cran: SAM | Projects | Ecosyste.ms: Papers

10.1186/1471-2105-15-S11-S10

SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data
Cited by: 7
Author(s): Yan Peng, Andrew S. Maxwell, Natalie D. Barker, Jennifer G. Laird, Alan J. Kennedy, Nan Wang, Chaoyang Zhang, Ping Gong
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-11-495

Gene signatures in wound tissue as evidenced by molecular profiling in the chick embryo model
Cited by: 15
Author(s): Fabienne Soulet, Witold W. Kilarski, Philipp Antczak, John Herbert, Roy Bicknell, Francesco Falciani, Andréas Bikfalvi
Software Mentions: 1
Published: almost 16 years ago

10.1038/s41598-018-23726-3

Insensitivity to atorvastatin is associated with increased accumulation of intracellular lipid droplets and fatty acid metabolism in breast cancer cells
Cited by: 23
Author(s): Barbara Lettiero, Maria Inasu, Siker Kimbung, Signe Borgquist
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1002195

Accelerated Profile HMM Searches
Cited by: 4,510
Author(s): Sean R. Eddy
Software Mentions: 1
Published: almost 15 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: about 14 years ago

10.1186/1471-2164-7-160

Gene expression profiling of Spodoptera frugiperda hemocytes and fat body using cDNA microarray reveals polydnavirus-associated variations in lepidopteran host genes transcript levels
Cited by: 59
Author(s): Mouna Barat‐Houari, Frédérique Hilliou, Jousset Fx, Luc Sofer, Emeline Deleury, Janick Rocher, Marc Ravallec, Lionel Galibert, Pierre Delobel, René Feyereisen, Philippe Fournier, A-N Volkoff
Software Mentions: 1
Published: about 20 years ago

10.1186/1471-2164-11-S3-S4

A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNT
Cited by: 6
Author(s): Sudhir Chowbina, Youping Deng, Junmei Ai, Xiaogang Wu, Xin Yuan Guan, Mitchell S. Wilbanks, B. Lynn Escalon, Sharon A. Meyer, Edward J. Perkins, Jake Y. Chen
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 16 years ago

10.1186/1471-2164-10-13

Reconstruction and functional analysis of altered molecular pathways in human atherosclerotic arteries
Cited by: 76
Author(s): Stefano Cagnin, Michele Biscuola, Cristina Patuzzo, Elisabetta Trabetti, Alessandra Pasquali, Paolo Laveder, Giuseppe Faggian, Mauro Iafrancesco, Alessandro Mazzucco, Pier Franco Pignatti, Gerolamo Lanfranchi
Software Mentions: 1
Published: over 17 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: about 13 years ago

10.1186/1471-2105-9-187

Significance analysis of microarray for relative quantitation of LC/MS data in proteomics
Cited by: 56
Author(s): Bryan A. P. Roxas, Qingbo Li
Software Mentions: 1
Published: over 18 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: over 10 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: over 19 years ago

10.1038/s41598-018-23978-z

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis
Cited by: 20
Author(s): Daichi Shigemizu, Fuyuki Miya, Shintaro Akiyama, Shujiro Okuda, Keith A. Boroevich, Akihiro Fujimoto, Hidewaki Nakagawa, Kouichi Ozaki, Shumpei Niida, Yonehiro Kanemura, Nobuhiko Okamoto, Shinji Saitoh, Mitsuhiro Kato, Mami Yamasaki, Tatsuo Matsunaga, Hideki Mutai, Kenjiro Kosaki, Tatsuhiko Tsunoda
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-26427-z

Chytridiomycosis causes catastrophic organism-wide metabolic dysregulation including profound failure of cellular energy pathways
Cited by: 16
Author(s): Laura F. Grogan, Lee F. Skerratt, Lee Berger, Scott D. Cashins, Robert D. Trengove, Joel Gummer
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-26425-1

Naturally occurring a loss of a giant plasmid from Mycobacterium ulcerans subsp. shinshuense makes it non-pathogenic
Cited by: 13
Author(s): Kazue Nakanaga, Yoshitoshi Ogura, Atsushi Toyoda, Mitsunori Yoshida, Hanako Fukano, Nagatoshi Fujiwara, Yuji Miyamoto, Noboru Nakata, Yuko Kazumi, Shingo Maeda, Tadasuke Ooka, Masamichi Goto, Kazunari Tanigawa, Satoshi Mitarai, Koichi Suzuki, Norihisa Ishii, Manabu Ato, Tetsuya Hayashi, Yoshihiko Hoshino
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2105-6-67

