cran: SAM | Projects | Ecosyste.ms: Papers

10.7554/eLife.02137

The quantitative architecture of centromeric chromatin
Cited by: 177
Author(s): Dani L. Bodor, João F. Mata, Mikhail Sergeev, Ana F. David, Kevan J. Salimian, Tanya Panchenko, Don W. Cleveland, Ben E. Black, Jagesh V. Shah, Lars Jansen
Software Mentions: 1
Published: about 12 years ago

10.7554/eLife.07901

A putative ATPase mediates RNA transcription and capping in a dsRNA virus
Cited by: 32
Author(s): Xuekui Yu, Junchen Jiang, Jingchen Sun, Z. Hong Zhou
Software Mentions: 1
Published: about 11 years ago

10.7554/eLife.43114

A causal role for the precuneus in network-wide theta and gamma oscillatory activity during complex memory retrieval
Cited by: 53
Author(s): Melissa Hebscher, Jed A. Meltzer, Asaf Gilboa
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.23493

Mating and male pheromone kill Caenorhabditis males through distinct mechanisms
Cited by: 54
Author(s): Cheng Shi, Alexi Runnels, Coleen T. Murphy
Software Mentions: 1
Published: over 9 years ago

10.7554/eLife.00822

A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis
Cited by: 72
Author(s): Virginie Olive, Erich Sabio, Margaux J Bennett, Caitlin S De Jong, Anne Biton, James C. McGann, Samantha K. Greaney, Nicole M. Sodir, Alicia Y. Zhou, Asha Balakrishnan, Mona Foth, Micah A. Luftig, Andrei Goga, Terence P. Speed, Zhenyu Xuan, Gérard I. Evan, Ying Wan, Alex C. Minella, Lin He
Software Mentions: 1
Published: almost 13 years ago

10.7554/eLife.19092

Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin
Cited by: 73
Author(s): Gudrun Böhmdorfer, Shriya Sethuraman, M. Jordan Rowley, Michał Krzysztoń, M. Hafiz Rothi, Lilia Bouzit, Andrzej Wierzbicki
Software Mentions: 1
Published: almost 10 years ago

10.7554/eLife.56611

Cohesion is established during DNA replication utilising chromosome associated cohesin rings as well as those loaded de novo onto nascent DNAs
Cited by: 31
Author(s): Manoj Srinivasan, Marco Fumasoni, Naomi J Petela, Andrew W. Murray, Kim Nasmyth
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.44736

Scc2 counteracts a Wapl-independent mechanism that releases cohesin from chromosomes during G1
Cited by: 28
Author(s): Manoj Srinivasan, Naomi J Petela, Johanna C. Scheinost, James E. Collier, Menelaos Voulgaris, Maurici B. Roig, Frédéric Beckouët, Bin Hu, Kim Nasmyth
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.46413

Insulin-like peptides and the mTOR-TFEB pathway protect Caenorhabditis elegans hermaphrodites from mating-induced death
Cited by: 24
Author(s): Cheng Shi, Lauren N. Booth, Coleen T. Murphy
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.19295

Inhibition in the auditory brainstem enhances signal representation and regulates gain in complex acoustic environments
Cited by: 32
Author(s): Christian Keine, Rudolf Rübsamen, Bernhard Englitz
Software Mentions: 1
Published: almost 10 years ago

10.3390/ijms13032744

Genome-Wide Analysis of a TaLEA-Introduced Transgenic Populus simonii × Populus nigra Dwarf Mutant
Cited by: 9
Author(s): Hongmei Yuan, Chen Su, Lin Lin, Rui Wei, Huiyu Li, Guifeng Liu, Jing Jiang
Software Mentions: 1
Published: over 14 years ago

10.3390/ijms131012857

Fragment-Based Screening by Protein Crystallography: Successes and Pitfalls
Cited by: 47
Author(s): Zorik Chilingaryan, Zhou Yin, Aaron J. Oakley
Software Mentions: 1
Published: about 14 years ago

10.3390/ijms14011105

Identification of Recurrence Related microRNAs in Hepatocellular Carcinoma after Surgical Resection
Cited by: 22
Author(s): Zhen Yang, Ruoyu Miao, Guangbing Li, Yan Wu, Simon C. Robson, Xiaobo Yang, Yi Zhao, Haitao Zhao, Yang Zhong
Software Mentions: 1
Published: almost 14 years ago

