pypi: house | Projects | Ecosyste.ms: Papers

10.15252/msb.20209438

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
Cited by: 49
Author(s): Carmen Bravo González-Blas, Xiao‐Jiang Quan, Ramon Duran-Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime De Waegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, Stein Aerts
Software Mentions: 19
Published: over 4 years ago

10.1111/eva.13246

Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest
Cited by: 11
Author(s): Djampa Kozlowski, Rahim Hassanaly‐Goulamhoussen, Martine Da Rocha, Georgios Koutsovoulos, Marc Bailly‐Bechet, Étienne Danchin
Software Mentions: 15
Published: over 3 years ago

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: over 5 years ago

10.1371/journal.pcbi.1003000

Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
Cited by: 55
Author(s): Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd
Software Mentions: 13
Published: over 11 years ago

10.3389/fgene.2020.580580

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)
Cited by: 20
Author(s): Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gažová, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan Archibald, Shannon Clarke, Brenda M. Murdoch, Emily L. Clark
Software Mentions: 11
Published: about 4 years ago

10.3390/plants10091921

UHPLC-Orbitrap-MS Tentative Identification of 51 Oleraceins (Cyclo-Dopa Amides) in Portulaca oleracea L. Cluster Analysis and MS2 Filtering by Mass Difference
Cited by: 2
Author(s): Yulian Voynikov, Paraskev Nedialkov, Reneta Gevrenova, Dimitrina Zheleva‐Dimitrova, Vessela Balabanova, Иван Димитров
Software Mentions: 10
Published: over 3 years ago

10.1186/s12859-017-1770-1

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction
Cited by: 24
Author(s): Carlos Guzmán, Iván D’Orso
Software Mentions: 10
Published: over 7 years ago

10.1186/s13040-019-0201-4

Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies
Cited by: 3
Author(s): Elisabetta Manduchi, Patryk Orzechowski, Marylyn D. Ritchie, Jason H. Moore
Software Mentions: 9
Published: over 5 years ago

10.3389/fmicb.2021.641643

Temporal Bacterial Community Diversity in the Nicotiana tabacum Rhizosphere Over Years of Continuous Monocropping
Cited by: 10
Author(s): Yan Ling, Wenyou Zhang, Wangjun Duan, Yizheng Zhang, Wen Zheng, Xianjun Lai
Software Mentions: 9
Published: over 3 years ago

10.1111/mec.15120

Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia
Cited by: 69
Author(s): Mary O’Neill, Abigail C. Shockey, Alex Zarley, William Aylward, Vegard Eldholm, Andrew Kitchen, Caitlin S. Pepperell
Software Mentions: 9
Published: over 5 years ago

10.1186/1471-2164-14-892

RNA-Seq optimization with eQTL gold standards
Cited by: 24
Author(s): Shannon Ellis, Saloni Gupta, Foram N. Ashar, Joel S. Bader, Andrew B. West, Dan E. Arking
Software Mentions: 9
Published: about 11 years ago

10.1186/s12864-019-5870-3

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods
Cited by: 56
Author(s): Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado‐Torres, Martha Kimos, Nicholas J. Brandon, A.J. Cross, Daniel R. Weinberger, Joo Heon Shin
Software Mentions: 9
Published: over 5 years ago

10.1016/j.cell.2017.04.013

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension
Cited by: 607
Author(s): Judith H.I. Haarhuis, Robin H. van der Weide, Vincent A. Blomen, J. Omar Yáñez-Cuna, Mario Amendola, Marjon S. van Ruiten, Peter H.L. Krijger, Hans Teunissen, René H. Medema, Bas van Steensel, Thijn R. Brummelkamp, Elzo de Wit, Benjamin D. Rowland
Software Mentions: 8
Published: over 7 years ago

10.1111/pbi.12958

The developmental dynamics of the Populus stem transcriptome
Cited by: 92
Author(s): Qing Chao, Zili Gao, Dong Zhang, Biligen-Gaowa Zhao, Fengqin Dong, Chunxiang Fu, Lijun Liu, Bai-Chen Wang
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pcbi.1004956

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis
Cited by: 38
Author(s): Rebeca Campos-Sánchez, Marzia A. Cremona, Alessia Pini, Francesca Chiaromonte, Kateryna D. Makova
Software Mentions: 8
Published: over 8 years ago

10.1038/s41598-020-68665-0

MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse
Cited by: 15
Author(s): Nicolas Bonhoure, Viviane Praz, Robyn D. Moir, Gilles Willemin, François Mange, Catherine Moret, Ian M. Willis, Nouria Hernandez
Software Mentions: 8
Published: over 4 years ago

