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10.1186/1471-2148-13-19

Impact of constitutional copy number variants on biological pathway evolution
Cited by: 14
Author(s): Maria Poptsova, Samprit Banerjee, Ömer Gökçümen, Mark A. Rubin, Francesca Demichelis
Software Mentions: 1
Published: over 13 years ago

10.1186/s12862-015-0528-5

Selective sweeps versus introgression - population genetic dynamics of the murine leukemia virus receptor Xpr1 in wild populations of the house mouse (Mus musculus)
Cited by: 9
Author(s): Natascha Hasenkamp, Terry Solomon, Diethard Tautz
Software Mentions: 1
Published: almost 11 years ago

10.1186/gb-2009-10-8-r86

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes
Cited by: 25
Author(s): Xianjun Dong, David Fredman, Boris Lenhard
Software Mentions: 1
Published: over 17 years ago

10.1098/rsob.180131

DNA methylation subpatterns at distinct regulatory regions in human early embryos
Cited by: 15
Author(s): Rongsong Luo, Chunling Bai, Lei Yang, Zhong Zheng, Guanghua Su, Guang Gao, Zhuying Wei, Yongchun Zuo, Guangpeng Li
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13015-019-0158-3

TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column
Cited by: 0
Author(s): Hisanori Kiryu, Yuto Ichikawa, Yasuhiro Kojima
Software Mentions: 1
Published: almost 7 years ago

10.1515/jib-2021-0001

Novel perspectives for SARS-CoV-2 genome browsing
Cited by: 2
Author(s): Visam Gültekin, Jens Allmer
Software Mentions: 1
Published: over 5 years ago

10.1194/jlr.M062497

miR-146a-5p inhibits TNF-α-induced adipogenesis via targeting insulin receptor in primary porcine adipocytes
Cited by: 36
Author(s): Di Wu, Qianyun Xi, Xiao Cheng, Tao Dong, Xiaotong Zhu, Gang Shu, Lina Wang, Qingyan Jiang, Yongliang Zhang
Software Mentions: 1
Published: about 10 years ago

10.1186/gb-2010-11-7-r70

Contrasting chromatin organization of CpG islands and exons in the human genome
Cited by: 101
Author(s): Jung Kyoon Choi
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2148-11-308

Abundance of ultramicro inversions within local alignments between human and chimpanzee genomes
Cited by: 11
Author(s): Yuichiro Hara, Tadashi Imanishi
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2011-12-9-r86

Mutation discovery in mice by whole exome sequencing
Cited by: 102
Author(s): Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R. Corrigan, Michelle Curtain, Yueming Ding, Mark D’Ascenzo, Daniel J. Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy B. Rowe, Frank J. Probst, David E. Bergstrom, Stephen A. Murray, Carol J. Bult, Joel E. Richardson, Benjamin T. Kile, Ivo Gut, Jörg Hager, Snaevar Sigurðsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad‐Toh, Michael L. Cunningham, Timothy C. Cox, Monica J. Justice, Mona S. Spector, Scott W. Lowe, Thomas Albert, Leah Rae Donahue, Jeffrey A. Jeddeloh, Jay Shendure
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2011-12-s1-p3

COSMIC: the catalogue of somatic mutations in cancer
Cited by: 5
Author(s): Nidhi Bindal, Simon Forbes, David Beare, Prasad Gunasekaran, Kenric Leung, Chai Yin Kok, Mingming Jia, Sally Bamford, Charlotte G. Cole, Sari Ward, Jon W. Teague, Michael R. Stratton, Peter J. Campbell, Andrew Futreal
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2011-12-s1-p24

Identification of functional genetic variants associated with prostate cancer through analysis of genome-wide genetic and epigenetic datasets
Cited by: 0
Author(s): McAnthony Tarway, Wei Tang, Ludmila Prokunina–Olsson
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2012-13-7-r66

Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation
Cited by: 201
Author(s): Markus Lommer, Michael Specht, Alexandra-Sophie Roy, Lars Kraemer, Reidar Andreson, Magdalena A. Gutowska, Juliane Wolf, Sonja Verena Bergner, Markus B. Schilhabel, Ulrich C. Klostermeier, Robert G. Beiko, Philip Rosenstiel, Michael Hippler, Julie LaRoche
Software Mentions: 1
Published: over 14 years ago

10.1186/gb-2012-13-10-r84

Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns
Cited by: 141
Author(s): Duncan Sproul, Robert Kitchen, Colm E. Nestor, JM Dixon, Andrew H. Sims, David J. Harrison, Bernard Ramsahoye, Richard R. Meehan
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2148-14-137

