cran: SAM | Projects | Ecosyste.ms: Papers

10.3389/fgene.2018.00250

GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data
Cited by: 15
Author(s): Mayur Divate, Edwin Cheung
Software Mentions: 7
Published: over 6 years ago

Agile parallel bioinformatics workflow management using Pwrake
Cited by: 20
Author(s): Hiroyuki Mishima, Kensaku Sasaki, M. Tanaka, Osamu Tatebe, Koh-ichiro Yoshiura
Software Mentions: 7
Published: about 13 years ago

10.1186/s12859-018-2445-2

Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance
Cited by: 44
Author(s): Alyssa Baccarella, Claire Williams, Jay Z. Parrish, Charles C. Kim
Software Mentions: 7
Published: about 6 years ago

10.7554/eLife.45403

The dynamic conformational landscape of the protein methyltransferase SETD8
Cited by: 37
Author(s): Shi Chen, Rafal Wiewiora, Fanwang Meng, Nicolas Babault, Anqi Ma, Wenyu Yu, Kun Qian, Hao Hu, Hua Zou, Junyi Wang, Shijie Fan, Gil Blum, Fábio Pittella Silva, Kyle A. Beauchamp, W. Tempel, Hualiang Jiang, Kaixian Chen, R.J. Skene, Y. George Zheng, Peter J. Brown, Jian Jin, Cheng Luo, John D. Chodera, Minkui Luo
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-019-6155-6

A framework using topological pathways for deeper analysis of transcriptome data
Cited by: 0
Author(s): Yue Zhao, Stephanie Piekos, Tham H. Hoang, Dong-Guk Shin
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0183933

Tensor decomposition-based unsupervised feature extraction applied to matrix products for multi-view data processing
Cited by: 24
Author(s): Y-h. Taguchi
Software Mentions: 7
Published: about 7 years ago

10.1186/s12859-021-03986-z

MSIFinder: a python package for detecting MSI status using random forest classifier
Cited by: 6
Author(s): Tao Zhou, Libin Chen, Jing Guo, Mengmeng Zhang, Yanrui Zhang, Shanbo Cao, Li Feng, Haijun Wang
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-9-46

EzArray: A web-based highly automated Affymetrix expression array data management and analysis system
Cited by: 16
Author(s): Yuerong Zhu, Yuelin J. Zhu, Wei Xu
Software Mentions: 7
Published: almost 17 years ago

10.3389/fgene.2020.00082

SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes
Cited by: 6
Author(s): Yue Xing, Alan R. Dabney, Xiao Li, Guosong Wang, C. A. Gill, Claudio Casola
Software Mentions: 7
Published: over 4 years ago

10.1186/s40168-017-0387-y

In-depth resistome analysis by targeted metagenomics
Cited by: 103
Author(s): Val F. Lanza, Fernando Baquero, José Luis Martínez, Ricardo Ramos-Ruíz, Bruno González‐Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, S. Dusko Ehrlich, Sean Kennedy, Étienne Ruppé, Willem van Schaik, Rob J. L. Willems, Fernando de la Cruz, Teresa M. Coque
Software Mentions: 7
Published: almost 7 years ago

10.1186/1471-2164-12-227

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing
Cited by: 144
Author(s): Susanne U. Franssen, Ranjit Shrestha, Andrea Bräutigam, Erich Bornberg‐Bauer, Andreas Weber
Software Mentions: 7
Published: over 13 years ago

10.1038/s41597-019-0261-9

A 2D hyperspectral library of mineral reflectance, from 900 to 2500 nm
Cited by: 7
Author(s): Laurent Fasnacht, Marie-Louise Vogt, Philippe Renard, Philip Brunner
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0025279

GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences
Cited by: 62
Author(s): Jason S. Cumbie, Jeffrey A. Kimbrel, Yanming Di, Daniel W. Schafer, Larry J. Wilhelm, Samuel E. Fox, Christopher Sullivan, Aron D. Curzon, James C. Carrington, Todd C. Mockler, Jeff H. Chang
Software Mentions: 6
Published: about 13 years ago