10.3390/microorganisms7120662

Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew
Cited by: 17
Author(s): Luca Nerva, Chiara Pagliarani, Massimo Pugliese, M. Monchiero, Solène Gonthier, M. L. Gullino, Giorgio Gambino, Walter Chitarra
Software Mentions: 8
Published: about 5 years ago

10.1038/s41598-021-87890-9

Epigenetic alteration contributes to the transcriptional reprogramming in T-cell prolymphocytic leukemia
Cited by: 2
Author(s): Shulan Tian, Henan Zhang, Pan Zhang, Michael Kalmbach, Jeong Heon Lee, Tamás Ördög, Paul J. Hampel, Timothy G. Call, Thomas E. Witzig, Neil E. Kay, Eric W. Klee, Susan L. Slager, Huihuang Yan, Wei Ding
Software Mentions: 8
Published: over 3 years ago

10.1186/s40168-019-0626-5

Choice of assembly software has a critical impact on virome characterisation
Cited by: 94
Author(s): Thomas D.S. Sutton, Adam G. Clooney, Feargal J. Ryan, R. Paul Ross, Colin Hill
Software Mentions: 8
Published: almost 6 years ago

10.1186/s12864-021-07595-1

Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats
Cited by: 15
Author(s): Xiangyu Pan, Zongjun Li, Bibo Li, Chen Zhao, Yu Wang, Yulin Chen, Yu Jiang
Software Mentions: 7
Published: over 3 years ago

10.1002/cti2.1127

High‐dimensional analyses reveal a distinct role of T‐cell subsets in the immune microenvironment of gastric cancer
Cited by: 18
Author(s): Minyu Wang, Yen-Yu Huang, Joseph C Kong, Yu Sun, Daniela Tantalo, Han Xian Aw Yeang, Le Ying, Feng Yan, Dakang Xu, Heloise M. Halse, Natasha Di Costanzo, Ian Gordon, Catherine Mitchell, Laura K. Mackay, Rita A. Busuttil, Paul J. Neeson, Alex Boussioutas
Software Mentions: 7
Published: almost 5 years ago

10.15698/mic2021.07.754

Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast
Cited by: 14
Author(s): Catalina A. Romila, StJohn Townsend, Michał Malecki, Stephan Kamrad, María Rodríguez-López, Olivia Hillson, Cristina Cotobal, Markus Ralser, Jürg Bähler
Software Mentions: 7
Published: over 3 years ago

10.1093/bioinformatics/btaa177

Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Cited by: 11
Author(s): Yaxin Xue, Anders Lanzén, Inge Jonassen
Software Mentions: 7
Published: almost 5 years ago

10.15252/msb.20177881

High‐resolution definition of humoral immune response correlates of effective immunity against <scp>HIV</scp>
Cited by: 33
Author(s): Galit Alter, Karen G. Dowell, Eric N. Brown, Todd J. Suscovich, Anastassia Mikhailova, Alison E. Mahan, Bruce D. Walker, Falk Nimmerjahn, Chris Bailey‐Kellogg, Margaret E. Ackerman
Software Mentions: 7
Published: almost 7 years ago

10.1038/s41598-021-96967-4

Parasites and diet as main drivers of the Malagasy gut microbiome richness and function
Cited by: 3
Author(s): Stanislas Mondot, Philippe Poirier, Ahmed Abou-Bacar, Valentin Greigert, Julie Brunet, Céline Nourrisson, Milijaona Randrianarivelojosia, Jean-Louis Razafindrakoto, Eugène Morel, Rivo Rakotomalala, Marion Leclerc, Karine Le Roux, Céline Monot, Patricia Lepage, Ermanno Candolfi
Software Mentions: 7
Published: over 3 years ago

10.1038/s42003-021-01785-z

Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization
Cited by: 42
Author(s): Mehrshad Golesorkhi, Javier Gómez‐Pilar, Shankar Tumati, Maia Fraser, Georg Northoff
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12864-021-07441-4

A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks
Cited by: 2
Author(s): Pedro Gabriel Nachtigall, Luiz Augusto Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke, Danillo Pinhal
Software Mentions: 7
Published: almost 4 years ago