Cited by: 28
Author(s): Li Fu, Casey S Fu-Liu
Software Mentions: 1
Published: over 21 years ago

10.1186/1471-2164-14-741

mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction
Cited by: 38
Author(s): Ricardo B. Leite, Massimo Milan, Alessandro Coppe, Stefania Bortoluzzi, António dos Anjos, Richard Reinhardt, Carlos Saavedra, Tomaso Patarnello, M. Leonor Cancela, Luca Bargelloni
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-016-3162-8

Analysis of gene expression in the midgut of Bombyx mori during the larval molting stage
Cited by: 20
Author(s): Bing Yang, Weixin Huang, Jie Zhang, Qiufang Xu, Shoulin Zhu, Chenglong Zhang, Brenda T. Beerntsen, Hui Song, Erjun Ling
Software Mentions: 1
Published: over 9 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: over 7 years ago

10.1186/1471-2164-9-37

Discovery of genes implicated in whirling disease infection and resistance in rainbow trout using genome-wide expression profiling
Cited by: 47
Author(s): Melinda R. Baerwald, Amy B. Welsh, Ronald P. Hedrick, Bernie May
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pgen.1007075

How well do you know your mutation? Complex effects of genetic background on expressivity, complementation, and ordering of allelic effects
Cited by: 45
Author(s): Christopher H. Chandler, Sudarshan Chari, Alycia Kowalski, Lin Choi, David C. Tack, Michael DeNieu, William Pitchers, Anne Sonnenschein, Leslie Marvin, Kristen Hummel, Christian Marier, Andrew Victory, Cody K. Porter, Anna Mammel, Julie Holms, Gayatri Sivaratnam, Ian Dworkin
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-29301-0

Transcriptome Profiles of Nod Factor-independent Symbiosis in the Tropical Legume Aeschynomene evenia
Cited by: 22
Author(s): Djamel Gully, Pierre Czernic, Stéphane Cruveiller, Frédéric Mahé, C. F. H. Longin, David Vallenet, Philippe François, Sabine Nidelet, Stéphanie Rialle, Éric Giraud, Jean‐François Arrighi, Moumita Dasgupta, Fabienne Cartieaux
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms221910600

Imatinib Regulates miR-483-3p and Mitochondrial Respiratory Complexes in Gastrointestinal Stromal Tumors
Cited by: 6
Author(s): Wen‐Shih Huang, Hao Shi, Pınar Akçakaya, Katarina Zeljić, Anastasia Gangaev, Stefano Caramuta, Chun‐Nan Yeh, Robert Bränström, Catharina Larsson, Weng‐Onn Lui
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-018-30067-8

Acute Physical Activity Enhances Executive Functions in Children with ADHD
Cited by: 64
Author(s): Valentin Benzing, Yu Kai Chang, Mirko Schmidt
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-31217-8

Identification of chronological and photoageing-associated microRNAs in human skin
Cited by: 15
Author(s): Ankit Srivastava, Magnus Karlsson, Claire Marionnet, Françoise Bernerd, Audrey Guéniche, Charles El Rawadi, Mona Ståhle, Enikö Sonkoly, Lionel Breton, Andor Pivarcsi
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1004097

CEP-1, the Caenorhabditis elegans p53 Homolog, Mediates Opposing Longevity Outcomes in Mitochondrial Electron Transport Chain Mutants
Cited by: 57
Author(s): Aiswarya Baruah, Hung‐Hao Chang, Mathew Hall, Jie Yuan, Sarah Gordon, Erik C. Johnson, Ludmila Shtessel, Callista Yee, Siegfried Hekimi, W. Brent Derry, Siu Sylvia Lee
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1002530

A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections between Pre–mRNA Splicing and 5′ and 3′ End Transcript Determinants
Cited by: 31
Author(s): Laura-Oana Albulescu, Nevin Sabet, Mohanram Gudipati, Nicholas Stepankiw, Zane J. Bergman, Tim C. Huffaker, Jeffrey A. Pleiss
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-9-231

