10.7554/eLife.68573

Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis
Cited by: 22
Author(s): Martin H Fabry, Federica A. Falconio, Fadwa Joud, Emily K Lythgoe, Benjamin Czech, Gregory J. Hannon
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.46919

FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory
Cited by: 63
Author(s): Kirsty Sawicka, Caryn Hale, Christopher Y. Park, John Fak, Jodi Gresack, Sarah J. Van Driesche, Jaw Jou Kang, Jennifer C. Darnell, Robert B. Darnell
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.64204

Single-PanIN-seq unveils that ARID1A deficiency promotes pancreatic tumorigenesis by attenuating KRAS-induced senescence
Cited by: 5
Author(s): Shou Liu, Wenjian Cao, Yichi Niu, Jiayi Luo, Yanhua Zhao, Zheng Hu, Chenghang Zong
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-021-04120-9

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences
Cited by: 15
Author(s): Sagnik Banerjee, Priyanka Bhandary, Margaret R. Woodhouse, Taner Z. Sen, Roger P. Wise, Carson M. Andorf
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-6161-8

Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat
Cited by: 17
Author(s): Ehsan Sari, Adrian L. Cabral, Brittany Polley, Yifang Tan, Emma Hsueh, David Konkin, Ron Knox, Yuefeng Ruan, Pierre R. Fobert
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.37892

DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis
Cited by: 57
Author(s): Amr Nassrallah, Martin Rougée, Clara Bourbousse, Stéphanie Drevensek, Sandra Fonseca, Elisa Iniesto, Ouardia Aït-Mohamed, Anne Flore Deton-Cabanillas, Gérald Zabulon, Ikhlak Ahmed, David Stroebel, Vanessa Masson, Bérangère Lombard, Dominique Eeckhout, Kris Gevaert, Damarys Loew, Auguste Genovesio, Cécile Breyton, Geert De Jaeger, Chris Bowler, Vicente Rubio, Frédy Barneche
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.68238

Neuronal calmodulin levels are controlled by CAMTA transcription factors
Cited by: 3
Author(s): Thanh Thi Kim Vuong-Brender, Sean M. Flynn, Yvonne Vallis, Mario de Bono
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.60987

Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons
Cited by: 9
Author(s): Bastien Saint-Leandre, Courtney J. Christopher, Mia T. Levine
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-018-4660-7

Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular
Cited by: 41
Author(s): Osagie Izuogu, Abd A. Alhasan, Carla Mellough, Joseph Collin, Richard Gallon, Jonathon Hyslop, Francesco K. Mastrorosa, Ingrid Ehrmann, Majlinda Lako, David Elliott, Mauro Santibanez‐Koref, Michael S. Jackson
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pcbi.1009411

ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
Cited by: 5
Author(s): Juan L. Trincado, Marina Reixachs‐Solé, Judith Pérez-Granado, Tim Fugmann, Ferrán Sanz, Jun Yokota, Eduardo Eyras
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1008422

Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells
Cited by: 2
Author(s): Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Akihiro Fujimoto, Jun-ichirou Yasunaga, Masao Matsuoka
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2020.00216

FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells
Cited by: 26
Author(s): Noudjoud Attaf, Iñaki Cervera-Marzal, Chuang Dong, Laurine Gil, Amédée Renand, Lionel Spinelli, Pierre Milpied
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.46418

Self-sperm induce resistance to the detrimental effects of sexual encounters with males in hermaphroditic nematodes
Cited by: 20
Author(s): Lauren N. Booth, Travis J. Maures, Robin Yeo, Cindy Tantilert, Anne Brunet
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-020-6483-6

Virus expression detection reveals RNA-sequencing contamination in TCGA
Cited by: 21
Author(s): Sara R. Selitsky, David Marron, Daniel P. Hollern, Lisle E. Mose, Katherine A. Hoadley, Corbin D. Jones, Joel S. Parker, Dirk P. Dittmer, Charles M. Perou
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-018-5255-z

Phenotypic plasticity and the evolution of azole resistance in Aspergillus fumigatus; an expression profile of clinical isolates upon exposure to itraconazole
Cited by: 23
Author(s): Margriet W.J. Hokken, Jan Zoll, Jordy P. M. Coolen, Bas J. Zwaan, Paul E. Verweij, Willem J. G. Melchers
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pbio.3000891

Interphase-arrested Drosophila embryos activate zygotic gene expression and initiate mid-blastula transition events at a low nuclear-cytoplasmic ratio
Cited by: 19
Author(s): I. Strong, Xianfu Lei, Fang Chen, Kai Yuan, Patrick H. O’Farrell
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1006903

Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements
Cited by: 17
Author(s): Elodie Thierion, Johan Le Men, Samuel Collombet, Céline Hernandez, Fanny Coulpier, Patrick Torbey, Morgane Thomas‐Chollier, Daan Noordermeer, Patrick Charnay, Pascale Gilardi-Hebenstreit
Software Mentions: 4
Published: about 9 years ago

10.1186/s12859-019-2676-x

SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package
Cited by: 5
Author(s): Taewoon Joo, Ji-Hye Choi, Jihye Lee, So Eun Park, Youngsic Jeon, Sae Hoon Jung, Hyun Goo Woo
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2020.580219

Host Transcriptomic Response Following Administration of Rotavirus Vaccine in Infants’ Mimics Wild Type Infection
Cited by: 4
Author(s): Alberto Gómez‐Carballa, Ruth Barral-Arca, Miriam Cebey-López, María José Currás-Tuala, Sara Pischedda, José Gómez-Rial, Dominic Habgood-Coote, Jethro Herberg, Myrsini Kaforou, Federico Martinón‐Torres, Antonio Salas
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.67932

Wnt signaling enhances macrophage responses to IL-4 and promotes resolution of atherosclerosis
Cited by: 25
Author(s): Ada Weinstock, Karishma Rahman, Or Yaacov, Hitoo Nishi, Prashanthi Menon, Cyrus Nikain, Michela L. Garabedian, Stephanie Pena, Naveed Akbar, Brian E. Sansbury, Sean Heffron, Jianhua Liu, Gregory Marecki, Dawn Fernandez, Emily J. Brown, Kelly V. Ruggles, Stephen A. Ramsey, Chiara Giannarelli, Matthew Spite, Robin P. Choudhury, P’ng Loke, Edward A. Fisher
Software Mentions: 4
Published: over 5 years ago

10.1016/j.ajhg.2016.05.030

BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription
Cited by: 116
Author(s): Cristina Dias, Sara Busquets Estruch, Sarah A. Graham, Jeremy F. McRae, Stephen J. Sawiak, Jane A. Hurst, Shelagh Joss, Susan Holder, Jenny Morton, Claire Turner, Julien Thévenon, Kelly Mellul, Gabriela Sánchez-Andrade, Ximena Ibarra-Soria, Pelagia Derizioti, Rui F. Santos, Song-Choon Lee, Laurence Faivre, Tjitske Kleefstra, Pentao Liu, Mathew E. Hurles, Simon E. Fisher, Darren W. Logan
Software Mentions: 4
Published: about 10 years ago

10.7554/eLife.27786

Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response
Cited by: 29
Author(s): Xu Zhang, Xiaoli Chen, Qiuying Liu, Shaojie Zhang, Wenqian Hu
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.58041

Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria
Cited by: 52
Author(s): Sara M. Nowinski, Ashley Solmonson, Scott F. Rusin, J. Alan Maschek, Claire Bensard, Sarah Fogarty, Mi Young Jeong, Sandra Lettlová, Jordan A. Berg, Jeffrey T. Morgan, Yeyun Ouyang, Bradley C. Naylor, João A. Paulo, Katsuhiko Funai, James E. Cox, Steven P. Gygi, Dennis R. Winge, Ralph J. DeBerardinis, Jared Rutter
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1008253

A Cyclin A—Myb-MuvB—Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles
Cited by: 24
Author(s): Michael D. Rotelli, Robert A. Policastro, Anna M. Bolling, Andrew W. Killion, Abraham J. Weinberg, Michael J. Dixon, Gabriel E. Zentner, Claire Walczak, Mary A. Lilly, Brian R. Calvi
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1007891

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
Cited by: 47
Author(s): A. Callegari, Christian Sieben, Alexander Benke, David M. Suter, Beat Fierz, Davide Mazza, Suliana Manley
Software Mentions: 4
Published: over 7 years ago

10.1093/hmg/ddab140

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
Cited by: 15
Author(s): Andrew P. Voigt, Nathaniel K. Mullin, S. Scott Whitmore, Adam P. DeLuca, Erin R Burnight, Xiuying Liu, Budd A. Tucker, Todd E. Scheetz, Edwin M Stone, Robert F. Mullins
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-5184-x

Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification
Cited by: 7
Author(s): Yung-Chih Lai, Ya-Chen Liang, Ting‐Xin Jiang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 4
Published: almost 8 years ago