10.1371/journal.pgen.1008905

Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase
Cited by: 5
Author(s): Richard Silva, María Ascensión Villar-Fernández, Gerben Vader
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.11491

Localized JNK signaling regulates organ size during development
Cited by: 37
Author(s): Helen Rankin Willsey, Xiaoyan Zheng, José Carlos Pastor-Pareja, A. Jeremy Willsey, Philip A. Beachy, Tian Xu
Software Mentions: 6
Published: over 8 years ago

10.18632/oncotarget.22942

S-adenosyl-methionine (SAM) alters the transcriptome and methylome and specifically blocks growth and invasiveness of liver cancer cells
Cited by: 33
Author(s): Yan Wang, Zhong Sheng Sun, Moshe Szyf
Software Mentions: 6
Published: almost 7 years ago

10.7554/eLife.53933

Heterogeneous T cell motility behaviors emerge from a coupling between speed and turning in vivo
Cited by: 33
Author(s): Elizabeth R. Jerison, Stephen R. Quake
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0123380

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

10.1007/s12275-020-9536-2

STATR: A simple analysis pipeline of Ribo-Seq in bacteria
Cited by: 7
Author(s): Donghui Choe, Bernhard Ø. Palsson, Byung-Kwan Cho
Software Mentions: 6
Published: almost 5 years ago

10.1186/1471-2105-10-201

A-MADMAN: Annotation-based microarray data meta-analysis tool
Cited by: 35
Author(s): Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi
Software Mentions: 6
Published: over 15 years ago

10.1186/1471-2105-12-92

Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies
Cited by: 5
Author(s): Paolo Martini, Davide Risso, Gabriele Sales, Chiara Romualdi, Gerolamo Lanfranchi, Stefano Cagnin
Software Mentions: 6
Published: over 13 years ago

10.1038/s41598-020-73376-7

RNA oxidation in chromatin modification and DNA-damage response following exposure to formaldehyde
Cited by: 17
Author(s): Juan C. Gonzalez-Rivera, Mark W. Sherman, Dongyu Wang, Jamie C. L. Chuvalo-Abraham, Lea Hildebrandt Ruiz, Lydia M. Contreras
Software Mentions: 6
Published: about 4 years ago

10.1038/srep32753

HIPSTR and thousands of lncRNAs are heterogeneously expressed in human embryos, primordial germ cells and stable cell lines
Cited by: 35
Author(s): Dinar Yunusov, Letícia Anderson, Luis DaSilva, Joanna Wysocka, Toshihiko Ezashi, R. M. Roberts, Sérgio Verjovski-Almeida
Software Mentions: 6
Published: about 8 years ago

10.1186/s12859-015-0664-3

Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications
Cited by: 5
Author(s): Fang Yu, Ming Hui Chen, Lynn Kuo, Heather Talbott, John S. Davis
Software Mentions: 6
Published: over 9 years ago

10.1186/1471-2105-11-279

Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver
Cited by: 12
Author(s): Tung Nguyen, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis
Software Mentions: 6
Published: over 14 years ago

10.1371/journal.pone.0072614

DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster
Cited by: 46
Author(s): Ram Vinay Pandey, Christian Schlötterer
Software Mentions: 6
Published: about 11 years ago

10.1038/s41598-020-74567-y

Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction
Cited by: 11
Author(s): Tong Li, Po-Yen Wu, John H. Phan, Hamid R Hassazadeh, Weida Tong, May D. Wang
Software Mentions: 6
Published: about 4 years ago

10.1186/1477-5956-8-66

A comparison of imputation procedures and statistical tests for the analysis of two-dimensional electrophoresis data
Cited by: 7
Author(s): Jeffrey C. Miecznikowski, Srinivasan Damodaran, Kimberly F. Sellers, Richard A. Rabin
Software Mentions: 6
Published: almost 15 years ago

