pypi: browser | Projects | Ecosyste.ms: Papers

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 12 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 13 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 16 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 16 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 4 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 10 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 16 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 16 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 16 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 16 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 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 18 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 9 years ago

10.1186/1471-2105-11-10

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement
Cited by: 52
Author(s): Guanqun Shi, Liqing Zhang, Tao Jiang
Software Mentions: 2
Published: almost 16 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 20 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 4 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 4 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 4 years ago

10.3390/genes11121486

citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement
Cited by: 8
Author(s): Naveen Duhan, Manish Meshram, Cristian D Loaiza, Rakesh Kaundal
Software Mentions: 2
Published: almost 5 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 18 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 5 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 9 years ago

10.3390/genes5041115

Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential
Cited by: 18
Author(s): Y. Kurihara, Yuko Makita, Mika Kawashima, Hidefumi Hamasaki, Yoshiharu Y. Yamamoto, Minami Matsui
Software Mentions: 2
Published: almost 11 years ago

10.1136/annrheumdis-2018-214930

Altered DNA methylation in children born to mothers with rheumatoid arthritis during pregnancy
Cited by: 7
Author(s): Hilal Ince-Askan, Pooja R. Mandaviya, Janine F. Felix, Liesbeth Duijts, Joyce B. J. van Meurs, Johanna M. W. Hazes, Radboud J E M Dolhain
Software Mentions: 2
Published: over 6 years ago

10.3390/genes7030011

Genome-Wide Identification and Characterization of Long Non-Coding RNAs from Mulberry (Morus notabilis) RNA-seq Data
Cited by: 35
Author(s): Xin Song, Liang Sun, Haitao Luo, Qingguo Ma, Yi Zhao, Dong Pei
Software Mentions: 2
Published: over 9 years ago

10.1534/g3.118.200901

Genetic, Inflammatory, and Epithelial Cell Differentiation Factors Control Expression of Human Calpain-14
Cited by: 14
Author(s): Daniel Miller, Carmy Forney, Mark Rochman, Stacey A Cranert, Jeffery Habel, Jeffrey K. Rymer, Arthur Lynch, Connor Schroeder, Josh Lee, Amber Sauder, Quinton Smith, Mehak Chawla, Michael Trimarchi, Xiaoming Lu, Ellen Fjellman, Michael Brusilovsky, Artem Barski, Stephen N. Waggoner, Matthew T. Weirauch, Marc E. Rothenberg, Leah C. Kottyan
Software Mentions: 2
Published: over 6 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 14 years ago

10.3390/genes8010014

mRNA Expression and DNA Methylation Analysis of Serotonin Receptor 2A (HTR2A) in the Human Schizophrenic Brain
Cited by: 29
Author(s): Sern-Yih Cheah, Bruce R. Lawford, Ross McD. Young, Charles P. Morris, Joanne Voisey
Software Mentions: 2
Published: almost 9 years ago

10.1534/g3.112.003194

Microarray-Based Capture of Novel Expressed Cell Type–Specific Transfrags (CoNECT) to Annotate Tissue-Specific Transcription in Drosophila melanogaster
Cited by: 0
Author(s): Xiaojing Hong, Harshavardhan Doddapaneni, Josep M. Comeron, Matthew J. Rodesch, Heather A. Halvensleben, Chung Yi Nien, F. Bolei, Raghu Metpally, Todd Richmond, Thomas Albert, J. Robert Manak
Software Mentions: 2
Published: over 13 years ago

10.3389/fpls.2019.00072

Cold Induced Antisense Transcription of FLOWERING LOCUS C in Distant Grasses
Cited by: 16
Author(s): Fuchao Jiao, Kanchan Pahwa, Murray Manning, Niklas Dochy, Koen Geuten
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2172-9-7

The Innate Immune Database (IIDB)
Cited by: 44
Author(s): Martin Korb, Alistair G. Rust, Vésteinn Thórsson, Christophe Battail, Bin Li, Daehee Hwang, Kathleen A. Kennedy, Jared C. Roach, Carrie M. Rosenberger, Mark Gilchrist, Daniel E. Zak, Carrie D. Johnson, Bruz Marzolf, Alan Aderem, Ilya Shmulevich, Hamid Bolouri
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pgen.1008026

Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency
Cited by: 13
Author(s): Jinli Li, Yi Chen, Tao Zheng, Lingxin Kong, Sucheng Zhu, Yihua Sun, Zixin Deng, Litao Yang, Delin You
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-11-119

Prodigal: prokaryotic gene recognition and translation initiation site identification
Cited by: 7,098
Author(s): Doreene R. Hyatt, Gwo Liang Chen, Philip F. LoCascio, Miriam Land, Frank W. Larimer, Loren Hauser
Software Mentions: 2
Published: over 15 years ago

10.1534/g3.115.021386

Identification of Genes Uniquely Expressed in the Germ-Line Tissues of the Jewel Wasp<i>Nasonia vitripennis</i>
Cited by: 15
Author(s): Patrick M. Ferree, Christopher Fang, Mariah Mastrodimos, Bruce A. Hay, Henry Amrhein, Omar S. Akbari
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pgen.1009290

Natural variation in temperature-modulated immunity uncovers transcription factor bHLH059 as a thermoresponsive regulator in Arabidopsis thaliana
Cited by: 19
Author(s): Friederike Bruessow, Jaqueline Bautor, Gesa Hoffmann, Ipek Yildiz, Jürgen Zeier, Jane E. Parker
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pgen.1004507

KDM6 Demethylase Independent Loss of Histone H3 Lysine 27 Trimethylation during Early Embryonic Development
Cited by: 94
Author(s): Karl B. Shpargel, Joshua Starmer, Della Yee, Michael Pohlers, Terry Magnuson
Software Mentions: 2
Published: over 11 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 5 years ago

10.1371/journal.pgen.1004885

Interactions of Chromatin Context, Binding Site Sequence Content, and Sequence Evolution in Stress-Induced p53 Occupancy and Transactivation
Cited by: 49
Author(s): Dan Su, Xuting Wang, Michelle R. Campbell, Lingyun Song, Alexias Safi, Gregory E. Crawford, Douglas A. Bell
Software Mentions: 2
Published: almost 11 years ago

10.3389/fpls.2017.02218

Nictaba Homologs from Arabidopsis thaliana Are Involved in Plant Stress Responses
Cited by: 13
Author(s): Lore Eggermont, Karolina Stefanowicz, Els J. M. Van Damme
Software Mentions: 2
Published: almost 8 years ago

10.1002/dvg.22963

Transcriptional regulation of the proto‐oncogene<i>Zfp521</i>by 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 9 years ago

10.3389/fnmol.2016.00013

Recombinant Human Myelin-Associated Glycoprotein Promoter Drives Selective AAV-Mediated Transgene Expression in Oligodendrocytes
Cited by: 35
Author(s): Georg von Jonquières, Dominik Fröhlich, Claudia B. Klugmann, Xin Wen, Anne E. Harasta, Roshini Ramkumar, Ziggy H. T. Spencer, Gary D. Housley, Matthias Klugmann
Software Mentions: 2
Published: over 9 years ago

10.3389/fmolb.2021.668402

Expression and Prognostic Value of MCM Family Genes in Osteosarcoma
Cited by: 12
Author(s): Jian Zhou, Mingyong Wang, Zhen Zhou, Wanchun Wang, Juan Duan, Gen Sheng Wu
Software Mentions: 2
Published: over 4 years ago

10.3389/fnmol.2017.00279

Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder
Cited by: 14
Author(s): Krzysztof J. Szkop, Peter I. C. Cooke, Joanne A. Humphries, Viktoria Kalna, David S. Moss, Eugene F. Schuster, Irene Nobeli
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2021.636284

Antimicrobial Resistance and Genomic Characterization of Two mcr-1-Harboring Foodborne Salmonella Isolates Recovered in China, 2016
Cited by: 4
Author(s): Yujie Hu, Scott V. Nguyen, Wei Wang, Xin Gan, Yinping Dong, Chang Liu, Xiquan Cui, Jin Xu, Fengqin Li, Séamus Fanning
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1001134

