pypi: browser | Projects | Ecosyste.ms: Papers

10.1016/j.csbj.2019.10.003

MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines
Cited by: 9
Author(s): Wei Zhou, Lei Wang, Wenming Zheng, Wen Yao
Software Mentions: 20
Published: almost 6 years ago

10.1016/j.xpro.2021.100768

A computational approach for identification of core modules from a co-expression network and GWAS data
Cited by: 0
Author(s): Olivia L. Sabik, Cheryl Ackert‐Bicknell, Charles R. Farber
Software Mentions: 16
Published: over 3 years ago

10.1371/journal.pone.0256196

Finding differentially expressed sRNA-Seq regions with srnadiff
Cited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: over 3 years ago

10.1093/bib/bbv080

Public data and open source tools for multi-assay genomic investigation of disease
Cited by: 47
Author(s): Lavanya Kannan, Marcel Ramos, Angela Re, Nehmé El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe‐Kains, Levi Waldron
Software Mentions: 15
Published: about 9 years ago

10.12688/f1000research.51477.2

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
Cited by: 2
Author(s): Ann Mc Cartney, Medhat Mahmoud, Michael D. Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K. Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev, Hakeem Almabrazi, Ahmed Arslan, Advait Balaji, Sairam Behera, Kimberley Billingsley, Daniel Cameron, Joyjit Daw, Eric T. Dawson, Wouter De Coster, Haowei Du, Christopher Dunn, Rocio Esteban, Angad Jolly, Divya Kalra, Chunxiao Liao, Yunxi Liu, Tsung-Yu Lu, James M Havrilla, Michael M. Khayat, Maximillian G. Marin, Jean Monlong, Stephen Price, Alejandro Rafael Gener, Jimin Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C. Soto, Arda Söylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin N. Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam C. English, Zev Kronenberg, Todd J. Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, Fritz J. Sedlazeck
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pcbi.1005158

Machine Learning for Characterization of Insect Vector Feeding
Cited by: 25
Author(s): Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski, Stephen L. Lapointe
Software Mentions: 14
Published: about 8 years ago

10.1371/journal.pcbi.1003118

Software for Computing and Annotating Genomic Ranges
Cited by: 2,902
Author(s): Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, Vincent J. Carey
Software Mentions: 14
Published: over 11 years ago

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: over 5 years ago

10.7554/eLife.54186

Epigenetic inheritance of circadian period in clonal cells
Cited by: 12
Author(s): Yan Li, Yongli Shan, Gokhul Kilaru, Stefano Berto, Guang-Zhong Wang, Kimberly Cox, Seung-Hee Yoo, Shao Nian Yang, Genevieve Konopka, Joseph S. Takahashi
Software Mentions: 13
Published: over 4 years ago

10.1099/mgen.0.000524

BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access
Cited by: 12
Author(s): Adrian Sven Geissler, Christian Anthon, Ferhat Alkan, Enrique González-Tortuero, Line Dahl Poulsen, Thomas Beuchert Kallehauge, Anne Breüner, Stefan E. Seemann, Jeppe Vinther, Jan Gorodkin
Software Mentions: 12
Published: almost 4 years ago

10.1074/mcp.TIR120.002155

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis
Cited by: 129
Author(s): Johannes Griss, Guilherme Viteri, Konstantinos Sidiropoulos, Vy Kim Nguyen, Antonio Fabregat, Henning Hermjakob
Software Mentions: 11
Published: about 4 years ago

10.1186/s13073-016-0285-0

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins
Cited by: 55
Author(s): Chan Zhou, Samuel R. York, Jennifer Y. Chen, Joshua V. Pondick, Daniel L. Motola, Raymond T. Chung, Alan C. Mullen
Software Mentions: 11
Published: almost 9 years ago

10.1038/s41421-021-00314-w

Single-cell RNA-Seq reveals transcriptional heterogeneity and immune subtypes associated with disease activity in human myasthenia gravis
Cited by: 12
Author(s): Jin Wu, Qi Yang, Yuyao Peng, Chengkai Yan, Yi Li, Zhaohui Luo, Bo Xiao, Liqun Xu, Huan Yang
Software Mentions: 11
Published: over 3 years ago

10.1016/j.celrep.2019.05.026

ZIC3 Controls the Transition from Naive to Primed Pluripotency
Cited by: 41
Author(s): Shen Hsi Yang, Munazah Andrabi, Rebecca Biss, Syed Murtuza Baker, Mudassar Iqbal, Andrew D. Sharrocks
Software Mentions: 11
Published: over 5 years ago

10.1093/database/bay027

Maser: one-stop platform for NGS big data from analysis to visualization
Cited by: 38
Author(s): Sonoko Kinjo, Norikazu Monma, Sadahiko Misu, Norikazu Kitamura, Junichi Imoto, Kazutoshi Yoshitake, Takashi Gojobori, Kazuho Ikeo
Software Mentions: 10
Published: almost 7 years ago

10.7554/eLife.10421

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain
Cited by: 115
Author(s): Claudia Scheckel, Elodie Drapeau, María A. Frías, Christopher Y. Park, John Fak, Ilana Zucker-Scharff, Yan Kou, Vahram Haroutunian, Avi Ma’ayan, Joseph D. Buxbaum, Robert B. Darnell
Software Mentions: 10
Published: almost 9 years ago

10.1186/s13059-020-02034-y

APEC: an accesson-based method for single-cell chromatin accessibility analysis
Cited by: 11
Author(s): Bin Li, Young Li, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin, Kun Qu
Software Mentions: 10
Published: over 4 years ago

10.3390/md18100515

Applying a Chemogeographic Strategy for Natural Product Discovery from the Marine Cyanobacterium Moorena bouillonii
Cited by: 6
Author(s): Christopher A. Leber, C. Benjamin Naman, Lena Keller, Jehad Almaliti, Eduardo J. E. Caro‐Diaz, Evgenia Glukhov, V. Joseph, Sajeevan Thavarool Puthiyedathu, Andres Joshua Reyes, Jason S. Biggs, Te Li, Ye Yuan, Shan He, Xiaojun Yan, William H. Gerwick
Software Mentions: 10
Published: about 4 years ago

10.1186/s13059-019-1647-x

Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma
Cited by: 48
Author(s): Domenico Alessandro Silvestris, Ernesto Picardi, Valeriana Cesarini, Bruno Fosso, Nicolò Mangraviti, Luca Massimi, Maurizio Martini, Graziano Pesole, Franco Locatelli, Angela Gallo
Software Mentions: 10
Published: almost 6 years ago

