pypi: TopHat | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-44302-3

Dose-dependent effects of chronic alcohol drinking on peripheral immune responses
Cited by: 41
Author(s): Suhas Sureshchandra, Anthony M. Raus, Allen Jankeel, Brian Jin Kee Ligh, Nicole A.R. Walter, Natali Newman, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pgen.1006840

Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks
Cited by: 54
Author(s): Syed Bukhari, Michael C. Saul, Christopher H. Seward, Huimin Zhang, Miles K. Bensky, Noelle James, Sihai Dave Zhao, Sriram Chandrasekaran, Lisa Stubbs, Alison M. Bell
Software Mentions: 6
Published: about 9 years ago

10.1038/s41598-019-47797-y

Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae
Cited by: 3
Author(s): John P. Lloyd, Megan J. Bowman, Christina B. Azodi, Rosalie P. Sowers, Gaurav D. Moghe, Kevin L. Childs, Shin-Han Shiu
Software Mentions: 6
Published: about 7 years ago

10.1038/s41598-018-37397-7

Temporal dynamics in meta longitudinal RNA-Seq data
Cited by: 4
Author(s): Sangwon Oh, Congjun Li, R.L. Baldwin, Seongho Song, Fang Liu, Robert W. Li
Software Mentions: 6
Published: over 7 years ago

10.3390/jpm9020021

The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis
Cited by: 6
Author(s): Marín de Evsikova C, Isaac Raplee, John H. Lockhart, G Jaimes, Evsikov Av
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2019.02491

Dynamic Changes in the Microbiome and Mucosal Immune Microenvironment of the Lower Respiratory Tract by Influenza Virus Infection
Cited by: 30
Author(s): Liming Gu, Huixiong Deng, Zhihui Ren, Ying Zhao, Shun Yu, Yingzhu Guo, Jianping Dai, Xiaoxuan Chen, Kangsheng Li, Rui Li, Gefei Wang
Software Mentions: 6
Published: almost 7 years ago

10.7554/eLife.19127

Regulation of X-linked gene expression during early mouse development by Rlim
Cited by: 36
Author(s): Feng Wang, Jongdae Shin, Jeremy Shea, Jun Yu, Ana Bošković, Meg Byron, Xiaochun Zhu, Alex K. Shalek, Aviv Regev, Jeanne B. Lawrence, Eduardo M. Torres, Lihua Julie Zhu, Oliver J. Rando, Ingolf Bach
Software Mentions: 6
Published: about 10 years ago

10.3389/fmicb.2019.01408

Chromatin Profiles of Chromosomally Integrated Human Herpesvirus-6A
Cited by: 19
Author(s): Anthony J. Saviola, Cosima Zimmermann, Michael Mariani, Sylvia Signorelli, Diana L. Gerrard, Joseph R. Boyd, Darren J. Wight, Guillaume Morissette, Annie Gravel, Isabelle Dubuc, Louis Flamand, Benedikt B. Kaufer, Seth Frietze
Software Mentions: 6
Published: over 7 years ago

10.1186/s12284-016-0098-1

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress
Cited by: 32
Author(s): Elena Baldoni, Paolo Bagnaresi, Franca Locatelli, Monica Mattana, Annamaria Genga
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pone.0053822

Efficient and Comprehensive Representation of Uniqueness for Next-Generation Sequencing by Minimum Unique Length Analyses
Cited by: 31
Author(s): Helena Storvall, Daniel Ramsköld, Rickard Sandberg
Software Mentions: 6
Published: over 13 years ago

10.1099/mgen.0.000320

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics
Cited by: 0
Author(s): Amol C. Shetty, John Mattick, Matthew Chung, Carrie McCracken, Anup Mahurkar, Scott G. Filler, Claire M. Fraser, David A. Rasko, Vincent M. Bruno, Julie C. Dunning Hotopp
Software Mentions: 6
Published: over 6 years ago

10.1534/g3.118.200865

Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi)
Cited by: 16
Author(s): Karen M. Kapheim, Hailin Pan, Cai Li, Charles Blatti, Brock A. Harpur, Panagiotis Ioannidis, Beryl M. Jones, Clement F. Kent, Livio Ruzzante, Laura Sloofman, Eckart Stolle, Robert M. Waterhouse, Amro Zayed, Guojie Zhang, William T. Wcislo
Software Mentions: 6
Published: over 7 years ago

