pypi: browser | Projects | Ecosyste.ms: Papers

10.1186/2041-1480-2-S2-S3

HyQue: evaluating hypotheses using Semantic Web technologies
Cited by: 33
Author(s): Alison Callahan, Michel Dumontier, Nigam H. Shah
Software Mentions: 2
Published: over 13 years ago

Using Semantic Web technologies for the generation of domain-specific templates to support clinical study metadata standards
Cited by: 7
Author(s): Guoqian Jiang, Julie Evans, Cory M. Endle, Harold R. Solbrig, Christopher G. Chute
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0006589

Integrated Expression Profiling and ChIP-seq Analyses of the Growth Inhibition Response Program of the Androgen Receptor
Cited by: 73
Author(s): Biaoyang Lin, Jun Wang, Hong Xu, Xiaowei Yan, Daehee Hwang, Ji Hoon Cho, Danielle Yi, Angelita G. Utleg, Xuefeng Fang, Dustin E. Schones, Keji Zhao, Gilbert S. Omenn, Leroy Hood
Software Mentions: 2
Published: over 15 years ago

10.1111/jcmm.14104

Genetic variant in miR‐21 binding sites is associated with colorectal cancer risk
Cited by: 6
Author(s): Le Xie, Shuwei Li, Jing Jin, Lei He, Kaili Xu, Lingjun Zhu, Mulong Du, Yanqing Liu, Haiyan Chu, Zhengdong Zhang, Meilin Wang, Danni Shi, Dongying Gu, Min Ni
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1006296

Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer
Cited by: 37
Author(s): Jian Gong, Carolyn M. Hutter, Polly A. Newcomb, Cornelia M. Ulrich, Stephanie A. Bien, Peter T. Campbell, John A. Baron, Sonja I. Berndt, Stéphane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang–Claude, Mengmeng Du, David Duggan, Jane C. Figueiredo, Steven Gallinger, Edward Giovannucci, Robert W. Haile, Tabitha A. Harrison, Richard B. Hayes, Michael Hoffmeister, John L. Hopper, Thomas J. Hudson, Jihyoun Jeon, Mark A. Jenkins, Jonathan Kocarnik, Sébastien Küry, Loı̈c Le Marchand, Yi Lin, Noralane M. Lindor, Reiko Nishihara, Shuji Ogino, John D. Potter, Anja Rudolph, Robert E. Schoen, Petra Schrotz‐King, Daniela Seminara, Martha L. Slattery, Stephen N. Thibodeau, Mark Thornquist, Réka Tóth, Robert B. Wallace, Emily White, Shuo Jiao, Mathieu Lemire, Li Hsu, Ulrike Peters
Software Mentions: 2
Published: about 8 years ago

10.1111/pbi.13327

High‐resolution expression profiling of selected gene sets during plant immune activation
Cited by: 19
Author(s): Pingtao Ding, Bruno Pok Man Ngou, Oliver J. Furzer, Toshiyuki Sakai, Ram Krishna Shrestha, Dan MacLean, Jonathan D. G. Jones
Software Mentions: 2
Published: almost 5 years ago

10.1093/pcp/pcw207

TOMATOMICS: A Web Database for Integrated Omics Information in Tomato
Cited by: 18
Author(s): Toru Kudo, Mariko Kobayashi, Shin Terashima, Minami Katayama, Soichi Ozaki, Maasa Kanno, Misa Saito, Koji Yokoyama, Hajime Ohyanagi, Koh Aoki, Yasutaka Kubo, Kentarô Yano
Software Mentions: 2
Published: almost 8 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 16 years ago

10.3390/jcm9061672

Association Analysis of TP53 rs1042522, MDM2 rs2279744, rs3730485, MDM4 rs4245739 Variants and Acute Myeloid Leukemia Susceptibility, Risk Stratification Scores, and Clinical Features: An Exploratory Study
Cited by: 6
Author(s): Florin Tripon, Mihaela Iancu, Adrian P. Trifa, George Andrei Crauciuc, Alina Bogliş, Beáta Balla, Adriana S Cosma, Delia Dima, Marcela Cândea, Erzsébet Lázár, Laura Jimbu, Claudia Bănescu
Software Mentions: 2
Published: over 4 years ago

