10.1186/1471-2105-11-73

BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets
Cited by: 11
Author(s): Mark Alston, John Seers, Jay C. D. Hinton, Sacha Lucchini
Software Mentions: 3
Published: over 16 years ago

10.1038/s41598-018-21484-w

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias
Cited by: 56
Author(s): Raga Krishnakumar, Anupama Sinha, Sara W. Bird, Harikrishnan Jayamohan, Harrison Edwards, Joseph S. Schoeniger, Kamlesh D. Patel, Steven S. Branda, Michael Bartsch
Software Mentions: 3
Published: over 8 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

10.1186/1746-4811-8-12

Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis
Cited by: 18
Author(s): Kun-Hsiang Liu, Matthew McCormack, Jenq-Yunn Sheen
Software Mentions: 3
Published: over 14 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: about 7 years ago

10.1371/journal.pone.0015617

A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology
Cited by: 61
Author(s): Martin Blythe, Damian Kao, Sunir Malla, Joanna Rowsell, Reginald H. Wilson, Deborah Evans, Jamie Jowett, Amy Hall, Virginie Lemay, Sabrina Lam, A. Aziz Aboobaker
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0040194

Microarray-Based Sketches of the HERV Transcriptome Landscape
Cited by: 46
Author(s): Philippe Pérot, Nathalie Mugnier, Cécile Montgiraud, Juliette Gimenez, Magali Jaillard, Bertrand Bonnaud, François Mallet
Software Mentions: 3
Published: about 14 years ago

10.3758/s13414-015-0860-2

The long and the short of priming in visual search
Cited by: 24
Author(s): Wouter Kruijne, Martijn Meeter
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0063946

Predicting Species Cover of Marine Macrophyte and Invertebrate Species Combining Hyperspectral Remote Sensing, Machine Learning and Regression Techniques
Cited by: 26
Author(s): Jonne Kotta, Tiit Kutser, Karolin Teeveer, Ele Vahtmäe, Merli Pärnoja
Software Mentions: 3
Published: over 13 years ago

10.1111/pbi.12685

Indel‐seq: a fast‐forward genetics approach for identification of trait‐associated putative candidate genomic regions and its application in pigeonpea (<i>Cajanus cajan</i>)
Cited by: 57
Author(s): Vikas K. Singh, Aamir W. Khan, Rachit K. Saxena, Pallavi Sinha, Sandip M. Kale, Swathi Parupalli, Vinay Kumar, Annapurna Chitikineni, Suryanarayana Vechalapu, C.V. Sameer Kumar, Mamta Sharma, G. Anuradha, K.N. Yamini, S. Muniswamy, Rajeev K. Varshney
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-018-23641-7

Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol
Cited by: 43
Author(s): Joseph A. Russell, Brittany Campos, Jennifer Stone, Erik M. Blosser, Nathan D. Burkett‐Cadena, Jonathan L. Jacobs
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2407-14-64

Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma
Cited by: 21
Author(s): Marion Fehlker, Matthew R. Huska, Thomas Jöns, Miguel A. Andrade‐Navarro, Wolfgang Kemmner
Software Mentions: 3
Published: over 12 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

10.7717/peerj.2105

Constant and seasonal drivers of bird communities in a wind farm: implications for conservation
Cited by: 7
Author(s): Zuzanna M. Rosin, Piotr Skórka, Paweł Szymański, Marcin Tobółka, Andrzej Łuczak, Piotr Tryjanowski
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-017-02824-8

High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor
Cited by: 8
Author(s): Masahito Yoshihara, Yuzuru Sasamoto, Ryuhei Hayashi, Yuki Ishikawa, Motokazu Tsujikawa, Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji, Kohji Nishida
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2407-7-61

Identification of a robust gene signature that predicts breast cancer outcome in independent data sets
Cited by: 37
Author(s): James E. Korkola, Ekaterini Blaveri, Sandy DeVries, Dan H. Moore, E. Shelley Hwang, Yunn Yi Chen, Anne L. Estep, Karen Chew, Ronald H. Jensen, Frederic M. Waldman
Software Mentions: 3
Published: over 19 years ago