10.1534/g3.113.006742

The Developmental Transcriptome of the Mosquito Aedes aegypti, an Invasive Species and Major Arbovirus Vector
Cited by: 184
Author(s): Omar S. Akbari, Igor Antoshechkin, Henry Amrhein, Brian A. Williams, Rose DiLoreto, Jeremy E. Sandler, Bruce A. Hay
Software Mentions: 6
Published: about 13 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: over 9 years ago

10.1038/s41598-020-70334-1

Developmental changes in the accessible chromatin, transcriptome and Ascl1-binding correlate with the loss in Müller Glial regenerative potential
Cited by: 20
Author(s): Leah S. VandenBosch, Stefanie G. Wohl, Matthew S. Wilken, Marcus Hooper, Connor Finkbeiner, Kristen E. Cox, Laura B. Chipman, Thomas A. Reh
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-020-65089-8

Immunorthodontics: in vivo gene expression of orthodontic tooth movement
Cited by: 28
Author(s): Yehuda Klein, Omer Fleissig, David Polak, Yechezkel Barenholz, Ofer Mandelboim, Stella Chaushu
Software Mentions: 6
Published: over 6 years ago

10.1534/g3.114.016196

A Multipurpose, High-Throughput Single-Nucleotide Polymorphism Chip for the Dengue and Yellow Fever Mosquito, Aedes aegypti
Cited by: 53
Author(s): Benjamin R. Evans, Andrea Gloria‐Soria, Lin Hou, Carolyn S. McBride, Mariangela Bonizzoni, Hongyu Zhao, Jeffrey R. Powell
Software Mentions: 6
Published: over 11 years ago

10.3389/fmicb.2018.02212

A Class 1 Histone Deacetylase as Major Regulator of Secondary Metabolite Production in Aspergillus nidulans
Cited by: 29
Author(s): Angelo Pidroni, Birgit Faber, Gerald Brosch, Ingo Bauer, Stefan Graessle
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-018-36840-z

Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas
Cited by: 28
Author(s): Susan K. Rathe, Flavia E. Popescu, James E. Johnson, Adrienne L. Watson, Tracy A. Marko, Branden S. Moriarity, John R. Ohlfest, David A. Largaespada
Software Mentions: 5
Published: over 7 years ago

10.1111/1755-0998.13257

High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae
Cited by: 19
Author(s): Simei He, Dong Xiao, Guanghui Zhang, Wei Fan, Shengchang Duan, Hong Shi, Dawei Li, Rui Li, Cuizhi Geng, Guangqiang Long, Yan Zhao, Mo Chen, Mi Yan, Jianli Yang, Yingchun Lu, Yanli Zhou, Wei Chen, Yang Dong, Shengchao Yang
Software Mentions: 5
Published: almost 6 years ago

10.3389/fonc.2019.01206

Exploration of the Transcriptional Landscape of ALPPS Reveals the Pathways of Accelerated Liver Regeneration
Cited by: 11
Author(s): Pieter Borger, Marcel Schneider, Lukas Frick, Magda Langiewicz, Maksim Sorokin, Anton Buzdin, Ekaterina Kachaylo, Rolf Graf, Bostjan Humar, Pierre‐Alain Clavien
Software Mentions: 5
Published: almost 7 years ago

10.1038/sdata.2015.51

De novo transcriptome profiling of highly purified human lymphocytes primary cells
Cited by: 34
Author(s): Raoul Jean Pierre Bonnal, Valeria Ranzani, Alberto Arrigoni, Serena Maria Curti, Ilaria Panzeri, Paola Gruarin, Sergio Abrignani, Grazisa Rossetti, Massimiliano Pagani
Software Mentions: 5
Published: about 11 years ago

10.1371/journal.pgen.1004648

Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements
Cited by: 36
Author(s): Robin P. Smith, Walter L. Eckalbar, Kari M. Morrissey, Marcelo R. Luizon, Thomas J. Hoffmann, Xinwei Sun, Stacy L. Jones, Shelley Force Aldred, Anuradha Ramamoorthy, Zeruesenay Desta, Yunlong Liu, Todd C. Skaar, Nathan D. Trinklein, Kathleen M. Giacomini, Nadav Ahituv
Software Mentions: 5
Published: almost 12 years ago

10.7150/jca.29958

TGFBI Promotes Tumor Growth and is Associated with Poor Prognosis in Oral Squamous Cell Carcinoma
Cited by: 16
Author(s): Bingjie Wang, Kun-Ping Chi, Ruling Shen, Saiwei Zheng, Yang Guo, Jianfeng Li, Jian Fei, Yuan He
Software Mentions: 5
Published: over 7 years ago

