pypi: browser | Projects | Ecosyste.ms: Papers

10.1186/s12864-016-3110-7

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

10.1155/2014/893501

AmalgamScope: Merging Annotations Data across the Human Genome
Cited by: 0
Author(s): Georgia Tsiliki, Konstantinos Tsaramirsis, Σοφία Κοσσίδα
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12864-016-2389-8

Cascade: an RNA-seq visualization tool for cancer genomics
Cited by: 2
Author(s): Aaron R. Shifman, Radia Marie Johnson, Brian T. Wilhelm
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-14-477

Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq
Cited by: 64
Author(s): Md. Shamimuzzaman, Lila O. Vodkin
Software Mentions: 2
Published: almost 14 years ago

10.7554/eLife.11155

Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway
Cited by: 112
Author(s): Zhiyun Ge, Bao Lin Quek, Karen Beemon, J. Robert Hogg
Software Mentions: 2
Published: almost 11 years ago

10.3390/biology9070157

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

10.3390/biology1020370

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

10.3390/biology10060500

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

10.1038/s41598-017-04642-4

Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population
Cited by: 56
Author(s): Sang Moon Lee, Jihae Seo, Jinman Park, Jae Yong Nam, Ahyoung Choi, Jason S. Ignatius, Robert Bjornson, Jong Hee Chae, In Jin Jang, Sanghyuk Lee, Woong-Yang Park, Daehyun Baek, Murim Choi
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.29550

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo
Cited by: 76
Author(s): Michael Stadler, Jenna E. Haines, Michael B. Eisen
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13293-017-0150-x

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

10.1038/s41598-017-14336-6

Unravelling pathways downstream Sox6 induction in K562 erythroid cells by proteomic analysis
Cited by: 6
Author(s): Gloria Barbarani, Antonella Ronchi, Margherita Ruoppolo, Lucia Santorelli, Robert S. Steinfelder, Sudharshan Elangovan, Cristina Fugazza, Marianna Caterino
Software Mentions: 2
Published: almost 9 years ago

10.1242/bio.011585

The canonical eIF4E isoform ofC. elegansregulates growth, embryogenesis, and germline sex-determination
Cited by: 8
Author(s): Richard S. Mangio, SarahBeth Votra, David Pruyne
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2105-11-611

SIDEKICK: Genomic data driven analysis and decision-making framework
Cited by: 4
Author(s): Mark Doderer, Kihoon Yoon, Kay A. Robbins
Software Mentions: 2
Published: almost 16 years ago

10.7554/eLife.56697

Trait-associated noncoding variant regions affect TBX3 regulation and cardiac conduction
Cited by: 5
Author(s): Jan Hendrik van Weerd, Rajiv A Mohan, Karel van Duijvenboden, Ingeborg B. Hooijkaas, Vincent Wakker, Bastiaan J. Boukens, Phil Barnett, Vincent M. Christoffels
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-019-6087-1

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

10.1038/srep33779

SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster
Cited by: 12
Author(s): Jinumary Mathai, Smriti Mittal, Aftab Alam, Payal Ranade, Devraj Mogare, Sonal Patel, Smita Saxena, Suvankar Ghorai, Abhijeet Kulkarni, Samit Chattopadhyay
Software Mentions: 2
Published: about 10 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 10 years ago

10.1186/1745-6150-5-67

Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers
Cited by: 5
Author(s): Georg Fuellen, Stephan Struckmann
Software Mentions: 2
Published: almost 17 years ago

10.1186/s12859-014-0412-0

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

10.1093/bioinformatics/btt330

Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation
Cited by: 9
Author(s): Colin Veal, Hang Xu, Katherine Reekie, Robert C. Free, Robert J. Hardwick, David G. McVey, Anthony J. Brookes, Edward J. Hollox, Chris J. Talbot
Software Mentions: 2
Published: over 13 years ago