10.1038/s41598-017-14418-5

Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis
Cited by: 10
Author(s): Emiko Yoshida, Yasuhisa Terao, Noriko Hayashi, Kaoru Mogushi, Atsushi Arakawa, Yuji Tanaka, Yoshiaki Ito, Hiroko Ohmiya, Yoshihide Hayashizaki, Satoru Takeda, Masayoshi Itoh, Hideya Kawaji
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2105-16-S7-S5

Heterozygous genome assembly via binary classification of homologous sequence
Cited by: 13
Author(s): Paul Bodily, Mao Fujimoto, Cameron Ortega, Nozomu Okuda, Joseph Price, Mark J. Clement, Quinn Snell
Software Mentions: 3
Published: over 11 years ago

10.7717/peerj.8275

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers
Cited by: 9
Author(s): Daniel Liu
Software Mentions: 3
Published: over 6 years ago

10.1029/2019RG000686

Spaceborne Cloud and Precipitation Radars: Status, Challenges, and Ways Forward
Cited by: 65
Author(s): Alessandro Battaglia, Pavlos Kollias, Ranvir Dhillon, Richard Roy, Simone Tanelli, Katia Lamer, Mircea Grecu, Matthew Lebsock, Daniel Watters, Kamil Mróz, Gerald M. Heymsfield, Lihua Li, Katsuko Furukawa
Software Mentions: 3
Published: about 6 years ago

10.3390/ani11092557

Identification of Circular RNAs in the Anterior Pituitary in Rats Treated with GnRH
Cited by: 3
Author(s): Haixiang Guo, Bao Yuan, Meng-Ting Su, Yi Zheng, Jinyu Zhang, Dong-Xu Han, Hao-Qi Wang, Yongping Huang, Hao Jiang, Jiabao Zhang
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.382

Characterisation of the horse transcriptome from immunologically active tissues
Cited by: 6
Author(s): Joanna Moreton, Sunir Malla, A. Aziz Aboobaker, Rachael Tarlinton, Richard D. Emes
Software Mentions: 3
Published: over 12 years ago

10.7717/peerj.830

The effect of listening to music on human transcriptome
Cited by: 32
Author(s): Chakravarthi Kanduri, Pirre Raijas, Minna Ahvenainen, Anju K. Philips, Liisa Ukkola-Vuoti, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 3
Published: over 11 years ago

10.1002/prot.25697

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13
Cited by: 142
Author(s): Jie Hou, Tai Tsun Wu, Renzhi Cao, Jianlin Cheng
Software Mentions: 3
Published: over 7 years ago

10.1128/mBio.00731-20

Differential Alphavirus Defective RNA Diversity between Intracellular and Extracellular Compartments Is Driven by Subgenomic Recombination Events
Cited by: 11
Author(s): Rose M. Langsjoen, Antonio E. Muruato, S. R. Kunkel, Elizabeth Jaworski, Andrew Routh
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-017-02329-4

Expression Profiling of mRNAs and Long Non-Coding RNAs in Aged Mouse Olfactory Bulb
Cited by: 11
Author(s): Ming Wang, Wei Liu, Jian Jiao, Jingyun Li, Chengshuo Wang, Luo Zhang
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.ppat.1009175

Escalation in the host-pathogen arms race: A host resistance response corresponds to a heightened bacterial virulence response
Cited by: 5
Author(s): Qi Wang, Nadia Shakoor, Adam Boyher, Kira M. Veley, Jeffrey C. Berry, Todd C. Mockler, Rebecca Bart
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.7156

Spread of the non-native anemone <i>Anemonia alicemartinae</i> Häussermann &amp; Försterra, 2001 along the Humboldt-current large marine ecosystem: an ecological niche model approach
Cited by: 7
Author(s): Javier Pinochet, Reinaldo Rivera, Paula E. Neill, Antonio Brante, Cristián E. Hernández
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2105-10-418

TransportTP: A two-phase classification approach for membrane transporter prediction and characterization
Cited by: 57
Author(s): Haiquan Li, Vagner A. Benedito, Michael K. Udvardi, Patrick Xuechun Zhao
Software Mentions: 3
Published: almost 17 years ago