10.1074/mcp.RA118.000832

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets
Cited by: 17
Author(s): Zhe Ren, Da Qi, Nina Pugh, Kai Li, Bo Wen, Ruo Zhou, Shaohang Xu, Siqi Liu, Andrew R. Jones
Software Mentions: 5
Published: over 7 years ago

10.3892/or.2015.4023

Integrated analysis of DNA methylation and microRNA regulation of the lung adenocarcinoma transcriptome
Cited by: 20
Author(s): Jie Du, Lin Zhang
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0238924

Exploring the potential of comparative de novo transcriptomics to classify Saccharomyces brewing yeasts
Cited by: 1
Author(s): Jürgen Behr, Meike Kliche, Andreas Geißler, Rudi F. Vogel
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pgen.1005819

Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
Cited by: 21
Author(s): Н. А. Иванов, Ran Tao, Joshua G. Chenoweth, Anna C. Brandtjen, Michelle I. Mighdoll, John D. Genova, Ronald D.G. McKay, Yankai Jia, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde, Andrew E. Jaffe
Software Mentions: 5
Published: over 10 years ago

10.7150/jca.47698

Mass Spectrometry Imaging Differentiates Chromophobe Renal Cell Carcinoma and Renal Oncocytoma with High Accuracy
Cited by: 7
Author(s): Mark Kriegsmann, Rita Casadonte, Nadine Maurer, Christine Stoehr, Franziska Erlmeier, Holger Moch, Kerstin Junker, Christiane Zgorzelski, Wilko Weichert, Kristina Schwamborn, Sören‐Oliver Deininger, Matthias M. Gaida, Gunhild Mechtersheimer, Albrecht Stenzinger, Peter Schirmacher, Arndt Hartmann, Joerg Kriegsmann, Katharina Kriegsmann
Software Mentions: 5
Published: over 6 years ago

10.1186/s12934-015-0226-4

An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture
Cited by: 17
Author(s): Bat-Erdene Jugder, Zhiliang Chen, Darren Tan Tek Ping, Hélène Lebhar, Jeffrey Welch, Christopher P. Marquis
Software Mentions: 5
Published: over 11 years ago

10.3390/molecules25214894

Study on Molecular Profiles of Staphylococcus aureus Strains: Spectrometric Approach
Cited by: 8
Author(s): Michał Złoch, Paweł Pomastowski, Ewelina Maślak, Fernanda Monedeiro
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2016.01335

Visual Comparative Omics of Fungi for Plant Biomass Deconstruction
Cited by: 31
Author(s): Shingo Miyauchi, David Navarro, Igor V. Grigoriev, Anna Lipzen, Robert Riley, Didier Chevret, Sacha Grisel, Jean‐Guy Berrin, Bernard Henrissat, Marie‐Noëlle Rosso
Software Mentions: 5
Published: about 10 years ago

10.1002/1878-0261.12314

Induced <scp>PTF</scp> 1a expression in pancreatic ductal adenocarcinoma cells activates acinar gene networks, reduces tumorigenic properties, and sensitizes cells to gemcitabine treatment
Cited by: 17
Author(s): Brad L. Jakubison, Patrick G. Schweickert, Sarah E. Moser, Yi Yang, Hongyu Gao, Kathleen M. Scully, Pamela Itkin-Ansari, Yunlong Liu, Stephen F. Konieczny
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0088515

Extensive Expression Differences along Porcine Small Intestine Evidenced by Transcriptome Sequencing
Cited by: 29
Author(s): Núria Mach, Mustapha Berri, Diane Esquerré, Claire Chevaleyre, Gaëtan Lemonnier, Yvon Billon, Patricia Lepage, Isabelle P. Oswald, Joël Doré, Claire Rogel–Gaillard, Jordi Estellé
Software Mentions: 5
Published: over 12 years ago

10.1155/2017/6218353

Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers
Cited by: 105
Author(s): Luka Bolha, Metka Ravnik‐Glavač, Damjan Glavač
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0206844

Clustering-local-unique-enriched-signals (CLUES) promotes identification of novel regulators of ES cell self-renewal and pluripotency
Cited by: 1
Author(s): Chao Wu, Jiao Yang, Minhong Shen, Ci Pan, Cheng Guo, Danmei Jia, Jing Zhu, Long Zhang, Min Zheng, Junling Jia
Software Mentions: 5
Published: almost 8 years ago