The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms
Cited by: 6
Author(s): Kathryn B. Walters-Conte, Diana Johnson, Warren E. Johnson, Stephen J. O’Brien, Jill Pecon-Slattery
Software Mentions: 1
Published: over 12 years ago

10.1155/2013/517943

Association of RXR-Gamma Gene Variants with Familial Combined Hyperlipidemia: Genotype and Haplotype Analysis
Cited by: 17
Author(s): Federica Sentinelli, Ilenia Minicocci, Anna Mestice, Luisa Nanni, Stefano Romeo, Michela Incani, Maria Gisella Cavallo, Andrea Lenzi, Marcello Arca, Marco Giorgio Baroni
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2148-10-73

A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution
Cited by: 26
Author(s): Morgane Thomas‐Chollier, Valérie Ledent, Luc Leyns, Michel Vervoort
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2148-10-157

Functional conservation of a forebrain enhancer from the elephant shark (Callorhinchus milii) in zebrafish and mice
Cited by: 11
Author(s): R. Macdonald, Mélanie Debiais-Thibaud, Kyle J. Martin, Luc Poitras, Boon-Hui Tay, Byrappa Venkatesh, Marc Ekker
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2148-9-195

A fungal phylogeny based on 82 complete genomes using the composition vector method
Cited by: 185
Author(s): Hao Wang, Zhonghui Xu, Lei Gao, Bailin Hao
Software Mentions: 1
Published: about 17 years ago

10.1186/gb-2013-14-5-r45

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing
Cited by: 115
Author(s): Shivendra Kishore, Andreas Gruber, Dominik J. Jedlinski, Afzal Pasha Syed, Hadi Jorjani, Mihaela Zavolan
Software Mentions: 1
Published: over 13 years ago

10.1186/gb-2013-14-3-r25

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes
Cited by: 199
Author(s): James P. Reddington, Sara Maria Perricone, Colm E. Nestor, Judith Reichmann, Neil A. Youngson, Masako Suzuki, Diana Reinhardt, Donncha S. Dunican, James Prendergast, Heidi K. Mjoseng, Bernard Ramsahoye, Emma Whitelaw, John M. Greally, Ian R. Adams, Wendy A. Bickmore, Richard R. Meehan
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2148-8-17

A genome-wide screen for noncoding elements important in primate evolution
Cited by: 91
Author(s): Eliot C. Bush, Bruce T. Lahn
Software Mentions: 1
Published: over 18 years ago

10.1186/gb-2014-15-1-r5

Mammalian conserved ADAR targets comprise only a small fragment of the human editosome
Cited by: 146
Author(s): Yishay Pinto, Haim Y. Cohen, Erez Y. Levanon
Software Mentions: 1
Published: over 12 years ago

10.1186/s13256-018-1608-0

Novel compound heterozygote mutations in the ATP7B gene in an Iranian family with Wilson disease: a case report
Cited by: 8
Author(s): Omid Daneshjoo, Masoud Garshasbi
Software Mentions: 1
Published: over 8 years ago

10.1111/acel.12607

The PPARγ-SETD8 axis constitutes an epigenetic, p53-independent checkpoint on p21-mediated cellular senescence
Cited by: 21
Author(s): Chieh Tien Shih, Ian Yi‐Feng Chang, Yi Tung Chen, Chung Pei, Hui-Wen Chen, Chang Ching Yang, Juu Chin Lu, Yau Sheng Tsai, Hua Chien Chen, Bertrand Chin‐Ming Tan
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2148-14-74

An evolutionarily biased distribution of miRNA sites toward regulatory genes with high promoter-driven intrinsic transcriptional noise
Cited by: 18
Author(s): Hossein Zare, Arkady B. Khodursky, Vittorio Sartorelli
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2148-13-238

The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications
Cited by: 103
Author(s): David Lagman, Daniel Ocampo Daza, Jenny Widmark, Xesús M. Abalo, Görel Sundström, Dan Larhammar
Software Mentions: 1
Published: almost 13 years ago

10.1186/gb-2013-14-7-r79

PARma: identification of microRNA target sites in AGO-PAR-CLIP data
Cited by: 52
Author(s): Florian Erhard, Lars Dölken, Łukasz Jaśkiewicz, Ralf Zimmer
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2148-7-S1-S14

Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human
Cited by: 20
Author(s): Zhaolei Zhang, Andy Wing Chun Pang, Mark Gerstein
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2148-14-11

Evolutionary classification of ammonium, nitrate, and peptide transporters in land plants
Cited by: 107
Author(s): Neil J J B von Wittgenstein, Cuong H. Le, Barbara J. Hawkins, Jürgen Ehlting
Software Mentions: 1
Published: over 12 years ago

