pypi: browser | Projects | Ecosyste.ms: Papers

10.1038/srep12062

Differential and coherent processing patterns from small RNAs
Cited by: 21
Author(s): Sachin Pundhir, Jan Gorodkin
Software Mentions: 3
Published: about 11 years ago

Uncovering RNA Editing Sites in Long Non-Coding RNAs
Cited by: 41
Author(s): Ernesto Picardi, Anna Maria D’Erchia, Angela Gallo, Antonio Montalvo, Graziano Pesole
Software Mentions: 3
Published: almost 12 years ago

10.1093/database/bax009

HopBase: a unified resource for Humulus genomics
Cited by: 27
Author(s): Steven T. Hill, Ramcharan Sudarsanam, Jimmy C. Henning, David A. Hendrix
Software Mentions: 3
Published: over 9 years ago

10.1016/j.dib.2015.10.033

Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model
Cited by: 6
Author(s): Joel B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William Stafford Noble, Christine M. Distèche, Xinxian Deng
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13072-017-0123-7

Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA
Cited by: 64
Author(s): Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M. Gould, Shalima S. Nair, Susan J. Clark, Clare Stirzaker
Software Mentions: 3
Published: over 9 years ago

10.1038/srep19615

Overlapping signatures of chronic pain in the DNA methylation landscape of prefrontal cortex and peripheral T cells
Cited by: 67
Author(s): Renaud Massart, Sergiy Dymov, Magali Millecamps, Matthew Suderman, Stéphanie Grégoire, Kevin Koenigs, Sebastian Alvarado, Maral Tajerian, Laura S. Stone, Moshe Szyf
Software Mentions: 3
Published: over 10 years ago

10.1038/s42003-019-0488-1

Systematic discovery of conservation states for single-nucleotide annotation of the human genome
Cited by: 16
Author(s): Adriana Arneson, Jason Ernst
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.40364

PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells
Cited by: 27
Author(s): Shuchi Agrawal-Singh, Mads Lerdrup, Ana-Luisa R Gomes, Harmen J.G. van de Werken, Jens Vilstrup Johansen, Robin Andersson, Albin Sandelin, Kristian Helin, Klaus Hansen
Software Mentions: 3
Published: over 7 years ago

10.1186/s13148-020-00876-8

Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets
Cited by: 34
Author(s): Julia Krushkal, Thomas Silvers, William C. Reinhold, Dmitriy Sonkin, Suleyman Vural, John W. Connelly, Sudhir Varma, Paul S. Meltzer, Mark W. Kunkel, Annamaria Rapisarda, David M. Evans, Yves Pommier, Beverly A. Teicher
Software Mentions: 3
Published: about 6 years ago

10.1186/s13148-019-0699-9

Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing
Cited by: 14
Author(s): Xiaojian Shao, Marie Hudson, Inés Colmegna, Celia Greenwood, Marvin J. Fritzler, Philip Awadalla, Tomi Pastinen, Sasha Bernatsky
Software Mentions: 3
Published: about 7 years ago

10.26508/lsa.202000663

Splicing of enhancer-associated lincRNAs contributes to enhancer activity
Cited by: 22
Author(s): Jennifer Y. Tan, Adriano Biasini, Robert S. Young, Ana C. Marques
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0222432

The intermediate proteasome is constitutively expressed in pancreatic beta cells and upregulated by stimulatory, low concentrations of interleukin 1 β
Cited by: 13
Author(s): Muhammad Saad Khilji, Danielle Verstappen, Tina Dahlby, Michala Prause, Celina Pihl, Sophie Emilie Bresson, Tenna Holgersen Bryde, Phillip Alexander Keller Andersen, Kristian Klindt, Dušan Živković, Marie‐Pierre Bousquet, Björn Tyrberg, Thomas Mandrup‐Poulsen, Michał Marzec
Software Mentions: 3
Published: over 6 years ago

10.1186/s13148-017-0344-4

Genome-wide DNA methylation analysis reveals loci that distinguish different types of adipose tissue in obese individuals
Cited by: 27
Author(s): Donia Macartney-Coxson, Miles C. Benton, R. A. J. Blick, Richard S. Stubbs, R. D. Hagan, Michael A. Langston
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-8-113

Discovery and characterization of 91 novel transcripts expressed in cattle placenta
Cited by: 9
Author(s): Charu G. Kumar, Joshua H. Larson, Mark Band, Harris A. Lewin
Software Mentions: 3
Published: over 19 years ago

