10.1186/1471-2105-9-415

BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments
Cited by: 53
Author(s): Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli, Marianna Pensky
Software Mentions: 3
Published: almost 18 years ago

10.1186/1471-2105-8-346

A framework for significance analysis of gene expression data using dimension reduction methods
Cited by: 41
Author(s): Lars Gidskehaug, Endre Anderssen, Arnar Flatberg, Bjørn K. Alsberg
Software Mentions: 3
Published: almost 19 years ago

10.3390/microorganisms9091845

High Throughput Analysis Reveals Changes in Gut Microbiota and Specific Fecal Metabolomic Signature in Hematopoietic Stem Cell Transplant Patients
Cited by: 3
Author(s): Soumaya Kouidhi, Nessrine Souai, Oumaima Zidi, Ahmed Mosbah, Amel Lakhal, Tarek Ben Othmane, Dorra Belloumi, Farhat Ben Ayed, Elias Asimakis, Panagiota Stathopoulou, Ameur Chérif, George Tsiamis
Software Mentions: 3
Published: almost 5 years ago

10.1186/s40168-017-0341-z

Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats
Cited by: 39
Author(s): Hong Shen, Zhongyan Lu, Zhihui Xu, Zhan Chen, Zongzhuan Shen
Software Mentions: 3
Published: almost 9 years ago

10.1111/1751-7915.13863

Transcriptome analysis reveals the roles of nitrogen metabolism and sedoheptulose bisphosphatase pathway in methanol‐dependent growth of Corynebacterium glutamicum
Cited by: 4
Author(s): Liwen Fan, Yu Wang, Jin Qian, Ning Gao, Zhihui Zhang, Xiaomeng Ni, Letian Sun, Qianqian Yuan, Ping Zheng, Jibin Sun
Software Mentions: 3
Published: about 5 years ago

10.3389/fcvm.2021.658915

Common Variants Associated With OSMR Expression Contribute to Carotid Plaque Vulnerability, but Not to Cardiovascular Disease in Humans
Cited by: 3
Author(s): Daniëlle van Keulen, Ian D. van Koeverden, Arjan Boltjes, H.M.G. Princen, Alain J. van Gool, Gert J. de Borst, Folkert W. Asselbergs, Dennie Tempel, Gérard Pasterkamp, Sander W. van der Laan
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giy168

New<i>de novo</i>assembly of the Atlantic bottlenose dolphin (<i>Tursiops truncatus</i>) improves genome completeness and provides haplotype phasing
Cited by: 5
Author(s): Karine A. Martinez-Viaud, Cindy Lawley, Milmer Martinez Vergara, Gil Ben-Zvi, Tammy Biniashvili, Kobi Baruch, Judy St. Leger, Jennie Le, Aparna Natarajan, Marlem Rivera, Marbie Guillergan, Erich B. Jaeger, Brian Steffy, Aleksey V. Zimin
Software Mentions: 3
Published: over 7 years ago

10.1093/gigascience/giab008

Twelve years of SAMtools and BCFtools
Cited by: 3,237
Author(s): Petr Danecek, James K. Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M. Keane, Shane McCarthy, Robert M. Davies, Heng Li
Software Mentions: 3
Published: over 5 years ago

10.1007/s00251-014-0820-3

Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics
Cited by: 15
Author(s): Wouter J. Veneman, Jan de Sonneville, Kees-Jan van der Kolk, Anita Ordas, Zaid Al-Ars, Annemarie H. Meijer, Herman P. Spaink
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-017-04786-3

sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Cited by: 25
Author(s): Julie Bronsard, Gaëtan Pascreau, Mohamed Sassi, Tony Mauro, Yoann Augagneur, Brice Felden
Software Mentions: 3
Published: about 9 years ago

10.1186/gm130

Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes
Cited by: 228
Author(s): Iain J. Gallagher, Camilla Schéele, Pernille Keller, Annemette Nielsen, Judit Reményi, Christian P. Fischer, Karim Roder, John Babraj, Claes Wahlestedt, György Hutvágner, Bente Klarlund Pedersen, James A. Timmons
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2164-9-333

Structure and properties of transcriptional networks driving selenite stress response in yeasts
Cited by: 74
Author(s): Hélène Salin, Vivienne Fardeau, Eugenia Piccini, Gaëlle Lelandais, Véronique Tanty, Sophie Lemoine, Claude Jacq, Frédéric Devaux
Software Mentions: 3
Published: about 18 years ago