10.3390/ijms140611560

MicroRNA-Regulated Protein-Protein Interaction Networks and Their Functions in Breast Cancer
Cited by: 55
Author(s): Chia Hsien Lee, Wen-Hsing Kuo, Lin Chen, Yen Jen Oyang, Hsuan‐Cheng Huang, Hsueh‐Fen Juan
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-9-591

Transcriptome analysis of mammary epithelial subpopulations identifies novel determinants of lineage commitment and cell fate
Cited by: 153
Author(s): Howard Kendrick, Joseph L. Regan, Fiona-Ann Magnay, Anita Grigoriadis, Costas Mitsopoulos, Marketa Zvelebil, Matthew J. Smalley
Software Mentions: 1
Published: almost 18 years ago

10.3390/ijms141020326

MicroRNA Expression Profiling of the Porcine Developing Hypothalamus and Pituitary Tissue
Cited by: 18
Author(s): Lifan Zhang, Zhaowei Cai, Song Wei, Huiyun Zhou, Hongmei Zhou, Xiaoling Jiang, N. Xu
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-016-2558-9

A genome-wide expression profile analysis reveals active genes and pathways coping with phosphate starvation in soybean
Cited by: 18
Author(s): Qing Wang, Jiao Wang, Yuming Yang, Wenkai Du, Dan Zhang, Deyue Yu, Hao Cheng
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-8-29

Identification of rat lung-specific microRNAs by microRNA microarray: valuable discoveries for the facilitation of lung research
Cited by: 66
Author(s): Yang Wang, Tingting Weng, Deming Gou, Zhongming Chen, Narendranath Reddy Chintagari, Lin Liu
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2164-7-87

Operon information improves gene expression estimation for cDNA microarrays
Cited by: 12
Author(s): Guanghua Xiao, Betsy Martinez‐Vaz, Wei Pan, Arkady B. Khodursky
Software Mentions: 1
Published: over 20 years ago

10.1186/1471-2164-14-353

Transcription analysis of the porcine alveolar macrophage response to porcine circovirus type 2
Cited by: 33
Author(s): Wentao Li, Shuqing Liu, Yang Wang, Feng Deng, Weidong Yan, Kun Yang, Huanchun Chen, Qigai He, Catherine Charreyre, Jean-Christophe Audoneet
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-16-S9-S2

A computational framework for the prioritization of disease-gene candidates
Cited by: 16
Author(s): Fiona Browne, Haiying Wang, Huiru Zheng
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-8-305

Genome-wide genetic aberrations of thymoma using cDNA microarray based comparative genomic hybridization
Cited by: 31
Author(s): Gui Youn Lee, Woo Ick Yang, Hei Cheul Jeung, Sang Chul Kim, Min Young Seo, Chan Hee Park, Hyun Cheol Chung, Sun Young Rha
Software Mentions: 1
Published: about 19 years ago

10.1186/z

Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background
Cited by: 0
Author(s): Fan Zhang, Liying Huang, Wensheng Wang, Xiuqin Zhao, Linghua Zhu, Binying Fu, Zhikang Li
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-13-663

Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties
Cited by: 64
Author(s): Ramasamy S Annadurai, Vasanthan Jayakumar, Raja C. Mugasimangalam, Mohan A. V. S. K. Katta, Sanchita Anand, Sreeja Gopinathan, Santosh Prasad Sarma, Sunjay Jude Fernandes, Nandita Mullapudi, M. Senthilkumar, Sudha Rao
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-8-384

A systems-biology analysis of isogenic megakaryocytic and granulocytic cultures identifies new molecular components of megakaryocytic apoptosis
Cited by: 19
Author(s): Chi Chen, Peter G. Fuhrken, Li Chi Huang, Pani A. Apostolidis, Min Wang, Carlos J. Paredes, William M. Miller, Eleftherios T. Papoutsakis
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2164-11-505

Homoeolog-specific transcriptional bias in allopolyploid wheat
Cited by: 120
Author(s): Alina Akhunova, R. T. Matniyazov, Hanquan Liang, Eduard Akhunov
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-14-731

Reversible, interrelated mRNA and miRNA expression patterns in the transcriptome of Rasless fibroblasts: functional and mechanistic implications
Cited by: 11
Author(s): Sami Azrak, Alicia Ginel-Picardo, Matthias Drosten, Mariano Barbacid, Eugenio Santos
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-020-06953-9

