cran: SAM | Projects | Ecosyste.ms: Papers

10.1186/1471-2105-11-205

Predicting conserved protein motifs with Sub-HMMs
Cited by: 9
Author(s): Kevin Horan, Christian R. Shelton, Thomas Girke
Software Mentions: 3
Published: about 16 years ago

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

10.7150/ijms.51743

Identifying daily changes in circRNAs and circRNA-associated-ceRNA networks in the rat pineal gland
Cited by: 5
Author(s): Yi Zheng, Hao Jiang, Hao-Qi Wang, Haixiang Guo, Dong-Xu Han, Yongping Huang, Yan Gao, Bao Yuan
Software Mentions: 3
Published: over 5 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: almost 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

10.1038/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: almost 5 years ago

10.1038/s41598-021-90243-1

Metabolomics and computational analysis of the role of monoamine oxidase activity in delirium and SARS-COV-2 infection
Cited by: 17
Author(s): Miroslava Čuperlović-Culf, Emma Cunningham, Hossen Teimoorinia, Anuradha Surendra, Xiaobei Pan, Steffany A. L. Bennett, Mijin Jung, Bernadette McGuiness, Anthony Peter Passmore, David Beverland, Brian D. Green
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-83459-8

Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
Cited by: 5
Author(s): M. Joseph Tomlinson, Shawn W. Polson, Jing Qiu, Juniper A. Lake, William Lee, Behnam Abasht
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-91503-w

Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
Cited by: 12
Author(s): Jessica Gray, P. Scott Chandry, Mandeep Kaur, Chawalit Kocharunchitt, Séamus Fanning, John P. Bowman, Edward M. Fox
Software Mentions: 3
Published: almost 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: almost 5 years ago

10.1038/s41598-020-77600-2

Genetic mapping and candidate gene analysis for melon resistance to Phytophthora capsici
Cited by: 4
Author(s): Pingyong Wang, Xiuhong Xu, Guangwei Zhao, Yue He, C. T. Hou, Weihu Kong, Jian Zhang, Shuimiao Liu, Yong Xu, Zhigao Xu
Software Mentions: 3
Published: over 5 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

10.1186/1471-2105-7-286

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: almost 20 years ago

10.1038/s41598-020-74877-1

Low E2F2 activity is associated with high genomic instability and PARPi resistance
Cited by: 4
Author(s): Jonathan Rennhack, Eran R. Andrechek
Software Mentions: 3
Published: over 5 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: over 8 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: over 5 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: about 5 years ago

10.1038/s41598-021-93555-4

The conserved ASTN2/BRINP1 locus at 9q33.1–33.2 is associated with major psychiatric disorders in a large pedigree from Southern Spain
Cited by: 1
Author(s): Josep Pol-Fuster, Francesca Cañellas, Laura Ruiz-Guerra, Aina Medina-Dols, Bàrbara Bisbal-Carrió, Bernat Ortega-Vila, Jaume Llinàs, Jessica Hernández-Rodríguez, Jerònia Lladó, Gabriel Olmos, Konstantin Strauch, Damián Heine-Suñer, Cristòfol Vives-Bauzà, Antònia Flaquer
Software Mentions: 3
Published: almost 5 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

10.1038/srep41238

Patient-specific hepatocyte-like cells derived from induced pluripotent stem cells model pazopanib-mediated hepatotoxicity
Cited by: 43
Author(s): Yukti Choudhury, Yi‐Chin Toh, Jiangwa Xing, Yinghua Qu, Jonathan Poh, Huan Li, Hui Shan Tan, Ravindran Kanesvaran, Hanry Yu, Min‐Han Tan
Software Mentions: 3
Published: over 9 years ago

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: over 5 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

10.1038/s41598-020-65724-4

Simultaneous identification of animal-derived components in meats using high-throughput sequencing in combination with a custom-built mitochondrial genome database
Cited by: 6
Author(s): Yinan Zhang, Qinfeng Qu, RAO Mingzhen, Zhang Nana, Yu Zhao, Fei Tao
Software Mentions: 3
Published: about 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: over 12 years ago

