Ecosyste.ms: Papers

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

10.12688/f1000research.15398.3

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Cited by: 53
Author(s): Michael I. Love, Charlotte Soneson, Rob Patro
Software Mentions: 16
Published: about 6 years ago

10.12688/f1000research.8900.2

DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics
Cited by: 105
Author(s): Małgorzata Nowicka, Mark D. Robinson
Software Mentions: 14
Published: almost 8 years ago

10.1186/s13059-020-02151-8

Alignment and mapping methodology influence transcript abundance estimation
Cited by: 80
Author(s): Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Software Mentions: 13
Published: about 4 years ago

10.1371/journal.pone.0190152

RNA-Seq differential expression analysis: An extended review and a software tool
Cited by: 389
Author(s): Juliana Costa-Silva, Douglas Silva Domingues, Fabrício Martins Lopes
Software Mentions: 12
Published: almost 7 years ago

10.1186/s12859-020-03846-2

ARPIR: automatic RNA-Seq pipelines with interactive report
Cited by: 10
Author(s): Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini, Maria Paola Martelli
Software Mentions: 11
Published: almost 4 years ago

10.1186/s13073-020-0710-2

Interactions between the gut microbiome and host gene regulation in cystic fibrosis
Cited by: 65
Author(s): Gargi Dayama, Sambhawa Priya, David Niccum, Alexander Khoruts, Ran Blekhman
Software Mentions: 10
Published: almost 5 years ago

10.1186/s13059-021-02360-9

Role of epigenetics in unicellular to multicellular transition in Dictyostelium
Cited by: 8
Author(s): Simon Yuan Wang, Elizabeth A. Pollina, I‐Hao Wang, Lindsay K. Pino, Henry L. Bushnell, Ken Takashima, Colette Fritsche, George Sabin, Benjamin A. Garcia, Paul L. Greer, Eric Lieberman Greer
Software Mentions: 10
Published: over 3 years ago

10.1186/s13059-021-02337-8

Best practices on the differential expression analysis of multi-species RNA-seq
Cited by: 36
Author(s): Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo, José F. Muñoz, Jonathan Livny, Amol Shetty, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 10
Published: over 3 years ago

10.1534/g3.120.401436

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat
Cited by: 18
Author(s): Sophie A Harrington, Anna E Backhaus, Ajit Singh, Keywan Hassani‐Pak, Cristóbal Uauy
Software Mentions: 9
Published: about 4 years ago

10.1186/s12859-019-2852-z

Differential analysis of combinatorial protein complexes with CompleXChange
Cited by: 4
Author(s): Thorsten Will, Volkhard Helms
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pcbi.1006792

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis
Cited by: 25
Author(s): Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison J. Miller, Anne Fennell, Qin Ma
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-019-41315-w

Novel Data Transformations for RNA-seq Differential Expression Analysis
Cited by: 23
Author(s): Zeyu Zhang, Danyang Yu, Minseok Seo, Craig P. Hersh, Scott T. Weiss, Weiliang Qiu
Software Mentions: 6
Published: over 5 years ago

10.1093/dnares/dsz015

Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning model
Cited by: 8
Author(s): Antônio Pedro Camargo, Thiago S. Nakahara, Luiz E R Firmino, Paulo H.M. Netto, João Batista Plácido do Nascimento, Elisa Donnard, Pedro A. F. Galante, Marcelo Falsarella Carazzolle, Bettina Malnic, Fábio Papes
Software Mentions: 6
Published: over 5 years ago

10.1038/s42003-020-0916-2

Tankyrase inhibition sensitizes melanoma to PD-1 immune checkpoint blockade in syngeneic mouse models
Cited by: 23
Author(s): Jo Waaler, Line Mygland, Anders Aune Tveita, Martin Frank Strand, Nina Solberg, Petter Olsen, Aleksandra Aizenshtadt, Marte Fauskanger, Kaja Lund, Jo Waaler, Max Lycke, Elisabeth Dybing, Vegard Nygaard, Sigurd Leinæs Bøe, Karen‐Marie Heintz, Eivind Hovig, Clara Hammarström, Alexandre Corthay, Stefan Krauß
Software Mentions: 6
Published: over 4 years ago