10.1186/1471-2105-15-S1-S7

Reducing bias in RNA sequencing data: a novel approach to compute counts
Cited by: 39
Author(s): Francesca Finotello, Enrico Lavezzo, Luca Bianco, Luisa Barzon, Paolo Emilio Mazzon, Paolo Fontana, Stefano Toppo, Barbara Di Camillo
Software Mentions: 3
Published: over 12 years ago

10.3758/s13421-020-01082-w

The simultaneous recognition of multiple words: A process analysis
Cited by: 4
Author(s): Anne Voormann, Mikhail S. Spektor, Karl Christoph Klauer
Software Mentions: 3
Published: over 5 years ago

10.1186/gm340

Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets
Cited by: 141
Author(s): Piyush B. Madhamshettiwar, Stefan Maetschke, Melissa J. Davis, Antônio Reverter, Mark A. Ragan
Software Mentions: 3
Published: over 14 years ago

10.1186/s12864-017-4430-y

The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes
Cited by: 38
Author(s): Deepak Kumar Gupta, Martin Rühl, Bagdevi Mishra, Vanessa Kleofas, Martin Hofrichter, Robert Herzog, Marek J. Pecyna, Rahul Sharma, Harald Kellner, Florian Hennicke, Marco Thines
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-8-157

Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures
Cited by: 21
Author(s): Xin Lü, David L. Perkins
Software Mentions: 3
Published: about 19 years ago

10.1093/gbe/evt199

The Standing Pool of Genomic Structural Variation in a Natural Population of Mimulus guttatus
Cited by: 40
Author(s): Lex E. Flagel, John H. Willis
Software Mentions: 3
Published: over 12 years ago

10.3390/metabo11090627

Comparative Untargeted Metabolomic Profiling of Induced Mitochondrial Fusion in Pancreatic Cancer
Cited by: 0
Author(s): Nathalie Nguyen, Meifang Yu, Vinit Y. Reddy, Ariana Carolina Acevedo-Diaz, Enzo C. Mesarick, Joseph Abi Jaoude, Min Yuan, John M. Asara, Cullen M. Taniguchi
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2164-14-337

Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver
Cited by: 48
Author(s): Logan J. Everett, John Le Lay, Sabina Lukovac, Diana Bernstein, David J. Steger, Mitchell A. Lazar, Klaus H. Kaestner
Software Mentions: 3
Published: about 13 years ago

10.1186/s12859-021-03955-6

IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner
Cited by: 2
Author(s): Ana Maria Martins Alves Vasconcelos, Maria Beatriz Carmo, Beatriz Quintino Ferreira, Inês Viegas, Margarida Gama‐Carvalho, António E. N. Ferreira, Andreia J. Amaral
Software Mentions: 3
Published: over 5 years ago

10.1111/tpj.14468

An ‘ <scp>eFP</scp> ‐Seq Browser’ for visualizing and exploring <scp>RNA</scp> sequencing data
Cited by: 31
Author(s): Alexander Sullivan, Priyank Purohit, Nowlan H. Freese, Asher Pasha, Eddi Esteban, Jamie Waese, Alison Wu, Michelle Chen, Chih Ying Chin, Richard Song, Sneha Ramesh Watharkar, Agnes P. Chan, Vivek Krishnakumar, Matthew Vaughn, Chris Town, Ann E. Loraine, Nicholas J. Provart
Software Mentions: 3
Published: almost 7 years ago

10.1093/gbe/evu272

Evolutionary Dynamics of GLD-1–mRNA Complexes in Caenorhabditis Nematodes
Cited by: 7
Author(s): Alana V. Beadell, Eric S. Haag
Software Mentions: 3
Published: over 11 years ago

10.1186/s13073-020-00809-3

Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier
Cited by: 49
Author(s): Eiru Kim, Traver Hart
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-020-02045-9

Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing
Cited by: 11
Author(s): Naveen Ramesh, Emi Sei, Pei Ching Tsai, Shanshan Bai, Yuehui Zhao, Patricia Troncoso, Paul G. Corn, Christopher J. Logothetis, Amado J. Zurita, Nicholas E. Navin
Software Mentions: 3
Published: about 6 years ago

