bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.3390/microorganisms8010061

Prenatal Transfer of Gut Bacteria in Rock Pigeon
Cited by: 14
Author(s): Maurine W. Dietz, Joana Falcão Salles, Bin‐Yan Hsu, Cor Dijkstra, Ton G. G. Groothuis, Marco van der Velde, Yvonne I. Verkuil, B. Irene Tieleman
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pgen.1006864

Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder
Cited by: 101
Author(s): Tom S. Koemans, Tjitske Kleefstra, Melissa C. Chubak, Max H. Stone, Margot R.F. Reijnders, Sonja de Munnik, Marjolein H. Willemsen, Michaela Fencková, Connie Stumpel, Levinus A. Bok, Margarita Saenz, Kyna A. Byerly, Linda B. Baughn, Alexander P.A. Stegmann, Rolph Pfundt, Huiqing Zhou, Hans van Bokhoven, Annette Schenck, Jamie M. Kramer
Software Mentions: 7
Published: almost 9 years ago

10.1016/j.cell.2021.01.002

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition
Cited by: 412
Author(s): Kevin Litchfield, James L. Reading, Clare Puttick, Krupa Thakkar, Chris Abbosh, Robert Bentham, Thomas B.K. Watkins, Rachel Rosenthal, Dhruva Biswas, Andrew Rowan, Emilia L. Lim, Maise Al Bakir, Virginia Turati, José Afonso Guerra-Assunção, Lucía Conde, Andrew J.S. Furness, Sunil Kumar Saini, Sine Reker Hadrup, Javier Herrero, Se‐Hoon Lee, Peter Van Loo, Tariq Enver, James Larkin, Matthew D. Hellmann, Samra Turajlic, Sergio A. Quezada, Nicholas McGranahan, Charles Swanton
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0233899

Recapitulation of prostate tissue cell type-specific transcriptomes by an in vivo primary prostate tissue xenograft model
Cited by: 2
Author(s): Nelson T. Gross, Jianmin Wang, Michael V. Fiandalo, Eduardo Cortes Gomez, Anica Watts, Alejandro Godoy, Gary J. Smith, Yue Wu
Software Mentions: 7
Published: about 6 years ago

10.1038/s41388-021-01876-5

The FLI portion of EWS/FLI contributes a transcriptional regulatory function that is distinct and separable from its DNA-binding function in Ewing sarcoma
Cited by: 12
Author(s): Megann A. Boone, Cenny Taslim, Julie Crow, Julia Selich‐Anderson, Andrea K. Byrum, Iftekhar A. Showpnil, Benjamin D. Sunkel, Meng Wang, Benjamin Z. Stanton, Emily R. Theisen, Stephen L. Lessnick
Software Mentions: 7
Published: over 5 years ago

10.3390/microorganisms8020270

In Vitro Zika Virus Infection of Human Neural Progenitor Cells: Meta-Analysis of RNA-Seq Assays
Cited by: 15
Author(s): Rossella Gratton, Paola Maura Tricarico, Almerinda Agrelli, Heverton Valentim Colaço da Silva, Lucas Coêlho Bernardo, Sérgio Crovella, Antônio Victor Campos Coelho, Ronald Moura, Lucas André Cavalcanti Brandão
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.59610

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos
Cited by: 29
Author(s): Theodora Koromila, Fan Gao, Yohei Iwasaki, Peng He, Lior Pachter, J. Peter Gergen, Angelike Stathopoulos
Software Mentions: 7
Published: about 6 years ago

10.1128/mBio.03396-20

Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes
Cited by: 21
Author(s): Rozlyn C.T. Boutin, Hind Sbihi, Ryan J. McLaughlin, Aria S. Hahn, Kishori M. Konwar, Rachelle Loo, Darlene Dai, Charisse Petersen, Fiona S. L. Brinkman, Geoffrey L. Winsor, Malcolm R. Sears, Theo J. Moraes, Allan B. Becker, Meghan B. Azad, Piush J. Mandhane, Padmaja Subbarao, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 7
Published: about 5 years ago

10.12688/f1000research.14880.4

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
Cited by: 0
Author(s): Syed Hussain Ather, Olaitan I. Awe, Thomas J. Butler, Tamiru Denka, Stephen A. Semick, Wanhu Tang, Ben Busby
Software Mentions: 7
Published: almost 6 years ago

10.3390/microorganisms8060961

The Bacterial Gut Microbiota of Schoolchildren from High and Low Socioeconomic Status: A Study in an Urban Area of Makassar, Indonesia
Cited by: 10
Author(s): Aldian Irma Amaruddin, Firdaus Hamid, J. Koopman, Munawir Muhammad, Eric A. T. Brienen, Lisette van Lieshout, A. R. Geelen, Sitti Wahyuni, Ed J. Kuijper, Erliyani Sartono, Maria Yazdanbakhsh, Romy D. Zwittink
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0258157

Dynamically expressed genes provide candidate viability biomarkers in a model coccidian
Cited by: 4
Author(s): Matthew S. Tucker, Celia O’Brien, Mark C. Jenkins, Benjamin M. Rosenthal
Software Mentions: 7
Published: almost 5 years ago

