pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1006639

The highly buffered Arabidopsis immune signaling network conceals the functions of its components
Cited by: 102
Author(s): Rachel Hillmer, Kazuhiko Tsuda, Ghanasyam Rallapalli, Shuji Asai, William Truman, Matthew D Papke, Hitoshi Sakakibara, Jonathan D. G. Jones, Chad L. Myers, Fumiaki Katagiri
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pgen.1009010

Candidate variants in TUB are associated with familial tremor
Cited by: 2
Author(s): M. Reza Sailani, Fereshteh Jahanbani, Charles W. Abbott, Hayan Lee, Amin Zia, Shannon Rego, Juliane Winkelmann, Franziska Hopfner, Tahir Naeem Khan, Nicholas Katsanis, Stefanie H. Müller, Daniela Berg, Katherine M. Lyman, Christian Mychajliw, G. Deuschl, Jonathan A. Bernstein, Gregor Kuhlenbäumer, M Snyder
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-015-1739-2

De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil
Cited by: 20
Author(s): Bree K. Yednock, Timothy J. Sullivan, Joseph E. Neigel
Software Mentions: 5
Published: over 11 years ago

10.1186/s12859-018-2019-3

Closha: bioinformatics workflow system for the analysis of massive sequencing data
Cited by: 15
Author(s): Gun Hwan Ko, Pan Gyu Kim, Jong-Cheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song, Byung-Wook Lee
Software Mentions: 5
Published: almost 9 years ago

10.12688/f1000research.21779.2

A role for MIR828 in pineapple fruit development
Cited by: 6
Author(s): Christopher D. Rock
Software Mentions: 5
Published: over 6 years ago

10.15252/embr.201846960

Nucleosome dynamics of human iPSC during neural differentiation
Cited by: 5
Author(s): Janet Harwood, Nicholas A. Kent, Nicholas Denby Allen, Adrian J. Harwood
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.32537

The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture
Cited by: 57
Author(s): Athma A. Pai, Telmo Henriques, Kayla McCue, Adam Burkholder, Karen Adelman, Christopher B. Burge
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12859-019-3219-1

uap: reproducible and robust HTS data analysis
Cited by: 12
Author(s): Christoph Kämpf, Michael Specht, Alexander Scholz, Sven-Holger Puppel, Gero Doose, Kristin Reiche, Jana Schor, Jörg Hackermüller
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.63093

MITF reprograms the extracellular matrix and focal adhesion in melanoma
Cited by: 42
Author(s): Ramile Dilshat, Valerie Fock, Colin Kenny, Ilse Gerritsen, Romain Lasseur, Jana Trávníčková, Ossia M. Eichhoff, Philipp Cerny, Katrín Möller, Sara Sigurbjörnsdóttir, Kritika Kirty, Berglind O. Einarsdottir, Phil F. Cheng, Mitchell P. Levesque, Robert A. Cornell, E. Elizabeth Patton, Lionel Larue, Marie de Tayrac, Erna Magnúsdóttir, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.02200

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms
Cited by: 206
Author(s): Mary A. Allen, Zdeněk Andrysík, Veronica L. Dengler, Hestia Mellert, Anna L. Guarnieri, John H. Freeman, Kelly D. Sullivan, Matthew D. Galbraith, Xin Luo, W. Lee Kraus, Robin D. Dowell, Joaquín M. Espinosa
Software Mentions: 5
Published: over 12 years ago

10.7554/eLife.02024

MOF-associated complexes ensure stem cell identity and Xist repression
Cited by: 73
Author(s): Tomasz Chelmicki, Friederike Dündar, Matthew James Turley, Tasneem Khanam, Tuğçe Aktaş, Fidel Ramírez, Anne-Valérie Gendrel, Patrick R. Wright, Pavankumar Videm, Rolf Backofen, Edith Heard, Thomas Manke, Asifa Akhtar
Software Mentions: 5
Published: over 12 years ago

10.3390/ijms17060956

Human Milk Cells Contain Numerous miRNAs that May Change with Milk Removal and Regulate Multiple Physiological Processes
Cited by: 58
Author(s): Mohammed Alsaweed, Ching Tat Lai, Peter Hartmann, Donna T. Geddes, Foteini Kakulas
Software Mentions: 5
Published: over 10 years ago

