10.1038/s41598-018-19684-5

Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
Cited by: 23
Author(s): Jelle van Wesemael, Yann Hueber, Ewaut Kissel, Nádia Alves Campos, Rony Swennen, Sébastien Carpentier
Software Mentions: 4
Published: over 8 years ago

10.18632/oncotarget.21378

Progesterone receptor isoforms, agonists and antagonists differentially reprogram estrogen signaling
Cited by: 48
Author(s): Hari Singhal, Mark E. Greene, Allison L. Zarnke, Muriel Lainé, Rose Al Abosy, Yung-Fu Chang, Anna Dembo, Kelly Q. Schoenfelt, Raga Vadhi, Xintao Qiu, Prakash K. Rao, Bindu Santhamma, Hareesh B. Nair, Klaus Nickisch, Henry W. Long, Lev Becker, Myles Brown, Geoffrey L. Greene
Software Mentions: 4
Published: about 9 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

10.3390/jpm9020018

Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research
Cited by: 12
Author(s): Isaac Raplee, Alexei V. Evsikov, Caralina Marín de Evsikova
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-017-19072-5

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs
Cited by: 45
Author(s): Yuliaxis Ramayo-Caldas, María Ballester, Juan Pablo Sánchez, Olga González‐Rodríguez, Manuel Revilla, Henry Reyer, Klaus Wimmers, D. Torrallardona, Raquel Quintanilla
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12862-017-0902-6

Transcriptomic insights into the genetic basis of mammalian limb diversity
Cited by: 19
Author(s): Jennifer Maier, Marcelo Rivas‐Astroza, Jenny Deng, Anna Dowling, Paige Oboikovitz, Xiaoyi Cao, Richard R. Behringer, Chris J. Cretekos, John J. Rasweiler, Sheng Zhong, Karen E. Sears
Software Mentions: 4
Published: over 9 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/s41598-017-15822-7

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease
Cited by: 23
Author(s): Chao Ren, Feng Liu, Zhangyi Ouyang, Gaole An, Chenghui Zhao, Jun Shuai, Shuhong Cai, Xiaochen Bo, Wenjie Shu
Software Mentions: 4
Published: almost 9 years ago

10.18632/oncotarget.12180

The transcriptional signature of human ovarian carcinoma macrophages is associated with extracellular matrix reorganization
Cited by: 72
Author(s): Florian Finkernagel, Silke Reinartz, Sonja Lieber, Till Adhikary, Annika Wortmann, Nathalie Hoffmann, Tim Bieringer, Andrea Nist, Thorsten Stiewe, Julia M. Jansen, Uwe Wagner, Sabine Müller‐Brüsselbach, Rolf Müller
Software Mentions: 4
Published: about 10 years ago

10.1038/s41598-017-13462-5

Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
Cited by: 54
Author(s): Michaela Asp, Fredrik Salmén, Patrik L. Ståhl, Sanja Vicković, Ulrika Felldin, Marie Löfling, José Fernández Navarro, Jonas Maaskola, Maria Eriksson, Bengt Persson, Matthias Corbascio, Hans Persson, Cecilia Linde, Joakim Lundeberg
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-021-07615-0

Identification of the conserved long non-coding RNAs in myogenesis
Cited by: 0
Author(s): Anupam Bhattacharya, Simang Champramary, Tanya Tripathi, Debajit Thakur, Ilya Ioshikhes, Satyendra Kumar Singh, Soumyadeep Nandi
Software Mentions: 4
Published: over 5 years ago

10.26508/lsa.201900332

Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma
Cited by: 4
Author(s): Elena Afanasyeva, Moritz Gartlgruber, Tatsiana Ryl, Bieke Decaesteker, Geertrui Denecker, Gregor Mönke, Umut Toprak, Andrés Flórez, Alica Torkov, Daniel Dreidax, Carl Herrmann, Konstantin Okonechnikov, Sara Ek, Ashwini Kumar Sharma, Vitaliya Sagulenko, Frank Speleman, Kai Oliver Henrich, Frank Westermann
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-017-4359-1