10.3389/fimmu.2019.03065

Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells
Cited by: 17
Author(s): Jessica Vázquez, Deborah Chasman, Gladys López, Chanel T. Tyler, Irene M. Ong, Aleksandar K. Stanic
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pbio.2003648

A direct link between MITF, innate immunity, and hair graying
Cited by: 37
Author(s): Melissa L. Harris, Temesgen Fufa, Joseph W. Palmer, Sandeep S. Joshi, Denise M. Larson, Arturo Incao, Derek Gildea, Niraj Trivedi, Autumne N Lee, Chi-Ping Day, Helen Michael, Thomas J. Hornyak, Glenn Merlino, Nisc Comparative Sequencing Program, William J. Pavan
Software Mentions: 4
Published: over 8 years ago

10.1016/j.ajhg.2015.11.018

Autosomal-Dominant Corneal Endothelial Dystrophies CHED1 and PPCD1 Are Allelic Disorders Caused by Non-coding Mutations in the Promoter of OVOL2
Cited by: 65
Author(s): Alice E. Davidson, Petra Lišková, Cerys J. Evans, Ľubica Ďuďáková, Lenka Nosková, Nikolas Pontikos, Hana Hartmannová, Kateřina Hodaňová, Viktor Stránecký, Zbyněk Kozmík, Hannah J. Levis, Nwamaka Juliana Idigo, Noriaki Sasai, Geoffrey J. Maher, James Bellingham, Neyme Veli, Neil D. Ebenezer, Michael E. Cheetham, Julie T. Daniels, Caroline Thaung, Kateřina Jirsová, Vincent Plagnol, Martin Filipec, Stanislav Kmoch, Stephen Tuft, Alison J. Hardcastle
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12859-018-2261-8

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
Cited by: 43
Author(s): Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pgen.1009055

Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon
Cited by: 25
Author(s): Jukka‐Pekka Verta, Paul V. Debes, Nikolai Piavchenko, Annukka Ruokolainen, Outi Ovaskainen, Jacqueline Emmanuel Moustakas-Verho, Seija Tillanen, Noora Parre, Tutku Aykanat, Jaakko Erkinaro, Craig R. Primmer
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pbio.3000187

Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses
Cited by: 49
Author(s): Bo Lv, Qin An, Qiao Zeng, Xunyi Zhang, Ping Lü, Yanqiu Wang, Xianmin Zhu, Yao Ji, Guoping Fan, Zhigang Xue
Software Mentions: 4
Published: about 7 years ago

10.1128/mSystems.00495-20

The Stringent Stress Response Controls Proteases and Global Regulators under Optimal Growth Conditions in Pseudomonas aeruginosa
Cited by: 21
Author(s): Daniel Pletzer, Travis M. Blimkie, Heidi Wolfmeier, Yicong Li, Arjun Baghela, Ahwon Lee, Reza Falsafi, Robert E. W. Hancock
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1007216

The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation
Cited by: 20
Author(s): Sean L. Beckwith, Erich Schwartz, Pablo E. García-Nieto, D. A. King, Graeme J. Gowans, Ka Man Wong, Tessa L. Eckley, Alexander P. Paraschuk, Egan Peltan, Laura R. Lee, Wei Yao, Ashby J. Morrison
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1009734

Recovery from heat shock requires the microRNA pathway in Caenorhabditis elegans
Cited by: 10
Author(s): Delaney C Pagliuso, Devavrat M Bodas, Amy E. Pasquinelli
Software Mentions: 4
Published: about 5 years ago

10.1186/s40478-021-01204-8

CSF1R inhibition rescues tau pathology and neurodegeneration in an A/T/N model with combined AD pathologies, while preserving plaque associated microglia
Cited by: 20
Author(s): Chritica Lodder, Isabelle Scheyltjens, Ilie-Cosmin Stancu, Pablo Botella Lucena, Manuel Gutiérrez de Ravé, Sarah Vanherle, Tim Vanmierlo, Niels Cremers, Hannah Vanrusselt, Bert Brône, Bernard Hanseeuw, Jean‐Noël Octave, Astrid Bottelbergs, Kiavash Movahedi, Ilse Dewachter
Software Mentions: 4
Published: over 5 years ago

10.1016/j.ajhg.2019.03.025

Cell-Type Heterogeneity in Adipose Tissue Is Associated with Complex Traits and Reveals Disease-Relevant Cell-Specific eQTLs
Cited by: 76
Author(s): Craig A. Glastonbury, Alexessander Couto Alves, Julia S. El-Sayed Moustafa, Kerrin S. Small
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1009097