10.1002/1878-0261.12853

Genome‐scale CRISPR screening identifies cell cycle and protein ubiquitination processes as druggable targets for erlotinib‐resistant lung cancer
Cited by: 10
Author(s): Jieun Lee, Ahyoung Choi, Sung Yup Cho, Yukyung Jun, Deukchae Na, Ahra Lee, Giyong Jang, Jee Young Kwon, Jaesang Kim, Sanghyuk Lee, Charles Lee
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.58305

Damage-responsive, maturity-silenced enhancers regulate multiple genes that direct regeneration in Drosophila
Cited by: 38
Author(s): Robin E. Harris, Michael J. Stinchfield, Spencer L. Nystrom, Daniel J. McKay, Iswar K. Hariharan
Software Mentions: 5
Published: over 6 years ago

10.1084/jem.20171738

A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets
Cited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: almost 9 years ago

10.7717/peerj.6660

Music-performance regulates microRNAs in professional musicians
Cited by: 7
Author(s): Preethy Sasidharan Nair, Tuire Kuusi, Minna Ahvenainen, Anju K. Philips, Irma Järvelä
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-015-2246-1

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants
Cited by: 12
Author(s): Anna Aulicino, Adam M. Dinan, Aleksandra A. Miranda-CasoLuengo, John A. Browne, Kévin Rue-Albrecht, David E. MacHugh, Brendan J. Loftus
Software Mentions: 5
Published: almost 11 years ago

10.1155/2021/8880585

Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells
Cited by: 3
Author(s): Szabolcs Éliás, Angelika Schmidt, David Green, Jesper Tegnér
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-86919-3

Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis
Cited by: 3
Author(s): Tongqiang Fan, Yajiang Huang
Software Mentions: 5
Published: over 5 years ago

10.1016/j.molcel.2018.09.033

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Cited by: 73
Author(s): Lorea Blázquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, André Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Software Mentions: 5
Published: about 8 years ago

10.1038/s41598-021-92448-w

Focused CRISPR-Cas9 genetic screening reveals USO1 as a vulnerability in B-cell acute lymphoblastic leukemia
Cited by: 8
Author(s): Amit Jaiswal, Hellen Truong, Tiffany Tran, Tasha Lin, David Casero, Michael O. Alberti, Dinesh S. Rao
Software Mentions: 5
Published: over 5 years ago

10.1242/dev.146811

Epigenetic resetting of human pluripotency
Cited by: 210
Author(s): Ge Guo, Ferdinand von Meyenn, Maria Rostovskaya, James Clarke, Sabine Dietmann, Duncan Baker, Anna Sahakyan, Samuel A. Myers, Paul Bertone, Wolf Reik, Kathrin Plath, Austin Smith
Software Mentions: 5
Published: over 9 years ago

10.15252/embj.2020105776

Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency
Cited by: 22
Author(s): Andreas Lackner, Robert Sehlke, Marius Garmhausen, Giuliano Giuseppe Stirparo, Michelle Huth, Fabian Titz-Teixeira, Petra van der Lelij, Julia Ramesmayer, Henry F. Thomas, Markus Ralser, Laura Santini, Elena Galimberti, Mihail Sarov, A. Francis Stewart, Austin Smith, Andreas Beyer, Martin Leeb
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-93297-3

Zfp57 inactivation illustrates the role of ICR methylation in imprinted gene expression during neural differentiation of mouse ESCs
Cited by: 7
Author(s): Basilia Acurzio, Ankit Verma, Alessia Polito, Carlo Giaccari, Francesco Cecere, Salvatore Fioriniello, Floriana Della Ragione, Annalisa Fico, Flavia Cerrato, Claudia Angelini, Robert Feil, Andrea Riccio
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.04530

The long non-coding RNA Dali is an epigenetic regulator of neural differentiation
Cited by: 142
Author(s): Vladislava Chalei, Stephen N. Sansom, Lesheng Kong, Sheena Lee, Juan Montiel, Keith W. Vance, Chris P. Ponting
Software Mentions: 5
Published: almost 12 years ago