10.1186/s12870-021-02894-x

A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors
Cited by: 14
Author(s): Lara Brian, Ben Warren, Peter A. McAtee, Jessica A. Rodrigues, Niels J. Nieuwenhuizen, Asher Pasha, Karine David, Annette Richardson, Nicholas J. Provart, Andrew C. Allan, Erika Varkonyi‐Gasic, Robert J. Schaffer
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2148-10-90

Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes
Cited by: 56
Author(s): Chenhong Li, Jean-Jack M. Riethoven, Lan Ma
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2148-9-252

Positive selection for the male functionality of a co-retroposed gene in the hominoids
Cited by: 13
Author(s): Yong Zhang, Shujuan Lu, Shuqi Zhao, Xiaofeng Zheng, Manyuan Long, Liping Wei
Software Mentions: 3
Published: almost 17 years ago

10.1186/s12870-019-1672-7

Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume
Cited by: 35
Author(s): Xinxin Wu, Ting Shi, Shahid Iqbal, Yong Zhang, Lin Liu, Zhihong Gao
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.08954

The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development
Cited by: 110
Author(s): Thomas W. Bebee, Juw Won Park, Katherine I Sheridan, Claude C. Warzecha, Benjamin Cieply, Alex M Rohacek, Yi Xing, Russ P. Carstens
Software Mentions: 3
Published: about 11 years ago

10.3390/cells8060623

Functionally Significant Features in the 5′ Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates
Cited by: 10
Author(s): Pavel Dvořák, Sarah Leupen, Pavel Souček
Software Mentions: 3
Published: about 7 years ago

10.3390/cells10092375

Transcriptome and Methylome Analysis Reveal Complex Cross-Talks between Thyroid Hormone and Glucocorticoid Signaling at Xenopus Metamorphosis
Cited by: 10
Author(s): Nicolas Buisine, Alexis Grimaldi, Vincent Jonchère, Muriel Rigolet, Corinne Blugeon, Juliette Hamroune, Laurent M. Sachs
Software Mentions: 3
Published: about 5 years ago

10.1074/mcp.O115.048777

Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics*
Cited by: 28
Author(s): Jun Fan, Shyamasree Saha, Gary Barker, Kate J Heesom, Fawaz Ghali, Andrew R. Jones, David A. Matthews, Conrad Bessant
Software Mentions: 3
Published: almost 11 years ago

10.1016/j.celrep.2020.108533

USP15 Deubiquitinase Safeguards Hematopoiesis and Genome Integrity in Hematopoietic Stem Cells and Leukemia Cells
Cited by: 10
Author(s): Paul van den Berk, Cesare Lancini, Michela Serresi, María Pilar Sánchez-Bailón, Danielle Hulsman, Colin C. Pritchard, Ji‐Ying Song, Matthias Jürgen Schmitt, Ellen Tanger, Oliver Popp, Philipp Mertins, Ivo J. Huijbers, Heinz Jacobs, Maarten van Lohuizen, Gaetano Gargiulo, Elisabetta Citterio
Software Mentions: 3
Published: almost 6 years ago

10.1038/cr.2017.134

Derivation of hypermethylated pluripotent embryonic stem cells with high potency
Cited by: 39
Author(s): Siqin Bao, Walfred W.C. Tang, Baojiang Wu, Shinseog Kim, Jingyun Li, Lin Li, Toshihiro Kobayashi, Caroline Lee, Yanglin Chen, Mengyi Wei, Shudong Li, Sabine Dietmann, Fuchou Tang, Xihe Li, M. Azim Surani
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.celrep.2018.07.104

Simultaneous Measurement of Transcriptional and Post-transcriptional Parameters by 3′ End RNA-Seq
Cited by: 9
Author(s): Manfred Schmid, Agnieszka Tudek, Torben Heick Jensen
Software Mentions: 3
Published: about 8 years ago

10.1186/s12943-020-01293-4

Long non-coding RNA NEAT1 promotes bone metastasis of prostate cancer through N6-methyladenosine
Cited by: 154
Author(s): Simeng Wen, Yulei Wei, Chong Zen, Wei Xiong, Yuanjie Niu, Yu Zhao
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12885-021-07900-x

Super-enhancer-associated long noncoding RNA AC005592.2 promotes tumor progression by regulating OLFM4 in colorectal cancer
Cited by: 7
Author(s): Yan Liu, Huanhuan Chen, Li Tang, Pan Jiang, Feng Yan
Software Mentions: 3
Published: over 5 years ago