10.1371/journal.pbio.3001053

Identification of 3′ UTR motifs required for mRNA localization to myelin sheaths in vivo
Cited by: 13
Author(s): Katie M. Yergert, Caleb A. Doll, Rebecca O’Rouke, Jacob H. Hines, Bruce Appel
Software Mentions: 10
Published: almost 4 years ago

10.3389/fchem.2021.722087

PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems
Cited by: 0
Author(s): Matej Medvecký, Manolis Mandalakis
Software Mentions: 10
Published: over 3 years ago

10.1242/dev.193060

Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish
Cited by: 4
Author(s): Stefan Redl, António Miguel de Jesus Domingues, Edoardo Caspani, Stefanie Möckel, Willi Salvenmoser, María Méndez-Lago, René F. Ketting
Software Mentions: 10
Published: almost 5 years ago

10.7554/eLife.40757

Targets and genomic constraints of ectopic Dnmt3b expression
Cited by: 24
Author(s): Yingying Zhang, Jocelyn Charlton, Rahul Karnik, Isabel Beerman, Zachary D. Smith, Hongcang Gu, Patrick Boyle, Xiaoli Mi, Kendell Clement, Ramona Pop, Andreas Gnirke, Derrick J. Rossi, Alexander Meissner
Software Mentions: 9
Published: about 6 years ago

10.1186/s13059-020-02008-0

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Cited by: 24
Author(s): Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan
Software Mentions: 9
Published: over 4 years ago

10.1126/sciadv.abc8492

Persistent epigenetic reprogramming of sweet taste by diet
Cited by: 29
Author(s): Anoumid Vaziri, Morteza Khabiri, Brendan T. Genaw, Christina E. May, Peter L. Freddolino, Monica Dus
Software Mentions: 9
Published: about 4 years ago

10.3389/fgene.2014.00325

DaVIE: Database for the Visualization and Integration of Epigenetic data
Cited by: 6
Author(s): Anthony P. Fejes, Meaghan J. Jones, Michæl S. Kobor
Software Mentions: 9
Published: over 10 years ago

10.3390/ijms22063200

Identification of Transcriptomic Differences between Lower Extremities Arterial Disease, Abdominal Aortic Aneurysm and Chronic Venous Disease in Peripheral Blood Mononuclear Cells Specimens
Cited by: 4
Author(s): Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Przemysław Kołodziej, Jolanta Szymańska, Bartosz J. Płachno, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki, Anna Bogucka‐Kocka
Software Mentions: 9
Published: almost 4 years ago

10.3389/fgene.2015.00339

Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome
Cited by: 23
Author(s): Emanuele Libertini, Alice Lebreton, Goran Lakisic, Marie‐Agnès Dillies, Stephan Beck, Jean‐Yves Coppée, Pascale Cossart, Hélène Bierne
Software Mentions: 9
Published: about 9 years ago

10.18632/oncotarget.10834

Dysregulated long intergenic non-coding RNA modules contribute to heart failure
Cited by: 15
Author(s): Lin Pang, Jing Hu, Guanxiong Zhang, Xiang Li, Xinxin Zhang, Fulong Yu, Yujia Lan, Jiu Hua Xu, Bo Pang, Dong Han, Yun Xiao, Xia Li
Software Mentions: 8
Published: over 8 years ago

10.1038/s41598-018-29378-7

Epigenetic and transcriptional dysregulation of VWA2 associated with a MYC-driven oncogenic program in colorectal cancer
Cited by: 7
Author(s): Beatríz González, Ferran Fece de la Cruz, Johanna Samuelsson, Andreu Alibés, Sergio Alonso
Software Mentions: 8
Published: over 6 years ago

10.3389/fphys.2021.662132

Liver Transcriptome Dynamics During Hibernation Are Shaped by a Shifting Balance Between Transcription and RNA Stability
Cited by: 10
Author(s): Austin E. Gillen, Rui Fu, Kent Riemondy, Jennifer Jager, Bin Fang, Mitchell A. Lazar, Sandra L. Martin
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-020-67870-1

Investigating the influence of mtDNA and nuclear encoded mitochondrial variants on high intensity interval training outcomes
Cited by: 6
Author(s): Nicholas R. Harvey, Sarah Voisin, Rodney Arthur Lea, Xu Yan, Miles C. Benton, ID Papadimitriou, Jacques Michaux, Larisa M. Haupt, Kevin J. Ashton, Nir Eynon, Lyn R. Griffiths
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-021-98889-7

Productive visualization of high-throughput sequencing data using the SeqCode open portable platform
Cited by: 7
Author(s): Enrique Blanco, Mar González-Ramírez, Luciano Di Croce
Software Mentions: 8
Published: about 3 years ago

10.1371/journal.pbio.2002054

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells
Cited by: 76
Author(s): Colin R. Lickwar, J. Gray Camp, Matthew Weiser, Jordan L. Cocchiaro, David M. Kingsley, Terrence S. Furey, Shehzad Z. Sheikh, John F. Rawls
Software Mentions: 8
Published: over 7 years ago

10.3390/vaccines9030217

HIV-Exposed Seronegative Sex Workers Express Low T-Cell Activation and an Intact Ectocervical Tissue Microenvironment
Cited by: 2
Author(s): Maria Röhl, Annelie Tjernlund, Julie Lajoie, Gabriella Edfeldt, Frideborg Bradley, Sofia Bergström, Vilde Kaldhusdal, Alexandra Åhlberg, Anna Månberg, Kenneth Omollo, Geneviève Boily-Larouche, Muhammad Asghar, Douglas S. Kwon, Julius Oyugi, Joshua Kimani, Peter Nilsson, Keith R. Fowke, Kristina Broliden
Software Mentions: 8
Published: almost 4 years ago

10.1186/s13072-020-00353-9

Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells
Cited by: 20
Author(s): Nicole L. Arruda, Zachary Carico, Megan Justice, Ying Frances Liu, Junjie Zhou, Holden C. Stefan, Jill M. Dowen
Software Mentions: 8
Published: over 4 years ago

10.1186/s12864-021-07760-6

UniBind: maps of high-confidence direct TF-DNA interactions across nine species
Cited by: 31
Author(s): Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime A Castro-Mondragón, Anthony Mathelier
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.05005

Predicting effective microRNA target sites in mammalian mRNAs
Cited by: 5,158
Author(s): Vikram Agarwal, George W. Bell, Jin Wu Nam, David P. Bartel
Software Mentions: 8
Published: over 9 years ago

