pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1007376

Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment
Cited by: 59
Author(s): Michael B. Burns, Emmanuel Montassier, Juan E. Abrahante, Sambhawa Priya, David Niccum, Alexander Khoruts, Timothy K. Starr, Dan Knights, Ran Blekhman
Software Mentions: 4
Published: about 8 years ago

10.1186/s13059-019-1918-6

Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes
Cited by: 4
Author(s): Maroun Bou Sleiman, Michael Frochaux, Tommaso Andreani, Dani Osman, Roderic Guigó, Bart Deplancke
Software Mentions: 4
Published: over 6 years ago

10.26508/lsa.202000961

A role for condensin in mediating transcriptional adaptation to environmental stimuli
Cited by: 4
Author(s): Lucy Lancaster, Harshil Patel, Gavin Kelly, Frank Uhlmann
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1007905

Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment
Cited by: 21
Author(s): Alexandra Bezler, Fabian Braukmann, Sean M. West, Arthur Duplan, Raffaella Conconi, Frédéric Schütz, Pierre Gönczy, Fabio Piano, Kristin C. Gunsalus, Eric A. Miska, Laurent Keller
Software Mentions: 4
Published: over 7 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: almost 8 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13073-021-00826-w

Comprehensive molecular characterization of gastric cancer patients from phase II second-line ramucirumab plus paclitaxel therapy trial
Cited by: 16
Author(s): Seung Tae Kim, K. Jason, Sung Yong Oh, Kyung Kim, Jung Yong Hong, Won Ki Kang, Jeeyun Lee
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pbio.3001306

Dynamic landscape of protein occupancy across the Escherichia coli chromosome
Cited by: 18
Author(s): Peter L. Freddolino, Haley M. Amemiya, Thomas J. Goss, Saeed Tavazoie
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pbio.3000166

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival
Cited by: 32
Author(s): Oliver Smith, Glenn Dunshea, Mikkel‐Holger S. Sinding, Sergey Fedorov, Mietje Germonpré, Hervé Bocherens, M. Thomas P. Gilbert
Software Mentions: 4
Published: about 7 years ago

10.1016/j.cmet.2020.09.001

Bone Marrow Mesenchymal Stem Cells Support Acute Myeloid Leukemia Bioenergetics and Enhance Antioxidant Defense and Escape from Chemotherapy
Cited by: 107
Author(s): Dorian Forte, María García-Fernández, Abel Sánchez-Aguilera, Vaia Stavropoulou, Claire Fielding, Daniel Martín-Pérez, Juan Antonio López, Ana S. H. Costa, Laura Tronci, Efterpi Nikitopoulou, M. Barber, Paolo Gallipoli, Ludovica Marando, Carlos L.F. de Castillejo, Alexandar Tzankov, Sabine Dietmann, Michèle Cavo, Lucia Catani, Antonio Curti, Jesús Vázquez, Christian Frezza, Brian J. P. Huntly, Juerg Schwaller, Simón Méndez-Ferrer
Software Mentions: 4
Published: almost 6 years ago

10.3390/nu12041063

Specific Dietary Components and Gut Microbiota Composition are Associated with Obesity in Children and Adolescents with Prader–Willi Syndrome
Cited by: 16
Author(s): Sonika Garcia-Ribera, Montse Amat-Bou, Eric Climent, M. Villangómez Llobet, Empar Chenoll, Raquel Corripio, Lourdes Ibáñez, Marta Ramón-Krauel, Carles Lerín
Software Mentions: 4
Published: over 6 years ago

10.1016/j.isci.2021.102783

AMPK activation reverts mouse epiblast stem cells to naive state
Cited by: 4
Author(s): Yajing Liu, Junko Yamane, Akito Tanaka, Wataru Fujibuchi, Jun Yamashita
Software Mentions: 4
Published: about 5 years ago

10.1155/2020/5974157

Comparative Transcriptome Analysis Reveals the Protective Mechanism of Glycyrrhinic Acid for Deoxynivalenol-Induced Inflammation and Apoptosis in IPEC-J2 Cells
Cited by: 14
Author(s): Xiaoxiang Xu, Guorong Yan, Juan Chang, Ping Wang, Qingqiang Yin, Chaoqi Liu, Qun Zhu, Fushan Lu
Software Mentions: 4
Published: almost 6 years ago

10.1093/gbe/evw262

Salmonid chromosome evolution as revealed by a novel method for comparing RADseq linkage maps
Cited by: 38
Author(s): Ben J. G. Sutherland, Thierry Gosselin, Éric Normandeau, Manuel Lamothe, Nathalie Isabel, Céline Audet, Louis Bernatchez
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41421-020-00218-1