10.3390/genes10100734

Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James)
Cited by: 4
Author(s): Bharti Sharma, Timothy A. Batz, Rakesh Kaundal, Elena M. Kramer, Uriah R. Sanders, Valerie J. Mellano, Naveen Duhan, Rousselene B. Larson
Software Mentions: 6
Published: about 5 years ago

10.3390/genes11060655

Transcriptional Basis for Differential Thermosensitivity of Seedlings of Various Tomato Genotypes
Cited by: 5
Author(s): Yangjie Hu, Sotirios Fragkostefanakis, Enrico Schleiff, Stefan Simm
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-020-07013-y

Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework
Cited by: 3
Author(s): Tanveer Ahmad, Nauman Ahmed, Zaid Al-Ars, H. Peter Hofstee
Software Mentions: 6
Published: about 4 years ago

10.3389/fmicb.2018.01888

Infection-Induced Changes Within the Endocytic Recycling Compartment Suggest a Roadmap of Human Cytomegalovirus Egress
Cited by: 16
Author(s): William L. Close, James Glassbrook, Stephen J. Gurczynski, Philip E. Pellett
Software Mentions: 6
Published: over 6 years ago

10.1186/s40168-021-01136-4

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes
Cited by: 24
Author(s): Chhedi Lal Gupta, Shlomo E. Blum, Karuppasamy Kattusamy, Tali Daniel, S. Druyan, Roni Shapira, O. Krifucks, Yan Zhu, Xinyuan Zhou, Jian‐Qiang Su, Eddie Cytryn
Software Mentions: 6
Published: about 3 years ago

10.1534/g3.117.300152

Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (<i>Phylloscopus collybita abietinus/P. tristis</i>)
Cited by: 4
Author(s): Venkat Talla, Faheema Kalsoom, Daria Shipilina, И. М. Марова, Niclas Backström
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0015581

Therapeutic Implications of GIPC1 Silencing in Cancer
Cited by: 21
Author(s): Thomas Chittenden, Jane Pak, Renee Rubio, Hai‐Ling Margaret Cheng, Kristina M. Holton, Niall Prendergast, Vladimir Glinskii, Yi Cai, Aedín C. Culhane, Stefan Bentink, Mathew Schwede, Jessica C. Mar, Eleanor Howe, Martin J. Aryee, Răzvan Sultana, Anthony A. Lanahan, Jennifer Taylor, Chris Holmes, William C. Hahn, Jean J. Zhao, J. Dirk Iglehart, John Quackenbush
Software Mentions: 6
Published: almost 14 years ago

10.1038/sdata.2016.8

Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice
Cited by: 8
Author(s): Xing Tang, Huayang Liu, Arunima Srivastava, Thierry Pécot, Zhong Chen, Qianben Wang, Kun Huang, Maria Teresa Sáenz-Robles, Paul G. Cantalupo, James M. Pipas, Gustavo Leone
Software Mentions: 6
Published: almost 9 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 5 years ago

10.3389/fgene.2021.647653

DysPIA: A Novel Dysregulated Pathway Identification Analysis Method
Cited by: 1
Author(s): Limei Wang, Weixin Xie, Kongning Li, Zhenzhen Wang, Xia Li, Weixing Feng, Li Jin
Software Mentions: 6
Published: over 3 years ago

10.1111/febs.13690

Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8-demethyl-8-amino-<scp>d</scp> -riboflavin to the antibiotic roseoflavin
Cited by: 13
Author(s): Chanakan Tongsook, M. Uhl, Frank Jankowitsch, Matthias Mack, Karl Gruber, Peter Macheroux
Software Mentions: 6
Published: over 8 years ago

10.3389/fvets.2021.733357

Chytridiomycosis Outbreak in a Chilean Giant Frog (Calyptocephalella gayi) Captive Breeding Program: Genomic Characterization and Pathological Findings
Cited by: 5
Author(s): Mario Alvarado‐Rybak, Paz Acuña, Alexandra Peñafiel‐Ricaurte, Thomas R. Sewell, Simon J. O’Hanlon, Matthew C. Fisher, Andrés Valenzuela‐Sánchez, Andrew A. Cunningham, Claudio Soto‐Azat
Software Mentions: 6
Published: about 3 years ago