10.3390/microorganisms9050996

Unrelated Fungal Rust Candidate Effectors Act on Overlapping Plant Functions
Cited by: 1
Author(s): Karen Cristine Gonçalves dos Santos, G. Pelletier, Armand Séguin, François Guillemette, Jeffrey A. Hawkes, Isabel Desgagné‐Penix, Hugo Germain
Software Mentions: 7
Published: over 3 years ago

10.3389/fimmu.2020.585168

Distinct Age-Related Epigenetic Signatures in CD4 and CD8 T Cells
Cited by: 40
Author(s): Bin Hu, Rohit R. Jadhav, Claire E. Gustafson, Sabine Le Saux, Zhongde Ye, Xuanying Li, Lu Tian, Cornelia M. Weyand, Jörg J. Goronzy
Software Mentions: 7
Published: about 4 years ago

10.1038/s41598-017-05377-y

Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes
Cited by: 33
Author(s): Zupeng Wang, Yifei Liu, Li Li, Dawei Li, Qiong Zhang, Yangtao Guo, Shuaibin Wang, Caihong Zhong, Hongwen Huang
Software Mentions: 7
Published: over 7 years ago

10.1186/1758-2946-6-35

Proteochemometric modeling in a Bayesian framework
Cited by: 39
Author(s): Isidro Cortés-Ciriano, Gerard J. P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender, Thérèse E. Malliavin
Software Mentions: 7
Published: over 10 years ago

10.3389/fmicb.2020.00765

Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes
Cited by: 10
Author(s): Paula Luize Camargos Fonseca, Fernanda Badotti, Ruth B De-Paula, Daniel S. Araújo, Dener Eduardo Bortolini, Luiz-Eduardo Del-Bem, Vasco Azevedo, Bertram Brenig, Eric Roberto Guimarães Rocha Aguiar, Aristóteles Goés-Neto
Software Mentions: 7
Published: over 4 years ago

10.1002/2211-5463.13057

Long noncoding RNAs implicated in embryonic development in Ybx1 knockout zebrafish
Cited by: 5
Author(s): Chen Huang, Bo Zhu, Dongliang Leng, Wei Ge, Xiaohua Douglas Zhang
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12864-019-5927-3

Alternative polyadenylation produces multiple 3’ untranslated regions of odorant receptor mRNAs in mouse olfactory sensory neurons
Cited by: 5
Author(s): Mohamed Doulazmi, Cyril Cros, Isabelle Dusart, Alain Trembleau, Caroline Dubacq
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-018-5266-9

Host microRNA analysis in cyprinid Herpesvirus-3 (CyHV-3) infected common carp
Cited by: 10
Author(s): M. Reichert, Anna Łukasik, Piotr Zielenkiewicz, Marek Matras, Joanna Maj‐Paluch, Magdalena Stachnik, Ewa Borzym
Software Mentions: 6
Published: almost 6 years ago

10.15252/embj.2021108345

Piwi–piRNA complexes induce stepwise changes in nuclear architecture at target loci
Cited by: 4
Author(s): Yuka W. Iwasaki, Sira Sriswasdi, Yasuha Kinugasa, Jun Adachi, Yasunori Horikoshi, Aoi Shibuya, Wataru Iwasaki, Satoshi Tashiro, Takeshi Tomonaga, Haruhiko Siomi
Software Mentions: 6
Published: over 3 years ago

10.15252/embj.2020104569

Translation is required for miRNA‐dependent decay of endogenous transcripts
Cited by: 15
Author(s): Adriano Biasini, Baroj Abdulkarim, Stefano de Pretis, Jennifer Y. Tan, Rajika Arora, Harry Wischnewski, René Dreos, Mattia Pelizzola, Constance Ciaudo, Ana C. Marques
Software Mentions: 6
Published: about 4 years ago

10.1093/jxb/erab072

Dynamic histone acetylation in floral volatile synthesis and emission in petunia flowers
Cited by: 19
Author(s): Ryan M. Patrick, Xing-Qi Huang, Natalia Dudareva, Ying Liu
Software Mentions: 6
Published: almost 4 years ago

10.1099/mgen.0.000042

Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan
Cited by: 11
Author(s): Maia A. Rabaa, Duy Pham Thanh, Sirigade Ruekit, Sonam Wangchuk, Tandin Dorji, Kinzang Pem Tshering, To Nguyen Thi Nguyen, Phat Voong Vinh, Tuyen Ha Thanh, Chau Nguyen Ngoc Minh, Paul Turner, Pinaki Sar, Guy Thwaites, Kathryn E. Holt, Nicholas R. Thomson, Ladaporn Bodhidatta, Carl J. Mason, Stephen Baker
Software Mentions: 6
Published: about 9 years ago