10.1111/1751-7915.12757

Relative abundance of ‘ Candidatus Tenderia electrophaga’ is linked to cathodic current in an aerobic biocathode community
Cited by: 25
Author(s): Anthony P. Malanoski, Baochuan Lin, Brian J. Eddie, Zheng Wang, W. Judson Hervey, Sarah M. Glaven
Software Mentions: 5
Published: over 9 years ago

10.1016/j.stem.2019.03.017

Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency
Cited by: 78
Author(s): Tüzer Kalkan, Susanne Bornelöv, Carla Mulas, Evangelia Diamanti, Tim Lohoff, Markus Ralser, Sjors Middelkamp, Patrick Lombard, Jennifer Nichols, Austin Smith
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pcbi.1002887

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling
Cited by: 46
Author(s): S. Huang, David Clarke, Sara J.C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel
Software Mentions: 5
Published: almost 14 years ago

10.1371/journal.pcbi.1006982

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Cited by: 83
Author(s): Ivan Jurić, Miao Yu, Armen Abnousi, Ramya Raviram, Rongxin Fang, Yuan Zhao, Yanxiao Zhang, Yunjiang Qiu, Yuchen Yang, Yun Li, Bing Ren, Maowen Hu
Software Mentions: 5
Published: over 7 years ago

10.1186/gb-2013-14-10-r112

Genome-wide analysis of condensin binding in Caenorhabditis elegans
Cited by: 74
Author(s): Anna-Lena Kranz, Chenyu Jiao, Lara Winterkorn, Sarah Elizabeth Albritton, Maxwell Kramer, Sevinç Ercan
Software Mentions: 5
Published: almost 14 years ago

10.1186/s12862-019-1572-3

The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish
Cited by: 4
Author(s): Mauricio Losilla, David Luecke, Jason R. Gallant
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-021-81297-2

CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants
Cited by: 3
Author(s): Victor Aprilyanto, Redi Aditama, Zulfikar Achmad Tanjung, Condro Utomo, Tony Liwang
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-017-17408-9

Model-based genome-wide determination of RNA chain elongation rates in Escherichia coli
Cited by: 7
Author(s): Peter Großmann, Anja Lück, Christoph Kaleta
Software Mentions: 5
Published: almost 9 years ago

10.1093/molbev/msz099

Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae)
Cited by: 72
Author(s): Marc Tollis, Jooke Robbins, Andrew E. Webb, Lukas F. K. Kuderna, Aleah F. Caulin, Jacinda D Garcia, Martine Bérubé, Nader Pourmand, Tomàs Marquès-Bonet, Mary J. O’Connell, Per Palsbøll, Carlo C. Maley
Software Mentions: 5
Published: over 7 years ago

10.1016/j.celrep.2021.109101

Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation
Cited by: 18
Author(s): Nicholas T. Crump, Andreas V. Hadjinicolaou, Meng Xia, John Walsby-Tickle, Uzi Gileadi, Ji‐Li Chen, Mashiko Setshedi, Lars Rønn Olsen, I-Jun Lau, Laura Godfrey, Lynn Quek, Zhanru Yu, Erica Ballabio, Mike Bogetofte Barnkob, Giorgio Napolitani, Mariolina Salio, Hashem Koohy, Benedikt M. Kessler, Stephen Taylor, Paresh Vyas, James McCullagh, Thomas A. Milne, Vincenzo Cerundolo
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-19984-w

Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage
Cited by: 51
Author(s): Jun Wang, Zhu Jun, Yadong Zhang, Fangjun Fan, Wenqi Li, Fangquan Wang, Zhong WeiGong, Cailin Wang, Jie Yang
Software Mentions: 5
Published: almost 9 years ago

10.1038/s41598-021-82136-0

A high-throughput RNA-Seq approach to elucidate the transcriptional response of Piriformospora indica to high salt stress
Cited by: 13
Author(s): Nivedita, Abdul Rawoof, Nirala Ramchiary, M. Z. Abdin
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.ppat.1009217

EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape
Cited by: 14
Author(s): Nathan Ungerleider, Whitney Bullard, Mehmet Kara, Xia Wang, Claire Roberts, Rolf Renne, Scott A. Tibbetts, Erik K. Flemington
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cell.2021.03.062

Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing
Cited by: 88
Author(s): Mateusz Mendel, Kamila Delaney, Radha Raman Pandey, Kuan-Ming Chen, Joanna M. Wenda, Cathrine Broberg Vågbø, Florian Steiner, David Homolka, Ramesh S. Pillai
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0105097

Transcriptome of American Oysters, Crassostrea virginica, in Response to Bacterial Challenge: Insights into Potential Mechanisms of Disease Resistance
Cited by: 64
Author(s): Ian C. McDowell, Chamilani Nikapitiya, Derek Aguiar, Christopher E. Lane, Sorin Istrail, Marta Gómez-Chiarri
Software Mentions: 5
Published: about 12 years ago

10.1371/journal.pone.0151917

Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns
Cited by: 9
Author(s): Yayoi Natsume-Kitatani, Hiroshi Mamitsuka
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0159093

Molecular Mechanism for Stress-Induced Depression Assessed by Sequencing miRNA and mRNA in Medial Prefrontal Cortex
Cited by: 57
Author(s): Ke Ma, Li Guo, Aiping Xu, Shan Cui, Jinhui Wang
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0119027

Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss Mutant
Cited by: 17
Author(s): Zhiying Li, Jiabin Wang, Xuequan Zhang, Li Xu
Software Mentions: 5
Published: over 11 years ago

10.1186/gm377

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival
Cited by: 47
Author(s): Pär G. Engström, Diva Tommei, Stefan H. Stricker, Christine Ender, Steven M. Pollard, Paul Bertone
Software Mentions: 5
Published: almost 15 years ago

10.1371/journal.pbio.3000396

Inverted translational control of eukaryotic gene expression by ribosome collisions
Cited by: 39
Author(s): Heungwon Park, Arvind R. Subramaniam
Software Mentions: 5
Published: about 7 years ago

10.1093/gbe/evz150

Evolution of Phototransduction Genes in Lepidoptera
Cited by: 26
Author(s): Aide Macias-Muñoz, Aline G. Rangel Olguin, Adriana D. Briscoe
Software Mentions: 5
Published: over 7 years ago

10.1093/gigascience/giz145

Benchmark of long non-coding RNA quantification for RNA sequencing of cancer samples
Cited by: 31
Author(s): Hong Zheng, Kevin Brennan, Mikel Hernáez, Olivier Gevaert
Software Mentions: 5
Published: almost 7 years ago

10.1038/srep43793

Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome
Cited by: 24
Author(s): Guogui Ning, Cheng Xu, Ping Luo, Fan Liang, Zhen Wang, Guoliang Yu, Xin Li, Depeng Wang, Manzhu Bao
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.23645

Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation
Cited by: 27
Author(s): Sarah Elizabeth Albritton, Anna Lena Kranz, Lara Winterkorn, Lena Annika Street, Sevinç Ercan
Software Mentions: 5
Published: over 9 years ago

10.1111/pbi.12615

A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution
Cited by: 149
Author(s): James K. Hane, Ming Yao, Lars G. Kamphuis, Matthew N. Nelson, Gagan Garg, Craig A. Atkins, Philipp E. Bayer, Armando Bravo, Scott Bringans, Steven B. Cannon, David Edwards, Rhonda C. Foley, Ling Gao, Maria J. Harrison, Wei Huang, Bhavna Hurgobin, Sean Li, Cheng-Wu Liu, Annette McGrath, Grant Morahan, Jeremy D. Murray, James L. Weller, Jianbo Jian, Karam B. Singh
Software Mentions: 5
Published: about 10 years ago

10.7717/peerj.5089

Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci
Cited by: 31
Author(s): Bruno A. S. de Medeiros, Brian D. Farrell
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-016-0882-7

Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay
Cited by: 50
Author(s): Brandon C. Sos, Ho-Lim Fung, Derek Gao, Trina Osothprarop, Amirali Kia, M.M. He, Kun Zhang
Software Mentions: 4
Published: almost 11 years ago

10.1002/pld3.241

Control of translation during the unfolded protein response in maize seedlings: Life without PERKs
Cited by: 9
Author(s): Pulkit Kanodia, Paramasivan Vijayapalani, Renu Srivastava, Ran Bi, Peng Liu, W. Allen Miller, Stephen H. Howell
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-015-0746-6

Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
Cited by: 74
Author(s): Adler R. Dillman, Marissa Macchietto, Camille F. Porter, Alicia K. Rogers, Brian A. Williams, Igor Antoshechkin, Ming Min Lee, Z. Goodwin, Xiaojun Lu, Edwin E. Lewis, Heidi Goodrich-Blair, S. Patricia Stock, Byron J. Adams, Paul W. Sternberg, A Mortazavi
Software Mentions: 4
Published: about 11 years ago

10.1186/s13059-021-02390-3

Transcription shapes DNA replication initiation to preserve genome integrity
Cited by: 17
Author(s): Yang Liu, Chen Ai, Tingting Gan, Jinchun Wu, Yongpeng Jiang, Xuhao Liu, Ru-Sen Lu, Ning Gao, Qing Li, Ji Xiong, Jiazhi Hu
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-S1-S9

Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information
Cited by: 2
Author(s): Ellis Patrick, Michael Buckley, David M. Lin, Jean Yee Hwa Yang
Software Mentions: 4
Published: almost 14 years ago

10.1186/s12870-016-0788-2

Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication
Cited by: 33
Author(s): Fantao Zhang, Tao Xu, Linyong Mao, Shuangyong Yan, Xiwen Chen, Zhenfeng Wu, Rui Chen, Xiangdong Luo, Jingzhong Xie, Shan Gao
Software Mentions: 4
Published: over 10 years ago

10.1186/gb-2014-15-4-r57

Evidence for the biogenesis of more than 1,000 novel human microRNAs
Cited by: 214
Author(s): Marc R. Friedländer, Esther Lizano, Anna J.S. Houben, Daniela Bezdan, Mónica Báñez-Coronel, Grzegorz Kudla, Elisabet Mateu-Huertas, Birgit Kagerbauer, Justo González, Kevin C. Chen, Emily LeProust, Eulàlia Martı́, Xavier Estivill
Software Mentions: 4
Published: almost 13 years ago

10.1186/s12870-015-0632-0

Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet
Cited by: 10
Author(s): Fei Yi, Jian Chen, Jingjuan Yu
Software Mentions: 4
Published: about 11 years ago

10.1186/gb-2013-14-11-r131

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
Cited by: 162
Author(s): Ana C. Marques, Jim R. Hughes, Bryony Graham, Monika S. Kowalczyk, Douglas R. Higgs, Chris P. Ponting
Software Mentions: 4
Published: almost 14 years ago

10.1186/s13059-014-0410-6

Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
Cited by: 278
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 4
Published: over 12 years ago

10.1186/s12870-019-2193-0

Variation in plastid genomes in the gynodioecious species Silene vulgaris
Cited by: 7
Author(s): Manuela Krüger, Oushadee A. J. Abeyawardana, Miloslav Juříček, Claudia Krüger, Helena Štorchová
Software Mentions: 4
Published: almost 7 years ago

10.1186/1471-2105-14-326

snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing
Cited by: 6
Author(s): Ali Al‐Shahib, Anthony Underwood
Software Mentions: 4
Published: almost 13 years ago

10.1186/gb-2011-12-8-r76

The head-regeneration transcriptome of the planarian Schmidtea mediterranea
Cited by: 110
Author(s): Thomas Sandmann, Matthias Christian Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer
Software Mentions: 4
Published: almost 16 years ago

10.1371/journal.pone.0242516

The small RNA locus map for Chlamydomonas reinhardtii
Cited by: 4
Author(s): Sebastian Müller, Nicholas E. Matthews, Adrián Vallí, David C. Baulcombe
Software Mentions: 4
Published: almost 6 years ago

10.1186/gb-2014-15-2-r32

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation
Cited by: 112
Author(s): Benjamin L. Kidder, Gangqing Hu, Keji Zhao
Software Mentions: 4
Published: almost 13 years ago

10.1111/tpj.15250

The chemical compound ‘Heatin’ stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1‐subfamily of nitrilases
Cited by: 7
Author(s): Lennard van der Woude, Markus Piotrowski, Gruson Klaasse, Judith K Paulus, Daniel Krahn, Sabrina Ninck, Farnusch Kaschani, Markus Kaiser, Ondřej Novák, Karin Ljung, Suzanne Bulder, Marcel van Verk, L. Basten Snoek, Martijn Fiers, Nathaniel I. Martin, R.A.L. van der Hoorn, Stéphanie Robert, Sjef Smeekens, Martijn van Zanten
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.2056