10.1186/s12859-016-1195-2

A fuzzy method for RNA-Seq differential expression analysis in presence of multireads
Cited by: 16
Author(s): Arianna Consiglio, Corrado Mencar, Giorgio Grillo, Flaviana Marzano, Mariano Francesco Caratozzolo, Sabino Liuni
Software Mentions: 6
Published: about 8 years ago

10.1186/s13059-018-1419-z

Gene-level differential analysis at transcript-level resolution
Cited by: 97
Author(s): Lynn Yi, Harold Pimentel, Nicolas Bray, Lior Pachter
Software Mentions: 6
Published: over 6 years ago

10.1093/jxb/erz546

Transcriptional and biochemical analyses of gibberellin expression and content in germinated barley grain
Cited by: 16
Author(s): Natalie S. Betts, Christoph Dockter, Oliver Berkowitz, Helen Collins, Michelle Hooi, Qiongxian Lu, Rachel A. Burton, Vincent Bulone, Birgitte Skadhauge, James Whelan, Geoffrey B. Fincher
Software Mentions: 5
Published: almost 5 years ago

10.12688/wellcomeopenres.14735.2

Mapping targets for small nucleolar RNAs in yeast
Cited by: 16
Author(s): Tatiana Dudnakova, Hywel Dunn-Davies, Rosie Peters, David Tollervey
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pgen.1006619

Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum
Cited by: 46
Author(s): Yi Jin Liew, Yong Li, Sebastian Baumgarten, Christian R. Voolstra, Manuel Aranda
Software Mentions: 5
Published: over 7 years ago

10.1016/j.devcel.2018.10.004

SETDB1 Links the Meiotic DNA Damage Response to Sex Chromosome Silencing in Mice
Cited by: 60
Author(s): Takayuki Hirota, Paul Blakeley, Mahesh N. Sangrithi, Shantha K. Mahadevaiah, Vesela Encheva, Ambrosius P. Snijders, Elias ElInati, Obah A. Ojarikre, Dirk G. de Rooij, Kathy K. Niakan, James M. A. Turner
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.39188

Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury
Cited by: 27
Author(s): Jordan W. Squair, Seth Tigchelaar, Kyung‐Mee Moon, Jie Liu, Wolfram Tetzlaff, Brian K. Kwon, Andrei V. Krassioukov, Christopher R. West, Leonard J. Foster, Michael A. Skinnider
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.66904

Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology
Cited by: 14
Author(s): Markus Terrey, Scott I. Adamson, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 5
Published: over 3 years ago

10.18632/oncotarget.25330

Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma
Cited by: 14
Author(s): Michael Hamilton, Thomas Girke, Ernest Martinez
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.62731

GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis
Cited by: 22
Author(s): Markus Terrey, Scott I. Adamson, Alana L. Gibson, Tianda Deng, Ryuta Ishimura, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-020-3484-z

Short paired-end reads trump long single-end reads for expression analysis
Cited by: 13
Author(s): Adam H. Freedman, John Gaspar, Timothy B. Sackton
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pgen.1008189

Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia
Cited by: 66
Author(s): Guoxin Cui, Yi Jin Liew, Yong Li, Najeh M. Kharbatia, Noura Ibrahim Omar Zahran, Abdul‐Hamid Emwas, Vı́ctor M. Eguı́luz, Manuel Aranda
Software Mentions: 4
Published: over 5 years ago

10.1093/jxb/erw105

The<i>Cer-cqu</i>gene cluster determines three key players in a β-diketone synthase polyketide pathway synthesizing aliphatics in epicuticular waxes
Cited by: 80
Author(s): Lizette M. Schneider, Nikolai M Adamski, Claus Bo Vöge Christensen, David Stuart, Sonia Vautrin, Mats Hansson, Cristóbal Uauy, Penny von Wettstein-Knowles
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-019-5579-3