10.3390/nu11020325

Divergent Effectiveness of Multispecies Probiotic Preparations on Intestinal Microbiota Structure Depends on Metabolic Properties
Cited by: 26
Author(s): Michele Biagioli, Daniela Capobianco, Adriana Carino, Silvia Marchianò, Federica Chiara, Patrizia Ricci, Eleonora Distrutti, Stefano Fiorucci
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2148-8-46

Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals
Cited by: 42
Author(s): Christina M. Laukaitis, Andreas Heger, Tyler D Blakley, Pavel Munclinger, Chris P. Ponting, Robert C. Karn
Software Mentions: 1
Published: over 18 years ago

10.1007/s12031-018-1044-z

The Regulation of Monoamine Oxidase A Gene Expression by Distinct Variable Number Tandem Repeats
Cited by: 19
Author(s): Maurizio Manca, Veridiana Pessoa, Ana Illera Lopez, Patrick T. Harrison, Fábio Miyajima, Helen Sharp, Andrew Pickles, Jonathan Hill, Chris Murgatroyd, Vivien J. Bubb, John P. Quinn
Software Mentions: 1
Published: over 8 years ago

10.1186/s12862-018-1147-8

Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa
Cited by: 16
Author(s): Alyssa D. Lokits, Henrike Indrischek, Jens Meiler, Heidi E. Hamm, Peter F. Stadler
Software Mentions: 1
Published: over 8 years ago

10.1186/s13059-015-0672-7

Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression
Cited by: 130
Author(s): Ruslan Strogantsev, Felix Krueger, Kazuki Yamazawa, Hui Shi, Poppy A. Gould, Megan Goldman-Roberts, Kirsten McEwen, Bowen Sun, Roger A. Pedersen, Anne C. Ferguson-Smith
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2148-12-62

Genomic characterization of the European sea bass Dicentrarchus labrax reveals the presence of a novel uncoupling protein (UCP) gene family member in the teleost fish lineage
Cited by: 11
Author(s): Mbaye Tine, Heiner Kuhl, Martin Jastroch, Richard Reinhardt
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2148-9-217

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC
Cited by: 26
Author(s): Rahul Satija, Adam M. Novak, István Miklós, Rune B. Lyngsø, Jotun Hein
Software Mentions: 1
Published: over 17 years ago

10.2174/1874192401711010084

Interpreting the Mechanism of APOE (p.Leu167del) Mutation in the Incidence of Familial Hypercholesterolemia; An In-silico Approach
Cited by: 11
Author(s): Omran M. Rashidi, Fatima Amanullah H.Nazar, Mohamed Nabil Alama, Zuhier Awan
Software Mentions: 1
Published: almost 9 years ago

10.18632/aging.101470

Integrated DNA methylation and gene expression analysis identifies SLAMF7 as a key regulator of atherosclerosis
Cited by: 13
Author(s): Zhangyong Xia, Minghong Gu, Xiaodong Jia, Xiaoting Wang, Chunxia Wu, Jiangwen Guo, Liyong Zhang, Yifeng Du, Jiyue Wang
Software Mentions: 1
Published: about 8 years ago

10.1186/s13059-015-0768-0

Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells
Cited by: 175
Author(s): A. Rasim Barutcu, Bryan R. Lajoie, Rachel Patton McCord, Coralee E. Tye, Deli Hong, Terri L. Messier, Gillian Browne, André J. van Wijnen, Jane B. Lian, Janet L. Stein, Job Dekker, Anthony N. Imbalzano
Software Mentions: 1
Published: almost 11 years ago

10.18502/jovr.v15i2.6730

Screening for Novel LOX and SOD1 Variants in Keratoconus Patients from Brazil
Cited by: 8
Author(s): Diego Nery Benevides Gadelha, Alex Felipe Barbosa Feitosa, Rafaela Gomes da Silva, Luana Talita Antunes, Matheus Cavalcanti Muniz, Matheus Alencar de Oliveira, Dáfine de Oliveira Andrade, Nathalia Mayanna da Paz Silva, Sebastião Cronemberger, Bruno Luiz Fonseca Schamber-Reis
Software Mentions: 1
Published: over 6 years ago

10.1186/s13059-015-0842-7

High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction
Cited by: 106
Author(s): Joseph L. McClay, Andrey A. Shabalin, Mikhail G. Dozmorov, Daniel E. Adkins, Gaurav Kumar, Srilaxmi Nerella, Shaunna L. Clark, Sarah E. Bergen, Christina M. Hultman, Patrik K. E. Magnusson, Patrick F. Sullivan, Karolina A. Åberg, Edwin J. C. G. van den Oord
Software Mentions: 1
Published: almost 11 years ago