Automating dChip: toward reproducible sharing of microarray data analysis
Cited by: 61
Author(s): Cheng Li
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2164-8-258

EGFR associated expression profiles vary with breast tumor subtype
Cited by: 246
Author(s): Katherine A. Hoadley, Victor Weigman, Cheng Fan, Lynda R. Sawyer, Xiaping He, Melissa A. Troester, Carolyn I. Sartor, Thais Rieger-House, Philip S. Bernard, Lisa A. Carey, Charles M. Perou
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pgen.0030174

Signalling Pathways Involved in Adult Heart Formation Revealed by Gene Expression Profiling in Drosophila
Cited by: 70
Author(s): Bruno Zeitouni, Sébastien Sénatore, Dany Séverac, Cindy Aknin, Michel Sémériva, Laurent Perrin
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pgen.1003389

Molecular Networks of Human Muscle Adaptation to Exercise and Age
Cited by: 149
Author(s): Bethan E. Phillips, John P. Williams, Thomas Gustafsson, Claude Bouchard, Tuomo Rankinen, Steen Knudsen, Kenneth Smith, James A. Timmons, Philip J. Atherton
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-8-400

Innate gene repression associated with Mycobacterium bovis infection in cattle: toward a gene signature of disease
Cited by: 62
Author(s): Kieran G. Meade, Eamonn Gormley, Mairead B. Doyle, Tara Fitzsimons, Cliona O’Farrelly, Eamon Costello, Joseph Keane, Yingdong Zhao, David E. MacHugh
Software Mentions: 1
Published: over 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: about 17 years ago

10.1186/1471-2164-14-556

De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach
Cited by: 77
Author(s): Venkatramana Pegadaraju, Rick Nipper, Brent S. Hulke, Lili Qi, Quentin Schultz
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.1000999

Amplification of a Cytochrome P450 Gene Is Associated with Resistance to Neonicotinoid Insecticides in the Aphid Myzus persicae
Cited by: 380
Author(s): Alin M. Puinean, S. P. Foster, L. Oliphant, I. Denholm, L. M. Field, Neil S. Millar, Martin S. Williamson, Chris Bass
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pgen.1003369

MTL–Independent Phenotypic Switching in Candida tropicalis and a Dual Role for Wor1 in Regulating Switching and Filamentation
Cited by: 40
Author(s): Allison M. Porman, Matthew P. Hirakawa, Stephen K. Jones, Na Wang, Richard J. Bennett
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-018-5025-y

Revealing post-transcriptional microRNA–mRNA regulations in Alzheimer’s disease through ensemble graphs
Cited by: 2
Author(s): Rubén Armañanzas
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.0020203

Impact of Nonsense-Mediated mRNA Decay on the Global Expression Profile of Budding Yeast
Cited by: 119
Author(s): Qiaoning Guan, Wei Zheng, Shijie Tang, Xiaosong Liu, Robert A. Zinkel, Kam‐Wah Tsui, Brian S. Yandell, Michael R. Culbertson
Software Mentions: 1
Published: over 20 years ago

10.1186/1471-2164-14-628

BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower
Cited by: 41
Author(s): M. Livaja, Yu Wang, Silke Wieckhorst, Grit Haseneyer, Michael Seidel, Volker Hahn, Steven J. Knapp, Stefan Taudien, Chris‐Carolin Schön, Eva Bauer
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.1000450

A Regulated Response to Impaired Respiration Slows Behavioral Rates and Increases Lifespan in Caenorhabditis elegans
Cited by: 144
Author(s): David Cristina, Michael Cary, Adam Lunceford, Catherine F. Clarke, Cynthia Kenyon
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pgen.1004589

A Gain-of-Function Mutation in Tnni2 Impeded Bone Development through Increasing Hif3a Expression in DA2B Mice
Cited by: 26
Author(s): Xiaoquan Zhu, Fengchao Wang, Yang Zhao, Peng Yang, Jun Chen, Hanzi Sun, Lei Liu, Wenjun Li, Pei Lin, Yafei Guo, Zhaohui Kou, Yu Zhang, Cheng Zhou, Jiang He, Xue Zhang, Jianxin Li, Han Wang, Jian Li, Guanghui Liu, Shaorong Gao, Ze Yang
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-11-360