Physiological and transcriptomic responses of water spinach (Ipomoea aquatica) to prolonged heat stress
Cited by: 12
Author(s): R. S. Guo, Xingru Wang, Xiao Han, Xiao Chen, Gefu Wang‐Pruski
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-9-S2-S14

Selecting informative genes for discriminant analysis using multigene expression profiles
Cited by: 9
Author(s): Xin Yan, Zheng Tian
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2164-10-644

A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum
Cited by: 70
Author(s): Tarun Kumar Bhatt, Charu Kapil, Sameena Khan, Mohamad Aman Jairajpuri, Vinay Sharma, Daniele Santoni, Francesco Silvestrini, Elisabetta Pizzi, Amit Sharma
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-7-118

Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes
Cited by: 191
Author(s): Valerie W. Hu, Bryan Frank, Shannon J. Heine, Norman H. Lee, John Quackenbush
Software Mentions: 1
Published: over 20 years ago

10.1186/s12864-018-5290-9

iMGEins: detecting novel mobile genetic elements inserted in individual genomes
Cited by: 7
Author(s): Jong Woon Bae, Kyeong Won Lee, Mohammad Nazrul Islam, Hyung-Soon Yim, Heejin Park, Mina Rho
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-15-708

Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly
Cited by: 97
Author(s): Amit Deokar, Larissa Ramsay, Andrew Sharpe, Marwan Diapari, Anoop Sindhu, Kirstin E. Bett, Thomas D. Warkentin, Bunyamin Tar’an
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-10-370

The steady-state transcriptome of the four major life-cycle stages of Trypanosoma cruzi
Cited by: 119
Author(s): Todd Minning, D. Brent Weatherly, James Atwood, Ron Orlando, Rick L. Tarleton
Software Mentions: 1
Published: about 17 years ago

10.1186/s12864-015-2256-z

De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.)
Cited by: 29
Author(s): Liwu Zhang, Ray Ming, Jisen Zhang, Aifen Tao, Pingping Fang, Jianmin Qi
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12864-016-3147-7

Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences
Cited by: 19
Author(s): Damarius S. Fleming, James E. Koltes, Eric R. Fritz-Waters, Max F. Rothschild, Carl J. Schmidt, C. M. Ashwell, Michael E. Persia, James M. Reecy, Susan J. Lamont
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-15-1016

Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells
Cited by: 15
Author(s): Masahiro Tokunaga, Chikara Kokubu, Yusuke Maeda, Jun Sese, Kyoji Horie, Nakaba Sugimoto, Taroh Kinoshita, Kosuke Yusa, Junji Takeda
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-14-15

Saccharopolyspora erythraea’sgenome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch
Cited by: 25
Author(s): Esteban Marcellin, Tim R. Mercer, Cuauhtémoc Licona-Cassani, Robin W. Palfreyman, Marcel E. Dinger, Jennifer A. Steen, John S. Mattick, Lars K. Nielsen
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-15-1145

Genomic and transcriptomic differences in community acquired methicillin resistant Staphylococcus aureus USA300 and USA400 strains
Cited by: 18
Author(s): Marcus B. Jones, Christopher P. Montgomery, Susan Boyle-Vavra, Kenneth Shatzkes, Rosslyn Maybank, Bryan Frank, Scott N. Peterson, Robert S. Daum
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-14-104

A highly expressed miR-101 isomiR is a functional silencing small RNA
Cited by: 93
Author(s): Franc Llorens, Mónica Báñez-Coronel, Lorena Pantano, José Antonio del Rı́o, Isidre Ferrer, Xavier Estivill, Eulàlia Martı́
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-7-208

Cell organisation, sulphur metabolism and ion transport-related genes are differentially expressed in Paracoccidioides brasiliensis mycelium and yeast cells
Cited by: 17
Author(s): Rosângela Viana Andrade, Hugo Costa Paes, André Moraes Nicola, Maria José A. Carvalho, Ana Lúcia Fachin, Renato Cardoso, Simoneide S. Silva, Larissa Fernandes, Silvana P. Silva, Eduardo Antônio Donadi, Elza T. Sakamoto-Hojo, Geraldo A. S. Passos, C. M. A. Soares, Marcelo M. Brígido, Maria Sueli Soares Felipe
Software Mentions: 1
Published: about 20 years ago

