cran: SAM | Projects | Ecosyste.ms: Papers

10.3390/vaccines8030495

Estimating the Fiscal Consequences of National Immunization Programs Using a “Government Perspective” Public Economic Framework
Cited by: 3
Author(s): Mark P. Connolly, Nikolaos Kotsopoulos
Software Mentions: 1
Published: about 4 years ago

10.1111/vop.12597

Optical coherence tomography and molecular analysis of sudden acquired retinal degeneration syndrome ( <scp>SARDS</scp> ) eyes suggests the immune‐mediated nature of retinal damage
Cited by: 26
Author(s): Siniša D. Grozdanić, Tatjana Lazic, Helga Kecova, Kabhilan Mohan, Markus H. Kuehn
Software Mentions: 1
Published: over 6 years ago

10.14202/vetworld.2016.1287-1293

Value added by Spirulina platensis in two different diets on growth performance, gut microbiota, and meat quality of Japanese quails
Cited by: 20
Author(s): Mohamed S. Yusuf, Marwa A. Hassan, Mohamed M. Abdel-Daim, Adel S. El Nabtiti, Amira Ahmed, Sherief A Moawed, Ahmed K. Elsayed, Hengmi Cui
Software Mentions: 1
Published: almost 8 years ago

10.14202/vetworld.2017.880-887

Influence of microclimatic ammonia levels on productive performance of different broilers' breeds estimated with univariate and multivariate approaches
Cited by: 15
Author(s): Essam S. Soliman, Sherif A. Moawed, Rania Hassan
Software Mentions: 1
Published: over 7 years ago

10.14202/vetworld.2018.259-267

Modeling the potential risk factors of bovine viral diarrhea prevalence in Egypt using univariable and multivariable logistic regression analyses
Cited by: 27
Author(s): Abdelfattah Selim, Mahmoud M. Elhaig, Sherif A. Moawed, E. M. El-Nahas
Software Mentions: 1
Published: over 6 years ago

10.14202/vetworld.2019.664-670

Isolation and molecular characterization of Mycoplasma spp. in sheep and goats in Egypt
Cited by: 8
Author(s): Mounier mohamed Abdel Halium, Fayez Awadalla Salib, Sherif Marouf, Emil saad Abdel Massieh
Software Mentions: 1
Published: over 5 years ago

10.1186/1743-422X-4-97

Comparative genomics of Bacillus thuringiensis phage 0305φ8-36: defining patterns of descent in a novel ancient phage lineage
Cited by: 25
Author(s): Stephen C. Hardies, Julie A. Thomas, Philip Serwer
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2105-10-131

SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip
Cited by: 7
Author(s): Hironori Fujisawa, Youko Horiuchi, Yoshiaki Harushima, Toyoyuki Takada, Shinto Eguchi, Takako Mochizuki, Takayuki Sakaguchi, Toshihiko Shiroishi, Nori Kurata
Software Mentions: 1
Published: over 15 years ago

10.18632/oncotarget.19674

Whole-exome sequencing reveals novel mutations and epigenetic regulation in hypopharyngeal carcinoma
Cited by: 11
Author(s): Ping Wu, Honglong Wu, Yurong Tang, Shi Luo, Xing Fang, Chubo Xie, Jian He, Suping Zhao, Xiaofeng Wang, Jiajia Xu, Xi Chen, Dongfang Li, Huanming Yang, Jian Wang
Software Mentions: 1
Published: over 7 years ago

10.1186/1472-6963-6-95

Development and testing of innovative patient resources for the management of coronary heart disease (CHD): a descriptive study
Cited by: 24
Author(s): Julie Redfern, Elizabeth Ellis, Tom Briffa, Ben Freedman
Software Mentions: 1
Published: almost 18 years ago

10.1186/1743-422X-10-164

A remarkable synergistic effect at the transcriptomic level in peach fruits doubly infected by prunus necrotic ringspot virus and peach latent mosaic viroid
Cited by: 32
Author(s): M. C. Herranz, Annette Niehl, Merlín Rosales, Nicola Fiore, Alan Zamorano, Antonio Granell, Vicente Pallás
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-14-S14-S10

Towards human-computer synergetic analysis of large-scale biological data
Cited by: 6
Author(s): Rahul Singh, Hui Yang, Ben Dalziel, Daniel Asarnow, William Murad, David Foote, Matthew Gormley, Jonathon H. Stillman, Susan J. Fisher
Software Mentions: 1
Published: about 11 years ago