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome
Cited by: 461
Author(s): Robert S. Illingworth, Ulrike Gruenewald-Schneider, Shaun Webb, Alastair Kerr, Keith James, Daniel J. Turner, Colin Smith, David J. Harrison, Robert Andrews, Adrian Bird
Software Mentions: 2
Published: about 15 years ago

10.1186/1471-2105-13-253

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
Cited by: 15
Author(s): Danielle G. Lemay, William Martin, Angie S. Hinrichs, Monique Rijnkels, J. Bruce German, Ian F Korf, Katherine S. Pollard
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2156-12-27

PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila
Cited by: 10
Author(s): Ram Vinay Pandey, Robert Kofler, Pablo Orozco‐terWengel, Viola Nolte, Christian Schlötterer
Software Mentions: 2
Published: over 14 years ago

10.1186/s12864-015-1533-1

Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea
Cited by: 17
Author(s): Gustavo Rodríguez-Esteban, Alejandro González-Sastre, José Ignacio Rojo-Laguna, Emili Saló, Josep F. Abril
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2018.00965

Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts
Cited by: 25
Author(s): M. A. Eldarov, Alexey V. Beletsky, Tatiana N. Tanashchuk, Svetlana A. Kishkovskaya, Nikolai V. Ravin, Andrey V. Mardanov
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-021-04359-2

Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders
Cited by: 0
Author(s): Quentin Ferré, Jeanne Chèneby, Denis Puthier, Cécile Capponi, Benoît Ballester
Software Mentions: 2
Published: about 4 years ago

10.3389/fimmu.2015.00616

Bad News: Analysis of the Quality of Information on Influenza Prevention Returned by Google in English and Italian
Cited by: 21
Author(s): Ali Maki, Roger Evans, Pietro Ghezzi
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pgen.1008694

WHIMP links the actin nucleation machinery to Src-family kinase signaling during protrusion and motility
Cited by: 7
Author(s): Shail Kabrawala, Margaret D. Zimmer, Kenneth Campellone
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1001116

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data
Cited by: 484
Author(s): Abigail W. Bigham, Marc Bauchet, Dalila Pinto, Xiaole Mao, Joshua M. Akey, Rui Mei, Stephen W. Scherer, Colleen G. Julian, Megan J. Wilson, David López Herráez, Tom D. Brutsaert, Esteban J. Parra, Lorna G. Moore, Mark D. Shriver
Software Mentions: 2
Published: about 15 years ago

10.1186/1471-2164-15-765

Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature
Cited by: 80
Author(s): Alba Nicoletta Mininni, Massimo Milan, Serena Ferraresso, T. Petochi, Patrizia Di Marco, G. Marino, Silvia Livi, Chiara Romualdi, Luca Bargelloni, Tomaso Patarnello
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1006700

Probing the canonicity of the Wnt/Wingless signaling pathway
Cited by: 37
Author(s): Alexandra Franz, Daria Shlyueva, Erich Brunner, Alexander Stark, Konrad Basler
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2015.00167

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds
Cited by: 56
Author(s): Beatriz Gutiérrez-Gil, Juan José Arranz, Pamela Wiener
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.0020024

SPA: A Probabilistic Algorithm for Spliced Alignment
Cited by: 25
Author(s): Erik van Nimwegen, Nicodème Paul, Robert P. Sheridan, Mihaela Zavolan
Software Mentions: 2
Published: over 19 years ago

10.3389/fgene.2018.00214

Screening of the LAMB2, WT1, NPHS1, and NPHS2 Genes in Pediatric Nephrotic Syndrome
Cited by: 6
Author(s): Aiysha Abid, Saba Shahid, Madiha Shakoor, Ali Lanewala, Seema Hashmi, Shagufta Khaliq
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2020.00766

Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice
Cited by: 12
Author(s): Nannan Zhao, Kang Zhang, Chunchao Wang, Hengyu Yan, Yue Liu, Wenying Xu, Zhen Su
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2018.00025

Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2
Cited by: 8
Author(s): Øivind Skare, Rolv Terje Lie, Øystein Ariansen Haaland, Miriam Gjerdevik, Julia Romanowska, Håkon K. Gjessing, Astanand Jugessur
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2148-9-207

Whole genome duplications and expansion of the vertebrate GATA transcription factor gene family
Cited by: 47
Author(s): William J. Gillis, John St. John, Bruce Bowerman, Stephan Schneider
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pgen.1005947

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies
Cited by: 91
Author(s): Qiongshi Lu, Ryan L. Powles, Qian Wang, B. Julie He, Hongyu Zhao
Software Mentions: 2
Published: over 9 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 6 years ago

10.1093/database/bat034

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
Cited by: 120
Author(s): Deeksha Bhartiya, Koustav Pal, Sourav Ghosh, Shruti Kapoor, Saakshi Jalali, Bharat Panwar, Sakshi Jain, Satish Sati, Shantanu Sengupta, Chetana Sachidanandan, Gajendra P. S. Raghava, Sridhar Sivasubbu, Vinod Scaria
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2148-9-85

Origin and evolution of the RIG-I like RNA helicase gene family
Cited by: 224
Author(s): Jun Zou, Ming Chang, Pin Nie, Chris J. Secombes
Software Mentions: 2
Published: almost 17 years ago

10.1093/database/baz056

LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species
Cited by: 6
Author(s): Leiming You, Jiaqi Chi, Shengfeng Huang, Ting Yu, Guangrui Huang, Yuchao Feng, Xiaopu Sang, Xinhui Gao, Tingan Li, Zirui Yue, Aijie Liu, Shangwu Chen, Anlong Xu
Software Mentions: 2
Published: almost 7 years ago

10.1093/database/bav103

WaspAtlas: aNasonia vitripennisgene database and analysis platform
Cited by: 17
Author(s): Nathaniel J. Davies, Eran Tauber
Software Mentions: 2
Published: almost 11 years ago

10.1093/database/bax074

Echinobase: an expanding resource for echinoderm genomic information
Cited by: 60
Author(s): Parul Kudtarkar, R. Andrew Cameron
Software Mentions: 2
Published: almost 9 years ago

10.1093/database/baw162

viruSITE—integrated database for viral genomics
Cited by: 47
Author(s): Matej Stano, Gábor Beke, Ľuboš Klučár
Software Mentions: 2
Published: almost 10 years ago

10.1093/database/bax059

BioSearch: a semantic search engine for Bio2RDF
Cited by: 19
Author(s): Wei Hu, Honglei Qiu, Junhui Huang, Michel Dumontier
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2164-11-68

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing
Cited by: 57
Author(s): Heiner Kuhl, Alfred Beck, Grzegorz Woźniak, Adelino V.M. Canário, Filip Volckaert, Richard Reinhardt
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2164-15-526

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals
Cited by: 61
Author(s): Seung Gu Park, Sridhar Hannenhalli, Sun Shim Choi
Software Mentions: 2
Published: over 11 years ago

10.1093/database/bat067

BBGRE: brain and body genetic resource exchange
Cited by: 3
Author(s): Joo Wook Ahn, Abhishek Dixit, Caroline Johnston, Caroline Mackie Ogilvie, David A. Collier, Sarah Curran, Richard Dobson
Software Mentions: 2
Published: almost 13 years ago

10.1093/database/baz009

The radish genome database (RadishGD): an integrated information resource for radish genomics
Cited by: 11
Author(s): Hee‐Ju Yu, Seung-Hoon Baek, Young-Joon Lee, Ara Cho, Jeong‐Hwan Mun
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1002641

Patterns of Ancestry, Signatures of Natural Selection, and Genetic Association with Stature in Western African Pygmies
Cited by: 121
Author(s): Joseph P. Jarvis, Laura B. Scheinfeldt, Sameer Soi, Charla Lambert, Larsson Omberg, Bart Ferwerda, Alain Froment, Jean-Marie Bodo, William Beggs, Gabriel E. Hoffman, Jason G. Mezey, Sarah A. Tishkoff
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1000081