10.1186/s13059-020-01968-7

NanoVar: accurate characterization of patients’ genomic structural variants using low-depth nanopore sequencing
Cited by: 53
Author(s): Cheng Yong Tham, Roberto Tirado-Magallanes, Yufen Goh, Melissa J. Fullwood, Bryan T. H. Koh, Wilson Wang, Chin Hin Ng, Wee Joo Chng, Alexandre H. Thiéry, Daniel G. Tenen, Touati Benoukraf
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-14-S14-S17

mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis
Cited by: 17
Author(s): Cory B. Giles, G. Reshmi, Mikhail G. Dozmorov, Jonathan D. Wren
Software Mentions: 3
Published: almost 13 years ago

10.1186/gb-2005-6-2-r16

Cited by: 335
Author(s): Sung Choe, Michael Boutros, Alan D. Michelson, George M. Church, Marc S. Halfon
Software Mentions: 3
Published: over 21 years ago

10.1186/1471-2105-7-286

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology
Cited by: 53
Author(s): Bruz Marzolf, Eric W. Deutsch, Patrick Moss, D. S. Campbell, Michael H. Johnson, Timothy Galitski
Software Mentions: 3
Published: about 20 years ago

10.1186/gb-2005-6-2-r20

Cited by: 18
Author(s): Stephen R. Master, Alexander J. Stoddard, Leonard C. Bailey, Tien-Chi Pan, Katherine D. Dugan, Lewis A. Chodosh
Software Mentions: 3
Published: over 21 years ago

10.1186/s12859-021-04068-w

RiboA: a web application to identify ribosome A-site locations in ribosome profiling data
Cited by: 2
Author(s): Danying Shao, Nabeel Ahmed, Nishant Soni, Edward P. O’Brien
Software Mentions: 3
Published: over 5 years ago

10.1186/2049-3002-2-13

Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer
Cited by: 27
Author(s): Debarshi Roy, Susmita Mondal, Chen Wang, Xiaoping He, Ashwani Khurana, Shailendra Giri, Robert Hoffmann, Deok‐Beom Jung, Sung Hyun Kim, Eduardo N. Chini, Juliana Camacho Periera, Clifford D.L. Folmes, Andrea Mariani, Sean C. Dowdy, Jamie N. Bakkum-Gamez, Shaun M. Riska, Ann L. Oberg, Edward D. Karoly, Lauren N. Bell, Jeremy Chien, Viji Shridhar
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13059-021-02270-w

simATAC: a single-cell ATAC-seq simulation framework
Cited by: 12
Author(s): Zeinab Navidi, Lin Zhang, Bo Wang
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-014-0571-3

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification
Cited by: 780
Author(s): Yuan Gao, Jinfeng Wang, Fangqing Zhao
Software Mentions: 3
Published: over 11 years ago

10.1186/s12859-018-2315-y

bioSyntax: syntax highlighting for computational biology
Cited by: 2
Author(s): Artem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin Jeffrey Kam, Gherman Novakovsky, Jasper Wong, Dylan Aïssi, Yao Li
Software Mentions: 3
Published: almost 8 years ago

10.1186/gb-2014-15-5-r71

A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions
Cited by: 28
Author(s): Alayne Brunner, Jun Li, Xiangqian Guo, Robert T. Sweeney, Sushama Varma, Shirley Zhu, Rui Li, Robert Tibshirani, Robert B. West
Software Mentions: 3
Published: over 12 years ago

10.1186/1752-0509-8-S1-S5

Detection of type 2 diabetes related modules and genes based on epigenetic networks
Cited by: 6
Author(s): Liu Hui, Tongtong Wang, Hongbo Liu, Yanjun Wei, Guofeng Zhao, Jianzhong Su, Qiong Wu, Hong Qiao, Yan Zhang
Software Mentions: 3
Published: over 12 years ago

10.1186/s13059-014-0540-x

Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity
Cited by: 33
Author(s): Stuart Dowall, David A. Matthews, Isabel García-Dorival, Irene Taylor, John Kenny, Christiane Hertz‐Fowler, Neil Hall, Kara Corbin-Lickfett, Cyril Empig, Kyle Schlunegger, John N. Barr, Miles W. Carroll, Roger Hewson, Julian A. Hiscox
Software Mentions: 3
Published: over 11 years ago