10.1089/cmb.2018.0199

INDEX-db: The Indian Exome Reference Database (Phase I)
Cited by: 11
Author(s): Parvez Ahmed, More Rp, Biju Viswanath, Sanjeev Jain, Rao Ms, Odity Mukherjee
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-13-S15-S4

Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
Cited by: 12
Author(s): Joseph S. Reddy, Ranjit Kumar, James Watt, Mark L. Lawrence, Shane C. Burgess, Bindu Nanduri
Software Mentions: 2
Published: about 12 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 15 years ago

10.1186/1756-0500-7-845

Experience of using an open source clinical trials data management software system in Kenya
Cited by: 15
Author(s): Moses Ngari, Naomi Waithira, Roma Chilengi, Patricia Njuguna, Trudie Lang, Greg Fegan
Software Mentions: 2
Published: almost 11 years ago

10.1186/1746-4811-7-31

Maize microarray annotation database
Cited by: 9
Author(s): Nanette Coetzer, Alexander Andrew Myburg, David Kenneth Berger
Software Mentions: 2
Published: about 13 years ago

10.1186/1756-0500-4-405

EcoBrowser: a web-based tool for visualizing transcriptome data of Escherichia coli
Cited by: 3
Author(s): Xiao Chang, Yun Li, Jie Ping, Xiaobin Xing, Han Sun, Peng Jia, Chuan Wang, Yuanyuan Li, Yixue Li
Software Mentions: 2
Published: about 13 years ago

10.1093/jxb/eraa550

Abundance of metalloprotease FtsH12 modulates chloroplast development in Arabidopsis thaliana
Cited by: 16
Author(s): Kati Mielke, Raik Wagner, Laxmi S. Mishra, Fatih Demir, Andreas Perrar, Pitter F. Huesgen, Christiane Funk
Software Mentions: 2
Published: about 4 years ago

10.1007/s11103-016-0508-1

Elucidating and mining the Tulipa and Lilium transcriptomes
Cited by: 16
Author(s): Natalia M. Moreno-Pachon, Hendrika A.C.F. Leeggangers, Harm Nijveen, Edouard Severing, Henk W. M. Hilhorst, Richard G. H. Immink
Software Mentions: 2
Published: over 8 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 14 years ago

10.1186/s12864-016-2794-z

MBDDiff: an R package designed specifically for processing MBDcap-seq datasets
Cited by: 3
Author(s): Yuanhang Liu, Desiree Wilson, Robin J. Leach, Yidong Chen
Software Mentions: 2
Published: over 8 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 6 years ago

10.1186/1471-2105-6-95

Cited by: 12
Author(s): Judith E. Stenger, Hong Xu, Carol Haynes, Elizabeth R. Hauser, Margaret A. Pericak‐Vance, Pascal J. Goldschmidt‐Clermont, Jeffery M. Vance
Software Mentions: 2
Published: almost 20 years ago

10.1371/journal.ppat.1009615

A parasitoid wasp of Drosophila employs preemptive and reactive strategies to deplete its host’s blood cells
Cited by: 6
Author(s): Johnny R. Ramroop, Mary Ellen Heavner, Zubaidul H. Razzak, Shubha Govind
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.ppat.1009796

Cytomegalovirus late transcription factor target sequence diversity orchestrates viral early to late transcription
Cited by: 12
Author(s): Ming Li, Qiaolin Hu, Geoffrey S Collins, Mrutyunjaya Parida, Christopher B. Ball, David H. Price, Jeffery L. Meier
Software Mentions: 2
Published: over 3 years ago

10.1155/2020/1783564

Association of Peroxisome Proliferator-Activated Receptors (PPARs) with Diabetic Retinopathy in Human and Animal Models: Analysis of the Literature and Genome Browsers
Cited by: 4
Author(s): Špela Tajnšek, Danijel Petrovič, Mojca Globočnik Petrovič, Tanja Kunej
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0173723

Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability
Cited by: 28
Author(s): Anna C. Salzberg, Abigail Harris-Becker, Evgenya Y. Popova, Nikki Keasey, Thomas P. Loughran, David F. Claxton, Sergei A. Grigoryev
Software Mentions: 2
Published: over 7 years ago

10.1007/s13238-017-0497-0

Antisense transcription regulates the expression of sense gene via alternative polyadenylation
Cited by: 3
Author(s): Ting Shen, Huan Li, Yifan Song, Jun Yao, Moonsik Han, Ming Yu, Gang Wei, Ting Ni
Software Mentions: 2
Published: almost 7 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 3 years ago

10.1186/s12870-019-1651-z

Transcriptomic analysis of Citrus clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness
Cited by: 21
Author(s): Javier Terol, María José Nueda, Daniel Ventimilla, Francisco R. Tadeo, Manuel Talón
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-12-165

Rice-Map: a new-generation rice genome browser
Cited by: 12
Author(s): Jun Wang, Lei Kong, Shuqi Zhao, He Zhang, Liang Tang, Zhe Li, Xiaocheng Gu, Jianxun Luo, Ge Gao
Software Mentions: 2
Published: over 13 years ago

10.1002/jrsm.1408

“statcheck”: Automatically detect statistical reporting inconsistencies to increase reproducibility of <scp>meta‐analyses</scp>
Cited by: 9
Author(s): Michèle B. Nuijten, Joshua R. Polanin
Software Mentions: 2
Published: over 4 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 14 years ago

10.1186/s12864-018-5376-4

GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution
Cited by: 9
Author(s): Peter J. Hansen, Salaheddine Ali, Hannah Blau, Daniel Daniš, Jochen Hecht, Uwe Kornak, Darío G. Lupiáñez, Stefan Mundlos, Robin Steinhaus, Peter N. Robinson
Software Mentions: 2
Published: almost 6 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 9 years ago

10.1038/s41598-017-09810-0

Evidence-based tailoring of bioinformatics approaches to optimize methods that predict the effects of nonsynonymous amino acid substitutions in glucokinase
Cited by: 9
Author(s): Daniela Šimčíková, Lucie Kocková, Kateřina Vackářová, Miroslav Těšínský, Petr Heneberg
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2105-11-239

Using caching and optimization techniques to improve performance of the Ensembl website
Cited by: 7
Author(s): Anne Parker, Eugene Bragin, Simon Brent, Bethan Pritchard, James Smith, Stephen J. Trevanion
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2105-9-432

easyExon – A Java-based GUI tool for processing and visualization of Affymetrix exon array data
Cited by: 18
Author(s): Ting‐Yu Chang, Yin-Yi Li, C.-L. Jen, Tsun-Po Yang, Chi‐Hung Lin, Ming Hsu, Hsei‐Wei Wang
Software Mentions: 2
Published: about 16 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 16 years ago

10.1371/journal.pone.0238179

Genome-wide identification and expression profiling of the carotenoid cleavage dioxygenase (CCD) gene family in Brassica napus L
Cited by: 12
Author(s): Xin-Tong Zhou, Longfei Jia, Mouzheng Duan, Xue Chen, Cailin Qiao, Jinqi Ma, Chao Zhang, Fuyu Jing, Shengsen Zhang, Bo Yang, Liyuan Zhang, Jiana Li
Software Mentions: 2
Published: about 4 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 4 years ago

10.1371/journal.pone.0097568

Genome-Wide Quantitative Analysis of Histone H3 Lysine 4 Trimethylation in Wild House Mouse Liver: Environmental Change Causes Epigenetic Plasticity
Cited by: 12
Author(s): Angelika Börsch-Haubold, Inka Montero, Kathryn Konrad, Bernhard Haubold
Software Mentions: 2
Published: over 10 years ago