10.1038/srep41598

Genome-wide Regulatory Roles of the C2H2-type Zinc Finger Protein ZNF764 on the Glucocorticoid Receptor
Cited by: 14
Author(s): Abeer A. Fadda, Najeeb Syed, Rafah Mackeh, Anna Papadopoulou, Shigeru Suzuki, Puthen V. Jithesh, Tomoshige Kino
Software Mentions: 2
Published: over 9 years ago

10.1093/bioinformatics/bts382

REVEAL--visual eQTL analytics
Cited by: 0
Author(s): Günter Jäger, Florian Battke, Kay Nieselt
Software Mentions: 2
Published: about 14 years ago

10.1038/s41598-017-06351-4

Integrin α6β4 Upregulates Amphiregulin and Epiregulin through Base Excision Repair-Mediated DNA Demethylation and Promotes Genome-wide DNA Hypomethylation
Cited by: 9
Author(s): Brittany L. Carpenter, Jinpeng Liu, Lei Qi, Chi Wang, Kathleen L. O’Connor
Software Mentions: 2
Published: about 9 years ago

10.1093/bioinformatics/btx007

ASCIIGenome: a command line genome browser for console terminals
Cited by: 3
Author(s): Dario Beraldi
Software Mentions: 2
Published: over 9 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 10 years ago

10.1038/srep41474

Genome-wide DNA methylation reprogramming in response to inorganic arsenic links inhibition of CTCF binding, DNMT expression and cellular transformation
Cited by: 29
Author(s): Matthew Rea, Meredith Eckstein, Rebekah Eleazer, Caroline N. Smith, Yvonne Fondufe‐Mittendorf
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.40811

Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis
Cited by: 60
Author(s): Shuo-Chien Ling, Somasish Ghosh Dastidar, Seiya Tokunaga, Wan Yun Ho, Kenneth Teck Kiat Lim, Hristelina Ilieva, Philippe A. Parone, Sheue Houy Tyan, Tsemay M. Tse, Jer Cherng Chang, Oleksandr Platoshyn, Ngoc B. Bui, Anh Bui, Anne P. Vetto, Shuying Sun, Melissa McAlonis-Downes, Joo Seok Han, Debbie Swing, Katannya Kapeli, G Yeo, Lino Tessarollo, Martin Mars̆ala, Christopher E. Shaw, Greg Tucker‐Kellogg, Albert R. La Spada, Clotilde Lagier‐Tourenne, Sandrine Da Cruz, Don W. Cleveland
Software Mentions: 2
Published: over 7 years ago

10.1186/s13040-021-00251-0

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

10.1186/1471-2105-13-S3-S13

Comparative analysis and visualization of multiple collinear genomes
Cited by: 54
Author(s): Jeremy Wang, Fernando Pardo Manuel de Villena, Leonard McMillan
Software Mentions: 2
Published: over 14 years ago

10.1186/s12917-018-1752-1

Inherited selective cobalamin malabsorption in Komondor dogs associated with a CUBN splice site variant
Cited by: 9
Author(s): John C. Fyfe, Shelby L. Hemker, Alycia Frampton, Karthik Raj, Péter L. Nagy, Kristi J. Gibbon, Urs Giger
Software Mentions: 2
Published: almost 8 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 9 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 6 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 9 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: about 5 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: over 7 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 6 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 13 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 5 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 9 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: almost 15 years ago

10.18632/aging.101867

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

10.1186/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: over 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 16 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 7 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 6 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: almost 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 17 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 8 years ago

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 15 years ago

10.1186/s13326-016-0053-5

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 10 years ago

10.1186/s12870-014-0412-2

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

10.1007/s13361-015-1269-9

High Resolution Mass Spectrometry of Polyfluorinated Polyether-Based Formulation
Cited by: 36
Author(s): Ian Ken D. Dimzon, Xenia Trier, Tobias Frömel, Rick Helmus, Thomas P. Knepper, P. de Voogt
Software Mentions: 2
Published: almost 11 years ago