Genomic Profiling Identifies GATA6 as a Candidate Oncogene Amplified in Pancreatobiliary Cancer
Cited by: 94
Author(s): Kevin Kwei, Murali D. Bashyam, Jennifer L. Kao, Raman Ratheesh, E. Chandrakanth Reddy, Young H. Kim, Kelli Montgomery, Craig P. Giacomini, Yoon La Choi, Sreejata Chatterjee, Collins Karikari, Keyan Salari, Pei Wang, Tina Hernandez‐Boussard, G Swarnalata, Matt van de Rijn, Anirban Maitra, Jonathan R. Pollack
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2105-10-215

Regression based predictor for p53 transactivation
Cited by: 7
Author(s): Sivakumar Gowrisankar, Anil G. Jegga
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2148-11-267

Visualization and Exploration of Conserved Regulatory Modules Using ReXSpecies 2
Cited by: 4
Author(s): Stephan Struckmann, Daniel Esch, Hans R. Schöler, Georg Fuellen
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-11-519

Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated
Cited by: 99
Author(s): Mun-Kit Choy, Mehregan Movassagh, Hock Guan Goh, Martin R. Bennett, Thomas A. Down, Roger Foo
Software Mentions: 2
Published: about 15 years ago

10.1186/1471-2164-9-398

Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray
Cited by: 54
Author(s): Hongying Jiang, Ming Yi, Jianbing Mu, Louie Zhang, Alasdair Ivens, Leszek J. Klimczak, Yentram Huyen, Robert M. Stephens, Xin-zhuan Su
Software Mentions: 2
Published: about 17 years ago

10.1186/s13148-016-0269-3

MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics
Cited by: 10
Author(s): Ram Vinay Pandey, Walter Pulverer, Rainer Kallmeyer, Gabriel Beikircher, Stephan Pabinger, Albert Kriegner, Andreas Weinhäusel
Software Mentions: 2
Published: about 9 years ago

10.1186/s13148-018-0470-7

Methylated genomic loci encoding microRNA as a biomarker panel in tissue and saliva for head and neck squamous cell carcinoma
Cited by: 15
Author(s): Yu Cao, Katherine Green, Steve Quattlebaum, Ben Milam, Ling Lu, Dexiang Gao, Hui He, Ningning Li, Liwei Gao, F. De Havilland Hall, Matthew Whinery, Elyse Handley, Yi Ma, Tao Xu, Feng Jin, Jing Xiao, Minjie Wei, Derek E. Smith, Sophia Bornstein, Neil D. Gross, Dohun Pyeon, John I. Song, Shi Lu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1000843

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq
Cited by: 55
Author(s): Augix Guohua Xu, Lin He, Zhongshan Li, Ying Xu, Mingfeng Li, Xing Fu, Yanyan Zheng, Yuan Yuan, Corinna Menzel, Na Li, Mehmet Somel, Hao Hu, Wei Chen, Svante Pääbo, Philipp Khaitovich
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pcbi.1007399

Direct prediction of regulatory elements from partial data without imputation
Cited by: 12
Author(s): Yu Zhang, Shaun Mahony
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1003153

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations
Cited by: 350
Author(s): Umadevi Paila, Brad Chapman, Rory Kirchner, Aaron R. Quinlan
Software Mentions: 2
Published: over 12 years ago

10.1186/s13148-017-0386-7

CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel
Cited by: 44
Author(s): Luca Morandi, Davide Bartolomeo Gissi, Achille Tarsitano, Sofia Asioli, Andrea Gabusi, Claudio Marchetti, Lucio Montebugnoli, Maria Pia Foschini
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pcbi.1005840

Significant associations between driver gene mutations and DNA methylation alterations across many cancer types
Cited by: 38
Author(s): Yunching Chen, Valer Gotea, Gennady Margolin, Laura Elnitski
Software Mentions: 2
Published: about 8 years ago

10.3390/cells9010147

IGF-1 Signalling Regulates Mitochondria Dynamics and Turnover through a Conserved GSK-3β–Nrf2–BNIP3 Pathway
Cited by: 46
Author(s): Sarah Riis, Jack Murray, Rosemary O’Connor
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1007863

