Ecosyste.ms: Papers

10.7554/eLife.69431

Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2
Cited by: 18
Author(s): Elektra Kantzari Robinson, Pratibha Jagannatha, Sergio Covarrubias, Matthew Cattle, Valeriya Smaliy, Rojin Safavi, Barbara Shapleigh, Robin Abu-Shumays, Miten Jain, Suzanne M. Cloonan, Mark Akeson, Angela N. Brooks
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.52690

Sphingosine 1-phosphate-regulated transcriptomes in heterogenous arterial and lymphatic endothelium of the aorta
Cited by: 28
Author(s): Eric Engelbrecht, Michel V. Levesque, Liqun He, Michael Vanlandewijck, Anja Nitzsche, Hira Niazi, Andrew Kuo, Sasha A Singh, Masamichi Aikawa, Kristina M. Holton, Richard L. Proia, Mari Kono, William T. Pu, Eric Camerer, Christer Betsholtz, Timothy Hla
Software Mentions: 8
Published: over 4 years ago

10.1093/gigascience/giz003

Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
Cited by: 21
Author(s): Stefan Prost, Ellie E. Armstrong, Johan A. A. Nylander, Gregg W.C. Thomas, Alexander Suh, Bent Petersen, Love Dalén, Brett W. Benz, Mozes P. K. Blom, Eleftheria Palkopoulou, Per G. P. Ericson, Martin Irestedt
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.pgen.1009435

A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression
Cited by: 14
Author(s): Zachary Carico, Holden C. Stefan, Megan Justice, Askar Yimit, Jill M. Dowen
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.53360

Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice
Cited by: 25
Author(s): Mohamed Mahgoub, Jacob Paiano, Melania Bruno, Wei Wu, Sarath Pathuri, Xing Zhang, Sherry Ralls, Xiaodong Cheng, André Nussenzweig, Todd S. Macfarlan
Software Mentions: 7
Published: over 4 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 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/s41422-019-0168-1

Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate
Cited by: 64
Author(s): Rui Gao, Xingqun Liang, Sirisha Cheedipudi, Julio Cordero, Xiyi Jiang, Qingquan Zhang, Luca Caputo, Stefan Günther, Carsten Kuenne, Yongcheng Ren, Shoumo Bhattacharya, Xuejun Yuan, Guillermo Barreto, Yihan Chen, Thomas Braun, Sylvia M. Evans, Yunfu Sun, Gergana Dobreva
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-020-03739-4

MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates
Cited by: 5
Author(s): Nathaniel Delos Santos, Lorane Texari, Christopher Benner
Software Mentions: 6
Published: about 4 years ago

10.1186/s12859-016-1204-5

LMAP: Lightweight Multigene Analyses in PAML
Cited by: 12
Author(s): Emanuel Maldonado, Daniela Almeida, Tibisay Escalona, Imran Khan, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 6
Published: about 8 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

10.1186/s12864-021-07656-5

Species and population specific gene expression in blood transcriptomes of marine turtles
Cited by: 8
Author(s): Shreya M. Banerjee, Jamie Adkins Stoll, Camryn D. Allen, Jennifer M. Lynch, Heather Harris, Lauren Kenyon, Richard E. Connon, Eleanor J. Sterling, Eugênia Naro‐Maciel, Kathryn M. McFadden, Margaret M. Lamont, James Benge, Nadia B. Fernández, Jeffrey A. Seminoff, Scott R. Benson, Rebecca L. Lewison, Tomoharu Eguchi, Tammy M. Summers, Jessy R. Hapdei, Marc Rice, Summer L. Martin, T. Todd Jones, Peter H. Dutton, George H. Balazs, Lisa M. Komoroske
Software Mentions: 6
Published: over 3 years ago

10.1093/database/bay014

TransAtlasDB: an integrated database connecting expression data, metadata and variants
Cited by: 2
Author(s): Modupeore O. Adetunji, Susan J. Lamont, Carl J. Schmidt
Software Mentions: 6
Published: almost 7 years ago