10.1186/s12985-019-1242-5

Whole-genome sequencing of human Pegivirus variant from an Egyptian patient co-infected with hepatitis C virus: a case report
Cited by: 2
Author(s): Hany Soliman, Mohamed Abouelhoda, Mahmoud N. El Rouby, Ola Ahmed, Gamal Esmat, Zeinab K. Hassan, Mohammed M. Hafez, Dina A. Mehaney, Manojkumar Selvaraju, Rania K. Darwish, Yehia A. Osman, Abdel-Rahman N. Zekri
Software Mentions: 1
Published: about 5 years ago

10.1186/s12985-019-1274-x

Decay of infectious adenovirus and coliphages in freshwater habitats is differentially affected by ambient sunlight and the presence of indigenous protozoa communities
Cited by: 44
Author(s): Brian R. McMinn, Eric R. Rhodes, Emma M. Huff, Asja Korajkic
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12985-020-1280-z

Whole genome sequencing and genetic variations in several dengue virus type 1 strains from unusual dengue epidemic of 2017 in Vietnam
Cited by: 14
Author(s): Thuy Thi Dang, My Ha Pham, Huy Vu Bui, Duyet Van Le
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12877-020-01535-6

“Study protocol for the ≥65 years NOrthern jutland Cohort of Fall risk Assessment with Objective measurements (the NOCfao study)”
Cited by: 1
Author(s): Morten Villumsen, Bo Grarup, Steffan Wittrup Christensen, Thorvaldur Skuli Palsson, Rogério Pessoto Hirata
Software Mentions: 1
Published: over 4 years ago

10.1093/ve/veab003

Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution
Cited by: 25
Author(s): Masashi Iwamoto, Yukino Shibata, Jun Kawasaki, Shohei Kojima, Yung‐Tsung Li, Shingo Iwami, Masamichi Muramatsu, Hui‐Lin Wu, Kazuhiro Wada, Keizō Tomonaga, Koichi Watashi, Masayuki Horie
Software Mentions: 1
Published: almost 4 years ago

10.3390/v8010019

Complete Genome Sequence of Germline Chromosomally Integrated Human Herpesvirus 6A and Analyses Integration Sites Define a New Human Endogenous Virus with Potential to Reactivate as an Emerging Infection
Cited by: 43
Author(s): Joshua Tweedy, Maria A. Spyrou, Max Pearson, Dirk Laßner, Uwe Kühl, Ursula A. Gompels
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-020-59523-0

RNA cargos in extracellular vesicles derived from blood serum in pancreas associated conditions
Cited by: 44
Author(s): Sudeep Kumar, Eric T. Kimchi, Yariswamy Manjunath, Saivaroon Gajagowni, Alexei J. Stuckel, Jussuf T. Kaifi
Software Mentions: 1
Published: almost 5 years ago

10.3390/v10010040

CRISPR-Cas Targeting of Host Genes as an Antiviral Strategy
Cited by: 32
Author(s): Shuliang Chen, Xijie Yu, Deyin Guo
Software Mentions: 1
Published: almost 7 years ago

10.3390/v10060313

The Odd “RB” Phage—Identification of Arabinosylation as a New Epigenetic Modification of DNA in T4-Like Phage RB69
Cited by: 16
Author(s): Julie A. Thomas, Jared Orwenyo, Lai-Xi Wang, Lindsay W. Black
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-9-344

Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803
Cited by: 69
Author(s): Zhigang Zhang, Ninad D Pendse, Katherine N. Phillips, James B. Cotner, Arkady B. Khodursky
Software Mentions: 1
Published: over 16 years ago

10.1038/s41598-020-60250-9

Glycation changes molecular organization and charge distribution in type I collagen fibrils
Cited by: 38
Author(s): Sneha Bansode, Uliana Bashtanova, Rui Li, Jonathan Clark, Karin H. Müller, Anna M. Puszkarska, Ieva Goldberga, Holly H. Chetwood, David G. Reid, Lucy Colwell, Jeremy N. Skepper, Catherine M. Shanahan, Georg Schitter, Patrick Mesquida, Melinda J. Duer
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-60361-3

