Ecosyste.ms: Papers

10.1093/jme/tjaa151

A Low-Powered and Highly Selective Trap for Male Aedes (Diptera: Culicidae) Surveillance: The Male Aedes Sound Trap
Cited by: 9
Author(s): Kyran M. Staunton, Jacob E. Crawford, Jianyi Liu, Michael Townsend, Yu Han, Mark Desnoyer, Paul Howell, Xiang Wang, Thomas R. Burkot, Nigel Snoad, Scott A. Ritchie
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-021-07435-2

Blinatumomab-induced T cell activation at single cell transcriptome resolution
Cited by: 11
Author(s): Yi Huo, Zhonghua Sheng, Daniel Lu, Daniel C. Ellwanger, Chi-Ming Li, Oliver Homann, Songli Wang, Hong Mei Yin, Ruibao Ren
Software Mentions: 6
Published: over 3 years ago

10.1186/1752-0509-5-S2-S3

Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite
Cited by: 7
Author(s): Xi Wang, Xuegong Zhang
Software Mentions: 6
Published: almost 14 years ago

10.1128/mSystems.00329-20

Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum
Cited by: 8
Author(s): Adrián López García de Lomana, Ulrike Kusebauch, Arjun V. Raman, Min Pan, Serdar Turkarslan, Alan Péricles Rodrigues Lorenzetti, Robert L. Moritz, Nitin S. Baliga
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0132798

Partial Hepatectomy Induced Long Noncoding RNA Inhibits Hepatocyte Proliferation during Liver Regeneration
Cited by: 20
Author(s): Lulu Huang, Sagar S. Damle, Sheri Booten, Priyam Singh, Mahyar Sabripour, Jeff Hsu, Minji Jo, Melanie Katz, Andy Watt, Christopher E. Hart, Susan M. Freier, Brett P. Monia, Shuling Guo
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0149891

Identification and Characterization of msf, a Novel Virulence Factor in Haemophilus influenzae
Cited by: 15
Author(s): Jennifer M. Kress-Bennett, N. Luisa Hiller, Rory Eutsey, Evan Powell, Mark Longwell, Todd A. Hillman, Tenisha Blackwell, Barbara Byers, Joshua Chang Mell, J. Christopher Post, Fang Hu, Garth D. Ehrlich, Benjamin Janto
Software Mentions: 6
Published: over 8 years ago

10.3390/plants10061039

Comparative Analysis of Re-Annotated Genes Provides Insight into Evolutionary Divergence and Expressions of Aquaporin Family in Pepper
Cited by: 2
Author(s): Yeon Mi Lee, Geun Young Chae, Min Kyung Kim, Seungill Kim
Software Mentions: 6
Published: over 3 years ago

10.1136/jitc-2021-002856

IL-6 contributes to metastatic switch via the differentiation of monocytic-dendritic progenitors into prometastatic immune cells
Cited by: 15
Author(s): Ksenia Magidey-Klein, Tim J. Cooper, Ksenya Kveler, Rachelly Normand, Tongwu Zhang, Michael Timaner, Ziv Raviv, Brian P. James, Roi Gazit, Ze’ev Ronai, Shai S. Shen-Orr, Yuval Shaked
Software Mentions: 6
Published: over 3 years ago

10.1093/bioinformatics/btz726

bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data
Cited by: 59
Author(s): Wenhao Tang, François Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-017-3936-7

Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
Cited by: 35
Author(s): Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D. G. Jones, Matt Clark
Software Mentions: 5
Published: over 7 years ago

10.3389/fgene.2019.00958

Single-Cell Analysis of Circulating Tumor Cells: How Far Have We Come in the -Omics Era?
Cited by: 52
Author(s): Elisabetta Rossi, Rita Zamarchi
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.612670

Non-linear Normalization for Non-UMI Single Cell RNA-Seq
Cited by: 3
Author(s): Zhijin Wu, Kenong Su, Hao Wu
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2020.588041

Identification of Differential Gene Groups From Single-Cell Transcriptomes Using Network Entropy
Cited by: 3
Author(s): Yanglan Gan, Shanshan Liang, Qingting Wei, Guobing Zou
Software Mentions: 5
Published: about 4 years ago