10.1038/sdata.2016.8

Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice
Cited by: 8
Author(s): Xing Tang, Huayang Liu, Arunima Srivastava, Thierry Pécot, Zhong Chen, Qianben Wang, Kun Huang, Maria Teresa Sáenz-Robles, Paul G. Cantalupo, James M. Pipas, Gustavo Leone
Software Mentions: 6
Published: almost 9 years ago

10.1093/gbe/evab069

Synteny-Based Genome Assembly for 16 Species of <i>Heliconius</i> Butterflies, and an Assessment of Structural Variation across the Genus
Cited by: 13
Author(s): Fernando Seixas, Nathaniel B. Edelman, James Mallet
Software Mentions: 6
Published: over 3 years ago

10.1038/s41392-020-00378-2

Loss of FOXC1 contributes to the corneal epithelial fate switch and pathogenesis
Cited by: 11
Author(s): Mingsen Li, Liqiong Zhu, Jiafeng Liu, Huaxing Huang, Huizhen Guo, Li Wang, Lingyu Li, Sijie Gu, Jieying Tan, Jing Zhong, Bowen Wang, Zhen Mao, Yong Fan, Chunqiao Liu, Jing Yuan, Hong Ouyang
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-021-07774-0

Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
Cited by: 10
Author(s): Aileen R Ferraro, Abigail J Ameri, Zefu Lu, Masayuki Kamei, Robert J. Schmitz, Zachary A. Lewis
Software Mentions: 5
Published: over 3 years ago

10.1038/s42003-018-0094-7

Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis
Cited by: 53
Author(s): Taro Maeda, Yuuki Kobayashi, Hiromu Kameoka, Nao Okuma, Nobuo Takeda, Katsushi Yamaguchi, Takahiro Bino, Shuji Shigenobu, Masayoshi Kawaguchi
Software Mentions: 5
Published: over 6 years ago

10.1016/j.celrep.2021.109423

RHOX10 drives mouse spermatogonial stem cell establishment through a transcription factor signaling cascade
Cited by: 11
Author(s): Kun Tan, H. C. Song, Miles Wilkinson
Software Mentions: 5
Published: over 3 years ago

10.1186/s13073-021-00938-3

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability
Cited by: 9
Author(s): Jennifer Derrien, Catherine Guérin‐Charbonnel, Victor Gaborit, Loı̈c Campion, Martine Devic, Elise Douillard, Nathalie Roi, Hervé Avet‐Loiseau, Olivier Decaux, Thierry Facon, Jan‐Philipp Mallm, Roland Eils, Nikhil C. Munshi, Philippe Moreau, Carl Herrmann, Florence Magrangeas, Stέphane Minvielle
Software Mentions: 5
Published: over 3 years ago

10.1186/s12915-017-0412-4

Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution
Cited by: 96
Author(s): Damien J. Lightfoot, David E. Jarvis, Thiruvarangan Ramaraj, R. Lee, Eric N. Jellen, Peter J. Maughan
Software Mentions: 5
Published: about 7 years ago

10.3390/jcm9082452

Insight in miRNome of Long-Term Non-Progressors and Elite Controllers Exposes Potential RNAi Role in Restraining HIV-1 Infection
Cited by: 9
Author(s): Rubén Ayala-Suárez, Francisco Díez-Fuertes, Esther Calonge, Humberto Erick De La Torre Tarazona, M Gracia-Ruiz de Alda, Laura Capa, José Alcamı́
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0015925

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals
Cited by: 526
Author(s): Robert Kofler, Pablo Orozco‐terWengel, Nicola De Maio, Ram Vinay Pandey, Viola Nolte, Andreas Futschik, Carolin Kosiol, Christian Schlötterer
Software Mentions: 5
Published: almost 14 years ago

10.1371/journal.pone.0169087

The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population
Cited by: 74
Author(s): Axel Künstner, Maria Hoffmann, Bonnie A. Fraser, Verena A. Kottler, Eshita Sharma, Detlef Weigel, Christine Dreyer
Software Mentions: 5
Published: almost 8 years ago

10.3390/ijms21051630

Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines
Cited by: 1
Author(s): Dóra Bojcsuk, Gergely Nagy, Bálint László Bálint
Software Mentions: 5
Published: over 4 years ago