10.1155/2020/7658342

A Comprehensive Network Pharmacology-Based Strategy to Investigate Multiple Mechanisms of HeChan Tablet on Lung Cancer
Cited by: 6
Author(s): Zhenjie Zhuang, Qianying Chen, Cihui Huang, Junping Wen, Huayi Huang, Zhanhua Liu
Software Mentions: 7
Published: over 6 years ago

10.1186/s40168-020-00813-0

Disinfection exhibits systematic impacts on the drinking water microbiome
Cited by: 37
Author(s): Zihan Dai, Maria C. Sevillano-Rivera, Szymon T. Calus, Quyen Melina Bautista-de los Santos, A. Murat Eren, P.W.J.J. van der Wielen, Umer Zeeshan Ijaz, Ameet J. Pinto
Software Mentions: 7
Published: over 6 years ago

10.1038/s42003-021-01990-w

Multi-omics phenotyping of the gut-liver axis reveals metabolic perturbations from a low-dose pesticide mixture in rats
Cited by: 26
Author(s): Robin Mesnage, Maxime Teixeira, Daniele Mandrioli, Laura Falcioni, Mariam Ibragim, Quinten R Ducarmon, Romy D. Zwittink, Caroline Amiel, Jean-Michel Panoff, Emma Bourne, Emanuel Savage, Charles A. Mein, Fiorella Belpoggi, Michael Antoniou
Software Mentions: 7
Published: over 5 years ago

10.1038/s42003-021-02095-0

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis
Cited by: 28
Author(s): Mariana Galvão Ferrarini, Avantika Lal, Rita Rebollo, Andreas J. Gruber, Andrea Guarracino, Itziar Martinez Gonzalez, Taylor Floyd, Daniel Siqueira de Oliveira, Justin Shanklin, Ethan Beausoleil, Taneli Pusa, Brett E. Pickett, Vanessa Aguiar‐Pulido
Software Mentions: 7
Published: over 5 years ago

10.3390/cancers13081934

Cannabinoid Receptor Type-2 in B Cells Is Associated with Tumor Immunity in Melanoma
Cited by: 3
Author(s): Thomas Gruber, Steve Robatel, Mirela Kremenovic, Lukas Bäriswyl, Jürg Gertsch, Mirjam Schenk
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.11985

Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields
Cited by: 14
Author(s): Ademir Durrer, Thiago Gumière, Maurício Rumenos Guidetti Zagatto, Henrique Petry Feiler, Antônio Marcos Miranda Silva, Rodrigo Henriques Longaresi, Sérgio Kenji Homma, Elke Jurandy Bran Nogueira Cardoso
Software Mentions: 7
Published: almost 5 years ago

10.3390/biomedicines9050454

mRNA Profiles of Porcine Parathyroid Glands Following Variable Phosphorus Supplies throughout Fetal and Postnatal Life
Cited by: 8
Author(s): Michael Oster, Henry Reyer, Christian Gerlinger, Nares Trakooljul, Puntita Siengdee, Jonas Keiler, Siriluck Ponsuksili, Petra Wolf, Klaus Wimmers
Software Mentions: 7
Published: over 5 years ago

10.1093/bib/bbt086

Comparison of software packages for detecting differential expression in RNA-seq studies
Cited by: 317
Author(s): Fatemeh Seyednasrollah, Asta Laiho, Laura L. Elo
Software Mentions: 7
Published: almost 13 years ago

10.1093/bib/bbx143

Bioinformatics for precision oncology
Cited by: 49
Author(s): Jochen Singer, Anja Irmisch, Hans‐Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
Software Mentions: 7
Published: over 8 years ago

10.7554/eLife.22631

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells
Cited by: 184
Author(s): Hamish W King, Robert J. Klose
Software Mentions: 7
Published: over 9 years ago

10.1016/j.csbj.2020.12.012

Virulence factor-related gut microbiota genes and immunoglobulin A levels as novel markers for machine learning-based classification of autism spectrum disorder
Cited by: 17
Author(s): Mingbang Wang, Ceymi Doenyas, Jing Wan, Shujuan Zeng, Chunquan Cai, Jiaxiu Zhou, Yanqing Liu, Yin Zhen, Wenhao Zhou
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.8103

Acquisition of fungi from the environment modifies ambrosia beetle mycobiome during invasion
Cited by: 33
Author(s): Davide Rassati, Lorenzo Marini, Antonino Malacrinò
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pgen.1009587

The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency
Cited by: 17
Author(s): Kazutoshi Takahashi, Michiko Nakamura, Chikako Okubo, Zane Kliesmete, Mari Ohnuki, Megumi Narita, Akira Watanabe, Mai Ueda, Yasuhiro Takashima, Ines Hellmann, Shinya Yamanaka
Software Mentions: 7
Published: over 5 years ago