10.1186/s40064-015-1356-1

Accurate mobile malware detection and classification in the cloud
Cited by: 26
Author(s): Xiaolei Wang, Yuexiang Yang, Yingzhi Zeng
Software Mentions: 5
Published: about 9 years ago

10.1186/s12864-020-07302-6

JOINT for large-scale single-cell RNA-sequencing analysis via soft-clustering and parallel computing
Cited by: 4
Author(s): Tao Cui, Tingting Wang
Software Mentions: 5
Published: almost 4 years ago

10.1186/1471-2164-15-555

piRNAQuest: searching the piRNAome for silencers
Cited by: 49
Author(s): Arijita Sarkar, Ranjan Kumar Maji, Sudipto Saha, Zhumur Ghosh
Software Mentions: 5
Published: over 10 years ago

10.21203/rs.3.rs-25639/v1

A potential role for AHR in SARS-CoV-2 pathology
Cited by: 12
Author(s): Federico Giovannoni, Zhaorong Li, Cybele C. Garcı́a, Francisco J. Quintana
Software Mentions: 5
Published: over 4 years ago

10.1126/sciimmunol.abe4782

Severely ill patients with COVID-19 display impaired exhaustion features in SARS-CoV-2–reactive CD8 ⁺ T cells
Cited by: 163
Author(s): Anthony Kusnadi, Ciro Ramírez-Suástegui, Vicente Fajardo, Serena Chee, Benjamin J Meckiff, Hayley Simon, Emanuela Pelosi, Grégory Seumois, Ferhat Ay, Pandurangan Vijayanand, Christian Ottensmeier
Software Mentions: 5
Published: almost 4 years ago

10.15252/msb.20209844

Integrative characterization of the near‐minimal bacterium <i>Mesoplasma florum</i>
Cited by: 8
Author(s): Dominick Matteau, Jean-Christophe Lachance, Frédéric Grenier, Samuel Gauthier, James M. Daubenspeck, Kevin Dybvig, Daniel Garneau, Thomas F. Knight, Pierre-Étienne Jacques, Sébastien Rodrigue
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0011471

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
Cited by: 263
Author(s): Elizabeth G. Wilbanks, Marc T. Facciotti
Software Mentions: 5
Published: over 14 years ago

10.1186/s13073-021-00885-z

Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis
Cited by: 24
Author(s): Sunny Z. Wu, Daniel Roden, Ghamdan Al-Eryani, Nenad Bartoniček, Kate Harvey, Aurélie Cazet, Chia-Ling Chan, Simon Junankar, Mun Hui, Ewan A. Millar, Julia Beretov, Lisa Kristina Horvath, Anthony M. Joshua, Phillip D. Stricker, James S. Wilmott, Camelia Quek, Georgina V. Long, Richard A. Scolyer, Bertrand Z. Yeung, Davendra Segara, Cindy Mak, Sanjay Warrier, Joseph E. Powell, Sandra A. O’Toole, Elgene Lim, Alexander Swarbrick
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0057170

General Patterns of Diversity in Major Marine Microeukaryote Lineages
Cited by: 51
Author(s): Massimo C. Pernice, Ramiro Logares, Laure Guillou, Ramón Massana
Software Mentions: 5
Published: over 11 years ago

10.1186/s13059-019-1922-x

DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing
Cited by: 31
Author(s): Zilu Zhou, Baocheng Xu, Andy J. Minn, Nancy R. Zhang
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13059-016-1010-4

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index
Cited by: 229
Author(s): Lan Jiang, Huidong Chen, Luca Pinello, Guo‐Cheng Yuan
Software Mentions: 5
Published: over 8 years ago

10.15252/msb.20199005

Combinatorial prediction of marker panels from single‐cell transcriptomic data
Cited by: 54
Author(s): Conor P. Delaney, Alexandra Schnell, Louis Cammarata, Aaron Yao-Smith, Aviv Regev, Vijay K. Kuchroo, Meromit Singer
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1005693

Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome
Cited by: 24
Author(s): Luke Isbel, Richa Srivastava, Harald Oey, Alex Spurling, Lucia Daxinger, Hamsa Puthalakath, Emma Whitelaw
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13059-016-0930-3