A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells
Cited by: 19
Author(s): Jialiang Yang, Jacob Hagen, Kalyani V. P. Guntur, Kimaada Allette, Sarah Schuyler, Jyoti Ranjan, Francesca Petralia, Stéphane Gesta, Robert Sebra, Milind Mahajan, Bin Zhang, Jun Zhu, Sander M. Houten, Andrew Kasarskis, Vivek K. Vishnudas, Viatcheslav R. Akmaev, Rangaprasad Sarangarajan, Niven R. Narain, Eric E. Schadt, Carmen Argmann, Zhidong Tu
Software Mentions: 4
Published: almost 9 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/s12864-017-4011-0

A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression
Cited by: 54
Author(s): Nicholas F. Lahens, Emanuela Ricciotti, Olga Smirnova, Erik Toorens, Young Ho Kim, Giacomo Baruzzo, Katharina E. Hayer, Tapan Ganguly, Jonathan Schug, Gregory R. Grant
Software Mentions: 4
Published: about 9 years ago

10.1186/s12864-017-3566-0

Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development
Cited by: 51
Author(s): Steven Ge
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-019-5793-z

Identification of genes underlying phenotypic plasticity of wing size via insulin signaling pathway by network-based analysis in Sogatella furcifera
Cited by: 7
Author(s): Xinlei Gao, Yating Fu, Olugbenga Emmanuel Ajayi, Dongyang Guo, Liqin Zhang, Qingfa Wu
Software Mentions: 4
Published: over 7 years ago

10.1186/s12974-020-01797-2

Glioblastoma hijacks microglial gene expression to support tumor growth
Cited by: 63
Author(s): Sybren L. N. Maas, Erik R. Abels, Lieke L van de Haar, Xuan Zhang, Liza M. Morsett, Srinjoy Sil, Joana Guedes, Pritha Sen, Shilpa Prabhakar, Suzanne E. Hickman, Charles P. Lai, David T. Ting, Xandra O. Breakefield, Marike L. D. Broekman, Joseph El Khoury
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-07757-w

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Cited by: 63
Author(s): Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-017-07100-3

Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcription
Cited by: 59
Author(s): Yumiko Oishi, Shinichiro Hayashi, Takayuki Isagawa, Motohiko Oshima, Atsushi Iwama, Shigeki Shimba, Hitoshi Okamura, Ichiro Manabe
Software Mentions: 4
Published: about 9 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

10.1038/s41598-017-03390-9

Aberrant plasticity of peripheral sensory axons in a painful neuropathy
Cited by: 30
Author(s): Takashi Hirai, Yatendra Mulpuri, Yanbing Cheng, Zheng Xia, Wei Li, Supanigar Ruangsri, Igor Spigelman, Ichiro Nishimura
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-020-07334-y

scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets
Cited by: 9
Author(s): Hongyu Liu, N M Prashant, Liam F. Spurr, Pavlos Bousounis, Nawaf Alomran, Helen Ibeawuchi, Justin Sein, Piotr Słowiński, Krasimira Tsaneva-Atanasova, Anélia Horvath
Software Mentions: 4
Published: almost 6 years ago

10.26508/lsa.202000848

Polycomb mutant partially suppresses DNA hypomethylation–associated phenotypes in Arabidopsis
Cited by: 19
Author(s): Martin Rougée, Leandro Quadrana, Jérôme Zervudacki, Valentin Hure, Vincent Colot, Lionel Navarro, Angélique Deleris
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-017-4002-1

Evaluation and comparison of computational tools for RNA-seq isoform quantification
Cited by: 132
Author(s): Chi Zhang, Baohong Zhang, Lih-Ling Lin, Shanrong Zhao
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0143496

Human Breast Milk miRNA, Maternal Probiotic Supplementation and Atopic Dermatitis in Offspring
Cited by: 56
Author(s): Melanie Rae Simpson, Gaute Brede, Jostein Johansen, Roar Johnsen, Ola Storrø, Pål Sætrom, Torbjørn Øien
Software Mentions: 4
Published: almost 11 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/s41598-017-02391-y

Whole blood transcriptome analysis reveals potential competition in metabolic pathways between negative energy balance and response to inflammatory challenge
Cited by: 13
Author(s): Juliette Bouvier-Muller, Charlotte Allain, Guillaume Tabouret, Francis Enjalbert, David Portes, Céline Noirot, Rachel Rupp, Gilles Foucras
Software Mentions: 4
Published: over 9 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

