cran: SAM | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-76533-0

High definition transcranial direct current stimulation modulates abnormal neurophysiological activity in post-stroke aphasia
Cited by: 16
Author(s): Priyanka P. Shah-Basak, Gayatri Sivaratnam, Selina Teti, Alexander Francois-Nienaber, Maryam Yossofzai, Sabrina E M Armstrong, Sumiti Nayar, Regina Jokel, Jed A. Meltzer
Software Mentions: 3
Published: about 4 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 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: over 4 years ago

10.1371/journal.pone.0020924

The Reconstruction of Condition-Specific Transcriptional Modules Provides New Insights in the Evolution of Yeast AP-1 Proteins
Cited by: 17
Author(s): Christel Goudot, Catherine Etchebest, Frédéric Devaux, Gaëlle Lelandais
Software Mentions: 3
Published: over 13 years ago

10.18632/aging.103184

Plasma proteomic profiling of young and old mice reveals cadherin-13 prevents age-related bone loss
Cited by: 14
Author(s): Yong Ryoul Yang, Mohammad Humayun Kabir, Jin Hee Park, Jae-Il Park, Jae Sook Kang, Shinyeong Ju, Yeo Jin Shin, Seung Min Lee, Jaemin Lee, Seokho Kim, Kwang-Pyo Lee, Soo Young Lee, Cheolju Lee, Kideok D. Kwon
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0113862

The Accuracy, Feasibility and Challenges of Sequencing Short Tandem Repeats Using Next-Generation Sequencing Platforms
Cited by: 26
Author(s): Monika Závodná, Andrew T. M. Bagshaw, Rüdiger Bräuning, Neil J. Gemmell
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0081468

Quantitative Identification of Mutant Alleles Derived from Lung Cancer in Plasma Cell-Free DNA via Anomaly Detection Using Deep Sequencing Data
Cited by: 62
Author(s): Yoji Kukita, Junji Uchida, Shigeyuki Oba, Kazumi Nishino, Toru Kumagai, Koki Taniguchi, Takako Okuyama, Fumio Imamura, Kikuya Kato
Software Mentions: 3
Published: about 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 7 years ago

10.1186/1471-2105-12-411

EPEPT: A web service for enhanced P-value estimation in permutation tests
Cited by: 5
Author(s): Theo Knijnenburg, Jake Lin, Hector Rovira, John P. Boyle, Ilya Shmulevich
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pone.0090240

A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene
Cited by: 33
Author(s): Yvette A. Halley, Scot E. Dowd, Jared E. Decker, Paul Seabury, Eric K. Bhattarai, Charles D. Johnson, Dale Rollins, Ian R. Tizard, Donald J. Brightsmith, Markus J. Peterson, Jeremy F. Taylor, Christopher M. Seabury
Software Mentions: 3
Published: over 10 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 19 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 9 years ago

10.1186/s12859-015-0812-9

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles
Cited by: 5
Author(s): Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie Verbist, Joke Reumers, Herman van Vlijmen, Jeroen Aerssens
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0048743

Internal Habitat Quality Determines the Effects of Fragmentation on Austral Forest Climbing and Epiphytic Angiosperms
Cited by: 9
Author(s): Ainhoa Magrach, Asier R. Larrinaga, Luis Santamarı́a
Software Mentions: 3
Published: about 12 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: about 16 years ago

10.1186/s12859-021-03980-5

ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data
Cited by: 7
Author(s): Elisa Pischedda, Cristina M. Crava, Martina Carlassara, Susanna Zucca, Laila Gasmi, Mariangela Bonizzoni
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12862-019-1353-z

Origin and diversification of the plasminogen activation system among chordates
Cited by: 26
Author(s): Andrés Chana-Muñoz, Agnieszka Jendroszek, Malene Sønnichsen, Tobias Wang, Michael Ploug, Jan K. Jensen, Peter A. Andreasen, Christian Berthou, Frank Panitz
Software Mentions: 3
Published: almost 6 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: over 19 years ago

10.1371/journal.pone.0249859

Physiological and genetic characterization of heat stress effects in a common bean RIL population
Cited by: 17
Author(s): Yulieth Vargas, Víctor Manuel Mayor-Durán, Hector Fabio Buendia, Henry Alonso Ruiz-Guzman, Bodo Raatz
Software Mentions: 3
Published: over 3 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 6 years ago

