermúdez-Barrientos, Cei Abreu‐Goodger, Noelina Hernández, Nélson Simões, Rafaél Montiel
Software Mentions: 3
Published: almost 8 years ago

10.1002/pld3.240

Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater
Cited by: 10
Author(s): Rejbana Alam, Maureen Hummel, Euson Yeung, Anna M. Locke, John Carlos I. Ignacio, Miriam D. Baltazar, Zhenyu Jia, Ismail Am, Endang M. Septiningsih, Julia Bailey‐Serres
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.581660

The Effect of Iodine-Containing Nano-Micelles, FS-1, on Antibiotic Resistance, Gene Expression and Epigenetic Modifications in the Genome of Multidrug Resistant MRSA Strain Staphylococcus aureus ATCC BAA-39
Cited by: 9
Author(s): Oleg N. Reva, Ilya S. Korotetskiy, Monique Joubert, Sergey V. Shilov, Ardak B. Jumagaziyeva, Natalya A. Suldina, А. И. Ильин
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-021-81030-z

Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika
Cited by: 4
Author(s): Christoph Fischer, Stephan Koblmüller, Christine Börger, Gabriele Michelitsch, Slave Trajanoski, Christian Schlötterer, Christian Godballe, Gerhard Thallinger, Christian Sturmbauer
Software Mentions: 3
Published: over 3 years ago

10.1186/1753-6561-8-S1-S88

Gene analysis for longitudinal family data using random-effects models
Cited by: 3
Author(s): Jeanine J. Houwing-Duistermaat, Quinta Helmer, Bruna Balliu, Erik B. van den Akker, Roula Tsonaka, Hae‐Won Uh
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-019-6313-x

Secretory RING finger proteins function as effectors in a grapevine galling insect
Cited by: 13
Author(s): Chaoyang Zhao, Claude Rispe, Paul D. Nabity
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-015-1583-4

Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae
Cited by: 44
Author(s): Isabelle Rosinski‐Chupin, Elisabeth Sauvage, Odile Sismeiro, Adrien Villain, Violette Da Cunha, Marie-Elise Caliot, Marie‐Agnès Dillies, Patrick Trieu-Cuot, Philippe Bouloc, Marie‐Frédérique Lartigue, Philippe Glaser
Software Mentions: 3
Published: over 9 years ago

10.1186/gb-2014-15-6-r86

IVT-seq reveals extreme bias in RNA sequencing
Cited by: 135
Author(s): Nicholas F. Lahens, İbrahim Halil Kavaklı, Ray Zhang, Katharina E. Hayer, Michael B. Black, Hannah Dueck, Angel Pizarro, Junhyong Kim, Rafael A. Irizarry, Russell S. Thomas, Gregory R. Grant, John B. Hogenesch
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12862-018-1199-9

The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish
Cited by: 28
Author(s): Masato Yoshizawa, Alexander Settle, Meredith C. Hermosura, Lillian J. Tuttle, Nicolas Cetraro, Courtney N. Passow, Suzanne E. McGaugh
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.00615

A Long Non-coding RNA, LOC157273, Is an Effector Transcript at the Chromosome 8p23.1-PPP1R3B Metabolic Traits and Type 2 Diabetes Risk Locus
Cited by: 14
Author(s): Alisa K. Manning, Anton Scott Goustin, Erica L. Kleinbrink, Pattaraporn Thepsuwan, Juan Cai, Donghong Ju, Aaron Leong, Miriam S. Udler, James Brown, Mark O. Goodarzi, Jerome I. Rotter, Robert Sladek, James B. Meigs, Leonard Lipovich
Software Mentions: 3
Published: over 4 years ago

10.1093/database/baaa071

Exploring functionally annotated transcriptional consensus regulatory elements with CONREL
Cited by: 1
Author(s): Davide Dalfovo, Samuel Valentini, Alessandro Romanel
Software Mentions: 3
Published: almost 5 years ago

10.1186/s40246-021-00318-3

Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability
Cited by: 6
Author(s): Xi Long, Hong Xue
Software Mentions: 3
Published: over 3 years ago

10.3390/genes10020138

Spatio-Temporal Transcriptional Dynamics of Maize Long Non-Coding RNAs Responsive to Drought Stress
Cited by: 34
Author(s): Junling Pang, Xia Zhang, Xuhui Ma, Jun Zhao
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0128969

Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene
Cited by: 29
Author(s): Ben Dorshorst, Corneliu Hénégar, Xiaoping Liao, Markus Sällman Almén, Carl-Johan Rubin, Shosuke Ito, Kazumasa Wakamatsu, Paul Stothard, Brian Van Doormaal, Graham Plastow, Gregory S. Barsh, Leif Andersson
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0160975

Understanding the Pathogenicity of Burkholderia contaminans, an Emerging Pathogen in Cystic Fibrosis
Cited by: 28
Author(s): Jaroslav Nunvář, Lucie Kalferstová, Ruhi A. M. Bloodworth, Michal Kolář, José Degrossi, S. Lubovich, Silvia T. Cardona, Pavel Dřevı́nek
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2021.637956