10.1534/g3.117.040170

A Chromosome-Scale Assembly of the<i>Bactrocera cucurbitae</i>Genome Provides Insight to the Genetic Basis of<i>white pupae</i>
Cited by: 30
Author(s): Sheina B. Sim, Scott M. Geib
Software Mentions: 5
Published: over 7 years ago

10.1186/gb-2011-12-7-r69

ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
Cited by: 38
Author(s): Brad A. Friedman, Tom Maniatis
Software Mentions: 5
Published: over 13 years ago

10.1186/1471-2164-15-1081

Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator
Cited by: 137
Author(s): Laura M. Jones, Summaira Riaz, Abraham Morales‐Cruz, Katherine C. H. Amrine, Brianna McGuire, W. D. Gubler, Michael Walker, Dario Cantu
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.19893

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status
Cited by: 16
Author(s): Dongming Li, Ana Marie S. Palanca, So Youn Won, Lei Gao, Ying Feng, Ajay A. Vashisht, Li Liu, Yuanyuan Zhao, Xigang Liu, Xiuyun Wu, Shaofang Li, Brandon H. Le, Yun Ju Kim, Guodong Yang, Shengben Li, Jinyuan Liu, James A. Wohlschlegel, Hongwei Guo, Beixin Mo, Xuemei Chen, Julie A. Law
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-13-670

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria
Cited by: 49
Author(s): Laura Hobley, Thomas R. Lerner, Laura E. Williams, Carey Lambert, Rob Till, David S. Milner, Sarah M. Basford, Michael J. Capeness, Andrew K. Fenton, Robert J. Atterbury, Maximilian A. T. S. Harris, R. Elizabeth Sockett
Software Mentions: 4
Published: almost 12 years ago

10.1038/s41598-020-61678-9

Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues
Cited by: 23
Author(s): Michelle M. Halstead, Colin Kern, Perot Saelao, Ganrea Chanthavixay, Y. Wang, Mary E. Delany, Huaijun Zhou, Pablo J. Ross
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0213278

A common genomic code for chromatin architecture and recombination landscape
Cited by: 17
Author(s): Kamel Jabbari, Johannes Wirtz, Martina Rauscher, Thomas Wiehe
Software Mentions: 4
Published: over 5 years ago

10.1016/j.immuni.2021.05.016

A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression
Cited by: 22
Author(s): Francesco Cilenti, Giulia Barbiera, Nicoletta Caronni, Dario Iodice, Elisa Montaldo, Simona Barresi, Eleonora Lusito, Vincenzo Cuzzola, Francesco Maria Vittoria, Luca Mezzanzanica, Paolo Miotto, Pietro Di Lucia, Dejan Lazarevic, Daniela María Cirillo, Matteo Iannacone, Marco Genua, Renato Ostuni
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-014-0536-6

TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning
Cited by: 41
Author(s): Sarah D. Diermeier, Petros Kolovos, Leonhard Heizinger, Uwe Schwartz, Theodore Georgomanolis, Anne Zirkel, Gero Wedemann, Frank Grosveld, Tobias Knoch, Rainer Merkl, Peter R. Cook, Gernot Längst, Argyris Papantonis
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12859-016-1055-0

DensityMap: a genome viewer for illustrating the densities of features
Cited by: 13
Author(s): Sébastien Guizard, Benoît Piégu, Yves Bigot
Software Mentions: 4
Published: over 8 years ago

10.1534/genetics.118.301482

Diverse Lineages of <i>Candida albicans</i> Live on Old Oaks
Cited by: 54
Author(s): Douda Bensasson, Jo Dicks, John M. Ludwig, Christopher J. Bond, Adam Elliston, Ian N. Roberts, Stephen A. James
Software Mentions: 4
Published: about 6 years ago

10.3389/fpls.2017.00184

Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species
Cited by: 60
Author(s): Bruno Contreras‐Moreira, Carlos Pérez Cantalapiedra, María Jesús García-Pereira, Sean P. Gordon, John P. Vogel, Ernesto Igartua, Ana M. Casas, Pablo Vinuesa
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2020.01259