3D landscape of Hepatitis B virus interactions with human chromatins
Cited by: 20
Author(s): Bo Yang, Boyuan Li, Lingfei Jia, Yongpeng Jiang, Xin Wang, Shaodong Jiang, Shunda Du, Ji Xiong, Pengyuan Yang
Software Mentions: 4
Published: over 5 years ago

10.3390/ani10040577

Improvement of Cecal Commensal Microbiome Following the Insect Additive into Chicken Diet
Cited by: 30
Author(s): Agata Józefiak, Abdelbasset Benzertiha, Bartosz Kierończyk, Anna Łukomska, Izabela Wesołowska, Mateusz Rawski
Software Mentions: 4
Published: over 6 years ago

10.1186/s12974-018-1170-0

Novel insights into neuroinflammation: bacterial lipopolysaccharide, tumor necrosis factor α, and Ureaplasma species differentially modulate atypical chemokine receptor 3 responses in human brain microvascular endothelial cells
Cited by: 15
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Mathias Buttmann, Kirsten Glaser
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2164-14-586

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions
Cited by: 46
Author(s): Brian R. Johnson, Joel Atallah, David C. Plachetzki
Software Mentions: 4
Published: over 13 years ago

10.3389/fmicb.2021.643904

Predominant Microbial Colonizers in the Root Endosphere and Rhizosphere of Turfgrass Systems: Pseudomonas veronii, Janthinobacterium lividum, and Pseudogymnoascus spp.
Cited by: 10
Author(s): Qing Xia, Thomas W. Rufty, Wei Shi
Software Mentions: 4
Published: over 5 years ago

10.1186/s12974-019-1413-8

More than just inflammation: Ureaplasma species induce apoptosis in human brain microvascular endothelial cells
Cited by: 18
Author(s): Christine Silwedel, Axel Haarmann, Markus Fehrholz, Heike Claus, Christian P. Speer, Kirsten Glaser
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2018.02094

Application of MootralTM Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation Technique
Cited by: 27
Author(s): Melanie Eger, Michael Graz, Susanne Riede, Gerhard Breves
Software Mentions: 4
Published: about 8 years ago

10.1098/rstb.2015.0040

Loss of neurogenesis inHydraleads to compensatory regulation of neurogenic and neurotransmission genes in epithelial cells
Cited by: 42
Author(s): Yvan Wenger, Wanda Christa Buzgariu, Brigitte Galliot
Software Mentions: 4
Published: over 10 years ago

10.3390/ijms21238898

MicroRNA Profiling in Oesophageal Adenocarcinoma Cell Lines and Patient Serum Samples Reveals a Role for miR-451a in Radiation Resistance
Cited by: 8
Author(s): Frederike Butz, Ann-Kathrin Eichelmann, George C. Mayne, Tingting Wang, Isabell Bastian, Karen Chiam, Shashikanth Marri, Pamela J. Sykes, Bas P. L. Wijnhoven, Eelke Toxopeus, Michael Michael, Christos S. Karapetis, Richard Hummel, David I. Watson, Damian J. Hussey
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms21124453

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Cited by: 7
Author(s): Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan‐Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21186946

Proteomic and Transcriptomic Patterns during Lipid Remodeling in Nannochloropsis gaditana
Cited by: 13
Author(s): Chris J. Hulatt, Irina Smolina, Adam Dowle, Martina Kopp, Ghana Kalerammana Vasanth, Galice Hoarau, René H. Wijffels, Viswanath Kiron
Software Mentions: 4
Published: almost 6 years ago

10.1080/20002297.2021.1946316

Microbial characteristics across different tongue coating types in a healthy population
Cited by: 5
Author(s): Hairong Chen, Qingwei Li, Min Li, Sheng Liu, Chensi Yao, Zixiong Wang, Zhixin Zhao, Ping Liu, Fan Yang, Xinjian Li, Jun Wang, Yi-Xin Zeng, Xiaolin Tong
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.01305

Seasonal Dynamics of Pelagic Mycoplanktonic Communities: Interplay of Taxon Abundance, Temporal Occurrence, and Biotic Interactions
Cited by: 21
Author(s): Stefanos Banos, Deisy Morselli Gysi, Tim Richter-Heitmann, Frank Oliver Glöckner, Maarten Boersma, Karen Helen Wiltshire, Gunnar Gerdts, Antje Wichels, M. Reich
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2019.01576