10.3390/cells9061435

Altered Transcription Factor Binding and Gene Bivalency in Islets of Intrauterine Growth Retarded Rats
Cited by: 13
Author(s): Yu‐Chin Lien, Paul Zhiping Wang, Xueqing Maggie Lu, Rebecca A. Simmons
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms22105335

INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison
Cited by: 11
Author(s): Monika Chanu Chongtham, Tamer Butto, Kanak Mungikar, Susanne Gerber, Jennifer Winter
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.20851

Age-dependent diastolic heart failure in an in vivo Drosophila model
Cited by: 32
Author(s): Matthew P. Klassen, Christian J. Peters, Shiwei Zhou, Hannah H Williams, Yuh Nung Jan
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms19113607

Methylation-Based Classification of Cervical Squamous Cell Carcinoma into Two New Subclasses Differing in Immune-Related Gene Expression
Cited by: 4
Author(s): Xia Li, Yunpeng Cai
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41419-019-1892-7

Epigenetic re-wiring of breast cancer by pharmacological targeting of C-terminal binding protein
Cited by: 7
Author(s): Jung S. Byun, Samson Park, Dae Ik Yi, Jee-Hye Shin, Sara Gil Hernandez, Stephen M. Hewitt, Marc C. Nicklaus, Megan L. Peach, Laura Guasch, Binwu Tang, Lalage M. Wakefield, Tingfen Yan, Ambar Caban, Alana Jones, Mohamed Kabbout, Nasreen A. Vohra, Anna María Nápoles, Sandeep K. Singhal, Ryan Yancey, Adriana De Siervi, Kevin Gardner
Software Mentions: 3
Published: almost 7 years ago

10.1038/celldisc.2015.8

The PRC2-associated factor C17orf96 is a novel CpG island regulator in mouse ES cells
Cited by: 26
Author(s): Robert Liefke, Yang Shi
Software Mentions: 3
Published: over 11 years ago

10.3390/ijms19030738

The Coordinated Activities of nAChR and Wnt Signaling Regulate Intestinal Stem Cell Function in Mice
Cited by: 25
Author(s): Toshio Takahashi, Akira Shiraishi, Jun Murata
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms21124378

Discovery of Isoplumbagin as a Novel NQO1 Substrate and Anti-Cancer Quinone
Cited by: 19
Author(s): Yen-Chi Tsao, Yu‐Jung Chang, Chun-Hsien Wang, Linyi Chen
Software Mentions: 3
Published: about 6 years ago

10.3390/cancers11030284

Gliosarcoma Is Driven by Alterations in PI3K/Akt, RAS/MAPK Pathways and Characterized by Collagen Gene Expression Signature
Cited by: 15
Author(s): Bartosz Wojtaś, Bartłomiej Gielniewski, Kamil Wojnicki, Marta Maleszewska, Shamba S. Mondal, Paweł Nauman, Wiesława Grajkowska, Rainer Glaß, Ulrich Schüller, Christel Herold‐Mende, Bożena Kamińska
Software Mentions: 3
Published: over 7 years ago

10.3390/cancers12030764

Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability
Cited by: 41
Author(s): Wa Zhang, David Klinkebiel, Carter J. Barger, Sanjit Pandey, Chittibabu Guda, Austin Miller, Stacey N. Akers, Kunle Odunsi, Adam R. Karpf
Software Mentions: 3
Published: over 6 years ago

10.3390/cancers13133176

Epigenetic Upregulation of MAGE-A Isoforms Promotes Breast Cancer Cell Aggressiveness
Cited by: 4
Author(s): Chaeun Oh, Hwa Ryeon Kim, Seungmin Oh, Je Yeong Ko, Yesol Kim, Keunsoo Kang, Young Yang, Jongmin Kim, Jae Seok Roe, Kyung Hyun Yoo
Software Mentions: 3
Published: about 5 years ago

10.1016/j.cell.2019.04.038

SCAF4 and SCAF8, mRNA Anti-Terminator Proteins
Cited by: 78
Author(s): Lea H. Gregersen, Richard Mitter, Alejandro P. Ugalde, Takayuki Nojima, Nick J. Proudfoot, Reuven Agami, Aengus Stewart, Jesper Q. Svejstrup
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms21165743

Premature Activation of Immune Transcription Programs in Autoimmune-Predisposed Mouse Embryonic Stem Cells and Blastocysts
Cited by: 0
Author(s): Oktay Kirak, Eugene Ke, Kevin Yi Yang, Anna Schwarz, Lars Plate, Amy Nham, Justin R. Abadejos, Anna Valencia, R. Luke Wiseman, Kathy O. Lui, Manching Ku
Software Mentions: 3
Published: about 6 years ago