10.1186/s12862-019-1522-0

RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea)
Cited by: 11
Author(s): Akira Iguchi, Yuki Yoshioka, Zac H. Forsman, Ingrid S. Knapp, Robert J. Toonen, Yuki Hongo, Satoshi Nagai, Nina Yasuda
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0039951

Effects of Eutrophication, Seasonality and Macrofouling on the Diversity of Bacterial Biofilms in Equatorial Coral Reefs
Cited by: 42
Author(s): Yvonne Sawall, Claudio Richter, Alban Ramette
Software Mentions: 3
Published: over 12 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: over 17 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 (Cajanus cajan)
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: almost 8 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 5 years ago

10.1128/mBio.02096-17

The Essential Genome of Escherichia coli K-12
Cited by: 204
Author(s): Emily C. A. Goodall, Ashley Robinson, Iain G. Johnston, Sara Jabbari, A. Keith Turner, Adam F. Cunningham, Peter A. Lund, Jeffrey A. Cole, Ian R. Henderson
Software Mentions: 3
Published: over 6 years ago

10.1186/1472-6815-14-9

Combined examination of sequence and copy number variations in human deafness genes improves diagnosis for cases of genetic deafness
Cited by: 23
Author(s): Haiying Ji, Jingqiao Lü, Jianjun Wang, Huawei Li, Xiaobo Lin
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0062547

p63 Attenuates Epithelial to Mesenchymal Potential in an Experimental Prostate Cell Model
Cited by: 29
Author(s): Jan Roger Olsen, Anne Margrete Øyan, Kari Rostad, Margrete R. Hellem, Jie Liu, Lisha Li, David Micklem, Hallvard Haugen, James B. Lorens, Varda Rotter, Xisong Ke, Biaoyang Lin, Karl‐Henning Kalland
Software Mentions: 3
Published: over 11 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 4 years ago

10.1186/1471-2105-16-S18-S16

Identification of aberrant gene expression associated with aberrant promoter methylation in primordial germ cells between E13 and E16 rat F3 generation vinclozolin lineage
Cited by: 23
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0002737

Type I Interferon: Potential Therapeutic Target for Psoriasis?
Cited by: 253
Author(s): Yihong Yao, Laura K. Richman, Chris Morehouse, Melissa de los Reyes, Brandon W. Higgs, Anmarie Boutrin, Barbara White, Anthony J. Coyle, James G. Krueger, Peter A. Kiener, Bahija Jallal
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2164-10-342

Gene expression profile of rat left ventricles reveals persisting changes following chronic mild exercise protocol: implications for cardioprotection
Cited by: 23
Author(s): Betti Giusti, Marina Marini, Luciana Rossi, Ilaria Lapini, Alberto Magi, Andrea Capalbo, Rosa Lapalombella, Simona di Tullio, Michele Samaja, Fabio Esposito, V. Margonato, Maria Boddi, Rosanna Abbate, Arsenio Veicsteinas
Software Mentions: 3
Published: almost 16 years ago

10.1186/1471-2164-11-13

Sex-dimorphic gene expression and ineffective dosage compensation of Z-linked genes in gastrulating chicken embryos
Cited by: 55
Author(s): Shaobing O. Zhang, Sachin Mathur, Gaye Hattem, Olivier Tassy
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pone.0010247

Evaluation of the Psoriasis Transcriptome across Different Studies by Gene Set Enrichment Analysis (GSEA)
Cited by: 153
Author(s): Mayte Suárez‐Fariñas, Michelle A. Lowes, Lisa C. Zaba, James G. Krueger
Software Mentions: 3
Published: over 14 years ago

10.3390/ani11071863

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep
Cited by: 8
Author(s): Aiju Liu, Xiaoyong Chen, Menghe Liu, Limeng Zhang, Xiaofei Ma, Shujun Tian
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0084231

Identification of the Third Binding Site of Arsenic in Human Arsenic (III) Methyltransferase
Cited by: 12
Author(s): Xiangli Li, Zhirong Geng, Jiayin Chang, Shuping Wang, Xiaoli Song, Xin Hu, Zhilin Wang
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0238311