10.1038/sdata.2017.107

FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies
Cited by: 58
Author(s): Imad Abugessaisa, Shuhei Noguchi, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Marina Lizio, Jessica Severin, Piero Carninci, Hideya Kawaji, Takeya Kasukawa
Software Mentions: 2
Published: about 7 years ago

10.1038/sdata.2017.112

FANTOM5 CAGE profiles of human and mouse samples
Cited by: 169
Author(s): Shuhei Noguchi, Takahiro Arakawa, Shiro Fukuda, Masaaki Furuno, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Kaoru Kaida, Ai Kaiho, Mutsumi Kanamori-Katayama, Tsugumi Kawashima, Miki Kojima, Atsutaka Kubosaki, Ri Ichiroh Manabe, Mitsuyoshi Murata, Sayaka Nagao-Sato, Kenichi Nakazato, Noriko Ninomiya, Hiromi Nishiyori-Sueki, Shohei Noma, Eri Saijyo, Akiko Saka, Mizuho Sakai, Christophe Simon, Naoki Suzuki, Michihira Tagami, Shoko Watanabe, Shigehiro Yoshida, Peter Arner, Richard Axton, Magda Babina, J Kenneth Baillie, Timothy C. Barnett, Anthony G Beckhouse, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, Ailsa J Carlisle, Hans Clevers, Carrie A. Davis, Michael Detmar, Taeko Dohi, B. Albert S. Edge, Matthias Edinger, Anna Ehrlund, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Afsaneh Eslami, Michela Fagiolini, Lynsey Fairbairn, Mary C. Farach-Carson, Geoffrey J. Faulkner, Carmelo Ferrai, Malcolm E Fisher, Lesley M. Forrester, Rie Fujita, Jun Furusawa, Teunis B. H. Geijtenbeek, T Gingeras, Daniel Goldowitz, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas Ha, Masahide Hamaguchi, Mitsuko Hara, Yuki Hasegawa, Meenhard Herlyn, Peter Heutink, Kelly J Hitchens, David Hume, Tomokatsu Ikawa, Yuri Ishizu, Chieko Kai, Hiroshi Kawamoto, Yuki I. Kawamura, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, Sarah Klein, S. Peter Klinken, Alan J. Knox, Soichi Kojima, Haruhiko Koseki, Shigeo Koyasu, Weon-Ju Lee, Andreas Lennartsson, Alan Mackay‐Sim, Niklas Mejhert, Yosuke Mizuno, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Kelly J. Morris, Hozumi Motohashi, Christine L. Mummery, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Tomohiro Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada‐Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Robert Passier, Margaret Patrikakis, Ana Pombo, Swati Pradhan-Bhatt, Xian Qin, Michael Rehli, Patrizia Rizzu, Sugata Roy, Antti Sajantila, Shimon Sakaguchi, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Christian Schmidl, Claudio Schneider, Gundula Schulze‐Tanzil, Anita Schwegmann, Guojun Sheng, Jay W. Shin, Daisuke Sugiyama, Takaaki Sugiyama, Kim M. Summers, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Andru Tomoiu, Hiroo Toyoda, Marcvande Wetering, Linda Berg, Roberto Verardo, Dipti Vijayan, Christine A. Wells, Louise N. Winteringham, Ernst J. Wolvetang, Yoko Yamaguchi, Masayuki Yamamoto, Chiyo Yanagi-Mizuochi, Misako Yoneda, Yohei Yonekura, Peter G. Zhang, S. Zucchelli, Imad Abugessaisa, Peter Arner, Jayson Harshbarger, Atsushi Kondo, Timo Lassmann, Marina Lizio, Serkan Sahin, Thierry Sengstag, Jessica Severin, Hisashi Shimoji, Masanori Suzuki, Harukazu Suzuki, Jun Kawai, Naoto Kondo, Masayoshi Itoh, Carsten O. Daub, Takeya Kasukawa, Hideya Kawaji, Piero Carninci, Alistair R.R. Forrest, Yoshihide Hayashizaki
Software Mentions: 2
Published: about 7 years ago