Beyond comparisons of means: understanding changes in gene expression at the single-cell level
Cited by: 89
Author(s): Catalina A. Vallejos, Sylvia Richardson, John C. Marioni
Software Mentions: 5
Published: over 8 years ago

10.1186/s12936-020-03512-1

Characterisation of plasmodial transketolases and identification of potential inhibitors: an in silico study
Cited by: 5
Author(s): Rita Afriyie Boateng, Özlem Tastan Bishop, Thommas M. Musyoka
Software Mentions: 5
Published: almost 4 years ago

10.1534/g3.115.019166

Genome-Wide Analysis of<i>Drosophila</i>RBf2 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 9 years ago

10.1371/journal.pgen.1006619

Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum
Cited by: 46
Author(s): Yi Jin Liew, Yong Li, Sebastian Baumgarten, Christian R. Voolstra, Manuel Aranda
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-015-0844-5

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
Cited by: 1,843
Author(s): Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian H. Gersuk, Alex K. Shalek, Chloe K. Slichter, Hannah W. Miller, M. Juliana McElrath, Martin Prlic, Peter S. Linsley, Raphaël Gottardo
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2164-15-1072

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column
Cited by: 18
Author(s): Satadal Chatterjee, V. Sivakamasundari, Sook Peng Yap, Petra Kraus, Vibhor Kumar, Xing Xing, Siew Lan Lim, Joel Sng, Shyam Prabhakar, Thomas Lufkin
Software Mentions: 5
Published: almost 10 years ago

10.3389/fpls.2018.00018

Genome-Wide Identification of Cyclic Nucleotide-Gated Ion Channel Gene Family in Wheat and Functional Analyses of TaCNGC14 and TaCNGC16
Cited by: 37
Author(s): Jia Guo, Md. Ashraful Islam, Haocheng Lin, Changan Ji, Yinghui Duan, Peng Liu, Qingdong Zeng, Brad Day, Zhensheng Kang, Jun Guo
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2019.02628

Strong Seasonality in Arctic Estuarine Microbial Food Webs
Cited by: 22
Author(s): Colleen T. E. Kellogg, J. W. McClelland, Kenneth H. Dunton, Byron C. Crump
Software Mentions: 5
Published: almost 5 years ago

10.1186/1471-2164-15-966

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants
Cited by: 29
Author(s): Johannes A. Hofberger, Beifei Zhou, Haibao Tang, Jonathan D. G. Jones, M. Eric Schranz
Software Mentions: 5
Published: about 10 years ago

10.1186/s12964-019-0363-1

Systematic expression analysis of ligand-receptor pairs reveals important cell-to-cell interactions inside glioma
Cited by: 31
Author(s): Dongsheng Yuan, Yiran Tao, Geng Chen, Tieliu Shi
Software Mentions: 5
Published: over 5 years ago

10.1038/s41419-021-03936-w

Valproic acid stimulates myogenesis in pluripotent stem cell-derived mesodermal progenitors in a NOTCH-dependent manner
Cited by: 9
Author(s): Natacha Breuls, Nefele Giarratana, Laura Yedigaryan, Gabriel Miró Garrido, Paolo Carai, Stéphane Heymans, Adrian Ranga, Christophe M. Deroose, Maurilio Sampaolesi
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0196987

Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel)
Cited by: 11
Author(s): Sara Rachik, Urania Christaki, Luen Luen Li, Savvas Genitsaris, Elsa Breton, Sébastien Monchy
Software Mentions: 5
Published: over 6 years ago

10.3389/fnmol.2021.712609

NMDARs Drive the Expression of Neuropsychiatric Disorder Risk Genes Within GABAergic Interneuron Subtypes in the Juvenile Brain
Cited by: 7
Author(s): Vivek Mahadevan, Apratim Mitra, Yajun Zhang, Xitong Yuan, Areg Peltekian, Ramesh Chittajallu, Caroline Esnault, Dragan Maric, C. T. Rhodes, Kenneth A. Pelkey, Ryan Dale, Timothy J. Petros, Chris J. McBain
Software Mentions: 5
Published: about 3 years ago