10.1073/pnas.1921055117

ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in <i>Arabidopsis</i>
Cited by: 54
Author(s): Christophe Lambing, Pallas Kuo, Andrew J. Tock, Stephanie D. Topp, Ian Henderson
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1003341

Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy
Cited by: 132
Author(s): Michael J. Strong, Guiyin Xu, Joseph Coco, Carl Baribault, Dass S. Vinay, Michelle Lacey, Amy L. Strong, Teresa A. Lehman, Michael Seddon, Zhen Lin, Monica Concha, Melody Baddoo, MaryBeth Ferris, Kenneth F. Swan, Deborah E. Sullivan, Matthew E. Burow, Christopher M. Taylor, Erik K. Flemington
Software Mentions: 3
Published: over 13 years ago

10.1186/1471-2105-13-S14-S5

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis
Cited by: 12
Author(s): Ivan Merelli, Federica Viti, Luciano Milanesi
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.ppat.1005943

Cathelicidin Insufficiency in Patients with Fatal Leptospirosis
Cited by: 21
Author(s): Janet C. Lindow, Elsio A. Wunder, Stephen J. Popper, Jinsoo Min, Praveen Mannam, Anup Srivastava, Yi Yao, Kathryn P. Hacker, Khadir Raddassi, Patty J Lee, Ruth R. Montgomery, Albert C. Shaw, José E. Hagan, Guilherme C. Araújo, Nívison Nery, David A. Relman, Charles C. Kim, Mitermayer Galvão dos Reis, Albert I. Ko
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.ppat.1006510

Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
Cited by: 50
Author(s): Gustavo H. Kijak, Eric Sanders‐Buell, Agnès‐Laurence Chenine, Michael A. Eller, Nilu Goonetilleke, Rasmi Thomas, Sivan Leviyang, Elizabeth A. Harbolick, Meera Bose, Phuc Pham, Celina Oropeza, Kultida Poltavee, Anne Marie O’Sullivan, Erik Billings, Mélanie Merbah, Margaret C. Costanzo, Joanna Warren, Bonnie M. Slike, Hui Li, Kristina K. Peachman, Will Fischer, Feng Gao, Claudia Cicala, James Arthos, Leigh Anne Eller, Robert J. O’Connell, Samuel Sinei, Lucas Maganga, Hannah Kibuuka, Sorachai Nitayaphan, Mangala Rao, Mary Marovich, Shelly J. Krebs, Morgane Rolland, Bette T. Korber, George M. Shaw, Nelson L. Michael, Merlin L. Robb, Sodsai Tovanabutra, Jerome H. Kim
Software Mentions: 3
Published: about 9 years ago

10.1038/s41396-018-0332-5

Niche-directed evolution modulates genome architecture in freshwater Planctomycetes
Cited by: 55
Author(s): Adrian‐Ştefan Andrei, Michaela M. Salcher, Maliheh Mehrshad, Pavel Rychtecký, Petr Znachor, Rohit Ghai
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-31064-7

Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis
Cited by: 33
Author(s): Johnny A. Sena, Giulia Galotto, Nico Devitt, Melanie C. Connick, Jennifer L. Jacobi, Pooja Umale, Luis Vidali, Callum J. Bell
Software Mentions: 3
Published: about 8 years ago

10.1186/s12863-017-0568-5

IntroMap: a signal analysis based method for the detection of genomic introgressions
Cited by: 3
Author(s): Daniel J. Shea, Mitsuru Shimizu, Namiko Nishida, Eigo Fukai, Takashi Abe, Ryo Fujimoto, Keiichi Okazaki
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12885-016-2453-4

Context dependent regulatory patterns of the androgen receptor and androgen receptor target genes
Cited by: 26
Author(s): Jan Roger Olsen, Waqas Azeem, Margrete R. Hellem, Kristo Marvyin, Yaping Hua, Yi Qu, Lisha Li, Biaoyang Lin, Xiaoting Ke, Anne Margrete Øyan, Karl H. Kalland
Software Mentions: 3
Published: about 10 years ago