Diversified regulation of circadian clock gene expression following whole genome duplication
Cited by: 9
Author(s): Alexander C. West, Marianne Iversen, Even H. Jørgensen, Simen Rød Sandve, David G. Hazlerigg, Shona H. Wood
Software Mentions: 4
Published: about 6 years ago

10.1128/mBio.01959-21

Multifactorial Role of Mitochondria in Echinocandin Tolerance Revealed by Transcriptome Analysis of Drug-Tolerant Cells
Cited by: 13
Author(s): Rocio Garcia-Rubio, Cristina Jiménez‐Ortigosa, Lucius DeGregorio, Christopher Quinteros, Erika Shor, David S. Perlin
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0251121

Melanocytes determine angiogenesis gene expression across human tissues
Cited by: 3
Author(s): Shirly Freilikhman, Marianna Halasi, Alal Eran, Irit Adini
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-4362-6

Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii
Cited by: 20
Author(s): Musa A. Hassan, Juan J. Vasquez, Guo-Liang Chew, Markus Meissner, T. Nicolai Siegel
Software Mentions: 4
Published: almost 9 years ago

10.3389/fimmu.2021.649458

Transcriptome and IgH Repertoire Analyses Show That CD11chi B Cells Are a Distinct Population With Similarity to B Cells Arising in Autoimmunity and Infection
Cited by: 16
Author(s): Robert W. Maul, Michelle D. Catalina, Varsha Kumar, Prathyusha Bachali, Amrie C. Grammer, Shu Wang, William W. Yang, Sarfaraz Hasni, Rachel Ettinger, Peter E. Lipsky, Patricia J. Gearhart
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.672168

Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy
Cited by: 18
Author(s): Sandra Hellberg, Johanna Raffetseder, Olof Rundquist, Rasmus Magnusson, Georgia Papapavlou, Maria C. Jenmalm, Jan Ernerudh, Mika Gustafsson
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-3755-x

Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults
Cited by: 3
Author(s): Haiwang Yang, Denis Basquin, Daniel Pauli, Brian Oliver
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-021-07592-4

RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish
Cited by: 8
Author(s): Matt J. Thorstensen, Melinda R. Baerwald, Ken M. Jeffries
Software Mentions: 4
Published: over 5 years ago

10.1186/s13195-020-00598-2

Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model
Cited by: 24
Author(s): Yaqi Wang, Xiaomin Zhang, Shan Qiao, Yuli Hou, Jing Liu, Yu Sun, Peichang Wang
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2021.664249

Over-Generalizing About GC (Hypoxia): Pitfalls of Limiting Breadth of Experimental Systems and Analyses in Framing Informatics Conclusions
Cited by: 7
Author(s): Mark Boothby, Ariel Raybuck, Sung Hoon Cho, Kristy R. Stengel, Volker H. Haase, Scott W. Hiebert, Jingxin Li
Software Mentions: 4
Published: over 5 years ago

10.15252/msb.20209596

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation
Cited by: 108
Author(s): Erika Kelmer Sacramento, Joanna Kirkpatrick, Mariateresa Mazzetto, Mario Baumgart, Aleksandar Bartolome, Simone Di Sanzo, Cinzia Caterino, Michele Sanguanini, Nikoletta Papaevgeniou, Maria Lefaki, Dorothee Childs, Sara Bagnoli, Eva Terzibasi Tozzini, Domenico Di Fraia, Natalie Romanov, Peter H. Sudmant, Wolfgang Huber, Niki Chondrogianni, Michele Vendruscolo, Alessandro Cellerino, Alessandro Ori
Software Mentions: 4
Published: over 6 years ago

10.15252/msb.20209946

The transcriptome dynamics of single cells during the cell cycle
Cited by: 28
Author(s): Daniel Schwabe, Sara Formichetti, Jan Philipp Junker, Martin Falcke, Nikolaus Rajewsky
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-018-5393-3

A comparison between whole transcript and 3’ RNA sequencing methods using Kapa and Lexogen library preparation methods
Cited by: 55
Author(s): Feiyang Ma, Brie K. Fuqua, Yehudit Hasin, Clara Yukhtman, Chris D. Vulpe, Aldons J. Lusis, Matteo Pellegrini
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0213535

Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Cited by: 22
Author(s): Mio Takeuchi, Haruka Ozaki, Satoshi Hiraoka, Yoichi Kamagata, Susumu Sakata, Hideyoshi Yoshioka, Wataru Iwasaki
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-021-07989-1

Global identification of long non-coding RNAs involved in the induction of spinach flowering
Cited by: 11
Author(s): Fatemeh Ghorbani, Reza Abolghasemi, Maryam Haghighi, Nematollah Etemadi, Shui Wang, Marzieh Karimi, Aboozar Soorni
Software Mentions: 4
Published: about 5 years ago

10.1128/mBio.02613-19

The Cyclic AMP Receptor Protein Regulates Quorum Sensing and Global Gene Expression in Yersinia pestis during Planktonic Growth and Growth in Biofilms
Cited by: 23
Author(s): Jeremy T. Ritzert, G. Minasov, Ryan B. Embry, Matthew J. Schipma, K.J.F. Satchell
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12859-017-1816-4

mmquant: how to count multi-mapping reads?
Cited by: 29
Author(s): Matthias Zytnicki
Software Mentions: 4
Published: about 9 years ago

10.3389/fimmu.2020.00445

Perirenal Adipose Tissue Displays an Age-Dependent Inflammatory Signature Associated With Early Graft Dysfunction of Marginal Kidney Transplants
Cited by: 6
Author(s): Romain Boissier, Pauline François, B. Gondran Tellier, Meunier Maité, Luc Lyonnet, Stéphanie Simoncini, Jéremy Magalon, Tristan Legris, Alexis Laurent, Laurent Guy, Françoise Dignat-George, G. Karsenty, Stéphane Burtey, É. Lechevallier, Florence Sabatier, Pascale Paul
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-020-07218-1

Targeted mutagenesis of ∆5 and ∆6 fatty acyl desaturases induce dysregulation of lipid metabolism in Atlantic salmon (Salmo salar)
Cited by: 6
Author(s): Yang Jin, Alex K. Datsomor, Rolf Erik Olsen, Jon Olav Vik, Jacob Torgersen, Rolf B. Edvardsen, Anna Wargelius, Per Winge, Fabian Grammes
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-015-1308-8

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
Cited by: 109
Author(s): Shanrong Zhao, Baohong Zhang
Software Mentions: 4
Published: over 11 years ago

10.1111/acer.14259

Chronic Voluntary Ethanol Drinking in Cynomolgus Macaques Elicits Gene Expression Changes in Prefrontal Cortical Area 46
Cited by: 4
Author(s): Nicole A.R. Walter, Christina Zheng, Robert P. Searles, Shannon K. McWeeney, Kathleen A. Grant, Robert Hitzemann
Software Mentions: 4
Published: over 6 years ago

10.1002/1878-0261.12982

<i>CDX2</i> expression in the hematopoietic lineage promotes leukemogenesis via TGFβ inhibition
Cited by: 6
Author(s): Anne Galland, Victor Gourain, Karima Habbas, Yonca Güler, Elisabeth Martin, Claudine Ebel, Manuela Tavian, Laurent Vallat, Marie‐Pierre Chenard, Laurent Mauvieux, Jean–Noël Freund, Isabelle Duluc, Claire Domon‐Dell
Software Mentions: 4
Published: over 5 years ago

10.1038/s41398-019-0426-5

Alcohol-responsive genes identified in human iPSC-derived neural cultures
Cited by: 15
Author(s): Kevin P. Jensen, Richard Lieberman, Henry R. Kranzler, Joel Gelernter, Kaitlin Clinton, Jonathan Covault
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0251611

Transcriptome analyses reveal tau isoform-driven changes in transposable element and gene expression
Cited by: 7
Author(s): Jennifer Grundman, Brian Spencer, Floyd Sarsoza, Robert A. Rissman
Software Mentions: 4
Published: about 5 years ago

10.1016/j.tranon.2018.04.002

Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers
Cited by: 7
Author(s): Anthony J. Cesnik, Bing Yang, Andrew Truong, Tyler Etheridge, Michele Spiniello, Maisie I. Steinbrink, Michael R. Shortreed, Brian L. Frey, David F. Jarrard, Lloyd M. Smith
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-018-4632-y

Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils
Cited by: 18
Author(s): Marcella Sabino, Victor Adriano Okstoft Carmelo, Gianluca Mazzoni, Katia Cappelli, Stefano Capomaccio, Paolo Ajmone‐Marsan, Andrea Verini-Supplizi, Massimo Trabalza‐Marinucci, Haja N. Kadarmideen
Software Mentions: 4
Published: over 8 years ago