10.1186/s13059-021-02300-7

riboCIRC: a comprehensive database of translatable circRNAs
Cited by: 39
Author(s): Huihui Li, Mingzhe Xie, Yan Wang, Ludong Yang, Zhi Xie
Software Mentions: 6
Published: almost 4 years ago

10.1099/mgen.0.000585

Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey
Cited by: 2
Author(s): Marcus M. Dillon, Tatiana Ruiz-Bedoya, Cedoljub Bundalovic-Torma, Kevin Guttman, Haejin Angela Kwak, Maggie A. Middleton, Pauline W. Wang, Sümer Horuz, Y. Aysan, David S. Guttman
Software Mentions: 6
Published: over 3 years ago

10.1016/j.jbc.2021.100804

Droplet and fibril formation of the functional amyloid Orb2
Cited by: 8
Author(s): Kidist Ashami, Alexander S. Falk, Connor Hurd, Samridhi Garg, Silvia A. Cervantes, Anoop Rawat, Ansgar B. Siemer
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-016-2381-3

Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida
Cited by: 40
Author(s): Antony T. Vincent, Mélanie V. Trudel, Luca Freschi, Vandan Nagar, Cynthia Gagné-Thivierge, Roger C. Levesque, Steve J. Charette
Software Mentions: 6
Published: almost 9 years ago

10.1038/s41598-019-39866-z

Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions
Cited by: 10
Author(s): Adrian I. Campos-González, Julio A. Freyre-González
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12870-014-0315-2

The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes
Cited by: 8
Author(s): Gopal Misra, Piyush Priya, Nitesh Bandhiwal, Neha Bareja, Mukesh Jain, Sabhyata Bhatia, Debasis Chattopadhyay, Akhilesh K. Tyagi, Gitanjali Yadav
Software Mentions: 6
Published: about 10 years ago

10.1111/1751-7915.13519

Raman–deuterium isotope probing to study metabolic activities of single bacterial cells in human intestinal microbiota
Cited by: 44
Author(s): Yi Wang, Jiabao Xu, Lingchao Kong, Tang Liu, Lingbo Yi, Hongjuan Wang, Wei E. Huang, Kewei Chen
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-018-2013-9

TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association
Cited by: 8
Author(s): Seo Won Choi, Jin Wu Nam
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13293-015-0056-4

Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development
Cited by: 24
Author(s): Martin M. Johansson, E. Lundin, Xiaoyan Qian, Mohammadreza Mirzazadeh, Jonatan Halvardson, Elisabeth Darj, Lars Feuk, Mats Nilsson, Elena Jazin
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13072-016-0079-z

Epigenetic dynamics of monocyte-to-macrophage differentiation
Cited by: 71
Author(s): Stefan Wallner, Christopher Schröder, Elsa Leitão, Tea Berulava, Claudia Haak, Daniela Beißer, Sven Rahmann, Andreas S. Richter, Thomas Manke, Ulrike Bönisch, Laura Arrigoni, Sebastian Fröhler, Filippos Klironomos, Wei Chen, Nikolaus Rajewsky, Fabian Müller, Peter Ebert, Thomas Lengauer, Matthias Barann, Philip Rosenstiel, Gilles Gasparoni, Karl Nordström, Jörn Walter, Benedikt Brors, Gideon Zipprich, Bärbel Felder, Ludger Klein-Hitpaß, Corinna Attenberger, Gerd Schmitz, Bernhard Horsthemke
Software Mentions: 5
Published: over 8 years ago

10.7717/peerj.3091

Effect of method of deduplication on estimation of differential gene expression using RNA-seq
Cited by: 20
Author(s): Anna V. Klepikova, Artem S. Kasianov, Mikhail S. Chesnokov, Н. Л. Лазаревич, Aleksey A. Penin, Maria D. Logacheva
Software Mentions: 5
Published: almost 8 years ago

10.1002/ece3.3148

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi)
Cited by: 80
Author(s): Andrea Springer, Claudia Fichtel, Gabriel A. Al‐Ghalith, Flávia Koch, Katherine R. Amato, Jonathan B. Clayton, Dan Knights, Peter M. Kappeler
Software Mentions: 5
Published: over 7 years ago

10.1186/1471-2105-14-174

PMTED: a plant microRNA target expression database
Cited by: 46
Author(s): Xiaofan Sun, Boquan Dong, Lingjie Yin, Rongzhi Zhang, Wei Du, Dongfeng Liu, Nan Shi, Aili Li, Yanchun Liang, Long Mao
Software Mentions: 5
Published: over 11 years ago