10.1186/s13100-021-00233-3

RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs
Cited by: 17
Author(s): Erica M. Briggs, Wilson McKerrow, Paolo Mita, Jef D. Boeke, Susan K. Logan, David Fenyö
Software Mentions: 3
Published: over 5 years ago

10.1161/CIRCRESAHA.120.316770

Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics
Cited by: 239
Author(s): Marie A.C. Depuydt, K.H.M. Prange, Lotte Slenders, Tiit Örd, D. Elbersen, Arjan Boltjes, Saskia C.A. de Jager, Folkert W. Asselbergs, Gert J. de Borst, Einari Aavik, Tapio Lönnberg, Esther Lutgens, Christopher K. Glass, Hester M. den Ruijter, Minna U. Kaikkonen, Ilze Bot, Bram Slütter, Sander W. van der Laan, Seppo Ylä‐Herttuala, Michal Mokrý, Johan Kuiper, Menno P.J. de Winther, Gérard Pasterkamp
Software Mentions: 3
Published: almost 6 years ago

10.3390/microorganisms7100420

Reduced Virulence of an Introduced Forest Pathogen over 50 Years
Cited by: 6
Author(s): Rosie E. Bradshaw, Shannon Ormond, Pierre‐Yves Dupont, Pranav Chettri, I. Kutay Ozturk, Rebecca McDougal, L. S. Bulman, Murray P. Cox
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-10-148

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes
Cited by: 17
Author(s): Wonhoon Lee, Jongsun Park, Jaeyoung Choi, Ki Won Jung, Bong Soo Park, Donghan Kim, Jae-Young Lee, Kyohun Ahn, Wonho Song, Seogchan Kang, Yong Hwan Lee, Seung Hwan Lee
Software Mentions: 3
Published: over 17 years ago

10.1371/journal.pone.0102968

Role of Polycomb Group Proteins in the DNA Damage Response – A Reassessment
Cited by: 12
Author(s): Hollie Chandler, Harshil Patel, Richard D. Palermo, Sharon Brookes, Nik Matthews, Gordon Peters
Software Mentions: 3
Published: about 12 years ago

10.1186/s12864-015-1959-5

Development of ListeriaBase and comparative analysis of Listeria monocytogenes
Cited by: 8
Author(s): Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh V.R. Mutha, Wei Yee Wee, Hamed Heydari, Shi Tan, Mia Yang Ang, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: almost 11 years ago

10.7554/eLife.25787

Repression by PRDM13 is critical for generating precision in neuronal identity
Cited by: 34
Author(s): Bishakha Mona, Ana Uruena, Rahul K. Kollipara, Zhenzhong Ma, Mark D. Borromeo, Joshua C. Chang, Jane E. Johnson
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0247402

DeepSRE: Identification of sterol responsive elements and nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network analysis
Cited by: 0
Author(s): Davide Noto, Antonina Giammanco, Rossella Spina, Francesca Fayer, Angelo B. Cefalù, Maurizio Averna
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.15635

Sox9 and Sox8 protect the adult testis from male-to-female genetic reprogramming and complete degeneration
Cited by: 65
Author(s): Francisco Barrionuevo, Alicia Hurtado, Gwang-Jin Kim, Francisca M. Real, Mohammed Bakkali, Janel L. Kopp, Maike Sander, Gerd Scherer, Miguel Burgos, Rafael Jiménez
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0047216

A Hybrid Distance Measure for Clustering Expressed Sequence Tags Originating from the Same Gene Family
Cited by: 5
Author(s): Keng-Hoong Ng, Chin-Kuan Ho, Somnuk Phon-Amnuaisuk
Software Mentions: 3
Published: almost 14 years ago

10.3389/fbioe.2014.00088

Discovery of Proteinâ€“lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets
Cited by: 55
Author(s): Junhao Li, Shun Liu, Ling‐Ling Zheng, Jie Wu, Wenju Sun, Zelin Wang, Hui Zhou, Liang‐Hu Qu, Jianhua Yang
Software Mentions: 3
Published: over 11 years ago

10.1097/MD.0000000000012679

Comprehensive assessment gene signatures for clear cell renal cell carcinoma prognosis
Cited by: 11
Author(s): Po-Ya Chang, Zhitong Bing, Jinhui Tian, Jingyun Zhang, Xiuxia Li, Long Ge, Juan Ling, Kun Yang, Yumin Li
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12885-017-3252-2

Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns
Cited by: 47
Author(s): Marie K. Kirby, Ryne C. Ramaker, Brian S. Roberts, Brittany N. Lasseigne, David S. Gunther, Todd C. Burwell, Nicholas S. Davis, Zulfiqar Gulzar, Devin Absher, Sara J. Cooper, James D. Brooks, R Myers
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.44642

Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila
Cited by: 51
Author(s): Ane Martín Anduaga, Naveh Evantal, Inés Lucía Patop, Osnat Bartok, Ron Weiss, Sebastián Kadener
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms21218383

Trans-Ancestral Fine-Mapping and Epigenetic Annotation as Tools to Delineate Functionally Relevant Risk Alleles at IKZF1 and IKZF3 in Systemic Lupus Erythematosus
Cited by: 6
Author(s): Timothy J. Vyse, Deborah S. Cunninghame Graham
Software Mentions: 3
Published: almost 6 years ago

10.3390/biology9090295

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing
Cited by: 33
Author(s): Girum Fitihamlak Ejigu, Jaehee Jung
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12915-019-0679-8

Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response
Cited by: 13
Author(s): Xiaoman Xie, Casey Hanson, Saurabh Sinha
Software Mentions: 3
Published: about 7 years ago

10.1186/s12920-018-0453-8

Identification of exon skipping events associated with Alzheimer’s disease in the human hippocampus
Cited by: 17
Author(s): Seonggyun Han, Jason E. Miller, Seyoun Byun, Dokyoon Kim, Shannon L. Risacher, Andrew J. Saykin, Younghee Lee, Kwangsik Nho
Software Mentions: 3
Published: over 7 years ago

10.1016/j.jsb.2016.02.012

Web-based volume slicer for 3D electron-microscopy data from EMDB
Cited by: 14
Author(s): José Salavert-Torres, A. Iudin, Ingvar Lagerstedt, Eduardo Sanz-García, Gerard J. Kleywegt, Ardan Patwardhan
Software Mentions: 3
Published: over 10 years ago

10.1038/s41388-018-0659-4

Histoepigenetic analysis of HPV- and tobacco-associated head and neck cancer identifies both subtype-specific and common therapeutic targets despite divergent microenvironments
Cited by: 20
Author(s): Ivenise Carrero, Hsuan-Chen Liu, Andrew G. Sikora, Aleksandar Milosavljevic
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1007274

A benchmark of computational CRISPR-Cas9 guide design methods
Cited by: 23
Author(s): Jacob Bradford, Dimitri Perrin
Software Mentions: 3
Published: about 7 years ago

10.18632/oncotarget.14843

Relationship between LINC00341 expression and cancer prognosis
Cited by: 13
Author(s): Meijian Liao, Bing Li, Shikuan Zhang, Qing Liu, Weijie Liao, Weidong Xie, Yaou Zhang
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-018-4869-5

Limitations of alignment-free tools in total RNA-seq quantification
Cited by: 61
Author(s): Douglas C. Wu, Jun Yao, Kevin S. Ho, Alan M. Lambowitz, Claus O. Wilke
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0190992

HAfTs are novel lncRNA transcripts from aflatoxin exposure
Cited by: 9
Author(s): B. Alex Merrick, Justin Chang, Dhiral Phadke, Meredith A. Bostrom, Ruchir Shah, Xinguo Wang, Oksana Gordon, Garron M. Wright
Software Mentions: 3
Published: over 8 years ago

10.1128/JVI.00980-17

ZIC2 Is Essential for Maintenance of Latency and Is a Target of an Immediate Early Protein during Kaposi's Sarcoma-Associated Herpesvirus Lytic Reactivation
Cited by: 10
Author(s): Yuanzhi Lyu, K. Nakano, Ryan R. Davis, Clifford G. Tepper, Mel Campbell, Yoshihiro Izumiya
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41389-020-00285-9

Triptolide targets super-enhancer networks in pancreatic cancer cells and cancer-associated fibroblasts
Cited by: 32
Author(s): Pawan Noel, Shaimaa Hussein, Serina Ng, Corina E. Antal, Wei Lin, Emily Rodela, Priscilla Delgado, Sanna Naveed, Michael Downes, Yin Lin, Ronald M. Evans, Daniel D. Von Hoff, Haiyong Han
Software Mentions: 3
Published: almost 6 years ago

10.1186/1756-8722-6-25

Structurally differentiated cis-elements that interact with PU.1 are functionally distinguishable in acute promyelocytic leukemia
Cited by: 12
Author(s): Maoxiang Qian, Ji Wen, Xuehua Zhu, Xiaohong Jia, Xian‐Wen Yang, Yanzhi Du, Kankan Wang, Ji Zhang
Software Mentions: 3
Published: over 13 years ago