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals
Cited by: 9
Author(s): Yevgeny Nikolaichik, Aliaksandr U. Damienikan
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0187542

Effects of glucose availability in Lactobacillus sakei; metabolic change and regulation of the proteome and transcriptome
Cited by: 10
Author(s): Anette McLeod, Ellen Færgestad Mosleth, Ida Rud, Filipe Branco dos Santos, Lars-Gustav Snipen, Kristian Hovde Liland, Lars Axelsson
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-015-0742-x

Extensive identification and analysis of conserved small ORFs in animals
Cited by: 162
Author(s): Sebastian D. Mackowiak, Henrik Zauber, Chris Bielow, Denise Thiel, Kamila Kutz, Lorenzo Calviello, Guido Mastrobuoni, Nikolaus Rajewsky, Stefan Kempa, Matthias Selbach, Benedikt Obermayer
Software Mentions: 4
Published: about 11 years ago

10.1186/s12864-018-4783-x

The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum
Cited by: 27
Author(s): Chuanlin Yin, Meizhen Li, Jian Hu, Kun Lang, Qiming Chen, Jinding Liu, Dan Guo, Kang He, Yipei Dong, Jiapeng Luo, Zhenkun Song, James R. Walters, Wenqing Zhang, Fĕi Li, Xue-Xin Chen
Software Mentions: 4
Published: over 8 years ago

10.1534/g3.118.200789

Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophila simulans Wild-Type Strains
Cited by: 4
Author(s): Marie Fablet, Angelo Jacquet, Rita Rebollo, Annabelle Haudry, Colette Rey, Judit Salces-Ortiz, Prajakta Bajad, Nelly Burlet, Michael F. Jantsch, Maria Pilar García Guerreiro, Cristina Vieira
Software Mentions: 4
Published: over 7 years ago

10.3390/genes8020068

Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts
Cited by: 34
Author(s): Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, Kumiko Ui-Tei
Software Mentions: 4
Published: over 9 years ago

10.1534/g3.114.013508

De Novo Assembly and Annotation of the Transcriptome of the Agricultural Weed Ipomoea purpurea Uncovers Gene Expression Changes Associated with Herbicide Resistance
Cited by: 41
Author(s): Trent A Leslie, Regina S. Baucom
Software Mentions: 4
Published: about 12 years ago

10.3390/pathogens8040183

Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus
Cited by: 12
Author(s): Soo Jin Oh, Soo Yeon Lim, Mee Hyun Song, Jinhee Ahn, Chan Hee Lee, Ok Sarah Shin
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0238546

MITF and TFEB cross-regulation in melanoma cells
Cited by: 12
Author(s): Josué Ballesteros‐Álvarez, Ramile Dilshat, Valerie Fock, Katrín Möller, Ludwig Karl, Lionel Larue, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 4
Published: about 6 years ago

10.3389/fpls.2020.01003

The MADS-Box Gene MdDAM1 Controls Growth Cessation and Bud Dormancy in Apple
Cited by: 33
Author(s): Mirko Moser, Elisa Asquini, Giulia Valentina Miolli, Kathleen Weigl, Magda‐Viola Hanke, Henryk Flachowsky, Azeddine Si‐Ammour
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2021.727302

Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses
Cited by: 4
Author(s): Minsu Park, Wookap Choi, Sang Yoon Shin, Hongman Moon, Dowhan Lee, Yun Shil Gho, Ki Hong Jung, Jong Seong Jeon, Chanseok Shin
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2012.00202

A High-Throughput Method for Illumina RNA-Seq Library Preparation
Cited by: 134
Author(s): Ravi Kumar, Yasunori Ichihashi, Seisuke Kimura, Daniel H. Chitwood, Lauren R. Headland, Jie Peng, Julin N. Maloof, Neelima Sinha
Software Mentions: 4
Published: almost 15 years ago

10.1186/s12859-018-2279-y

Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data
Cited by: 8
Author(s): Yasunobu Okamura, Kengo Kinoshita
Software Mentions: 4
Published: over 8 years ago