10.1371/journal.pone.0164461

Responses of Bovine Innate Immunity to Mycobacterium avium subsp. paratuberculosis Infection Revealed by Changes in Gene Expression and Levels of MicroRNA
Cited by: 40
Author(s): M. Malvisi, Fiorentina Palazzo, Nicola Morandi, Barbara Lazzari, J. L. Williams, G. Pagnacco, Giulietta Minozzi
Software Mentions: 4
Published: almost 10 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

10.1371/journal.pone.0256471

Radiology- and gene-based risk stratification in small renal cell carcinoma: A preliminary study
Cited by: 0
Author(s): Takao Sugiyama, Yasuhiro Ushijima, Yuki Motomura, Katsumi Sakamoto, Masakazu Hirakawa, Akihiro Nishie, Koshi Mimori, Yasuo Yamashita, Takashi Tsutsumi, Kousei Ishigami
Software Mentions: 4
Published: about 5 years ago

10.1038/srep38820

Acfs: accurate circRNA identification and quantification from RNA-Seq data
Cited by: 67
Author(s): Xintian You, Tim Conrad
Software Mentions: 4
Published: almost 10 years ago

10.1038/srep29122

The transcriptomes of novel marmoset monkey embryonic stem cell lines reflect distinct genomic features
Cited by: 16
Author(s): Katharina Debowski, Charis Drummer, Jana Lentes, Maren Cors, Ralf Dressel, Thomas Lingner, Gabriela Salinas-Riester, Sigrid Fuchs, Erika Sasaki, Rüdiger Behr
Software Mentions: 4
Published: over 10 years ago

10.3389/fcell.2021.615950

The Novel Non-coding Transcriptional Regulator Gm18840 Drives Cardiomyocyte Apoptosis in Myocardial Infarction Post Ischemia/Reperfusion
Cited by: 1
Author(s): Changjun Luo, Si Xiong, Yiteng Huang, Ming Deng, Jing Zhang, Jianlin Chen, Rongfeng Yang, Xiaoyan Ke
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0230566

Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease
Cited by: 35
Author(s): Elena Buglo, Evan Sarmiento, Nicole Belliard Martuscelli, David W. Sant, Matt C. Danzi, A. Jeanine Abrams, Julia E. Dallman, Stephan Züchner
Software Mentions: 4
Published: over 6 years ago

10.1038/srep20759

Comparative transcriptome analysis of peripheral blood mononuclear cells in hepatitis B-related acute-on-chronic liver failure
Cited by: 10
Author(s): Qian Zhou, Wenchao Ding, Liangliang Jiang, Jiaojiao Xin, Tianzhou Wu, Dongyan Shi, Jing Jiang, Cao H, Lanjuan Li, Jun Li
Software Mentions: 4
Published: over 10 years ago

10.1186/s40104-019-0340-y

Flutamide-induced alterations in transcriptional profiling of neonatal porcine ovaries
Cited by: 14
Author(s): Katarzyna Knapczyk-Stwora, Anna Nynca, Renata E. Ciereszko, Łukasz Paukszto, J Jastrzebski, Elzbieta Czaja, Patrycja Witek, Marek Koziorowski, Maria Słomczyńska
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0141910

Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?
Cited by: 25
Author(s): Shanrong Zhao, Li Xi, Baohong Zhang
Software Mentions: 4
Published: almost 11 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

10.1172/jci.insight.151621

Combinatorial transcription factor profiles predict mature and functional human islet α and β cells
Cited by: 21
Author(s): Shristi Shrestha, Diane Saunders, John T. Walker, Joan Camunas-Soler, Xiao-Qing Dai, Rachana Haliyur, Radhika Aramandla, Greg Poffenberger, Nripesh Prasad, Rita Bottino, Roland Stein, Jean‐Philippe Cartailler, Stephen C. J. Parker, Patrick E. MacDonald, Shawn Levy, Alvin C. Powers, Marcela Briššová
Software Mentions: 4
Published: about 5 years ago