10.1186/s12862-020-01679-4

Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species
Cited by: 9
Author(s): Erica S. Nielsen, Romina Henriques, Maria Beger, Robert J. Toonen, Sophie von der Heyden
Software Mentions: 6
Published: about 4 years ago

10.12688/f1000research.28608.2

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
Cited by: 6
Author(s): Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø. Arntzen, Benoît J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 6
Published: over 3 years ago

10.1186/s13072-018-0250-9

Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infection
Cited by: 29
Author(s): José Luis Ruiz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Jean-Bosco Ouédraogo, Victor G. Corcés, Elena Gómez-Díaz
Software Mentions: 6
Published: almost 6 years ago

10.12688/f1000research.6157.2

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines
Cited by: 21
Author(s): Michael T. Wolfinger, Jörg Fallmann, Florian Eggenhofer, Fabian Amman
Software Mentions: 6
Published: over 9 years ago

10.3390/genes11121465

Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining
Cited by: 2
Author(s): Giacomo Mutti, Alessandro Raveane, Andrea Pagano, Francesco Bertolini, Ornella Semino, Alma Balestrazzi, Anca Macovei
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.ppat.1008754

JNK pathway restricts DENV2, ZIKV and CHIKV infection by activating complement and apoptosis in mosquito salivary glands
Cited by: 37
Author(s): Avisha Chowdhury, Cassandra M. Modahl, Siok Thing Tan, Benjamin Wong Wei Xiang, Dorothée Missé, Thomas Vial, R. Manjunatha Kini, Julien Pompon
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0116095

ICan: An Integrated Co-Alteration Network to Identify Ovarian Cancer-Related Genes
Cited by: 9
Author(s): Yuanshuai Zhou, Yongjing Liu, Kening Li, Rui Zhang, Fujun Qiu, Ning Zhao, Yan Xu
Software Mentions: 6
Published: over 9 years ago

10.1186/2045-9769-3-1

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

10.1186/s12859-016-1195-2

A fuzzy method for RNA-Seq differential expression analysis in presence of multireads
Cited by: 16
Author(s): Arianna Consiglio, Corrado Mencar, Giorgio Grillo, Flaviana Marzano, Mariano Francesco Caratozzolo, Sabino Liuni
Software Mentions: 6
Published: about 8 years ago

10.1186/s12870-017-1070-y

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions
Cited by: 12
Author(s): Martin Schmidt, Michiel Van Bel, Magdalena Wołoszyńska, Bram Slabbinck, Cindy Martens, Marc De Block, Frederik Coppens, Mieke Van Lijsebettens
Software Mentions: 6
Published: over 7 years ago

10.15252/msb.20156520

Environment‐induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children
Cited by: 93
Author(s): Tobias Bauer, Saskia Trump, Naveed Ishaque, Loreen Thürmann, Lei Gu, Mario Bauer, Matthias Bieg, Zuguang Gu, Dieter Weichenhan, Jan‐Philipp Mallm, Stefan Röder, Gunda Herberth, Eiko Takada, Oliver Mücke, Marcus Winter, Kristin M. Junge, Konrad Grützmann, Ulrike Rolle-Kampczyk, Qi Wang, Christian Lawerenz, Michael Borte, Tobias Polte, Matthias Schlesner, Michaela Schanné, Stefan Wiemann, Christina Geörg, Hendrik G. Stunnenberg, Christoph Plass, Karsten Rippe, Junichiro Mizuguchi, Carl Herrmann, Roland Eils, Irina Lehmann
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0190279

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment
Cited by: 12
Author(s): Sven Warris, N. Roshan N. Timal, Marcel Kempenaar, Arne M. Poortinga, Henri van de Geest, Ana Lucia Vărbănescu, Jan-Peter Nap
Software Mentions: 6
Published: almost 7 years ago