10.1038/srep37563

A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing
Cited by: 21
Author(s): Marcus Davidsson, Paula Díaz-Fernández, Oliver D. Schwich, Marcos Torroba, Gang Wang, Tomas Björklund
Software Mentions: 3
Published: over 9 years ago

10.1038/srep38096

Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus)
Cited by: 81
Author(s): Fang-Nong Lai, Hong-Li Zhai, Ming Cheng, Jun‐Yu Ma, Shun‐Feng Cheng, Wei Ge, Guoliang Zhang, Junjie Wang, Ruiqian Zhang, Xue Wang, Min Liu, Jiuzhou Song, Wei Shen
Software Mentions: 3
Published: over 9 years ago

10.1038/srep32965

Predicting the synergy of multiple stress effects
Cited by: 157
Author(s): Matthias Liess, Kaarina Foit, Saskia Knillmann, Ralf B. Schäfer, Hans-Dieter Ließ
Software Mentions: 3
Published: over 9 years ago

10.1038/srep33262

Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
Cited by: 13
Author(s): Chenchen Feng, Jian Zhang, Xuecang Li, Bo Ai, Junwei Han, Qiuyu Wang, Taiming Wei, Yong Xu, Meng Li, Shang Li, Chao Song, Chunquan Li
Software Mentions: 3
Published: over 9 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

10.1038/srep39487

Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach
Cited by: 24
Author(s): Li Li, Ilana Greene, Benjamin Readhead, Madhav C. Menon, Brian Kidd, Andrew Uzilov, Chengguo Wei, Nimrod Philippe, Bernd Schröppel, John Cijiang He, Rong Chen, Joel T. Dudley, Barbara Murphy
Software Mentions: 3
Published: over 9 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: over 12 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

10.1038/srep27623

Multiplex giant magnetoresistive biosensor microarrays identify interferon-associated autoantibodies in systemic lupus erythematosus
Cited by: 31
Author(s): J. Lee, D. James Haddon, Hannah Wand, J. M. Price, Vivian K. Diep, Drew A. Hall, Michelle Petri, Emily C. Baechler, Imelda Balboni, Paul J. Utz, Shan X. Wang
Software Mentions: 3
Published: almost 10 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

10.3390/molecules24030631

Stratification of Breast Cancer by Integrating Gene Expression Data and Clinical Variables
Cited by: 8
Author(s): Zongzhen He, Junying Zhang, Xiguo Yuan, Jianing Xi, Zhaowen Liu, Yuanyuan Zhang
Software Mentions: 3
Published: over 7 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: almost 10 years ago

10.1186/1471-2105-12-13

A Platform for Processing Expression of Short Time Series (PESTS)
Cited by: 16
Author(s): Ayan Sinha, Marianthi Markatou
Software Mentions: 3
Published: over 15 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: almost 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

10.1186/1471-2105-13-42

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: about 14 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: over 16 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: almost 13 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: about 14 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: almost 6 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

10.1038/s41597-020-0427-5

Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample
Cited by: 35
Author(s): Joan Mas-Lloret, Mireia Obón-Santacana, Gemma Ibáñez‐Sanz, Elisabet Guinó, Miguel L Pato, Francisco Rodríguez-Moranta, Alfredo Mata, Ana García-Rodríguez, Vı́ctor Moreno, Ville N. Pimenoff
Software Mentions: 3
Published: about 6 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

10.1073/pnas.1921055117

ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in Arabidopsis
Cited by: 54
Author(s): Christophe Lambing, Pallas Kuo, Andrew J. Tock, Stephanie D. Topp, Ian Henderson
Software Mentions: 3
Published: about 6 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: about 7 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: almost 9 years ago