Interactive Gene Expression Patterns of Susceptible and Resistant Lens ervoides Recombinant Inbred Lines and the Necrotroph Ascochyta lentis
Cited by: 1
Author(s): Zhe Cao, Karan Kapoor, Li Li, Sabine Banniza
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-57071-w

Genome- and transcriptome-derived microsatellite loci in lumpfish Cyclopterus lumpus: molecular tools for aquaculture, conservation and fisheries management
Cited by: 7
Author(s): Simo N. Maduna, Adam Vivian‐Smith, Ólöf Dóra Bartels Jónsdóttir, Albert K. Imsland, Cornelya F. C. Klütsch, Tommi Nyman, Hans Geir Eiken, Snorre B. Hagen
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-019-3019-7

HH-suite3 for fast remote homology detection and deep protein annotation
Cited by: 602
Author(s): Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-9-122

Strategies for measuring evolutionary conservation of RNA secondary structures
Cited by: 67
Author(s): Andreas Gruber, Stephan H. Bernhart, Ivo L. Hofacker, Stefan Washietl
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2148-11-211

Evidence for a high mutation rate at rapidly evolving yeast centromeres
Cited by: 28
Author(s): Douda Bensasson
Software Mentions: 3
Published: over 13 years ago

10.1136/bmjdrc-2019-000751

Peritoneal macrophages have an impaired immune response in obesity which can be reversed by subsequent weight loss
Cited by: 10
Author(s): Lisa Willemsen, Annette E. Neele, Saskia van der Velden, K.H.M. Prange, Myrthe den Toom, Cindy P. A. A. van Roomen, Myrthe E. Reiche, Guillermo R. Griffith, Marion J.J. Gijbels, Esther Lutgens, Menno P.J. de Winther
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1005395

Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma
Cited by: 35
Author(s): Sarah A. Gilmore, Mark Voorhies, Dana Gebhart, Anita Sil
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.0030022

Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes
Cited by: 138
Author(s): Irene Keller, Douda Bensasson, Richard A. Nichols
Software Mentions: 3
Published: almost 18 years ago

10.1371/journal.pone.0209846

Bioinformatic analysis of long-lasting transcriptional and translational changes in the basolateral amygdala following acute stress
Cited by: 19
Author(s): Stephanie E. Sillivan, Meghan E. Jones, Sarah E. Jamieson, Gavin Rumbaugh, Courtney A. Miller
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0060458

Assessing the Consequences of Denoising Marker-Based Metagenomic Data
Cited by: 53
Author(s): John Gaspar, W. Kelley Thomas
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0131787

Quantitative Analysis of MicroRNAs in Vaccinia virus Infection Reveals Diversity in Their Susceptibility to Modification and Suppression
Cited by: 5
Author(s): Amy H. Buck, Alasdair Ivens, Katrina Gordon, Nicky Craig, Alexandre Houzelle, Alice Roche, Neil Turnbull, Philippa M. Beard
Software Mentions: 3
Published: over 9 years ago

10.1038/s42003-021-02351-3

Tag-seq: a convenient and scalable method for genome-wide specificity assessment of CRISPR/Cas nucleases
Cited by: 10
Author(s): Hongxin Huang, Yongfei Hu, Guanjie Huang, Shufeng Ma, Jianqi Feng, Dong Wang, Ying Lin, Jiajian Zhou, Zhili Rong
Software Mentions: 3
Published: over 3 years ago

10.15252/embr.201642958

Changing <scp>POU</scp> dimerization preferences converts Oct6 into a pluripotency inducer
Cited by: 39
Author(s): Stepan Jerabek, Calista K.L. Ng, Guangming Wu, Marcos J. Araúzo‐Bravo, Kee‐Pyo Kim, Daniel Esch, Vikas Malik, Yanpu Chen, Sergiy Velychko, Caitlin M. MacCarthy, Xiaoxiao Yang, Vlad Cojocaru, Hans R. Schöler, Ralf Jauch
Software Mentions: 3
Published: almost 8 years ago