10.1016/j.molcel.2020.01.007

Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation
Cited by: 74
Author(s): Alex Tuck, Aneliya Rankova, Alaaddin Bulak Arpat, Luz Angélica Liechti, Daniel Heß, Vytautas Iešmantavičius, Violeta Castelo-Szekely, David Gatfield, Marc Bühler
Software Mentions: 7
Published: almost 5 years ago

10.1126/sciimmunol.abg0833

SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation
Cited by: 127
Author(s): Bingyu Yan, Tilo Freiwald, Daniel Chauss, Luopin Wang, Erin E. West, Carmen Mirabelli, Zhang Cj, Eva-Maria Nichols, Nazish T. Malik, Richard I. Gregory, Marcus Bantscheff, Sonja Ghidelli-Disse, Martin Kolev, Tristan Frum, Jason R. Spence, Jonathan Z. Sexton, Konstantinos D. Alysandratos, Darrell N. Kotton, Stefania Pittaluga, Jack Bibby, Nathalie Niyonzima, Matthew R. Olson, Shahram Kordasti, Didier Portilla, Christiane E. Wobus, Arian Laurence, Michail S Lionakis, Claudia Kemper, Behdad Afzali, Majid Kazemian
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-021-07488-3

Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP
Cited by: 7
Author(s): Thomas M. Adams, Tjelvar S. G. Olsson, Ricardo H. Ramírez-González, Ruth Bryant, R. J. Bryson, Pablo E. Campos, Paul Fenwick, David Feuerhelm, Charlotte Hayes, Tina Henriksson, Amelia Hubbard, Radivoje Jevtić, Christopher Judge, Matthew Kerton, Jean-Luc Da Lage, Clare M. Lewis, Christine Lilly, Udi Meidan, Dario Novoselović, Colin Patrick, R. Wanyera, Diane G. O. Saunders
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-017-10853-6

The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages
Cited by: 39
Author(s): Elton J. R. Vasconcelos, Luis DaSilva, David S. Pires, Guilherme M. Lavezzo, Adriana S. A. Pereira, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 7
Published: over 7 years ago

10.1038/s41597-020-00659-z

lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA
Cited by: 35
Author(s): Fayaz Seifuddin, Komudi Singh, Abhilash Suresh, Jennifer Judy, Yun Ching Chen, Vijender Chaitankar, Ilker Tunc, Xiangbo Ruan, Ping Li, Yi Chen, Haiming Cao, Richard S. Lee, Fernando S. Goes, Peter P. Zandi, M. Saleet Jafri, Mehdi Pirooznia
Software Mentions: 7
Published: about 4 years ago

10.1093/gigascience/giaa153

Significantly improving the quality of genome assemblies through curation
Cited by: 540
Author(s): Kerstin Howe, William Chow, Joanna Collins, Sarah Pelan, Damon-Lee Pointon, Ying Sims, James Torrance, Alan S. Tracey, Jonathan Wood
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13007-021-00791-w

Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture
Cited by: 3
Author(s): Amir Mahboubi, Nicolas Delhomme, Sara Lea Häggström, Johannes Hanson
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.66668

GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo
Cited by: 66
Author(s): Marissa M Gaskill, Tyler J. Gibson, Elizabeth D Larson, Melissa M. Harrison
Software Mentions: 7
Published: almost 4 years ago

10.1155/2012/876976

A High-Throughput Computational Framework for Identifying Significant Copy Number Aberrations from Array Comparative Genomic Hybridisation Data
Cited by: 1
Author(s): Ian Roberts, Stephanie A. Carter, Cinzia G. Scarpini, Konstantina Karagavriilidou, Jenny Barna, M. Calleja, Nicholas Coleman
Software Mentions: 7
Published: over 12 years ago

10.1186/gb-2013-14-2-r18

The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila
Cited by: 29
Author(s): Tobias Kockmann, Moritz Gerstung, Tommy Beat Schlumpf, Zhu Xhinzhou, Daniel Heß, Niko Beerenwinkel, Christian Beisel, Renato Paro
Software Mentions: 7
Published: almost 12 years ago

10.15698/mic2021.07.754

Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast
Cited by: 14
Author(s): Catalina A. Romila, StJohn Townsend, Michał Malecki, Stephan Kamrad, María Rodríguez-López, Olivia Hillson, Cristina Cotobal, Markus Ralser, Jürg Bähler
Software Mentions: 7
Published: over 3 years ago

10.3389/fgene.2020.00082

SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes
Cited by: 6
Author(s): Yue Xing, Alan R. Dabney, Xiao Li, Guosong Wang, C. A. Gill, Claudio Casola
Software Mentions: 7
Published: almost 5 years ago

10.7554/eLife.28275

Concentration dependent chromatin states induced by the bicoid morphogen gradient
Cited by: 76
Author(s): Colleen E Hannon, Shelby A. Blythe, Eric Wieschaus
Software Mentions: 7
Published: over 7 years ago

10.3389/fgene.2021.664424

Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues
Cited by: 5
Author(s): Eliah Overbey, Theros T Ng, Pietro Catini, Lisa Griggs, Paul A. Stewart, Suzana Tkalčić, R. David Hawkins, Yvonne Drechsler
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.47809

Free circular introns with an unusual branchpoint in neuronal projections
Cited by: 11
Author(s): Harleen Saini, Alicia A. Bicknell, Sean R. Eddy, Melissa J. Moore
Software Mentions: 7
Published: about 5 years ago

10.1186/1471-2105-16-S11-S4

Epiviz: a view inside the design of an integrated visual analysis software for genomics
Cited by: 3
Author(s): Florin Chelaru, Héctor Corrada Bravo
Software Mentions: 7
Published: over 9 years ago

10.1186/s12864-018-4835-2

Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)
Cited by: 15
Author(s): Julien Richard Albert, Takao Koike, Hamid Younesy, Iain Thompson, Aaron B. Bogutz, Mehdi Karimi, Matthew C. Lorincz
Software Mentions: 7
Published: over 6 years ago

10.1186/1471-2105-16-S5-S10

Using epigenomics data to predict gene expression in lung cancer
Cited by: 40
Author(s): Jeffery Li, Travers Ching, Sijia Huang, Lana X. Garmire
Software Mentions: 7
Published: almost 10 years ago

10.1242/dev.178590

Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan
Cited by: 13
Author(s): Julien Rougeot, Naomi D. Chrispijn, Marco Aben, Dei M. Elurbe, Karolina M. Andralojc, Patrick J. Murphy, Pascal W.T.C. Jansen, Michiel Vermeulen, Bradley R. Cairns, Leonie M. Kamminga
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0014524