Length of stay to recover from severe acute malnutrition and associated factors among under-five years children admitted to public hospitals in Aksum, Ethiopia
Cited by: 10
Author(s): Wagnew Tesfay, Mebrahtu Abay, Solomon Hintsa, Tekia Zafu
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0163832

The Role of Vitamin D in the Transcriptional Program of Human Pregnancy
Cited by: 30
Author(s): Amal Al-Garawi, Vincent J. Carey, Divya Chhabra, Hooman Mirzakhani, Jarrett Morrow, Jessica Lasky‐Su, Weiliang Qiu, Nancy Laranjo, Augusto A. Litonjua, Scott T. Weiss
Software Mentions: 3
Published: about 8 years ago

10.1186/s12859-018-2592-5

IMOS: improved Meta-aligner and Minimap2 On Spark
Cited by: 7
Author(s): Mostafa Hadadian Nejad Yousefi, Maziar Goudarzi, Seyed Abolfazl Motahari
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0015595

A Novel Statistical Algorithm for Gene Expression Analysis Helps Differentiate Pregnane X Receptor-Dependent and Independent Mechanisms of Toxicity
Cited by: 8
Author(s): M. Ann Mongan, Robert T. Dunn, Steven Vonderfecht, Nancy E. Everds, Guang Chen, Cheng Su, Marnie Higgins-Garn, Yuan Chen, Cynthia A. Afshari, Toni Williamson, Linda L. Carlock, Christopher DiPalma, Suzanne T. Moss, Jeanine L. Bussiere, Charles W. Qualls, Yudong He, Hisham K. Hamadeh
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12859-020-3491-0

Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure
Cited by: 6
Author(s): Jad Abbass, Jean‐Christophe Nebel
Software Mentions: 3
Published: over 4 years ago

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: almost 15 years ago

10.1186/s12864-021-07505-5

Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle
Cited by: 12
Author(s): Paulina G. Eusebi, Natalia Sevane, Thomas O’Rourke, Manuel Pizarro, Cédric Boeckx, S. Dunner
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-9-131

The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution
Cited by: 127
Author(s): Kirstin Replogle, Arthur P. Arnold, Gregory F. Ball, Mark Band, Staffan Bensch, Eliot A. Brenowitz, Shu Dong, Jenny Drnevich, Margaret Ferris, Julia M. George, George Gong, Dennis Hasselquist, Álvaro Gonzalez Hernández, Ryan Kim, Harris A. Lewin, Lei Liu, Peter V. Lovell, Claudio V. Mello, Sara Naurin, Sandra L. Rodriguez-Zas, Jyothi Thimmapuram, Juli Wade, David F. Clayton
Software Mentions: 3
Published: over 16 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 9 years ago

10.1371/journal.pone.0010770

Integrative Genome Comparison of Primary and Metastatic Melanomas
Cited by: 159
Author(s): Omar Kabbarah, Cristina Nogueira, Bin Feng, Rosalynn M. Nazarian, Marcus W. Bosenberg, Min Wu, Kenneth L. Scott, Lawrence N. Kwong, Yonghong Xiao, Carlos Cordón-Cardo, Scott R. Granter, Sridhar Ramaswamy, Todd R. Golub, Lyn M. Duncan, Stephan N. Wagner, Cameron Brennan, Lynda Chin
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2164-15-969

MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence
Cited by: 9
Author(s): Turki Turki, Usman Roshan
Software Mentions: 3
Published: almost 11 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: almost 11 years ago

10.1371/journal.pone.0087499

Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress
Cited by: 80
Author(s): Henry D. Priest, Samuel E. Fox, Erik R. Rowley, Jessica R. Murray, Todd P. Michael, Todd C. Mockler
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-14-666

Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees
Cited by: 62
Author(s): Pablo Cingolani, Xiaoyi Cao, Radhika S. Khetani, Chieh Chun Chen, Melissa Coon, Alya’a Sammak, Aliccia Bollig‐Fischer, Susan Land, Yun Huang, Matthew E. Hudson, Mark D. Garfinkel, Sheng Zhong, Gene E. Robinson, Douglas M. Ruden
Software Mentions: 3
Published: about 11 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 17 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 9 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 12 years ago