10.3389/fcell.2021.668833

Detection of Hematopoietic Stem Cell Transcriptome in Human Fetal Kidneys and Kidney Organoids Derived From Human Induced Pluripotent Stem Cells
Cited by: 3
Author(s): Jin Wook Hwang, Christophe Desterke, Julien Loisel‐Duwattez, Frank Griscelli, Annelise Bennaceur‐Griscelli, Ali G Turhan
Software Mentions: 4
Published: over 5 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

10.1242/dmm.049044

Comparison of the oncogenomic landscape of canine and feline hemangiosarcoma shows novel parallels with human angiosarcoma
Cited by: 16
Author(s): Kim Wong, Latasha Ludwig, Oscar Krijgsman, David J. Adams, Geoffrey A. Wood, Louise van der Weyden
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0236771

Transcriptome analysis of sevoflurane exposure effects at the different brain regions
Cited by: 6
Author(s): Hiroto Yamamoto, Yasuzo Uchida, Tomoki Chiba, Ryota Kurimoto, Taijiro Matsushima, Maiko Inotsume, Chihiro Ishikawa, Haiyan Li, Takashi Shiga, Masafumi Muratani, Tatsuo Uchida, Hiroshi Asahara
Software Mentions: 4
Published: almost 6 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

10.1186/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

10.1172/jci.insight.150107

IL-13 is a driver of COVID-19 severity
Cited by: 74
Author(s): Alexandra N Donlan, Tara E. Sutherland, Chelsea Marie, Saskia Preissner, Benjamin T. Bradley, Rebecca Carpenter, Jeffrey M. Sturek, Z. Jennie, G. Brett Moreau, Jeffrey R. Donowitz, Gregory A. Buck, Myrna G. Serrano, Stacey L. Burgess, Mayuresh M. Abhyankar, Cameron Mura, Philip E. Bourne, Robert Preißner, Mary K. Young, Genevieve Lyons, Johanna Loomba, Sarah J. Ratcliffe, Melinda D. Poulter, Amy J Mathers, Anthony J. Day, Barbara J. Mann, Judith E. Allen, William A. Petri
Software Mentions: 4
Published: over 5 years ago

10.1172/jci.insight.147703

Integration of spatial and single-cell transcriptomics localizes epithelial cell–immune cross-talk in kidney injury
Cited by: 68
Author(s): Ricardo Melo Ferreira, Angela R Sabo, Seth Winfree, Kimberly S. Collins, Danielle Janosevic, Connor J. Gulbronson, Ying‐Hua Cheng, Lauren Casbon, Daria Barwinska, Michael J. Ferkowicz, Xiaoling Xuei, Chi Zhang, Kenneth W. Dunn, Katherine J. Kelly, Timothy A. Sutton, Takashi Hato, Pierre C. Dagher, Tarek M. El‐Achkar, Michael T. Eadon
Software Mentions: 4
Published: over 5 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

10.1172/jci.insight.145346

Systemic and adipocyte transcriptional and metabolic dysregulation in idiopathic intracranial hypertension
Cited by: 39
Author(s): Connar Westgate, Hannah Botfield, Zerin Alimajstorovic, Andreas Yiangou, Mark D. Walsh, Gabrielle Smith, Rishi Singhal, James Mitchell, Olivia Grech, Keira Markey, Daniel Hebenstreit, Daniel A. Tennant, Jeremy W. Tomlinson, Susan P Mollan, Christian Ludwig, İldem Akerman, Gareth G. Lavery, Alexandra J Sinclair
Software Mentions: 4
Published: over 5 years ago

10.1172/jci.insight.145029

Nrf2 overexpression rescues the RPE in mouse models of retinitis pigmentosa
Cited by: 30
Author(s): David M. Wu, Xuke Ji, Maryna V. Ivanchenko, M. S. Chung, Mary E. Piper, Parimal Rana, Sean K. Wang, Y. Y. Xue, Emma R. West, Sophia R. Zhao, Hongbin Xu, Marcelo Cicconet, Wenjun Xiong, Constance L. Cepko
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.50901

A genetic, genomic, and computational resource for exploring neural circuit function
Cited by: 151
Author(s): Fred P. Davis, Aljoscha Nern, Serge Picard, Michael B. Reiser, Gerald M. Rubin, Sean R. Eddy, Gilbert L. Henry
Software Mentions: 4
Published: over 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