10.1007/s12035-019-01643-4

Altered Levels of Proteins and Phosphoproteins, in the Absence of Early Causative Transcriptional Changes, Shape the Molecular Pathogenesis in the Brain of Young Presymptomatic Ki91 SCA3/MJD Mouse
Cited by: 14
Author(s): Kalina Wiatr, Piotr Piasecki, Łukasz Marczak, Paweł Wojciechowski, Małgorzata Kurkowiak, Rafał Płoski, Małgorzata Rydzanicz, Luiza Handschuh, Johannes Jungverdorben, Oliver Brüstle, Marek Figlerowicz, Maciej Figiel
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.41305

Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
Cited by: 114
Author(s): Gerard L. Brien, David Remillard, Junwei Shi, Matthew L. Hemming, Jonathon Chabon, Kieran Wynne, Eugene Dillon, Gerard Cagney, Guido van Mierlo, Marijke P Baltissen, Michiel Vermeulen, Jun Qi, Stefan Fröhling, Nathanael S. Gray, James E. Bradner, Christopher R. Vakoc, Scott A. Armstrong
Software Mentions: 4
Published: almost 8 years ago

10.7150/thno.55645

Deciphering the autophagy regulatory network via single-cell transcriptome analysis reveals a requirement for autophagy homeostasis in spermatogenesis
Cited by: 18
Author(s): Mei Wang, Yanwen Xu, Yuncong Zhang, Yuhan Chen, Gang Chang, Geng An, Xinyan Yang, Caihong Zheng, Jiexiang Zhao, Zhaoting Liu, Dazhuang Wang, Masahiro Kai, Rao S, Meng Dai, Dong Wang, Xiaoyang Zhao
Software Mentions: 4
Published: almost 6 years ago

10.1186/s10020-019-0102-5

Gut microbiota promote the inflammatory response in the pathogenesis of systemic lupus erythematosus
Cited by: 68
Author(s): Yinglong Ma, Xiaoxue Xu, Mengtao Li, Jun Cai, Qiang Wang, Haitao Niu
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-021-07491-8

A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis
Cited by: 8
Author(s): Zofia Bakuła, Paweł Siedlecki, Robert Gromadka, Jan Gawor, Agnieszka Gromadka, Jan J. Pomorski, Hanna Panagiotopoulou, Tomasz Jagielski
Software Mentions: 4
Published: over 5 years ago

10.1038/s41398-017-0058-6

Enriched expression of genes associated with autism spectrum disorders in human inhibitory neurons
Cited by: 43
Author(s): Ping Wang, Dejian Zhao, Herbert M. Lachman, Deyou Zheng
Software Mentions: 4
Published: almost 9 years ago

10.1128/mBio.00586-21

Intraspecies Transcriptional Profiling Reveals Key Regulators of Candida albicans Pathogenic Traits
Cited by: 13
Author(s): Joshua M. Wang, Andrew L. Woodruff, Matthew J. Dunn, Robert J. Fillinger, Richard J. Bennett, Matthew Anderson
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-6541-0

iREAD: a tool for intron retention detection from RNA-seq data
Cited by: 33
Author(s): Hong Dong Li, Cory C. Funk, Nathan D. Price
Software Mentions: 4
Published: over 6 years ago

10.1002/mgg3.1346

Dysregulated expression of androgen metabolism genes and genetic analysis in hypospadias
Cited by: 7
Author(s): Zhongzhong Chen, Xiaoling Lin, Yaping Wang, Hua Xie, Fang Chen
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-69182-w

Identification of TNFAIP3 as relapse biomarker and potential therapeutic target for MOG antibody associated diseases
Cited by: 9
Author(s): Shrishti Saxena, Hrishikesh Lokhande, Grace Gombolay, Radhika Raheja, Timothy B. Rooney, Tanuja Chitnis
Software Mentions: 4
Published: about 6 years ago

10.7150/thno.40650

A mouse model of MSU-induced acute inflammation <i>in vivo</i> suggests imiquimod-dependent targeting of <i>Il-1β</i> as relevant therapy for gout patients
Cited by: 26
Author(s): Alexandre Mariotte, Aurore De Cauwer, Chrystelle Po, Cherine Abou-Fayçal, Angélique Pichot, Nicodème Paul, Ismael Aouadi, Raphaël Carapito, Benoı̂t Frisch, Cécile Macquin, Emmanuel Chatelus, Jean Sibilia, Jean‐Paul Armspach, Seiamak Bahram, Philippe Georgel
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2019.01036