Fecal Microbiota Transplant From Highly Feed Efficient Donors Affects Cecal Physiology and Microbiota in Low- and High-Feed Efficient Chickens
Cited by: 30
Author(s): Barbara U. Metzler‐Zebeli, Sina-Catherine Siegerstetter, Elizabeth Magowan, Peadar G. Lawlor, Niamh O’Connell, Qendrim Zebeli
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms20143583

Ureaplasma Species Modulate Cytokine and Chemokine Responses in Human Brain Microvascular Endothelial Cells
Cited by: 6
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Nicolas Schlegel, Kirsten Glaser
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms19092500

Co-Expression Network Analysis Identifies miRNA–mRNA Networks Potentially Regulating Milk Traits and Blood Metabolites
Cited by: 12
Author(s): Adolf A. Ammah, Duy Ngoc, Nathalie Bissonnette, Nicolas Gévry, Eveline M. Ibeagha‐Awemu
Software Mentions: 4
Published: about 8 years ago

10.3389/fmicb.2021.628437

Volatile Compounds From Bacillus, Serratia, and Pseudomonas Promote Growth and Alter the Transcriptional Landscape of Solanum tuberosum in a Passively Ventilated Growth System
Cited by: 8
Author(s): Darren Heenan-Daly, Simone Coughlan, Eileen Dillane, Barbara Doyle Prestwich
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms20236040

Whole Genome Expression Analyses of miRNAs and mRNAs Suggest the Involvement of miR-320a and miR-155-3p and their Targeted Genes in Lithium Response in Bipolar Disorder
Cited by: 27
Author(s): Claudia Pisanu, Eleni Merkouri Papadima, Carla Melis, Donatella Congiu, Annalisa Loizedda, Nicola Orrù, Stefano Calza, Sandro Orrù, Carlo Carcassi, Giovanni Severino, Raffaella Ardau, Caterina Chillotti, Maria Del Zompo, Alessio Squassina
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.63545

Mutations in SKI in Shprintzen–Goldberg syndrome lead to attenuated TGF-β responses through SKI stabilization
Cited by: 20
Author(s): Ilaria Gori, Roger George, A. Purkiss, Stephanie Strohbuecker, Rebecca A. Randall, R.W. Ogrodowicz, Virginie Carmignac, Laurence Faivre, Dhira Joshi, Svend Kjær, Caroline S. Hill
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2017.01656

Linseed Oil Supplementation of Lambs’ Diet in Early Life Leads to Persistent Changes in Rumen Microbiome Structure
Cited by: 36
Author(s): Tamsin Lyons, T. M. Boland, Sean Storey, Evelyn Doyle
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.28625

The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis
Cited by: 30
Author(s): Sarah N. Deffit, Brian A. Yee, Aidan C. Manning, Suba Rajendren, Pranathi Vadlamani, Emily C. Wheeler, Alain Domissy, Michael C. Washburn, G Yeo, Heather A. Hundley
Software Mentions: 4
Published: almost 9 years ago

10.3389/fmicb.2021.675048

A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments
Cited by: 6
Author(s): Zhongdong Huang, Shiqing Mo, Lifei Yan, Xiaomei Wei, Yangze Huang, Lizhen Zhang, Shuhui Zhang, Jianzong Liu, Qing Xiao, Hong Lin, Yu Guo
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers13071494

Musashi1 Contribution to Glioblastoma Development via Regulation of a Network of DNA Replication, Cell Cycle and Division Genes
Cited by: 9
Author(s): Mirella Baroni, Caihong Yi, Saket Choudhary, Xiufen Lei, Adam Kosti, Denise Grieshober, Mitzli X. Velasco, Mu Qiao, Suzanne Burns, Patrícia Rosa de Araújo, Talia Delambre, Mi‐Young Son, Michelina Plateroti, Marco A. R. Ferreira, Paul Hasty, Luiz O. F. Penalva
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.50530

Viral miRNA adaptor differentially recruits miRNAs to target mRNAs through alternative base-pairing
Cited by: 5
Author(s): Carlos Gorbea, Tim Mosbruger, David A. Nix, Demián Cazalla
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms21062079

Whole-Genome Uterine Artery Transcriptome Profiling and Alternative Splicing Analysis in Rat Pregnancy
Cited by: 4
Author(s): Kathirvel Gopalakrishnan, Sathish Kumar
Software Mentions: 4
Published: over 6 years ago