10.1186/s12864-019-6147-6

The role of nitric oxide during embryonic wound healing
Cited by: 16
Author(s): Pavel Abaffy, Silvie Tománková, Ravindra Naraine, Mikael Kubista, Radek Šindelka
Software Mentions: 4
Published: almost 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

10.1172/jci.insight.141341

Shear stress associated with cardiopulmonary bypass induces expression of inflammatory cytokines and necroptosis in monocytes
Cited by: 17
Author(s): Lan N. Tu, Lance Hsieh, Masaki Kajimoto, Kevin Charette, Nataliya Kibiryeva, Adriana Forero, Sarah E. Hampson, Jennifer Marshall, James E. O’Brien, Marta Scatena, Michael A. Portman, Ram Savan, Christopher Benner, Alberto Aliseda, Muhammad Nuri, Douglas C. Bittel, Peter Pastuszko, Vishal Nigam
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

10.1186/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

10.1172/jci.insight.140332

ETV6 germline mutations cause HDAC3/NCOR2 mislocalization and upregulation of interferon response genes
Cited by: 12
Author(s): Marlie H Fisher, Gregory D. Kirkpatrick, Brett M. Stevens, Courtney L. Jones, Michael U. Callaghan, Madhvi Rajpurkar, Joy M. Fulbright, Megan A. Cooper, Jesse W. Rowley, Christopher C. Porter, Arthur Gutierrez‐Hartmann, Kenneth L. Jones, Craig T. Jordan, Eric M. Pietras, Jorge Di Paola
Software Mentions: 4
Published: about 6 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

10.1371/journal.pone.0238202

Immune and sex-biased gene expression in the threatened Mojave desert tortoise, Gopherus agassizii
Cited by: 2
Author(s): Cindy Xu, Greer A. Dolby, K. Kristina Drake, Todd C. Esque, Kenro Kusumi
Software Mentions: 4
Published: about 6 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

10.1172/jci.insight.138443

Epigenetic regulation of the PGE2 pathway modulates macrophage phenotype in normal and pathologic wound repair
Cited by: 31
Author(s): Frank M. Davis, Lam C. Tsoi, Rachael Wasikowski, Aaron D. denDekker, Amrita Joshi, Carol A. Wilke, Hongping Deng, Sonya Wolf, Andrea Obi, Steven K. Huang, Allison C. Billi, Scott T. Robinson, Jay H Lipinski, William J. Melvin, Christopher O. Audu, Stephan Weidinger, Steven L. Kunkel, Andrew M. Smith, Jóhann E. Guðjónsson, Bethany B. Moore, Katherine A. Gallagher
Software Mentions: 4
Published: about 6 years ago

10.1007/s00125-018-4612-4

Patterns of differential gene expression in a cellular model of human islet development, and relationship to type 2 diabetes predisposition
Cited by: 12
Author(s): Marta Perez-Alcantara, Christian Honoré, Agata Wesolowska-Andersen, Anna L. Gloyn, Mark I. McCarthy, Mattias Hansson, Nicola L. Beer, Martijn van de Bunt
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0206948

Comparative mRNA and miRNA transcriptome analysis of a mouse model of IGFIR-driven lung cancer
Cited by: 4
Author(s): Robert A. Jones, S. Elizabeth Franks, Roger A. Moorehead
Software Mentions: 4
Published: almost 8 years ago

10.1016/j.immuni.2021.03.002

Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses
Cited by: 40
Author(s): Hong Zheng, A. Koneti Rao, Denis Đermadi, Jiaying Toh, Lara Jones, Michèle Donato, Yiran E. Liu, Yapeng Su, Dai Cl, Sergey A. Kornilov, Minas Karagiannis, Theodoros Marantos, Yehudit Hasin-Brumshtein, Yudong He, Evangelos J. Giamarellos‐Bourboulis, James R. Heath, Purvesh Khatri
Software Mentions: 4
Published: over 5 years ago

10.1093/molbev/msab197

Functional Characterization of the Cnidarian Antiviral Immune Response Reveals Ancestral Complexity
Cited by: 13
Author(s): Magda Lewandowska, Ton Sharoni, Yael Admoni, Reuven Aharoni, Yehu Moran
Software Mentions: 4
Published: over 5 years ago