10.3390/ijms22020787

Full-Length Transcriptome Analysis of Four Different Tissues of Cephalotaxus oliveri
Cited by: 13
Author(s): Ziqing He, Yingjuan Su, Ting Wang
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0245324

InsectOR—Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes
Cited by: 10
Author(s): Snehal D. Karpe, Vikas Tiwari, R. Sowdhamini
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.59095

Constitutive activation of cellular immunity underlies the evolution of resistance to infection in Drosophila
Cited by: 17
Author(s): Alexandre B. Leitão, Ramesh Arunkumar, Jonathan P. Day, Emma M Geldman, Ismaël Morin-Poulard, Michèle Crozatier, Francis M. Jiggins
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.51796

A MAC2-positive progenitor-like microglial population is resistant to CSF1R inhibition in adult mouse brain
Cited by: 44
Author(s): Lihong Zhan, Li Fan, Lay Kodama, Peter Sohn, Man Ying Wong, Gergey Alzaem Mousa, Yungui Zhou, Yaqiao Li, Li Gan
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0016294

Plasmodium vivax Tryptophan-Rich Antigen PvTRAg33.5 Contains Alpha Helical Structure and Multidomain Architecture
Cited by: 12
Author(s): Hema Bora, Satpal Garg, Priyankar Sen, Deepak Kumar, Punit Kaur, Rizwan Hasan Khan, Yagya D. Sharma
Software Mentions: 5
Published: almost 14 years ago

10.1186/1471-2229-12-106

Genome-wide analysis of the MYB transcription factor superfamily in soybean
Cited by: 320
Author(s): Hongwu Du, Sisi Yang, Zhe Liang, Bo-Run Feng, Lei Liu, Yubi Huang, Yixiong Tang
Software Mentions: 5
Published: over 12 years ago

10.3389/fgene.2021.648898

A Novel Method to Identify the Differences Between Two Single Cell Groups at Single Gene, Gene Pair, and Gene Module Levels
Cited by: 1
Author(s): Lingyu Cui, Bo Wang, Caixia Ren, Ailan Wang, Hong An, Wei Liang
Software Mentions: 5
Published: over 3 years ago

10.1038/s41396-020-00885-8

Comparative genomics reveals new functional insights in uncultured MAST species
Cited by: 17
Author(s): Aurélie Labarre, Lior David, Francisco Latorre, Guy Leonard, François Bucchini, Aleix Obiol, Corinne Cruaud, Michael E. Sieracki, Olivier Jaillon, Patrick Wincker, Klaas Vandepoele, Ramiro Logares, Ramón Massana
Software Mentions: 5
Published: almost 4 years ago

10.3390/plants9091176

Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling
Cited by: 19
Author(s): Ivan Tsers, Vladimir Gorshkov, Natalia Gogoleva, Olga Parfirova, Olga Petrova, Alexander A. Kamnev
Software Mentions: 5
Published: about 4 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: about 10 years ago

10.1038/s41598-020-74598-5

Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19
Cited by: 36
Author(s): Anna A. Valyaeva, Anastasia A. Zharikova, Artem S. Kasianov, Yegor S. Vassetzky, Eugene V. Sheval
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-021-81381-7

Towards validation of combined-accelerated stress testing through failure analysis of polyamide-based photovoltaic backsheets
Cited by: 16
Author(s): Michael Owen‐Bellini, Stephanie L. Moffitt, Archana Sinha, Ashley Maes, Joseph J. Meert, Todd Karin, Chris Takacs, Donald R. Jenket, James Yuan Hartley, David C. Miller, Peter Hacke, Laura T. Schelhas
Software Mentions: 4
Published: almost 4 years ago

10.1186/1741-7015-11-163

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease
Cited by: 56
Author(s): Adam E. Handel, Geir Kjetil Sandve, Giulio Disanto, Antonio J. Berlanga‐Taylor, Giuseppe Gallone, Heather Hanwell, Finn Drabløs, Gavin Giovannoni, George C. Ebers, Sreeram Ramagopalan
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-020-58779-w