10.1038/s42003-020-0969-2

Integrative genome-wide analysis reveals the role of WIP proteins in inhibition of growth and development
Cited by: 11
Author(s): Maria Victoria Gómez Roldán, Farhaj Izhaq, Marion Verdenaud, John Saviour Yaw Eleblu, Aimen Haraghi, Vivien Sommard, Pierre Chambrier, David Latrasse, Teddy Jégu, Moussa Benhamed, Judit Szécsi, Mohammed Bendahmane, Adnane Boualem, Abdelhafid Bendahmane
Software Mentions: 7
Published: over 6 years ago

10.1186/s13059-020-1930-x

CUBIC: an atlas of genetic architecture promises directed maize improvement
Cited by: 49
Author(s): Haijun Liu, Xiaqing Wang, Yingjie Xiao, Jingyun Luo, Feng Qiao, Wenyu Yang, Ruyang Zhang, Yijiang Meng, Jiamin Sun, Shijuan Yan, Yong Peng, Luyao Niu, Liumei Jian, Wei Song, Jiali Yan, Chunhui Li, Yanxin Zhao, Liu Ya, Marilyn L. Warburton, Jiuran Zhao
Software Mentions: 7
Published: over 6 years ago

10.1038/s42003-020-01175-x

Genetic alterations in the 3q26.31-32 locus confer an aggressive prostate cancer phenotype
Cited by: 3
Author(s): Benjamin S. Simpson, Niedzica Camacho, Hayley J. Luxton, Hayley Pye, Ron Finn, Susan Heavey, Jason J. Pitt, Caroline M. Moore, Hayley C. Whitaker
Software Mentions: 7
Published: about 6 years ago

10.7554/eLife.56523

DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors
Cited by: 25
Author(s): Maria M. Mikedis, Yuting Fan, Peter K. Nicholls, Toshihiko Endo, Emily Jackson, Sarah A. Cobb, Dirk G. de Rooij, David C. Page
Software Mentions: 7
Published: about 6 years ago

10.3390/microorganisms8101528

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria
Cited by: 14
Author(s): Mathilde Lebas, Peggy Garault, Daniel Carrillo, Francisco M. Codoñer, Muriel Derrien
Software Mentions: 7
Published: almost 6 years ago

10.26508/lsa.202000897

Tissue-selective alternate promoters guide NLRP6 expression
Cited by: 1
Author(s): Nathan A. Bracey, Jaye M. Platnich, Arthur Lau, Hyunsoo Chung, M. Eric Hyndman, Justin A. MacDonald, Justin Chun, Paul L. Beck, Stephen E. Girardin, Paul M. Gordon, Daniel A. Muruve
Software Mentions: 7
Published: over 5 years ago

10.3389/fpls.2021.693039

Far-Red Light-Induced Azolla filiculoides Symbiosis Sexual Reproduction: Responsive Transcripts of Symbiont Nostoc azollae Encode Transporters Whilst Those of the Fern Relate to the Angiosperm Floral Transition
Cited by: 5
Author(s): Laura W. Dijkhuizen, Badraldin Ebrahim Sayed Tabatabaei, Paul Brouwer, Niels Rijken, Valerie A. Buijs, Erbil Güngör, Henriette Schluepmann
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.52511

ERK3/MAPK6 controls IL-8 production and chemotaxis
Cited by: 23
Author(s): Katarzyna Bogucka, Malvika Pompaiah, Fédérico Marini, Harald Binder, Gregory S. Harms, Manuel Kaulich, Matthias Klein, Christian Michel, Markus P. Radsak, Sebastian Rosigkeit, Peter Grimminger, Hansjörg Schild, Krishnaraj Rajalingam
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0240512

Bone biodeterioration—The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community
Cited by: 19
Author(s): Anne Eriksen, Tue Kjærgaard Nielsen, Henning Matthiesen, Christian Carøe, Lars Hestbjerg Hansen, David Gregory, Gordon Turner‐Walker, Matthew J. Collins, M. Thomas P. Gilbert
Software Mentions: 7
Published: almost 6 years ago

10.26508/lsa.202101080

Glucocorticoid signaling induces transcriptional memory and universally reversible chromatin changes
Cited by: 9
Author(s): Melissa Bothe, René Buschow, Sebastiaan H. Meijsing
Software Mentions: 7
Published: about 5 years ago

10.1002/glia.23767

Transcriptional profiling of microglia; current state of the art and future perspectives
Cited by: 72
Author(s): Emma Gerrits, Yang Heng, Erik Boddeke, Bart J. L. Eggen
Software Mentions: 7
Published: almost 7 years ago

10.1111/pbi.13205

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass
Cited by: 45
Author(s): Linkai Huang, Guangyan Feng, Haidong Yan, Zhongren Zhang, B. Shaun Bushman, Jianping Wang, Aureliano Bombarely, Mingzhou Li, Zhongfu Yang, Gang Nie, Wengang Xie, Lei Xu, Peilin Chen, Xinxin Zhao, Wenkai Jiang, Xinquan Zhang
Software Mentions: 7
Published: about 7 years ago