10.1038/sdata.2018.235

De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing
Cited by: 50
Author(s): Fabien Dutreux, Corinne Da Silva, Léo d'Agata, Arnaud Couloux, Benjamin Istace, Nicolas Lapalu, Arnaud Lemainque, Juliette Linglin, Benjamin Noël, Patrick Wincker, Corinne Cruaud, Thierry Rouxel, Marie‐Hélène Balesdent, Jean‐Marc Aury
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2229-9-50

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences
Cited by: 54
Author(s): Martin Trick, Foo Cheung, Nizar Drou, F C Fråser, Edward K. Lobenhofer, Patrick Hurban, Andreas Magusin, Christopher D. Town, Ian Bancroft
Software Mentions: 2
Published: over 15 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 7 years ago

10.1371/journal.pone.0099844

OccuPeak: ChIP-Seq Peak Calling Based on Internal Background Modelling
Cited by: 10
Author(s): Bouke A. de Boer, Karel van Duijvenboden, Malou van den Boogaard, Vincent M. Christoffels, Phil Barnett, Jan M. Ruijter
Software Mentions: 2
Published: over 10 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 10 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 11 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 5 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 14 years ago

10.1371/journal.pone.0053452

From QTL to QTN: Candidate Gene Set Approach and a Case Study in Porcine IGF1-FoxO Pathway
Cited by: 9
Author(s): Minghui Wang, Qishan Wang, Yuchun Pan
Software Mentions: 2
Published: almost 12 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 4 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 15 years ago

10.18632/oncotarget.25536

Prostate cancer susceptibility gene HIST1H1A is a modulator of androgen receptor signaling and epithelial to mesenchymal transition
Cited by: 6
Author(s): Kendra A. Williams, Minnkyong Lee, Jean M. Winter, Derek Gildea, Carla Calagua, Natasha Curry, Jens Lichtenberg, Huihui Ye, Nigel P.S. Crawford
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0012362

Profiling and Functional Analyses of MicroRNAs and Their Target Gene Products in Human Uterine Leiomyomas
Cited by: 65
Author(s): Jiří Zavadil, Huihui Ye, Zhaojian Liu, Jingjing Wu, Peng Lee, Eva Hernando, Patricia Soteropoulos, Gokce Toruner, Jian Jun Wei
Software Mentions: 2
Published: about 14 years ago

10.1186/s12870-014-0412-2

NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome
Cited by: 16
Author(s): Hamed Bostan, Maria Luisa Chiusano
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep25954

CNV analysis in Chinese children of mental retardation highlights a sex differentiation in parental contribution to de novo and inherited mutational burdens
Cited by: 19
Author(s): Binbin Wang, Taoyun Ji, Xueya Zhou, Jing Wang, Xi Wang, Jingmin Wang, Dandan Zhu, Xuejun Zhang, Pak C. Sham, Xuegong Zhang, Xu Ma, Yuwu Jiang
Software Mentions: 2
Published: over 8 years ago

10.1038/srep32348

Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection
Cited by: 20
Author(s): Rajesh Pandey, Aniket Bhattacharya, Vivek Bhardwaj, Vineet Jha, Amit Kumar Mandal, Mitali Mukerji
Software Mentions: 2
Published: about 8 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 8 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 8 years ago

10.18632/oncotarget.11324

The cytokine-cosmc signaling axis upregulates the tumor-associated carbohydrate antigen Tn
Cited by: 4
Author(s): Chia Wen Ho, Chia‐Hua Lin, Yi Wei Liaw, Hsiao Ling Chiang, Yu Tang Chin, Rui Huang, Hung Cheng Lai, Yaw Wen Hsu, Po Jan Kuo, Chiao-En Chen, Hung Yun Lin, Jacqueline Whang‐Peng, Shin Nieh, Earl Fu, Leroy F. Liu, Jaulang Hwang
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.13746

An annotated list of bivalent chromatin regions in human ES cells: a new tool for cancer epigenetic research
Cited by: 41
Author(s): Franck Court, Philippe Arnaud
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.13720