10.3389/fcell.2020.00448

miR-205 Expression Elevated With EDS Treatment and Induced Leydig Cell Apoptosis by Targeting RAP2B via the PI3K/AKT Signaling Pathway
Cited by: 3
Author(s): Chunrong Yang, Rui Chen, Lin Ma, Wenjing Yang, Mingyue Chen, Yanghai Zhang, Shuai Yu, Wuzi Dong, Wenxian Zeng, Xianyong Lan, Chuanying Pan
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2019.00659

Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements
Cited by: 8
Author(s): Iliyas Rashid, Ajey Kumar Pathak, Ravindra Kumar, Prachi Srivastava, Mahender Singh, S. Murali, Basdeo Kushwaha
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2021.732511

T-BET and EOMES Accelerate and Enhance Functional Differentiation of Human Natural Killer Cells
Cited by: 19
Author(s): L. Kiekens, Wouter Van Loocke, Sylvie Taveirne, Sigrid Wahlen, Eva Persyn, Els Van Ammel, Zenzi De Vos, Patrick Matthys, Filip Van Nieuwerburgh, Tom Taghon, Pieter Van Vlierberghe, Bart Vandekerckhove, Georges Leclercq
Software Mentions: 3
Published: about 3 years ago

10.1534/g3.111.000240

<i>Stacks</i>: Building and Genotyping Loci <i>De Novo</i> From Short-Read Sequences
Cited by: 1,474
Author(s): Julian M. Catchen, Angel Amores, Paul A. Hohenlohe, William A. Cresko, John H. Postlethwait
Software Mentions: 3
Published: over 13 years ago

10.1186/s13059-015-0729-7

Exploiting single-molecule transcript sequencing for eukaryotic gene prediction
Cited by: 115
Author(s): André E. Minoche, Juliane C. Dohm, Jessica Schneider, Daniela Holtgräwe, Prisca Viehöver, Magda Montfort, Thomas Rosleff Sörensen, Bernd Weißhaar, Heinz Himmelbauer
Software Mentions: 3
Published: about 9 years ago

10.1186/1756-8935-6-13

ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes
Cited by: 65
Author(s): Adam Blattler, Lijing Yao, Yao Wang, Zhenqing Ye, Victor X. Jin, Peggy J. Farnham
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0000741

Genome Dynamics of Short Oligonucleotides: The Example of Bacterial DNA Uptake Enhancing Sequences
Cited by: 15
Author(s): Mohammed Bakkali
Software Mentions: 2
Published: over 17 years ago

10.1186/s12859-018-2154-x

ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements
Cited by: 31
Author(s): Egon A. Ozer
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2020.00675

rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output
Cited by: 1
Author(s): Marek Schwarz, Jiřı́ Vohradský, Martin Modrák, Josef Pánek
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-020-3537-3

VADR: validation and annotation of virus sequence submissions to GenBank
Cited by: 45
Author(s): Alejandro A. Schäffer, Eneida L. Hatcher, Linda Yankie, Lara Shonkwiler, J. Rodney Brister, Ilene Karsch-Mizrachi, Eric P. Nawrocki
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0212947

Tracking dengue virus type 1 genetic diversity during lineage replacement in an hyperendemic area in Colombia
Cited by: 7
Author(s): Mauricio A. Salvo, Matthew T. Aliota, Louise H. Moncla, Iván Darío Vélez, Andrea Trujillo, Thomas C. Friedrich, Jorge E. Osorio
Software Mentions: 2
Published: over 5 years ago

10.1128/genomeA.00670-13

Genome Sequences of Six Wheat-Infecting <i>Fusarium</i> Species Isolates
Cited by: 26
Author(s): Paula Moolhuijzen, John M. Manners, Stephen Wilcox, M. Bellgard, Donald M. Gardiner
Software Mentions: 2
Published: about 11 years ago

10.1128/genomeA.00594-14

Draft Genome Sequence of Kozakia baliensis SR-745, the First Sequenced <i>Kozakia</i> Strain from the Family <i>Acetobacteraceae</i>
Cited by: 4
Author(s): Jochen Schmid, Steven Koenig, André Pick, Fabian Steffler, Shosuke Yoshida, Kenji Miyamoto, Volker Sieber
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1008213