Profiling Transcriptional Regulation and Functional Roles of Schistosoma mansoni c-Jun N-Terminal Kinase
Cited by: 5
Author(s): Sandra Grossi Gava, Naiara Clemente Tavares, Franco H. Falcone, Guilherme Oliveira, Marina Moraes Mourão
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0115740

Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression
Cited by: 10
Author(s): Carol Soderlund, William M. Nelson, Stephen A. Goff
Software Mentions: 4
Published: almost 12 years ago

10.1074/mcp.RA118.001141

Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition
Cited by: 45
Author(s): Piotr Grabowski, Sebastian Hesse, Sebastian Hollizeck, Meino Rohlfs, Uta Behrends, Roya Sherkat, Hannah Tamary, Ekrem Ünal, Raz Somech, Türkan Patıroğlu, Stefan Canzar, Jutte van der Werff ten Bosch, Christoph Klein, Juri Rappsilber
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2020.00867

Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic Fibroblasts
Cited by: 13
Author(s): Wei Chen, Xuefei Wang, Gang Wei, Yin Huang, Yufang Shi, Dan Li, Shengnu Qiu, Bin Zhou, Junhong Cao, Meng Chen, Pengfei Qin, Wenfei Jin, Ting Ni
Software Mentions: 4
Published: about 6 years ago

10.1016/j.molcel.2018.09.023

Phosphorylation of Histone H4T80 Triggers DNA Damage Checkpoint Recovery
Cited by: 20
Author(s): Gonzalo Millán-Zambrano, Helena Santos‐Rosa, Fabio Puddu, Samuel Robson, Stephen Jackson, Tony Kouzarides
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-020-07141-5

Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii
Cited by: 9
Author(s): Peter M. Henry, Sukhwinder Kaur, Quyen Anh Tran Pham, Radwan Barakat, Samuel Brinker, Hannah Haensel, Oleg Daugovish, Lynn Epstein
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-021-07699-8

Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome
Cited by: 8
Author(s): Stefania Bertazzoni, Darcy A. B. Jones, H. Phan, Kar‐Chun Tan, James K. Hane
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-68373-9

Increased predominance of the matured ventricular subtype in embryonic stem cell-derived cardiomyocytes in vivo
Cited by: 22
Author(s): Hajime Ichimura, Shin Kadota, Toshihide Kashihara, Mitsuhiko Yamada, Kyoko Ito, Hideki Kobayashi, Yuki Tanaka, Naoko Shiba, Shinichiro Chuma, Shugo Tohyama, Takashi Seto, Kenji Okada, Koichiro Kuwahara, Yuji Shiba
Software Mentions: 4
Published: about 6 years ago

10.1016/j.molcel.2019.03.010

A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal Jelly
Cited by: 35
Author(s): Eyal Maori, Isabela Cunha Navarro, Humberto Boncristiani, David J. Seilly, Konrad L. M. Rudolph, Alexandra Sapetschnig, Chi-Chuan Lin, John E. Ladbury, Jay D. Evans, Jonathan L. Heeney, Eric A. Miska
Software Mentions: 4
Published: over 7 years ago

10.1016/j.molcel.2021.04.028

Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease
Cited by: 46
Author(s): Evgeniia Prokhorova, Thomas Agnew, Anne R. Wondisford, Michael Tellier, Nicole Kaminski, Danique Beijer, James Holder, Joséphine Groslambert, Marcin Suskiewicz, Kang Zhu, Julia M Reber, Sarah C. Krassnig, Luca Palazzo, Shona Murphy, Michael L. Nielsen, Aswin Mangerich, Dragana Ahel, Jonathan Baets, Roderick J. O’Sullivan, Ivan Ahel
Software Mentions: 4
Published: over 5 years ago

10.1016/j.molcel.2021.06.020

BAP1 enhances Polycomb repression by counteracting widespread H2AK119ub1 deposition and chromatin condensation
Cited by: 38
Author(s): E. J. Conway, Federico Rossi, Daniel Fernández-Pérez, Eleonora Ponzo, Karin Johanna Ferrari, Marika Zanotti, Daria Manganaro, Simona Rodighiero, Simone Tamburri, Diego Pasini
Software Mentions: 4
Published: about 5 years ago

10.1016/j.molcel.2021.06.016

Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination
Cited by: 31
Author(s): Ashwin Narain, Pranjali Bhandare, Bikash Adhikari, Simone Backes, Martin Eilers, Lars Dölken, Andreas Schlösser, Florian Erhard, Apoorva Baluapuri, Elmar Wolf
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-66309-x