10.3390/pathogens10050555

Microeukaryotic Communities on the Fruit of Gardenia thunbergia Thunb. with a Focus on Pathogenic Fungi
Cited by: 0
Author(s): Bastian Steudel, Himansu Baijnath, Thorben Schwedt, Armin O. Schmitt
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers13184687

Bacteria-Derived Extracellular Vesicles in Urine as a Novel Biomarker for Gastric Cancer: Integration of Liquid Biopsy and Metagenome Analysis
Cited by: 7
Author(s): Jae Yong Park, Chil Sung Kang, Ho Chan Seo, Jin Chul Shin, Sung Min Kym, Young Soo Park, Tae Seop Shin, Jae Gyu Kim, Yoon Keun Kim
Software Mentions: 4
Published: about 5 years ago

10.3389/fmed.2021.675842

Exosomal Circular RNA RNA-seq Profiling and the Carcinogenic Role of Exosomal circ-CYP24A1 in Cutaneous Squamous Cell Carcinoma
Cited by: 9
Author(s): Zheng Zhang, Hao Guo, Wen‐Jia Yang, Jiu‐Hong Li
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.41337

Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni
Cited by: 83
Author(s): Wannaporn Ittiprasert, Victoria H. Mann, Shannon E. Karinshak, Avril Coghlan, Gabriel Rinaldi, Geetha Sankaranarayanan, Apisit Chaidee, Toshihiko Tanno, Chutima Kumkhaek, Pannathee Prangtaworn, Margaret M. Mentink–Kane, Christina J Cochran, Patrick Driguez, Nancy Holroyd, Alan S. Tracey, Rutchannee Rodpai, Bart Everts, Cornelis H. Hokke, Karl F. Hoffmann, Matthew Berriman, Paul J. Brindley
Software Mentions: 4
Published: over 7 years ago

10.3390/cancers13030527

Radiosensitizing Pancreatic Cancer with PARP Inhibitor and Gemcitabine: An In Vivo and a Whole-Transcriptome Analysis after Proton or Photon Irradiation
Cited by: 7
Author(s): Waisse Waissi, Anaïs Nicol, Matthieu Jung, M. Rousseau, D. Jarnet, Georges Noël, Hélène Burckel
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.38014

Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells
Cited by: 52
Author(s): Jacob W. Freimer, TJ Hu, Robert Blelloch
Software Mentions: 4
Published: about 8 years ago

10.1242/bio.047829

Heterogeneous beta-catenin activation is sufficient to cause hepatocellular carcinoma in zebrafish
Cited by: 13
Author(s): Sharanya Maanasi Kalasekar, Srishti Kotiyal, Christopher J. Conley, Cindy Phan, Annika Young, Kimberley Evason
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.58041

Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria
Cited by: 52
Author(s): Sara M. Nowinski, Ashley Solmonson, Scott F. Rusin, J. Alan Maschek, Claire Bensard, Sarah Fogarty, Mi Young Jeong, Sandra Lettlová, Jordan A. Berg, Jeffrey T. Morgan, Yeyun Ouyang, Bradley C. Naylor, João A. Paulo, Katsuhiko Funai, James E. Cox, Steven P. Gygi, Dennis R. Winge, Ralph J. DeBerardinis, Jared Rutter
Software Mentions: 4
Published: about 6 years ago

10.3390/cancers12082210

Human FBXL8 Is a Novel E3 Ligase Which Promotes BRCA Metastasis by Stimulating Pro-Tumorigenic Cytokines and Inhibiting Tumor Suppressors
Cited by: 10
Author(s): Shu Chun Chang, Wei‐Hsiu Hsu, Emily Chia Yu Su, Chin Sheng Hung, Jeak Ling Ding
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.65760

Morphological and genomic shifts in mole-rat ‘queens’ increase fecundity but reduce skeletal integrity
Cited by: 8
Author(s): Rachel A Johnston, Philippe Vullioud, Jack Thorley, Henry Kirveslahti, Leyao Shen, Sayan Mukherjee, Courtney M. Karner, Tim Clutton‐Brock, Jenny Tung
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms21093262

Whole-Genome Deep Sequencing Reveals Host-Driven in-planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations
Cited by: 5
Author(s): Parichate Tangkanchanapas, Annelies Haegeman, Tom Ruttink, Monica Höfte, Kris De Jonghe
Software Mentions: 4
Published: over 6 years ago

10.3390/v11111041

Viruses in the Invasive Hornet Vespa velutina
Cited by: 36
Author(s): Anne Dalmon, Philippe Gayral, Damien Decante, Christophe Klopp, Diane Bigot, Maxime Thomasson, Elisabeth A. Herniou, Cédric Alaux, Yves Le Conte
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0187150

RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma
Cited by: 13
Author(s): Jennifer K. Grenier, Polly Foureman, Erica A. Sloma, Andrew D. Miller
Software Mentions: 4
Published: almost 9 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: about 8 years ago

10.7554/eLife.67577

Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila
Cited by: 57
Author(s): Heather E. Machado, Alan O. Bergland, Ryan W. Taylor, Susanne Tilk, Emily L. Behrman, Kelly A. Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Bernard Kim, Iryna Kozeretska, Brian P. Lazzaro, Thomas J. S. Merritt, John E. Pool, Katherine R. O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul S. Schmidt, Dmitri A. Petrov
Software Mentions: 4
Published: about 5 years ago

10.1080/21505594.2021.1958057

Transcriptional response of Aspergillus fumigatus to copper and the role of the Cu chaperones
Cited by: 6
Author(s): Duaa Anabosi, Zohar Meir, Yana Shadkchan, Mariana Handelman, Ammar Abou-Kandil, Annie Yap, Daniel Urlings, Morgan Gold, Sven Krappmann, Hubertus Haas, Nir Osherov
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0215986

Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq
Cited by: 27
Author(s): Sebastian Laaß, Vivian Monzon, Jana Kliemt, M Hammelmann, Friedhelm Pfeiffer, Konrad U. Förstner, Jörg Soppa
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2020.00867

Single-Cell Transcriptome Analysis Reveals Six Subpopulations Reflecting Distinct Cellular Fates in Senescent Mouse Embryonic Fibroblasts
Cited by: 13
Author(s): Wei Chen, Xuefei Wang, Gang Wei, Yin Huang, Yufang Shi, Dan Li, Shengnu Qiu, Bin Zhou, Junhong Cao, Meng Chen, Pengfei Qin, Wenfei Jin, Ting Ni
Software Mentions: 4
Published: about 6 years ago

10.1186/s12870-016-0926-x

Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq
Cited by: 9
Author(s): Nikolay A. Shmakov, Gennady V. Vasiliev, Natalya V. Shatskaya, А. В. Дорошков, Е. И. Гордеева, D. A. Afonnikov, Е. К. Хлесткина
Software Mentions: 4
Published: almost 10 years ago

10.3389/fcimb.2020.594778

Biliary Microbial Structure of Gallstone Patients With a History of Endoscopic Sphincterotomy Surgery
Cited by: 6
Author(s): Haikang Shen, Juanjuan Zhu, Fuqiang Ye, Danyi Xu, Liang Fang, Jianfeng Yang, Huijie Lv, Qifeng Lou, Hangbin Jin, Ming Ni, Xiaofeng Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2019.00854

New Recurrent Structural Aberrations in the Genome of Chronic Lymphocytic Leukemia Based on Exome-Sequencing Data
Cited by: 7
Author(s): Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, José Ángel Díaz Arias, Marta Sonia González Pérez, José Luis Bello López
Software Mentions: 4
Published: almost 7 years ago

10.1186/s40303-016-0017-9

αT-catenin in restricted brain cell types and its potential connection to autism
Cited by: 20
Author(s): Stephen Sai Folmsbee, Douglas R. Wilcox, Koen Tyberghein, Pieter De Bleser, Warren G. Tourtellotte, Jolanda van Hengel, Frans van Roy, Cara J. Gottardi
Software Mentions: 4
Published: about 10 years ago

10.1038/s41380-018-0271-6

Alterations in sperm long RNA contribute to the epigenetic inheritance of the effects of postnatal trauma
Cited by: 106
Author(s): Katharina Gapp, Gretchen van Steenwyk, Pierre-Luc Germain, Wayo Matsushima, Konrad L. M. Rudolph, Francesca Manuella, Martin Roszkowski, Grégoire Vernaz, Tanay Ghosh, Paweł Pelczar, Isabelle M. Mansuy, Eric A. Miska
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.47891

Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation
Cited by: 54
Author(s): Jered M. Wendte, Yinwen Zhang, Lexiang Ji, Xiulin Shi, Rashmi R. Hazarika, Yadollah Shahryary, Frank Johannes, Robert J. Schmitz
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-016-2694-2

RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures
Cited by: 21
Author(s): Maurizio Pellegrino, Adam Sciambi, Jamie Yates, Joshua D. Mast, Charles Silver, Dennis J. Eastburn
Software Mentions: 4
Published: over 10 years ago