10.1371/journal.pone.0086869

CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
Cited by: 46
Author(s): Yong-Chao Liu, Bernt Popp, Bertil Schmidt
Software Mentions: 3
Published: almost 11 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 3 years ago

10.1371/journal.pone.0067410

Boosting Probabilistic Graphical Model Inference by Incorporating Prior Knowledge from Multiple Sources
Cited by: 10
Author(s): Paurush Praveen, Holger Fröhlich
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-10-420

Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation
Cited by: 13
Author(s): Tamara Aid-Pavlidis, Pavlos Pavlidis, Tõnis Timmusk
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.pone.0117006

Spatial Transferability of Habitat Suitability Models of Nephrops norvegicus among Fished Areas in the Northeast Atlantic: Sufficiently Stable for Marine Resource Conservation?
Cited by: 24
Author(s): Valentina Lauria, Anne Marie Power, Colm Lordan, Adrian Weetman, Mark P. Johnson
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0046847

lociNGS: A Lightweight Alternative for Assessing Suitability of Next-Generation Loci for Evolutionary Analysis
Cited by: 6
Author(s): Sarah M. Hird
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0236197

Family-based exome sequencing combined with linkage analyses identifies rare susceptibility variants of MUC4 for gastric cancer
Cited by: 3
Author(s): Young-Wook Choi, Jung Hun Ohn, Nayoung Kim, Wonji Kim, Kyungtaek Park, Sungho Won, Lee Sael, Cheol Min Shin, Sun Min Lee, Sejoon Lee, Hyun Joo An, Dong Man Jang, Byung Woo Han, Hye Seung Lee, Seung Joo Kang, Sang Woo Kim, Dong Hoon Lee
Software Mentions: 3
Published: over 4 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 15 years ago

10.1371/journal.pone.0125201

Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data
Cited by: 55
Author(s): Lilit Nersisyan, Arsen Arakelyan
Software Mentions: 3
Published: over 9 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: over 10 years ago

10.3390/cancers13153889

Chromosomal Translocations in NK-Cell Lymphomas Originate from Inter-Chromosomal Contacts of Active rDNA Clusters Possessing Hot Spots of DSBs
Cited by: 6
Author(s): Nickolai A. Tchurikov, Л. А. Урошлев, Elena S. Klushevskaya, Ildar R. Alembekov, Maria A. Lagarkova, Galina I. Kravatskaya, Vsevolod J. Makeev, Yuri V. Kravatsky
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0002126

Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance
Cited by: 162
Author(s): David G. Hendrickson, Daniel J. Hogan, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: over 16 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: about 14 years ago

10.1371/journal.pone.0121730

Gene Expression Profiles Associated with Pediatric Relapsed AML
Cited by: 23
Author(s): Costa Bachas, Gerrit Jan Schuurhuis, C. Michel Zwaan, Marry M. van den Heuvel‐Eibrink, Monique L. den Boer, Eveline S.J.M. de Bont, Zinia J. Kwidama, Dirk Reinhardt, Ursula Creutzig, Valérie de Haas, Gertjan J. L. Kaspers, Jacqueline Cloos
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0102185

Embryonic miRNA Profiles of Normal and Ectopic Pregnancies
Cited by: 30
Author(s): Francisco Domı́nguez, Juan Manuel Moreno-Moya, Teresa Lozoya, Ainhoa Romero, Sebastián Martínez, Mercedes Monterde, Marta Gurrea, Blanca Ferri, Marı́a José Núñez, Carlos Simón, António Pellicer
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0022226

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology
Cited by: 70
Author(s): Xun Lan, Christopher M. Adams, Mark Landers, Miroslav Dudas, Daniel Krissinger, George Marnellos, Russell Bonneville, Maoxiong Xu, Junbai Wang, Tim H-M. Huang, Gavin Meredith, Victor X. Jin
Software Mentions: 3
Published: over 13 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: over 8 years ago

10.1186/1471-2164-8-428

Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison
Cited by: 226
Author(s): S. Pilati, Michele Perazzolli, A. Malossini, Alessandro Cestaro, L. Dematté, Paolo Fontana, A. Dal Rì, Roberto Viola, Riccardo Velasco, C. Moser
Software Mentions: 3
Published: almost 17 years ago