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
Cited by: 493
Author(s): Fabienne Brenet, Michelle Moh, Patricia Funk, Erika Feierstein, Agnès Viale, Nicholas D. Socci, Joseph M. Scandura
Software Mentions: 7
Published: almost 14 years ago

10.1371/journal.pone.0132866

swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing
Cited by: 43
Author(s): Zhen Wang, Xianfeng Li, Yi Jiang, Qianzhi Shao, Qi Liu, Bingyu Chen, Dongsheng Huang
Software Mentions: 7
Published: over 9 years ago

10.1371/journal.pgen.1009587

The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency
Cited by: 17
Author(s): Kazutoshi Takahashi, Michiko Nakamura, Chikako Okubo, Zane Kliesmete, Mari Ohnuki, Megumi Narita, Akira Watanabe, Mai Ueda, Yasuhiro Takashima, Ines Hellmann, Shinya Yamanaka
Software Mentions: 7
Published: over 3 years ago

10.3390/cancers11060759

Detection of Epstein-Barr Virus Infection in Non-Small Cell Lung Cancer
Cited by: 31
Author(s): Fayez Kheir, Mengmeng Zhao, Michael J. Strong, Yi Yu, Asuka Nanbo, Erik K. Flemington, Gilbert F. Morris, Krzysztof Reiss, Li Li, Zhen Lin
Software Mentions: 7
Published: over 5 years ago