A Group of Olfactory Receptor Alleles that Encode Full Length Proteins are Down-Regulated as Olfactory Sensory Neurons Mature
Cited by: 1
Author(s): Richard C. Krolewski, Brian M. Lin, Samuel D. Stampfer, Adam Packard, James E. Schwob
Software Mentions: 4
Published: almost 5 years ago

10.3389/fcvm.2021.628885

Single-Cell Transcriptome Analysis Decipher New Potential Regulation Mechanism of ACE2 and NPs Signaling Among Heart Failure Patients Infected With SARS-CoV-2
Cited by: 13
Author(s): Mengqiu Ma, Yanhua Xu, Yang Su, Sang‐Bing Ong, Xingdong Hu, Min Chai, Maojun Zhao, Hong Li, Xiaojuan Fan, Yingjie Chen, Dan Xu, Xiaojiang Xu
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-8-265

Inference of transcriptional regulation using gene expression data from the bovine and human genomes
Cited by: 8
Author(s): Amonida Zadissa, John C. McEwan, Chris M. Brown
Software Mentions: 4
Published: over 17 years ago

10.3389/fcell.2018.00108

Experimental Considerations for Single-Cell RNA Sequencing Approaches
Cited by: 125
Author(s): Quy Nguyen, Nicholas Pervolarakis, Kevin Nee, Kai Kessenbrock
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2105-13-317

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs
Cited by: 18
Author(s): Phillip Seitzer, Elizabeth G. Wilbanks, David Larsen, Marc T. Facciotti
Software Mentions: 4
Published: almost 12 years ago

10.1038/s41598-017-11804-x

Phylogenetic implications of nuclear rRNA IGS variation in Stipa L. (Poaceae)
Cited by: 21
Author(s): Katarzyna Krawczyk, Marcin Nobis, Arkadiusz Nowak, Monika Szczecińska, Jakub Sawicki
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-31371-z

Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440
Cited by: 37
Author(s): Esther Blanco-Romero, Miguel Redondo‐Nieto, Francisco Martínez‐Granero, Daniel Garrido‐Sanz, Marı́a Isabel Ramos-González, Marta Martín, Rafael Rivilla
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2164-6-68

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals
Cited by: 45
Author(s): Sven Nelander, Erik Larsson, Erik Kristiansson, Robert Månsson, Olle Nerman, Mikael Sigvardsson, Petter Mostad, Per Lindahl
Software Mentions: 4
Published: over 19 years ago

10.1038/s42003-020-1028-8

Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures
Cited by: 31
Author(s): Åsa Wallén-Mackenzie, Sylvie Dumas, Maria Papathanou, Mihaela M. Martis, Bianca Vlcek, Niclas König, Åsa K. Björklund
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.ppat.1009665

Single-cell RNA-seq landscape midbrain cell responses to red spotted grouper nervous necrosis virus infection
Cited by: 17
Author(s): Qing Wang, Cheng Yuan Peng, Min Yang, Fengqi Huang, Xuzhuo Duan, Shaowen Wang, Huitao Cheng, Huirong Yang, Haifeng Zhao, Qiwei Qin
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-021-07679-y

Global investigation of estrogen-responsive genes regulating lipid metabolism in the liver of laying hens
Cited by: 14
Author(s): Jingyao Ren, Weihua Tian, Keren Jiang, Zhang Wang, Dandan Wang, Zhuanjian Li, Fengbin Yan, Yanbin Wang, Yadong Tian, Kepeng Ou, Hongjun Wang, Xiangtao Kang, Hong Li, Xiaojun Liu
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2105-12-139

PeakRanger: A cloud-enabled peak caller for ChIP-seq data
Cited by: 146
Author(s): Xin Feng, Robert L. Grossman, Lincoln Stein
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.ppat.1008671

Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection
Cited by: 44
Author(s): Jiayi Sun, J. Cristobal Vera, Jenny Drnevich, Yen Ting Lin, Ruian Ke, Christopher B. Brooke
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.ppat.1009804