Design and implementation of a mobile system for lung cancer patient follow-up in China and initial report of the ongoing patient registry
Cited by: 10
Author(s): Xiangyun Ye, Wei Hua Jia, Ziming Li, Xiaomin Niu, Jiemin Wang, Yunqin Chen, Zong-Ming Guo, Shun Lü
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.15571

Predictive analysis of long non-coding RNA expression profiles in diffuse large B-cell lymphoma
Cited by: 19
Author(s): Dan-Xia Zhu, Cheng Fang, Xiaodong Li, Yiting Geng, Ruiqi Li, Chen Wu, Jingting Jiang, Changping Wu
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.15478

NOMO-1 gene is deleted in early-onset colorectal cancer
Cited by: 16
Author(s): José Perea, Juan Luis Garcı́a, Javier Bajo Pérez, Daniel Rueda, María Arriba, Yolanda Rodríguez, Miguel Urioste, Rogelio González-Sarmiento
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.15695

Immunocompetent mouse allograft models for development of therapies to target breast cancer metastasis
Cited by: 72
Author(s): Yuan Yang, Howard H. Yang, Ying Hu, Peter H. Watson, Huaitian Liu, Thomas Geiger, Miriam R. Anver, Diana C. Haines, Philip Martin, Jeffrey E. Green, Maxwell P. Lee, Kent W. Hunter, Lalage M. Wakefield
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.17399

Clinically significant sub-clonality for common drivers can be detected in 26% of KRAS/EGFR mutated lung adenocarcinomas
Cited by: 4
Author(s): Einav Simon, Tova Bick, Shada Sarji, Talia Shentzer, Elad Prinz, Liza Yehiam, Edmond Sabo, Ofer Ben‐Izhak, Dov Hershkovitz
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.14175

Expression analysis of microRNA as prognostic biomarkers in colorectal cancer
Cited by: 46
Author(s): Jie Yang, Dongling Ma, Andrew Fesler, Haiyan Zhai, Apisri Leamniramit, Wenzhe Li, Song Wu, Jingfang Ju
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.17826

C1orf64 is a novel androgen receptor target gene and coregulator that interacts with 14-3-3 protein in breast cancer
Cited by: 11
Author(s): Ali Naderi
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.17740

TUBB3 overexpression has a negligible effect on the sensitivity to taxol in cultured cell lines
Cited by: 17
Author(s): Mihoko A. Tame, Anna G. Manjón, Daria Belokhvostova, Jonne A. Raaijmakers, René H. Medema
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.20340

LINC00461, a long non-coding RNA, is important for the proliferation and migration of glioma cells
Cited by: 35
Author(s): Yong Yang, Mingxin Ren, Song Chen, Dan Li, Shahid Hussain Soomro, Yajie Xiong, Hongfeng Zhang, Hui Fu
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.21272

MicroRNA-212/ABCG2-axis contributes to development of imatinib-resistance in leukemic cells
Cited by: 19
Author(s): Meike Kaehler, Johanna Ruemenapp, Daniel Gonnermann, Inga Nagel, Oliver Bruhn, Sierk Haenisch, Ole Ammerpohl, Daniela Wesch, Ingolf Cascorbi, Henrike Bruckmueller
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.20115

Long non-coding RNA polymorphisms in 6p21.1 are associated with atrophic gastritis risk and gastric cancer prognosis
Cited by: 9
Author(s): Zhi Lv, Liping Sun, Qian Xu, Yuehua Gong, Jingjing Jing, Chengzhong Xing, Yuan Yuan
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.21469

Deregulated c-Myc requires a functional HSF1 for experimental and human hepatocarcinogenesis
Cited by: 15
Author(s): Antonio Cigliano, Maria G. Pilo, Lei Li, Gavinella Latte, Marta Szydlowska, Maria M. Simile, Panagiotis Paliogiannis, Li Che, Giovanni Mario Pes, Giuseppe Palmieri, Maria Cristina Sini, Antonio Cossu, Alberto Porcu, Gianpaolo Vidili, Maria A. Seddaiu, Rosa M. Pascale, Silvia Ribback, Frank Dombrowski, Xin Chen, Diego F. Calvisi
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.22245