10.1016/j.celrep.2019.12.057

Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells
Cited by: 118
Author(s): James Rhodes, Angelika Feldmann, Benjamín Hernández-Rodríguez, Noèlia Díaz, Jill M. Brown, Nadezda A. Fursova, Neil P. Blackledge, Praveen Prathapan, Paula Dobrinić, Miles K. Huseyin, Aleksander Szczurek, Kai Kruse, K Nasmyth, Veronica J. Buckle, Juan M. Vaquerizas, Robert J. Klose
Software Mentions: 7
Published: over 6 years ago

10.3389/fimmu.2021.568729

Evolution and Expression of the Immune System of a Facultatively Anadromous Salmonid
Cited by: 7
Author(s): Thomas J. Colgan, Peter Moran, Louise C. Archer, Robert Wynne, Stephen A. Hutton, Philip McGinnity, Thomas E. Reed
Software Mentions: 7
Published: over 5 years ago

10.1093/gigascience/gix129

Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags
Cited by: 15
Author(s): Xianfeng Chen, Stephen Johnson, Patricio Jeraldo, Junwen Wang, Nicholas Chia, Jean Pierre A. Kocher, Jun Chen
Software Mentions: 7
Published: almost 9 years ago

10.1038/s41598-018-29373-y

Experimentally induced metamorphosis in highly regenerative axolotl (ambystoma mexicanum) under constant diet restructures microbiota
Cited by: 25
Author(s): Turan Demircan, Guvanch Ovezmyradov, Berna Yıldırım, İlknur Keskin, Ayşe Elif İlhan, Ece Cana Fesçioğlu, Gürkan Öztürk, Süleyman Yıldırım
Software Mentions: 7
Published: about 8 years ago

10.3389/fmolb.2020.565530

Cross-Sectional Transcriptional Analysis of the Aging Murine Heart
Cited by: 4
Author(s): Matthew Greenig, Andrew Melville, Derek Huntley, Mark Isalan, Michał Mielcarek
Software Mentions: 7
Published: almost 6 years ago

10.3389/fcell.2021.702046

Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast
Cited by: 17
Author(s): Robert Morey, Omar Farah, Sampada Kallol, Daniela F. Requena, Morgan Meads, Matteo Moretto-Zita, Francesca Soncin, Louise C. Laurent, Mana M. Parast
Software Mentions: 7
Published: about 5 years ago

10.1093/gigascience/giaa068

Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution
Cited by: 8
Author(s): Michael Kluge, Marie-Sophie Friedl, Amrei L Menzel, Caroline C. Friedel
Software Mentions: 7
Published: over 6 years ago

10.1186/s13007-021-00791-w

Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture
Cited by: 3
Author(s): Amir Mahboubi, Nicolas Delhomme, Sara Lea Häggström, Johannes Hanson
Software Mentions: 7
Published: about 5 years ago

10.1016/j.devcel.2017.07.002

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription
Cited by: 59
Author(s): Alper Akay, Tomás Di Domenico, Kin Man Suen, Amena Nabih, Guillermo E. Parada, Mark Larance, Ragini Medhi, Ahmet C. Berkyurek, Xinlian Zhang, Christopher J. Wedeles, Konrad L. M. Rudolph, Jan Engelhardt, Martin Hemberg, Ping Ma, Angus I. Lamond, Julie M. Claycomb, Eric A. Miska
Software Mentions: 7
Published: about 9 years ago

10.1080/19490976.2021.1927634

Influence of pig farming on human Gut Microbiota: role of airborne microbial communities
Cited by: 5
Author(s): Julia Moor, Tsering Wüthrich, Suzanne Aebi, Nadezda Mostacci, Gudrun Overesch, Anne Oppliger, Markus Hilty
Software Mentions: 7
Published: over 5 years ago

10.1128/mSystems.00280-19

Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition
Cited by: 7
Author(s): Shen Jean Lim, Louie C. Alexander, Annette Summers Engel, Audrey Paterson, Laurie C. Anderson, Barbara J. Campbell
Software Mentions: 7
Published: about 7 years ago

10.3389/fmicb.2017.02624

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica
Cited by: 15
Author(s): Juan G. Abarca, Ibrahim Zuñiga, Gilmary Ortiz-Morales, Armando Lugo, Mariel Viquez-Cervilla, Natalia Rodríguez-Hernández, Frances Vázquez-Sánchez, Catalina Murillo‐Cruz, Ernesto A. Torres-Rivera, Adrián A. Pinto‐Tomás, Filipa Godoy-Vitorino
Software Mentions: 7
Published: over 8 years ago

10.3389/fcell.2021.659294

Ubiquitin Modification Patterns of Clear Cell Renal Cell Carcinoma and the Ubiquitin Score to Aid Immunotherapy and Targeted Therapy
Cited by: 5
Author(s): Peng Zhou, Yuchao Lu, Xiufen Yang, Jin‐Zhou Xu, Chen‐Qian Liu, Qi‐Dong Xia, Junlin Lu, Shaogang Wang, Jia Hu
Software Mentions: 7
Published: over 5 years ago

10.1002/mc.23147

Loss of myeloid‐specific lamin A/C drives lung metastasis through Gfi‐1 and C/EBPε‐mediated granulocytic differentiation
Cited by: 3
Author(s): Hiroki Ishii, Woo‐Yong Park, Jae-Young So, Skyler Kuhn, Vishal N. Kopardé, Yanli Pang, Tim F. Greten, M. Christine Hollander, Li Yang
Software Mentions: 7
Published: over 6 years ago