Identification of immune correlates of fatal outcomes in critically ill COVID-19 patients
Cited by: 34
Author(s): Jonathan Youngs, Nicholas M. Provine, Nicholas Lim, Hannah Sharpe, Ali Amini, Yi‐Ling Chen, Jian Luo, Matthew Edmans, Panagiota Zacharopoulou, Wentao Chen, Oliver Sampson, Robert S Paton, William J Hurt, David A. Duncan, Anna L McNaughton, Vincent N. Miao, Susannah Leaver, Duncan Wyncoll, Jonathan Ball, P Hopkins, Donal Skelly, Eleanor Barnes, Susanna Dunachie, Graham Ogg, Teresa Lambe, Ian D. Pavord, Alex K. Shalek, Craig Thompson, Luzheng Xue, Derek C. Macallan, Philip Goulder, Paul Klenerman, Tihana Bicanic
Software Mentions: 4
Published: about 3 years ago

10.1093/jxb/eru119

Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences
Cited by: 81
Author(s): Salma Balazadeh, Jörg Schildhauer, Wagner L. Araújo, Sergi Munné‐Bosch, Alisdair R. Fernie, Sebastian Proost, Klaus Humbeck, Bernd Mueller‐Roeber
Software Mentions: 4
Published: over 10 years ago

10.1186/s13619-021-00083-7

Defining cell identity beyond the premise of differential gene expression
Cited by: 2
Author(s): Hani Jieun Kim, Patrick Tam, Pengyi Yang
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.ppat.1000846

SREB, a GATA Transcription Factor That Directs Disparate Fates in Blastomyces dermatitidis Including Morphogenesis and Siderophore Biosynthesis
Cited by: 57
Author(s): Gregory M. Gauthier, Thomas D. Sullivan, Sergio S. Gallardo, T. Tristan Brandhorst, Amber J. Vanden Wymelenberg, Christina A. Cuomo, Garret Suen, Cameron R. Currie, Bruce S. Klein
Software Mentions: 4
Published: over 14 years ago

10.1038/s41421-021-00271-4

Single-cell analysis of pancreatic ductal adenocarcinoma identifies a novel fibroblast subtype associated with poor prognosis but better immunotherapy response
Cited by: 90
Author(s): Yu Wang, Yongfeng Liang, Haiyan Xu, Xiao Zhang, Tiebo Mao, Jiujie Cui, Jiyong Yao, Yongchao Wang, Feng Jiao, Xiuying Xiao, Jiong Hu, Qing Xia, Xiaofei Zhang, Xujun Wang, Yongwei Sun, Deliang Fu, Lei Shen, Ximing Xu, Jing Xue, Liwei Wang
Software Mentions: 4
Published: over 3 years ago

10.1038/s41422-020-00445-x

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing
Cited by: 88
Author(s): Luca Mazzurana, Paulo Czarnewski, Viktor Jönsson, Leif Wigge, Markus Ringnér, Teresa C. Williams, Avinash Ravindran, Åsa K. Björklund, Jesper Säfholm, Gunnar Nilsson, Sven Erik Dahlén, Ann Charlotte Orre, Mamdoh Al‐Ameri, Charlotte Höög, Charlotte Hedin, Sylwester Szczegielniak, Sven Almér, Jenny Mjösberg
Software Mentions: 4
Published: almost 4 years ago

10.1007/s00401-021-02322-2

Altered oligodendroglia and astroglia in chronic traumatic encephalopathy
Cited by: 25
Author(s): Kevin Blake Chancellor, Sarah E. Chancellor, Joseph E. Duke-Cohan, Bertrand R. Huber, Thor D. Stein, Victor E. Alvarez, Benjamin W. Okaty, Susan M. Dymecki, Ann C. McKee
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.ppat.1004959

Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis
Cited by: 16
Author(s): Amber J. Marty, Aimee Teo Broman, Robert Żarnowski, Teigan G. Dwyer, Laura M. Bond, Anissa Lounès-Hadj Sahraoui, Joël Fontaine, James M. Ntambi, Sündüz Keleş, Christina Kendziorski, Gregory M. Gauthier
Software Mentions: 4
Published: over 9 years ago

10.1186/s13059-021-02438-4

CoCoA-diff: counterfactual inference for single-cell gene expression analysis
Cited by: 6
Author(s): Yongjin Park, M Kellis
Software Mentions: 4
Published: over 3 years ago