10.1038/sdata.2016.25

Extensive sequencing of seven human genomes to characterize benchmark reference materials
Cited by: 535
Author(s): Justin M. Zook, David Catoe, Jennifer McDaniel, Lindsay K. Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E. Mason, Noah Alexander, Elizabeth Hénaff, Alexa B. R. McIntyre, Dhruva Chandramohan, Feng Chen, Erich B. Jaeger, Ali Moshrefi, Khoa Pham, William Stedman, Tiffany Y. Liang, Michael Saghbini, Željko Džakula, Alex Hastie, Han Cao, Gintaras Deikus, Eric E. Schadt, Robert Sebra, Ali Kashif Bashir, Rebecca Truty, Christopher Chang, Natali Gulbahce, Keyan Zhao, Srinka Ghosh, Fiona Hyland, Yutao Fu, Mark Chaisson, Chunlin Xiao, Jonathan Trow, Stephen T. Sherry, Alexander Wait Zaranek, Madeleine Ball, Jason Bobe, Preston W. Estep, George M. Church, Patrick Marks, Sofia Kyriazopoulou-Panagiotopoulou, Grace Zheng, Michael Schnall-Levin, Heather Ordonez, Patrice A Mudivarti, Kristina Giorda, Ying Sheng, Karoline Bjarnesdatter Rypdal, Marc Salit
Software Mentions: 6
Published: over 8 years ago

10.1186/s12859-018-2437-2

Adaptively capturing the heterogeneity of expression for cancer biomarker identification
Cited by: 1
Author(s): Xueping Xie, Yufeng Xie, Yitong Liu, Hongqiang Wang
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0164542

IGSA: Individual Gene Sets Analysis, including Enrichment and Clustering
Cited by: 3
Author(s): Lingxiang Wu, Xiujie Chen, Denan Zhang, Wubing Zhang, Lei Liu, Hongzhe Ma, Jingbo Yang, Hongbo Xie, Bo Liu, Qing Jin
Software Mentions: 6
Published: about 8 years ago

10.3390/ijms21249622

Novel Liver X Receptor Ligand GAC0001E5 Disrupts Glutamine Metabolism and Induces Oxidative Stress in Pancreatic Cancer Cells
Cited by: 7
Author(s): Shivangi Srivastava, Scott Widmann, Charles Ho, Donovan Nguyen, Alexis Nguyen, Asitha Premaratne, Jan‐Åke Gustafsson, Chin-Yo Lin
Software Mentions: 6
Published: almost 4 years ago

10.1101/2020.07.19.210955

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

10.1186/1745-6150-7-44

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods
Cited by: 21
Author(s): Frank Emmert‐Streib, Shailesh Tripathi, Ricardo de Matos Simoes
Software Mentions: 6
Published: almost 13 years ago

10.1371/journal.pone.0147426

Transcriptomic Profile of Whole Blood Cells from Elderly Subjects Fed Probiotic Bacteria Lactobacillus rhamnosus GG ATCC 53103 (LGG) in a Phase I Open Label Study
Cited by: 16
Author(s): Gloria Solano‐Aguilar, Aleksey Molokin, Christine Botelho, Anne‐Maria Fiorino, Bryan T. Vinyard, Robert Li, Celine Chen, Joseph F. Urban, Harry Dawson, Irina Andreyeva, Miriam Haverkamp, Patricia L. Hibberd
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pone.0251354

Altering mammalian transcription networking with ADAADi: An inhibitor of ATP-dependent chromatin remodeling
Cited by: 3
Author(s): Ramalingam Radhakrishnan, Upasana Bedi Chanana, Saddam Hussain, Soni Sharma, Kaveri Goel, Deepa Bisht, Ketki Patne, Pynskhem Bok Swer, Joel W. Hockensmith, Rohini Muthuswami
Software Mentions: 6
Published: over 3 years ago