10.3389/fimmu.2020.00538

5-Azacytidine Potentiates Anti-tumor Immunity in a Model of Pancreatic Ductal Adenocarcinoma
Cited by: 11
Author(s): Nancy D. Ebelt, Edith Zuniga, B. Lamar Johnson, Don J. Diamond, Edwin R. Manuel
Software Mentions: 3
Published: over 6 years ago

10.2196/resprot.9639

A Web-Based Telemanagement System for Patients With Complex Inflammatory Bowel Disease: Protocol for a Randomized Controlled Clinical Trial
Cited by: 9
Author(s): Mariam Aguas, Javier del Hoyo, Raquel Faubel, Diana Muñoz, Dana A. Dominguez, Guillermo Bastida, Belén Navarro, Alejandra Barrios, Bernardo Valdivieso, Marisa Correcher, Pilar Nos
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1004562

A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways
Cited by: 60
Author(s): Bode A. Olukolu, Guan‐Feng Wang, Vijay Vontimitta, Bala P. Venkata, Sandeep Marla, Jiabing Ji, Emma W. Gachomo, Kevin Chu, Adisu Negeri, Jacqueline Benson, Rebecca Nelson, Peter J. Bradbury, Dahlia M. Nielsen, James B. Holland, Peter Balint‐Kurti, Gurmukh S. Johal
Software Mentions: 3
Published: about 12 years ago

10.1186/1471-2105-13-85

DIPSBC - data integration platform for systems biology collaborations
Cited by: 13
Author(s): Felix Dreher, Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, K. Schellander, Hans Lehrach, Bodo Lange, Ralf Herwig
Software Mentions: 3
Published: over 14 years ago

10.1101/2021.07.09.21260221

Genetic regulation of<i>OAS1</i>nonsense-mediated decay underlies association with risk of severe COVID-19
Cited by: 8
Author(s): Abdul Rouf Banday, Megan L. Stanifer, Óscar Flórez-Vargas, Olusegun O. Onabajo, Muhammad Atif Zahoor, Brenen W. Papenberg, Timothy J. Ring, Chia-Han Lee, Evangelos Andreakos, Evgeny Arons, Greg Barsh, Leslie G. Biesecker, David L. Boyle, Andrea N. Burnett‐Hartman, Mary Carrington, Euijin Chang, Pyoeng Gyun Choe, Rex L Chrisholm, Clifton L. Dalgard, Jeff Edberg, Nathan Erdmann, Heather Spencer Feigelson, Gary S. Firestein, Adam J. Gehring, Michelle Ho, Steven M. Holland, Amy Hutchinson, Hogune Im, Michael G. Ison, Hong Bin Kim, Robert J. Kreitman, Bruce R. Korf, Lisa Mirabello, Jennifer A. Pacheco, Michael J. Peluso, Daniel J. Rader, David T. Redden, Marylyn D. Ritchie, Brooke Rosenbloom, Hanaisa P. Sant Anna, Sharon A. Savage, E. Siouti, Vasiliki Triantafyllia, Joselin M. Vargas, Anurag Verma, Vibha Vij, Duane R. Wesemann, Meredith Yeager, Xu G. Yu, Yu Zhang, Steeve Boulant, Stephen J. Chanock, Jordan J. Feld, Ludmila Prokunina–Olsson
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-016-1139-x

CerealsDB 3.0: expansion of resources and data integration
Cited by: 38
Author(s): Paul Wilkinson, Mark Winfield, Gary Barker, Simon Tyrrell, Xingdong Bian, Alexandra M. Allen, Amanda Burridge, Jane A. Coghill, Christy Waterfall, Mario Cáccamo, Robert P. Davey, Keith J. Edwards
Software Mentions: 3
Published: about 10 years ago

10.3389/fnmol.2017.00283

RNA-Sequencing Analysis Reveals a Regulatory Role for Transcription Factor Fezf2 in the Mature Motor Cortex
Cited by: 6
Author(s): Alison J Clare, Hollie E. Wicky, Ruth M. Empson, Stephanie M. Hughes
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0013020