10.18632/oncotarget.18162

Upregulation of long noncoding RNA HOXA-AS3 promotes tumor progression and predicts poor prognosis in glioma
Cited by: 53
Author(s): Fan Wu, Chuanbao Zhang, Jinquan Cai, Fan Yang, Tingyu Liang, Xiaoyan Yan, Haoyuan Wang, Wen Wang, Jing Chen, Tao Jiang
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.10947

Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression
Cited by: 22
Author(s): Zhiming Li, Zaozao Zheng, Jun Ruan, Zhi Li, Xuan Zhuang, Chi-Meng Tzeng
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0219551

Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes
Cited by: 16
Author(s): Han-Ming Liu, Dan Yang, Zhao-Fa Liu, Shengzhou Hu, Yan Shen-hai, Xian-Wen He
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.15604

NUSAP1 promotes invasion and metastasis of prostate cancer
Cited by: 49
Author(s): Catherine A. Gordon, Xue Gong, Durga Ganesh, James D. Brooks
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.19733

Overexpression of COL3A1 confers a poor prognosis in human bladder cancer identified by co-expression analysis
Cited by: 59
Author(s): Lushun Yuan, Bo Shu, Changhong Liang, Kaiyu Qian, Yongzhi Wang, Guofeng Qian, Yuan Zhu, Xinyue Cao, Conghua Xie, Yu Xiao, Xinghuan Wang
Software Mentions: 3
Published: over 7 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 11 years ago

10.1186/s12974-017-0858-x

Toll-like receptor 4 in glial inflammatory responses to air pollution in vitro and in vivo
Cited by: 99
Author(s): Nick Woodward, Morgan C. Levine, Amin Haghani, Farimah Shirmohammadi, Arian Saffari, Constantinos Sioutas, Todd E. Morgan, Caleb E. Finch
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.5876

KIAA0101 is associated with human renal cell carcinoma proliferation and migration induced by erythropoietin
Cited by: 27
Author(s): Shengjun Fan, Xin Li, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 3
Published: about 9 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: over 12 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: almost 14 years ago

10.3390/ijms22169081

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches
Cited by: 10
Author(s): Aljaž Gaber, Miha Pavšič
Software Mentions: 3
Published: about 3 years ago

10.3390/ijms22179246

Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus
Cited by: 8
Author(s): Nesma Shalby, Ibrahim A. A. Mohamed, Jie Xiong, Kaining Hu, Yuting Yang, Elsayed Nishawy, Bin Yi, Jing Wen, Chaozhi Ma, Tingdong Fu, Jinxing Tu
Software Mentions: 3
Published: about 3 years ago

10.1186/1471-2164-10-98

SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip® expression data
Cited by: 26
Author(s): Adriane Menßen, Götz Edinger, Joachim R. Grün, Ulrike Haase, Ria Baumgrass, Andreas Grützkau, Andreas Radbruch, G.-R. Burmester, Thomas Häupl
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.pone.0085583

Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming
Cited by: 36
Author(s): Thomas P. van Gurp, Lauren M. McIntyre, Koen J. F. Verhoeven
Software Mentions: 3
Published: almost 11 years ago

10.3390/ijms22041837

Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer
Cited by: 5
Author(s): Diamanto Skopelitou, Benchun Miao, Aayushi Srivastava, Abhishek Kumar, Magdalena Kuswick, Dagmara Dymerska, Nagarajan Paramasivam, Matthias Schlesner, Jan Lubiński, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0151522

Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
Cited by: 25
Author(s): Paul Pavlidis, Vignesh Dhandapani, Jana Jeevan Rameneni, Xiaonan Li, Ganesan Sivanandhan, Su Ryun Choi, Wenxing Pang, Subin Im, Yong Pyo Lim
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0000242

Epigenetic Activation of a Subset of mRNAs by eIF4E Explains Its Effects on Cell Proliferation
Cited by: 203
Author(s): Yaël Mamane, Emmanuel Petroulakis, Yvan Martineau, Takaaki Sato, Ola Larsson, Vinagolu K. Rajasekhar, Nahum Sonenberg
Software Mentions: 3
Published: almost 18 years ago