10.1186/1745-7580-2-4

Cited by: 42
Author(s): Emily Wong, Lauren J. Young, Anthony T. Papenfuss, Katherine Belov
Software Mentions: 2
Published: almost 21 years ago

10.1186/s12859-018-2219-x

mySyntenyPortal: an application package to construct websites for synteny block analysis
Cited by: 6
Author(s): Jongin Lee, Daehwan Lee, Mikang Sim, Daehong Kwon, Ju‐Yeon Kim, Yun Woong Ko, Jaebum Kim
Software Mentions: 2
Published: over 8 years ago

10.1038/s41438-020-0336-y

Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral buds
Cited by: 38
Author(s): Hong Zhu, Pao‐Yang Chen, Silin Zhong, Chris Dardick, Ann M. Callahan, Yong-Qiang An, Steve van Knocker, Yingzhen Yang, Gan-Yuan Zhong, Albert G. Abbott, Zongrang Liu
Software Mentions: 2
Published: about 6 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: almost 8 years ago

10.1186/s12864-015-1414-7

The salinity tolerant poplar database (STPD): a comprehensive database for studying tree salt-tolerant adaption and poplar genomics
Cited by: 7
Author(s): Ying Ma, Ting Xu, Dongshi Wan, Tao Ma, Shengjun Shi, Jianquan Liu, Quanjun Hu
Software Mentions: 2
Published: over 11 years ago

10.1016/j.heliyon.2020.e05243

Fast, easy, cheap, robust and safe method of analysis of Sudan dyes in chilli pepper powder
Cited by: 5
Author(s): Joseph Kweku Adjei, Vigil Ahormegah, Alex Kissi Boateng, Harry Kwaku Megbenu, Samuel Asiedu Owusu
Software Mentions: 2
Published: about 6 years ago

10.3390/ht9020008

DMETTM Genotyping: Tools for Biomarkers Discovery in the Era of Precision Medicine
Cited by: 11
Author(s): Giuseppe Agapito, Marzia Settino, Francesca Scionti, Emanuela Altomare, Pietro Hiram Guzzi, Pierfrancesco Tassone, Pierosandro Tagliaferri, Mario Cannataro, Mariamena Arbitrio, Maria Teresa Di Martino
Software Mentions: 2
Published: over 6 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 9 years ago

10.1186/1471-2105-8-320

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation
Cited by: 6
Author(s): Kathrin Klee, Rebecca Ernst, Manuel Spannagl, Klaus Mayer
Software Mentions: 2
Published: about 19 years ago

10.1186/s12860-021-00378-2

Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity
Cited by: 2
Author(s): Atefeh Atefi, Pendar Shojaei kojouri, Fereshteh Karamali, Shiva Irani, Mohammad Hossein Nasr-Esfahani
Software Mentions: 2
Published: about 5 years ago

10.1186/s13073-018-0562-1

Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Cited by: 36
Author(s): Sabrina Grasse, Matthias Lienhard, Steffen Frese, Martin Kerick, Anne Steinbach, Christina Grimm, Michelle Hussong, Jana Rolff, Michael W. Becker, Felix Dreher, Uwe Schirmer, Stefan Boerno, Anna Ramisch, Gunda Leschber, Bernd Timmermann, Christian Grohé, H Lüders, Martin Vingron, Iduna Fichtner, Sebastian Klein, Margarete Odenthal, Reinhard Büttner, Hans Lehrach, Holger Sültmann, Ralf Herwig, Michal R. Schweiger
Software Mentions: 2
Published: about 8 years ago

10.1186/s12859-020-03806-w

oposSOM-Browser: an interactive tool to explore omics data landscapes in health science
Cited by: 10
Author(s): Henry Loeffler‐Wirth, Jasmin Reikowski, Siras Hakobyan, Jonas Wagner, Hans Binder
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-13-206

CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes
Cited by: 39
Author(s): Ivan Borozan, Shane Wilson, Paola Blanchette, Philippe Laflamme, Stuart Watt, Paul M. Krzyzanowski, Fabrice Sircoulomb, Robert Rottapel, Philip E. Branton, Vincent Ferretti
Software Mentions: 2
Published: about 14 years ago

10.1186/gm486

BAIT: Organizing genomes and mapping rearrangements in single cells
Cited by: 31
Author(s): Matthew J. Hills, Kieran O’Neill, Ester Falconer, Ryan R. Brinkman, Peter M. Lansdorp
Software Mentions: 2
Published: almost 14 years ago

10.1186/s13073-016-0320-1

Comprehensive promoter level expression quantitative trait loci analysis of the human frontal lobe
Cited by: 19
Author(s): Cornelis Blauwendraat, Margherita Francescatto, J. Raphael Gibbs, Iris E. Jansen, Javier Simón‐Sánchez, Dena G. Hernandez, Allissa Dillman, Andrew B. Singleton, Mark Cookson, Patrizia Rizzu, Peter Heutink
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-12-305

A tissue-specific landscape of sense/antisense transcription in the mouse intestine
Cited by: 19
Author(s): Ulrich C. Klostermeier, Matthias Barann, Michael Wittig, Robert Häsler, André Franke, Olga Gavrilova, Benjamin Kreck, Christian Sina, Markus B. Schilhabel, Stefan Schreiber, Philip Rosenstiel
Software Mentions: 2
Published: over 15 years ago

10.1186/s12874-016-0164-9

ODMedit: uniform semantic annotation for data integration in medicine based on a public metadata repository
Cited by: 28
Author(s): Martin Dugas, Alexandra Meidt, Philipp Neuhaus, Michael Storck, Julian Varghese
Software Mentions: 2
Published: over 10 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: about 10 years ago

10.1371/journal.pone.0005008

Transcriptional Network of p63 in Human Keratinocytes
Cited by: 42
Author(s): Silvia Pozzi, Federico Zambelli, Daniele Merico, Giulio Pavesi, Amélie Robert, Peggy Maltère, Xavier Gidrol, Roberto Mantovani, M. Alessandra Viganò
Software Mentions: 2
Published: over 17 years ago

10.1093/gbe/evab183

nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over
Cited by: 7
Author(s): Andrea Talenti, James Prendergast
Software Mentions: 2
Published: about 5 years ago

10.1038/s41438-018-0078-2

PGD: Pineapple Genomics Database
Cited by: 22
Author(s): Huimin Xu, Qingyi Yu, Yan Shi, Xiuting Hua, Haibao Tang, Long Yang, Ray Ming, Jisen Zhang
Software Mentions: 2
Published: about 8 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 12 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 15 years ago

10.1186/1755-8794-6-1

Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C
Cited by: 72
Author(s): Daria Grafodatskaya, Barian H Y Chung, Darci T. Butcher, Andrei L. Turinsky, Sarah J. Goodman, Sana Choufani, Yi‐An Chen, Youliang Lou, Cheng Zhao, Rageen Rajendram, Fatima Abidi, Cindy Skinner, James Stavropoulos, Carolyn A. Bondy, Jill Hamilton, Shoshana J. Wodak, Stephen W. Scherer, Charles E. Schwartz, Rosanna Weksberg
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-13-636

Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects
Cited by: 184
Author(s): Kristel R. van Eijk, Simone de Jong, Marco P. Boks, Terry Langeveld, Fabrice Colas, Jan H. Veldink, Carolien G.F. de Kovel, Esther Janson, Eric Strengman, Peter Langfelder, René S. Kahn, Leonard H van den Berg, Steve Horvath, Roel A. Ophoff
Software Mentions: 2
Published: almost 14 years ago