10.1186/s13071-016-1341-8

Reconstruction of the insulin-like signalling pathway of Haemonchus contortus
Cited by: 14
Author(s): Namitha Mohandas, Min Hu, Andreas J. Stroehlein, Neil D. Young, Paul W. Sternberg, James B. Lok, Robin B. Gasser
Software Mentions: 3
Published: over 10 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: almost 12 years ago

10.1029/2020MS002138

Clouds and Convective Self‐Aggregation in a Multimodel Ensemble of Radiative‐Convective Equilibrium Simulations
Cited by: 69
Author(s): Allison A. Wing, Catherine L. Stauffer, Tobias Becker, Kevin A. Reed, Min‐Seop Ahn, Nathan Arnold, Sandrine Bony, Mark Branson, G. H. Bryan, Jean‐Pierre Chaboureau, Stephan R. de Roode, Gayatri Kulkarni, Cathy Hohenegger, I‐Kuan Hu, Fredrik Jansson, Todd R. Jones, Marat Khairoutdinov, Dae Hyun Kim, Zane Martin, Shuhei Matsugishi, Brian Medeiros, Hiroaki Miura, Yumin Moon, Sebastian K. Müller, Tomoki Ohno, Max Popp, Thara Prabhakaran, David A. Randall, Rosimar Ríos-Berríos, Nicolas Rochetin, Romain Roehrig, David M. Romps, James H. Ruppert, Masaki Satoh, Levi G. Silvers, Martin S. Singh, Björn Stevens, Lorenzo Tomassini, Chiel C. van Heerwaarden, Shuguang Wang, Ming Zhao
Software Mentions: 3
Published: about 6 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

10.1093/gigascience/giz040

Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls
Cited by: 41
Author(s): Brent S. Pedersen, Aaron R. Quinlan
Software Mentions: 3
Published: over 7 years ago

10.1007/s13361-016-1544-4

Prognostic Metabolite Biomarkers for Soft Tissue Sarcomas Discovered by Mass Spectrometry Imaging
Cited by: 37
Author(s): Sha Lou, Benjamin Balluff, Arjen H.G. Cleven, Judith V.M.G. Bovée, Liam A. McDonnell
Software Mentions: 3
Published: almost 10 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

10.3390/v11010033

A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium
Cited by: 5
Author(s): Wei Zou, Min Xiong, Xuefeng Deng, John F. Engelhardt, Ziying Yan, Jianming Qiu
Software Mentions: 3
Published: over 7 years ago

10.3390/v12070782

High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics
Cited by: 4
Author(s): Sílvia Inês Sardi, Renata Carvalho, Luis Gustavo Carvalho Pacheco, João Fernando Lourenço de Almeida, Emilia M M D A Belitardo, Carina S. Pinheiro, Gúbio Soares Campos, Eric Roberto Guimarães Rocha Aguiar
Software Mentions: 3
Published: about 6 years ago

10.1186/s12859-020-03665-5

SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles
Cited by: 11
Author(s): Zhenhua Yu, Fang Du, Rongjun Ban, Yuanwei Zhang
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-13-74

GemSIM: general, error-model based simulator of next-generation sequencing data
Cited by: 141
Author(s): Kerensa McElroy, Fabio Luciani, Torsten Thomas
Software Mentions: 3
Published: over 14 years ago

10.1186/s12859-018-2319-7

BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs
Cited by: 21
Author(s): Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
Software Mentions: 3
Published: about 8 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

10.1093/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

10.1120/jacmp.v17i3.6370

2016 AAPM Spring Clinical Meeting - Abstracts
Cited by: 0
Author(s):
Software Mentions: 3
Published: over 10 years ago

10.1186/s12859-021-04267-5

Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing
Cited by: 8
Author(s): Lior Galanti, Dennis Shasha, Kristin C. Gunsalus
Software Mentions: 3
Published: about 5 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: almost 12 years ago