10.3389/fphys.2019.01305

The Regulation of Ruminal Short-Chain Fatty Acids on the Functions of Rumen Barriers
Cited by: 28
Author(s): Hong Shen, Zhihui Xu, Zanming Shen, Zhongyan Lu
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.31683

Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm
Cited by: 36
Author(s): Xinan Yang, Rangarajan D. Nadadur, Catharina R.E. Hilvering, Valerio Bianchi, Michael S. Werner, Stefan R. Mazurek, Margaret Gadek, Karen Shen, Joseph D. Goldman, Leonid Tyan, Jenna C. Bekeny, Johnathon M Hall, Nutishia Lee, Carlos Perez-Cervantes, Ozanna Burnicka-Turek, Kenneth D. Poss, Christopher R. Weber, Wouter de Laat, Alexander J. Ruthenburg, Ivan P. Moskowitz
Software Mentions: 5
Published: almost 9 years ago

10.1093/gigascience/giaa143

High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis
Cited by: 7
Author(s): Qionghua Gao, Zijun Xiong, Rasmus Stenbak Larsen, Long Zhang, Jie Zhao, Guo Ding, Ruoping Zhao, Chengyuan Liu, Ran Hao, Guojie Zhang
Software Mentions: 5
Published: almost 6 years ago

10.3390/ijms21031067

Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress
Cited by: 32
Author(s): Zhaoyang Hu, Yufei Zhang, Yue Ping He, Qingqing Cao, Ting Zhang, Laiqing Lou, Qingqing Cai
Software Mentions: 5
Published: over 6 years ago

10.26508/lsa.202000946

Prognostic accuracy of MALDI-TOF mass spectrometric analysis of plasma in COVID-19
Cited by: 23
Author(s): Lucas Cardoso Lázari, Fábio Ghilardi, Lívia Rosa-Fernandes, Diego M. Assis, José Carlos Nicolau, Verônica Feijoli Santiago, Talia Falcão Dalçóquio, Cláudia Blanes Angeli, Adriádne Justi Bertolin, Cláudio Romero Farias Marinho, Carsten Wrenger, Edison Luiz Durigon, Rinaldo Focaccia Siciliano, Giuseppe Palmisano
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0101374

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads
Cited by: 21
Author(s): Shanrong Zhao
Software Mentions: 5
Published: about 12 years ago

10.3390/ijms22052353

ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast Cancer
Cited by: 3
Author(s): Leqin Yan, Sally Gaddis, Luis Della Coletta, John Repass, Katherine Powell, Melissa S. Simper, Yueping Chen, Michelle Byrom, Yi Zhong, Kevin Lin, Bin Liu, Yao Lu, Jianjun Shen, Michael C. MacLeod
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1008566

The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants
Cited by: 54
Author(s): Takashi Akagi, Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle Henry
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.50541

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons
Cited by: 62
Author(s): Rita A Batista, Jordi Moreno‐Romero, Yue Qiu, Joram van Boven, Juan Santos‐González, Duarte D. Figueiredo, Claudia Köhler
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13041-020-00603-7

Ocular hypertension suppresses homeostatic gene expression in optic nerve head microglia of DBA/2 J mice
Cited by: 28
Author(s): James R. Tribble, Jeffrey M. Harder, Pete A. Williams, Simon W. M. John
Software Mentions: 5
Published: over 6 years ago

10.1523/ENEURO.0288-18.2019

Brain Region-Specific Gene Signatures Revealed by Distinct Astrocyte Subpopulations Unveil Links to Glioma and Neurodegenerative Diseases
Cited by: 26
Author(s): Raquel Cuevas-Diaz Duran, Chih Yen Wang, Hui Zheng, Benjamin Deneen, Jia Qian Wu
Software Mentions: 5
Published: over 7 years ago

10.3390/ijms19020593

Luminal lncRNAs Regulation by ERα-Controlled Enhancers in a Ligand-Independent Manner in Breast Cancer Cells
Cited by: 13
Author(s): Valentina Miano, Giulio Ferrero, Valentina Rosti, Eleonora Manitta, Jamal Elhasnaoui, Giulia Basile, Michele De Bortoli
Software Mentions: 5
Published: over 8 years ago

10.3390/genes5040957

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis
Cited by: 57
Author(s): Vahan Simonyan, Raja Mazumder
Software Mentions: 5
Published: about 12 years ago