10.1016/j.molcel.2020.01.007

Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation
Cited by: 74
Author(s): Alex Tuck, Aneliya Rankova, Alaaddin Bulak Arpat, Luz Angélica Liechti, Daniel Heß, Vytautas Iešmantavičius, Violeta Castelo-Szekely, David Gatfield, Marc Bühler
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-020-77727-2

Gene expression in diapausing rotifer eggs in response to divergent environmental predictability regimes
Cited by: 21
Author(s): Eva Tarazona, José Ignacio Lucas-Lledó, Marı́a José Carmona, Eduardo M. García‐Roger
Software Mentions: 7
Published: almost 6 years ago

10.3389/fmicb.2019.00675

Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study
Cited by: 29
Author(s): Jordan Espenshade, Sofie Thijs, S.W. Gawroński, Hannelore Bové, Nele Weyens, Jaco Vangronsveld
Software Mentions: 7
Published: over 7 years ago

10.3389/fimmu.2020.588411

Distinctive Cellular and Metabolic Reprogramming in Porcine Lung Mononuclear Phagocytes Infected With Type 1 PRRSV Strains
Cited by: 6
Author(s): Elisa Crisci, Marco Moroldo, Thien‐Phong Vu Manh, Ammara Mohammad, Laurent Jourdren, Céline Urien, Edwige Bouguyon, Elise Bordet, Claudia Bevilacqua, Mickaël Bourge, Jérémy Pezant, Alexis Pléau, Olivier Boulesteix, Isabelle Schwartz, Nicolas Bertho, Elisabetta Giuffra
Software Mentions: 7
Published: almost 6 years ago

10.3389/fimmu.2021.651475

Novel Insights Into Rheumatoid Arthritis Through Characterization of Concordant Changes in DNA Methylation and Gene Expression in Synovial Biopsies of Patients With Differing Numbers of Swollen Joints
Cited by: 5
Author(s): Andrew Y. Li Yim, Enrico Ferrero, Klio Maratou, Huw D. Lewis, George C. Royal, David F. Tough, Chris Larminie, Marcel M.A.M. Mannens, Peter Henneman, Wouter J. de Jonge, Marleen G H van de Sande, Daniëlle M. Gerlag, Rab K. Prinjha, Paul P. Tak
Software Mentions: 7
Published: over 5 years ago

10.3389/fimmu.2020.596514

Intestinal Transcriptome Analysis Reveals Soy Derivative-Linked Changes in Atlantic Salmon
Cited by: 26
Author(s): Viswanath Kiron, Youngjin Park, Prabhugouda Siriyappagouder, Dalia Dahle, Ghana Kalerammana Vasanth, Jorge Dias, Jorge M. O. Fernandes, Mette Sørensen, Viviane Verlhac Trichet
Software Mentions: 7
Published: almost 6 years ago

10.1038/srep45369

Soil classification predicts differences in prokaryotic communities across a range of geographically distant soils once pH is accounted for
Cited by: 12
Author(s): Rachel Kaminsky, Blandine Trouche, Sergio E. Morales
Software Mentions: 7
Published: over 9 years ago

10.3389/fimmu.2020.578505

Preparing for Life: Plasma Proteome Changes and Immune System Development During the First Week of Human Life
Cited by: 18
Author(s): Tue Bjerg Bennike, Benoit Fatou, Asimenia Angelidou, Joann Diray‐Arce, Reza Falsafi, Rebecca Ford, Erin E. Gill, Simon D. van Haren, Olubukola T. Idoko, Ahwon Lee, Rym Ben‐Othman, William Pomat, Casey P. Shannon, Kinga K. Smolen, Scott J. Tebbutt, Al Ozonoff, Peter Richmond, Anita H. J. van den Biggelaar, Robert E. W. Hancock, Beate Kampmann, Tobias R. Kollmann, Ofer Levy, Hanno Steen
Software Mentions: 7
Published: almost 6 years ago

10.3390/plants9121700

Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots
Cited by: 8
Author(s): Evgeny A. Zorin, Alexey М. Afonin, Olga A. Kulaeva, Emma S. Gribchenko, O. Y. Shtark, Vladimir A. Zhukov
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-020-70967-2

Transcriptomics uncovers substantial variability associated with alterations in manufacturing processes of macrophage cell therapy products
Cited by: 14
Author(s): Olga L. Gurvich, Katja A. Puttonen, Aubrey Bailey, Anssi Kailaanmäki, Vita Skirdenko, Minna Sivonen, Sanna Pietikäinen, Nigel R. Parker, Seppo Ylä‐Herttuala, Tuija Kekarainen
Software Mentions: 7
Published: about 6 years ago