Dual-molecular barcode sequencing detects rare variants in tumor and cell free DNA in plasma
Cited by: 21
Author(s): Yosuke Hirotsu, Sotaro Otake, Hiroshi Ohyama, Kenji Amemiya, Rumi Higuchi, Toshio Oyama, Hitoshi Mochizuki, Taichiro Goto, Masao Omata
Software Mentions: 1
Published: over 4 years ago

10.3390/v12060666

Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing
Cited by: 6
Author(s): Marc Noguera-Julián, Emma R. Lee, Robert W. Shafer, Rami Kantor, Hezhao Ji
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-020-07222-5

Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition
Cited by: 3
Author(s): Hemant Gupta, Khyati Chandratre, Siddharth Sinha, Teng Huang, Xiaobing Wu, Jian Cui, Michael Q. Zhang, San Ming Wang
Software Mentions: 1
Published: almost 4 years ago

10.3390/v13040620

Multiple Viral Infections Detected in Phytophthora condilina by Total and Small RNA Sequencing
Cited by: 17
Author(s): Leticia Botella, T. Jung
Software Mentions: 1
Published: over 3 years ago

10.3390/v13071288

Lentiviral Vectors for Delivery of Gene-Editing Systems Based on CRISPR/Cas: Current State and Perspectives
Cited by: 25
Author(s): Wendy Dong, Boris Kantor
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-14-383

Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells
Cited by: 19
Author(s): Sheila Z. Kimaro Mlacha, Sandra Romero-Steiner, Julie C. Dunning Hotopp, Nikhil Kumar, Nadeeza Ishmael, David R. Riley, Umar Farooq, Todd Creasy, Luke J. Tallon, Xinyue Liu, Cynthia S. Goldsmith, Jacquelyn S. Sampson, George M. Carlone, Susan K. Hollingshead, J. Anthony G. Scott, Hervé Tettelin
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-015-2058-3

Blood transcriptomics of drug-naïve sporadic Parkinson’s disease patients
Cited by: 61
Author(s): Raffaella Calligaris, Mihaela Banica, Paola Roncaglia, Elisa Robotti, Sara Finaurini, Christina Vlachouli, Lucia Antonutti, Francesco Iorio, Annamaria Carissimo, Tatiana Cattaruzza, Andrea Ceiner, Dejan Lazarevic, Alberto Cucca, Nicola Pangher, Emílio Marengo, Diego di Bernardo, Gilberto Pizzolato, Stefano Gustincich
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-7-333

A methodology for global validation of microarray experiments
Cited by: 69
Author(s): Mathieu Miron, Owen Z. Woody, Alexandre Marcil, Carl Murie, Robert Sladek, Robert Nadon
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-5-71

Inter-Platform comparability of microarrays in acute lymphoblastic leukemia
Cited by: 31
Author(s): Stephanie A Mitchell, Kevin M. Brown, M. M. Henry, Michelle Mintz, Daniel Catchpoole, Bonnie LaFleur, Dietrich A. Stephan
Software Mentions: 1
Published: about 20 years ago

10.3897/zookeys.67.704

Revision of the rove beetle genus Antimerus (Coleoptera, Staphylinidae, Staphylininae), a puzzling endemic Australian lineage of the tribe Staphylinini
Cited by: 7
Author(s): Alexey Solodovnikov, Alfred F. Newton
Software Mentions: 1
Published: about 14 years ago

10.3897/zookeys.100.1540

Belowground carabid beetle diversity in the western Palaearctic – effects of history and climate on range-restricted taxa (Coleoptera, Carabidae)
Cited by: 21
Author(s): Andreas Schuldt, Thorsten Aßmann
Software Mentions: 1
Published: over 13 years ago

10.3897/zookeys.147.2047

Carabidae diversity along an altitudinal gradient in a Peruvian cloud forest (Coleoptera)
Cited by: 47
Author(s): Sarah A. Maveety, Robert A. Browne, Terry L. Erwin
Software Mentions: 1
Published: about 13 years ago

10.3897/zookeys.172.1889

Review of Australasian spider flies (Diptera, Acroceridae) with a revision of Panops Lamarck
Cited by: 10
Author(s): Shaun L. Winterton
Software Mentions: 1
Published: over 12 years ago