10.1186/s12859-017-1705-x

An evaluation of copy number variation detection tools for cancer using whole exome sequencing data
Cited by: 121
Author(s): Fatima Zare, Michelle Dow, Nicholas J. Monteleone, Abdelrahman Hosny, Sheida Nabavi
Software Mentions: 3
Published: about 9 years ago

10.1186/gb-2013-14-3-r30

CRAC: an integrated approach to the analysis of RNA-seq reads
Cited by: 70
Author(s): Philippe Naveilhan, Mikaël Salson, Thérèse Commes, Éric Rivals
Software Mentions: 3
Published: over 13 years ago

10.1186/gb-2013-14-5-r51

Characterizing and measuring bias in sequence data
Cited by: 708
Author(s): Michael G. Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J. Lennon, Ryan Hegarty, Chad Nusbaum, David B. Jaffe
Software Mentions: 3
Published: over 13 years ago

10.1186/gb-2011-12-3-r22

Improving RNA-Seq expression estimates by correcting for fragment bias
Cited by: 1,136
Author(s): Anjeanette Roberts, Cole Trapnell, Julie Donaghey, John L. Rinn, Lior Pachter
Software Mentions: 3
Published: over 15 years ago

10.1186/gb-2012-13-5-r34

A new approach for detecting low-level mutations in next-generation sequence data
Cited by: 87
Author(s): Mingkun Li, Mark Stoneking
Software Mentions: 3
Published: over 14 years ago

10.1186/bcr2632

Expression levels of uridine 5'-diphospho-glucuronosyltransferase genes in breast tissue from healthy women are associated with mammographic density
Cited by: 37
Author(s): Vilde Drageset Haakensen, Margarethe Biong, Ole Christian Lingjærde, Marit Muri Holmen, Jan Ole Frantzen, Ying Chen, Dina Navjord, Linda Romundstad, Torben Lüders, Ida K. Bukholm, Hiroko Kato Solvang, Vessela N. Kristensen, Giske Ursin, Anne‐Lise Børresen‐Dale, Åslaug Helland
Software Mentions: 3
Published: almost 16 years ago

10.1186/s40478-016-0338-z

A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association
Cited by: 54
Author(s): Michael J. Strong, Eugene Blanchard, Zhen Lin, Cindy A. Morris, Melody Baddoo, Christopher M. Taylor, Marcus L. Ware, Erik K. Flemington
Software Mentions: 3
Published: about 10 years ago

10.1186/gb-2012-13-8-r75

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
Cited by: 220
Author(s): Alayne Brunner, Andrew H. Beck, Badreddin Edris, Robert T. Sweeney, Shirley Zhu, Rui Li, Kelli Montgomery, Sushama Varma, Thea Gilks, Xiangqian Guo, Joseph W. Foley, Daniela Witten, Craig P. Giacomini, Ryan A. Flynn, Jonathan R. Pollack, Robert Tibshirani, Howard Y. Chang, Matt van de Rijn, Robert B. West
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2105-13-42

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community
Cited by: 142
Author(s): Konstantinos Krampis, Tim Booth, Brad Chapman, Brijesh K. Tiwari, Mesude Bicak, Dawn Field, Karen E. Nelson
Software Mentions: 3
Published: over 14 years ago

10.1186/gb-2013-14-8-r93

Web Apollo: a web-based genomic annotation editing platform
Cited by: 312
Author(s): Eduardo Lee, Gregg Helt, Justin Reese, Monica Muñoz-Torres, Christopher P. Childers, Robert Buels, Lincoln Stein, Ian Holmes, Christine G. Elsik, Suzanna Lewis
Software Mentions: 3
Published: over 13 years ago

10.3389/fpls.2019.01624

Gene Expression Profiling of the Shoot Meristematic Tissues in Woodland Strawberry Fragaria vesca
Cited by: 8
Author(s): Yongping Li, Jia Feng, Laichao Cheng, Cheng Dai, Qi Gao, Zhongchi Liu, Chunying Kang
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2016.01020

Low Temperature and Short-Term High-CO2 Treatment in Postharvest Storage of Table Grapes at Two Maturity Stages: Effects on Transcriptome Profiling
Cited by: 30
Author(s): Raquel Rosales, Irene Romero, Carlos Fernández-Caballero, M. Isabel Escribano, Carmen Merodio, Marı́a T. Sanchez-Ballesta
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2105-10-300