10.1534/g3.116.030783

ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress
Cited by: 47
Author(s): Benoît Castandet, Amber M. Hotto, Susan R. Strickler, David B. Stern
Software Mentions: 5
Published: about 10 years ago

10.3390/ijms21051630

Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines
Cited by: 1
Author(s): Dóra Bojcsuk, Gergely Nagy, Bálint László Bálint
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0167488

Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial
Cited by: 46
Author(s): Leigh M. Howard, Kristen L. Hoek, Johannes Goll, Parimal Samir, Allison C. Galassie, Tara M. Allos, Xinnan Niu, Laura E. Gordy, C. Buddy Creech, Nripesh Prasad, Travis L. Jensen, Heather Hill, Shawn Levy, Sebastian Joyce, Andrew J. Link, Kathryn M. Edwards
Software Mentions: 5
Published: over 9 years ago

10.1038/onc.2016.382

Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer
Cited by: 125
Author(s): Alison Harrod, Janet S. Fulton, Van Nguyen, Manikandan Periyasamy, L Ramos-Garcia, C-F Lai, Gergana Metodieva, Alex de Giorgio, Richard Williams, Delfran Batista dos Santos, Pablo Gómez, M-L Lin, Metodi V. Metodiev, Justin Stebbing, Leandro Castellano, Luca Magnani, R. Charles Coombes, Laki Buluwela, Simak Ali
Software Mentions: 5
Published: almost 10 years ago

10.1534/g3.115.019166

Genome-Wide Analysis ofDrosophilaRBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis
Cited by: 15
Author(s): Yiliang Wei, Shamba S. Mondal, Rima Mouawad, Bartek Wilczyński, R. William Henry, David N. Arnosti
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0197162

A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells
Cited by: 15
Author(s): Alexander Wolff, Michaela Bayerlová, Jochen Gaedcke, Dieter Kube, Tim Beißbarth
Software Mentions: 5
Published: over 8 years ago

10.1084/jem.20191257

Combined deletion of Bap1, Nf2, and Cdkn2ab causes rapid onset of malignant mesothelioma in mice
Cited by: 28
Author(s): Jitendra Badhai, Gaurav Kumar Pandey, Ji‐Ying Song, Oscar Krijgsman, Rajith Bhaskaran, G. Chandrasekaran, Min-Chul Kwon, Lorenzo Bombardelli, Kim Monkhorst, Cristoforo Grasso, John Zevenhoven, Jan van der Vliet, Miranda Cozijnsen, Paul Krimpenfort, Daniel S. Peeper, Maarten van Lohuizen, Anton Berns
Software Mentions: 5
Published: over 6 years ago

10.1016/j.immuni.2017.12.010

The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages
Cited by: 153
Author(s): Zsolt Czimmerer, Bence Dániel, Attila Horváth, Dominik Rückerl, Gergely Nagy, Máté Kiss, Matthew Peloquin, Marietta Margit Budai, Ixchelt Cuaranta-Monroy, Zoltán Simándi, László Steiner, Béla Nagy, Szilárd Póliska, Csaba Bankó, Zsolt Bacsó, Ira G. Schulman, Sascha Sauer, Jean Deleuze, Judith E. Allen, Szilvia Benkő, László Nagy
Software Mentions: 5
Published: over 8 years ago

10.1186/s12979-020-00182-0

Effect of aging on the transcriptomic changes associated with the expression of the HERV-K (HML-2) provirus at 1q22
Cited by: 11
Author(s): Arttu Autio, Tapio Nevalainen, Binisha H. Mishra, Marja Jylhä, Heini Flinck, Mikko Hurme
Software Mentions: 5
Published: over 6 years ago

10.1186/s12967-020-02695-0

Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2
Cited by: 39
Author(s): Abul B.M.M.K. Islam, A. A. Khan, Rasel Ahmed, Md. Sabbir Hossain, Shah Md. Tamim Kabir, Md Shahidul Islam, Amam Zonaed Siddiki
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms8040559

Comparative Transcriptomics Reveals Distinct Gene Expressions of a Model Ciliated Protozoan Feeding on Bacteria-Free Medium, Digestible, and Digestion-Resistant Bacteria
Cited by: 9
Author(s): Songbao Zou, Qianqian Zhang, Jun Gong
Software Mentions: 5
Published: over 6 years ago

