pypi: browser | Projects | Ecosyste.ms: Papers

10.1186/1471-2105-9-145

ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts
Cited by: 8
Author(s): Kwangmin Choi, Sun Kim
Software Mentions: 1
Published: over 16 years ago

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan
Cited by: 38
Author(s): Jason C. Ting, Ying Ye, George H. Thomas, Ingo Ruczinski, Jonathan Pevsner
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2105-11-516

QTLminer: identifying genes regulating quantitative traits
Cited by: 24
Author(s): Rudi Alberts, Klaus Schughart
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2105-8-19

Statistical significance of cis-regulatory modules
Cited by: 70
Author(s): Dustin E. Schones, Andrew D. Smith, Michael Q. Zhang
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2105-8-94

Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements
Cited by: 13
Author(s): Sung Tae Doh, Yunyu Zhang, Matthew H Temple, Li Cai
Software Mentions: 1
Published: over 17 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 16 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: over 9 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: over 11 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 14 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 11 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 8 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 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 3 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: almost 15 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: over 15 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 6 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 3 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: about 13 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 11 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: almost 16 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 16 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: over 8 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: almost 16 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: almost 13 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 6 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: almost 17 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: almost 11 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: almost 18 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: about 11 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: almost 11 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: almost 17 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: over 15 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 14 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: almost 15 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: almost 11 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: almost 14 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: about 9 years ago

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: almost 12 years ago

10.1186/s12862-020-01624-5

The amylase gene cluster in house mice (Mus musculus) was subject to repeated introgression including the rescue of a pseudogene
Cited by: 2
Author(s): Miriam Linnenbrink, Kristian K. Ullrich, Ellen McConnell, Diethard Tautz
Software Mentions: 1
Published: over 4 years ago

10.1186/s12862-015-0437-7

Evolution of the unspliced transcriptome
Cited by: 7
Author(s): Jan Engelhardt, Peter F. Stadler
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2148-5-22

Cited by: 21
Author(s): Michael E. Bradley, Steven A. Benner
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2148-12-231

The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements
Cited by: 34
Author(s): Daniel Ocampo Daza, Görel Sundström, Christina Bergqvist, Dan Larhammar
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2156-8-78

SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
Cited by: 34
Author(s): Britta Mersch, Noa Sela, Gil Ast, Sándor Suhai, Agnes Hotz‐Wagenblatt
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2156-9-6

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples
Cited by: 24
Author(s): Paola Sebastiani, Zhenming Zhao, María M. Abad‐Grau, Alberto Riva, Stephen W. Hartley, Amanda Sedgewick, Alessandro Doria, Monty Montano, Efthymia Melista, Dellara F. Terry, Thomas T. Perls, Martin H. Steinberg, Clinton T. Baldwin
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12863-020-00913-8

Molecular basis of a new ovine model for human 3M syndrome-2
Cited by: 3
Author(s): Shernae A. Woolley, Steven Hayes, M. R. Shariflou, F. W. Nicholas, Cali E. Willet, Brendon A. O’Rourke, Imke Tammen
Software Mentions: 1
Published: about 4 years ago

10.1186/s12863-020-00868-w

Identification and genetic analysis of qCL1.2, a novel allele of the “green revolution” gene SD1 from wild rice (Oryza rufipogon) that enhances plant height
Cited by: 14
Author(s): Lizhen Zhang, Jingfen Huang, Yanyan Wang, Rui Xu, Ziyi Yang, Zhigang Zhao, Shijia Liu, Yunlu Tian, Xiaoming Zheng, Fĕi Li, Junrui Wang, Yue Song, Jiaqi Li, Yongxia Cui, Lifang Zhang, Yunlian Cheng, Jinhao Lan, Weihua Qiao, Qing Yang
Software Mentions: 1
Published: over 4 years ago

10.1186/s12863-016-0404-3

Multiple regulatory variants located in cell type-specific enhancers within the PKP2 locus form major risk and protective haplotypes for canine atopic dermatitis in German shepherd dogs
Cited by: 7
Author(s): Katarina Tengvall, Sergey V. Kozyrev, Marcin Kierczak, Kerstin Bergvall, Fabiana H.G. Farias, Brita Ardesjö-Lundgren, Mia Olsson, Eva Murén, Ragnvi Hagman, Tosso Leeb, Gerli Pielberg, Åke Hedhammar, Gerhard Andersson, Kerstin Lindblad‐Toh
Software Mentions: 1
Published: over 8 years ago

10.1186/s12863-019-0749-5

In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins
Cited by: 12
Author(s): Qiang Jiang, Han Zhao, Rongling Li, Yaran Zhang, Yong Liu, Jinpeng Wang, Xiuge Wang, Zhihua Ju, Wenhao Liu, Minghai Hou, Jinming Huang
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-13-688