10.18632/aging.202780

circRNA expression profiling of colon tissue from mesalazine-treated mouse of inflammatory bowel disease reveals an important circRNA-miRNA-mRNA pathway
Cited by: 8
Author(s): Wei Zhou, Haiyin Zhang, Y. B. Pan, Yingbin Xu, Yongqing Cao
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2020.551065

Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice
Cited by: 11
Author(s): Fang Cao, Yu Guo, Qiang Zhang, Yinchun Fan, Qian Liu, Jiancheng Song, Hua Zhong, Shengtao Yao
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-016-3227-8

Blood miRNomes and transcriptomes reveal novel longevity mechanisms in the long-lived bat, Myotis myotis
Cited by: 43
Author(s): Zixia Huang, David Jebb, Emma C. Teeling
Software Mentions: 4
Published: almost 10 years ago

10.3389/fimmu.2021.644350

Analysis of Bulk RNA Sequencing Data Reveals Novel Transcription Factors Associated With Immune Infiltration Among Multiple Cancers
Cited by: 5
Author(s): Lei Liu, Qiuchen Zhao, Chao Cheng, Jingwen Yi, Hongyan Sun, Qi Wang, Weili Quan, Yaqiang Xue, Luguo Sun, Xianling Cong, Yi Zhang
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.20983

A molecular portrait of maternal sepsis from Byzantine Troy
Cited by: 32
Author(s): Alison Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob Enk, G. Brian Golding, John Southon, Melanie Kuch, Ana T. Duggan, William Aylward, Shea N. Gardner, Jonathan Allen, Andrew King, Gerard D. Wright, Makoto Kuroda, Kengo Kato, Derek E. G. Briggs, Gino Fornaciari, Edward C. Holmes, Hendrik N. Poinar, Caitlin S. Pepperell
Software Mentions: 4
Published: over 9 years ago

10.3389/fbioe.2020.00155

Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
Cited by: 9
Author(s): Richou Han, Katie Haning, Juan C. Gonzalez-Rivera, Yongqiang Yang, Runxia Li, Seung Hee Cho, Ju Huang, Bobi A. Simonsen, Shihui Yang, Lydia M. Contreras
Software Mentions: 4
Published: over 6 years ago

10.1186/s12866-021-02230-1

A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants
Cited by: 12
Author(s): Christophe Lay, Collins Wenhan Chu, Rikky W. Purbojati, Enzo Acerbi, Daniela I. Drautz–Moses, Paola Flórez de Sessions, Jié Song, Eliza Xin Pei Ho, Yee Jiun Kok, Xinyan Bi, Shuwen Chen, Shi Ya Mak, Mei Chien Chua, Angela Goh, Wen Chin Chiang, Rajeshwar Rao, Surasith Chaithongwongwatthana, Nipon Khemapech, Voranush Chongsrisawat, Rocı́o Martı́n, Yanqing Koh, Sachin R. Lohar, Ivan Chin Hin Tan, Wong Anng Anng, Jie Chen, Nana Bartke, Kaouther Ben-Amor, Ingrid B. Renes, Fiona Wong, Guus Roeselers, Ying Swan Ho, Martin L. Hibberd, Stephan C. Schuster, Jan Knol
Software Mentions: 4
Published: about 5 years ago

10.1186/s12866-017-1092-5

Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone
Cited by: 43
Author(s): Stephanie L. Bond, Edouard Timsit, Matthew L. Workentine, Trevor W. Alexander, Renaud Léguillette
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0246367

Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis
Cited by: 6
Author(s): Lluís Revilla, Aida Mayorgas, A M Corraliza, Maria Carme Masamunt, Amira Metwaly, Dirk Haller, Eva Tristán, Anna Carrasco, María Esteve, Julián Panés, Elena Ricart, Juan José Lozano, Azucena Salas
Software Mentions: 4
Published: over 5 years ago

10.3389/fbioe.2015.00028

G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods
Cited by: 8
Author(s): Andrea Manconi, Elias Manca, Marco Moscatelli, Matteo Gnocchi, Alessandro Orro, Giuliano Armano, Luciano Milanesi
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0223397

Brief communication: Long-term absence of Langerhans cells alters the gene expression profile of keratinocytes and dendritic epidermal T cells
Cited by: 10
Author(s): Qingtai Su, Aurélie Bouteau, Jacob Cardenas, Uthra Balaji, Yuanyaun Wang, Cynthia Smitherman, Jin Gu, Botond Z. Igyártó
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-65638-1

Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels
Cited by: 11
Author(s): Saket Choudhary, Suzanne Perea Burns, Hoda Mirsafian, Wenzheng Li, Dat T. Vo, Mu Qiao, Xiufen Lei, Andrew D. Smith, Luiz O. F. Penalva
Software Mentions: 4
Published: over 6 years ago

10.12688/f1000research.10571.2

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
Cited by: 332
Author(s): Jason L. Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu‐Jie Wang, David Buck, Kin Fai Au
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-019-53892-x

Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles
Cited by: 46
Author(s): Celine Everaert, Hetty Helsmoortel, Anneleen Decock, Eva Hulstaert, Ruben Van Paemel, Kimberly Verniers, Justine Nuytens, Jasper Anckaert, Nele Nijs, Joeri Tulkens, Bert Dhondt, An Hendrix, Pieter Mestdagh, Jo Vandesompele
Software Mentions: 4
Published: almost 7 years ago

10.1155/2017/7183516

PEDF Is Associated with the Termination of Chondrocyte Phenotype and Catabolism of Cartilage Tissue
Cited by: 6
Author(s): Patricia Klinger, Söeren Lukassen, Fulvia Ferrazzi, Arif B. Ekici, Thilo Hotfiel, B. Swoboda, Thomas Aigner, Kolja Gelse
Software Mentions: 4
Published: over 9 years ago

10.1016/j.molcel.2019.03.010

A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal Jelly
Cited by: 35
Author(s): Eyal Maori, Isabela Cunha Navarro, Humberto Boncristiani, David J. Seilly, Konrad L. M. Rudolph, Alexandra Sapetschnig, Chi-Chuan Lin, John E. Ladbury, Jay D. Evans, Jonathan L. Heeney, Eric A. Miska
Software Mentions: 4
Published: over 7 years ago

10.1111/eva.12979

Estimating the contribution of Greenland Halibut (Reinhardtius hippoglossoides) stocks to nurseries by means of genotyping‐by‐sequencing: Sex and time matter
Cited by: 16
Author(s): Emilie Carrier, Anne‐Laure Ferchaud, Éric Normandeau, Pascal Sirois, Louis Bernatchez
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-42560-9

De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats
Cited by: 22
Author(s): Diana D. Moreno-Santillán, Carlos Machaín-Williams, Georgina Hernández-Montes, Jorge Ortega
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-42911-6

Habitat-dependent composition of bacterial and fungal communities in biological soil crusts from Oman
Cited by: 30
Author(s): Raeid M. M. Abed, Alexandra Tamm, Christiane Hassenrück, Ahmed Al‐Rawahi, Emilio Rodríguez‐Caballero, Sabine Fiedler, Stefanie Maier, Bettina Weber
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-42865-9

Differences in resource use lead to coexistence of seed-transmitted microbial populations
Cited by: 15
Author(s): Gloria Torres-Cortés, Benjamin J. Garcia, Stéphane Compant, Samir Rezki, Piet Jones, Anne Préveaux, Martial Briand, Alain Roulet, Olivier Bouchez, Daniel Jacobson, Matthieu Barret
Software Mentions: 4
Published: over 7 years ago

10.1016/j.molcel.2018.10.018

Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor
Cited by: 32
Author(s): Andrew Wu, Harshil Patel, Minghao Chia, Fabien Moretto, David Frith, Ambrosius P. Snijders, Folkert J. van Werven
Software Mentions: 4
Published: almost 8 years ago

10.1186/1471-2164-15-221

From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism
Cited by: 119
Author(s): Inès Zouari, Alessandra Salvioli, Matteo Chialva, Mara Novero, Laura Miozzi, Gian Carlo Tenore, Paolo Bagnaresi, Paola Bonfante
Software Mentions: 4
Published: over 12 years ago

10.3390/cancers13051126

Transformed Canine and Murine Mesenchymal Stem Cells as a Model for Sarcoma with Complex Genomics
Cited by: 5
Author(s): Natasja Franceschini, Bas Verbruggen, Marianna A. Tryfonidou, Alwine B. Kruisselbrink, Hans J. Baelde, Karin E. de Visser, Károly Szuhai, Anne‐Marie Cleton‐Jansen, Judith V.M.G. Bovée
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-51056-5

Down-regulation of CK2α correlates with decreased expression levels of DNA replication minichromosome maintenance protein complex (MCM) genes
Cited by: 4
Author(s): Susanne Schaefer, Thomas Koed Doktor, Sabrina B Frederiksen, Kathleen Chea, Mirka Hlavacova, Georg M. Bruun, Maj Rabjerg, Brage S. Andresen, Isabel Domı́nguez, Bárbara Guerra
Software Mentions: 4
Published: almost 7 years ago