10.1186/s40246-016-0063-5

Human genome meeting 2016
Cited by: 10
Author(s): Arpita Srivastava, Y. Wang, Raymond Y. Huang, Chris J. Skinner, Tommy G. Thompson, Lucille Addison Pollard, Teresa L. Wood, Feng Luo, Robert B. Stevenson, Renato Polimanti, Joel Gelernter, Xin-Ying Lin, I. Y. Lim, Yi-Chieh Wu, Ai Ling Teh, L. Chen, I. M. Aris, Soo-Youn Soh, Mya Thway Tint, Julia L. MacIsaac, Fui W Yap, Kenneth Kwek, S. M. Saw, Michael S. Kobor, Michael J. Meaney, Keith M. Godfrey, Yap Seng Chong, Joanna D. Holbrook, Y. S. Lee, P. D. Gluckman, Neerja Karnani, Ashish Kapoor, D. Lee, Aravinda Chakravarti, Christian Maercker, Fritz Graf, Michael Boutros, Georgios Stamoulis, Fabio Santoni, Periklis Makrythanasis, Audrey Letourneau, Michel Guipponi, Nikolaos Panousis, Marco Garieri, Pascale Ribaux, Emilie Falconnet, Christelle Borel, Stylianos E. Antonarakis, Sonia Kumar, Joanne E. Curran, John Blangero, Samit Chatterjee, Jennifer A. Akiyama, Dallas R. Auer, Courtney Berrios, L Pennacchio, Tarak Donti, Gerarda Cappuccio, Marcus J. Miller, Paldeep S. Atwal, A. L. Kennedy, Aaron L. Cardon, Carlos A. Bacino, Lisa Emrick, Jozef Hertecant, F Bäumer, Brenda E. Porter, Matthew N. Bainbridge, Penelope E. Bonnen, Brett H. Graham, Reid Sutton, Qin Sun, Sarah H. Elsea, Zhi-Liang Hu, P. Wang, Yun Zhu, Jinying Zhao, Momiao Xiong, David A. Bennett, Alfredo Hidalgo‐Miranda, Sandra Romero-Córdoba, Sergio Rodrı́guez-Cuevas, Rosa Rebollar-Vega, Elena Tagliabue, Maria Iorio, Elvira D’Ippolito, Stefano Baroni, Bogumił Kaczkowski, Yoïchi Tanaka, Hideya Kawaji, Albin Sandelin, Robin Andersson, Masumi Itoh, Timo Lassmann, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, Colin A. Semple, Elisabeth Rosenthal, Brian H. Shirts, Laura M. Amendola, Cecilia Gracia Gallego, Martha Horike‐Pyne, Amber Burt, Peggy D. Robertson, P. Beyers, Chris Nefcy, DL Veenstra, Fuki M. Hisama, Robin L. Bennett, Michael O. Dorschner, Deborah A. Nickerson, Joseph D. Smith, Karynne Patterson, David R. Crosslin, Rami Nassir, N. Zubair, Tom Harrison, Ulrike Peters, Gail P. Jarvik, Francesca Menghi, Koichiro Inaki, Xingyi Woo, Prerna Kumar, Krzysztof R. Grzęda, Ankit Malhotra, H. Kim, Duygu Ucar, Phung Trang Shreckengast, Krishna Karuturi, James Keck, James Chuang, E. T. Liu, Boyang Ji, Alioto Tyler, Guruprasad Ananda, G. Carter, Hamid Nikbakht, Martin Montagne, Michele Zeinieh, A. Harutyunyan, Melissa K. McConechy, Nada Jabado, Pierre Lavigne, Jacek Majewski, Jennifer B. Goldstein, Michael J. Overman, Gauri Varadhachary, Rachna T. Shroff, Robert A. Wolff, M. M. Javle, Andy Futreal, D. Fogelman, Leny Bravo, Williams Fajardo, Humberto Serna Gómez, Carlos Castañeda, Christian Rolfo, Joseph A. Pinto, Kadir C. Akdemir, Lynda Chin, Shanna Patterson, Cara Statz, Susan M. Mockus, S. N. Nikolaev, Ximena Bonilla, Laurent Parmentier, Bryan King, Fedor Bezrukov, Gulhan Kaya, Vincent Zoete, Vladimir B. Seplyarskiy, Heather Sharpe, Thomas W. McKee, Konstantin Popadin, Nicole Basset-Séguin, Rouaa Ben Chaabene, M. E. Andrianova, C Verdan, K. Grosdemange, Olga Sumara, Martin Eilers, Iannis Aifantis, Olivier Michielin, FJ de Sauvage, Stylianos E. Antonarakis, Somsak Likhitrattanapisal, Stephen E. Lincoln, Allison W. Kurian, Andrea Desmond, Shihui Yang, Yukio Kobayashi, James M. Ford, Leif W. Ellisen, Ted Peters, Karine Alvarez, Emporia Faith Hollingsworth, Dolores López‐Terrada, Alex Hastie, Željko Džakula, Andy Wing Chun Pang, Elaine T. Lam, Thomas Anantharaman, Michael Saghbini, Hua Cao, BioNano Genomics, Claudia Gonzaga‐Jauregui, Lijia Ma, Alejandra King, Erika B. Rosenzweig, U. B. Krishnan, Jeffrey G. Reid, J. D. Overton, Frederick E. Dewey, Woo-Keun Chung, Kathy M. Small, Adam P. DeLuca, Frans P.M. Cremers, Richard A. Lewis, V. Puech, Benjamin Bakall, R. Silva-Garcia, Klaus Rohrschneider, Marie Leys, Fadi Shaya, Edwin M Stone, Nara Sobreira, François Schiettecatte, Hong‐Qing Ling, Eric Pugh, David R. Witmer, Kyle M. Hetrick, P. Zhang, Kimberly F. Doheny, David Valle, Ada Hamosh, Shalini N. Jhangiani, Zeynep Coban Akdemir, Matthew N. Bainbridge, Wu‐Lin Charng, Wojciech Wiszniewski, Tomasz Gambin, Ender Karaca, Yavuz Bayram, Mohammad K. Eldomery, Jennifer E. Posey, Hv. Doddapaneni, Jingyuan Hu, V. Reid Sutton, Donna M. Muzny, Eric Boerwinkle, James R. Lupski, Richard A. Gibbs, Sandhya Shekar, William Salerno, Adam C. English, Adina Mangubat, Jeremy Bruestle, Adrian Thorogood, Bartha Maria Knoppers, Global Alliance for Genomics, Hazuki Takahashi, Kazuhiro R. Nitta, A. Kozhuharova, Ana Maria Suzuki, Hemant Sharma, Diego Cotella, Claudia Santoro, S. Zucchelli, Stefano Gustincich, J. J. Mulvihill, Gareth Baynam, W. A. Gahl, Stephen C. Groft, Kenjiro Kosaki, Paul Lasko, Béla Melegh, Domenica Taruscio, Rajarshi Ghosh, Sharon E. Plon, Steven E. Scherer, Xiang Qin, Rashesh Sanghvi, Kimberly Walker, Tsoyu Chiang, Donna M. Muzny, L. Wang, John L. Black, Eric Boerwinkle, Richard M. Weinshilboum, R.A. Gibbs, Tatiana V. Karpinets, Tiffany L. Calderone, Khalida Wani, Xiaoxing Yu, Caitlin Creasy, Cara L. Haymaker, Marie-Andrée Forget, Vashisht Gopal Yennu Nanda, Jason Roszik, Jennifer A. Wargo, Lauren E. Haydu, Xiaofei Song, Alexander J. Lazar, Jeffrey E. Gershenwald, M. A. Davies, Chantale Bernatchez, J. Zhang, Simon Woodman, Elissa J. Chesler, Todd B. Reynolds, Jason A Bubier, C M D Wendell Phillips, Michael A. Langston, Erich J. Baker, Nancy U. Lin, Christopher I. Amos, Vince D. Calhoun, Otto Dobretsberger, M. Egger, F. Leimgruber, Simon Sadedin, Alicia Oshlack, Victor Andrew A. Antonio, Noriaki Ono, Clark Kendrick Go, Zaheer Ahmed, Mohan Bolisetty, Saman Zeeshan, Esther Aguirre Anguiano, Abhishek Sarkar, Madhusudan R. Nandineni, Chao Zeng, Jie Shao, Tianzhu Liang, Kevin Pham, Y. Chee-Wei, Dongsheng Li, W. Lai-Ping, Duan Lian, Rick Ong Twee Hee, Yuzaimi Yunus, Farhang Aghakhanian, Siti Shuhada Mokhtar, C. V. Lok-Yung, Jong Bhak, Matthew Phipps, Xu Shuhua, T. Yik-Ying, Vinod Kumar, Hoh BoonPeng, Ian Campbell, Mary‐Anne Young, Pettengill James, Lifepool, Manjari