Transcriptomic responses in mouse brain exposed to chronic excess of the neurotransmitter glutamate
Cited by: 31
Author(s): Xinkun Wang, Xiaodong Bao, Ranu Pal, Abdulbakî Agbaş, Elias K. Michaelis
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pgen.1009119

Two cis-regulatory SNPs upstream of ABCG2 synergistically cause the blue eggshell phenotype in the duck
Cited by: 8
Author(s): Li Chen, Xiaorong Gu, Xuetao Huang, Rui Liu, Jinxiu Li, Yiqing Hu, Guoqin Li, Tao Zeng, Yong Tian, Xiaoxiang Hu, Lizhi Liu, Ning Li
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1003186

Rbfox1 Downregulation and Altered Calpain 3 Splicing by FRG1 in a Mouse Model of Facioscapulohumeral Muscular Dystrophy (FSHD)
Cited by: 32
Author(s): Mariaelena Pistoni, Lily Shiue, Melissa Cline, Sergia Bortolanza, Maria Victoria Neguembor, Alexandros Xynos, Manuel Ares, Davide Gabellini
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-14-597

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria
Cited by: 39
Author(s): Eric I. Sun, Semen A. Leyn, Marat D. Kazanov, Milton H. Saier, Pavel S. Novichkov, Dmitry A. Rodionov
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1006042

Heat Shock Protein Beta-1 Modifies Anterior to Posterior Purkinje Cell Vulnerability in a Mouse Model of Niemann-Pick Type C Disease
Cited by: 18
Author(s): Chan Chung, Matthew J. Elrick, Zhaohui S. Qin, Shanker Kalyana-Sundaram, Arul M. Chinnaiyan, Vikram G. Shakkottai, Andrew P. Lieberman
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1007500

Modulation of miR-210 alters phasing of circadian locomotor activity and impairs projections of PDF clock neurons in Drosophila melanogaster
Cited by: 27
Author(s): Paola Cusumano, Alberto Biscontin, Federica Sandrelli, Gabriella Mazzotta, Claudia Tregnago, Cristiano De Pittà, Rodolfo Costa
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.0010028

Differential Expression of Novel Potential Regulators in Hematopoietic Stem Cells
Cited by: 265
Author(s): Erik Forsberg, Susan Prohaska, Sol Katzman, Garrett C. Heffner, Joshua M. Stuart, Irving L. Weissman
Software Mentions: 1
Published: almost 21 years ago

10.1186/s12864-017-3723-5

A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions
Cited by: 164
Author(s): Matthew A. Conte, William J Gammerdinger, Kerry L. Bartie, David J. Penman, Thomas D. Kocher
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1004955

Pooled Sequencing of 531 Genes in Inflammatory Bowel Disease Identifies an Associated Rare Variant in BTNL2 and Implicates Other Immune Related Genes
Cited by: 58
Author(s): Natalie J. Prescott, Benjamin Lehne, Kristina Stone, James C. Lee, Kirstin M. Taylor, Jo Knight, Efterpi Papouli, Muddassar M. Mirza, Michael A. Simpson, Sarah L. Spain, Grace H C Lu, Franca Fraternali, Suzannah Bumpstead, Emma Gray, Ariella Amar, Hannah Bye, Peter Green, Guy Carrault, Bu’Hussain Hayee, Richard Pollok, Jack Satsangi, Miles Parkes, Jeffrey C. Barrett, John C. Mansfield, Jeremy Sanderson, Cathryn M. Lewis, Michael E. Weale, Thomas Schlitt, Christopher G. Mathew
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1000310

Genetic and Computational Identification of a Conserved Bacterial Metabolic Module
Cited by: 28
Author(s): Cara C. Boutte, Balaji Srinivasan, Jason Flannick, Antal F. Novak, Andrew T. Martens, Serafim Batzoglou, Patrick H. Viollier, Sean Crosson
Software Mentions: 1
Published: over 17 years ago

10.1038/s41598-018-32063-4

Affective computing in virtual reality: emotion recognition from brain and heartbeat dynamics using wearable sensors
Cited by: 220
Author(s): Javier Marín‐Morales, Alberto Greco, Jaime Guixeres, Carmen Llinares, Enzo Pasquale Scilingo, Mariano Alcañíz, Gaetano Valenza
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1003683

Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG
Cited by: 173
Author(s): François P. Douillard, Angela Ribbera, Ravi Kant, Taija E. Pietilä, Hanna Järvinen, Marcel Messing, Cinzia Lucia Randazzo, Lars Paulín, Pia Laine, Jarmo Ritari, Cinzia Caggia, Tanja Lähteinen, Stan J. J. Brouns, Reetta Satokari, Ingemar von Ossowski, Justus Reunanen, Airi Palva, Willem M. de Vos
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1002902

Polysome Profiling in Liver Identifies Dynamic Regulation of Endoplasmic Reticulum Translatome by Obesity and Fasting
Cited by: 47
Author(s): Suneng Fu, Jason Fan, Joshua Aaron Blanco, Alfredo Giménez-Cassina, Nika N. Danial, Simon Watkins, Gökhan S. Hotamışlıgil
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1007135

Histological subtypes of mouse mammary tumors reveal conserved relationships to human cancers
Cited by: 51
Author(s): Daniel P. Hollern, Matthew Swiatnicki, Eran R. Andrechek
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-11-98

Transcriptional profiling of Actinobacillus pleuropneumoniae during the acute phase of a natural infection in pigs
Cited by: 45
Author(s): Vincent Deslandes, Martine Denicourt, Christiane Girard, Josée Harel, John H. E. Nash, Mario Jacques
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pgen.1002862

The Yeast Rab GTPase Ypt1 Modulates Unfolded Protein Response Dynamics by Regulating the Stability of HAC1 RNA
Cited by: 31
Author(s): Nikoleta G. Tsvetanova, Daniel P. Riordan, Patrick O. Brown
Software Mentions: 1
Published: about 14 years ago

10.1038/s41598-018-32788-2

Scanning Acoustic Microscopy and Time-Resolved Fluorescence Spectroscopy for Characterization of Atherosclerotic Plaques
Cited by: 13
Author(s): Bükem Bilen, Belkıs Gökbulut, Ülkü Kafa, Emre Heves, Mehmet Nacı Incı, Mehmet Ünlü
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1000942

Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae
Cited by: 169
Author(s): Jared W. Wenger, Katja Schwartz, Gavin Sherlock
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pgen.1003027

Cooperativity of Rb, Brca1, and p53 in Malignant Breast Cancer Evolution
Cited by: 23
Author(s): Prashant Kumar, Malini Mukherjee, Jacob P. S. Johnson, Milan Patel, Bing Huey, Donna G. Albertson, Karl Simin
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-15-372

Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map
Cited by: 17
Author(s): Qiong Zhang, Leiting Li, Robert VanBuren, Yanling Liu, Mei Yang, Liming Xu, John E. Bowers, Caihong Zhong, Yuepeng Han, Shaohua Li, Ray Ming
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.0020119

Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs
Cited by: 410
Author(s): John L. Rinn, Chanda Bondre, Hayes B. Gladstone, Patrick O. Brown, Howard Y. Chang
Software Mentions: 1
Published: about 20 years ago

10.1371/journal.pgen.0030101

Laser Microdissection of Narrow Sheath Mutant Maize Uncovers Novel Gene Expression in the Shoot Apical Meristem
Cited by: 76
Author(s): Xiaolan Zhang, Shahinez Madi, Lisa A. Borsuk, Dan Nettleton, Robert J. Elshire, Brent Buckner, Diane Janick-Buckner, Jon Beck, Marja C.P. Timmermans, Patrick S. Schnable, Michael J. Scanlon
Software Mentions: 1
Published: about 19 years ago

10.2196/jmir.4384

Swab2know: An HIV-Testing Strategy Using Oral Fluid Samples and Online Communication of Test Results for Men Who Have Sex With Men in Belgium
Cited by: 35
Author(s): Tom Platteau, Katrien Fransen, Ludwig Apers, Chris Kenyon, Laura Albers, Tine Vermoesen, Jasna Loos, Éric Florence
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1006666

Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts
Cited by: 73
Author(s): Jean-Tristan Brandenburg, Tristan Mary‐Huard, Guillem Rigaill, Sarah Hearne, Hélène Corti, Johann Joets, Clémentine Vitte, Alain Charcosset, Stéphane Nicolas, Maud I. Tenaillon
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-15-S10-S3

Identification of conserved and polymorphic STRs for personal genomes
Cited by: 8
Author(s): Chien‐Ming Chen, Chi Pong Sio, Yu Lu, Hao Teng Chang, Chaofang Hu, Tun‐Wen Pai
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pgen.1002235

