pypi: browser | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1009613

A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila
Cited by: 4
Author(s): Clara Poupault, Diane Choi, Khanh Lam-Kamath, Deepshe Dewett, Ansa Razzaq, Joseph Bunker, Alexis Perry, Irene Cho, Jens Rister
Software Mentions: 2
Published: over 5 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 13 years ago

10.1186/1471-2105-13-2

ABrowse - a customizable next-generation genome browser framework
Cited by: 18
Author(s): Lei Kong, Jun Wang, Shuqi Zhao, Xiaocheng Gu, Jianxun Luo, Ge Gao
Software Mentions: 2
Published: almost 15 years ago

10.3390/ijms17111848

IBTK Differently Modulates Gene Expression and RNA Splicing in HeLa and K562 Cells
Cited by: 10
Author(s): Giuseppe Fiume, Annarita Scialdone, Francesca Rizzo, Maria Rosaria De Filippo, Carmelo Laudanna, Fabio Albano, Gaetanina Golino, Eleonora Vecchio, Marilena Pontoriero, Selena Mimmi, Simona Ceglia, Antonio Pisano, Enrico Iaccino, Camillo Palmieri, Sergio Paduano, Giuseppe Viglietto, Alessandro Weisz, Giuseppe Scala, Ileana Quinto
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0220378

Coordinated transcriptional regulation by thyroid hormone and glucocorticoid interaction in adult mouse hippocampus-derived neuronal cells
Cited by: 12
Author(s): Pia Bagamasbad, Jose Ezekiel C. Espina, Joseph R. Knoedler, Arasakumar Subramani, Ariel J. Harden, Robert J. Denver
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0117415

A Non-Parametric Peak Calling Algorithm for DamID-Seq
Cited by: 5
Author(s): Renhua Li, Leonie U. Hempel, Tingbo Jiang
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-9-21

LeARN: a platform for detecting, clustering and annotating non-coding RNAs
Cited by: 10
Author(s): Céline Noirot, Christine Gaspin, Thomas Schiex, Jérôme Gouzy
Software Mentions: 2
Published: almost 19 years ago

10.1371/journal.pgen.1005946

MiR144/451 Expression Is Repressed by RUNX1 During Megakaryopoiesis and Disturbed by RUNX1/ETO
Cited by: 17
Author(s): Nicole Kohrs, Stephan Kolodziej, Olga N. Kuvardina, Julia Herglotz, Jasmin Yillah, Stefanie Herkt, Alexander Piechatzek, Gabriela Salinas Riester, Thomas Lingner, Christian Wichmann, Halvard Bönig, Erhard Seifried, Uwe Platzbecker, Hind Medyouf, Manuel Grez, Jörn Lausen
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1008036

LINE-2 transposable elements are a source of functional human microRNAs and target sites
Cited by: 42
Author(s): Rebecca Petri, Per Ludvik Brattås, Yogita Sharma, Marie E. Jönsson, Karolina Pircs, Johan Bengzon, Johan Jakobsson
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0161414

Neuronal Calcium Sensor 1 Has Two Variants with Distinct Calcium Binding Characteristics
Cited by: 8
Author(s): Baisheng Wang, Göran Ramin Boeckel, Larry Huynh, Lien D. Nguyen, Wenxiang Cao, Enrique M. De La Cruz, Edward Kaftan, Barbara E. Ehrlich
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pgen.1005702

Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish
Cited by: 70
Author(s): Adi Shamay-Ramot, Khen Khermesh, Hagit T. Porath, Michal Barák, Yishay Pinto, Chaim Wachtel, Alona Zilberberg, Tali Lerer-Goldshtein, Sol Efroni, Erez Y. Levanon, Lior Appelbaum
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12870-014-0412-2

NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome
Cited by: 16
Author(s): Hamed Bostan, Maria Luisa Chiusano
Software Mentions: 2
Published: almost 12 years ago

10.3390/ijms19061722

Systematic Analysis of Long Non-Coding RNAs and mRNAs in the Ovaries of Duroc Pigs During Different Follicular Stages Using RNA Sequencing
Cited by: 30
Author(s): Yi Liu, Mengxun Li, Xiaochen Bo, Tao Li, Ligeng Ma, Tenjiao Zhai, Tao Huang
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-014-0412-0

Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs
Cited by: 10
Author(s): Anagha Joshi
Software Mentions: 2
Published: almost 12 years ago

10.3390/biology9070157

Role of B Cell Lymphoma 2 in the Regulation of Liver Fibrosis in miR-122 Knockout Mice
Cited by: 5
Author(s): Kun-Yu Teng, Juan M. Barajas, Peng Hu, Samson T. Jacob, Kalpana Ghoshal
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-6087-1

Α de novo 3.8-Mb inversion affecting the EDA and XIST genes in a heterozygous female calf with generalized hypohidrotic ectodermal dysplasia
Cited by: 5
Author(s): Clémentine Escouflaire, Emmanuelle Rebours, Mathieu Charles, Sébastien Orellana, Margarita Cano, Julie Rivière, Cécile Grohs, Hélène Hayes, Aurélien Capitan
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0099069

Genome at Juncture of Early Human Migration: A Systematic Analysis of Two Whole Genomes and Thirteen Exomes from Kuwaiti Population Subgroup of Inferred Saudi Arabian Tribe Ancestry
Cited by: 33
Author(s): Osama Alsmadi, Sumi Elsa John, Gaurav Thareja, Prashantha Hebbar, Dinu Antony, Kazem Behbehani, Thangavel Alphonse Thanaraj
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1002384

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
Cited by: 892
Author(s): A. P. Jason de Koning, Wanjun Gu, Todd A. Castoe, Mark A. Batzer, David D. Pollock
Software Mentions: 2
Published: almost 15 years ago

10.3390/biology1020370

Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP
Cited by: 59
Author(s): Michał T. Lorenc, Satomi Hayashi, Jiri Stiller, S. Hong Lee, Sahana Manoli, Pradeep Ruperao, Paul Visendi, Paul J. Berkman, Kaitao Lai, Jacqueline Batley, David Edwards
Software Mentions: 2
Published: about 14 years ago

10.3390/ijms21061908

Peripheral Circulating Exosomal miRNAs Potentially Contribute to the Regulation of Molecular Signaling Networks in Aging
Cited by: 13
Author(s): Hongxia Zhang, Kunlin Jin
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1006682

Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus
Cited by: 37
Author(s): Anchel de Jaime-Soguero, Francesco Aulicino, Gökhan Ertaylan, Anna Griego, Aniello Cerrato, Aravind Tallam, Antonio del Sol, María Pía Cosma, Frederic Lluı́s
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0054359

Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data
Cited by: 37
Author(s): Анна Герасимова, Lukas Chávez, Bin Li, Grégory Seumois, Jason A. Greenbaum, Anjana Rao, Pandurangan Vijayanand, Bjoern Peters
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0007479

Probe-Level Analysis of Expression Microarrays Characterizes Isoform-Specific Degradation during Mouse Oocyte Maturation
Cited by: 29
Author(s): Jesse Salisbury, Keith W. Hutchison, Karen Wigglesworth, John J. Eppig, Joel H. Graber
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0214816

SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome
Cited by: 21
Author(s): Kerstin Neininger, Tobias Marschall, Volkhard Helms
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0018180

Exploring Uncoupling Proteins and Antioxidant Mechanisms under Acute Cold Exposure in Brains of Fish
Cited by: 89
Author(s): Yung‐Che Tseng, Ruo Dong Chen, Magnus Lucassen, Maike Schmidt, Ralf Dringen, Doris Abele, Pung Pung Hwang
Software Mentions: 2
Published: over 15 years ago

10.3390/ijms21165831

BrassicaEDB: A Gene Expression Database for Brassica Crops
Cited by: 37
Author(s): Haoyu Chao, Li Tian, Chaoyu Luo, Hualei Huang, Yingfei Ruan, Xiaodong Li, Yue Niu, Yonghai Fan, Wei Sun, Kai Zhang, Jiana Li, Cunmin Qu, Kun Lü
Software Mentions: 2
Published: over 6 years ago

10.1186/1755-8794-2-31

Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease
Cited by: 8
Author(s): Charles G. Danko, Arkady M. Pertsov
Software Mentions: 2
Published: over 17 years ago

10.3390/ani10081399

TGF-β1-Mediated FDNCR1 Regulates Porcine Preadipocyte Differentiation via the TGF-β Signaling Pathway
Cited by: 6
Author(s): Zhe Zhang, Yu Meng, Fei Gao, Yue Xiao, Yi Zheng, Hao-Qi Wang, Yan Gao, Hao Jiang, Bao Yuan
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1006296

Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer
Cited by: 37
Author(s): Jian Gong, Carolyn M. Hutter, Polly A. Newcomb, Cornelia M. Ulrich, Stephanie A. Bien, Peter T. Campbell, John A. Baron, Sonja I. Berndt, Stéphane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang–Claude, Mengmeng Du, David Duggan, Jane C. Figueiredo, Steven Gallinger, Edward Giovannucci, Robert W. Haile, Tabitha A. Harrison, Richard B. Hayes, Michael Hoffmeister, John L. Hopper, Thomas J. Hudson, Jihyoun Jeon, Mark A. Jenkins, Jonathan Kocarnik, Sébastien Küry, Loı̈c Le Marchand, Yi Lin, Noralane M. Lindor, Reiko Nishihara, Shuji Ogino, John D. Potter, Anja Rudolph, Robert E. Schoen, Petra Schrotz‐King, Daniela Seminara, Martha L. Slattery, Stephen N. Thibodeau, Mark Thornquist, Réka Tóth, Robert B. Wallace, Emily White, Shuo Jiao, Mathieu Lemire, Li Hsu, Ulrike Peters
Software Mentions: 2
Published: about 10 years ago

10.18632/genesandcancer.113

Pathway analysis of bladder cancer genome-wide association study identifies novel pathways involved in bladder cancer development
Cited by: 12
Author(s): Meng Chen, Nathaniel Rothman, Yuanqing Ye, Jian Gu, Paul Scheet, Maosheng Huang, David W. Chang, Colin P.N. Dinney, Debra T. Silverman, Jonine D. Figueroa, Stephen J. Chanock, Xifeng Wu
Software Mentions: 2
Published: over 10 years ago

10.3390/genes12091388

A Recurrent De Novo Terminal Duplication of 14q32 in Korean Siblings Associated with Developmental Delay and Intellectual Disability, Growth Retardation, Facial Dysmorphism, and Cerebral Infarction: A Case Report and Literature Review
Cited by: 2
Author(s): Ji Yoon Han, Joonhong Park
Software Mentions: 2
Published: about 5 years ago

10.3390/v9070161

Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome
Cited by: 10
Author(s): Przemysław Decewicz, Monika Radlińska, Łukasz Dziewit
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-15-1060

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor
Cited by: 64
Author(s): Michael N Romanov, Marta Farré, Pamela E Lithgow, Katie E. Fowler, Benjamin M. Skinner, Rebecca E O'Connor, Gothami Fonseka, Niclas Backström, Yoichi Matsuda, Chizuko Nishida, Peter Houde, Erich D. Jarvis, Hans Ellegren, David W. Burt, Denis M. Larkin, Darren K. Griffin
Software Mentions: 2
Published: almost 12 years ago

10.1002/dvg.22963

Transcriptional regulation of the proto‐oncogeneZfp521by SPI1 (PU.1) and HOXC13
Cited by: 11
Author(s): Ming Yu, Salma Aldallal, Latifa Al‐Haj, Shiraj Panjwani, Akina S. McCartney, Sarah Edwards, Pooja Manjunath, Catherine Walker, Alexander Awgulewitsch, Kathryn E. Hentges
Software Mentions: 2
Published: about 10 years ago

10.3390/ijms21249701

Origin and Evolution of the Human Bcl2-Associated Athanogene-1 (BAG-1)
Cited by: 4
Author(s): Peter Q. Nguyen, Kyle Hess, Larissa Smulders, Dat Le, Carolina Briseno, Christina M Chavez, Nikolas Nikolaidis
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms22020602

Transposable Elements and Teleost Migratory Behaviour
Cited by: 8
Author(s): Elisa Carotti, Federica Carducci, Adriana Canapa, Marco Barucca, Samuele Greco, Marco Gerdol, Maria Assunta Biscotti
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12711-020-0528-9

pCADD: SNV prioritisation in Sus scrofa
Cited by: 16
Author(s): Christian Groß, Martijn F.L. Derks, Hendrik Jan Megens, Mirte Bosse, M.A.M. Groenen, Marcel J. T. Reinders, Dick de Ridder
Software Mentions: 2
Published: almost 7 years ago