10.1186/s40644-021-00406-6

“Real-world” radiomics from multi-vendor MRI: an original retrospective study on the prediction of nodal status and disease survival in breast cancer, as an exemplar to promote discussion of the wider issues
Cited by: 10
Author(s): Simon J. Doran, Santosh Kumar, Matthew Orton, James A. d’Arcy, Fenna Kwaks, Elizabeth O’Flynn, Zaki Ahmed, Kate Downey, Mitch Dowsett, Nicholas C. Turner, Christina Messiou, Dow‐Mu Koh
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-015-2174-0

Extensive variation between tissues in allele specific expression in an outbred mammal
Cited by: 67
Author(s): Amanda J. Chamberlain, Christy J. Vander Jagt, Ben J. Hayes, Majid Khansefid, L. C. Marett, Catriona A. Millen, Thuy Thi Thu Nguyen, Michael E. Goddard
Software Mentions: 5
Published: about 9 years ago

10.1186/s13071-015-0772-y

Dynamic expression of miRNAs across immature and adult stages of the malaria mosquito Anopheles stephensi
Cited by: 26
Author(s): Shanu Jain, Vandita Rana, T. Adak, Sujatha Sunil, Raj K. Bhatnagar
Software Mentions: 5
Published: over 9 years ago

10.1111/pbi.13085

Development of an integrated 200K <scp>SNP</scp> genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus)
Cited by: 43
Author(s): Xiaolong Li, Jugpreet Singh, Mengfan Qin, Siwei Li, Xun Zhang, Mingyue Zhang, Awais Khan, Shaoling Zhang
Software Mentions: 5
Published: almost 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 5 years ago

10.3390/metabo9060113

Cerebral Vitamin B5 (D-Pantothenic Acid) Deficiency as a Potential Cause of Metabolic Perturbation and Neurodegeneration in Huntington’s Disease
Cited by: 46
Author(s): Stefano Patassini, Paul Begley, Jiaolong Xu, Stephanie J. Church, Nina Kureishy, Suzanne J. Reid, Henry J. Waldvogel, Richard L.M. Faull, Russell G. Snell, Richard D. Unwin, Garth J. S. Cooper
Software Mentions: 5
Published: over 5 years ago

10.18632/oncotarget.21031

Genome-wide analysis and functional prediction of long non-coding RNAs in mouse uterus during the implantation window
Cited by: 22
Author(s): Qi Wang, Nan Wang, Rui Cai, Fan Zhao, Yi Xiong, Xiao Li, Aihua Wang, Peng Lin, Yaping Jin
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-021-07912-8

Quantitative analysis of the blood transcriptome of young healthy pigs and its relationship with subsequent disease resilience
Cited by: 8
Author(s): Kyu-Sang Lim, Jian Cheng, Austin M. Putz, Qian Dong, Xue Bai, Hamid Beiki, Christopher K. Tuggle, Michael K. Dyck, Pig Gen Canada, Frédéric Fortin, John C. S. Harding, Graham Plastow, Jack C. M. Dekkers
Software Mentions: 5
Published: over 3 years ago

10.18632/oncotarget.25218

Comprehensive identification of long noncoding RNAs in colorectal cancer
Cited by: 15
Author(s): Eric James de Bony, Martin Bizet, Olivier Van Grembergen, Bouchra Hassabi, Emilie Calonne, Pascale Putmans, Gianluca Bontempi, François Fuks
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-021-08036-9

Repertoire analysis of γδ T cells in the chicken enables functional annotation of the genomic region revealing highly variable pan-tissue TCR gamma V gene usage as well as identifying public and private repertoires
Cited by: 5
Author(s): Robert J. Dixon, Stephen G. Preston, Stefan Dascalu, Patrik G. Flammer, Steven R. Fiddaman, Kirstie McLoughlin, Amy Boyd, Jiřı́ Volf, Ivan Rychlı́k, Michael B. Bonsall, Bernd Kaspers, Adrian L. Smith
Software Mentions: 5
Published: about 3 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 3 years ago

10.1038/s41598-018-22734-7

Transcriptional landscape of human endogenous retroviruses (HERVs) and other repetitive elements in psoriatic skin
Cited by: 11
Author(s): Freddy Lättekivi, Sulev Kõks, Maris Keermann, Ene Reimann, Ele Prans, Kristi Abram, Helgi Silm, Gea Kõks, Külli Kingo
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0051292