Comparative targeting analysis of KLF1, BCL11A, and HBG1/2 in CD34+ HSPCs by CRISPR/Cas9 for the induction of fetal hemoglobin
Cited by: 35
Author(s): Andrés Lamsfus‐Calle, Alberto Daniel‐Moreno, Justin S. Antony, Thomas Epting, Lukas Heumos, Praveen Baskaran, Jakob Admard, Nicolas Casadei, Ngadhnjim Latifi, Darina M. Siegmund, Michael Kormann, Rupert Handgretinger, Markus Mezger
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2018.01061

Profiling of the Transcriptomic Responses of Clonostachys rosea Upon Treatment With Fusarium graminearum Secretome
Cited by: 26
Author(s): Zerihun A. Demissie, Simon J. Foote, Yifang Tan, Michèle C. Loewen
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-65916-y

Alterations of transcriptome signatures in head trauma-related neurodegenerative disorders
Cited by: 13
Author(s): Hyesun Cho, Seung Jae Hyeon, Jong-Yeon Shin, Victor E. Alvarez, Thor D. Stein, Jung‐Hee Lee, Neil W. Kowall, Ann C. McKee, Hoon Ryu, Jeong-Sun Seo
Software Mentions: 4
Published: over 6 years ago

10.1186/s12915-019-0646-4

Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons
Cited by: 15
Author(s): Pavan Agrawal, Phuong Chung, Ulrike Heberlein, Clement F. Kent
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-61177-x

RNA-seq analysis reveals TRPC genes to impact an unexpected number of metabolic and regulatory pathways
Cited by: 10
Author(s): Karina Formoso, Sebastián Susperreguy, Marc Freichel, Lutz Birnbaumer
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-66556-y

WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations
Cited by: 9
Author(s): Ian M. Rose, Mallikarjun Bidarimath, Alex Webster, Andrew K. Godwin, Andrea Flesken‐Nikitin, Alexander Yu. Nikitin
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-015-1704-0

A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells
Cited by: 6
Author(s): Juan González-Vallinas, Amadís Pagès, Babita Singh, Eduardo Eyras
Software Mentions: 4
Published: about 11 years ago

10.1186/s13041-020-00623-3

Differentiation and localization of interneurons in the developing spinal cord depends on DOT1L expression
Cited by: 6
Author(s): Angelica Gray de Cristoforis, Francesco Ferrari, Frédéric Clotman, Tanja Vogel
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-020-03888-6

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data
Cited by: 1
Author(s): Noel‐Marie Plonski, Emily Johnson, Madeline Frederick, Heather Mercer, Gail Fraizer, Richard S. Meindl, Gemma Casadesús, Helen Piontkivska
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-63434-5

Identification of tipifarnib sensitivity biomarkers in T-cell acute lymphoblastic leukemia and T-cell lymphoma
Cited by: 5
Author(s): Ruth Alonso‐Alonso, Rufino Mondéjar, Nerea Martínez, Nuria García-Díaz, Cristina Fernández Pérez, David Merino, Marta Rodríguez, Anna Esteve‐Codina, Berta Fusté, Marta Gut, Francis Burrows, Catherine Scholz, José P. Vaqué, Antonio Gualberto, Miguel Á. Piris
Software Mentions: 4
Published: over 6 years ago

10.1186/s12915-019-0677-x

Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes
Cited by: 19
Author(s): Eddie Rodríguez-Carballo, Lucille Lopez-Delisle, Nayuta Yakushiji-Kaminatsui, Asier Ullate-Agote, Denis Duboule
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-019-6384-8

Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach
Cited by: 6
Author(s): Frédéric Jehl, Colette Désert, Christophe Klopp, M. Brenet, Andrea Rau, Sophie Leroux, Morgane Boutin, Laëtitia Lagoutte, Kévin Muret, Yuna Blum, Diane Esquerré, David Gourichon, Thierry Burlot, Anne Collin, Frédérique Pitel, Alexandre Bénani, Tatiana Zerjal, Sandrine Lagarrigue
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-61678-9

Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues
Cited by: 23
Author(s): Michelle M. Halstead, Colin Kern, Perot Saelao, Ganrea Chanthavixay, Y. Wang, Mary E. Delany, Huaijun Zhou, Pablo J. Ross
Software Mentions: 4
Published: over 6 years ago