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes
Cited by: 1
Author(s): Enrique Blanco, Montserrat Corominas
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-5-99

Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
Cited by: 292
Author(s): Albin Sandelin, Peter J. Bailey, Sara Bruce, Pär G. Engström, Joanna M. Klos, Wyeth W. Wasserman, Johan Ericson, Boris Lenhard
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-10-46

A multiway analysis for identifying high integrity bovine BACs
Cited by: 2
Author(s): Abhirami Ratnakumar, Wesley C. Barris, Sean McWilliam, Rüdiger Bräuning, John C. McEwan, W. M. Snelling, Brian P. Dalrymple
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12864-020-6688-8

Discovering candidate imprinted genes and imprinting control regions in the human genome
Cited by: 4
Author(s): Minou Bina
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-018-4886-4

H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells
Cited by: 22
Author(s): Jian Xu, Benjamin L. Kidder
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-10-209

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii
Cited by: 80
Author(s): Patrick May, Jan-Ole Christian, Stefan Kempa, Dirk Walther
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12864-016-2627-0

CRISPRDetect: A flexible algorithm to define CRISPR arrays
Cited by: 245
Author(s): Ambarish Biswas, Raymond H.J. Staals, Sergio E. Morales, Peter C. Fineran, Chris M. Brown
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-10-S3-S9

TTS Mapping: integrative WEB tool for analysis of triplex formation target DNA Sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome
Cited by: 32
Author(s): Piroon Jenjaroenpun, Vladimir A. Kuznetsov
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-9-320

T2D-Db: An integrated platform to study the molecular basis of Type 2 diabetes
Cited by: 37
Author(s): Shipra Agrawal, Nevenka Dimitrova, Prasanthi Nathan, K. R. Udayakumar, Swathi Lakshmi, Sriram Subramaniam, N Manjusha, Urmi Sengupta
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12864-016-2441-8

The effects of sample size on population genomic analyses – implications for the tests of neutrality
Cited by: 50
Author(s): Sankar Subramanian
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-14-69

High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome
Cited by: 81
Author(s): Gianni Liti, Alex N Nguyen Ba, Martin Blythe, Carolin A. Müller, Anders Bergström, Francisco A. Cubillos, Felix Dafhnis-Calas, Shima Khoshraftar, Sunir Malla, Neel Mehta, Cheuk Chuen Siow, Jonas Warringer, Alan M. Moses, Edward J. Louis, Conrad A. Nieduszynski
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-8-470

Maintenance of transposon-free regions throughout vertebrate evolution
Cited by: 32
Author(s): Cas Simons, Igor V. Makunin, Michael Pheasant, John S. Mattick
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-14-122

Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers
Cited by: 15
Author(s): Nazia Parveen, Ayesha Masood, Nouman Iftikhar, Bushra Fazal Minhas, Rashid Minhas, Uzma Nawaz, Amir Ali Abbasi
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-015-2107-y

Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data
Cited by: 6
Author(s): Praveen F. Cherukuri, Valerie V. Maduro, Karin Fuentes-Fajardo, Kevin Lam, David R. Adams, Cynthia J. Tifft, James C. Mullikin, William A. Gahl, Cornelius F. Boerkoel
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-13-367

Evidence for sequence biases associated with patterns of histone methylation
Cited by: 11
Author(s): Zhong Wang, Huntington F. Willard
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-15-867

A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus)
Cited by: 19
Author(s): Anne‐Laure Ferchaud, Susanne Holst Pedersen, Dorte Bekkevold, Jianbo Jian, Yongchao Niu, Michael Møller Hansen
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-015-1847-z

MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data
Cited by: 240
Author(s): Alexander Koch, Tim De Meyer, Jana Jeschke, Wim Van Criekinge
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-15-1010

Insights into the miRNA regulations in human disease genes
Cited by: 36
Author(s): Jyotirmoy Das, Soumita Podder, Tapash Chandra Ghosh
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2164-11-293

Ensembl variation resources
Cited by: 114
Author(s): Yuan Chen, Fiona Cunningham, Daniel Ríos, William McLaren, James Smith, Bethan Pritchard, Giulietta Spudich, Simon Brent, Eugene Kulesha, Pablo Marín-Garcia, Damian Smedley, Ewan Birney, Paul Flicek
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-12-204

Recent acquisition of imprinting at the rodent Sfmbt2 locus correlates with insertion of a large block of miRNAs
Cited by: 49
Author(s): Qianwei Wang, Jacqueline Chow, Jenny H. Hong, Anne C. Ferguson-Smith, Carol Moreno, P. J. Seaby, Paul B. Vrana, Kamelia Miri, Joon Tak, Philip E.D. Chung, Gabriela F. Mastromonaco, Isabella Caniggia, Susannah Varmuza
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-14-229

Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array
Cited by: 77
Author(s): Jiasen Liu, Li Zhang, Lingyang Xu, Hangxing Ren, Jian Lü, Xiaoning Zhang, Shifang Zhang, Xinlei Zhou, Caihong Wei, Fuping Zhao, Lixin Du
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-017-3801-8

Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes
Cited by: 9
Author(s): Irene Bassano, Swee Hoe Ong, Nathan Lawless, Thomas James Whitehead, Mark Fife, Paul Kellam
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-018-5330-5

HumCFS: a database of fragile sites in human chromosomes
Cited by: 57
Author(s): Rajesh Kumar, Gandharva Nagpal, Vinod Kumar, Salman Sadullah Usmani, Piyush Agrawal, Gajendra P. S. Raghava
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-9-525

NemaPath: online exploration of KEGG-based metabolic pathways for nematodes
Cited by: 25
Author(s): Todd Wylie, John Martin, Sahar Abubucker, Yong Yin, David N. Messina, Zhengyuan Wang, James P. McCarter, Makedonka Mitreva
Software Mentions: 1
Published: about 16 years ago

10.1186/s12864-020-07063-2

CrustyBase: an interactive online database for crustacean transcriptomes
Cited by: 14
Author(s): Cameron J. Hyde, Quinn P. Fitzgibbon, Abigail Elizur, Gregory G. Smith, Tomer Ventura
Software Mentions: 1
Published: about 4 years ago

10.1186/s12864-015-1245-6

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution
Cited by: 60
Author(s): Olgert Denas, Richard Sandstrom, Yong Cheng, Kathryn Beal, Javier Herrero, Ross C. Hardison, James Taylor
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-11-580

ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome
Cited by: 8
Author(s): Yi Ling, Zhou Du, Zhenhai Zhang, Zhen Su
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2164-13-713

Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression
Cited by: 18
Author(s): Ana Ariza-Cosano, Axel Visel, Len A. Pennacchio, Hunter B. Fraser, José Luis Gómez-Skármeta, Manuel Irimia, José Bessa
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-016-3173-5

Co-activator candidate interactions for orphan nuclear receptor NR2E1
Cited by: 10
Author(s): Ximena Corso-Díaz, Charles N. de Leeuw, Vivian Alonso, Diana Melchers, Bibiana K. Y. Wong, René Houtman, Elizabeth M. Simpson
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2164-11-565

Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay
Cited by: 70
Author(s): Nicholas J. McGlincy, Lit-Yeen Tan, Nicodème Paul, Mihaela Zavolan, Kathryn S. Lilley, Christopher W. Smith
Software Mentions: 1
Published: about 14 years ago

10.1186/s12864-018-5311-8

Characterization of the Esi3/RCI2/PMP3 gene family in the Triticeae
Cited by: 11
Author(s): Sabrina C Brunetti, Michelle K.M. Arseneault, Patrick J. Gulick
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-9-529

Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays
Cited by: 67
Author(s): Amandine Bemmo, David Benovoy, Tony Kwan, Daniel J. Gaffney, Roderick V. Jensen, Jacek Majewski
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2164-12-71

Characterization of the past and current duplication activities in the human 22q11.2 region
Cited by: 26
Author(s): Xingyi Guo, Laina Freyer, Bernice E. Morrow, Deyou Zheng
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-11-206

The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues
Cited by: 28
Author(s): Peter Lorenz, Sabine Dietmann, Thomas Wilhelm, Dirk Koczan, Sandra Autran, Sophie Gad, Gaiping Wen, Guohui Ding, Yixue Li, Marie-Françoise Rousseau-Merck, Hans‐Juergen Thiesen
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-12-606

The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs
Cited by: 100
Author(s): Peter Arensburger, Robert H. Hice, Jennifer A. Wright, Nancy L. Craig, Peter W. Atkinson
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-018-4659-0

A machine learning model to determine the accuracy of variant calls in capture-based next generation sequencing
Cited by: 19
Author(s): Jeroen van den Akker, Gilad Mishne, Anjali D. Zimmer, Alicia Y. Zhou
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-10-291

Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)
Cited by: 259
Author(s): Roy R. Chaudhuri, Andrew G. Allen, Paul Owen, Gil Shalom, Karl Stone, Marcus Harrison, Timothy A. Burgis, M. Lockyer, Jorge García‐Lara, Simon J. Foster, Stephen J. Pleasance, Sarah Peters, Duncan J. Maskell, Ian G. Charles
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-8-42

Mapping of transcription start sites of human retina expressed genes
Cited by: 15
Author(s): Valeria Roni, Ronald Carpio, Bernd Wissinger
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-11-295

Touring Ensembl: A practical guide to genome browsing
Cited by: 34
Author(s): Giulietta Spudich, Xosé M. Fernández‐Suárez
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12864-018-4443-1

Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress
Cited by: 141
Author(s): Peng Zhao, Dongdong Wang, Ruoqiu Wang, Nana Kong, Chao Zhang, Chan Yang, Weihang Wu, Hongwei Ma, Qin Chen
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-021-07931-5

Genome-wide association study for deoxynivalenol production and aggressiveness in wheat and rye head blight by resequencing 92 isolates of Fusarium culmorum
Cited by: 3
Author(s): Thomas Miedaner, Andrea Vásquez, Valheria Castiblanco, Hilda Elena Castillo, Nora A. Foroud, Tobias Würschum, Willmar L. Leiser
Software Mentions: 1
Published: about 3 years ago

10.1186/1471-2164-8-316

Detection of RNA structures in porcine EST data and related mammals
Cited by: 13
Author(s): Stefan E. Seemann, Michael J. Gilchrist, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-10-614

Evidence of uneven selective pressure on different subsets of the conserved human genome; implications for the significance of intronic and intergenic DNA
Cited by: 24
Author(s): Scott Davidson, Andrew Starkey, Alasdair MacKenzie
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-15-729

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules
Cited by: 45
Author(s): Alice Grison, S. Zucchelli, Alice Urzì, Ilaria Zamparo, Dejan Lazarevic, Giovanni Pascarella, Paola Roncaglia, Alejandro Giorgetti, Paula Garcia‐Esparcia, Christina Vlachouli, Roberto Simone, Francesca Persichetti, Alistair R.R. Forrest, Yoshihide Hayashizaki, Paolo Carloni, Isidró Ferrer, Claudia Lodovichi, Charles Plessy, Stefano Gustincich
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2164-8-301

Glycerate kinase of the hyperthermophilic archaeon Thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes
Cited by: 23
Author(s): Kehrer Daniel, Hatim Ahmed, Henner Brinkmann, Bettina Siebers
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-10-341

Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase
Cited by: 122
Author(s): Elodie Fleury, Arnaud Huvet, Christophe Lelong, Julien de Lorgeril, Viviane Boulo, Yannick Gueguen, Evelyne Bachère, Arnaud Tanguy, Dario Moraga, Caroline Fabioux, Penelope K. Lindeque, J Shaw, Richard Reinhardt, Patrick Prunet, Grace Davey, Sylvie Lapègue, Christopher Sauvage, Charlotte Corporeau, Jeanne Moal, Frédérick Gavory, Patrick Wincker, François Moreews, Christophe Klopp, Michel Mathieu, Pierre Boudry, Pascal Favrel
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-9-399

Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution
Cited by: 47
Author(s): Wilfried Haerty, Carlo G. Artieri, Navid Khezri, Rama S. Singh, Bhagwati P. Gupta
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2164-15-308

Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology
Cited by: 76
Author(s): Ekaterina Chernyaeva, M. V. Shul'gina, Mikhail Rotkevich, Pavel Dobrynin, Serguei Simonov, Egor Shitikov, Dimitry D Ischenko, Irina Y. Karpova, Elena S. Kostryukova, Elena N. Ilina, Vadim M. Govorun, Viacheslav Zhuravlev, Olga Manicheva, Piotr Yablonsky, Yulia D Isaeva, Elena Nosova, Igor Mokrousov, Anna Vyazovaya, Olga Narvskaya, Alla Lapidus, Stephen J. O’Brien
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-015-1346-2

RNASeqBrowser: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks
Cited by: 8
Author(s): Jiyuan An, John Lai, David Wood, Atul Sajjanhar, Chenwei Wang, Gregor Tevz, Melanie Lehman, Colleen C. Nelson
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-8-195

Definition of the zebrafish genome using flow cytometry and cytogenetic mapping
Cited by: 44
Author(s): Jennifer L. Freeman, Adeola Adeniyi, Ruby Banerjee, Stephanie Dallaire, Sean Maguire, Jianxiang Chi, Bee Ling Ng, Cinthya Zepeda, Carol Scott, Sean Humphray, Jane Rogers, Yi Zhou, Leonard I. Zon, Nigel P. Carter, Fengtang Yang, Charles Lee
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-15-252

Implications of human genome structural heterogeneity: functionally related genes tend to reside in organizationally similar genomic regions
Cited by: 3
Author(s): Arnon Paz, Svetlana Frenkel, Sagi Snir, Valery Kirzhner, Abraham B. Korol
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-11-458

Using paired-end sequences to optimise parameters for alignment of sequence reads against related genomes
Cited by: 2
Author(s): Abhirami Ratnakumar, Sean McWilliam, Wesley C. Barris, Brian P. Dalrymple
Software Mentions: 1
Published: over 14 years ago

Projects: pypi: browser

Papers Mentioning browser 2,125