10.15252/embj.2019102808

HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer
Cited by: 36
Author(s): Jorge Ferrer, Edgar Bernardo, Anthony Beucher, Miguel A. Maestro, Natalia del Pozo, I.R. Hernández Millán, Lena Haeberle, Martin Schlensog, Sami-Alexander Safi, Wolfram Trudo Knoefel, Vanessa Grau, Matías De Vas, Karl B. Shpargel, Eva C. Vaquero, Terry Magnuson, Sagrario Ortega, Irene Espósito, Francisco X. Real, Jorge Ferrer
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0151895

Patterns of Species Richness and Turnover for the South American Rodent Fauna
Cited by: 57
Author(s): Renan Maestri, Bruce D. Patterson
Software Mentions: 6
Published: over 8 years ago

10.1186/s13059-020-02216-8

Histone modifications during the life cycle of the brown alga Ectocarpus
Cited by: 21
Author(s): Simon Bourdareau, Leïla Tirichine, Bérangère Lombard, Damarys Loew, Delphine Scornet, Yue Wu, Susana M. Coelho, J. Mark Cock
Software Mentions: 6
Published: almost 4 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

10.1371/journal.pcbi.1005515

Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates
Cited by: 17
Author(s): Andreas Tuerk, Gregor Wiktorin, Serhat Güler
Software Mentions: 6
Published: over 7 years ago

10.1111/pbi.12834

Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (<i>Triticum aestivum</i>)
Cited by: 21
Author(s): Amanda Burridge, Paul Wilkinson, Mark Winfield, Gary Barker, Alexandra M. Allen, Jane A. Coghill, Christy Waterfall, Keith J. Edwards
Software Mentions: 6
Published: about 7 years ago

10.1093/database/baaa082

Siberian sturgeon multi-tissue reference transcriptome database
Cited by: 2
Author(s): Christophe Klopp, Cédric Cabau, Gonzalo Greif, André Lasalle, Santiago Di Landro, Denise Vizziano-Cantonnet
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-018-22488-2

Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer
Cited by: 55
Author(s): Rogan Magee, Aristeidis G. Telonis, Phillipe Loher, Eric Londin, Isidore Rigoutsos
Software Mentions: 6
Published: over 6 years ago

10.1038/s42003-021-01673-6

Glacial melt disturbance shifts community metabolism of an Antarctic seafloor ecosystem from net autotrophy to heterotrophy
Cited by: 11
Author(s): Ulrike Braeckman, Francesca Pasotti, Ralf Hoffmann, Susana Vázquez, Angela Wulff, Irene R Schloss, Ulrike Falk, Dolores Deregibus, Nene Lefaible, Anders Torstensson, Adil Y. Al-Handal, Frank Wenzhöfer, Ann Vanreusel
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0086536

Dual Targeting of MEK and PI3K Pathways Attenuates Established and Progressive Pulmonary Fibrosis
Cited by: 22
Author(s): Satish K. Madala, Ramakrishna Edukulla, Mukta Phatak, Stephanie Schmidt, Cynthia Davidson, Thomas H. Acciani, Thomas R. Korfhagen, Mario Medvedovic, Timothy D. Le Cras, Kimberly Wagner, William D. Hardie
Software Mentions: 6
Published: almost 11 years ago

10.1371/journal.pcbi.1005950

HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cells
Cited by: 9
Author(s): Giulio Di Minin, Andreas Postlmayr, Anton Wutz
Software Mentions: 6
Published: almost 7 years ago

10.1155/2014/248090

MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality Control
Cited by: 49
Author(s): Yan Guo, Shilin Zhao, Fei Ye, Quanhu Sheng, Yu Shyr
Software Mentions: 6
Published: almost 11 years ago

10.1093/gbe/evaa143

The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis
Cited by: 5
Author(s): David C. Plachetzki, M. Sabrina Pankey, Matthew D. MacManes, Michael P. Lesser, Charles W. Walker
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0012657