10.3389/fimmu.2020.580373

Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults
Cited by: 13
Author(s): Rym Ben‐Othman, Bing Cai, Aaron C. Liu, Natallia Varankovich, Daniel He, Travis M. Blimkie, Ahwon Lee, Erin E. Gill, M. A. Novotny, Brian D. Aevermann, Sibyl Drissler, Casey P. Shannon, Sarah McCann, Kim Marty, Gordean Bjornson, Rachel D. Edgar, David Lin, Nicole Gladish, Julia L. Maclsaac, Nelly Amenyogbe, Queenie Chan, Alba Llibre, Collin Joyce, Elise Landais, Khoa Le, Samantha M. Reiss, Wayne C. Koff, Colin Havenar-Daughton, Manraj K.S. Heran, Bippan S. Sangha, David R. Walt, Mel Krajden, Shane Crotty, Devin Sok, Bryan Briney, Dennis R. Burton, Darragh Duffy, Leonard J. Foster, William W. Mohn, Michael S. Kobor, Scott J. Tebbutt, Ryan R. Brinkman, Richard H. Scheuermann, Robert E. W. Hancock, Tobias R. Kollmann, Manish Sadarangani
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-017-05927-4

Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity
Cited by: 35
Author(s): Handan Melike Dönertaş, Hamit İzgi, Altuğ Kamacıoğlu, Zhisong He, Philipp Khaitovich, Mehmet Somel
Software Mentions: 7
Published: about 9 years ago

10.3389/fmolb.2020.598583

SARS-CoV-2 Proteins Exploit Host’s Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways
Cited by: 29
Author(s): A. A. Khan, Abul B.M.M.K. Islam
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-018-26930-3

Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period
Cited by: 64
Author(s): Shebl E. Salem, Thomas W. Maddox, Adam Berg, Philipp Antczak, Julian M. Ketley, Nicola Williams, Debra Archer
Software Mentions: 7
Published: over 8 years ago

10.1371/journal.pone.0245626

Diversity of microbial communities and soil nutrients in sugarcane rhizosphere soil under water soluble fertilizer
Cited by: 20
Author(s): Huan Niu, Ziqin Pang, Nyumah Fallah, Yongmei Zhou, Caifang Zhang, Chaohua Hu, Wenxiong Lin, Zhaonian Yuan
Software Mentions: 7
Published: over 5 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: about 9 years ago

10.3390/life10090185

An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists
Cited by: 3
Author(s): Hamza Mbareche, Nathan Dumont-Leblond, Guillaume J. Bilodeau, Caroline Duchaine
Software Mentions: 7
Published: about 6 years ago

10.7717/peerj.2888

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
Cited by: 67
Author(s): Xun Zhu, Travers Ching, Xinghua Pan, Sherman M. Weissman, Lana X. Garmire
Software Mentions: 7
Published: over 9 years ago

10.1186/s12864-021-07489-2

Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture
Cited by: 5
Author(s): Alex Rajewski, Derreck Carter-House, Jason E. Stajich, Amy Litt
Software Mentions: 7
Published: over 5 years ago

10.1080/19490976.2020.1840764

Dynamics of the bacterial gut microbiota during controlled human infection with Necator americanus larvae
Cited by: 6
Author(s): Quinten R Ducarmon, Marie-Astrid Hoogerwerf, Jacqueline J. Janse, A. R. Geelen, J. Koopman, Romy D. Zwittink, Jelle J. Goeman, Ed J. Kuijper, Meta Roestenberg
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-018-26592-1

Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan
Cited by: 13
Author(s): Radek Šindelka, Pavel Abaffy, Yanyan Qu, Silvie Tománková, Monika Šídová, Ravindra Naraine, Michal Kolář, Elizabeth H. Peuchen, Liangliang Sun, Norman J. Dovic̀hi, Mikael Kubista
Software Mentions: 7
Published: over 8 years ago

10.3389/fimmu.2020.609891

Targeted De-Methylation of the FOXP3-TSDR Is Sufficient to Induce Physiological FOXP3 Expression but Not a Functional Treg Phenotype
Cited by: 26
Author(s): Christopher Kressler, Gilles Gasparoni, Karl Nordström, Dania Hamo, Abdulrahman Salhab, Christoforos Dimitropoulos, Sascha Tierling, Petra Reinke, Hans‐Dieter Volk, Jörn Walter, Alf Hamann, Julia K. Polansky
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.3944

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits
Cited by: 24
Author(s): Ara S. Winter, Jennifer J.M. Hathaway, Jason C. Kimble, Debbie C. Buecher, Ernest W. Valdez, Andrea Porras-Alfaro, Jesse M. Young, Kaitlyn J. H. Read, Diana E. Northup
Software Mentions: 7
Published: almost 9 years ago

10.1016/j.molcel.2021.03.013

Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression
Cited by: 17
Author(s): Amy Tresenrider, Kaitlin Morse, Victoria Jorgensen, Minghao Chia, Hanna Liao, Folkert J. van Werven, Elçin Ünal
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-017-13397-x

The effect of insecticide synergist treatment on genome-wide gene expression in a polyphagous pest
Cited by: 28
Author(s): Simon Snoeck, Robert Greenhalgh, Luc Tirry, Richard M. Clark, Thomas Van Leeuwen, Wannes Dermauw
Software Mentions: 7
Published: almost 9 years ago