The Evolutionarily Conserved Longevity Determinants HCF-1 and SIR-2.1/SIRT1 Collaborate to Regulate DAF-16/FOXO
Cited by: 105
Author(s): Gizem Rizki, Terri Iwata, J i Li, Christian G. Riedel, Colette L. Picard, Max Jan, Coleen T. Murphy, Siu Sylvia Lee
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pgen.1003368

Long Noncoding RNA MALAT1 Controls Cell Cycle Progression by Regulating the Expression of Oncogenic Transcription Factor B-MYB
Cited by: 637
Author(s): Vidisha Tripathi, Zhen Shen, Arindam Chakraborty, Sumanprava Giri, Susan M. Freier, Xiaolin Wu, Yongqing Zhang, Myriam Gorospe, Supriya G. Prasanth, Ashish Lal, Kannanganattu V. Prasanth
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.0020152

Analysis of Pleiotropic Transcriptional Profiles: A Case Study of DNA Gyrase Inhibition
Cited by: 43
Author(s): Kyeong Soo Jeong, Yang Xie, Hiroshi Hiasa, Arkady B. Khodursky
Software Mentions: 1
Published: almost 20 years ago

10.1371/journal.pgen.1002380

A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster
Cited by: 55
Author(s): Hang Yin, Sarah Sweeney, Debasish Raha, M Snyder, Haifan Lin
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1002974

SWI/SNF-Like Chromatin Remodeling Factor Fun30 Supports Point Centromere Function in S. cerevisiae
Cited by: 41
Author(s): Mickaël Durand-Dubief, William Ryan Will, Edoardo Petrini, Delphine Theodorou, Rachael Rebecca Harris, Margaret Crawford, Konrad Paszkiewicz, Felix Krueger, Rosa Maria Correra, Anna T. Vetter, Jim Miller, Nicholas A. Kent, Patrick Varga‐Weisz
Software Mentions: 1
Published: almost 14 years ago

10.1038/s41598-018-34004-7

Amplification of the Melanocortin-1 Receptor in Nephrotic Syndrome Identifies a Target for Podocyte Cytoskeleton Stabilization
Cited by: 13
Author(s): Lovisa Bergwall, Hanna Wallentin, Johannes Elvin, Peidi Liu, Roberto Boi, Carina Sihlbom, Kyle Hayes, Dale Wright, Börje Haraldsson, Jenny Nyström, Lisa Buvall
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1000680

p63 and p73 Transcriptionally Regulate Genes Involved in DNA Repair
Cited by: 130
Author(s): Yu Li Lin, Shomit Sengupta, Katherine Gurdziel, George W. Bell, Tyler Jacks, Elsa R. Flores
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pgen.1005407

A Genetic Incompatibility Accelerates Adaptation in Yeast
Cited by: 22
Author(s): Duyen Bui, Elliot Dine, James B. Anderson, Charles F. Aquadro, Eric Alani
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1000555

Distinct Roles of Non-Canonical Poly(A) Polymerases in RNA Metabolism
Cited by: 94
Author(s): Salvatore San Paolo, Štěpánka Vaňáčová, Luca Schenk, Tanja Scherrer, Diana Blank, Walter Keller, André P. Gerber
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pgen.1005471

The Arabidopsis RCC1 Family Protein TCF1 Regulates Freezing Tolerance and Cold Acclimation through Modulating Lignin Biosynthesis
Cited by: 89
Author(s): Hongtao Ji, Youning Wang, Catherine Cloix, Kexue Li, Gareth I. Jenkins, Shuangfeng Wang, Zhonglin Shang, Yiting Shi, Shuhua Yang, Xia Li
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1004430

Ex Uno Plures: Clonal Reinforcement Drives Evolution of a Simple Microbial Community
Cited by: 38
Author(s): Margie Kinnersley, Jared W. Wenger, Evgueny Kroll, Julian Adams, Gavin Sherlock, Frank Rosenzweig
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1000129

A Precisely Regulated Gene Expression Cassette Potently Modulates Metastasis and Survival in Multiple Solid Cancers
Cited by: 121
Author(s): Kun Yu, Kumaresan Ganesan, Lay Keng Tan, Mirtha Laban, Jeanie Wu, Xiao Dong Zhao, Hongmin Li, Carol Ho Wing Leung, Yuechun Zhu, Chia Lin Wei, Shing Chuan Hooi, Lance D. Miller, Patrick Tan
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pgen.1000626