Gene expression profiles at different stages for formation of pearl sac and pearl in the pearl oyster Pinctada fucata
Cited by: 15
Author(s): . Mariom, Saori Take, Yoji Igarashi, Kazutoshi Yoshitake, Shuichi Asakawa, Kaoru Maeyama, Kiyohito Nagai, Shugo Watabe, Shigeharu Kinoshita
Software Mentions: 3
Published: over 5 years ago

10.1128/mSphere.00129-19

Combined Transcriptome and Proteome Analysis of Immortalized Human Keratinocytes Expressing Human Papillomavirus 16 (HPV16) Oncogenes Reveals Novel Key Factors and Networks in HPV-Induced Carcinogenesis
Cited by: 21
Author(s): Ruwen Yang, Jana Klimentová, Elke Göckel-Krzikalla, Regina Ly, Nadine Gmelin, Agnes Hotz‐Wagenblatt, Helena Řehulková, Jiřı́ Stulı́k, Frank Rösl, Martina Niebler
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pbio.2002399

Hippo signaling controls cell cycle and restricts cell plasticity in planarians
Cited by: 31
Author(s): Nídia de Sousa, Gustavo Rodríguez-Esteban, José Ignacio Rojo-Laguna, Emili Saló, Teresa Adell
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms21197404

Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana
Cited by: 5
Author(s): Yanqiao Zhu, Oliver Berkowitz, Jennifer Selinski, Andreas Hartmann, Reena Narsai, Yan Wang, Peisheng Mao, James Whelan
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms22094449

Transcriptome Analysis of Seed Weight Plasticity in Brassica napus
Cited by: 5
Author(s): Javier Canales, José Verdejo, Gabriela Carrasco‐Puga, Francisca M. Castillo, Anita Arenas‐M, Daniel F. Calderini
Software Mentions: 3
Published: over 3 years ago

10.1186/s13068-021-01946-6

Transcriptome analysis revealed the regulation of gibberellin and the establishment of photosynthetic system promote rapid seed germination and early growth of seedling in pearl millet
Cited by: 6
Author(s): Bingchao Wu, Min Sun, Huan Zhang, Dan Yang, Chuang Lin, İmran Khan, Xiaoshan Wang, Xinquan Zhang, Gang Nie, Guangyan Feng, Yanhong Yan, Li Zhou, Yan Peng, Linkai Huang
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2019.01027

Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production
Cited by: 20
Author(s): Chee Kent Lim, Juan C. Villada, Annie Chalifour, Maria F. Duran, Hsu Feng Lu, Patrick K. H. Lee
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2021.632512

Enhanced Glycolysis Is Required for Antileishmanial Functions of Neutrophils Upon Infection With Leishmania donovani
Cited by: 12
Author(s): Mareike Ohms, Carolina Ferreira, Hauke Busch, Inken Wohlers, Ana Cristina Guerra Souza, Ricardo Silvestre, Tamás Laskay
Software Mentions: 3
Published: over 3 years ago

10.1186/s12870-020-02590-2

Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum
Cited by: 11
Author(s): Javier Canales, Felipe Uribe, Carlos Henríquez-Valencia, Carlos Lovazzano, Joaquı́n Medina, Elena A. Vidal
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0244025

Coronavirus genomes carry the signatures of their habitats
Cited by: 21
Author(s): Yulong Wei, Jordan R. Silke, Parisa Aris, Xuhua Xia
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2020.568630

IL-12-Induced Immune Suppressive Deficit During CD8+ T-Cell Differentiation
Cited by: 5
Author(s): Pranav S Renavikar, Sushmita Sinha, Ashley A. Brate, Nicholas Borcherding, Michael P. Crawford, Scott Steward-Tharp, Nitin J. Karandikar
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2019.01514

Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway
Cited by: 8
Author(s): Anne Catherine Ahn, L. Cavalca, Monica Colombo, J. Merijn Schuurmans, Dimitry Y. Sorokin, Gerard Muyzer
Software Mentions: 2
Published: over 5 years ago

10.1186/s13567-021-00914-0

A broadly neutralizing monoclonal antibody induces broad protection against heterogeneous PRRSV strains in piglets
Cited by: 7
Author(s): Zhigang Zhang, Tianshu Zhai, Mingshuo Li, Kun Zhang, Jingrui Li, Zheng Xu, Chaonan Tian, Chen Rui, Jianhui Dong, En‐Min Zhou, Yuchen Nan, Chunyan Wu
Software Mentions: 2
Published: over 3 years ago

10.1111/gbb.12721

Combined change of behavioral traits for domestication and <scp>gene‐networks</scp> in mice selectively bred for active tameness
Cited by: 5
Author(s): Yuki Matsumoto, Hiromichi Nagayama, Hirofumi Nakaoka, Atsushi Toyoda, Tatsuhiko Goto, Tsuyoshi Koide
Software Mentions: 2
Published: almost 4 years ago

10.3390/biom10060929

Genome-Wide Identification of RNA Silencing-Related Genes and Their Expressional Analysis in Response to Heat Stress in Barley (Hordeum vulgare L.)
Cited by: 10
Author(s): Éva Hamar, Henrik Mihály Szaker, András Kis, Ágnes Dalmadi, Fabio Miloro, György Szittya, János Taller, Péter Gyula, Tibor Csorba
Software Mentions: 2
Published: over 4 years ago

10.1038/s41597-019-0094-6

Long non-coding and coding RNA profiling using strand-specific RNA-seq in human hypertrophic cardiomyopathy
Cited by: 44
Author(s): Xuanyu Liu, Yi Ma, Kunlun Yin, Wenke Li, Wen Chen, Yujing Zhang, Changsheng Zhu, Tianjiao Li, Bianmei Han, Xuewen Li, Shuiyun Wang, Zhou Zhou
Software Mentions: 2
Published: over 5 years ago

10.1038/s41597-020-0541-4

RNA sequencing analysis of the human retina and associated ocular tissues
Cited by: 8
Author(s): Scott Schumacker, Krista R Coppage, Ray A. Enke
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-016-1357-2

The Lair: a resource for exploratory analysis of published RNA-Seq data
Cited by: 14
Author(s): Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted, Lior Pachter
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13395-019-0203-4

Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation
Cited by: 70
Author(s): Lance T. Denes, Lance A. Riley, Joseph R. Mijares, J. D. Arboleda, Kendra K. McKee, Karyn A. Esser, Eric T. Wang
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.01202-20

Molecular and Physiological Adaptations to Low Temperature in <i>Thioalkalivibrio</i> Strains Isolated from Soda Lakes with Different Temperature Regimes
Cited by: 2
Author(s): Anne-Catherine Ahn, Evelien Jongepier, J. Merijn Schuurmans, W. Irene C. Rijpstra, Jaap S. Sinninghe Damsté, Erwin A. Galinski, Pawel Roman, Dimitry Y. Sorokin, Gerard Muyzer
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers13153897

The Most Common VHL Point Mutation R167Q in Hereditary VHL Disease Interferes with Cell Plasticity Regulation
Cited by: 1
Author(s): Stéphanie Buart, Stéphane Terry, M’Boyba Diop, Philippe Dessen, Sophie Couvé, Abdérémane Abdou, Julien Adam, Jérôme Thiery, Pierre Savagner, Salem Chouaı̈b
Software Mentions: 2
Published: over 3 years ago