10.1128/mBio.01496-21

The Interspecific Fungal Hybrid Verticillium longisporum Displays Subgenome-Specific Gene Expression
Cited by: 6
Author(s): Jasper R L Depotter, Fabian van Beveren, Luis Rodríguez‐Moreno, Holger Kramer, Edgar A. Chavarro Carrero, Gabriel Lorencini Fiorin, Grardy C. M. van den Berg, Thomas A. Wood, Bart P.H.J. Thomma, Michael Seidl
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1005698

Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans
Cited by: 43
Author(s): Maxwell Kramer, Anna Lena Kranz, Amanda Su, Lara Winterkorn, Sarah Elizabeth Albritton, Sevinç Ercan
Software Mentions: 5
Published: almost 11 years ago

10.1155/2013/481545

Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies
Cited by: 13
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith
Software Mentions: 5
Published: about 13 years ago

10.7554/eLife.25762

Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution
Cited by: 102
Author(s): Yuh Chwen G Lee, Gary H. Karpen
Software Mentions: 5
Published: about 9 years ago

10.1186/s12983-015-0109-x

Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex
Cited by: 33
Author(s): Andrey Rozenberg, Mrutyunjaya Parida, Florian Leese, Linda C. Weiss, Ralph Tollrian, J. Robert Manak
Software Mentions: 5
Published: about 11 years ago

10.18632/oncotarget.21031

Genome-wide analysis and functional prediction of long non-coding RNAs in mouse uterus during the implantation window
Cited by: 22
Author(s): Qi Wang, Nan Wang, Rui Cai, Fan Zhao, Yi Xiong, Xiao Li, Aihua Wang, Peng Lin, Yaping Jin
Software Mentions: 5
Published: about 9 years ago

10.18632/oncotarget.8192

Integrated analysis of long non-coding RNAs in human colorectal cancer
Cited by: 32
Author(s): Xiaohua Chen, Binjian Liu, Rui Yang, Yong Guo, Feng Li, Lin Wang, Hanyang Hu
Software Mentions: 5
Published: over 10 years ago

10.3390/ijms22179146

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses
Cited by: 5
Author(s): Mirosław Tyrka, Beata Bakera, Magdalena Szeliga, Magdalena Święcicka, Paweł Krajewski, Monika Mokrzycka, Monika Rakoczy-Trojanowska
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.07103

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
Cited by: 103
Author(s): Irene Gallego Romero, Bryan J. Pavlovic, Irene Hernando-Herraez, Xiang Zhou, Michelle C. Ward, Nicholas E. Banovich, Courtney L Kagan, Jonathan E. Burnett, Constance H Huang, Amy Mitrano, Claudia Chavarria, Inbar Friedrich Ben-Nun, Yingchun Li, Karen Sabatini, Trevor R. Leonardo, Mana M. Parast, Tomàs Marquès‐Bonet, Louise C. Laurent, Jeanne F. Loring, Yoav Gilad
Software Mentions: 5
Published: over 11 years ago

10.1186/s12974-021-02154-7

Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder
Cited by: 11
Author(s): Fumie Horiuchi, Yuta Yoshino, Hiroshi Kumon, Rie Hosokawa, Kiwamu Nakachi, Kentaro Kawabe, Jun‐ichi Iga, Shu‐ichi Ueno
Software Mentions: 5
Published: over 5 years ago

10.1002/pld3.239

N6‐methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis
Cited by: 35
Author(s): Marianne C. Kramer, Kevin A. Janssen, Kyle Palos, Andrew D. L. Nelson, Lee E. Vandivier, Benjamin A. García, Eric Lyons, Mark A. Beilstein, Brian D. Gregory
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.21049

Proliferation-independent regulation of organ size by Fgf/Notch signaling
Cited by: 36
Author(s): Agnė Kozlovskaja-Gumbrienė, Yi Ren, Alexander Richard, Andy Aman, Ryan Jiskra, Danielle Nagelberg, Holger Knaut, Melainia McClain, Tatjana Piotrowski
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.44161

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition
Cited by: 30
Author(s): Andrew L. Hong, Yuen-Yi Tseng, Jeremiah A. Wala, Won-Jun Kim, Bryan D. Kynnap, Mihir B. Doshi, Guillaume Kugener, Gabriel J. Sandoval, Thomas P. Howard, Ji Li, Xiaoping Yang, Michelle Tillgren, Mahmhoud Ghandi, Abeer Sayeed, Rebecca Deasy, Abigail Ward, Brian McSteen, Katherine Labella, Paula Keskula, Adam Tracy, Cora Connor, Catherine Clinton, Alanna J. Church, Brian D. Crompton, Katherine A. Janeway, Barbara Van Hare, David Sandak, Ole Gjoerup, Pratiti Bandopadhayay, Paul A. Clemons, Stuart L. Schreiber, David E. Root, Prafulla C. Gokhale, N. Susan, Elizabeth Mullen, Charles W.M. Roberts, Cigall Kadoch, Rameen Beroukhim, Keith L. Ligon, Jesse S. Boehm, William C. Hahn
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.37184