The Fission Yeast Homeodomain Protein Yox1p Binds to MBF and Confines MBF-Dependent Cell-Cycle Transcription to G1-S via Negative Feedback
Cited by: 42
Author(s): Sofia Aligianni, Daniel H. Lackner, Steffi Klier, Gabriella Rustici, Brian T. Wilhelm, Samuel Marguerat, Sandra Codlin, Alvis Brāzma, Robertus A.M. de Bruin, Jürg Bähler
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pgen.1000713

E Unibus Plurum: Genomic Analysis of an Experimentally Evolved Polymorphism in Escherichia coli
Cited by: 62
Author(s): Margie Kinnersley, William E. Holben, Frank Rosenzweig
Software Mentions: 1
Published: over 16 years ago

10.18632/oncotarget.15253

CBX3 promotes colon cancer cell proliferation by CDK6 kinase-independent function during cell cycle
Cited by: 41
Author(s): Yu Fan, Haiping Li, Xiaolong Liang, Zheng Xiang
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1000476

Microdissection of Shoot Meristem Functional Domains
Cited by: 71
Author(s): Lionel Brooks, Josh Strable, Xiaolan Zhang, Kazuhiro Ohtsu, Rongyan Zhou, Ananda K. Sarkar, Sarah K. Hargreaves, Robert J. Elshire, Douglas M. Eudy, Teresa E. Pawlowska, Doreen Ware, Diane Janick-Buckner, Brent Buckner, Marja C.P. Timmermans, Patrick S. Schnable, Dan Nettleton, Michael J. Scanlon
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pmed.0030486

A Genome-Wide Screen for Promoter Methylation in Lung Cancer Identifies Novel Methylation Markers for Multiple Malignancies
Cited by: 229
Author(s): David S. Shames, Luc Girard, Boning Gao, Mitsuo Sato, Cheryl Lewis, Narayan Shivapurkar, Aixiang Jiang, Charles M. Perou, Young H. Kim, Jonathan R. Pollack, Kwun M. Fong, Chi Leung Lam, Maria Pik Wong, Yu Shyr, Rita Nanda, Olufunmilayo I. Olopade, William L. Gerald, David M. Euhus, Jerry W. Shay, Adi F. Gazdar, John D. Minna
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2164-8-438

Dynamic gene expression in fish muscle during recovery growth induced by a fasting-refeeding schedule
Cited by: 96
Author(s): Pierre‐Yves Rescan, Jérôme Montfort, Cécile Rallière, Aurélie Le Cam, Diane Esquerré, Karine Hugot
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pmed.1000307

A Six-Gene Signature Predicts Survival of Patients with Localized Pancreatic Ductal Adenocarcinoma
Cited by: 197
Author(s): Jeran K. Stratford, David J. Bentrem, Judy M. Anderson, Cheng Fan, Keith A. Volmar, J. S. Marron, Elizabeth D. Routh, Laura S. Caskey, Jonathan C. Samuel, Channing J. Der, Leigh B. Thorne, Benjamin F. Calvo, Hee Jin Kim, Mark S. Talamonti, Christine A. Iacobuzio–Donahue, Michael A. Hollingsworth, Charles M. Perou, Jen Jen Yeh
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pmed.0030254

Inflammatory Manifestations of Experimental Lymphatic Insufficiency
Cited by: 187
Author(s): Raymond Tabibiazar, Lauren Cheung, Jennifer Han, Jeffrey Swanson, Andreas Beilhack, Andrew An, Soheil S. Dadras, Ned B. Rockson, Smita Joshi, Roger A. Wagner, Stanley G. Rockson
Software Mentions: 1
Published: about 20 years ago

10.1371/journal.pmed.1002877

Impact on child acute malnutrition of integrating a preventive nutrition package into facility-based screening for acute malnutrition during well-baby consultation: A cluster-randomized controlled trial in Burkina Faso
Cited by: 22
Author(s): Elodie Becquey, Lieven Huybregts, Amanda Zongrone, Agnès Le Port, Jef L. Leroy, Rahul Raj, Mariama Touré, Marie T. Ruel
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-015-2120-1