10.1534/genetics.115.185363

Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae
Cited by: 27
Author(s): Katarzyna B. Hooks, Samina Naseeb, Steven J. Parker, Sam Griffiths-Jones, Daniela Delneri
Software Mentions: 2
Published: over 10 years ago

10.1186/gb-2006-7-7-r58

Cited by: 22
Author(s): Matthew D. Wilkerson, Shannon D. Schlueter, Volker Brendel
Software Mentions: 2
Published: almost 21 years ago

10.3390/v13091764

The Evolving Faces of the SARS-CoV-2 Genome
Cited by: 14
Author(s): Maria Schmidt, Mamoona Arshad, Stephan H. Bernhart, Siras Hakobyan, Arsen Arakelyan, Henry Loeffler‐Wirth, Hans Binder
Software Mentions: 2
Published: about 5 years ago

10.1186/gb-2006-7-s1-s9

Cited by: 59
Author(s): Jonathan Allen, William H. Majoros, Mihaela Pertea, Steven L. Salzberg
Software Mentions: 2
Published: almost 21 years ago

10.1186/1471-2148-9-286

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites
Cited by: 26
Author(s): Alan M. Moses
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pone.0000366

Human GLI3 Intragenic Conserved Non-Coding Sequences Are Tissue-Specific Enhancers
Cited by: 41
Author(s): Amir Ali Abbasi, Zissis Paparidis, Sajid Malik, Debbie K. Goode, Heather Callaway, Greg Elgar, Karl‐Heinz Grzeschik
Software Mentions: 2
Published: over 19 years ago

10.1371/journal.pgen.1000672

Genetic Determinants of Circulating Sphingolipid Concentrations in European Populations
Cited by: 185
Author(s): Andrew A. Hicks, Peter P. Pramstaller, Åsa Johansson, Véronique Vitart, Igor Rudan, Péter Ugocsai, Yurii S. Aulchenko, Christopher S. Franklin, Gerhard Liebisch, Jeanette Erdmann, Inger Jonasson, Irina V. Zorkoltseva, Cristian Pattaro, Caroline Hayward, Aaron Isaacs, Christian Hengstenberg, Susan Campbell, Carsten Gnewuch, A. Cecile J.W. Janssens, A. V. Kirichenko, Inke R. König, Fabio Marroni, Ozren Polašek, Ayşe Demirkan, Ivana Kolčić, Christine Schwienbacher, Wilmar Igl, Zrinka Biloglav, Jacqueline C. M. Witteman, Irene Pichler, Ghazal Zaboli, Tatiana I. Axenovich, Annette Peters, Stefan Schreiber, H‐Erich Wichmann, Heribert Schunkert, Nick Hastie, Ben A. Oostra, Sarah H. Wild, Thomas Meitinger, Ulf Gyllensten, Cornelia M. van Duijn, James F. Wilson, Alan F. Wright, Gerd Schmitz, Harry Campbell
Software Mentions: 2
Published: about 17 years ago

10.1186/1471-2105-11-382

Integration and visualization of systems biology data in context of the genome
Cited by: 35
Author(s): J. Christopher Bare, Tie Koide, David J Reiss, Dan Tenenbaum, Nitin S. Baliga
Software Mentions: 2
Published: over 16 years ago

10.3390/biology10060500

Gene Expression Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer
Cited by: 9
Author(s): Jeeyong Lee, Joshua Kwon, Dayeon Kim, Misun Park, Kwang‐Seok Kim, In-Hwa Bae, Hyunkyung Kim, Joonseog Kong, Younjoo Kim, Ui-Sup Shin, EunJu Kim
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-016-0938-4

Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators
Cited by: 12
Author(s): Marcin Piechota, Michał Korostyński, Joanna Ficek, Andrzej Tomski, Ryszard Przewłocki
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12862-018-1311-1

Rapid microevolution during recent range expansion to harsh environments
Cited by: 26
Author(s): Yiyong Chen, Noa Shenkar, Ping Ni, Ya‐Ping Lin, Shiguo Li, Aibin Zhan
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0171661

Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer
Cited by: 88
Author(s): Federica Conte, Giulia Fiscon, Matteo Chiara, Teresa Colombo, Lorenzo Farina, Paola Paci
Software Mentions: 2
Published: almost 10 years ago