Genome-Wide DNA Methylation Maps in Follicular Lymphoma Cells Determined by Methylation-Enriched Bisulfite Sequencing
Cited by: 36
Author(s): Jeong-Hyeon Choi, Yajun Li, Jiangtao Guo, Lirong Pei, Tibor A. Rauch, Robin Kramer, Simone Macmil, Graham B. Wiley, Lynda Bennett, Jennifer Schnabel, Kristen H. Taylor, Sun Il Kim, Dong Xu, Arun Sreekumar, Gerd P. Pfeifer, Bruce A. Roe, Charles W. Caldwell, Kapil N. Bhalla, Huidong Shi
Software Mentions: 3
Published: almost 16 years ago

10.1038/s41598-021-98708-z

AGO CLIP-based imputation of potent siRNA sequences targeting SARS-CoV-2 with antifibrotic miRNA-like activity
Cited by: 6
Author(s): Seung Hyun Ahn, Dowoon Gu, Yongjun Koh, Hye-Sook Lee, Sung Wook
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-014-0422-y

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
Cited by: 9
Author(s): Shi Tan, Avirup Dutta, Nicholas S. Jakubovics, Mia Yang Ang, Cheuk Chuen Siow, Naresh V.R. Mutha, Hamed Heydari, Wei Yee Wee, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0043652

Pitfalls of Establishing DNA Barcoding Systems in Protists: The Cryptophyceae as a Test Case
Cited by: 26
Author(s): Kerstin Hoef‐Emden
Software Mentions: 3
Published: about 14 years ago

10.1186/1471-2164-13-147

Genome-wide analysis of Pax8 binding provides new insights into thyroid functions
Cited by: 40
Author(s): Sergio Ruiz‐Llorente, Enrique Carrillo Santa de Pau, Ana Sastre-Perona, Cristina Montero‐Conde, Gonzalo Goméz-López, James A. Fagin, Alfonso Valencia, David G. Pisano, Pilar Santisteban
Software Mentions: 3
Published: over 14 years ago

10.1038/s41598-020-78555-0

Evolutionary divergence of novel open reading frames in cichlids speciation
Cited by: 5
Author(s): Shraddha Puntambekar, Rachel Newhouse, Jaime San-Miguel, Ruchi Chauhan, Grégoire Vernaz, Thomas W. Willis, Matthew T. Wayland, Yagnesh Umrania, Eric A. Miska, Sudhakaran Prabakaran
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-89798-w

Genomic selection signatures in autism spectrum disorder identifies cognitive genomic tradeoff and its relevance in paradoxical phenotypes of deficits versus potentialities
Cited by: 3
Author(s): Anil Prakash, Moinak Banerjee
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-10-26

Identifying differential exon splicing using linear models and correlation coefficients
Cited by: 19
Author(s): Sonia Shah, Jacqueline A. Pallas
Software Mentions: 3
Published: over 17 years ago

10.1038/s41598-018-22284-y

Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis
Cited by: 19
Author(s): Li Jin, Peng Yu
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-020-6697-7

iMarmot: an integrative platform for comparative and functional genomics of marmots
Cited by: 3
Author(s): Baoning Liu, Liang Bai, Qingqing Yu, Fang Hu, Jing Wu, Zhao Song, Rong Wang, Weirong Wang, Yuanqing Tao, Jianglin Fan, Enqi Liu
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-14-818

Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data
Cited by: 67
Author(s): Nameeta Shah, Michael Lankerovich, Hwahyung Lee, Jae-Geun Yoon, Brett Schroeder, Greg Foltz
Software Mentions: 3
Published: over 13 years ago

10.1186/s13073-017-0481-6

Nuclear Wiskott–Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells
Cited by: 16
Author(s): Nikolai V. Kuznetsov, Bader Almuzzaini, Joanna S. Kritikou, Marisa A. P. Baptista, Mariana M.S. Oliveira, Márton Keszei, Scott B. Snapper, Piergiorgio Percipalle, Lisa S. Westerberg
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1005652

Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals
Cited by: 69
Author(s): Gung Wei Chirn, Reazur Rahman, Yuliya A. Sytnikova, Jessica Matts, Mei Zeng, Daniel Gerlach, Michael Yu, Bonnie Berger, Mayumi Naramura, Benjamin T. Kile, Nelson C. Lau
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12859-020-03934-3

Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays
Cited by: 9
Author(s): Vandhana Krishnan, Sowmithri Utiramerur, Zena Ng, Somalee Datta, M Snyder, Euan A. Ashley
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2542-4

Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA
Cited by: 6
Author(s): Matt R. Paul, Nicholas P. Levitt, David E. Moore, Patricia M. Watson, Robert Wilson, Chadrick E. Denlinger, Dennis K. Watson, Paul E. Anderson
Software Mentions: 3
Published: over 10 years ago