10.1186/s12915-021-01108-y

Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
Cited by: 14
Author(s): Nicole Gruenheit, Amy Baldwin, Balint Stewart, Sarah Jaques, Thomas Keller, Katie Parkinson, William Salvidge, Robert Baines, Chris Brimson, Jason B. Wolf, Rex L. Chisholm, Adrian J. Harwood, Christopher Thompson
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0103515

Characterisation of Adaptive Genetic Diversity in Environmentally Contrasted Populations of Eucalyptus camaldulensis Dehnh. (River Red Gum)
Cited by: 40
Author(s): Shannon Dillon, Rachel McEvoy, Darren S. Baldwin, Gavin N. Rees, Y. M. Parsons, Simon G. Southerton
Software Mentions: 3
Published: about 12 years ago

10.1186/s12915-021-01114-0

Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species
Cited by: 7
Author(s): Lianggang Huang, Xuejie Li, Lü Dong, Bin Wang, Li Pan
Software Mentions: 3
Published: about 5 years ago

10.15252/msb.20188584

Path‐seq identifies an essential mycolate remodeling program for mycobacterial host adaptation
Cited by: 49
Author(s): Eliza J.R. Peterson, Rebeca Bailo, Alissa C. Rothchild, Mario L. Arrieta-Ortiz, Amardeep Kaur, Min Pan, Dat Mai, Abrar A. Abidi, Charlotte Cooper, Alan Aderem, Apoorva Bhatt, Nitin S. Baliga
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-015-0775-x

A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11
Cited by: 21
Author(s): Jilong Li, Renzhi Cao, Jianlin Cheng
Software Mentions: 3
Published: almost 11 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: almost 13 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/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/s13059-020-02045-9

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/s12859-020-03726-9

IonCRAM: a reference-based compression tool for ion torrent sequence files
Cited by: 2
Author(s): Moustafa Shokrof, Mohamed Abouelhoda
Software Mentions: 3
Published: about 6 years ago

10.1186/s12859-018-2318-8

Identification of differentially expressed genes by means of outlier detection
Cited by: 5
Author(s): Itziar Irigoien, C. Arenas
Software Mentions: 3
Published: about 8 years ago

10.1186/s12859-019-2683-y

RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets
Cited by: 17
Author(s): Giovanni Perconti, Patrizia Rubino, Flavia Contino, Serena Bivona, Giorgio Bertolazzi, Michele Tumminello, Salvatore Feo, Agata Giallongo, Claudia Coronnello
Software Mentions: 3
Published: over 7 years ago

10.1186/1743-422X-8-285

Cellular transcriptional profiling in human lung epithelial cells infected by different subtypes of influenza A viruses reveals an overall down-regulation of the host p53 pathway
Cited by: 38
Author(s): Benjamin Terrier, Laurence Josset, Julien Textoris, Virginie Marcel, Gaëlle Cartet, Olivier Ferraris, Catherine Nguyen, Bruno Lina, Jean‐Jacques Diaz, Jean-Christophe Bourdon, Manuel Rosa‐Calatrava
Software Mentions: 3
Published: over 15 years ago

10.3892/mmr.2015.3318

PUFA diets alter the microRNA expression profiles in an inflammation rat model
Cited by: 34
Author(s): Zheng Zhang, Yubin Ge, Jinyu Zhang, Meilan Xue, Quan Li, Dongliang Lin, Wenhui Ma
Software Mentions: 3
Published: over 11 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

10.1155/2020/3158108

Danhong Injection Alleviates Cardiac Fibrosis via Preventing the Hypermethylation of Rasal1 and Rassf1 in TAC Mice
Cited by: 7
Author(s): Sinai Li, Ping Li, Weihong Liu, Juju Shang, Sheng-Lei Qiu, Xiang Li, Wei Liu, Haoyue Shi, Mingxue Zhou, Hongxu Liu
Software Mentions: 3
Published: over 5 years ago

10.1002/mgg3.1503

Identification of common differentially expressed genes in Turner (45,X) and Klinefelter (47,XXY) syndromes using bioinformatics analysis
Cited by: 5
Author(s): María Carolina Manotas, Juan M. Calderón, Liliana López‐Kleine, Fernando Suárez‐Obando, Olga Moreno, Alejandra Rojas
Software Mentions: 3
Published: almost 6 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