10.3390/microorganisms9030584

Implications of Tributyrin on Gut Microbiota Shifts Related to Performances of Weaning Piglets
Cited by: 15
Author(s): Francesco Miragoli, Vania Patrone, Aldo Prandini, Samantha Sigolo, Matteo Dell’Anno, Luciana Rossi, Alice Senizza, L. Morelli, Maria Luisa Callegari
Software Mentions: 3
Published: about 5 years ago

10.1042/BSR20203204

FRZB as a key molecule in abdominal aortic aneurysm progression affecting vascular integrity
Cited by: 6
Author(s): Chang‐Kyu Oh, Yeji Ko, Jeong-Jun Park, Hye Jin Heo, Junmo Kang, Eun Jung Kwon, Ji Wan Kang, Yoonsung Lee, Kyungjae Myung, Jin Mo Kang, Dai Sik Ko, Yun Hak Kim
Software Mentions: 3
Published: over 5 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

10.3390/biomedicines9070845

Serum miRNA Profiling for Early PDAC Diagnosis and Prognosis: A Retrospective Study
Cited by: 7
Author(s): Ada Aita, Caterina Millino, Cosimo Sperti, Beniamina Pacchioni, Mario Plebani, Cristiano De Pittà, Daniela Basso
Software Mentions: 3
Published: almost 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: almost 19 years ago

10.1093/jxb/erx010

Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation
Cited by: 48
Author(s): Lekha T. Pazhamala, Shilp Purohit, Rachit K. Saxena, Vanika Garg, L. Krishnamurthy, Jérôme Verdier, Rajeev K. Varshney
Software Mentions: 3
Published: over 9 years ago

10.3390/biom8040182

Identification of the Genetic Variation and Gene Exchange between Citrus Trifoliata and Citrus Clementina
Cited by: 4
Author(s): Tianjia Liu, Jingjing Zhou, Fa-Yi Chen, Zhi-Meng Gan, Yongping Li, Jin‐Zhi Zhang, Chun-Gen Hu
Software Mentions: 3
Published: over 7 years ago

10.1093/jxb/erx349

Transfer of a starch phenotype from wild wheat to bread wheat by deletion of a locus controlling B-type starch granule content
Cited by: 21
Author(s): Tansy Chia, Nikolai M Adamski, Benedetta Saccomanno, Andrew J. Greenland, Alastair Nash, Cristóbal Uauy, Kay Trafford
Software Mentions: 3
Published: almost 9 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

10.1155/2015/746970

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

10.1155/2021/7326853

Identification of Genes Universally Differentially Expressed in Gastric Cancer
Cited by: 6
Author(s): Yidan Shi, Lishuang Qi, Haifeng Chen, Jiahui Zhang, Qingzhou Guan, Jun He, Meifeng Li, Zheng Guo, Haidan Yan, Ping Li
Software Mentions: 3
Published: over 5 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

10.1371/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: about 13 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: almost 6 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: over 9 years ago

10.1186/1471-2105-15-S1-S2

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information
Cited by: 11
Author(s): Marco Masseroli, Barend Mons, Erik Bongcam‐Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frédérique Lisacek, Paolo Romano
Software Mentions: 3
Published: over 12 years ago

10.1186/s13062-016-0152-3

Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes
Cited by: 14
Author(s): Suyan Tian, Howard H. Chang, Chi Wang
Software Mentions: 3
Published: over 9 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: about 12 years ago

10.3390/biom11050738

Metabolomics-Guided Hypothesis Generation for Mechanisms of Intestinal Protection by Live Biotherapeutic Products
Cited by: 11
Author(s): Jiayu Ye, Lauren A. E. Erland, Sandeep Singh Gill, Stephanie L. Bishop, Andrea Verdugo‐Meza, Susan J. Murch, Deanna L. Gibson
Software Mentions: 3
Published: about 5 years ago

10.1120/jacmp.v17i3.6370

2016 AAPM Spring Clinical Meeting - Abstracts
Cited by: 0
Author(s):
Software Mentions: 3
Published: about 10 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: over 9 years ago