10.3389/fnmol.2017.00091

Identification of the Spinal Expression Profile of Non-coding RNAs Involved in Neuropathic Pain Following Spared Nerve Injury by Sequence Analysis
Cited by: 114
Author(s): Jun Zhou, Qingming Xiong, Hongtao Chen, Cheng-xiang Yang, Yu Fan
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-019-5947-z

Small RNA discovery in the interaction between barley and the powdery mildew pathogen
Cited by: 26
Author(s): Matt Hunt, Sagnik Banerjee, Priyanka Surana, Meiling Liu, Greg Fuerst, Sandra M. Mathioni, Blake C. Meyers, Dan Nettleton, Roger P. Wise
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2021.668644

Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood
Cited by: 9
Author(s): Vojtěch Tláskal, Victor Satler Pylro, Lucia Žifčáková, Petr Baldrián
Software Mentions: 4
Published: over 5 years ago

10.1186/1741-7015-11-163

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease
Cited by: 56
Author(s): Adam E. Handel, Geir Kjetil Sandve, Giulio Disanto, Antonio J. Berlanga‐Taylor, Giuseppe Gallone, Heather Hanwell, Finn Drabløs, Gavin Giovannoni, George C. Ebers, Sreeram Ramagopalan
Software Mentions: 4
Published: over 13 years ago

10.1186/s12859-016-1158-7

DISMISS: detection of stranded methylation in MeDIP-Seq data
Cited by: 6
Author(s): Umar Niazi, Kathrin K. Geyer, Martin Vickers, Karl F. Hoffmann, Martin Swain
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0131504

A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco)
Cited by: 31
Author(s): Ming Zou, Xiaoting Zhang, Ze-Chao Shi, Li Lin, Gang Ouyang, Guirong Zhang, Huan Zheng, Kai-Jian Wei, Wei Ji
Software Mentions: 4
Published: over 11 years ago

10.1186/1471-2164-15-899

Characterization and comparative profiling of ovarian microRNAs during ovine anestrus and the breeding season
Cited by: 40
Author(s): Ran Di, Jianning He, Shuhui Song, Dongmei Tian, Qiuyue Liu, Xiaojun Liang, Qing Ma, Min Sun, Jiandong Wang, Wenming Zhao, G. L. Cao, Jinxin Wang, Ziyin Yang, Ying Ge, Mingxing Chu
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0204038

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period
Cited by: 3
Author(s): Ramona Krauss, Belinda Phipson, Alicia Oshlack, Nikita Prasad-Gupta, Michael Cheung, Joseph J. Smolich, Salvatore Pepe
Software Mentions: 4
Published: about 8 years ago

10.3389/fmicb.2018.00593

Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases
Cited by: 51
Author(s): Edoardo Piombo, Noa Sela, Michael Wisniewski, Maria Hoffmann, M. L. Gullino, Marc W. Allard, E.J. Levin, D. Spadaro, Samir Droby
Software Mentions: 4
Published: over 8 years ago

10.3390/v10070388

Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms
Cited by: 40
Author(s): Shaun T. Cross, Marylee Kapuscinski, Jacquelyn Perino, Bernadette L Maertens, James Weger-Lucarelli, Gregory D. Ebel, Mark D. Stenglein
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0128465

Connecting Anxiety and Genomic Copy Number Variation: A Genome-Wide Analysis in CD-1 Mice
Cited by: 6
Author(s): Julia Brenndörfer, André Altmann, Regina Widner-Andrä, Benno Pütz, Darina Czamara, Erik Tilch, Tony Kam‐Thong, Peter Weber, Monika Rex‐Haffner, Thomas Bettecken, Andrea Bultmann, Bertram Müller‐Myhsok, Elisabeth Binder, Rainer Landgraf, Ludwig Czibere
Software Mentions: 4
Published: over 11 years ago

10.3389/fimmu.2021.663736

MicroRNA Expression Differences in Blood-Derived CD19+ B Cells of Methotrexate Treated Rheumatoid Arthritis Patients
Cited by: 8
Author(s): Fatima Heinicke, Xiao Zhong, Siri Tennebø Flåm, Johannes Breidenbach, Magnus Leithaug, Marthe Thoresen Mæhlen, Siri Lillegraven, Anna‐Birgitte Aga, Ellen Sauar Norli, Maria D Mjaavatten, Espen A. Haavardsholm, Manuela Zucknick, Simon Rayner, Benedicte A. Lie
Software Mentions: 4
Published: over 5 years ago