10.1186/1471-2164-9-446

Molecular architecture of the fruit fly's airway epithelial immune system
Cited by: 58
Author(s): Christina Wagner, Kerstin Isermann, Heinz Fehrenbach, Thomas Roeder
Software Mentions: 3
Published: almost 18 years ago

10.1186/1471-2105-6-173

Normal uniform mixture differential gene expression detection for cDNA microarrays
Cited by: 74
Author(s): Nema Dean, Adrian E. Raftery
Software Mentions: 3
Published: about 21 years ago

10.3390/molecules22101734

Analysis of Genetic Diversity and Structure Pattern of Indigofera Pseudotinctoria in Karst Habitats of the Wushan Mountains Using AFLP Markers
Cited by: 6
Author(s): Yanting Fan, Chenglin Zhang, Wen Bing Wu, Wei He, Li Zhang, Xiao Ma
Software Mentions: 3
Published: almost 9 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

10.1016/j.mcpro.2021.100125

Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network
Cited by: 6
Author(s): Cristian V. A. Munteanu, Gabriela Chirițoiu, Marioara Chirițoiu, Simona Ghenea, Andrei-José Petrescu, Ștefana M. Petrescu
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-6-129

Considerations when using the significance analysis of microarrays (SAM) algorithm
Cited by: 110
Author(s): Ola Larsson, Claes Wahlestedt, James A. Timmons
Software Mentions: 3
Published: over 21 years ago

10.1186/1471-2105-16-S7-S10

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)
Cited by: 14
Author(s): Ruibang Luo, Jeanno Cheung, Edward Wu, Heng Wang, S. C. Chan, Wai-Chun Law, Guangzhu He, Chang Yu, Chi-Man Liu, Dazong Zhou, Yingrui Li, Ruiqiang Li, Jun Wang, Xinhua Zhu, Shaoliang Peng, Tak Wah Lam
Software Mentions: 3
Published: over 11 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

10.1186/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/s12859-019-2903-5

A comparison of three programming languages for a full-fledged next-generation sequencing tool
Cited by: 10
Author(s): Pascal Costanza, Charlotte Herzeel, Wilfried Verachtert
Software Mentions: 3
Published: over 7 years ago

10.1186/1476-4598-12-140

Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations
Cited by: 53
Author(s): Ângela Aguirres Fachel, Ana Carolina Tahira, Santiago A. Vilella-Arias, Vinicius Maracaja‐Coutinho, Etel Rp Gimba, Giselle Maria Vignal, Franz Campos, Eduardo M. Reis, Sérgio Verjovski-Almeida
Software Mentions: 3
Published: almost 13 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

10.1186/1471-2164-10-361

Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae)
Cited by: 18
Author(s): Richard H. Baker, Jenna Morgan, Xianhui Wang, Jeffrey L. Boore, Gerald S. Wilkinson
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2105-14-143

Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis
Cited by: 23
Author(s): Lifang Zhang, Juan Zhang, Gang Yang, Di Wu, Lina Jiang, Zhining Wen, Menglong Li
Software Mentions: 3
Published: over 13 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: almost 12 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

10.1186/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

10.3389/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: 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/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

10.3389/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

10.3389/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

10.1186/1471-2105-9-144

Empirical Bayes analysis of single nucleotide polymorphisms
Cited by: 21
Author(s): Holger Schwender, Katja Ickstadt
Software Mentions: 3
Published: over 18 years ago

10.1186/bcr3150

Relevance of PTEN loss in brain metastasis formation in breast cancer patients
Cited by: 87
Author(s): Harriet Wikman, Katrin Lamszus, Niclas Detels, Liubov Uslar, Michaela Wrage, Christian Benner, Ina Hohensee, Bauke Ylstra, Kathrin Eylmann, Marc Zapatka, Guido Sauter, Dirk Kemming, Markus Glatzel, Volkmar Müller, Manfred Westphal, Klaus Pantel
Software Mentions: 3
Published: over 14 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

10.3389/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: almost 7 years ago