10.1186/s12915-018-0585-5

Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions
Cited by: 8
Author(s): Xinyi Yang, Martin Vingron
Software Mentions: 4
Published: about 6 years ago

10.1099/mic.0.034538-0

Cholesterol utilization in mycobacteria is controlled by two TetR-type transcriptional regulators: kstR and kstR2
Cited by: 143
Author(s): Sharon L. Kendall, Philippa Burgess, Ricardo Balhana, Mike Withers, Annemieke Ten Bokum, J.S. Lott, Chen Gao, Iria Uhia-Castro, Neil G. Stoker
Software Mentions: 4
Published: over 14 years ago

10.1186/s12864-020-6687-9

Stable intronic sequence RNAs (sisRNAs) are selected regions in introns with distinct properties
Cited by: 2
Author(s): Jing Jin, Ximiao He, Elena M. Silva
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0219823

Structures of TOG1 and TOG2 from the human microtubule dynamics regulator CLASP1
Cited by: 11
Author(s): Jonathan B. Leano, Kevin C. Slep
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0017080

The Light Responsive Transcriptome of the Zebrafish: Function and Regulation
Cited by: 92
Author(s): Benjamin D. Weger, Meltem Sahinbas, G. Otto, Philipp Mracek, Olivier Armant, Dirk Dolle, Kajori Lahiri, Daniela Vallone, Laurence Ettwiller, Robert Geisler, Nicholas S. Foulkes, Thomas Dickmeis
Software Mentions: 4
Published: almost 14 years ago

10.1371/journal.pone.0041374

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome
Cited by: 121
Author(s): Hebing Chen, Yao Tian, Wenjie Shu, Xiaochen Bo, Shengqi Wang
Software Mentions: 4
Published: over 12 years ago

10.1186/s12859-019-2977-0

RESCUE: imputing dropout events in single-cell RNA-sequencing data
Cited by: 26
Author(s): Sam Tracy, Guo‐Cheng Yuan, Ruben Dries
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.0010044

Positive Selection of Iris, a Retroviral Envelope–Derived Host Gene in Drosophila melanogaster
Cited by: 61
Author(s): Harmit S. Malik, Steven Henikoff
Software Mentions: 4
Published: about 19 years ago

10.1186/1475-2859-6-29

Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1
Cited by: 107
Author(s): L.M. Serrano, Douwe Molenaar, Michiel Wels, Bas Teusink, Peter A. Bron, Willem M. de Vos, Eddy J. Smid
Software Mentions: 4
Published: about 17 years ago

10.1371/journal.pgen.1009669

Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids
Cited by: 5
Author(s): Romain Durand, Florence Deschênes, Vincent Burrus
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-018-1406-4

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
Cited by: 159
Author(s): Koen Van den Berge, Fanny Perraudeau, Charlotte Soneson, Michael I. Love, Davide Risso, Jean-Philippe Vert, Mark D. Robinson, Sandrine Dudoit
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2017.00819

Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach
Cited by: 37
Author(s): Mohd Aamir, Vinay Kumar Singh, Mukesh Meena, Ram Sanmukh Upadhyay, Vijai Kumar Gupta, Surendra Singh
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2015.00718

A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones
Cited by: 20
Author(s): Itziar Frades, Kibrom B. Abreha, Estelle Proux‐Wéra, Åsa Lankinen, Erik Andréasson, Erik Alexandersson
Software Mentions: 4
Published: about 9 years ago

10.3389/fphys.2017.00734

Distinct Subfamilies of Odorant Binding Proteins in Locust (Orthoptera, Acrididae): Molecular Evolution, Structural Variation, and Sensilla-Specific Expression
Cited by: 15
Author(s): Xingcong Jiang, Jürgen Krieger, Heinz Breer, Pablo Pregitzer
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2018.03259

Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing
Cited by: 10
Author(s): Feipeng Wang, Yuyuan Xie, Wenxue Wu, Ping Sun, Lei Wang, Bangqin Huang
Software Mentions: 4
Published: almost 6 years ago