10.1186/gb-2008-9-12-r170

FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease
Cited by: 75
Author(s): Rongrong Chen, Alex Morgan, Joel T. Dudley, Tarangini Deshpande, Li Li, Keiichi Kodama, An‐Jen Chiang, Atul J. Butte
Software Mentions: 2
Published: almost 19 years ago

10.7717/peerj.6028

Comprehensive tissue-specific transcriptome profiling of pineapple (Ananas comosus) and building an eFP-browser for further study
Cited by: 6
Author(s): Qi Mao, Chengjie Chen, Tongxin Xie, Aiping Luan, Chaoyang Liu, Yehua He
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0131296

BGD: A Database of Bat Genomes
Cited by: 3
Author(s): Jian‐an Fang, Xuan Wang, Shuo Mu, Shuyi Zhang, Dong Dong
Software Mentions: 2
Published: over 11 years ago

10.3390/ijms22168646

PPARγ-Induced Global H3K27 Acetylation Maintains Osteo/Cementogenic Abilities of Periodontal Ligament Fibroblasts
Cited by: 7
Author(s): Hang Yuan, Shigeki Suzuki, Shizu Hirata-Tsuchiya, Akiko Satô, Eiji Nemoto, Masahiro Saito, Hideki Shiba, Satoru Yamada
Software Mentions: 2
Published: over 5 years ago

10.2196/jmir.9644

Online Information Infrastructure Increases Inter-Rater Reliability of Medical Coders: A Quasi-Experimental Study (Preprint)
Cited by: 6
Author(s): Julian Varghese, Sarah Sandmann, Martin Dugas
Software Mentions: 2
Published: almost 9 years ago

10.1186/gb-2010-11-3-r34

Global and unbiased detection of splice junctions from RNA-seq data
Cited by: 87
Author(s): Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten
Software Mentions: 2
Published: almost 17 years ago

10.1186/gb-2010-11-2-r22

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
Cited by: 254
Author(s): Guoliang Li, Melissa J. Fullwood, Xu Han, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Vinsensius B. Vega, Pramila Ariyaratne, Yusoff Bin Mohamed, Hong Ooi, Chandana Tennakoon, Chia Lin Wei, Yijun Ruan, Wing-Kin Sung
Software Mentions: 2
Published: almost 17 years ago

10.1186/gb-2010-11-4-r36

Optimized design and data analysis of tag-based cytosine methylation assays
Cited by: 76
Author(s): Masako Suzuki, Jun Qiang, Daniel Lia, Marién Pascual, Andrew McLellan, John M. Greally
Software Mentions: 2
Published: almost 17 years ago

10.1186/gb-2010-11-4-r42

Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis
Cited by: 66
Author(s): Qiang Gan, Dustin E. Schones, Suk Ho Eun, Gang Wei, Kairong Cui, Keji Zhao, Xin Chen
Software Mentions: 2
Published: almost 17 years ago

10.7717/peerj.11052

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily
Cited by: 13
Author(s): Sushma Naithani, Daemon Dikeman, Priyanka Garg, Noor Al-Bader, Pankaj Jaiswal
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12081249

Proof of Gene Doping in a Mouse Model with a Human Erythropoietin Gene Transferred Using an Adenoviral Vector
Cited by: 7
Author(s): Takehito Sugasawa, Takuro Nakano, Shin‐ichiro Fujita, Yuki Matsumoto, Genki Ishihara, Kai Aoki, Koki Yanazawa, S. Ono, Shinsuke Tamai, Lev Manevich, Hiroshi Ueda, Noriyo Ishibashi, Kenshirou Tamai, Yasuharu Kanki, Yasuko Yoshida, Koichi Watanabe, Tohru Takemasa, Yasushi Kawakami, Kazuhiro Takekoshi
Software Mentions: 2
Published: about 5 years ago

10.1186/s12920-021-01007-9

Epigenetic landscapes of intracranial aneurysm risk haplotypes implicate enhancer function of endothelial cells and fibroblasts in dysregulated gene expression
Cited by: 5
Author(s): Kerry E. Poppenberg, Haley R Zebraski, Naval Avasthi, Muhammad Waqas, Adnan H. Siddiqui, James N. Jarvis, Vincent M. Tutino
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.6230

Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time
Cited by: 5
Author(s): Jonas S. Almeida, Janos Hajagos, Joel Saltz, Mary Saltz
Software Mentions: 2
Published: almost 8 years ago