10.1038/s41598-017-13601-y

Gut microbiome alterations in Alzheimer’s disease
Cited by: 1,108
Author(s): N. Vogt, Robert L. Kerby, Kimberly A. Dill‐McFarland, Sandra Harding, Andrew P. Merluzzi, Sterling C. Johnson, Cynthia M. Carlsson, Sanjay Asthana, Henrik Zetterberg, Kaj Blennow, Barbara B. Bendlin, Federico E. Rey
Software Mentions: 7
Published: almost 9 years ago

10.1093/gigascience/giy167

SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis
Cited by: 2
Author(s): Samuel Blanck, Guillemette Marot
Software Mentions: 7
Published: over 7 years ago

10.7554/eLife.62800

Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum
Cited by: 18
Author(s): Kathryn H. Milne, Alasdair Ivens, Adam J. Reid, Magda E. Lotkowska, Áine O’Toole, Geetha Sankaranarayanan, Diana Muñoz Sandoval, Wiebke Nahrendorf, Clément Regnault, Nick J. Edwards, Sarah E. Silk, Ruth Payne, Angela M. Minassian, Navin Venkatraman, Mandy Sanders, Adrian V. S. Hill, Michael P. Barrett, Matthew Berriman, Simon J. Draper, J. Alexandra Rowe, Philip J. Spence
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2020.560336

Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses
Cited by: 15
Author(s): Matthew A. Campbell, Kliti Grice, Pieter T. Visscher, Therese Morris, Hon Lun Wong, Richard Allen White, Brendan P. Burns, Marco J. L. Coolen
Software Mentions: 7
Published: almost 6 years ago

10.1002/1878-0261.12923

Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases
Cited by: 8
Author(s): Tesa Severson, Yanyun Zhu, Angelo M. De Marzo, Tracy Jones, Jonathan W. Simons, William G. Nelson, Srinivasan Yegnasubramanian, Matthew L. Freedman, Lodewyk F.A. Wessels, Andries M. Bergman, Michael C. Haffner, Wilbert Zwart
Software Mentions: 7
Published: over 5 years ago

10.3390/jcm9061974

Dysregulation of microRNA Modulatory Network in Abdominal Aortic Aneurysm
Cited by: 13
Author(s): Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Łukasz Komsta, Przemysław Kołodziej, Paulina Chmiel, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki, Anna Bogucka‐Kocka
Software Mentions: 7
Published: about 6 years ago

10.3389/fpls.2016.01446

A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea
Cited by: 149
Author(s): Josh Clevenger, Ye Chu, Brian E. Scheffler, Peggy Ozias‐Akins
Software Mentions: 7
Published: almost 10 years ago

10.1111/gcb.15302

Stream microbial communities and ecosystem functioning show complex responses to multiple stressors in wastewater
Cited by: 44
Author(s): Francis J. Burdon, Yaohui Bai, Marta Reyes, Manu Tamminen, Philipp Staudacher, Simon Mangold, Heinz Singer, Katja Räsänen, Adriano Joss, Scott D. Tiegs, Jukka Jokela, Rik I.L. Eggen, Christian Stamm
Software Mentions: 7
Published: about 6 years ago

10.3389/fpls.2021.637115

The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype
Cited by: 9
Author(s): Tatiana Arias, Chad E. Niederhuth, Paula McSteen, J. Chris Pires
Software Mentions: 7
Published: over 5 years ago

10.1016/j.celrep.2020.107930

Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras
Cited by: 17
Author(s): Nele Merret Hollmann, Pravin Kumar Ankush Jagtap, Paweł Masiewicz, Tanit Guitart, Bernd Simon, Jan Provazník, Frank Stein, Per Haberkant, Lara Sweetapple, Laura Villacorta, Dylan Mooijman, Vladimı́r Beneš, Mikhail M. Savitski, Fátima Gebauer, Janosch Hennig
Software Mentions: 7
Published: about 6 years ago

10.3389/fpls.2021.661361

Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks
Cited by: 2
Author(s): Laura Serrano-Ron, Javier Cabrera, Pablo Pérez-García, Miguel A. Moreno-Risueño
Software Mentions: 7
Published: over 5 years ago

10.1242/dev.178590

Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan
Cited by: 13
Author(s): Julien Rougeot, Naomi D. Chrispijn, Marco Aben, Dei M. Elurbe, Karolina M. Andralojc, Patrick J. Murphy, Pascal W.T.C. Jansen, Michiel Vermeulen, Bradley R. Cairns, Leonie M. Kamminga
Software Mentions: 7
Published: over 7 years ago

10.3389/fpls.2021.684192

Agrobacterium VirE2 Protein Modulates Plant Gene Expression and Mediates Transformation From Its Location Outside the Nucleus
Cited by: 7
Author(s): Rachelle A. Lapham, Lan‐Ying Lee, Eder Xhako, Esteban Gañán Gómez, V. M. Nivya, Stanton B. Gelvin
Software Mentions: 7
Published: over 5 years ago