Characterisation and Validation of Insertions and Deletions in 173 Patient Exomes
Cited by: 9
Author(s): Francesco Lescai, Silvia Bonfiglio, Chiara Bacchelli, Estelle Chanudet, Aoife Waters, Sanjay M. Sisodiya, Dalia Kasperavičiūtė, Julie Williams, Denise Harold, John Hardy, Robert Kleta, Sebahattin Çırak, Richard Williams, John C. Achermann, John Anderson, David P. Kelsell, Tom Vulliamy, Henry Houlden, Nicholas W. Wood, Una Marie Sheerin, Gian Paolo Tonini, Donna S. Mackay, Khalid Hussain, Jane C. Sowden, Veronica A. Kinsler, Justyna Osinska, Tony Brooks, Mike Hubank, Philip L. Beales, Elia Stupka
Software Mentions: 5
Published: about 12 years ago

10.1186/s12870-018-1316-3

UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study
Cited by: 43
Author(s): Peng Qi, Davis Gimode, Dipnarayan Saha, Stephan Schröder, Debkanta Chakraborty, Xuewen Wang, Mathews M. Dida, Russell L. Malmberg, Katrien M. Devos
Software Mentions: 5
Published: over 6 years ago

10.1186/s13100-020-00224-w

Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains
Cited by: 14
Author(s): Mahoko Takahashi Ueda, Kirill Kryukov, Satomi Mitsuhashi, Hiroaki Mitsuhashi, Tadashi Imanishi, So Nakagawa
Software Mentions: 5
Published: over 4 years ago

10.1186/s12870-018-1467-2

WRKY transcription factors in legumes
Cited by: 51
Author(s): Hui Song, Weihong Sun, Guofeng Yang, Juan Sun
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0235218

Transcriptome profiling of longissimus lumborum in Holstein bulls and steers with different beef qualities
Cited by: 17
Author(s): Yan Li, Meimei Wang, Qiufeng Li, Yanxia Gao, Qian Li, Jianguo Li, Yong Cao
Software Mentions: 5
Published: over 4 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: about 5 years ago

10.1186/s12868-021-00635-2

Early postnatal irradiation‐induced age‐dependent changes in adult mouse brain: MRI based characterization
Cited by: 5
Author(s): Bo Ren, Isaac Huen, Zi Jun Wu, Hong Wang, Meng Yun Duan, Ilonka Guenther, Kritika Prakash, Feng Ru Tang
Software Mentions: 5
Published: over 3 years ago

10.1093/gbe/evaa223

Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair
Cited by: 16
Author(s): Mohak Sharda, Anjana Badrinarayanan, Aswin Sai Narain Seshasayee
Software Mentions: 5
Published: about 4 years ago

10.1002/hbm.24568

Comparing MRI metrics to quantify white matter microstructural damage in multiple sclerosis
Cited by: 29
Author(s): Ilona Lipp, Derek K. Jones, Sonya Bells, Eleonora Sgarlata, Catherine Foster, Rachael Stickland, Alison E. Davidson, Emma Tallantyre, Neil Robertson, Richard G. Wise, Valentina Tomassini
Software Mentions: 5
Published: almost 6 years ago

10.1186/gb-2014-15-4-r56

Hypermethylation in the ZBTB20 gene is associated with major depressive disorder
Cited by: 84
Author(s): Matthew N. Davies, Lutz Krause, Jordana T. Bell, Fei Gao, Kirsten Ward, Honglong Wu, Hanlin Lu, Yuan Liu, Pei-Chien Tsai, David A. Collier, Therese M. Murphy, Emma Dempster, Jonathan Mill, Alexis Battle, Sara Mostafavi, Xiaowei Zhu, Anjali K. Henders, Enda M. Byrne, Naomi R. Wray, Nicholas G. Martin, Tim D. Spector, Jun Wang
Software Mentions: 5
Published: almost 11 years ago

10.3389/fpls.2021.695439

Genome-Wide Identification and Characterization of Small Peptides in Maize
Cited by: 15
Author(s): Yan Liang, Wanchao Zhu, Sijia Chen, Qidong Jia, Li Lin
Software Mentions: 5
Published: over 3 years ago

10.1093/gbe/evu251

Diversity and Variability of NOD-Like Receptors in Fungi
Cited by: 77
Author(s): Witold Dyrka, Marina Lamacchia, Pascal Durrens, Boštjan Kobe, Asen Daskalov, Mathieu Paoletti, David James Sherman, Sven J. Saupe
Software Mentions: 5
Published: about 10 years ago