10.1186/s13059-016-0876-5

The contribution of Alu exons to the human proteome
Cited by: 36
Author(s): Lan Lin, Peng Jiang, Juw Won Park, Jinkai Wang, Zhi-xiang Lu, Maggie P. Y. Lam, Peipei Ping, Yi Xing
Software Mentions: 1
Published: over 10 years ago

10.1186/s12861-016-0119-8

Expression and knockdown of zebrafish folliculin suggests requirement for embryonic brain morphogenesis
Cited by: 3
Author(s): Emma J. Kenyon, Monique Luijten, Harmeet Gill, Nan Li, Matthew Rawlings, James C. Bull, Yavor Hadzhiev, M.A.M. van Steensel, Eamonn R. Maher, Ferenc Müller
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-213X-8-46

Axon-bearing and axon-less horizontal cell subtypes are generated consecutively during chick retinal development from progenitors that are sensitive to follistatin
Cited by: 35
Author(s): Per-Henrík Edqvist, Madelen Lek, Henrik Boije, Sarah M Lindbäck, Finn Hallböök
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-213X-9-11

Trichostatin A treatment of cloned mouse embryos improves constitutive heterochromatin remodeling as well as developmental potential to term
Cited by: 79
Author(s): Walid E. Maalouf, Zichuan Liu, Vincent Brochard, Jean‐Paul Renard, Pascale Debey, Nathalie Beaujean, Daniele Zink
Software Mentions: 1
Published: over 17 years ago

10.1016/j.isci.2019.10.055

Deciphering the Gene Regulatory Landscape Encoded in DNA Biophysical Features
Cited by: 7
Author(s): Abhijeet Pataskar, Willem Vanderlinden, Johannes Friedrich Emmerig, Aditi Singh, Jan Lipfert, Vijay Tiwari
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-12532-y

SHH signaling directed by two oral epithelium-specific enhancers controls tooth and oral development
Cited by: 22
Author(s): Tomoko Sagai, Takanori Amano, Akiteru Maeno, Hiroshi Kanazawa, Hye-Jin Seo, Sung Won Cho, Toshihiko Shiroishi
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13059-017-1185-3

Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions
Cited by: 141
Author(s): John Cole, Neil Robertson, Mohammed Iqbal Rather, John P. Thomson, Tony McBryan, Duncan Sproul, Tina Wang, Claire Brock, William Clark, Trey Ideker, Richard R. Meehan, Richard A. Miller, Holly M. Brown–Borg, Peter D. Adams
Software Mentions: 1
Published: over 9 years ago

10.1186/s13059-017-1226-y

The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci
Cited by: 30
Author(s): Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Li, Jin‐Xing Zhou, Joe Ogas, Jian‐Kang Zhu, Xin‐Jian He, Heng Zhang
Software Mentions: 1
Published: over 9 years ago

10.1186/s13059-017-1225-z

Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements
Cited by: 21
Author(s): Cristina Vicente-García, Bárbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D. Acemel, Juan J. Tena, Peter Rigby, Damien P. Devos, José Luis Gómez-Skármeta, Jaime J. Carvajal
Software Mentions: 1
Published: about 9 years ago

10.1186/gb-2004-6-1-r9

Cited by: 253
Author(s): Frank Desiere, Eric W. Deutsch, Alexey I. Nesvizhskii, Parag Mallick, Nichole L. King, Jimmy K. Eng, Alan Aderem, Rose Boyle, Erich Brunner, Samuel Donohoe, Nelson Fausto, Ernst Hafen, Lee Hood, Michael G. Katze, Kathleen A. Kennedy, Floyd Kregenow, Hookeun Lee, Biaoyang Lin, Dan Martin, Jeffrey A. Ranish, David J. Rawlings, Lawrence E. Samelson, Yuzuru Shiio, Julian D. Watts, Bernd Wollscheid, M. Wright, Wei Yan, Lizhu Yang, Eugene C. Yi, Hui Zhang, Ruedi Aebersold
Software Mentions: 1
Published: over 22 years ago

10.1186/s13059-018-1393-5

The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages
Cited by: 30
Author(s): Eugenia D’Atanasio, Beniamino Trombetta, Maria Di Bonito, Andrea Finocchio, Genny Di Vito, Mara Seghizzi, Rita Romano, Gianluca Russo, Giacomo Maria Paganotti, Elizabeth E. Watson, Alfredo Coppa, Paolo Anagnostou, Jean‐Michel Dugoujon, Pedro Moral, Daniele Sellitto, Andrea Novelletto, Fulvio Cruciani
Software Mentions: 1
Published: over 8 years ago