Loss of p53-inducible long non-coding RNA LINC01021 increases chemosensitivity
Cited by: 13
Author(s): Markus Kaller, Ursula Götz, Heiko Hermeking
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.22630

Identification of potential genetic causal variants for rheumatoid arthritis by whole-exome sequencing
Cited by: 19
Author(s): Ying Liu, Elaine Lai‐Han Leung, Hudan Pan, Xiaojun Yao, Qingchun Huang, Min Wu, Ting Xu, Yuwei Wang, Jun Cai, Runze Li, Wei Liu, Liang Liu
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.23643

Zinc finger protein 598 inhibits cell survival by promoting UV-induced apoptosis
Cited by: 2
Author(s): Qinghua Yang, Romi Gupta
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.25940

A novel molecular mechanism for a long non-coding RNA PCAT92 implicated in prostate cancer
Cited by: 5
Author(s): Pushpinder Bawa, Samathmika Ravi, Swagatika Paul, Bibha Chaudhary, Subhashini Srinivasan
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.27152

Safety evaluation of conditionally immortalized cells for renal replacement therapy
Cited by: 5
Author(s): Milos Mihajlovic, Sam Hariri, Koen C.G. Westphal, Manoe J. Janssen, Miriam J Oost, Laura Bongiovanni, Lambertus P. van den Heuvel, Alain de Bruin, Luuk B. Hilbrands, Rosalinde Masereeuw
Software Mentions: 1
Published: about 5 years ago

10.18632/oncotarget.28037

Diverse transcriptional regulation and functional effects revealed by CRISPR/Cas9-directed epigenetic editing
Cited by: 3
Author(s): Miguel Vizoso, Jacco van Rheenen
Software Mentions: 1
Published: over 3 years ago

10.3390/jpm11060468

Association of LINC00673 Genetic Variants with Progression of Oral Cancer
Cited by: 15
Author(s): Shih‐Chi Su, Chiao‐Wen Lin, Po‐Chung Ju, Lun‐Ching Chang, Chun‐Yi Chuang, Yu-Fan Liu, Ming‐Ju Hsieh
Software Mentions: 1
Published: over 3 years ago

10.3390/jpm11030231

The Epidemiology and Genetics of Hyperuricemia and Gout across Major Racial Groups: A Literature Review and Population Genetics Secondary Database Analysis
Cited by: 45
Author(s): Faven Butler, Ali Alghubayshi, Youssef M Roman
Software Mentions: 1
Published: over 3 years ago

10.1186/s40101-018-0169-7

Association of EGLN1 genetic polymorphisms with SpO2 responses to acute hypobaric hypoxia in a Japanese cohort
Cited by: 13
Author(s): Yoshiki Yasukochi, Takayuki Nishimura, Midori Motoi, Shigeki Watanuki
Software Mentions: 1
Published: over 6 years ago

10.1098/rsob.120054

Transcriptome sequencing of black grouse ( Tetrao tetrix ) for immune gene discovery and microsatellite development
Cited by: 26
Author(s): Biao Wang, Robert Ekblom, Todd A. Castoe, Eleanor P. Jones, Radoslav Kozma, Erik Bongcam‐Rudloff, David D. Pollock, Jacob Höglund
Software Mentions: 1
Published: over 12 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: about 6 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: about 7 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: almost 13 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 9 years ago

10.1186/s12967-018-1708-z

Mutational and phenotypic spectrum of OTOF-related auditory neuropathy in Koreans: eliciting reciprocal interaction between bench and clinics
Cited by: 17
Author(s): Bong Jik Kim, Jeong Hun Jang, Jin Hee Han, Hye Rim Park, Doo Yi Oh, Seungmin Lee, Min Young Kim, Ah Reum Kim, Chung Lee, Nayoung K.D. Kim, Woong-Yang Park, Yun Hoon Choung, Byung Yoon Choi
Software Mentions: 1
Published: almost 6 years ago