Rain, Ghulam Mohammad, Ritushree Kukreti, Qadar Pasha, Ainur Akilzhanova, C. Guelly, Zhannur Abilova, Saule Rakhimova, Ainur Akhmetova, Ulykbek Kairov, Slave Trajanoski, Zhaxybay Zhumadilov, Makhabbat Bekbossynova, Cassie A. Schumacher, Sardul Singh Sandhu, Timothy T. Harkins, Vladimir Makarov, Robert Glenn, Zeineen Momin, B. Dilrukshi, Hsiao Tuan Chao, Qingchang Meng, Brent M. Gudenkauf, R. Kshitij, Joy C. Jayaseelan, Caitlin Nessner, S. Lee, K. Blankenberg, Lora Lewis, Yi Han, Huyen Dinh, S. Jireh, Christian Buhay, X. Liu, Q. Wang, Yao Ding, Narayanan Veeraraghavan, Ya Ping Yang, Arthur L. Beaudet, Christine M. Eng, Kim C. Worley, Y. Liu, Daniel Hughes, Shwetha C. Murali, R. Alan Harris, Adam C. English, Oliver A. Hampton, Peter A. Larsen, Christine R. Beck, M. Wang, Christie Kovar, William Salerno, Anne D. Yoder, Stephen M. Richards, Jeffrey Rogers, M. Raveenedran, Chenghai Xue, Mahmoud Dahdouli, Linda J. Cox, Guangyi Fan, Betsy Ferguson, J. Hovarth, Zachary P. Johnson, Sree Kanthaswamy, M. Kubisch, Martin Ward Platt, Daniel G. Smith, Eric J. Vallender, Roger W. Wiseman, Jennifer E. Below, Fuli Yu, Jaime Lin, Y. Zhang, Zhengqing Ouyang, Andrew Moore, Z. Wang, Johannes Hofmann, Purdue Mp, Rachael Z. Stolzenberg‐Solomon, Shelsey J. Weinstein, Demetrius Albanês, C. S. Liu, Wei‐Yi Cheng, Timothy Lin, Qiong Lan, Nathaniel Rothman, SI Berndt, E. S. Chen, Hoda Bahrami, A. Khoshzaban, S. Heidari Keshal, K. K. R. Alharbi, M. Zhalbinova, Ainur Akilzhanova, Mahabbat Bekbosynova, Ш.К. Мырзахметова, Maher Matar, N. Mili, Robert J. Molinari, Yussanne Ma, Stéphane Guerrier, Nasser A. Elhawary, Mohammed T. Tayeb, Neda M. Bogari, N. Qotb, Sarah A. McClymont, Paul W. Hook, Loyal A. Goff, Andrew S. McCallion, Yong Kong, Jacob Charette, Wanda L. Hicks, Jürgen Κ. Naggert, Lue Ping Zhao, Patsy M. Nishina, Burhan Edrees, Mohammad Athar, Faisal A. Al‐Allaf, Mohiuddin M. Taher, Wahab Khan, Abdellatif Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, Abeer Abdullah Al Anazi, N. Altayeb, Muhammad Ahmed, K. Alansary, Zainularifeen Abduljaleel, Anton Kratz, Pascal Béguin, Stéphane Poulain, Makoto Kaneko, C. Takahiko, Atsuko Matsunaga, Sachi Kato, Nicolas Bertin, Réjan Vigot, Charles Plessy, Thomas Lavstsen, Dan Graur, Jens Friis-Nielsen, Jose M. G. Izarzugaza, Søren Brunak, Anurupa Chakraborty, Jolly Basak, and Rajendrani Mukhopadhyay, Benjamin Soibam, Dhritishree Das, Nupur Biswas, Das S, Sinjini Sarkar, Anirban Maitra, Chandan Kumar Panda, Prasenjit Majumder, Heba Morsy, Ahmed Mohammed Gaballah, M Parikh Samir, M. Shamseya, Hisham Mahrous, Ayesha Ghazal, Waleed Arafat, M. Hashish, Joshua J. Gruber, Natalie Jaeger, Matthew Snyder, Kashyap Patel, Shannon Bowman, Trisha N. Davis, D Kraushaar, Amy B. Emerman, Salvatore Russello, Noa Henig, Cynthia L. Hendrickson, K. Zhang, Mauricio Rodríguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales, Natalie Jäger, J. Chen, Robert W. Haile, Megan P. Hitchins, Julia Brooks, Silvia Jiménez-Morales, Mónica Morales Ramírez, Javier Martín‐Núñez, Valerie Bekker, Yriana Rodrigues Leal, Esteban Jiménez, Aída Carolina Medina, Alfredo Hidalgo, Jorge Mejía, V. Halytskiy, Jürgen Κ. Naggert, Gayle B. Collin, K. DeMauro, R. Hanusek, K. Belhassa, Khadija Belhassan, Laila Bouguenouch, I. Samri, H. Sayel, Fz. moufid, I. El Bouchikhi, S. Trhanint, H. Hamdaoui, I. Elotmani, I. Khtiri, O. Kettani, L. Quibibo, M. Ahagoud, Mohammed Abdou Abbassi, Karim Ouldim, А. В. Марусин, А. Н. Корнетов, M. G. Swarovskaya, K. Vagaiceva, Vadim Stepanov, Eva Maria Cutiongco de la Paz, Rody G. Sy, Julián Nevado, Paul Ferdinand M. Reganit, L. C. S. dos Santos, Jose Donato A. Magno, Felix Eduardo R. Punzalan, Deborah Ignacia D. Ona, Erasmo Gonzalo D.V. Llanes, R. L. Santos-Cortes, Raphael Enrique Tiongco, Jaime Alfonso M. Aherrera, Lauro L. Abrahan, P. Pagauitan-Alan, Kathryn H. Morelli, J. S. Domire, Nibedita Pyne, Shirley F. Harper, Ralph Royal Burgess, Mamdooh Gari, Ashraf Dallol, Haneen Alsehli, Abdullah Gari, Mamdooh Gari, A. A. Abuzenadah, M. G. Thomas, Mahadeo A. Sukhai, Shruti Garg, Maksym Misyura, T. Zhang, Anna Schuh, Tracy Stockley, Suzanne Kamel‐Reid, Stephen T. Sherry, Chunlin Xiao, Douglas J. Slotta, Kurt Rodarmer, Michael Feolo, Michael Kimelman, Georgy Godynskiy, Christopher D. O’Sullivan, Eugene Yaschenko, Claudia Rangel‐Escareño, H. Rueda-Zarate, Iftikhar Aslam Tayubi, Reema R Mohammed, Iqbal Ike K. Ahmed, Tamar Ahmed, Sahil Seth, Samirkumar B. Amin, Xinjie Mao, Hui Sun, Roeland Verhaak, S. J. Whiite, Jesse Farek, Z. Kahn, Takeya Kasukawa, Marina Lizio, Jayson Harshbarger, S. Hisashi, Jessica Severin, A. Imad, Sedef Şahin, Thomas Charles Augustus Freeman, Katherine Unger Baillie, Sandhya Shekar, Abbes Salem, Mecheala Abbas Ali, Ahmed Ibrahim, M. Sofi Ibrahim, H Barrera, Lourdes Garza, Julian Torres, V. Barajas, Alfredo Ulloa‐Aguirre, David Kershenobich, Shahroj Mortaji, Pedro Guizar, Eliezer Loera, Karen Moreno, Adriana De León, Daniela Monsiváis, Jackeline Gómez, Raquel Cardiel, Jesús Carlos Fernández-López, V. Bonifaz-Peña, Andrew Contreras, Linda M. Polfus, X. Wang, Vivek Philip, A. A. Abuzenadah, Rola Turki, Asli Uyar, A. Kaygun, Sayed Zaman, E. García de Castro Márquez, Josna George, Cynthia L. Hendrickson, Dakota Starr, Mark E. Baird, Brian Kirkpatrick, Kent J. Sheets, Rainer Nitsche, L. Prieto-Lafuente, Melissa Landrum, J. Lee, Wendy S. Rubinstein, Donna Maglott, P. K. R. Thavanati, A. Escoto de Dios, Rolando Hernandez, M. E. Aguilar Aldrate, Mirna Mejia, K. R. R. Kanala, Neelum Shahzad, Elisabeth Huber, Alice J. Dan, Wolfgang Herr, G. Sprotte, Josef Köstler, Andreas Hiergeist, AE Gessner, Reinhard Andreesen, Elmar Holler, Faisal A. Al‐Allaf, Abdullah A. Al-Ashwal, Mohiuddin M. Taher, Halah Abalkhail, Ahmad F. Al-Allaf, R. Bamardadh, Olga Filiptsova, M. M. Kobets, Yu. M. Kobets, Ievgeniia Burlaka, I. Timoshyna, M. M. Kobets, Muhammad Mohiuddin, A. Zainularifeen, Alfaqih Samar Mohammed, Tarek Owaidah
Software Mentions: 7
Published: over 8 years ago