10.1186/1471-2105-15-280

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
Cited by: 49
Author(s): Huihuang Yan, Jared M. Evans, Mike Kalmbach, Raymond M. Moore, Sumit Middha, Stanislav Luban, Liguo Wang, Aditya Bhagwate, Ying Liu, Zhifu Sun, Xianfeng Chen, Jean-Pierre A. Kocher
Software Mentions: 5
Published: over 10 years ago

10.1186/s40168-015-0146-x

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality
Cited by: 91
Author(s): Yue Jiang, Xuejian Xiong, Jayne S. Danska, John Parkinson
Software Mentions: 5
Published: almost 9 years ago

10.3389/fimmu.2016.00499

Azithromycin Attenuates Pseudomonas-Induced Lung Inflammation by Targeting Bacterial Proteins Secreted in the Cultured Medium
Cited by: 6
Author(s): Teresinha Leal, Gabriella Bergamini, François Huaux, Nadtha Panin, Sabrina Noël, Barbara Dhooghe, Jérémy Boris Haaf, Pierluigi Mauri, Sara Motta, Dario Di Silvestre, Paola Melotti, Claudio Sorio
Software Mentions: 5
Published: about 8 years ago

10.3389/fmicb.2016.01221

Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales
Cited by: 23
Author(s): John Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar, Karen G. Lloyd
Software Mentions: 5
Published: over 8 years ago

10.1099/mgen.0.000201

Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry
Cited by: 9
Author(s): Sion C. Bayliss, David W. Verner–Jeffreys, David Ryder, Rudy Suárez, Roxana Olvera Ramírez, Jaime Romero, Ben Pascoe, Sam Sheppard, Marcos Godoy, Edward J. Feil
Software Mentions: 5
Published: over 6 years ago

10.1093/dnares/dsaa029

De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme, by long-read sequencing
Cited by: 19
Author(s): Hitomi Takei, Kenta Shirasawa, Kosuke Kuwabara, Atsushi Toyoda, Yuma Matsuzawa, Shinji Iioka, Tohru Ariizumi
Software Mentions: 5
Published: almost 4 years ago

10.1128/AEM.03074-15

Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay
Cited by: 13
Author(s): Zhao Jin, Sara C. Di Rienzi, Anders Janzon, Jeff J. Werner, Largus T. Angenent, Jeffrey L. Dangl, Douglas M. Fowler, Ruth E. Ley
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12864-019-6003-8

RNAi based transcriptome suggests genes potentially regulated by HSF1 in the Pacific oyster Crassostrea gigas under thermal stress
Cited by: 14
Author(s): Youli Liu, Li Li, Baoyu Huang, Wei Wang, Guofan Zhang
Software Mentions: 5
Published: over 5 years ago

10.1186/s12862-021-01753-5

Rapid evolution and molecular convergence in cryptorchidism-related genes associated with inherently undescended testes in mammals
Cited by: 4
Author(s): Simin Chai, Ran Tian, Juanjuan Bi, Shixia Xu, Wenhua Ren
Software Mentions: 5
Published: almost 4 years ago

10.1186/1471-2164-15-539

ChIPseek, a web-based analysis tool for ChIP data
Cited by: 59
Author(s): Ting-Wen Chen, Hsin Pai Li, Chi-Ching Lee, Ruei Chi Gan, Po-Jung Huang, Timothy Wu, Cheng Yang Lee, Ian Yi‐Feng Chang, Petrus Tang
Software Mentions: 4
Published: over 10 years ago

10.1111/1751-7915.12006

Tips and tricks for the assembly of aCorynebacterium pseudotuberculosisgenome using a semiconductor sequencer
Cited by: 12
Author(s): Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Siomar de Castro Soares, Anderson Santos, Síntia Almeida, Luís Carlos Guimarães, Flávia Figueira, Eudes Guilherme Vieria Barbosa, Andreas Tauch, Vasco Azevedo, Artur M. S. Silva
Software Mentions: 4
Published: about 12 years ago

10.3390/plants10040669

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine
Cited by: 4
Author(s): Shuchi Smita, Michael Robben, Anup Deuja, Monica Accerbi, Pamela J. Green, Senthil Subramanian, Anne Fennell
Software Mentions: 4
Published: over 3 years ago