A Comprehensive and Universal Method for Assessing the Performance of Differential Gene Expression Analyses
Cited by: 13
Author(s): Mikhail G. Dozmorov, Joel M. Guthridge, Robert E. Hurst, Igor Dozmorov
Software Mentions: 6
Published: about 14 years ago

10.1371/journal.pone.0003415

Gene Expression Profiling of Two Distinct Neuronal Populations in the Rodent Spinal Cord
Cited by: 10
Author(s): Jesper Ryge, Ann-Charlotte Westerdahl, Preben Alstrøm, Ole Kiehn
Software Mentions: 6
Published: about 16 years ago

10.1186/s13059-017-1367-z

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
Cited by: 9
Author(s): Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert, David Hot
Software Mentions: 6
Published: almost 7 years ago

10.1093/gbe/evu133

Settling Down: The Genome of Serratia symbiotica from the Aphid Cinara tujafilina Zooms in on the Process of Accommodation to a Cooperative Intracellular Life
Cited by: 77
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pcbi.1004393

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud
Cited by: 73
Author(s): Malachi Griffith, Jason Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith
Software Mentions: 6
Published: over 9 years ago

10.1186/s13059-021-02423-x

GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
Cited by: 58
Author(s): Daniel Cameron, Jonathan Baber, Charles Shale, Jose Espejo Valle-Inclán, Nicolle Besselink, Arne van Hoeck, Roel Janssen, Edwin Cuppen, Peter Priestley, Anthony T. Papenfuss
Software Mentions: 6
Published: over 3 years ago

10.18632/oncotarget.20405

Cancer cell line specific co-factors modulate the FOXM1 cistrome
Cited by: 8
Author(s): Yue Wang, Matthew Ung, Tian Xia, Wenqing Cheng, Chao Cheng
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-015-0734-x

Errors in RNA-Seq quantification affect genes of relevance to human disease
Cited by: 128
Author(s): Christelle Robert, Michael Watson
Software Mentions: 5
Published: about 9 years ago

10.1186/s13059-015-0716-z

Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays
Cited by: 191
Author(s): Matteo Dell’Acqua, Daniel M. Gatti, G. Pea, Federica Cattonaro, Frederik Coppens, Gabriele Magris, Aye L. Hlaing, Htay Htay Aung, Hilde Nelissen, Joke Baute, Elisabetta Frascaroli, Gary A. Churchill, Dirk Inzé, Michèle Morgante, Mario Enrico Pè
Software Mentions: 5
Published: about 9 years ago

10.1186/s13059-017-1285-0

Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Cited by: 66
Author(s): Oliver S. Burren, Arcadio Rubio Garćıa, Biola M. Javierre, Daniel B. Rainbow, Jonathan Cairns, Nicholas Cooper, John Lambourne, Ellen Schofield, Xaquín Castro Dopico, Ricardo C. Ferreira, Richard M. R. Coulson, Frances Burden, Sophia Rowlston, Kate Downes, Steven W. Wingett, Mattia Frontini, Willem H. Ouwehand, Peter Fraser, Mikhail Spivakov, John A. Todd, Linda S. Wicker, Antony J. Cutler, Chris Wallace
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-014-0579-8

Pancancer analysis of DNA methylation-driven genes using MethylMix
Cited by: 102
Author(s): Olivier Gevaert, Robert Tibshirani, Sylvia K. Plevritis
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13293-015-0056-4

Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development
Cited by: 24
Author(s): Martin M. Johansson, E. Lundin, Xiaoyan Qian, Mohammadreza Mirzazadeh, Jonatan Halvardson, Elisabeth Darj, Lars Feuk, Mats Nilsson, Elena Jazin
Software Mentions: 5
Published: almost 9 years ago

10.1093/bioinformatics/btv634

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes
Cited by: 54
Author(s): Sheida Nabavi, Daniel Schmolze, Mayinuer Maitituoheti, Sadhika Malladi, Andrew H. Beck
Software Mentions: 5
Published: about 9 years ago