10.1093/gbe/evu142

Sequence-Level Mechanisms of Human Epigenome Evolution
Cited by: 17
Author(s): James Prendergast, Emily Chambers, Colin A. Semple
Software Mentions: 2
Published: over 12 years ago

10.1186/s12920-015-0087-z

Systems biology of myasthenia gravis, integration of aberrant lncRNA and mRNA expression changes
Cited by: 19
Author(s): Zhaohui Luo, Ye Li, Xiaofang Liu, Mingyao Luo, Liqun Xu, Yue‐Bei Luo, Bo Xiao, Huan Yang
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pntd.0007871

GSMN-ML- a genome scale metabolic network reconstruction of the obligate human pathogen Mycobacterium leprae
Cited by: 8
Author(s): Khushboo Borah, Jacque-Lucca Kearney, Ruma Banerjee, Pankaj Vats, Huihai Wu, Sonal Dahale, Sunitha Manjari Kasibhatla, Rajendra Joshi, Bhushan Bonde, Olabisi Ojo, Ramanuj Lahiri, Diana L. Williams, Johnjoe McFadden
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-019-1893-y

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
Cited by: 44
Author(s): Lin An, Tao Yang, Jingquan Yang, Johannes Nuebler, Guanjue Xiang, R Hardison, Qunhua Li, Yu Zhang
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pntd.0000543

Anti-schistosomal Intervention Targets Identified by Lifecycle Transcriptomic Analyses
Cited by: 117
Author(s): Jennifer M. Fitzpatrick, Emily Peak, Samïrah Perally, Iain W. Chalmers, John Barrett, Timothy P. Yoshino, Alasdair Ivens, Karl F. Hoffmann
Software Mentions: 2
Published: almost 17 years ago

10.1186/s13059-016-1142-6

Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies
Cited by: 145
Author(s): Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Saixia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael Feolo, Nataliya Sharopova, Anne Sturcke, Alejandro A. Schäffer, Nancy L. Heard‐Costa, Han Chen, Poching Liu, Thomas J. Wang, Kimberly A. Woodhouse, Kahraman Tanrıverdi, Jane E. Freedman, Nalini Raghavachari, Josée Dupuis, Andrew D. Johnson, Christopher J. O’Donnell, Daniel Levy, Peter J. Munson
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-017-1161-y

Software tools for visualizing Hi-C data
Cited by: 49
Author(s): Galip Gürkan Yardımcı
Software Mentions: 2
Published: over 9 years ago

10.1093/gbe/evy029

Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome
Cited by: 15
Author(s): Larissa Maranhão Dias, Adriana Ribeiro Carneiro Folador, Amanda M.S. Oliveira, Rommel Thiago Jucá Ramos, Artur M. S. Silva, Rafael Azevedo Baraúna
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-14-611

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

10.1186/s13059-015-0727-9

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

10.1186/s13059-015-0736-8

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

10.1186/s12920-021-01007-9

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

10.1371/journal.pgen.1005117

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

10.1186/s13059-015-0835-6

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

10.1186/1755-8794-2-31

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

10.1371/journal.pgen.1000672

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

10.1186/1471-2164-16-S8-S2

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

10.1186/s13059-014-0578-9

Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds
Cited by: 51
Author(s): Carolina Frankl-Vilches, Heiner Kuhl, Martin Werber, Sven Klages, Martin Kerick, Antje Bakker, Edivaldo Herculano Corrêa de Oliveira, Christina Reusch, Floriana Capuano, Jakob Vowinckel, Stefan Leitner, Markus Ralser, Bernd Timmermann, Manfred Gahr
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1006296

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

10.1186/1471-2105-11-10

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement
Cited by: 52
Author(s): Guanqun Shi, Liqing Zhang, Tao Jiang
Software Mentions: 2
Published: almost 17 years ago

10.1186/s13059-014-0469-0

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

10.1371/journal.pgen.1002384

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

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