RCMAT: a regularized covariance matrix approach to testing gene sets
Cited by: 8
Author(s): Phillip D. Yates, Mark Reimers
Software Mentions: 3
Published: almost 17 years ago

10.1186/1471-2164-14-471

Analysis and annotation of the hexaploid oat seed transcriptome
Cited by: 60
Author(s): Juan J. Gutiérrez-González, Zheng Jin Tu, David F. Garvin
Software Mentions: 3
Published: about 13 years ago

10.3389/fpls.2018.01962

Early Detection of Magnaporthe oryzae-Infected Barley Leaves and Lesion Visualization Based on Hyperspectral Imaging
Cited by: 23
Author(s): Ruiqing Zhou, Juanjuan Jin, Qing-Mian Li, Zhen-Zhu Su, Xinjie Yu, Yu Tang, Shaoming Luo, Yong He, Yuanyuan Liu
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-018-5017-y

Genome wide transcriptome analysis provides bases on colonic mucosal immune system development affected by colostrum feeding strategies in neonatal calves
Cited by: 6
Author(s): Zhixiong He, Albert J. Fischer, Yang Song, M.A. Steele, Le Luo Guan
Software Mentions: 3
Published: almost 8 years ago

10.1186/1756-0500-1-80

Advanced spot quality analysis in two-colour microarray experiments
Cited by: 10
Author(s): Mikalai M. Yatskou, Eugene Novikov, Guillaume Vetter, Arnaud Muller, Emmanuel Barillot, Laurent Vallar, Evelyne Friederich
Software Mentions: 3
Published: over 18 years ago

10.3389/fpls.2016.01528

Invasive Shrub Mapping in an Urban Environment from Hyperspectral and LiDAR-Derived Attributes
Cited by: 29
Author(s): Curtis M. Chance, Nicholas C. Coops, Andrew Plowright, Thoreau Rory Tooke, Andreas Christen, Neal W. Aven
Software Mentions: 3
Published: almost 10 years ago

10.1186/bcr3672

A genomic analysis of mouse models of breast cancer reveals molecular features ofmouse models and relationships to human breast cancer
Cited by: 71
Author(s): Daniel P. Hollern, Eran R. Andrechek
Software Mentions: 3
Published: about 12 years ago

10.1186/1752-0509-7-S2-S9

Identifying novel glioma associated pathways based on systems biology level meta-analysis
Cited by: 10
Author(s): Yangfan Hu, Jinquan Li, Wenying Yan, Jiajia Chen, Yin Li, Guang Hu, Bairong Shen
Software Mentions: 3
Published: over 13 years ago

10.3389/fgene.2021.622886

Familial Psychosis Associated With a Missense Mutation at MACF1 Gene Combined With the Rare Duplications DUP3p26.3 and DUP16q23.3, Affecting the CNTN6 and CDH13 Genes
Cited by: 3
Author(s): Josep Pol-Fuster, Francesca Cañellas, Laura Ruiz-Guerra, Aina Medina-Dols, Bàrbara Bisbal-Carrió, Víctor J. Asensio, Bernat Ortega-Vila, Diego M. Marzese, Carme Vidal, Carmen Sofia Pedro dos Santos, Jerònia Lladó, Gabriel Olmos, Damián Heine-Suñer, Konstantin Strauch, Antònia Flaquer, Cristòfol Vives-Bauzà
Software Mentions: 3
Published: over 5 years ago

10.1186/1756-0500-3-298

KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data
Cited by: 22
Author(s): Jorma J. de Ronde, Christiaan Klijn, Arno Velds, Henne Holstege, Marcel J. T. Reinders, Jos Jonkers, Lodewyk Wessels
Software Mentions: 3
Published: over 15 years ago

10.3389/fphar.2019.01690

SAMbinder: A Web Server for Predicting S-Adenosyl-L-Methionine Binding Residues of a Protein From Its Amino Acid Sequence
Cited by: 3
Author(s): Piyush Agrawal, Gaurav Mishra, Gajendra P. S. Raghava
Software Mentions: 3
Published: over 6 years ago

10.3389/fpsyt.2021.685656

Metabolic Profiling Indicates Diversity in the Metabolic Physiologies Associated With Maternal Postpartum Depressive Symptoms
Cited by: 4
Author(s): Emma Bränn, Christina J. Malavaki, Emma Fransson, Maria-Konstantina Ioannidi, Hanna Henriksson, Fotios C. Papadopoulos, George P. Chrousos, Maria I. Klapa, Alkistis Skalkidou
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-8-195

Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips
Cited by: 20
Author(s): Andrew Harrison, Caroline Johnston, Christine A. Orengo
Software Mentions: 3
Published: about 19 years ago

10.1186/bcr3020

Genomic and phenotypic analysis of BRCA2mutated breast cancers reveals co-occurring changes linked to progression
Cited by: 22
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Katrín Ólafsdóttir, Hörður Bjarnason, Óskar T. Jóhannsson, Sigrídur K. Bödvarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 3
Published: almost 15 years ago

10.1186/1471-2164-13-355

Dose-dependent effects of small-molecule antagonists on the genomic landscape of androgen receptor binding
Cited by: 7
Author(s): Zhou Zhu, Minmin Shi, Wenyue Hu, Heather Estrella, Jon Engebretsen, Tim Nichols, David M. Briere, Natilie Hosea, Gerrit Los, Paul A. Rejto, Andrea Fanjul
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2105-14-S9-S1

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
Cited by: 84
Author(s): Xiao Xu, Yuanhao Zhang, Jennie L. Williams, Eric Antoniou, W. Richard McCombie, Song Wu, Wei Zhu, Nicholas O. Davidson, Paula Denoya, Ellen Li
Software Mentions: 3
Published: about 13 years ago

10.3389/fgene.2014.00043

Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models
Cited by: 12
Author(s): Andreia J. Amaral, Francisco Brito, Tamar Chobanyan, S. Yoshikawa, Takakazu Yokokura, David Van Vactor, Margarida Gama‐Carvalho
Software Mentions: 3
Published: over 12 years ago

10.3389/fgene.2019.01268

Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism
Cited by: 10
Author(s): Mette Juul Jacobsen, Jakob Hull Havgaard, Christian Anthon, Caroline M. Junker Mentzel, Susanna Cirera, Poula Maltha Krogh, Sachin Pundhir, Peter Karlskov-Mortensen, Camilla S. Bruun, Philippe Lesnik, Maryse Guérin, Jan Gorodkin, Claus B. Jørgensen, Merete Fredholm, Romain Barrès
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2014.00031

Multi-genome alignment for quality control and contamination screening of next-generation sequencing data
Cited by: 21
Author(s): James Hadfield, Matthew Eldridge
Software Mentions: 3
Published: over 12 years ago

10.1111/tpj.12307

Resistance gene enrichment sequencing (<scp>R</scp>en<scp>S</scp>eq) enables reannotation of the <scp>NB</scp>‐<scp>LRR</scp> gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
Cited by: 327
Author(s): Florian Jupe, Kamil Witek, Walter Verweij, Jadwiga Śliwka, Leighton Pritchard, Graham J. Etherington, Dan MacLean, Peter J. A. Cock, Richard M. Leggett, Glenn J. Bryan, Linda Cardle, Ingo Hein, Jonathan D. G. Jones
Software Mentions: 3
Published: almost 13 years ago

10.1186/1471-2202-9-93

Bioinformatic and statistical analysis of the optic nerve head in a primate model of ocular hypertension
Cited by: 40
Author(s): Kenneth S Kompass, Olga A. Agapova, Wenjun Li, Paul L. Kaufman, Carol A. Rasmussen, M. Rosario Hernandez
Software Mentions: 3
Published: almost 18 years ago

10.1186/1472-6807-11-16

Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: Possible misannotation of this tubercle bacilli-hemolysin
Cited by: 27
Author(s): Nelson E. Arenas, Luz Mary Salazar, Carlos Y. Soto, Carolina Vizcaíno, Manuel Elkín Patarroyo, Arley Gómez
Software Mentions: 3
Published: over 15 years ago

10.3389/fgene.2019.01260

Joint Transcriptomic Analysis of Lung Cancer and Other Lung Diseases
Cited by: 8
Author(s): Beatriz Andrea Otálora‐Otálora, Mauro Florez, Liliana López‐Kleine, Alejandra Cañas Arboleda, Diana Urrego, Alejandra Rojas
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-14-371

Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor
Cited by: 34
Author(s): Franc Llorens, Manuela Hummel, Lorena Pantano, Xavier Pastor, Ana Vivancos, Ester Castillo, Heidi Mattlin, Anna Ferrer, Matthew Ingham, María Noguera, Robert Kofler, Juliane C. Dohm, Raquel Pluvinet, Mònica Bayés, Heinz Himmelbauer, José Antonio del Río, Eulàlia Martı́, Lauro Sumoy
Software Mentions: 3
Published: about 13 years ago

10.3389/fpsyg.2020.00953

Global Image Properties Predict Ratings of Affective Pictures
Cited by: 17
Author(s): Christoph Redies, Maria Grebenkina, Mahdi Mohseni, Ali Kaduhm, Christian Dobel
Software Mentions: 3
Published: about 6 years ago

10.1186/s41687-020-00193-x

Advances in Patient Reported Outcomes: Integration and Innovation
Cited by: 5
Author(s):
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-8-123

STATc is a key regulator of the transcriptional response to hyperosmotic shock
Cited by: 32
Author(s): Jianbo Na, Budi Tunggal, Ludwig M. Eichinger
Software Mentions: 3
Published: about 19 years ago

10.7554/eLife.32920

Association mapping from sequencing reads using k-mers
Cited by: 82
Author(s): Atif Rahman, Ingileif B. Hallgrímsdóttir, Michael B. Eisen, Lior Pachter
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.23468

A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation
Cited by: 29
Author(s): Meng Amy Li, Paulo Amaral, Priscilla Cheung, Jan H. Bergmann, Masaki Kinoshita, Tüzer Kalkan, Markus Ralser, Sam Robson, Ferdinand von Meyenn, Maike Paramor, Fengtang Yang, Caifu Chen, Jennifer Nichols, David L. Spector, Tony Kouzarides, Lin He, Austin Smith
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pmed.0030047

Gene Expression Programs in Response to Hypoxia: Cell Type Specificity and Prognostic Significance in Human Cancers
Cited by: 549
Author(s): Jen‐Tsan Chi, Zhen Wang, Dimitry S.A. Nuyten, Edwin H. Rodriguez, Marci E. Schaner, Ali Salim, Yun Wang, Gunnar B. Kristensen, Åslaug Helland, Anne Lise Børresen-Dale, Amato J. Giaccia, Michael T. Longaker, Trevor Hastie, George P. Yang, Marc J. van de Vijver, Patrick O. Brown
Software Mentions: 3
Published: over 20 years ago

10.7554/eLife.22345

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition
Cited by: 83
Author(s): Yun Huang, Jong Kim, Dang Vinh, Caroline Lee, Christopher A. Penfold, J. Ż̷ylicz, John C. Marioni, Jim Hackett, M. Azim Surani
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.27529

A viral protein promotes host SAMS1 activity and ethylene production for the benefit of virus infection
Cited by: 55
Author(s): Shanshan Zhao, Wei Hong, Jiang Wu, Yu Wang, Shaoyi Ji, Shuyi Zhu, Chunhong Wei, Jinsong Zhang, Yang Li
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.29736

CDK9-dependent RNA polymerase II pausing controls transcription initiation
Cited by: 157
Author(s): Saskia Gressel, Björn Schwalb, Tim-Michael Decker, Weihua Qin, Heinrich Leonhardt, Dirk Eick, Patrick Cramer
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1003820

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
Cited by: 80
Author(s): Stefanie Traeger, Florian Altegoer, Michael Freitag, Toni Gabaldón, Frank Kempken, Abhishek Kumar, Marina Marcet‐Houben, Stefanie Pöggeler, Jason E. Stajich, Minou Nowrousian
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-021-94396-x

Niche partitioning among dead wood-dependent beetles
Cited by: 1
Author(s): Jakub Horák
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-11-592

Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray
Cited by: 55
Author(s): Stéphane Fénart, Yves-Placide Assoumou Ndong, Jorge Duarte, Nathalie Rivière, Jeroen Wilmer, Olivier Van Wuytswinkel, Anca Lucau, Emmanuelle Cariou, Godfrey Neutelings, Laurent Gutierrez, Brigitte Chabbert, Xavier Guillot, Reynald Tavernier, Simon Hawkins, Brigitte Thomasset
Software Mentions: 3
Published: almost 16 years ago

10.1038/s41598-021-92395-6

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction
Cited by: 1
Author(s): Tai Tsun Wu, Jian Liu, Zhiye Guo, Jie Hou, Jianlin Cheng
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-93893-3