10.1016/j.ccell.2019.08.008

An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer
Cited by: 314
Author(s): Marian L. Burr, Christina E Sparbier, Kah Lok Chan, Yih-Chih Chan, Ariena Kersbergen, Enid Y.N. Lam, Elizabeth Azidis-Yates, Dane Vassiliadis, Charles C. Bell, Omer Gilan, Susan Jackson, Lavinia Tan, Stephen Q. Wong, Sebastian Hollizeck, Ewa M. Michalak, Hannah V. Siddle, Michael T. McCabe, Rab K. Prinjha, Glen R Guerra, Benjamin Solomon, Shahneen Sandhu, Sarah‐Jane Dawson, Paul A. Beavis, Richard W. Tothill, Carleen Cullinane, Paul J. Lehner, Kate D. Sutherland, Mark A. Dawson
Software Mentions: 7
Published: almost 7 years ago

10.5808/GI.2019.17.1.e6

Statistical Analysis of Metagenomics Data
Cited by: 147
Author(s): M. Luz Calle
Software Mentions: 7
Published: over 7 years ago

10.15252/embj.2020105565

The RNA polymerase II subunit RPB‐9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription
Cited by: 13
Author(s): Ahmet C. Berkyurek, Giulia Furlan, Lisa Lampersberger, Toni Beltran, Eva-Maria Weick, Emily Nischwitz, Isabela Cunha Navarro, Fabian Braukmann, Alper Akay, Jonathan Price, Falk Butter, Peter Sarkies, Eric A. Miska
Software Mentions: 7
Published: over 5 years ago

10.3390/cells10071576

Transcriptomic Profiling of Femoral Veins in Deep Vein Thrombosis in a Porcine Model
Cited by: 7
Author(s): Leszek Gromadziński, Łukasz Paukszto, Agnieszka Skowrońska, Piotr Holak, Michał Smoliński, Elżbieta Łopieńska–Biernat, Ewa Lepiarczyk, Aleksandra Lipka, J Jastrzebski, Marta Majewska
Software Mentions: 7
Published: about 5 years ago

10.3390/ijms22136726

Analysis of the Role of FRMD5 in the Biology of Papillary Thyroid Carcinoma
Cited by: 4
Author(s): Agata M. Gaweł, Maciej Ratajczak, Ewa Gajda, Małgorzata Grzanka, Agnieszka Paziewska, Marta Cieślicka, Maria Kulecka, Małgorzata Oczko-Wojciechowska, Marlena Godlewska
Software Mentions: 7
Published: about 5 years ago

10.1186/s13007-019-0440-x

Comparing time series transcriptome data between plants using a network module finding algorithm
Cited by: 6
Author(s): Jiyoung Lee, Lenwood S. Heath, Ruth Grene, Song Li
Software Mentions: 7
Published: over 7 years ago

10.3390/ijms221910451

Differentiation of the High Night Temperature Response in Leaf Segments of Rice Cultivars with Contrasting Tolerance
Cited by: 1
Author(s): Stephanie Schaarschmidt, Ulrike Glaubitz, Alexander Erban, Joachim Kopka, Ellen Zuther
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12864-016-3260-7

DeSigN: connecting gene expression with therapeutics for drug repurposing and development
Cited by: 52
Author(s): Bernard Kok Bang Lee, Kai Hung Tiong, Jit Kang Chang, Chee Sun Liew, Zainal Ariff Abdul Rahman, Aik Choon Tan, Tsung Fei Khang, Sok Ching Cheong
Software Mentions: 7
Published: over 9 years ago

10.1186/s13073-020-00788-5

Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation
Cited by: 10
Author(s): Shi Yang Liu, Nathan Harmston, Trudy Lee Glaser, Yunka Wong, Zheng Zhong, Babita Madan, David M. Virshup, Enrico Petretto
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0227289

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach
Cited by: 27
Author(s): Aashish R. Jha, Justin Shmalberg, Jirayu Tanprasertsuk, Lee Ann M. Perry, Dan Massey, Ryan W. Honaker
Software Mentions: 7
Published: over 6 years ago

10.3389/fpls.2019.01405

Fungicides and the Grapevine Wood Mycobiome: A Case Study on Tracheomycotic Ascomycete Phaeomoniella chlamydospora Reveals Potential for Two Novel Control Strategies
Cited by: 16
Author(s): Giovanni Del Frari, Alex Gobbi, Marie Rønne Aggerbeck, Helena Oliveira, Lars Hestbjerg Hansen, Ricardo B. Ferreira
Software Mentions: 7
Published: almost 7 years ago

10.1016/j.molcel.2019.01.017

System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection
Cited by: 122
Author(s): Manuel García-Moreno, Marko Noerenberg, Shuai Ni, Aino I Järvelin, Esther González-Almela, Caroline E. Lenz, Marcel Bach-Pagés, Victoria Cox, Rosario Avolio, Thomas W. Davis, Svenja Hester, Thibault J.M. Sohier, Bingnan Li, Gregory Heikel, Gracjan Michlewski, Miguel Á. Sanz, Luís Carrasco, Emiliano P. Ricci, Vicent Pelechano, Ilan Davis, Bernd Fischer, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 7
Published: over 7 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

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Papers Mentioning DESeq2 9,583