10.1186/s12864-016-3136-x

Distinct transcriptome responses to water limitation in isohydric and anisohydric grapevine cultivars
Cited by: 43
Author(s): Silvia Dal Santo, Alberto Palliotti, Sara Zenoni, Giovanni Battista Tornielli, Marianna Fasoli, Paola Paci, Sergio Tombesi, Tommaso Frioni, O. Silvestroni, Andrea Bellincontro, Claudio D’Onofrio, Fabiola Matarese, Matteo Gatti, Stefano Poni, Mario Pezzotti
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-14-378

Transcriptional adaptation of pneumococci and human pharyngeal cells in the presence of a virus infection
Cited by: 13
Author(s): Sheila Z. Kimaro Mlacha, Teresa C. T. Peret, Nikhil Kumar, Sandra Romero-Steiner, Julie C. Dunning Hotopp, Nadeeza Ishmael, Valerie Grinblat-Huse, David R. Riley, Dean D. Erdman, George M. Carlone, Jacquelyn S. Sampson, J. Anthony G. Scott, Hervé Tettelin
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-11-265

Chronic activation of the epithelial immune system of the fruit fly's salivary glands has a negative effect on organismal growth and induces a peculiar set of target genes
Cited by: 14
Author(s): Ahmed Abdelsadik, Thomas Roeder
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12864-018-4582-4

Combining QTL-seq and linkage mapping to fine map a wild soybean allele characteristic of greater plant height
Cited by: 47
Author(s): Xiaoli Zhang, Wubin Wang, Na Guo, Youyi Zhang, Yuanpeng Bu, Jinming Zhao
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-016-2416-9

Comparative transcriptome analysis of wheat embryo and endosperm responses to ABA and H2O2 stresses during seed germination
Cited by: 23
Author(s): Yonglong Yu, Shoumin Zhen, Wang Shu, Yaping Wang, Hui Cao, Yanzhen Zhang, Jiarui Li, Yueming Yan
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-8-153

Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates
Cited by: 67
Author(s): Fang Liu, Tor Kristian Jenssen, Jeffrey M. Trimarchi, Claudio Punzo, Connie Cepko, Lucila Ohno-Machado, Eivind Hovig, Winston Patrick Kuo
Software Mentions: 1
Published: over 19 years ago

10.1186/s12864-016-3405-8

Genome-wide expression profiling in muscle and subcutaneous fat of lambs in response to the intake of concentrate supplemented with vitamin E
Cited by: 20
Author(s): L. González-Calvo, Elda Dervishi, M. Joy, P. Sarto, Roberto Martín‐Hernández, M. Serrano, José M. Ordovás, J.H. Calvo
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-016-3377-8

Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency
Cited by: 9
Author(s): Desalegn D. Serba, Srinivasa Rao Uppalapati, Nick Krom, Shreyartha Mukherjee, Yuhong Tang, Kirankumar S. Mysore, Malay C. Saha
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-13-S2-S4

Haplotype and minimum-chimerism consensus determination using short sequence data
Cited by: 19
Author(s): Shawn T. O’Neil, Scott J. Emrich
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12864-021-07772-2

A two-way rectification method for identifying differentially expressed genes by maximizing the co-function relationship
Cited by: 0
Author(s): Bolin Chen, Li Gao, Xuequn Shang
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-8-87

Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise
Cited by: 40
Author(s): Harkamal Walia, Clyde Wilson, Pascal Condamine, Abdelbagi M. Ismail, Jin Xu, Xinping Cui, Timothy J. Close
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-13-500

Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing
Cited by: 22
Author(s): Abdou ElSharawy, Jason Warner, Jeff Olson, Michael Förster, Markus B. Schilhabel, Darren R. Link, Stefan Rose-John, Stefan Schreiber, Philip Rosenstiel, James Brayer, André Franke
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2164-14-315

Exploring the larval transcriptome of the common sole (Solea solea L.)
Cited by: 42
Author(s): Serena Ferraresso, Alessio Bonaldo, Luca Parma, Stefano Cinotti, Paola Massi, Luca Bargelloni, Pier Paolo Gatta
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-15-180

Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution
Cited by: 38
Author(s): Biao Wang, Robert Ekblom, Ignas Bunikis, Heli Siitari, Jacob Höglund
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-018-4636-7

Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423
Cited by: 24
Author(s): Hadrien Máté de Gérando, François Wasels, Angélique Bisson, Benjamin Clément, Frédérique Bidard, Etienne Jourdier, Ana M. López-Contreras, Nicolas Lopes Ferreira
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-15-273

SNP Discovery for mapping alien introgressions in wheat
Cited by: 78
Author(s): Vijay K. Tiwari, Shichen Wang, Sunish K. Sehgal, Jan Vrána, Bernd Friebe, Marie Kubaláková, Praveen Chhuneja, Jaroslav Doležel, Eduard Akhunov, Bhanu Kalia, Jamal S. M. Sabir, Bikram S. Gill
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-12-405

Transcriptional responses to glucose in Saccharomyces cerevisiae strains lacking a functional protein kinase A
Cited by: 23
Author(s): Daniela Livas, Marinka J. H. Almering, Jean‐Marc Daran, Jack T. Pronk, Juana M. Gancedo
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2164-10-292

Disorders of sex development expose transcriptional autonomy of genetic sex and androgen-programmed hormonal sex in human blood leukocytes
Cited by: 22
Author(s): Paul‐Martin Holterhus, Jan-Hendrik Bebermeier, Ralf Werner, János Demeter, Annette Richter‐Unruh, Gunnar Cario, Mahesh Appari, Reiner Siebert, Felix G. Riepe, James D. Brooks, Olaf Hiort
Software Mentions: 1
Published: almost 18 years ago

10.1186/s12864-015-1277-y

Characterization of a novel RXR receptor in the salmon louse (Lepeophtheirus salmonis, Copepoda) regulating growth and female reproduction
Cited by: 17
Author(s): Christiane Eichner, Sussie Dalvin, Rasmus Skern‐Mauritzen, Ketil Malde, Heidi Kongshaug, Frank Nilsen
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-15-346

Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars
Cited by: 29
Author(s): Jun‐ichi Yonemaru, Ritsuko Mizobuchi, Hiroshi Katô, Tetsuro Yamamoto, Eiji Yamamoto, Kazuki Matsubara, Hideyuki Hirabayashi, Yoshinobu Takeuchi, Hiroshi Tsunematsu, Takuro Ishii, Hiroto Ohta, Hideo Maeda, Kaworu Ebana, Masahiro Yano
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-11-354

Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity
Cited by: 35
Author(s): Serena Ferraresso, Massimo Milan, Caterina Pellizzari, Nicola Vitulo, Richard Reinhardt, Adelino V.M. Canário, Tomaso Patarnello, Luca Bargelloni
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-10-404

Streptococcus pneumoniae nasopharyngeal colonization induces type I interferons and interferon-induced gene expression
Cited by: 42
Author(s): Elizabeth A. Joyce, Stephen J. Popper, Stanley Falkow
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-14-589

Impact of microRNAs on regulatory networks and pathways in human colorectal carcinogenesis and development of metastasis
Cited by: 136
Author(s): Silvia Pizzini, Andrea Bisognin, Susanna Mandruzzato, M. Biasiolo, Arianna Facciolli, Lisa Perilli, Elisabetta Rossi, Giovanni Esposito, Massimo Rugge, Pierluigi Pilati, Simone Mocellin, Donato Nitti, Stefania Bortoluzzi, Paola Zanovello
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-13-S8-S9

BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data
Cited by: 6
Author(s): Yuan Yuan, Clift Norris, Yanxun Xu, Kam Wah Tsui, Yuan Ji, Han Liang
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-10-275

7TMRmine: a Web server for hierarchical mining of 7TMR proteins
Cited by: 21
Author(s): Guoquing Lu, Zhifang Wang, Alan M. Jones, Etsuko N. Moriyama
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-8-281

Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis
Cited by: 174
Author(s): Yong‐Mei Bi, Rong-Lin Wang, Tong Zhu, Steven J. Rothstein
Software Mentions: 1
Published: about 19 years ago

10.1186/1471-2164-11-65

Tungsten carbide cobalt nanoparticles exert hypoxia-like effects on the gene expression level in human keratinocytes
Cited by: 41
Author(s): Wibke Busch, Dana Kühnel, Kristin Schirmer, Stefan Scholz
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-12-381

Combined analysis of transcriptome and metabolite data reveals extensive differences between black and brown nearly-isogenic soybean (Glycine max) seed coats enabling the identification of pigment isogenes
Cited by: 39
Author(s): Nik Kovinich, Ammar Saleem, John T. Arnason, Brian Miki
Software Mentions: 1
Published: about 15 years ago