10.1186/s13072-020-00368-2

Chromatin accessibility dynamics of Chlamydia-infected epithelial cells
Cited by: 4
Author(s): Regan J. Hayward, J. Wallis Marsh, Michael S. Humphrys, Wilhelmina M. Huston, Garry S. A. Myers
Software Mentions: 4
Published: about 4 years ago

10.1111/1751-7915.13496

Preventive antibiotic treatment of calves: emergence of dysbiosis causing propagation of obese state‐associated and mobile multidrug resistance‐carrying bacteria
Cited by: 15
Author(s): Dorota A. Dobrzanska, Matthew T F Lamaudière, Jess Rollason, Lauren Acton, Michael Duncan, Sharon Compton, John Simms, Gareth D. Weedall, Igor Y. Morozov
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pbio.1002512

Spatial Embedding and Wiring Cost Constrain the Functional Layout of the Cortical Network of Rodents and Primates
Cited by: 160
Author(s): Szabolcs Horvát, Răzvan Gămănuţ, Mária Ercsey-Ravasz, Loïc Magrou, Bianca Gămănuț, David C. Van Essen, Andreas Burkhalter, Kenneth Knoblauch, Zoltán Toroczkai, Henry Kennedy
Software Mentions: 4
Published: over 8 years ago

10.7717/peerj.3302

Body composition estimation from selected slices: equations computed from a new semi-automatic thresholding method developed on whole-body CT scans
Cited by: 19
Author(s): Alizé Lacoste Jeanson, Ján Dupej, Chiara Villa, Jaroslav Brůžek
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.7071

Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants
Cited by: 1
Author(s): Jakub Hynšt, Karla Plevová, Lenka Radová, Vojtěch Bystrý, Karol Pál, Šárka Pospı́šilová
Software Mentions: 4
Published: over 5 years ago

10.1186/1475-2859-6-29

Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1
Cited by: 107
Author(s): L.M. Serrano, Douwe Molenaar, Michiel Wels, Bas Teusink, Peter A. Bron, Willem M. de Vos, Eddy J. Smid
Software Mentions: 4
Published: over 17 years ago

10.1186/s13072-018-0186-0

Transient reduction of DNA methylation at the onset of meiosis in male mice
Cited by: 36
Author(s): Valeriya Gaysinskaya, Brendan Miller, Chiara De Luca, Godfried W. van der Heijden, Kasper D. Hansen, Alex Bortvin
Software Mentions: 4
Published: over 6 years ago

10.3389/fcimb.2021.652837

Potential Roles of Oral Microbiota in the Pathogenesis of Immunoglobin A Nephropathy
Cited by: 6
Author(s): Jiawei He, Xu‐Jie Zhou, Ping Hou, Yan-Na Wang, Tao Gan, Yang Li, Yang Liu, Lijun Liu, Sufang Shi, Li Zhu, Jicheng Lv, Hong Zhang
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-021-07666-3

Re-examination of two diatom reference genomes using long-read sequencing
Cited by: 19
Author(s): Gina V. Filloramo, Bruce A. Curtis, Emma Blanche, John M. Archibald
Software Mentions: 4
Published: over 3 years ago

10.1002/cti2.1087

Rapid sequencing‐based diagnosis of infectious bacterial species from meningitis patients in Zambia
Cited by: 26
Author(s): So Nakagawa, Shigeaki Inoue, Kirill Kryukov, Junya Yamagishi, Ayumu Ohno, Kyoko Hayashida, Ruth Nakazwe, Mox Kalumbi, Darlington Mwenya, Nana Asami, Chihiro Sugimoto, Mable Mutengo, Tadashi Imanishi
Software Mentions: 4
Published: almost 6 years ago

10.1155/2020/8162524

High-Throughput Sequencing and Exploration of the lncRNA-circRNA-miRNA-mRNA Network in Type 2 Diabetes Mellitus
Cited by: 39
Author(s): Fang Yang, Chen Yang, Zhiqiang Xue, Yaogai Lv, Ли Шен, Kexin Li, Pingping Zheng, Pan Pan, Tianyu Feng, Lina Jin, Yan Yao
Software Mentions: 4
Published: over 4 years ago

10.1111/mec.12521

Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps
Cited by: 89
Author(s): Martin C. Fischer, Christian Rellstab, Andrew Tedder, Stefan Zoller, Félix Gugerli, Kentaro Shimizu, Rolf Holderegger, Alex Widmer
Software Mentions: 4
Published: about 11 years ago

Projects: pypi: house

Papers Mentioning house 960