10.1038/srep13245

Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea
Cited by: 52
Author(s): Valentina Lauria, Michele Gristina, Martin J. Attrill, Fabio Fiorentino, Germana Garofalo
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1009600

Antagonistic fungal enterotoxins intersect at multiple levels with host innate immune defences
Cited by: 10
Author(s): Xing Zhang, Benjamin W. Harding, Dina Aggad, Damien Courtine, Jia‐Xuan Chen, Nathalie Pujol, Jonathan J. Ewbank
Software Mentions: 3
Published: almost 5 years ago

10.1093/bioinformatics/btab102

Genozip: a universal extensible genomic data compressor
Cited by: 15
Author(s): Divon Mordechai Lan, Raymond Tobler, Yassine Souilmi, Bastien Llamas
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0177662

Network based stratification of major cancers by integrating somatic mutation and gene expression data
Cited by: 11
Author(s): Zongzhen He, Junying Zhang, Xiguo Yuan, Zhaowen Liu, Baobao Liu, Shouheng Tuo, Yajun Liu
Software Mentions: 3
Published: about 9 years ago

10.1016/j.gdata.2014.10.008

Base-resolution DNA methylation landscape of zebrafish brain and liver
Cited by: 21
Author(s): Aniruddha Chatterjee, Peter A. Stockwell, Julia A. Horsfield, Ian M. Morison, Shinichi Nakagawa
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-015-0705-y

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data
Cited by: 7
Author(s): Gregory K. Farrant, Mark Hoebeke, Frédéric Partensky, Gwendoline Andres, Matthieu Le Corre, Laurence Garczarek
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12859-019-2996-x

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
Cited by: 178
Author(s): Grzegorz M. Boratyn, Jean Thierry‐Mieg, Danielle Thierry-Mieg, Ben Busby, Thomas Madden
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12859-020-3428-7

LCQS: an efficient lossless compression tool of quality scores with random access functionality
Cited by: 2
Author(s): Jiabing Fu, Bixin Ke, Sujun Dong
Software Mentions: 2
Published: about 6 years ago

10.1186/gb-2006-7-9-r83

Cited by: 53
Author(s): Nandini Krishnamurthy, D. Brown, Daniel Kirshner, Kimmen Sjölander
Software Mentions: 2
Published: over 20 years ago

10.1186/1471-2164-12-384

Temperature stress differentially modulates transcription in meiotic anthers of heat-tolerant and heat-sensitive tomato plants
Cited by: 96
Author(s): Craita E. Bita, Sara Zenoni, Wim H. Vriezen, Celestina Mariani, Mario Pezzotti, Tom Geräts
Software Mentions: 2
Published: almost 15 years ago

10.1128/AEM.01808-20

Mapping the Efficacy and Mode of Action of Ethylzingerone [4-(3-Ethoxy-4-Hydroxyphenyl) Butan-2-One] as an Active Agent against Burkholderia Bacteria
Cited by: 1
Author(s): Laura Rushton, Ahmad Khodr, Florence Ménard-Szczebara, Jean‐Yves Maillard, Sylvie Cupferman, Eshwar Mahenthiralingam
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-018-4475-6

Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome
Cited by: 6
Author(s): Fedor Naumenko, Irina Abnizova, Nathan Beka, Mikhail A. Genaev, Yuriy L. Orlov
Software Mentions: 2
Published: over 8 years ago

10.3390/genes12020167

Leishmania Sexual Reproductive Strategies as Resolved through Computational Methods Designed for Aneuploid Genomes
Cited by: 10
Author(s): Jahangheer Shaik, Deborah E. Dobson, David L. Sacks, Stephen M. Beverley
Software Mentions: 2
Published: over 5 years ago

10.1590/1678-4685-GMB-2017-0031

Ecological drivers of plant genetic diversity at the southern edge of geographical distributions: Forestal vines in a temperate region
Cited by: 7
Author(s): Michel J. F. Barros, José Alexandre Felizola Diniz‐Filho, Loreta B. Freitas
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-14-310