10.3389/fphar.2021.673831

MMP24 Contributes to Neuropathic Pain in an FTO-Dependent Manner in the Spinal Cord Neurons
Cited by: 6
Author(s): Longfei Ma, Yangyuxin Huang, Fengjiang Zhang, Dave Schwinn Gao, Na Sun, Jinxuan Ren, Suyun Xia, Jia Li, Xiujuan Peng, Yu Lu, Bao‐Chun Jiang, Min Yan
Software Mentions: 4
Published: over 5 years ago

10.1186/gb-2011-12-2-r16

Genomewide characterization of non-polyadenylated RNAs
Cited by: 358
Author(s): Li Yang, Michael O. Duff, Brenton R. Graveley, Gordon G. Carmichael, Lingling Chen
Software Mentions: 4
Published: almost 16 years ago

10.1371/journal.pgen.1004261

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation
Cited by: 329
Author(s): Guilhem Janbon, Kate L. Ormerod, Damien Paulet, Edmond J. Byrnes, Vikas Yadav, Gautam Chatterjee, Nandita Mullapudi, Chung-Chau Hon, R. Blake Billmyre, François Brunel, Yong-Sun Bahn, Weidong Chen, Yuan Chen, Eve W. L. Chow, Jean Yves Coppée, Anna Floyd-Averette, Claude Gaillardin, Kimberly J. Gerik, Jonathan M. Goldberg, Sara Gonzalez-Hilarion, Sharvari Gujja, Joyce L. Hamlin, Yu-Ting Hsueh, Giuseppe Ianiri, Steven J.M. Jones, Chinnappa D. Kodira, Lukasz Kozubowski, Woei C. Lam, Marco A. Marra, Larry D. Mesner, Piotr A. Mieczkowski, Frédérique Moyrand, Kirsten Nielsen, Caroline Proux, Tristan Rossignol, Jacqueline E. Schein, Sheng Sun, Carolin Wollschlaeger, Ian Wood, Qiandong Zeng, Cécile Neuvéglise, Carol S. Newlon, John R. Perfect, Jennifer K. Lodge, Alexander Idnurm, Jason E. Stajich, James W. Kronstad, Kaustuv Sanyal, Joseph Heitman, James A. Fraser, Christina A. Cuomo, Fred S. Dietrich
Software Mentions: 4
Published: over 12 years ago

10.1186/s12985-016-0659-3

Derivation of chicken induced pluripotent stem cells tolerant to Newcastle disease virus-induced lysis through multiple rounds of infection
Cited by: 7
Author(s): Leonardo Susta, Ying He, Jessica M. Hutcheson, Yangqing Lu, Franklin D. West, Steven L. Stice, Ping Yu, Zaid Abdo, Claudio L. Afonso
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2105-12-75

AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm
Cited by: 16
Author(s): Jihoon Kim, Kiltesh Patel, Hyunchul Jung, Winston Patrick Kuo, Lucila Ohno-Machado
Software Mentions: 4
Published: over 15 years ago

10.1186/1471-2164-14-266

Characterization of differential transcript abundance through time during Nematostella vectensis development
Cited by: 73
Author(s): Rebecca R. Helm, Stefan Siebert, Sarah Tulin, Joel Smith, Casey W. Dunn
Software Mentions: 4
Published: almost 14 years ago

10.3389/fgene.2021.662468

Hypoxia-Induced miR-148a Downregulation Contributes to Poor Survival in Colorectal Cancer
Cited by: 15
Author(s): Stepan Nersisyan, A. V. Galatenko, Milena Chekova, Alexander G. Tonevitsky
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2896-7

Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data
Cited by: 8
Author(s): Yongsheng Bai, Jeff Kinne, Brandon Donham, Feng Jiang, Lizhong Ding, Justin Hassler, Randal J. Kaufman
Software Mentions: 4
Published: over 10 years ago

Projects: pypi: bowtie

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Papers Mentioning bowtie 1,566