10.15252/emmm.202013074

Impairment of the ER/mitochondria compartment in human cardiomyocytes with PLN p.Arg14del mutation
Cited by: 25
Author(s): Friederike Cuello, Anika E. Knaust, Umber Saleem, Malte Loos, Janice Raabe, Diogo Mosqueira, Sandra D. Laufer, Michaela Schweizer, Petra van der Kraak, Frederik Flenner, Bärbel Ulmer, Ingke Braren, Xiaoke Yin, Konstantinos Theofilatos, Jorge Ruiz-Orera, Giannino Patone, Birgit Klampe, Thomas G. Schulze, Angelika Piasecki, Yigal M. Pinto, Aryan Vink, Norbert Hübner, Siân E. Harding, Manuel Mayr, Chris Denning, Thomas Eschenhagen, Arne Hansen
Software Mentions: 4
Published: over 5 years ago

10.1016/j.immuni.2020.08.004

Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver
Cited by: 243
Author(s): Anneleen Remmerie, Liesbet Martens, Tinne Thoné, Ângela Castoldi, Ruth Seurinck, Benjamin Pavie, Joris Roels, Bavo Vanneste, Sofie De Prijck, Mathias Vanhockerhout, Mushida Binte Abdul Latib, Lindsey Devisscher, Anne Hoorens, Johnny Bonnardel, Niels Vandamme, Anna Kremer, Peter Borghgraef, Hans Van Vlierberghe, Saskia Lippens, Edward J. Pearce, Yvan Saeys, Charlotte Scott
Software Mentions: 4
Published: about 6 years ago

10.1016/j.immuni.2018.07.004

The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages
Cited by: 142
Author(s): Charlotte Scott, Wouter T’Jonck, Liesbet Martens, Helena Todorov, Dorine Sichien, Bieke Soen, Johnny Bonnardel, Sofie De Prijck, Niels Vandamme, Robrecht Cannoodt, Wouter Saelens, Bavo Vanneste, Wendy Toussaint, Pieter De Bleser, Nozomi Takahashi, Peter Vandenabeele, Sandrine Henri, Clare Pridans, David Hume, Bart N. Lambrecht, Patrick De Baetseĺier, Simon Milling, Jo A. Van Ginderachter, Bernard Malissen, Geert Berx, Alain Beck, Yvan Saeys, Martin Guilliams
Software Mentions: 4
Published: about 8 years ago

10.1089/hum.2020.213

Genetic Rescue of X-Linked Retinoschisis Mouse (<i>Rs1</i>^−/y) Retina Induces Quiescence of the Retinal Microglial Inflammatory State Following AAV8-<i>RS1</i> Gene Transfer and Identifies Gene Networks Underlying Retinal Recovery
Cited by: 16
Author(s): Camasamudram Vijayasarathy, Yong Zeng, Matthew Brooks, Robert N Fariss, Paul A. Sieving
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0100250

Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion
Cited by: 8
Author(s): Tzintzuni Garcia, Isa Matos, Yingjia Shen, Vagmita Pabuwal, M. M. Coelho, Yuko Wakamatsu, Manfred Schartl, Ronald B. Walter
Software Mentions: 4
Published: over 12 years ago

10.26508/lsa.201900303

Rate of brain aging and <i>APOE ε4</i> are synergistic risk factors for Alzheimer’s disease
Cited by: 10
Author(s): Christin Glorioso, Andreas R. Pfenning, Sam S Lee, David A. Bennett, Etienne Sibille, M Kellis, Leonard Guarente
Software Mentions: 4
Published: over 7 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

10.1038/s41438-020-0338-9

Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics
Cited by: 43
Author(s): Junyang Yue, Jiacheng Liu, Wei Tang, Ya Qing Wu, Xiaofeng Tang, Wei Li, Ying Yang, Lihuan Wang, Shengxiong Huang, Congbing Fang, Kun Zhao, Zhangjun Fei, Yongsheng Liu, Yi Zheng
Software Mentions: 4
Published: about 6 years ago