10.3389/fpls.2014.00708

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants
Cited by: 19
Author(s): Deblina Patra, Mario Fasold, David Langenberger, Gerhard Steger, Ivo Große, Peter F. Stadler
Software Mentions: 7
Published: almost 10 years ago

10.1371/journal.pgen.1006864

Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder
Cited by: 101
Author(s): Tom S. Koemans, Tjitske Kleefstra, Melissa C. Chubak, Max H. Stone, Margot R.F. Reijnders, Sonja de Munnik, Marjolein H. Willemsen, Michaela Fencková, Connie Stumpel, Levinus A. Bok, Margarita Saenz, Kyna A. Byerly, Linda B. Baughn, Alexander P.A. Stegmann, Rolph Pfundt, Huiqing Zhou, Hans van Bokhoven, Annette Schenck, Jamie M. Kramer
Software Mentions: 7
Published: about 7 years ago

10.3389/fgene.2019.00309

Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions
Cited by: 26
Author(s): Simon A. Hardwick, Samuel D. Bassett, Dominik C. Kaczorowski, James Blackburn, Kirston Barton, Nenad Bartoniček, Shaun Carswell, Hagen Tilgner, Clement T. Loy, Glenda M. Halliday, Tim R. Mercer, Martin A. Smith, John S. Mattick
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2015.00287

Design, measurement and processing of region-specific DNA methylation assays: the mass spectrometry-based method EpiTYPER
Cited by: 56
Author(s): H. Eka D. Suchiman, Roderick C. Slieker, Dennis Kremer, P. Eline Slagboom, Bastiaan T. Heijmans, Elmar W. Tobi
Software Mentions: 7
Published: over 9 years ago

10.3389/fgene.2017.00013

The Pancreatic Islet Regulome Browser
Cited by: 28
Author(s): Loris Mularoni, Mireia Ramos-Rodríguez, Lorenzo Pasquali
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pgen.1006563

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing
Cited by: 163
Author(s): Rui Zhang, Patricia Deng, Jacobson Dionna, Jin Billy Li
Software Mentions: 6
Published: almost 8 years ago

10.1186/2045-9769-3-1

glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data
Cited by: 52
Author(s): Andrew P. Hutchins, Ralf Jauch, Mateusz Dyla, Diego Miranda‐Saavedra
Software Mentions: 6
Published: almost 11 years ago

10.3390/genes9080392

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates
Cited by: 16
Author(s): Bernhard C. Thiel, Roman Ochsenreiter, Veerendra P. Gadekar, Andrea Tanzer, Ivo L. Hofacker
Software Mentions: 6
Published: over 6 years ago

10.1016/j.celrep.2020.108545

CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
Cited by: 23
Author(s): Jonathan Martínez-Fábregas, Luopin Wang, Elizabeth Pöhler, Adeline Cozzani, Stephan Wilmes, Majid Kazemian, Suman Mitra, Ignacio Moraga
Software Mentions: 6
Published: about 4 years ago

10.3389/fimmu.2021.630389

Identification of Novel Genetic Regulatory Region for Proprotein Convertase FURIN and Interferon Gamma in T Cells
Cited by: 6
Author(s): Zsuzsanna Ortutay, Anna Grönholm, Melina Laitinen, Melinda Keresztes-Andrei, Ismaïl Hermelo, Marko Pesu
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.csbj.2021.07.010

Genome-wide mapping of binding sites of the transposase-derived SETMAR protein in the human genome
Cited by: 3
Author(s): Márton Miskei, Adrienn Horváth, Lívia Viola, L. Varga, Éva Nagy, Orsolya Feró, Zsolt Karányi, Jason Roszik, Csaba Miskey, Zoltán Ivics, Lóránt Székvölgyi
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pgen.1009338

Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization
Cited by: 15
Author(s): Margarita V. Brovkina, Rachel Duffié, Abbigayl E. C. Burtis, E. Josephine Clowney
Software Mentions: 6
Published: almost 4 years ago

10.1038/s42003-018-0219-z

RELACS nuclei barcoding enables high-throughput ChIP-seq
Cited by: 27
Author(s): Laura Arrigoni, Hoor Al-Hasani, Fidel Ramírez, Ilaria Panzeri, Devon P. Ryan, Diana Santacruz, Nadia Kress, J. Andrew Pospisilik, Ulrike Bönisch, Thomas Manke
Software Mentions: 6
Published: about 6 years ago

10.1186/s13148-018-0582-0

Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes
Cited by: 20
Author(s): Adeline Divoux, Katalin Sandor, Dóra Bojcsuk, Amlan Talukder, Xiaoman Li, Bálint László Bálint, Timothy F. Osborne, Steven R. Smith
Software Mentions: 6
Published: about 6 years ago

10.1101/2021.02.23.432450

The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation
Cited by: 4
Author(s): Jordan M. Meyers, Muthukumar Ramanathan, Ronald L. Shanderson, Laura K. Donohue, Ian Ferguson, Margaret Guo, Deepti Rao, Weili Miao, David L. Reynolds, Xue Yang, Yang Zhao, Yen-Yu Yang, Yinsheng Wang, Paul A. Khavari
Software Mentions: 6
Published: almost 4 years ago

10.1534/g3.119.400273

DPAC: A Tool for Differential Poly(A)–Cluster Usage from Poly(A)–Targeted RNAseq Data
Cited by: 16
Author(s): Andrew Routh
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-82989-5

CD4+ T cells from children with active juvenile idiopathic arthritis show altered chromatin features associated with transcriptional abnormalities
Cited by: 5
Author(s): Evan Tarbell, Kaiyu Jiang, Teresa Hennon, Lucy C Holmes, Sonja D. Williams, Yao Fu, Patrick M. Gaffney, Tao Liu, James N. Jarvis
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.cub.2018.09.026

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis
Cited by: 35
Author(s): Ignacio E. Schor, Giovanni Bussotti, Matilda Maleš, Mattia Forneris, Rebecca R. Viales, Anton J. Enright, Eileen E. M. Furlong
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pcbi.1009095

Identifying the combinatorial control of signal-dependent transcription factors
Cited by: 15
Author(s): Ning Wang, Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li, Alexander Hoffmann
Software Mentions: 6
Published: over 3 years ago

10.1002/stem.2521

Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells
Cited by: 37
Author(s): Agata Stryjewska, Ruben Dries, Tim Pieters, Griet Verstappen, Andrea Conidi, Kathleen Coddens, Annick Francis, Lieve Umans, Wilfred F. J. van IJcken, Geert Berx, Leo A. van Grunsven, Frank Grosveld, Steven Goossens, Jody J. Haigh, Danny Huylebroeck
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pgen.1008516