10.3390/ijms22105231

Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge
Cited by: 12
Author(s): Cristina Zamora-Ballesteros, Glória Pinto, Joana Amaral, Luís Valledor, Artur Alves, Julio J. Diez, Jorge Martín‐García
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms20010016

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools
Cited by: 34
Author(s): Dana Pascovici, Jemma X. Wu, Matthew J. McKay, Chitra Joseph, Zainab Noor, Karthik Shantharam Kamath, Yunqi Wu, Shoba Ranganathan, Vivek Gupta, Mehdi Mirzaei
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms16035975

RNA-Seq Transcriptome Analysis of Maize Inbred Carrying Nicosulfuron-Tolerant and Nicosulfuron-Susceptible Alleles
Cited by: 26
Author(s): Xiaomin Liu, Xiaogang Xu, Binghua Li, Xueqing Wang, Guiqi Wang, Yaqian Li
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0028275

The Global Transcriptional Response of Fission Yeast to Hydrogen Sulfide
Cited by: 8
Author(s): Jianmin Xu, Weizhi He, Alastair I. H. Murchie, Dongrong Chen
Software Mentions: 3
Published: almost 13 years ago

10.3390/ijms17050696

Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction
Cited by: 31
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: over 8 years ago

10.3390/ijms20235922

Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies
Cited by: 10
Author(s): Xiaoxiang Zhang, Juan Zhou, Niansheng Huang, Lanjing Mo, Minjia Lv, Yujiao Gao, Chen Chen, Yin Su, Jianhua Ju, Guichun Dong, Yong Zhou, Zefeng Yang, Aihong Li, Yulong Wang, Jianye Huang, Youli Yao
Software Mentions: 3
Published: almost 5 years ago

10.1186/s40246-019-0194-6

vi-HMM: a novel HMM-based method for sequence variant identification in short-read data
Cited by: 1
Author(s): Man Lai Tang, Mohammad Shabbir Hasan, Hongxiao Zhu, Liqing Zhang, Xiaowei Wu
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1007543

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
Cited by: 6
Author(s): Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Mitchell D. Probasco, Ning Leng, Bret Duffin, John Steill, Scott Swanson, Brian E. McIntosh, Ron Stewart, Christina Kendziorski, James A. Thomson, Rhonda Bacher
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-020-03658-4

Performance evaluation of lossy quality compression algorithms for RNA-seq data
Cited by: 1
Author(s): Rongshan Yu, Wenxian Yang, Wang Shun
Software Mentions: 3
Published: over 4 years ago

10.1101/2021.07.09.21260221

Genetic regulation ofOAS1nonsense-mediated decay underlies association with risk of severe COVID-19
Cited by: 8
Author(s): Abdul Rouf Banday, Megan L. Stanifer, Óscar Flórez-Vargas, Olusegun O. Onabajo, Muhammad Atif Zahoor, Brenen W. Papenberg, Timothy J. Ring, Chia-Han Lee, Evangelos Andreakos, Evgeny Arons, Greg Barsh, Leslie G. Biesecker, David L. Boyle, Andrea N. Burnett‐Hartman, Mary Carrington, Euijin Chang, Pyoeng Gyun Choe, Rex L Chrisholm, Clifton L. Dalgard, Jeff Edberg, Nathan Erdmann, Heather Spencer Feigelson, Gary S. Firestein, Adam J. Gehring, Michelle Ho, Steven M. Holland, Amy Hutchinson, Hogune Im, Michael G. Ison, Hong Bin Kim, Robert J. Kreitman, Bruce R. Korf, Lisa Mirabello, Jennifer A. Pacheco, Michael J. Peluso, Daniel J. Rader, David T. Redden, Marylyn D. Ritchie, Brooke Rosenbloom, Hanaisa P. Sant Anna, Sharon A. Savage, E. Siouti, Vasiliki Triantafyllia, Joselin M. Vargas, Anurag Verma, Vibha Vij, Duane R. Wesemann, Meredith Yeager, Xu G. Yu, Yu Zhang, Steeve Boulant, Stephen J. Chanock, Jordan J. Feld, Ludmila Prokunina–Olsson
Software Mentions: 3
Published: over 3 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 3 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 3 years ago

Projects: cran: SAM

Papers Mentioning SAM 4,566