10.1186/s13059-018-1434-0

Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome
Cited by: 73
Author(s): Luís Zapata, Oriol Pich, Luís Serrano, Fyodor A. Kondrashov, Stephan Ossowski, Martin H. Schaefer
Software Mentions: 1
Published: over 8 years ago

10.1186/s13059-018-1493-2

Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons
Cited by: 16
Author(s): Yuan Yuan, Shirley Xie, Jennifer C. Darnell, Andrew J. Darnell, Yuhki Saito, Hemali Phatnani, Elisabeth A. Murphy, Chaolin Zhang, Tom Maniatis, Robert B. Darnell
Software Mentions: 1
Published: about 8 years ago

10.1186/s13059-018-1491-4

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data
Cited by: 181
Author(s): Michaël Alaux, Jane Rogers, Thomas Letellier, Raphaël Flores, Françoise Alfama, Cyril Pommier, Nacer Mohellibi, Sophie Durand, Erik Kimmel, Célia Michotey, Claire Guerche, Mikaël Loaec, Mathilde Lainé, Delphine Steinbach, Frédéric Choulet, Hélène Rimbert, Philippe Leroy, Nicolas Guilhot, Jérôme Salse, Catherine Feuillet, Etienne Paux, Kellye Eversole, Anne-Françoise Adam-Blondon, Hadi Quesneville
Software Mentions: 1
Published: about 8 years ago

10.1186/s13059-018-1544-8

Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes
Cited by: 40
Author(s): Joana Damas, Jaebum Kim, Marta Farré, Darren K. Griffin, Denis M. Larkin
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-213X-13-18

Expression of phosphatase of regenerating liver family genes during embryogenesis: an evolutionary developmental analysis among Drosophila, amphioxus, and zebrafish
Cited by: 22
Author(s): Ming‐Der Lin, Hsun-Tzu Lee, Szu-Chieh Wang, Han-Ru Li, Hsin-Lun Hsien, Kai-Wen Cheng, Yu-Di Chang, Min-Lang Huang, Jr-Kai Yu, Yau‐Hung Chen
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-213X-11-63

Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes
Cited by: 25
Author(s): Satadal Chatterjee, Guillaume Bourque, Thomas Lufkin
Software Mentions: 1
Published: almost 15 years ago

10.1186/s13059-019-1889-7

Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution
Cited by: 28
Author(s): Huizhong Fan, Qi Wu, Fuwen Wei, Fengtang Yang, Bee Ling Ng, Yibo Hu
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13059-019-1897-7

PASTMUS: mapping functional elements at single amino acid resolution in human cells
Cited by: 6
Author(s): Xinyi Zhang, Di Yue, Yinan Wang, Yan Zhou, Ying Liu, Yu Qiu, Feng Tian, Ying Yu, Zhuo Zhou, Wensheng Wei
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13048-021-00834-9

p38β - MAPK11 and its role in female cancers
Cited by: 11
Author(s): Periklis Katopodis, Rachel Kerslake, Athanasios Zikopoulos, Nefeli Eirini Beri, Vladimir Anikin
Software Mentions: 1
Published: about 5 years ago

10.1186/s12906-021-03310-5

Echinacea purpurea (L.) Moench treatment of monocytes promotes tonic interferon signaling, increased innate immunity gene expression and DNA repeat hypermethylated silencing of endogenous retroviral sequences
Cited by: 5
Author(s): Ken Declerck, Claudina Pérez Novo, Lisa Grielens, Guy Van Camp, Andy Suter, Wim Vanden Berghe
Software Mentions: 1
Published: over 5 years ago

10.1186/s13059-020-02017-z

ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data
Cited by: 91
Author(s): Egor Dolzhenko, Mark F Bennett, Phillip A. Richmond, Brett Trost, Sai Chen, Joke J.F.A. van Vugt, Charlotte Nguyen, Giuseppe Narzisi, Vladimir G. Gainullin, Andrew M. Gross, Bryan R. Lajoie, Ryan J. Taft, Wyeth W. Wasserman, Stephen W. Scherer, Jan H. Veldink, David Bentley, Ryan K. C. Yuen, Melanie Bahlo, Michael A. Eberle
Software Mentions: 1
Published: over 6 years ago

10.1186/s12906-018-2396-1

Topical anti-inflammatory and anti-oxidative effects of porcine placenta extracts on 2,4-dinitrochlorobenzene-induced contact dermatitis
Cited by: 15
Author(s): Jae-Hyeok Heo, Yoonki Heo, Hee Jung Lee, Min-Jee Kim, Ha Youn Shin
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2407-9-198