10.2196/10227

What People “Like”: Analysis of Social Media Strategies Used by Food Industry Brands, Lifestyle Brands, and Health Promotion Organizations on Facebook and Instagram
Cited by: 106
Author(s): Karen Klassen, Emily S. Borleis, Louis Brennan, Mike Reid, Tracy A. McCaffrey, Megan S C Lim
Software Mentions: 2
Published: over 8 years ago

10.1186/s13293-017-0150-x

Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells
Cited by: 50
Author(s): Rachael J. Werner, Bryant M. Schultz, Jacklyn Huhn, Jaroslav Jelı́nek, Jozef Madžo, Nora Engel
Software Mentions: 2
Published: about 9 years ago

10.3390/genes12060870

Age Prediction of Human Based on DNA Methylation by Blood Tissues
Cited by: 5
Author(s): Jiansheng Zhang, Hongli Fu, Yan Xu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1005117

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis
Cited by: 20
Author(s): Erin Osborne Nishimura, Jay C. Zhang, Adam D. Werts, Bob Goldstein, Jason D. Lieb
Software Mentions: 2
Published: over 11 years ago

10.1186/gb-2013-14-6-r59

Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome
Cited by: 251
Author(s): Emanuela Sani, Paweł Herzyk, Giorgio Perrella, Vincent Colot, Anna Amtmann
Software Mentions: 2
Published: over 13 years ago

10.1186/s12864-016-3110-7

Short- and long-term effects of 56Fe irradiation on cognition and hippocampal DNA methylation and gene expression
Cited by: 47
Author(s): Soren Impey, Timothy Jopson, Carl Pelz, Amanuel Tafessu, Fatema Fareh, Damian G. Zuloaga, Tessa Marzulla, Lara Kirstie Riparip, Blair Stewart, Susanna Rosi, Mitchell S. Turker, Jacob Raber
Software Mentions: 2
Published: about 10 years ago

10.1186/s12859-016-0942-8

Intra- and interspecies gene expression models for predicting drug response in canine osteosarcoma
Cited by: 30
Author(s): Jared S. Fowles, Kristen C. Brown, Ann Hess, Dawn L. Duval, Daniel L. Gustafson
Software Mentions: 2
Published: over 10 years ago

10.3390/genes12020221

Evaluation of OpenArray™ as a Genotyping Method for Forensic DNA Phenotyping and Human Identification
Cited by: 7
Author(s): Michele Reni, Giulio Puleri, Valeria Errichiello, L Manzo, Laura Luzzi, Saverio Potenza, Claudia Strafella, Cristina Peconi, Fabio Nicastro, Valerio Caputo, Emiliano Giardina
Software Mentions: 2
Published: almost 6 years ago

10.1038/mt.2016.112

Long Non-coding RNA BGas Regulates the Cystic Fibrosis Transmembrane Conductance Regulator
Cited by: 26
Author(s): Sheena Saayman, Amanda Ackley, Jon Burdach, Matthew Clemson, Dieter C. Gruenert, Kiyoshi Tachikawa, Pad Chivukula, Marc S. Weinberg, Kevin V. Morris
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2148-7-199

Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies
Cited by: 37
Author(s): Aurora Ruiz‐Herrera, Terence J. Robinson
Software Mentions: 2
Published: almost 20 years ago

10.1186/1471-2164-16-S8-S2

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction
Cited by: 68
Author(s): Adam Frankish, Barbara Uszczyńska, Graham R. S. Ritchie, Jose M. Gonzalez, Dmitri D. Pervouchine, Robert Petryszak, Jonathan M. Mudge, Nuno A. Fonseca, Alvis Brāzma, Roderic Guigó, Jennifer Harrow
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1006754

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
Cited by: 52
Author(s): Wareed Ahmed, Claudia Sala, Shubhada R. Hegde, Rajiv Kumar Jha, Stewart T. Cole, Valakunja Nagaraja
Software Mentions: 2
Published: over 9 years ago

10.1186/gb-2014-15-1-r8

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast
Cited by: 153
Author(s): Shaun Webb, Ralph D. Hector, Grzegorz Kudla, Sander Granneman
Software Mentions: 2
Published: almost 13 years ago