10.1155/2018/7640272

Myoblast Myogenic Differentiation but Not Fusion Process Is Inhibited via MyoD Tetraplex Interaction
Cited by: 5
Author(s): Stefano Testa, Pietro D’Addabbo, Ersilia Fornetti, Roberta Belli, Claudia Fuoco, Sergio Bernardini, Stefano Cannata, Domenico Frezza, Cesare Gargioli
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12986-015-0050-1

Epigenetic effects of casein-derived opioid peptides in SH-SY5Y human neuroblastoma cells
Cited by: 25
Author(s): Malav Suchin Trivedi, Nathaniel Hodgson, Stephen J. Walker, Geert Trooskens, Vineeth Nair, Richard C. Deth
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12986-021-00600-0

Modulation and bioinformatics screening of hepatic mRNA-lncRNAs (HML) network associated with insulin resistance in prediabetic and exercised mice
Cited by: 6
Author(s): Fatemeh Kazeminasab, Seyed Mohammad Marandi, Maryam Baharlooie, Mohammad Hossein Nasr-Esfahani, Kamran Ghaedi
Software Mentions: 1
Published: over 3 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: almost 6 years ago

10.1038/s41598-017-00301-w

MKL1 defines the H3K4Me3 landscape for NF-κB dependent inflammatory response
Cited by: 47
Author(s): Liming Yu, Fei Fang, Xin Dai, Huihui Xu, Xinming Qi, Mingming Fang, Yong Xu
Software Mentions: 1
Published: over 7 years ago

10.3390/nu5051706

Genome-Wide Association Study of Serum Selenium Concentrations
Cited by: 9
Author(s): Jian Gong, Li Hsu, Tabitha A. Harrison, Irena B. King, Stefan Stürup, Xiaoling Song, David Duggan, Yan Liu, Carolyn M. Hutter, Stephen J. Chanock, Charles B. Eaton, James R. Marshall, Ulrike Peters
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-017-03067-3

Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis
Cited by: 23
Author(s): Yuki Hitomi, Kazuyuki Kojima, M. Kawashima, Yosuke Kawai, Nao Nishida, Yoshihiro Aiba, Michio Yasunami, Masao Nagasaki, Minoru Nakamura, Katsushi Tokunaga
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-04657-x

Genetic targeting and anatomical registration of neuronal populations in the zebrafish brain with a new set of BAC transgenic tools
Cited by: 56
Author(s): Dominique Förster, Irene Arnold-Ammer, Eva Laurell, Alison J. Barker, António M. Fernandes, Karin Finger‐Baier, Alessandro Filosa, Thomas O. Helmbrecht, Yvonne Kölsch, Enrico Kühn, Estuardo Robles, Krasimir Slanchev, Tod R. Thiele, Herwig Baier, Fumi Kubo
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-10339-5

The PDK1 Inhibitor Dichloroacetate Controls Cholesterol Homeostasis Through the ERK5/MEF2 Pathway
Cited by: 23
Author(s): Asaad Khan, Nerea Allende-Vega, Delphine Gitenay, Sabine Gerbal‐Chaloin, Claire Gondeau, Dang Nghiem Vo, Sana Belkahla, Stefania Orecchioni, Giovanna Talarico, Francesco Bertolini, Milica Božić, José M. Valdivielso, Fabienne Bejjani, Isabelle Jariel, Isabel C. López-Mejía, Lluís Fajas, Charles-Henri Lecellier, Javier Hernandez, Martine Daujat, Martín Villalba
Software Mentions: 1
Published: about 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: about 7 years ago

10.1007/s13205-012-0063-7

Vertebrate patatin-like phospholipase domain-containing protein 4 (PNPLA4) genes and proteins: a gene with a role in retinol metabolism
Cited by: 7
Author(s): Roger S. Holmes
Software Mentions: 1
Published: over 12 years ago

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