10.1093/molbev/msab096

Novelty and Convergence in Adaptation to Whole Genome Duplication
Cited by: 20
Author(s): Magdalena Bohutínská, Mark Alston, Patrick J. Monnahan, Terezie Mandáková, Sian Bray, Pirita Paajanen, Filip Kolář, Levi Yant
Software Mentions: 4
Published: over 5 years ago

10.1093/molbev/msx144

Recent Sex Chromosome Divergence despite Ancient Dioecy in the Willow Salix viminalis
Cited by: 55
Author(s): Pascal Pucholt, Alison E. Wright, Lei Liu Conze, Judith E. Mank, Sofia Berlin
Software Mentions: 4
Published: over 9 years ago

10.1093/molbev/msw161

Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation
Cited by: 82
Author(s): Sara Pinosio, Stefania Giacomello, Patricia Faivre-Rampant, Gail Taylor, Véronique Jorge, Marie Christine Le Paslier, Giusi Zaina, Catherine Bastien, Federica Cattonaro, Fabio Marroni, Michèle Morgante
Software Mentions: 4
Published: about 10 years ago

10.7717/peerj.8133

The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity
Cited by: 19
Author(s): Lauren V. Carruthers, Moses Arinaitwe, Moses Adriko, Christina L. Faust, Edridah M. Tukahebwa, Lindsay J. Hall, Lisa Ranford-Cartwright, Poppy H. L. Lamberton
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0232715

PIWI-interacting RNAs are differentially expressed during cardiac differentiation of human pluripotent stem cells
Cited by: 11
Author(s): Alejandro La Greca, María Agustina Scarafia, María Clara Hernández Cañás, Nelba Pérez, Sheila Castañeda, Carolina Colli, Alan Miqueas Möbbs, Natalia Lucía Santín Velazque, Gabriel Neiman, Ximena Garate, Cyntia Abán, Ariel Waisman, Lucía Moro, Gustavo Sevlever, Carlos Luzzani, Santiago Gabriel Miriuka
Software Mentions: 4
Published: over 6 years ago

10.1093/molbev/msab141

Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution
Cited by: 14
Author(s): Alexander S. T. Papadopulos, Andrew J. Helmstetter, Owen G. Osborne, Aaron A. Comeault, Daniel P. Wood, Edward A. Straw, Laurence Mason, Michael F. Fay, Joe Parker, Luke T. Dunning, Andrew Foote, Rhian J. Smith, Jackie Lighten
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.10231

Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture
Cited by: 22
Author(s): John K. Pearman, Nigel Keeley, Susanna A. Wood, Olivier Laroche, Anastasija Zaiko, Georgia Thomson‐Laing, Laura Biessy, Javier Atalah, Xavier Pochon
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0216366

Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia
Cited by: 11
Author(s): Daniel Fernandes, Kendra Sirak, Olivia Cheronet, Rachel Howcroft, Mislav Čavka, Dženi Los, Josip Burmaz, Ron Pinhasi, Mario Novak
Software Mentions: 4
Published: about 7 years ago

10.1093/molbev/msaa172

Gene Loss Predictably Drives Evolutionary Adaptation
Cited by: 49
Author(s): Jana Helsen, Karin Voordeckers, Laura Vanderwaeren, Toon Santermans, Maria Tsontaki, Kevin J. Verstrepen, Rob Jelier
Software Mentions: 4
Published: about 6 years ago

10.1002/ece3.1720

The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development
Cited by: 34
Author(s): Svjetlana Vojvodic, Brian R. Johnson, Brock A. Harpur, Clement F. Kent, Amro Zayed, Kirk E. Anderson, Timothy A. Linksvayer
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-017-15955-9

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome
Cited by: 64
Author(s): María‐Soledad Benítez, Shannon L. Osborne, R. Michael Lehman
Software Mentions: 4
Published: almost 9 years ago

10.1002/ece3.3976

Brain gene expression analyses in virgin and mated queens of fire ants reveal mating-independent and socially regulated changes
Cited by: 14
Author(s): Travis L. Calkins, Mei Er Chen, Arinder K. Arora, Chloë Hawkings, Cécilia Tamborindeguy, Patricia V. Pietrantonio
Software Mentions: 4
Published: over 8 years ago

Projects: pypi: cutadapt

Enhanced Analysis

Science Score: 100/100

Bonuses:

Penalties:

Papers Mentioning cutadapt 1,562