A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth
Cited by: 52
Author(s): Hiroaki Mitsuya, Minoru Toyota, Fugaku Aoki, Hirofumi Akashi, Reo Maruyama, Yasushi Sasaki, Hiromu Suzuki, Masashi Idogawa, Lisa Kashima, Kazuyoshi Yanagihara, Masahiro Fujita, Masao Hosokawa, Masanobu Kusano, Sorin V. Sabau, Haruyuki Tatsumi, Kohzoh Imai, Yasuhisa Shinomura, Takashi Tokino
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2407-10-40

Orphan receptor GPR110, an oncogene overexpressed in lung and prostate cancer
Cited by: 63
Author(s): Amy Lum, Bruce B. Wang, Gabriele Beck-Engeser, Lauri Li, Namitha Channa, Matthias Wabl
Software Mentions: 1
Published: over 16 years ago

10.1186/s13059-020-02184-z

Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus
Cited by: 7
Author(s): Prithvi Raj, Ran Song, Honglin Zhu, Linley Riediger, Dong Jae Jun, Chao Liang, Carlos Arana, Bo Zhang, Yajing Gao, Benjamin Wakeland, Igor Dozmorov, Jianuan Zhou, Jennifer A. Kelly, Bernard Lauwerys, Joel M. Guthridge, Nancy J. Olsen, Swapan K. Nath, Chandrashekhar Pasare, Nicolai S. C. van Oers, Gary S. Gilkeson, Betty P. Tsao, Patrick M. Gaffney, Peter K. Gregersen, Judith A. James, Xiaoxia Zuo, David R. Karp, Quan Zhen Li, Edward K. Wakeland
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12885-021-08332-3

Prognostic and clinicopathological insights of phosphodiesterase 9A gene as novel biomarker in human colorectal cancer
Cited by: 10
Author(s): Tasmina Ferdous Susmi, Atikur Rahman, Md. Moshiur Rahman Khan, Farzana Yasmin, Md. Shariful Islam, Omaima Nasif, Sulaiman Ali Alharbi, Gaber El‐Saber Batiha, Mohammad Uzzal Hossain
Software Mentions: 1
Published: over 5 years ago

10.1186/s12885-018-5050-x

TRPM7 overexpression enhances the cancer stem cell-like and metastatic phenotypes of lung cancer through modulation of the Hsp90α/uPA/MMP2 signaling pathway
Cited by: 34
Author(s): Kai Li, Shaohua Xu, Zhao Chun-hua, Qingxin Zeng, Zhijun Li, Zhoumiao Chen
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12915-016-0320-z

Coordinated inhibition of C/EBP by Tribbles in multiple tissues is essential for Caenorhabditis elegans development
Cited by: 30
Author(s): Kyung Won Kim, Nishant Thakur, Christopher A. Piggott, Shizue Omi, Jolanta Polanowska, Yishi Jin, Nathalie Pujol
Software Mentions: 1
Published: almost 10 years ago

10.1186/1741-7007-11-24

Copy-number variation of cancer-gene orthologs is sufficient to induce cancer-like symptoms in Saccharomyces cerevisiae
Cited by: 17
Author(s): Michaela de Clare, Stephen G. Oliver
Software Mentions: 1
Published: over 13 years ago

10.1093/gbe/evu139

The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome
Cited by: 54
Author(s): Samuel H. Aeschlimann, Franziska Jönsson, Jan Postberg, Nicholas A. Stover, Robert L. Petera, Hans-Joachim Lipps, Mariusz Nowacki, Estienne C. Swart
Software Mentions: 1
Published: about 12 years ago

10.18632/oncotarget.7715

P300 acetyltransferase regulates fatty acid synthase expression, lipid metabolism and prostate cancer growth
Cited by: 41
Author(s): Xiaokun Gang, Yinhui Yang, Jian Zhong, Kui Jiang, Yunqian Pan, Jeffrey Karnes, Jun Zhang, Wanhai Xu, Guixia Wang, Haojie Huang
Software Mentions: 1
Published: over 10 years ago

10.1093/gbe/evv012

The Role of DNA Insertions in Phenotypic Differentiation between Humans and Other Primates
Cited by: 4
Author(s): Elizabeth Hellen, Andrew D. Kern
Software Mentions: 1
Published: over 11 years ago

10.1093/gbe/evv142

A Genome-Wide Landscape of Retrocopies in Primate Genomes
Cited by: 44
Author(s): Fábio C. P. Navarro, Pedro A. F. Galante
Software Mentions: 1
Published: about 11 years ago