A method to identify differential expression profiles of time-course gene data with Fourier transformation
Cited by: 12
Author(s): Jaehee Kim, R. Todd Ogden, Haseong Kim
Software Mentions: 2
Published: over 12 years ago

10.1093/bioinformatics/btv524

RNF: a general framework to evaluate NGS read mappers
Cited by: 8
Author(s): Karel Břinda, Valentina Boeva, Grégory Kucherov
Software Mentions: 2
Published: over 10 years ago

10.1093/bioinformatics/bts408

Accurate estimation of short read mapping quality for next-generation genome sequencing
Cited by: 30
Author(s): Matthew Ruffalo, Mehmet Koyutürk, Soumya Ray, Thomas LaFramboise
Software Mentions: 2
Published: almost 14 years ago

10.1093/bioinformatics/btaa051

BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis
Cited by: 6
Author(s): Gianvito Urgese, Emanuele Parisi, Orazio Maria Scicolone, Santa Di Cataldo, Elisa Ficarra
Software Mentions: 2
Published: over 6 years ago

10.3390/genes12010046

DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification
Cited by: 8
Author(s): Αθανάσιος Αλεξίου, Dimitrios Zisis, Ioannis Kavakiotis, Marios Miliotis, Antonis Koussounadis, Dimitra Karagkouni, Artemis G. Hatzigeorgiou
Software Mentions: 2
Published: over 5 years ago

10.1155/2018/3797214

CRISPR/Cas9 System: A Bacterial Tailor for Genomic Engineering
Cited by: 15
Author(s): Bilal Ahmad Lone, Shibendra Kumar Lal Karna, Fawad Ahmad, Nerina Shahi, Yuba Raj Pokharel
Software Mentions: 2
Published: over 7 years ago

10.1186/gb-2007-8-5-r69

Towards the uniform distribution of null P values on Affymetrix microarrays
Cited by: 29
Author(s): Anthony A. Fodor, Timothy L. Tickle, Christine Richardson
Software Mentions: 2
Published: over 19 years ago

10.1186/s12859-018-2579-2

NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors
Cited by: 119
Author(s): John Gaspar
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-021-07610-5

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs
Cited by: 13
Author(s): Adéla Nosková, Meenu Bhati, Naveen Kumar Kadri, Danang Crysnanto, Stefan Neuenschwander, Andreas Höfer, Hubert Pausch
Software Mentions: 2
Published: about 5 years ago

10.3390/genes10090650

Affinity Purification of NF1 Protein–Protein Interactors Identifies Keratins and Neurofibromin Itself as Binding Partners
Cited by: 11
Author(s): Rachel M. Carnes, Robert A. Kesterson, Bruce R. Korf, James A. Mobley, Deeann Wallis
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2105-14-S7-S11

WEP: a high-performance analysis pipeline for whole-exome data
Cited by: 42
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Daniele Paoletti, B Elmi, Matteo Pallocca, Nico Sanna, Ernesto Picardi, Graziano Pesole, Tiziana Castrignanò
Software Mentions: 2
Published: about 13 years ago

10.3390/genes11050534

Investigating Human Mitochondrial Genomes in Single Cells
Cited by: 8
Author(s): Maria Angela Diroma, Angelo Sante Varvara, Marcella Attimonelli, Graziano Pesole, Ernesto Picardi
Software Mentions: 2
Published: about 6 years ago

10.3390/genes9060313

CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads
Cited by: 2
Author(s): Dongmei Ai, Hongfei Pan, Ruocheng Huang, Xia Li
Software Mentions: 2
Published: almost 8 years ago

10.1093/bioinformatics/btt422

DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments
Cited by: 1
Author(s): Chiao‐Feng Lin, Otto Valladares, Daniel Micah Childress, Egor Klevak, Evan Geller, Yi‐Ting Hwang, Ellen Tsai, Gerard D. Schellenberg, Li-San Wang
Software Mentions: 2
Published: almost 13 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566