Transcriptome profiling reveals that feeding wild zooplankton to larval Atlantic cod (Gadus morhua) influences suites of genes involved in oxidation-reduction, mitosis, and selenium homeostasis
Cited by: 15
Author(s): Matthew L. Rise, Jennifer R. Hall, Gordon W. Nash, Xi Xue, Marije Booman, Tomer Katan, A. Kurt Gamperl
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-018-37480-z

Determination of Ultrastructural Properties of Human Carotid Atherosclerotic Plaques by Scanning Acoustic Microscopy, Micro-Computer Tomography, Scanning Electron Microscopy and Energy Dispersive X-Ray Spectroscopy
Cited by: 8
Author(s): Bükem Bilen, Leyla Türker Şener, Işıl Albeniz, Meltem Sezen, Mehmet Ünlü, Murat Uğurlucan
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-36859-2

Cellular and animal models of skin alterations in the autism-related ADNP syndrome
Cited by: 26
Author(s): Pilar Mollinedo, Oxana Kapitansky, Domingo González‐Lamuño, Adi Zaslavsky, Pedro J. Real, Illana Gozes, Alberto Gandarillas, José L. Fernández-Luna
Software Mentions: 1
Published: over 7 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: almost 13 years ago

10.1038/s41598-019-38702-8

Comparative Physiological and Metabolic Analysis Reveals a Complex Mechanism Involved in Drought Tolerance in Chickpea (Cicer arietinum L.) Induced by PGPR and PGRs
Cited by: 162
Author(s): Naeem Khan, Asghari Bano, Rahman Ma, J. Guo, Zhiyu Kang, Babar Ma
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pntd.0007489

Phlebotomus papatasi sand fly predicted salivary protein diversity and immune response potential based on in silico prediction in Egypt and Jordan populations
Cited by: 1
Author(s): Catherine M. Flanley, Marcelo Ramalho-Ortigão, Iliano V. Coutinho-Abreu, Rami Mukbel, Hanafi A. Hanafi, Shabaan S. El-Hossary, Emadeldin Y. Fawaz, David F. Hoel, Alexander W. Bray, Gwen Stayback, Douglas A. Shoue, Shaden Kamhawi, Scott J. Emrich, Mary Ann McDowell
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pntd.0000086

Host Gene Expression Profiling of Dengue Virus Infection in Cell Lines and Patients
Cited by: 203
Author(s): Joshua Fink, Feng Gu, Ling Ling, Thomas Tolfvenstam, Farzad O. Olfat, Keh Chuang Chin, Pauline Aw, Joshy George, Vladimir A. Kuznetsov, Mark Schreiber, Subhash G. Vasudevan, Martin L. Hibberd
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pntd.0000648

Delineation of Diverse Macrophage Activation Programs in Response to Intracellular Parasites and Cytokines
Cited by: 91
Author(s): Shuyi Zhang, Charles C. Kim, Sajeev Batra, James H. McKerrow, P’ng Loke
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pntd.0000556

Identification of the Schistosoma mansoni TNF-Alpha Receptor Gene and the Effect of Human TNF-Alpha on the Parasite Gene Expression Profile
Cited by: 32
Author(s): Kátia C. Oliveira, Mariana Carvalho, Thiago M. Venancio, Patrícia A. Miyasato, Toshie Kawano, Ricardo DeMarco, Sérgio Verjovski-Almeida
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pntd.0004086

Synergy of Omeprazole and Praziquantel In Vitro Treatment against Schistosoma mansoni Adult Worms
Cited by: 17
Author(s): Giulliana T. Almeida, Regina Coeli Gonçalves Lage, Letícia Anderson, Thiago M. Venancio, Hidehiko Nakaya, Patrícia A. Miyasato, Henrique K. Rofatto, Adhemar Zerlotini, Eliana Nakano, Guilherme Oliveira, Sérgio Verjovski-Almeida
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-13-707

Insights into the regulation of human CNV-miRNAs from the view of their target genes
Cited by: 17
Author(s): Xudong Wu, Dinglin Zhang, Guohui Li
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-11-248

Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum
Cited by: 72
Author(s): Ines Yang, Uwe John, Sára Beszteri, Gernot Glöckner, Bernd Krock, Alexander Goesmann, Allan Cembella
Software Mentions: 1
Published: over 16 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566