A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes
Cited by: 7
Author(s): Cerys Jones, Jose De Vega, Margaret Worthington, Ann Thomas, Dagmara Gasior, John A. Harper, John Doonan, Yuan Fu, Marina Bosch, Fiona Corke, Jacobo Arango, Juan Andrés Cardoso, Juan de la Cruz Jiménez, Ian Armstead, Narcís Fernández-Fuentes
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.ppat.1003962

Reversible Silencing of Cytomegalovirus Genomes by Type I Interferon Governs Virus Latency
Cited by: 55
Author(s): Franziska Dağ, Lars Dölken, Julia Holzki, Anja Drabig, Adrien Weingärtner, Johannes Schwerk, Stefan Lienenklaus, Ianina Conte, Robert Geffers, Colin Davenport, Ulfert Rand, Mario Köster, Siegfried Weiß, Barbara Adler, Dagmar Wirth, Martin Messerle, Hansjörg Hauser, Luka Čičin‐Šain
Software Mentions: 2
Published: almost 11 years ago

10.3389/fendo.2021.713961

Neuromedins NMU and NMS: An Updated Overview of Their Functions
Cited by: 18
Author(s): Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-019-41234-w

Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis
Cited by: 49
Author(s): Emily J. Blair, Titouan Bonnot, Maureen Hummel, Erika Hay, Jill M. Marzolino, Ivan A. Quijada, Dawn H. Nagel
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12050660

Sorghum Brown Midrib19 (Bmr19) Gene Links Lignin Biosynthesis to Folate Metabolism
Cited by: 7
Author(s): Adedayo Adeyanju, Scott E. Sattler, Patrick J. Rich, Luis A. Rivera-Burgos, Xiaochen Xu, Gebisa Ejeta
Software Mentions: 2
Published: over 3 years ago

10.1038/s41597-019-0136-0

Temporally replicated DNA methylation patterns in great tit using reduced representation bisulfite sequencing
Cited by: 16
Author(s): Hannu Mäkinen, Heidi M. Viitaniemi, Marcel E. Visser, Irene Verhagen, Kees van Oers, Arild Husby
Software Mentions: 2
Published: over 5 years ago

10.3390/nu11020407

Next-Generation Sequencing Identifies Polyunsaturated Fatty Acid Responsive Genes in the Juvenile Rat Cerebellum
Cited by: 1
Author(s): Aaron A. Mehus, Aaron M. Dickey, Timothy P. L. Smith, Kathleen M. Yeater, Matthew J. Picklo
Software Mentions: 2
Published: almost 6 years ago

10.1093/gbe/evw004

Dosage compensation in the African malaria mosquitoAnopheles gambiae
Cited by: 26
Author(s): Graham Rose, Elzbieta Krzywińska, Jan Kim, Loic Revuelta, Luca Ferretti, Jaroslaw Krzywinski
Software Mentions: 2
Published: almost 9 years ago

10.1155/2014/893501

AmalgamScope: Merging Annotations Data across the Human Genome
Cited by: 0
Author(s): Georgia Tsiliki, Konstantinos Tsaramirsis, Σοφία Κοσσίδα
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0150427

Information Thermodynamics of Cytosine DNA Methylation
Cited by: 13
Author(s): Robersy Sánchez, Sally A. Mackenzie
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.29815

Context-dependent deposition and regulation of mRNAs in P-bodies
Cited by: 58
Author(s): Congwei Wang, Fabian Schmich, Sumana Srivatsa, Julie Weidner, Niko Beerenwinkel, Anne Spang
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13073-016-0366-0

A case study of an integrative genomic and experimental therapeutic approach for rare tumors: identification of vulnerabilities in a pediatric poorly differentiated carcinoma
Cited by: 15
Author(s): Filemon S. Dela Cruz, Daniel Diolaiti, Andrew T. Turk, Allison Rainey, Alberto Ambesi-Impiombato, Stuart Andrews, Mahesh Mansukhani, Péter L. Nagy, Mariano J. Alvarez, Andrea Califano, F. Forouhar, Beata Modzelewski, Chelsey M. Mitchell, Darrell J. Yamashiro, Lianna J. Marks, Julia Glade Bender, Andrew L. Kung
Software Mentions: 2
Published: about 8 years ago

10.1186/s12859-016-1293-1

RGmatch: matching genomic regions to proximal genes in omics data integration
Cited by: 11
Author(s): P. Furió-Tarí, Ana Conesa, Sonia Tarazona
Software Mentions: 2
Published: about 8 years ago

10.1186/s12859-021-04243-z

Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants
Cited by: 1
Author(s): Ching-Yu Shih, Amrita Chattopadhyay, Chien-Hui Wu, Yu‐Wen Tien, Tzu-Pin Lu
Software Mentions: 1
Published: over 3 years ago

10.3390/plants10050946

Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula
Cited by: 5
Author(s): José Luís Carballo, Diego Zappacosta, G. Marconi, Jimena Gallardo, Marco Di Marsico, Cristian Gallo, Mario Cáccamo, Emidio Albertini, Viviana Echenique
Software Mentions: 1
Published: over 3 years ago

Projects: bioconductor: GenomicFeatures

Papers Mentioning GenomicFeatures 141