An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer
Cited by: 68
Author(s): Ji Li, Peter S. Choi, Christine L. Chaffer, Katherine Labella, Justin Hwang, Andrew O. Giacomelli, Jong Wook Kim, Nina Ilić, John G. Doench, Seav Huong Ly, Chao Dai, Kimberly R. Hagel, Andrew L. Hong, Ole Gjoerup, Shom Goel, Jennifer Y Ge, David E. Root, Jean J. Zhao, Angela N. Brooks, Robert A. Weinberg, William C. Hahn
Software Mentions: 5
Published: about 8 years ago

10.1038/s41421-017-0003-0

ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
Cited by: 46
Author(s): Si Wang, Boqiang Hu, Zicheng Ding, Yujiao Dang, Jun Wu, Di Li, Xiaoling Liu, Bailong Xiao, Weiqi Zhang, Rui Ren, Jinghui Lei, Huifang Hu, Chang Chen, Piu Chan, Dong Liu, Jing Qu, Fuchou Tang, Guang Hui Liu
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.14997

Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons
Cited by: 326
Author(s): Mark S. Cembrowski, Lihua Wang, Ken Sugino, Brenda C. Shields, Nelson Spruston
Software Mentions: 5
Published: over 10 years ago

10.7554/eLife.64317

Evolutionary shifts in taste coding in the fruit pest Drosophila suzukii
Cited by: 33
Author(s): Hany K.M. Dweck, Gaëlle J.S. Talross, Wanyue Wang, John R. Carlson
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.07295

Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100
Cited by: 179
Author(s): Shouan Liu, Barbara Kracher, J. Ziegler, Rainer P. Birkenbihl, Imre E. Somssich
Software Mentions: 5
Published: over 11 years ago

10.7554/eLife.39054

New insights into the cellular temporal response to proteostatic stress
Cited by: 40
Author(s): Justin Rendleman, Zhe Cheng, Shuvadeep Maity, Nicolai Kastelic, Mathias Munschauer, Kristina Allgoewer, Guoshou Teo, Yun Bin Matteo Zhang, Amy Lei, Brian J. Parker, Markus Landthaler, Lindsay Freeberg, Scott Kuersten, Hyungwon Choi, Christine Vogel
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.15657

An integrative transcriptomic atlas of organogenesis in human embryos
Cited by: 55
Author(s): Dave T. Gerrard, Andrew Berry, Rachel Jennings, Karen Piper Hanley, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 5
Published: about 10 years ago

10.1186/s12870-020-02702-y

Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development
Cited by: 3
Author(s): Xiaobo Zhao, Chunjuan Li, Hao Zhang, Yan Cheng, Quanxi Sun, Juan Wang, Cuiling Yuan, Shiguang Shan
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.51373

PHF19 mediated regulation of proliferation and invasiveness in prostate cancer cells
Cited by: 18
Author(s): Payal Jain, Cecilia Ballaré, Enrique Blanco, Pedro Vizán, Luciano Di Croce
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-86544-0

An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
Cited by: 5
Author(s): Gabriel Jiménez-Domínguez, Patrice Ravel, Stéphan Jalaguier, Vincent Cavaillès, Jacques Colinge
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0109715

Genome-Wide Identification and Tissue-Specific Expression Analysis of UDP-Glycosyltransferases Genes Confirm Their Abundance in Cicer arietinum (Chickpea) Genome
Cited by: 33
Author(s): Ranu Sharma, Vimal Rawat, C.G. Suresh
Software Mentions: 5
Published: almost 12 years ago

10.1038/s41598-021-92610-4

Identification of biological pathway and process regulators using sparse partial least squares and triple-gene mutual interaction
Cited by: 2
Author(s): Jun-Yan Hong, T.D.C.P. Gunasekara, Cheng He, Sanzhen Liu, Jianqin Huang, Hairong Wei
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-213X-12-33

Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst
Cited by: 82
Author(s): Manabu Ozawa, Miki Sakatani, Jiqiang Yao, Savita Shanker, Fahong Yu, Rui Yamashita, Shokichi Wakabayashi, Kenta Nakai, Kyle B. Dobbs, Mateus José Sudano, William G. Farmerie, Peter J. Hansen
Software Mentions: 5
Published: almost 14 years ago

10.1038/s41420-019-0184-4

A six-inhibitor culture medium for improving naïve-type pluripotency of porcine pluripotent stem cells
Cited by: 15
Author(s): Ye Yuan, Jin‐Kyu Park, Yuchen Tian, Jungmin Choi, Rolando Pasquariello, Andrei P. Alexenko, Aihua Dai, Susanta K. Behura, R. Michael Roberts, Toshihiko Ezashi
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0159093

Molecular Mechanism for Stress-Induced Depression Assessed by Sequencing miRNA and mRNA in Medial Prefrontal Cortex
Cited by: 57
Author(s): Ke Ma, Li Guo, Aiping Xu, Shan Cui, Jinhui Wang
Software Mentions: 5
Published: about 10 years ago

10.1186/1748-7188-8-25

Data compression for sequencing data
Cited by: 84
Author(s): Sebastian Deorowicz, Szymon Grabowski
Software Mentions: 5
Published: over 13 years ago

10.7554/eLife.49044

NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress
Cited by: 22
Author(s): Dongdong Han, Lars Schomacher, Katrin M. Schüle, Medhavi Mallick, Michael U. Musheev, Emil Karaulanov, Laura Krebs, Annika von Seggern, Christof Niehrs
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0182270

Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans
Cited by: 4
Author(s): Kapil Dev Singh, Xue Zheng, Stuart Milstein, Martin Keller, Bernd Roschitzki, Jonas Grossmann, Michael O. Hengartner
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-018-20262-y

Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes
Cited by: 15
Author(s): Austin Alleman, Barbara Feldmeyer, Susanne Foitzik
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-018-33718-y

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat
Cited by: 40
Author(s): Yongpeng Li, Xing Fu, Meicheng Zhao, Wei Zhang, Bo Li, Diaoguo An, Junming Li, Aimin Zhang, Renyi Liu, Xigang Liu
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-017-11036-z

SRSF1 suppresses selection of intron-distal 5′ splice site of DOK7 intron 4 to generate functional full-length Dok-7 protein
Cited by: 3
Author(s): Khalid Ahsan, Akio Matsubara, Mohammad Alinoor Rahman, Jun‐ichi Takeda, Mohammad Nazim, Bisei Ohkawara, Mikako Ito, Kinji Ohno
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0227303

Transcriptome analysis of Actinidia chinensis in response to Botryosphaeria dothidea infection
Cited by: 8
Author(s): Yuanxiu Wang, Guihong Xiong, Zhe He, Mingfeng Yan, M. Q. Zou, Junxi Jiang
Software Mentions: 5
Published: over 6 years ago

10.1038/srep46203

Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection
Cited by: 25
Author(s): Arun Kommadath, Hua Bao, Igseo Choi, James M. Reecy, James E. Koltes, Eric R. Fritz-Waters, Christopher J. Eisley, Jason R. Grant, R. Rowland, Christopher K. Tuggle, Jack C. M. Dekkers, Joan K. Lunney, Le Luo Guan, Paul Stothard, Graham Plastow
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0151917

Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns
Cited by: 9
Author(s): Yayoi Natsume-Kitatani, Hiroshi Mamitsuka
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-017-03478-2

Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasis
Cited by: 5
Author(s): Hong Shen, Zhongyan Lu, Zhihui Xu, Zongzhuan Shen
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0225180

Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation
Cited by: 10
Author(s): Aisling M. Redmond, Soleilmane Omarjee, Igor Chernukhin, Muriel Le Romancer, Jason S. Carroll
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.ppat.1008221

PDGFRA defines the mesenchymal stem cell Kaposi’s sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment
Cited by: 23
Author(s): Julián Naipauer, Santas Rosario, Sachin Gupta, Courtney Premer, Omayra Méndez-Solís, Mariana Schlesinger, Virginia Ponzinibbio, Vaibhav Jain, Rolf Renne, Ho Lam Chan, Lluís Morey, Daria Salyakina, Martı́n C. Abba, Siôn L. Williams, Joshua M. Hare, Pascal J. Goldschmidt‐Clermont, Enrique A. Mesri
Software Mentions: 5
Published: almost 7 years ago

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