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation
Cited by: 3
Author(s): Luke Sargent, Yating Liu, Wilson Leung, Nathan T. Mortimer, David Lopatto, Jeremy Goecks, Sarah C. R. Elgin
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1000147

A General Definition and Nomenclature for Alternative Splicing Events
Cited by: 211
Author(s): Michael Sammeth, Sylvain Foissac, Roderic Guigó
Software Mentions: 2
Published: over 17 years ago

10.3390/cells1041029

A Novel Type III Endosome Transmembrane Protein, TEMP
Cited by: 1
Author(s): Rajith Aturaliya, Markus C. Kerr, Rohan D. Teasdale
Software Mentions: 2
Published: about 13 years ago

10.1186/s13148-019-0666-5

DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer
Cited by: 20
Author(s): Christoph Weigel, Jittiporn Chaisaingmongkol, Yassen Assenov, Christine Kuhmann, Volker Winkler, Irene Santi, Olga Bogatyrova, Simone Kaucher, Justo Lorenzo Bermejo, Suet Yi Leung, Tsun Leung Chan, Felix Lasitschka, M. Bohrer, Alexander Marx, Roland Heyny-von Haußen, Christel Herold‐Mende, Gerhard Dyckhoff, Petra Boukamp, K.-W. Delank, K. Hörmann, Burkhard M. Lippert, G. Baier, Andreas Dietz, Christopher C. Oakes, Christoph Plass, Heiko Becher, Peter Schmezer, Heribert Ramroth, Odilia Popanda
Software Mentions: 2
Published: over 6 years ago

10.1186/s12862-018-1306-y

The evolution of ependymin-related proteins
Cited by: 15
Author(s): Carmel McDougall, Michael Hammond, Simon Christopher Dailey, Ildikó Maureen Lara Somorjai, Scott F. Cummins, Bernard M. Degnan
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1000163

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq
Cited by: 518
Author(s): Alexandra Sittka, Sacha Lucchini, Kai Papenfort, Cynthia M. Sharma, Katarzyna Rolle, Tim T. Binnewies, Jay C. D. Hinton, Jörg Vogel
Software Mentions: 2
Published: about 17 years ago

10.1016/j.cellsig.2007.01.010

Genomic tagging of endogenous Type IIβ Phosphatidylinositol 5-phosphate 4-kinase in DT40 cells reveals a nuclear localisation
Cited by: 31
Author(s): Jonathan P. Richardson, Minchuan Wang, Jonathan H. Clarke, Ketan Patel, Robin F. Irvine
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pbio.1000371

Most “Dark Matter” Transcripts Are Associated With Known Genes
Cited by: 384
Author(s): Harm van Bakel, Corey Nislow, Benjamin J. Blencowe, Timothy R. Hughes
Software Mentions: 2
Published: over 15 years ago

10.1038/s41598-017-07539-4

Reactivity of human AGO2 monoclonal antibody 11A9 with the SWI/SNF complex: A case study for rigorously defining antibody selectivity
Cited by: 9
Author(s): Roderick A. P. M. van Eijl, Teun van den Brand, Luan N. Nguyen, Klaas W. Mulder
Software Mentions: 2
Published: over 8 years ago

10.1016/j.celrep.2015.10.030

Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis
Cited by: 33
Author(s): Mayuri Rege, Vidya Subramanian, Chenchen Zhu, Tsung Han Hsieh, Assaf Weiner, Nir Friedman, Sandra Clauder‐Münster, Lars M. Steinmetz, Oliver J. Rando, Laurie A. Boyer, Craig L. Peterson
Software Mentions: 2
Published: about 10 years ago

10.1038/cr.2017.25

De novo DNA methylation during monkey pre-implantation embryogenesis
Cited by: 42
Author(s): Fei Gao, Yuyu Niu, Yi Sun, Hanlin Lu, Yongchang Chen, Siguang Li, Yu Kang, Yuan Luo, Chenyang Si, Juehua Yu, Li Chang, Nianqin Sun, Wei Si, Hong Wang, Weizhi Ji, Tao Tan
Software Mentions: 2
Published: over 8 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 11 years ago

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Papers Mentioning browser 2,125