10.18632/oncotarget.16417

Interaction of Epstein-Barr virus genes with human gastric carcinoma transcriptome
Cited by: 10
Author(s): Ruiyuan Zhang, Michael J. Strong, Melody Baddoo, Zhen Lin, Yuping Wang, Erik K. Flemington, Yaozhong Liu
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-014-0577-x

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics
Cited by: 109
Author(s): Benjamin J. Kelly, James Fitch, Yangqiu Patrick Hu, Donald J. Corsmeier, Huachun Zhong, Amy Wetzel, Russell D Nordquist, David L. Newsom, Peter White
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13059-017-1302-3

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination
Cited by: 127
Author(s): Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V. Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G. Lewsey, James Whelan
Software Mentions: 5
Published: about 7 years ago

10.1093/bioinformatics/btt016

Grape RNA-Seq analysis pipeline environment
Cited by: 28
Author(s): David G. Knowles, Maik Röder, Angelika Merkel, Roderic Guigó
Software Mentions: 5
Published: almost 12 years ago

10.1084/jem.20171738

A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets
Cited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: almost 7 years ago

10.1128/mBio.02079-16

Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus-Associated Merkel Cell Carcinoma
Cited by: 87
Author(s): Gabriel J. Starrett, Christina Marcelus, Paul G. Cantalupo, Joshua P. Katz, Jingwei Cheng, Keiko Akagi, Manisha Thakuria, Guilherme Rabinowits, Linda C. Wang, David E. Symer, James M. Pipas, Reuben S. Harris, James A. DeCaprio
Software Mentions: 5
Published: over 7 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: about 6 years ago

10.6026/97320630013327

Robust Feature Selection Approach for Patient Classification using Gene Expression Data
Cited by: 6
Author(s): Shahjaman, Nishith Kumar, Shakil Ahmed, AnjumanAra Begum, S. M. Shahinul Islam, Md. Nurul Haque Mollah
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pbio.1002585

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process
Cited by: 192
Author(s): Richard Angélique, Boullu Loïs, Ulysse Herbach, Bonnafoux Arnaud, Valérie Morin, Elodie Vallin, Anissa Guillemin, Nan Gao, Gunawan Rudiyanto, Jérémie Cosette, Ophélie Arnaud, Jean-Jacques Kupiec, Thibault Espinasse, Sandrine Gonin-Giraud, Olivier Gandrillon
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-020-61158-0

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus
Cited by: 46
Author(s): Bas Berbers, Assia Saltykova, Cristina Garcı́a-Graells, Patrick Philipp, F Arella, Kathleen Marchal, Raf Winand, Kevin Vanneste, Nancy Roosens, Sigrid C. J. De Keersmaecker
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms19010071

Transcriptome-Wide Identification and Characterization of Potato Circular RNAs in Response to Pectobacterium carotovorum Subspecies brasiliense Infection
Cited by: 42
Author(s): Ran Zhou, Yong‐Guan Zhu, Jiao Zhao, Zhengwu Fang, Shuping Wang, Jia Yin, Chu Zhang, Dongfang Ma
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-018-37679-0

Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level
Cited by: 46
Author(s): Petra Patáková, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Katerina Jureckova, Jan Kolek, Pavlína Koščová, Ivo Provazník
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.ebiom.2019.06.041

Metabolomics in plasma of Malawian children 7 years after surviving severe acute malnutrition: “ChroSAM” a cohort study
Cited by: 14
Author(s): Céline Bourdon, Natasha Lelijveld, Debbie Thompson, Prasad S. Dalvi, Gerard Bryan Gonzales, Dominic Wang, Misagh Alipour, Eytan Wine, Emmanuel Chimwezi, Jonathan C. K. Wells, Marko Kerac, Robert Bandsma, Moffat Nyirenda
Software Mentions: 5
Published: over 5 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 7 years ago

Projects: cran: SAM

Papers Mentioning SAM 4,566