10.1186/s12864-015-1524-2

Microarray: a global analysis of biomineralization-related gene expression profiles during larval development in the pearl oyster, Pinctada fucata
Cited by: 45
Author(s): Jun Li, Dong Yang, Shiting Liu, Shiguo Li, Guangrui Xu, Guilan Zheng, Liping Xie, Rongqing Zhang
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-8-63

Target genes of myostatin loss-of-function in muscles of late bovine fetuses
Cited by: 69
Author(s): Isabelle Cassar-Malek, Florent Passelaigue, Carine Bernard, Jean J. Léger, Jean-François Hocquette
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-13-177

Improving the performance of true single molecule sequencing for ancient DNA
Cited by: 39
Author(s): Aurélien Ginolhac, Julia T. Vilstrup, Jesper Stenderup, Morten Rasmussen, Mathias Stiller, Beth Shapiro, Grant D. Zazula, Duane G. Froese, Kathleen E. Steinmann, John F. Thompson, Khaled A. S. Al-Rasheid, M. Thomas P. Gilbert, Eske Willerslev, Ludovic Orlando
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-6-122

Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains
Cited by: 87
Author(s): Stefano Campanaro, Alessandro Vezzi, Nicola Vitulo, Federico M. Lauro, Michela D’Angelo, Francesca Simonato, Alessandro Cestaro, G Malacrida, Giulio Bertoloni, Giorgio Valle, Douglas H. Bartlett
Software Mentions: 1
Published: about 21 years ago

10.1186/1471-2164-9-369

Peripheral arterial occlusive disease: Global gene expression analyses suggest a major role for immune and inflammatory responses
Cited by: 57
Author(s): Shijun Fu, Hulin Zhao, Jiantao Shi, Arhat Abzhanov, Keith Crawford, Lucila Ohno-Machado, Jianqin Zhou, Yanzhi Du, Winston Patrick Kuo, Ji Zhang, Mier Jiang, Jiamin Jin
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2164-8-264

Genomic expression during human myelopoiesis
Cited by: 30
Author(s): Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Dario Basso, Silvio Bicciato, Roberta Zini, Claudia Gemelli, Gian Antonio Danieli, Sérgio Ferrari
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-8-72

Transcriptional profiling of Actinobacillus pleuropneumoniae under iron-restricted conditions
Cited by: 59
Author(s): Vincent Deslandes, John H. E. Nash, Josée Harel, James W. Coulton, Mario Jacques
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2164-14-195

5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea
Cited by: 60
Author(s): Chi Keung Cheng, Chun Hang Au, Sarah K. Wilke, Jason E. Stajich, Miriam E. Zolan, Patricia J. Pukkila, Hoi Shan Kwan
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-10-398

Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress
Cited by: 47
Author(s): Harkamal Walia, Clyde Wilson, Abdelbagi M. Ismail, Timothy J. Close, Xinping Cui
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-12-37

The sex-biased brain: sexual dimorphism in gene expression in two species of songbirds
Cited by: 60
Author(s): Sara Naurin, Bengt Hansson, Dennis Hasselquist, Yong Hwan Kim, Staffan Bensch
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-7-69

Specific age related signatures in Drosophila body parts transcriptome
Cited by: 97
Author(s): Fabrice Girardot, Christelle Lasbleiz, Véronique Monnier, Hervé Tricoire
Software Mentions: 1
Published: over 20 years ago

10.1186/s12864-018-4445-z

EOGD: the Euplotes octocarinatus genome database
Cited by: 13
Author(s): Ruanlin Wang, Wei Miao, Wei Wang, Jie Xiong, Aihua Liang
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-14-504

REACTIN: Regulatory activity inference of transcription factors underlying human diseases with application to breast cancer
Cited by: 20
Author(s): Mingzhu Zhu, Chun-Chi Liu, Chao Cheng
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-8-94

Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation
Cited by: 40
Author(s): Carl Trygve Stansberg, Audun Osland Vik‐Mo, Rita Holdhus, Harald Breilid, Boleslaw Srebro, Kjell Petersen, Hugo A. Jørgensen, Inge Jonassen, Vidar M. Steen
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-8-85