10.1242/dev.175265

A gene expression atlas of embryonic neurogenesis in <i>Drosophila</i> reveals complex spatiotemporal regulation of lncRNAs
Cited by: 21
Author(s): Alexandra L. McCorkindale, Philipp Wahle, Irwin Jungreis, Peter Menzel, Chinmay Shukla, Rúben Lopes Pereira Abreu, Rafael A. Irizarry, Irmtraud M. Meyer, M Kellis, Robert P. Zinzen
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0236348

Unraveling the molecular pathobiology of vocal fold systemic dehydration using an in vivo rabbit model
Cited by: 8
Author(s): Naíla Cannes do Nascimento, Andrea Pires dos Santos, M. Preeti Sivasankar, Abigail Cox
Software Mentions: 4
Published: about 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

10.7554/eLife.66522

Ketogenic diet restrains aging-induced exacerbation of coronavirus infection in mice
Cited by: 33
Author(s): Seungjin Ryu, Irina Shchukina, Yun‐Hee Youm, Hua Qing, Brandon Hilliard, Tamara Dlugos, Xinbo Zhang, Yuki Yasumoto, Carmen J. Booth, Carlos Fernández‐Hernando, Yajaira Suárez, Kamal M. Khanna, Tamás L. Horváth, Marcelo O Dietrich, Maxim N. Artyomov, Andrew Wang, Vishwa Deep Dixit
Software Mentions: 4
Published: over 5 years ago

10.1038/s41418-019-0285-x

CBP and SRF co-regulate dendritic growth and synaptic maturation
Cited by: 25
Author(s): Beatriz del Blanco, Deisy Guiretti, Romana Tomasoni, María T. Lopez-Cascales, Rafael Muñoz‐Viana, Michał Lipiński, Marilyn Scandaglia, Yaiza Coca, Román Olivares, Luis M. Valor, Eloı́sa Herrera, Ángel Barco
Software Mentions: 4
Published: over 7 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

10.1038/s41419-020-03020-9

Intracellular amyloid toxicity induces oxytosis/ferroptosis regulated cell death
Cited by: 51
Author(s): Ling Huang, Daniel B. McClatchy, Pamela Maher, Zhibin Liang, Jolene K. Diedrich, David Soriano-Castell, Joshua Goldberg, Maxim N. Shokhirev, John R. Yates, David Schubert, António Currais
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0233841

Whole blood transcriptional responses of very preterm infants during late-onset sepsis
Cited by: 16
Author(s): Sherrianne Ng, Tobias Strunk, Ahwon Lee, Erin E. Gill, Reza Falsafi, Tabitha Woodman, Julie Hibbert, Robert E. W. Hancock, Andrew Currie
Software Mentions: 4
Published: over 6 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

10.1093/gigascience/giab037

The genome of the venomous snail <i>Lautoconus ventricosus</i> sheds light on the origin of conotoxin diversity
Cited by: 21
Author(s): José Ramón Pardos-Blas, Iker Irisarri, Samuel Abalde, Carlos M.L. Afonso, Manuel Jiménez‐Tenorio, Rafael Zardoya
Software Mentions: 4
Published: over 5 years ago

10.1038/s41419-019-2040-0

Severe head dysgenesis resulting from imbalance between anterior and posterior ontogenetic programs
Cited by: 2
Author(s): Emmanuelle Grall, Victor Gourain, Asmaa Naïr, Elisabeth Martin, Marie‐Christine Birling, Jean–Noël Freund, Isabelle Duluc
Software Mentions: 4
Published: almost 7 years ago

10.26508/lsa.202000825

The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells
Cited by: 13
Author(s): Maria Inês Alvelos, Mirko Brüggemann, F. X. Reymond Sutandy, Jonàs Juan-Mateu, Máikel Luís Colli, Anke Busch, Miguel Lopes, Ângela Castela, Annemieke Aartsma‐Rus, Julian König, Kathi Zarnack, Décio L. Eizirik
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0169648

The Smc5/6 Complex Restricts HBV when Localized to ND10 without Inducing an Innate Immune Response and Is Counteracted by the HBV X Protein Shortly after Infection
Cited by: 107
Author(s): Congrong Niu, Christine M. Livingston, Li Li, Rudolf K. F. Beran, Stéphane Daffis, Dhivya Ramakrishnan, Dara Burdette, Leanne Peiser, Eduardo Salas, Hilario J. Ramos, Mei Yu, Guofeng Cheng, Michel Strubin, William E. Delaney, Simon P. Fletcher
Software Mentions: 4
Published: over 9 years ago