10.1155/2017/8932583

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos
Cited by: 9
Author(s): Wenqing Jean Lee, Satadal Chatterjee, Sook Peng Yap, Siew Lan Lim, Xing Xing, Petra Kraus, Wenjie Sun, Xiaoming Hu, V. Sivakamasundari, Hsiao Yun Chan, Prasanna R. Kolatkar, Shyam Prabhakar, Thomas Lufkin
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2018.03183

Iron Regulation in Clostridioides difficile
Cited by: 42
Author(s): Mareike Berges, Annika-Marisa Michel, Christian Lassek, Aaron M. Nuss, Michael Beckstette, Petra Dersch, Katharina Riedel, Susanne Sievers, Dörte Becher, Andreas Otto, Sandra Maaß, Manfred Rohde, Denitsa Eckweiler, José Manuel Borrero‐de Acuña, Martina Jahn, Meina Neumann‐Schaal, Dieter Jahn
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-018-2217-z

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data
Cited by: 175
Author(s): Shuonan Chen, Jessica C. Mar
Software Mentions: 4
Published: over 6 years ago

10.1038/s41419-018-0841-1

The detrimental effects of glucocorticoids exposure during pregnancy on offspring’s cardiac functions mediated by hypermethylation of bone morphogenetic protein-4
Cited by: 13
Author(s): Jun Peng, Yuhao Zhou, Zhiyu Zhang, Zhiming Wang, Ling-Tong Gao, Xiao Zhang, Fang Zhou, Guangyao Li, Huaiyan Chen, Hongxing Yang, Lu Gao
Software Mentions: 4
Published: over 6 years ago

10.3389/fmed.2018.00034

Beyond Enumeration: Functional and Computational Analysis of Circulating Tumor Cells to Investigate Cancer Metastasis
Cited by: 10
Author(s): Francesc Castro-Giner, Manuel C. Scheidmann, Nicola Aceto
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12859-019-2732-6

The cis-trans binding strength defined by motif frequencies facilitates statistical inference of transcriptional regulation
Cited by: 4
Author(s): Yance Feng, Sheng Zhang, Liang Li, Lei M. Li
Software Mentions: 4
Published: over 5 years ago

10.6026/97320630014123

Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice from co-expressed gene interaction networks
Cited by: 15
Author(s): Pragya Mishra, Nisha Singh, Ajay Jain, Neha Jain, S. R. Mishra, Sandhya Kp, Rai
Software Mentions: 4
Published: over 6 years ago

10.1016/j.cell.2020.10.002

Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics
Cited by: 57
Author(s): Dylan Kotliar, Aaron E. Lin, James Logue, Travis Hughes, Nadine M. Khoury, Siddharth S. Raju, Marc H. Wadsworth, Han Chen, Jonathan R. Kurtz, Bonnie Dighero-Kemp, Zach B. Bjornson, Nilanjan Mukherjee, Brian Sellers, Nancy Tran, Matthew R. Bauer, Gordon Adams, Ricky Adams, John L. Rinn, Marta Melé, Stephen F. Schaffner, Garry P. Nolan, Kayla G. Barnes, Lisa E. Hensley, David R. McIlwain, Alex K. Shalek, Pardis C. Sabeti, Richard S. Bennett
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0181671

Broad-range lytic bacteriophages that kill Staphylococcus aureus local field strains
Cited by: 36
Author(s): Virginia Abatángelo, Natalia Peressutti Bacci, Carina Andrea Boncompain, Ariel Fernando Amadío, Soledad Telma Carrasco, Cristian Alejandro Suárez, Héctor Ricardo Morbidoni
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-019-5570-z

Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica
Cited by: 18
Author(s): Sarah Naiyer, Devinder Kaur, Jamaluddin Ahamad, Sanjai Singh, Yatendra Pratap Singh, Vivek Thakur, Alok Bhattacharya, Sudha Bhattacharya
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers11101533

17β-Estradiol Activates HSF1 via MAPK Signaling in ERα-Positive Breast Cancer Cells
Cited by: 22
Author(s): Natalia Vydra, Patryk Janus, Agnieszka Toma-Jonik, Tomasz Stokowy, Katarzyna Mrowiec, Joanna Korfanty, Anna Długajczyk, Bartosz Wojtaś, Bartłomiej Gielniewski, Wiesława Widłak
Software Mentions: 4
Published: about 5 years ago