10.1186/gb-2014-15-1-r1

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis
Cited by: 1,195
Author(s): Peng Cui, Shoudong Zhang, Feng Ding, Shahjahan Ali, Liming Xiong
Software Mentions: 2
Published: almost 13 years ago

10.3389/fgene.2013.00209

A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells
Cited by: 9
Author(s): Ramakrishna Sompallae, Oliver Hofmann, Christopher A. Maher, Craig Gedye, Andreas Behren, Morana Vitezic, Carsten O. Daub, Sylvie Devalle, Otávia L. Caballero, Piero Carninci, Yoshihide Hayashizaki, Elizabeth R. Lawlor, Jonathan Cebon, Winston Hide
Software Mentions: 2
Published: almost 14 years ago

10.3389/fgene.2017.00170

HOTAIR: A Promising Long Non-coding RNA with Potential Role in Breast Invasive Carcinoma
Cited by: 22
Author(s): Niloofar Avazpour, Mohammadreza Hajjari, Maryam Tahmasebi Birgani
Software Mentions: 2
Published: almost 9 years ago

10.15252/msb.20177548

Pervasive coexpression of spatially proximal genes is buffered at the protein level
Cited by: 78
Author(s): Georg Kustatscher, Piotr Grabowski, Juri Rappsilber
Software Mentions: 2
Published: over 9 years ago

10.3389/fgene.2021.641620

Gene Expression Modification by an Autosomal Inversion Associated With Three Male Mating Morphs
Cited by: 8
Author(s): Jasmine Lopez Loveland, David B. Lank, Clemens Küpper
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0031621

High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region
Cited by: 80
Author(s): Satish Sati, Vinay Singh Tanwar, Kalle Anand Kumar, Ashok Patowary, Vaibhav Jain, Sourav Ghosh, Shadab Ahmad, Meghna Singh, Sujatha Reddy, Giriraj Ratan Chandak, Manchala Raghunath, Sridhar Sivasubbu, Kausik Chakraborty, Vinod Scaria, Shantanu Sengupta
Software Mentions: 2
Published: over 14 years ago

10.1186/s13059-014-0469-0

Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes
Cited by: 137
Author(s): Adam Blattler, Lijing Yao, Heather Witt, Yu Guo, Charles M. Nicolet, Benjamin P. Berman, Peggy J. Farnham
Software Mentions: 2
Published: about 12 years ago

10.1186/1471-2229-9-50

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences
Cited by: 54
Author(s): Martin Trick, Foo Cheung, Nizar Drou, F C Fråser, Edward K. Lobenhofer, Patrick Hurban, Andreas Magusin, Christopher D. Town, Ian Bancroft
Software Mentions: 2
Published: over 17 years ago

10.1186/s13059-014-0578-9

Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds
Cited by: 51
Author(s): Carolina Frankl-Vilches, Heiner Kuhl, Martin Werber, Sven Klages, Martin Kerick, Antje Bakker, Edivaldo Herculano Corrêa de Oliveira, Christina Reusch, Floriana Capuano, Jakob Vowinckel, Stefan Leitner, Markus Ralser, Bernd Timmermann, Manfred Gahr
Software Mentions: 2
Published: almost 12 years ago

10.3389/fgene.2019.01305

A Pretraining-Retraining Strategy of Deep Learning Improves Cell-Specific Enhancer Predictions
Cited by: 11
Author(s): Xiaohui Niu, Kun Yang, Ge Zhang, Zhiquan Yang, Xuehai Hu
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj-cs.433

Multi-level aspect based sentiment classification of Twitter data: using hybrid approach in deep learning
Cited by: 6
Author(s): Sadaf Hussain Janjua, Ghazanfar Farooq Siddiqui, Muddassar Azam Sindhu, Umer Rashid
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2013.00092

The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation
Cited by: 52
Author(s): Armand Valsesia, Aurélien Macé, Sébastien Jacquemont, Jacques S. Beckmann, Zoltán Kutalik
Software Mentions: 2
Published: almost 14 years ago

10.3389/fgene.2019.01190

Whole Genome Resequencing Reveals Selection Signatures Associated With Important Traits in Ethiopian Indigenous Goat Populations
Cited by: 6
Author(s): Haile Berihulay, Yefang Li, Berihu Gebrekidan, Gebremedhin Gebreselassie, Xuexue Liu, Lin Jiang, Yue Ma
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13059-015-0727-9