10.18632/aging.202780

circRNA expression profiling of colon tissue from mesalazine-treated mouse of inflammatory bowel disease reveals an important circRNA-miRNA-mRNA pathway
Cited by: 8
Author(s): Wei Zhou, Haiyin Zhang, Y. B. Pan, Yingbin Xu, Yongqing Cao
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giaa158

ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
Cited by: 4
Author(s): Pavankumar Videm, Anup Kumar, Oleg Zharkov, Björn Grüning, Rolf Backofen
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giaa108

Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis
Cited by: 5
Author(s): Florian Heyl, Daniel Maticzka, Michaël Uhl, Rolf Backofen
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.101691

SNCA overexpression disturbs hippocampal gene expression trajectories in midlife
Cited by: 6
Author(s): Thomas Hentrich, Zinah Wassouf, Olaf Rieß, Julia M. Schulze‐Hentrich
Software Mentions: 4
Published: almost 8 years ago

10.1093/gigascience/giaa111

IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
Cited by: 134
Author(s): Katrina Kalantar, Tiago Rodrigues De Carvalho, Charles F. A. de Bourcy, Boris Dimitrov, Greg Dingle, Rebecca Egger, Julie Han, Olivia B. Holmes, Yun Fang Juan, Ryan J. King, Andrey Kislyuk, Michael Lin, Maria Mariano, Todd Morse, Lucia V. Reynoso, David Rissato Cruz, Jonathan Sheu, Jennifer Tang, James Wang, Mark A. Zhang, Emily Zhong, Vida Ahyong, Sreyngim Lay, Sophana Chea, Jennifer A. Bohl, Jessica E. Manning, Cristina M. Tato, Joseph L. DeRisi
Software Mentions: 4
Published: about 6 years ago

10.3390/antiox10040618

Differential and Overlapping Effects of Melatonin and Its Metabolites on Keratinocyte Function: Bioinformatics and Metabolic Analyses
Cited by: 4
Author(s): Joanna Stefan, Tae Kang Kim, Fiona Schedel, Zorica Janjetovic, David K. Crossman, Kerstin Steinbrink, Radomir M. Slominski, Jaroslaw W. Żmijewski, Meri K. Tulić, Russel J. Reíter, Konrad Kleszczyński, Andrzej Słomiński
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-4671-4

Indel detection from DNA and RNA sequencing data with transIndel
Cited by: 23
Author(s): Rendong Yang, Jamie L. Van Etten, Scott M. Dehm
Software Mentions: 4
Published: over 8 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

10.1242/dev.172916

Capacitation of human naïve pluripotent stem cells for multi-lineage differentiation
Cited by: 78
Author(s): Maria Rostovskaya, Giuliano Giuseppe Stirparo, Austin Smith
Software Mentions: 4
Published: over 7 years ago

10.1038/s41419-021-03826-1

Gata2-L359V impairs primitive and definitive hematopoiesis and blocks cell differentiation in murine chronic myelogenous leukemia model
Cited by: 7
Author(s): Yanbin Fu, Yun Tan, Baichang Wu, Yuting Dai, Xiaoguang Xu, Mengmeng Pan, Zhiwei Chen, Na Qiao, Jing Wu, Lu Jiang, Jing Lu, Bing Chen, Avigail Rein, Shai Izraeli, Xiao Jian Sun, Jinyan Huang, Qiu-Hua Huang, Zhu Chen, Sai‐Juan Chen
Software Mentions: 4
Published: over 5 years ago

10.18632/oncotarget.27632

Validated limited gene predictor for cervical cancer lymph node metastases
Cited by: 1
Author(s): Joshua Bloomstein, Rie von Eyben, Avis Chan, Erinn B. Rankin, Daniel R. Fregoso, Jing Wang-Chiang, Lisa Lee, Li Xie, Shannon MacLaughlan David, Henning Stehr, Mohammad Shahrokh Esfahani, Amato J. Giaccia, Elizabeth A. Kidd
Software Mentions: 4
Published: over 6 years ago