10.1186/s13059-020-02186-x

Cis-acting lnc-eRNA SEELA directly binds histone H4 to promote histone recognition and leukemia progression
Cited by: 17
Author(s): Ke Fang, Wei Huang, Yu-Meng Sun, Tian-Qi Chen, Zhan-Cheng Zeng, Qianqian Yang, Qi Pan, Cai Han, Lin-Yu Sun, Xue-Qun Luo, Wen-Tao Wang, Yue‐Qin Chen
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-020-02201-1

Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
Cited by: 28
Author(s): Yue Feng, Yao Wang, Xiangnan Wang, Xiaohong He, Chen Yang, Ardalan Naseri, Thoru Pederson, Jing Zheng, Shaojie Zhang, Xiao Xiao, Wei Xie, Hanhui Ma
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-016-1023-z

Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells
Cited by: 54
Author(s): Xiaoli Zhang, Jun Wu, Jian Wang, Tingting Shen, Hua Li, Jun Lü, Yunzhao Gu, Yani Kang, Chee-Hong Wong, Chew Yee Ngan, Zongshu Shao, Ji Wu, Xiaodong Zhao
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2105-14-18

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
Cited by: 9
Author(s): Phillip Seitzer, Tu Anh Ngoc Huynh, Marc T. Facciotti
Software Mentions: 3
Published: over 13 years ago

10.1186/s13059-014-0414-2

Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes
Cited by: 67
Author(s): Antony M. Chettoor, Scott A. Givan, Rex A. Cole, Clayton T Coker, Erica Unger-Wallace, Zuzana Vejlupkova, Erik Vollbrecht, John E. Fowler, Evans Mulenga
Software Mentions: 3
Published: about 12 years ago

10.1186/gb-2014-15-1-r3

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
Cited by: 76
Author(s): Ian M. Silverman, Liancheng Fan, A Vinogradov Alexander, Loyal A. Goff, Cole Trapnell, John L. Rinn, Brian D. Gregory
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-018-4556-6

The deregulated microRNAome contributes to the cellular response to aneuploidy
Cited by: 12
Author(s): Milena Dürrbaum, Christine Kruse, K. Julia Nieken, Bianca Habermann, Zuzana Storchová
Software Mentions: 3
Published: over 8 years ago

10.1186/gb-2012-13-8-r75

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
Cited by: 220
Author(s): Alayne Brunner, Andrew H. Beck, Badreddin Edris, Robert T. Sweeney, Shirley Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W. Foley, Daniela Witten, Craig P. Giacomini, Ryan A. Flynn, Jonathan R. Pollack, Robert Tibshirani, Howard Y. Chang, Matt van de Rijn, Robert B. West
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2164-15-86

Finding the missing honey bee genes: lessons learned from a genome upgrade
Cited by: 349
Author(s): Christine G. Elsik, Kim C. Worley, Anna Bennett, Martin Beye, Francisco Câmara, Christopher P. Childers, Dirk C. de Graaf, Griet Debyser, Jixin Deng, Bart Devreese, Eran Elhaik, Jay D. Evans, Leonard J. Foster, Dan Graur, Roderic Guigó, Katharina J. Hoff, Michael Holder, Matthew E. Hudson, Greg J. Hunt, Huaiyang Jiang, Vandita Joshi, Radhika S. Khetani, Peter Kosarev, Christie Kovar, Jian Ma, Ryszard Maleszka, Robin F. A. Moritz, Monica Muñoz-Torres, Terence Murphy, Donna M. Muzny, Irene Newsham, Justin Reese, Hugh M. Robertson, Gene E. Robinson, Olav Rueppell, Victor Solovyev, Mario Stanke, Eckart Stolle, Jennifer M. Tsuruda, Matthias Van Vaerenbergh, Robert M. Waterhouse, Daniel Weaver, Charles W. Whitfield, Yuanqing Wu, Evgeny M. Zdobnov, Lan Zhang, Dianhui Zhu, Richard A. Gibbs
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-016-2539-z

A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome
Cited by: 117
Author(s): Laurence Ettwiller, John A. Buswell, Erbay Yigit, Ira Schildkraut
Software Mentions: 3
Published: over 10 years ago

10.1186/gb-2012-13-11-r102

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs
Cited by: 63
Author(s): Ana C. Marques, Jennifer Y. Tan, Sheena Lee, Lesheng Kong, Andreas Heger, Chris P. Ponting
Software Mentions: 3
Published: over 14 years ago

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Papers Mentioning browser 2,125