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution
Cited by: 107
Author(s): Pelin Sahlén, Ilgar Abdullayev, Daniel Ramsköld, Liudmila Matskova, Nemanja Rilakovic, Britta Lötstedt, Thomas Albert, Joakim Lundeberg, Rickard Sandberg
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-015-0736-8

Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions
Cited by: 83
Author(s): Elena M. Pugacheva, Samuel Rivero-Hinojosa, Celso A. Espinoza, Claudia Fabiola Méndez-Catalá, Sungyun Kang, Tomohiko Suzuki, Natsuki Kosaka-Suzuki, Susan Robinson, Vijayaraj Nagarajan, Zhen Ye, Abdelhalim Boukaba, John E.J. Rasko, Alexander Strunnikov, Dmitri Loukinov, Bing Ren, Victor Lobanenkov
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1002390

Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development
Cited by: 61
Author(s): Sushma Nagaraja Grellscheid, Caroline Dalgliesh, Markus Storbeck, Andrew Best, Yilei Liu, Miriam Jakubik, Ylva Mende, Ingrid Ehrmann, Tomaž Curk, Kristina Roßbach, Cyril F. Bourgeois, James Stévenin, David Grellscheid, Michael S. Jackson, Brunhilde Wirth, David J. Elliott
Software Mentions: 2
Published: almost 15 years ago

10.1186/s13059-015-0835-6

Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2
Cited by: 30
Author(s): Young Chae Kim, Sangwon Byun, Yang Zhang, Sunmi Seok, Byron Kemper, Jian Ma, Jongsook Kim Kemper
Software Mentions: 2
Published: almost 11 years ago

10.3389/fgene.2020.533052

Discovery of Genomic Characteristics and Selection Signatures in Southern Chinese Local Cattle
Cited by: 12
Author(s): Yuqiang Liu, Lingyang Xu, Yang Liu, Guangshan Zhao, Junya Li, Dewu Liu, Yaokun Li
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.isci.2020.101741

The PWWP2A Histone Deacetylase Complex Represses Intragenic Spurious Transcription Initiation in mESCs
Cited by: 8
Author(s): Guifeng Wei, Neil Brockdorff, Tianyi Zhang
Software Mentions: 2
Published: about 6 years ago

10.18632/aging.101867

Tubastatin A inhibits HDAC and Sirtuin activity rather than being a HDAC6-specific inhibitor in mouse oocytes
Cited by: 8
Author(s): Yun‐Jung Choi, Min-Hee Kang, Kwonho Hong, Jin‐Hoi Kim
Software Mentions: 2
Published: over 7 years ago

10.1186/s13040-021-00251-0

Indels in SARS-CoV-2 occur at template-switching hotspots
Cited by: 23
Author(s): Brianna Chrisman, Kelley Paskov, Nate Stockham, Kevin Tabatabaei, Jae-Yoon Jung, Peter Washington, Maya Varma, Min Sun, Sepideh Maleki, Dennis P. Wall
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-14-611

Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes
Cited by: 159
Author(s): James R. Doroghazi, William W. Metcalf
Software Mentions: 2
Published: almost 14 years ago

10.1186/s13059-016-1142-6

Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies
Cited by: 145
Author(s): Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Saixia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael Feolo, Nataliya Sharopova, Anne Sturcke, Alejandro A. Schäffer, Nancy L. Heard‐Costa, Han Chen, Poching Liu, Thomas J. Wang, Kimberly A. Woodhouse, Kahraman Tanrıverdi, Jane E. Freedman, Nalini Raghavachari, Josée Dupuis, Andrew D. Johnson, Christopher J. O’Donnell, Daniel Levy, Peter J. Munson
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13059-017-1161-y

Software tools for visualizing Hi-C data
Cited by: 49
Author(s): Galip Gürkan Yardımcı
Software Mentions: 2
Published: almost 10 years ago

10.3389/fcell.2021.715674

Decreased m6A Modification of CD34/CD276(B7-H3) Leads to Immune Escape in Colon Cancer
Cited by: 7
Author(s): Yiran Zhou, Haodong Zhou, Jianlin Shi, Aoran Guan, Yankun Zhu, Zhen Hou, Ruhong Li
Software Mentions: 2
Published: over 5 years ago

Projects: pypi: browser

Enhanced Analysis

Science Score: 65/100

Penalties:

Papers Mentioning browser 2,125