The gene regulatory basis of genetic compensation during neural crest induction
Cited by: 31
Author(s): Christopher M. Dooley, Neha Wali, Ian Sealy, Richard White, Derek L. Stemple, John Collins, Elisabeth M Busch-Nentwich
Software Mentions: 2
Published: over 5 years ago

10.1186/s12866-020-01821-8

Nanopore sequencing reveals genomic map of CTX-M-type extended-spectrum β-lactamases carried by Escherichia coli strains isolated from blue mussels (Mytilus edulis) in Norway
Cited by: 13
Author(s): Didrik H. Grevskott, Francisco Salvà‐Serra, Edward R. B. Moore, Nachiket P. Marathe
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-14-180

A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus)
Cited by: 43
Author(s): Laia Ribas, Belén G. Pardo, Carlos Fernández, José Antonio Álvarez‐Dios, María Isabel Quiroga, Josep V. Planas, Ariadna Sitjà‐Bobadilla, Paulino Martı́nez, Francesc Piferrer
Software Mentions: 2
Published: over 11 years ago

10.1111/jcmm.15799

Somatic mutations in colorectal cancer are associated with the epigenetic modifications
Cited by: 4
Author(s): Hongwei Lei, Kaixiong Tao
Software Mentions: 2
Published: about 4 years ago

10.1186/s12864-015-2024-0

Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize
Cited by: 86
Author(s): Chunxiao Fan, Zhiqiang Hao, Jiahong Yan, Guanglin Li
Software Mentions: 2
Published: about 9 years ago

10.1002/pmic.201200412

Quantitative analysis of chaperone network throughput in budding yeast
Cited by: 33
Author(s): Philip Brownridge, Craig Lawless, Aishwarya Payapilly, Karin Lanthaler, Stephen W. Holman, Victoria M. Harman, Chris M. Grant, Robert J. Beynon, Simon J. Hubbard
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-016-3328-4

ESAP plus: a web-based server for EST-SSR marker development
Cited by: 9
Author(s): Piyarat Ponyared, Jiradej Ponsawat, Sissades Tongsima, Pusadee Seresangtakul, C. Akkasaeng, N. Tantisuwichwong
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2164-13-S7-S13

Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs
Cited by: 29
Author(s): Jia-Shiun Khoo, San Jiun Chai, Rahmah Mohamed, Sheila Nathan, Mohd Firdaus-Raih
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2164-15-901

Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation
Cited by: 10
Author(s): Andrew Toseland, Simon Moxon, Thomas Möck, Vincent Moulton
Software Mentions: 2
Published: almost 11 years ago

10.3390/ijerph13020152

Diversity of Bacterial Communities on Four Frequently Used Surfaces in a Large Brazilian Teaching Hospital
Cited by: 19
Author(s): Tairacan Augusto Pereira da Fonseca, Rodrigo Pessôa, Alvina Clara Félix, Sabri Saeed Sanabani
Software Mentions: 2
Published: almost 9 years ago

10.1038/s42003-020-1043-9

Dissecting myogenin-mediated retinoid X receptor signaling in myogenic differentiation
Cited by: 5
Author(s): Saadia Khilji, Munerah Hamed, Jihong Chen, Qiao Li
Software Mentions: 2
Published: over 4 years ago

10.3390/cancers12071870

SNAIL Promotes Metastatic Behavior of Rhabdomyosarcoma by Increasing EZRIN and AKT Expression and Regulating MicroRNA Networks
Cited by: 13
Author(s): Klaudia Skrzypek, Marta Kot, Paweł Konieczny, Artur Nieszporek, Anna Kusienicka, Małgorzata Lasota, Wojciech Bobela, Urszula Jankowska, Sylwia Kędracka–Krok, Marcin Majka
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0243905

Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome
Cited by: 3
Author(s): Paul B. Finn, Devesh Bhimsaria, Asfa Ali, Asuka Eguchi, Aseem Z. Ansari, Peter B. Dervan
Software Mentions: 2
Published: almost 4 years ago