10.3897/zookeys.365.5859

Reviewing population studies for forensic purposes: Dog mitochondrial DNA
Cited by: 9
Author(s): Sophie Verscheure, Thierry Backeljau, Stijn Desmyter
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-021-07892-9

InvertypeR: Bayesian inversion genotyping with Strand-seq data
Cited by: 3
Author(s): Vincent C.T. Hanlon, Carl-Adam Mattsson, Diana C.J. Spierings, Victor Guryev, Peter M Lansdorp
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-020-60376-w

A phylogenetic comparative analysis on the evolution of sequential hermaphroditism in seabreams (Teleostei: Sparidae)
Cited by: 18
Author(s): Susanna Pla, Chiara Benvenuto, Isabella Capellini, Francesc Piferrer
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2105-9-357

Impact of residue accessible surface area on the prediction of protein secondary structures
Cited by: 42
Author(s): Amir Momen-Roknabadi, Mehdi Sadeghi, Hamid Pezeshk, Sayed-Amir Marashi
Software Mentions: 1
Published: about 16 years ago

10.1097/PR9.0000000000000944

The methyl donor S-adenosyl methionine reverses the DNA methylation signature of chronic neuropathic pain in mouse frontal cortex
Cited by: 6
Author(s): Lucas Topham, Stéphanie Grégoire, HyungMo Kang, Mali Salmon‐Divon, Elad Lax, Magali Millecamps, Moshe Szyf, Laura S. Stone
Software Mentions: 1
Published: over 3 years ago

10.1097/PR9.0000000000000620

Impact of patient information leaflets on pain medication intake behavior: a pilot study
Cited by: 13
Author(s): Julia Schmitz, Sandra Kamping, Janine Wiegratz, Maike Müller, Jan Stork, Luana Colloca, Herta Flor, Regine Klinger
Software Mentions: 1
Published: about 7 years ago

10.12669/pjms.37.4.3618

Treatment of Chronic Large and Persistent Macular Hole by a new technique in a Tertiary Care Hospital
Cited by: 3
Author(s): Tanweer Hasan Khan, Fawad Rizvi Syed, Asaad Mahmood Syed, Lubna Feroz
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-8-242

Improving gene set analysis of microarray data by SAM-GS
Cited by: 240
Author(s): Irina Dinu, John D. Potter, Thomas Mueller, Qi Liu, Adeniyi J. Adewale, Gian S. Jhangri, G. Einecke, Konrad S. Famulski, Philip F. Halloran, Yutaka Yasui
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pcbi.1000274

A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations
Cited by: 35
Author(s): Charles J. Vaske, Carrie D. House, Truong Luu, Bryan Frank, Chen Hsiang Yeang, Norman H. Lee, Joshua M. Stuart
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2105-6-172

The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
Cited by: 87
Author(s): Jan Kosiński, Marcin Feder, Janusz M. Bujnicki
Software Mentions: 1
Published: over 19 years ago

10.1186/s12864-016-3402-y

An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.)
Cited by: 24
Author(s): Ye Jiang, Yuhua Yang, Bin Chen, Jiaqin Shi, Meizhong Luo, Jiasui Zhan, Xinfa Wang, Guihua Liu, Hanzhong Wang
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-020-60892-9

Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken
Cited by: 26
Author(s): Khin K. Z. Mon, Yuhua Zhu, Ganrea Chanthavixay, Colin Kern, Huaijun Zhou
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pcbi.1002195

Accelerated Profile HMM Searches
Cited by: 4,510
Author(s): Sean R. Eddy
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pcbi.1002564

Coding Conspecific Identity and Motion in the Electric Sense
Cited by: 51
Author(s): Na Yu, Ginette J. Hupé, Charles J. Garfinkle, John E. Lewis, André Longtin
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-10-495

Transcriptome analysis of differentiating trypanosomes reveals the existence of multiple post-transcriptional regulons
Cited by: 132
Author(s): Rafael Queiroz, Corinna Benz, Kurt Fellenberg, Jörg D. Hoheisel, Christine Clayton
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2164-9-98

A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy
Cited by: 21
Author(s): Xiangrong Kong, Valeria R. Mas, Kellie J. Archer
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pcbi.1000730

Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis
Cited by: 141
Author(s): Younghee Lee, Xinan Yang, Yong Huang, Huiying Fan, Qingbei Zhang, Youngfei Wu, Jiànróng Lǐ, Rifat Hasina, Chao Cheng, Mark W. Lingen, Mark Gerstein, Ralph R. Weichselbaum, H. Rosie Xing, Yves A. Lussier
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-10-141