10.1093/gbe/evv161

Comparative Genomics of Environmental and Clinical<i>Stenotrophomonas maltophilia</i>Strains with Different Antibiotic Resistance Profiles
Cited by: 72
Author(s): Benjamin Youenou, Sabine Favre-Bonté, Josselin Bodilis, Elisabeth Brothier, Audrey Dubost, Daniel Müller, Sylvie Nazaret
Software Mentions: 1
Published: about 11 years ago

10.1093/gbe/evx237

The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine
Cited by: 9
Author(s): Eran Elhaik, Leeban Yusuf, Ainan I J Anderson, Mehdi Pirooznia, Dimitrios Arnellos, Gregory Vilshansky, Gunes Ercal, Yontao Lu, Teresa A. Webster, Michael L. Baird, Umberto Esposito
Software Mentions: 1
Published: almost 9 years ago

10.18632/oncotarget.7937

Tumor-promoting function and prognostic significance of the RNA-binding protein T-cell intracellular antigen-1 in esophageal squamous cell carcinoma
Cited by: 17
Author(s): Junichi Hamada, Katsutoshi Shoda, Kiyoshi Masuda, Yuji Fujita, Takuya Naruto, Tomohiro Kohmoto, Yuko Miyakami, Miki Watanabe, Yasusei Kudo, Hitoshi Fujiwara, Daisuke Ichikawa, Eigo Otsuji, Issei Imoto
Software Mentions: 1
Published: over 10 years ago

10.1093/gbe/evy199

Turning Vice into Virtue: Using Batch-Effects to Detect Errors in Large Genomic Data Sets
Cited by: 7
Author(s): Fabrizio Mafessoni, Rashmi B. Prasad, Leif Groop, Ola Hansson, Kay Prüfer
Software Mentions: 1
Published: almost 8 years ago

10.1093/gbe/evz228

A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona
Cited by: 69
Author(s): Yutaka Satou, Ryohei Nakamura, Dejie Yu, Reiko Yoshida, Mayuko Hamada, Manabu Fujie, Kanako Hisata, Hiroyuki Takeda, Noriyuki Satoh
Software Mentions: 1
Published: almost 7 years ago

10.1093/gbe/evz254

Genome Assembly of the Dogface Butterfly Zerene cesonia
Cited by: 7
Author(s): Luis Rodriguez-Caro, Jennifer Fenner, Caleb Benson, Steven M. Van Belleghem, Brian A. Counterman
Software Mentions: 1
Published: almost 7 years ago

10.1093/gbe/evaa045

Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome
Cited by: 9
Author(s): Michael Emmett Kartje, Peicheng Jing, Bret A. Payseur
Software Mentions: 1
Published: over 6 years ago

10.1186/1741-7007-8-149

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
Cited by: 246
Author(s): Philipp Kapranov, Georges St. Laurent, Tal Raz, Fatih Ozsolak, C. Patrick Reynolds, Poul H. Sorensen, Gregory H. Reaman, Patrice M. Milos, Robert J. Arceci, John F. Thompson, Timothy J. Triche
Software Mentions: 1
Published: almost 16 years ago

10.18632/oncotarget.7764

Associations between polymorphisms of long non-coding RNA MEG3 and risk of colorectal cancer in Chinese
Cited by: 53
Author(s): Xin Cao, Shulin Zhuang, Yong Hu, Xi Liu, Lichun Deng, Sheng Huaming, Weisheng Shen
Software Mentions: 1
Published: over 10 years ago

10.1186/2041-9414-2-6

Assessment of genome integrity with array CGH in cattle transgenic cell lines produced by homologous recombination and somatic cell cloning
Cited by: 7
Author(s): George E. Liu, Yali Hou, James M. Robl, Yoshimi Kuroiwa, Zhongde Wang
Software Mentions: 1
Published: over 15 years ago

10.1186/gm137

Collaboratively charting the gene-to-phenotype network of human congenital heart defects
Cited by: 28
Author(s): Roland Barriot, Jeroen Breckpot, Bernard Thienpont, Sylvain Brohée, Steven Van Vooren, Bert Coessens, Léon-Charles Tranchevent, Peter Van Loo, Marc Gewillig, Koenraad Devriendt, Yves Moreau
Software Mentions: 1
Published: over 16 years ago

10.1186/1750-1172-7-S2-A11

Speeding up research with the Semantic Web
Cited by: 1
Author(s): Marco Roos, Erik Schultes, Barend Mons
Software Mentions: 1
Published: over 14 years ago