Ligand dependent gene regulation by transient ERα clustered enhancers
Cited by: 17
Author(s): Bharath Saravanan, Deepanshu Soota, Zubairul Islam, Sudeshna Majumdar, Rajat Mann, Sweety Meel, Umer Farooq, Kaivalya Walavalkar, Srimonta Gayen, Anurag Kumar Singh, Sridhar Hannenhalli, Dimple Notani
Software Mentions: 6
Published: almost 5 years ago

10.1101/2020.07.19.210955

Interferons and viruses induce a novel primate-specific isoform dACE2 and not the SARS-CoV-2 receptor ACE2
Cited by: 19
Author(s): Olusegun O. Onabajo, Abdul Rouf Banday, Wusheng Yan, Adeola Obajemu, Megan L. Stanifer, Deanna M. Santer, Óscar Flórez-Vargas, Helen Piontkivska, Joselin M. Vargas, Carmon Kee, D. Lorne Tyrrell, Juan L. Mendoza, Steeve Boulant, Ludmila Prokunina‐Olsson
Software Mentions: 6
Published: over 4 years ago

10.1186/s13148-020-00881-x

Gene–methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk
Cited by: 7
Author(s): Julia Romanowska, Øystein Ariansen Haaland, Astanand Jugessur, Miriam Gjerdevik, Zongli Xu, Jack A. Taylor, Allen J. Wilcox, Inge Jonassen, Rolv Terje Lie, Håkon K. Gjessing
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.57189

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma
Cited by: 11
Author(s): Connor Rogerson, Samuel Ogden, Edward Britton, Yeng Ang, Andrew D. Sharrocks
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0123380

Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1)
Cited by: 41
Author(s): Christopher Terranova, Sridhar T. Narla, Yu Wei Lee, Jonathan Bard, Abhirath Parikh, Ewa K. Stachowiak, Emmanuel S. Tzanakakis, Michael Buck, Barbara Birkaya, Michal K. Stachowiak
Software Mentions: 6
Published: over 9 years ago

10.1038/s41598-017-17407-w

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation
Cited by: 37
Author(s): Mariana Fontes, Ayşegül Güvenek, Riki Kawaguchi, Dinghai Zheng, Alden Huang, Victoria M. Ho, Patrick B. Chen, Xiaochuan Liu, Thomas J. O’Dell, Giovanni Coppola, Bin Tian, Kelsey C. Martin
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pbio.2003903

Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development
Cited by: 62
Author(s): Hong Zhang, Shengqian Dou, Feng He, Junjie Luo, Liping Wei, Jian Lü
Software Mentions: 6
Published: over 6 years ago

10.1186/1471-2105-13-102

Workflows for microarray data processing in the Kepler environment
Cited by: 14
Author(s): Thomas Stropp, Timothy M. McPhillips, Bertram Ludäscher, Mark Bieda
Software Mentions: 6
Published: over 12 years ago

10.1371/journal.pbio.3001077

Cell-level metadata are indispensable for documenting single-cell sequencing datasets
Cited by: 5
Author(s): Sidhant Puntambekar, Jay R. Hesselberth, Kent Riemondy, Rui Fu
Software Mentions: 6
Published: over 3 years ago

10.3390/plants10061123

Genome-Wide Association Analysis for Stem Cross Section Properties, Height and Heading Date in a Collection of Spanish Durum Wheat Landraces
Cited by: 9
Author(s): Carmen M. Ávila, María Dolores Requena-Ramírez, Cristina Rodríguez-Suárez, Fernando Flores, Josefina C. Sillero, Sergio G. Atienza
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giaa137

Long-read assembly of the <i>Brassica napus</i> reference genome Darmor-bzh
Cited by: 50
Author(s): Mathieu Rousseau‐Gueutin, Caroline Belser, Corinne Da Silva, Gautier Richard, Benjamin Istace, Corinne Cruaud, Cyril Falentin, Franz Boideau, Julien Boutte, Régine Delourme, Gwenaëlle Deniot, Stéfan Engelen, Julie Ferreira de Carvalho, Arnaud Lemainque, Loeiz Maillet, Jérôme Morice, Patrick Wincker, Anne‐Marie Chèvre, Jean‐Marc Aury
Software Mentions: 6
Published: about 4 years ago

10.1111/tpj.14184

An updated gene atlas for maize reveals organ‐specific and stress‐induced genes
Cited by: 91
Author(s): Genevieve M. Hoopes, John Hamilton, Joshua C. Wood, Eddi Esteban, Asher Pasha, Brieanne Vaillancourt, Nicholas J. Provart, C. Robin Buell
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13073-015-0226-3

The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical–genomic driver associations
Cited by: 70
Author(s): HoJoon Lee, Jennifer Palm, Susan M. Grimes, Hanlee P. Ji
Software Mentions: 6
Published: about 9 years ago

10.1002/1878-0261.12829

Identification of RUNX1T1 as a potential epigenetic modifier in small‐cell lung cancer
Cited by: 10
Author(s): He Tian, Gary Wildey, Karen McColl, Alyssa Savadelis, Kyle B. Spainhower, Cassidy McColl, Adam Kresak, Aik Choon Tan, Michael Yang, Ata Abbas, Afshin Dowlati
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1008414

Modelling thalamocortical circuitry shows that visually induced LTP changes laminar connectivity in human visual cortex
Cited by: 4
Author(s): Rachael L. Sumner, Meg J. Spriggs, Alexander D Shaw
Software Mentions: 6
Published: almost 4 years ago

10.7554/eLife.66321

Channel nuclear pore complex subunits are required for transposon silencing in Drosophila
Cited by: 10
Author(s): Marzia Munafò, Victoria R Lawless, Alessandro Passera, Serena MacMillan, Susanne Bornelöv, Irmgard U. Haussmann, Matthias Soller, Gregory J. Hannon, Benjamin Czech
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-017-3568-y

Conserved expression of transposon-derived non-coding transcripts in primate stem cells
Cited by: 41
Author(s): LeeAnn Ramsay, Maria C. Marchetto, Maxime Caron, Shu-Huang Chen, Stephan Busche, Tony Kwan, Tomi Pastinen, Fred H. Gage, Guillaume Bourque
Software Mentions: 6
Published: almost 8 years ago

10.1186/s13059-018-1589-8

Enhancers in the Peril lincRNA locus regulate distant but not local genes
Cited by: 20
Author(s): Abigail F. Groff, A. Rasim Barutcu, Jordan P. Lewandowski, John L. Rinn
Software Mentions: 6
Published: about 6 years ago

Projects: pypi: browser

Papers Mentioning browser 2,125