10.1007/s00018-020-03750-1

HIF1α is a direct regulator of steroidogenesis in the adrenal gland
Cited by: 13
Author(s): Deepika Watts, Johanna Stein, Ana Meneses, Nicole Bechmann, Aleš Neuwirth, Denise Kaden, Anja Krüger, Anupam Sinha, Vasileia Ismini Alexaki, Luis Gustavo Pérez-Rivas, Stefan Kircher, Antoine Martinez, Marily Theodoropoulou, Graeme Eisenhofer, Mirko Peitzsch, Ali El‐Armouche, Triantafyllos Chavakis, Ben Wielockx
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0175744

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways
Cited by: 8
Author(s): Lynn Yi, Harold Pimentel, Lior Pachter
Software Mentions: 2
Published: over 7 years ago

10.1186/s12870-018-1241-5

Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat
Cited by: 26
Author(s): Jemima Brinton, James Simmonds, Cristóbal Uauy
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12870-019-2158-3

Direct comparison of Arabidopsis gene expression reveals different responses to melatonin versus auxin
Cited by: 31
Author(s): Sajal F. Zia, Oliver Berkowitz, Frank Bedon, James Whelan, Ashley E. Franks, Kim M. Plummer
Software Mentions: 1
Published: almost 5 years ago

10.3389/fcimb.2020.00437

Transcriptional Analyses Identify Genes That Modulate Bovine Macrophage Response to Toxoplasma Infection and Immune Stimulation
Cited by: 5
Author(s): Anton Gossner, Musa A. Hassan
Software Mentions: 1
Published: over 4 years ago

10.3389/fpls.2018.01830

Knock-Down of the Phosphoserine Phosphatase Gene Effects Rather N- Than S-Metabolism in Arabidopsis thaliana
Cited by: 10
Author(s): Sladjana Samuilov, Nadine Rademacher, Dominik Brilhaus, Samantha Flachbart, Leila Arab, Stanislav Kopriva, Andreas P.M. Weber, Tabea Mettler‐Altmann, Heinz Rennenberg
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-018-24290-6

Low-level mitochondrial heteroplasmy modulates DNA replication, glucose metabolism and lifespan in mice
Cited by: 25
Author(s): Misa Hirose, Paul Schilf, Yask Gupta, Kim Zarse, Axel Künstner, Anke Fähnrich, Hauke Busch, Youlun Ju, Marvin N. Wright, Andreas Ziegler, Marie Vallier, Meriem Belheouane, John F. Baines, Diethard Tautz, Kornelia Johann, Rebecca Oelkrug, Jens Mittag, Hendrik Lehnert, Alaa Othman, Olaf Jöhren, Markus Schwaninger, Cornelia Prehn, Jerzy Adamski, Kensuke Shima, Jan Rupp, Robert Häsler, Georg Fuellen, Rüdiger Köhling, Michael Ristow, Saleh M. Ibrahim
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2018.01709

The Photorespiratory BOU Gene Mutation Alters Sulfur Assimilation and Its Crosstalk With Carbon and Nitrogen Metabolism in Arabidopsis thaliana
Cited by: 20
Author(s): Sladjana Samuilov, Dominik Brilhaus, Nadine Rademacher, Samantha Flachbart, Leila Arab, Saleh Alfarraj, Franziska Kuhnert, Stanislav Kopriva, Andreas P.M. Weber, Tabea Mettler‐Altmann, Heinz Rennenberg
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms22179378

Reconnoitering the Role of Long-Noncoding RNAs in Hypertrophic Cardiomyopathy: A Descriptive Review
Cited by: 7
Author(s): Syeda Kiran Shahzadi, Nerissa Naidoo, Alawi A. Alsheikh‐Ali, Manfredi Rizzo, Ali A. Rizvi, Raul D. Santos, Yajnavalka Banerjee
Software Mentions: 1
Published: about 3 years ago

10.1093/genetics/iyaa020

Characterizing the genetic basis of copper toxicity in <i>Drosophila</i> reveals a complex pattern of allelic, regulatory, and behavioral variation
Cited by: 11
Author(s): Elizabeth R. Everman, Kristen M Cloud-Richardson, Stuart J. Macdonald
Software Mentions: 1
Published: almost 4 years ago