10.1186/1741-7007-11-90

Transcription of a protein-coding gene on B chromosomes of the Siberian roe deer (Capreolus pygargus)
Cited by: 55
Author(s): Vladimir A. Trifonov, Polina Dementyeva, Denis M. Larkin, Patrícia C. M. O’Brien, Polina L. Perelman, Fengtang Yang, Malcolm A. Ferguson‐Smith, Alexander S. Graphodatsky
Software Mentions: 1
Published: about 13 years ago

10.1186/s12915-015-0147-z

Nuclear myosin 1 contributes to a chromatin landscape compatible with RNA polymerase II transcription activation
Cited by: 46
Author(s): Bader Almuzzaini, Aishe A. Sarshad, Ann Kristin Östlund Farrants, Piergiorgio Percipalle
Software Mentions: 1
Published: about 11 years ago

10.18632/aging.101671

A CREB1/miR-433 reciprocal feedback loop modulates proliferation and metastasis in colorectal cancer
Cited by: 31
Author(s): Yan Li, Weiqiang You, Nengquan Sheng, Jianfeng Gong, Landian Hu, Gewen Tan, Hongqi Chen, Zhigang Wang
Software Mentions: 1
Published: over 7 years ago

10.1186/s13073-017-0427-z

PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories
Cited by: 24
Author(s): Kenneth D. Doig, Andrew Fellowes, Anthony Bell, Andrei Seleznev, Dávid Ma, Jason Ellul, Jason Li, Maria A. Doyle, Ella R. Thompson, Amit Kumar, Luis F. Lara, Ravikiran Vedururu, Gareth Reid, Thomas Conway, Anthony T. Papenfuss, Stephen B. Fox
Software Mentions: 1
Published: over 9 years ago

10.1186/s13073-017-0453-x

Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells
Cited by: 20
Author(s): Maykel López Rodríguez, Dorota Kaminska, Kati Lappalainen, Jussi Pihlajamäki, Minna U. Kaikkonen, Markku Laakso
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-9-S12-S19

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
Cited by: 13
Author(s): Jin Yang, Shin Hwang, Jeongsu Oh, Jong Bhak, Tae-Kwon Sohn
Software Mentions: 1
Published: almost 18 years ago

10.1186/s13023-015-0251-8

Rare diseases in ICD11: making rare diseases visible in health information systems through appropriate coding
Cited by: 84
Author(s): Ségolène Aymé, Bertrand Bellet, Ana Rath
Software Mentions: 1
Published: over 11 years ago

10.1016/j.ygeno.2009.10.004

Genome-wide end-sequenced BAC resources for the NOD/MrkTac☆ and NOD/ShiLtJ☆☆ mouse genomes
Cited by: 15
Author(s): Charles A. Steward, Sean Humphray, Bob Plumb, Matthew C. Jones, Michael A. Quail, Stephen V. Rice, Tony Cox, Robert M. Davies, James K. Bonfield, Thomas M. Keane, Michael Nefedov, Pieter J. de Jong, Paul Lyons, Linda S. Wicker, John A. Todd, Yoshihide Hayashizaki, Omid M. Gulban, Jayne S. Danska, Jennifer Harrow, Tim Hubbard, Jane Rogers, David J. Adams
Software Mentions: 1
Published: over 16 years ago

10.1016/j.gpb.2019.03.006

Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production
Cited by: 34
Author(s): Lin Zhang, Meilan Liu, Hongxu Long, Wei Dong, Asher Pasha, Eddi Esteban, Wenying Li, Xiaoming Yang, Ze Li, Aixia Song, Duo Ran, Guang Zhao, Yanwei Zeng, Hao Chen, Ming Zou, Jingjing Li, Fan Liang, Meili Xie, Jiang Hu, Depeng Wang, Heping Cao, Nicholas J. Provart, Liangsheng Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1111/1751-7915.12135

Microbial strain collections and information
Cited by: 3
Author(s): Lawrence P. Wackett
Software Mentions: 1
Published: about 12 years ago

10.3390/metabo11040238

A Medicago truncatula Metabolite Atlas Enables the Visualization of Differential Accumulation of Metabolites in Root Tissues
Cited by: 2
Author(s): Clayton Kranawetter, Shuai Zeng, Trupti Joshi, Lloyd W. Sumner
Software Mentions: 1
Published: over 5 years ago

10.1186/1475-2859-8-53

Open access to sequence: Browsing the Pichia pastoris genome
Cited by: 54
Author(s): Diethard Mattanovich, Nico Callewaert, Pierre Rouzé, Yao‐Cheng Lin, Alexandra B. Graf, Andréas Redl, Petra Tiels, Brigitte Gasser, Kristof De Schutter
Software Mentions: 1
Published: over 17 years ago

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