Microarray-based selection of a serum biomarker panel that can discriminate between latent and active pulmonary TB
Cited by: 6
Author(s): Zhihui Li, Jianjun Hu, Pengchong Liu, Dan Cui, Hongqin Di, Shucai Wu
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-12-126

Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions
Cited by: 178
Author(s): Bart A. Eijkelkamp, Karl A. Hassan, Ian T. Paulsen, Melissa H. Brown
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pgen.1005265

The Developmental Intestinal Regulator ELT-2 Controls p38-Dependent Immune Responses in Adult C. elegans
Cited by: 42
Author(s): Dena H. S. Block, Kwame Twumasi-Boateng, Hae Sung Kang, Jolie A Carlisle, Alexandru Hanganu, Ty Yu-Jen Lai, Michael Y. Shapira
Software Mentions: 3
Published: about 11 years ago

10.3892/ijo.2014.2648

Microarray phosphatome profiling of breast cancer patients unveils a complex phosphatase regulatory role of the MAPK and PI3K pathways in estrogen receptor-negative breast cancers
Cited by: 13
Author(s): Ramón González Manzano, E. Martinez-Navarro, Jerónimo Forteza, Antonio Brugarolas
Software Mentions: 3
Published: almost 12 years ago

10.3390/s18051465

Smart Waste Collection System with Low Consumption LoRaWAN Nodes and Route Optimization
Cited by: 48
Author(s): Álvaro Lozano, Javier Caridad, Juan F. De Paz, Gabriel Villarrubia González, Javier Bajo
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pgen.1007949

Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
Cited by: 38
Author(s): Dmytro Kryvokhyzha, Adriana Salcedo, Mimmi C. Eriksson, Tianlin Duan, Nilesh R. Tawari, Jun Chen, Maria Guerrina, Julia M. Kreiner, Tyler V. Kent, Ulf Lagercrantz, John R. Stinchcombe, Sylvain Glémin, Stephen I. Wright, Martin Lascoux
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1000812

Altered Gene Expression and DNA Damage in Peripheral Blood Cells from Friedreich's Ataxia Patients: Cellular Model of Pathology
Cited by: 95
Author(s): Astrid C. Haugen, Nicholas A. Di Prospero, Joel S. Parker, Rick D. Fannin, Jeff W. Chou, Joel N. Meyer, Christopher Halweg, Jennifer B. Collins, Alexandra Dürr, Kenneth H. Fischbeck, Bennett Van Houten
Software Mentions: 3
Published: over 16 years ago

10.7554/eLife.17903

A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading
Cited by: 32
Author(s): Chun-Min Shan, Jiyong Wang, Ke Xu, Huijie Chen, Jia-Xing Yue, Stuart Andrews, James J. Moresco, John R. Yates, Péter L. Nagy, Liang Tong, Songtao Jia
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-017-3679-5

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies
Cited by: 21
Author(s): William W. Greenwald, Niels Klitgord, Victor Seguritan, Shibu Yooseph, J. Craig Venter, Chad Garner, Karen E. Nelson, Weizhong Li
Software Mentions: 3
Published: over 9 years ago

10.1155/2015/746970

Identification of Novel Breast Cancer Subtype-Specific Biomarkers by Integrating Genomics Analysis of DNA Copy Number Aberrations and miRNA-mRNA Dual Expression Profiling
Cited by: 15
Author(s): Dongguo Li, Hong Xia, Zhen‐Ya Li, Lin Hua, Lin Li
Software Mentions: 3
Published: over 11 years ago

10.3390/s18020474

Design and Implementation of Cloud-Centric Configuration Repository for DIY IoT Applications
Cited by: 37
Author(s): Shabir Ahmad, Hang Lei, Do‐Hyeun Kim
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1004142

Genetic Basis of Metabolome Variation in Yeast
Cited by: 50
Author(s): J. Scott Breunig, Sean R. Hackett, Joshua D. Rabinowitz, Leonid Kruglyak
Software Mentions: 3
Published: over 12 years ago

10.3390/s18124330

Variational Pansharpening for Hyperspectral Imagery Constrained by Spectral Shape and Gram–Schmidt Transformation
Cited by: 10
Author(s): Z. J. Huang, Qihao Chen, Xiuguo Liu
Software Mentions: 3
Published: over 7 years ago