Revealing genes associated with vitellogenesis in the liver of the zebrafish (Danio rerio) by transcriptome profiling
Cited by: 61
Author(s): Liraz Levi, Irena Pekarski, Ellen Gutman, Paolo Fortina, Terry Hyslop, Jakob Biran, Berta Levavi‐Sivan, Esther Lubzens
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1003069

The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
Cited by: 24
Author(s): Wei Huang, Joohyun Kim, Shantenu Jha, Fareed Aboul‐ela
Software Mentions: 1
Published: over 11 years ago

10.1523/ENEURO.0022-19.2019

Transcriptomic Signatures of Postnatal and Adult Intrinsically Photosensitive Ganglion Cells
Cited by: 17
Author(s): Daniel Berg, Katherine Kartheiser, Megan L. Leyrer, Alexandra Saali, David M. Berson
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1004344

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
Cited by: 0
Author(s): Donatien Fotso Chedom, Pablo R. Murcia, Chris Greenman
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pcbi.0030003

Using Phylogeny to Improve Genome-Wide Distant Homology Recognition
Cited by: 6
Author(s): Sanne Abeln, Carlo Teubner, Charlotte M. Deane
Software Mentions: 1
Published: almost 18 years ago

10.18632/oncotarget.20843

MAPK, NFκB, and VEGF signaling pathways regulate breast cancer liver metastasis
Cited by: 16
Author(s): Xinhua Chen, Zhihong Zheng, Limin Chen, Hongyu Zheng
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.22495

Identification of the genetic and clinical characteristics of neuroblastomas using genome-wide analysis
Cited by: 21
Author(s): Kumiko Uryu, Riki Nishimura, Keisuke Kataoka, Yusuke Sato, Atsuko Nakazawa, Hiromichi Suzuki, Kenichi Yoshida, Masafumi Seki, Mitsuteru Hiwatari, Tomoya Isobe, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Katsuyoshi Koh, Ryoji Hanada, Akira Oka, Yasuhide Hayashi, Miki Ohira, Takehiko Kamijo, Hiroki Nagase, Tetsuya Takimoto, Tatsuro Tajiri, Akira Nakagawara, Seishi Ogawa, Junko Takita
Software Mentions: 1
Published: about 7 years ago

10.18632/aging.101625

Identification of an energy metabolism-related signature associated with clinical prognosis in diffuse glioma
Cited by: 47
Author(s): Zhengui Zhou, Ruoyu Huang, Rui‐Chao Chai, Xiaohong Zhou, Zhiping Hu, Wenbiao Wang, Baoguo Chen, Lintao Deng, Yuqing Liu, Fan Wu
Software Mentions: 1
Published: about 6 years ago

10.3390/s20164543

Emotion Variation from Controlling Contrast of Visual Contents through EEG-Based Deep Emotion Recognition
Cited by: 4
Author(s): Heekyung Yang, Jongdae Han, Kyungha Min
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-018-4963-8

Gene editing in the context of an increasingly complex genome
Cited by: 9
Author(s): Kevin Blighe, Larry DeDionisio, Kathleen A. Christie, Bo Chawes, Salar Shareef, Thomais Kakouli‐Duarte, Connie Chao-Shern, Victoria Harding, Rachel S. Kelly, Leandro Castellano, Justin Stebbing, Jessica Lasky‐Su, M. Andrew Nesbit, Tara Moore
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-020-06896-1

Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium
Cited by: 20
Author(s): Hye Seon Kim, Jessica M. Lohmar, Mark Busman, Daren W. Brown, Todd A. Naumann, Hege H. Divon, Erik Lysøe, Silvio Uhlig, Robert H. Proctor
Software Mentions: 1
Published: over 4 years ago

10.3390/s20174962

Underwater Hyperspectral Imaging Technology and Its Applications for Detecting and Mapping the Seafloor: A Review
Cited by: 42
Author(s): Bohan Liu, Zhaojun Liu, Shaojie Men, Yongfu Li, Zhongjun Ding, Jiahao He, Zhigang Zhao
Software Mentions: 1
Published: about 4 years ago

Projects: cran: SAM

Papers Mentioning SAM 4,566