Gene function in early mouse embryonic stem cell differentiation
Cited by: 129
Author(s): Kagnew Hailesellasse Sene, Christopher J. Porter, Gareth Palidwor, Carolina Perez‐Iratxeta, Enrique M. Muro, Pearl A. Campbell, Michael A. Rudnicki, Miguel A. Andrade‐Navarro
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2164-9-54

Glioma cells on the run – the migratory transcriptome of 10 human glioma cell lines
Cited by: 59
Author(s): Tim Demuth, Jessica L. Rennert, Dominique B. Hoelzinger, Linsey B. Reavie, Mitsutoshi Nakada, Christian Beaudry, Satoko Nakada, Eric M. Anderson, Amanda Henrichs, Wendy S. McDonough, David R. Holz, Anna Joy, Richard Lin, Kuang Hung Pan, Chih Jian Lih, Stan N Cohen, Michael E. Berens
Software Mentions: 1
Published: over 18 years ago

10.1186/s12864-015-1544-y

Mutations upstream of fabI in triclosan resistant Staphylococcus aureus strains are associated with elevated fabI gene expression
Cited by: 17
Author(s): Denis Grandgirard, Leonardo Furi, Maria Laura Ciusa, Lucilla Baldassarri, Daniel R. Knight, Ian Morrissey, Carlo R. Largiadèr, Stephen L. Leib, Marco R. Oggioni
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-9-225

Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells identifies novel immune response players in T-Cell activation
Cited by: 84
Author(s): Min Wang, Dirk Windgassen, Eleftherios T. Papoutsakis
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-11-85

MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori
Cited by: 59
Author(s): Shiping Liu, Song Gao, Danyu Zhang, Jiyun Yin, Xiang Zhang, Qingyou Xia
Software Mentions: 1
Published: over 16 years ago

10.1136/bmjopen-2018-027548

TAME trial: a multi-arm phase II randomised trial of four novel interventions for malnutrition enteropathy in Zambia and Zimbabwe - a study protocol
Cited by: 5
Author(s): Paul Kelly, Lauren N. Bell, Beatrice Amadi, Mutsa Bwakura‐Dangarembizi, Kelley VanBuskirk, Kanta Chandwe, Miyoba Chipunza, Deophine Ngosa, Nivea Chulu, Susan Hill, Simon Murch, Raymond J. Playford, Andrew J. Prendergast
Software Mentions: 1
Published: almost 7 years ago

10.29252/NIRP.BCN.9.2.107

Stress and Perception of Emotional Stimuli: Long-term Stress Rewiring the Brain
Cited by: 14
Author(s): Reza Khosrowabadi
Software Mentions: 1
Published: over 8 years ago

10.1186/1744-9081-4-8

MEG event-related desynchronization and synchronization deficits during basic somatosensory processing in individuals with ADHD
Cited by: 55
Author(s): Colleen Dockstader, William Gaetz, Douglas Cheyne, Frank Wang, F. Xavier Castellanos, Rosemary Tannock
Software Mentions: 1
Published: over 18 years ago

10.1186/1744-9081-10-32

Multilevel analysis of facial expressions of emotion and script: self-report (arousal and valence) and psychophysiological correlates
Cited by: 17
Author(s): Michela Balconi, Maria Elide Vanutelli, Roberta Finocchiaro
Software Mentions: 1
Published: almost 13 years ago

10.3758/s13428-014-0509-4

Affective norms for 1,586 polish words (ANPW): Duality-of-mind approach
Cited by: 73
Author(s): Kamil K. Imbir
Software Mentions: 1
Published: about 12 years ago

10.3390/bs10050092

Eye Movements in Response to Pain-Related Feelings in the Presence of Low and High Cognitive Loads
Cited by: 1
Author(s): Ramtin Zargari Marandi, Camilla Ann Fjelsted, Iris Hrustanovic, Rikke Olesen, Parisa Gazerani
Software Mentions: 1
Published: over 6 years ago

10.1186/1756-0381-5-4

Weighted multiple testing procedures for genomic studies
Cited by: 13
Author(s): Jiang Gui, Tor D. Tosteson, Mark E. Borsuk
Software Mentions: 1
Published: over 14 years ago

10.1093/bioinformatics/btt113

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
Cited by: 208
Author(s): Jon C. Ison, Matúš Kalaš, Inge Jonassen, Dan Bolser, Mahmut Uludağ, Hamish McWilliam, James Malone, Rodrigo López, Steve Pettifer, Peter Rice
Software Mentions: 1
Published: over 13 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566