10.1186/1741-7007-10-12

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates
Cited by: 341
Author(s): Katrin Nyakatura, Olaf R. P. Bininda‐Emonds
Software Mentions: 2
Published: over 12 years ago

10.7554/eLife.32110

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
Cited by: 88
Author(s): Samuel T. Coradetti, Dominic Pinel, Gina M. Geiselman, Masakazu Ito, Stephen J. Mondo, Morgann C. Reilly, Yafang Cheng, Štefan Bauer, Igor V. Grigoriev, John M. Gladden, Blake A. Simmons, Rachel B. Brem, Adam P. Arkin, Jeffrey M. Skerker
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0168023

An Isochore Framework Underlies Chromatin Architecture
Cited by: 57
Author(s): Kamel Jabbari, Giorgio Bernardi
Software Mentions: 2
Published: almost 8 years ago

10.3389/fpls.2020.600788

Quantitative Trait Locus (QTLs) Mapping for Quality Traits of Wheat Based on High Density Genetic Map Combined With Bulked Segregant Analysis RNA-seq (BSR-Seq) Indicates That the Basic 7S Globulin Gene Is Related to Falling Number
Cited by: 9
Author(s): Li Qiao, Zhifen Pan, Yuan Gao, Tao Li, Jinsong Liang, Zijin Zhang, Haili Zhang, Guangbing Deng, Hai Long, Maoqun Yu
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0106314

Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray
Cited by: 66
Author(s): Yoshiki Murakami, Takao Tanahashi, Ryosuke Okada, Hidenori Toyoda, Takashi Kumada, Masaru Enomoto, Akihiro Tamori, Norifumi Kawada, Y-h. Taguchi, Takeshi Azuma
Software Mentions: 2
Published: about 10 years ago

10.1186/s12859-019-3292-5

LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation
Cited by: 1
Author(s): Emanuel Maldonado, Agostinho Antunes
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0131312

Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons &amp; miRNAs, and Genetic Marker Potential
Cited by: 14
Author(s): Manosh Kumar Biswas, Yuxuan Liu, Chunyu Li, Ou Sheng, Christoph Mayer, Ganjun Yi
Software Mentions: 1
Published: over 9 years ago

10.1155/2011/657341

NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels
Cited by: 4
Author(s): Jens Aßmus, Armin O. Schmitt, Ralf Bortfeldt, Gudrun A. Brockmann
Software Mentions: 1
Published: about 13 years ago

10.3389/fmicb.2016.01042

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts
Cited by: 33
Author(s): Lars Schreiber, Kasper Urup Kjeldsen, Peter Funch, J. Jensen, Matthias Obst, Susanna López‐Legentil, Andreas Schramm
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2015.01267

Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences
Cited by: 3
Author(s): Michal Strejcek, Qiong Wang, Jakub Rídl, Ondřej Uhlík
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.gpb.2020.11.005

Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models
Cited by: 12
Author(s): Jie Wang, Michael W. Itgen, Hui-Ju Wang, Yuzhou Gong, Jianping Jiang, Jia‐Tang Li, Cheng Sun, Stanley K. Sessions, Rachel Lockridge Mueller
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13742-015-0097-y

GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists
Cited by: 30
Author(s): Lauris Kaplinski, Maarja Lepamets, Maido Remm
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-016-2775-2

Elucidation of the genetic basis of variation for stem strength characteristics in bread wheat by Associative Transcriptomics
Cited by: 29
Author(s): Charlotte N. Miller, Andrea L. Harper, Martin Trick, P. Werner, Keith W. Waldron, Ian Bancroft
Software Mentions: 1
Published: over 8 years ago

10.1038/s42003-020-1067-1

Geometric regulation of histone state directs melanoma reprogramming
Cited by: 19
Author(s): Junmin Lee, Thomas G. Molley, Christopher H. Seward, Amr A. Abdeen, Huimin Zhang, Xiaochun Wang, Hetvi Gandhi, Jia-Lin Yang, Katharina Gaus, Kristopher A. Kilian
Software Mentions: 1
Published: over 4 years ago

10.1534/g3.116.037275

<i>De Novo</i> Transcriptome Characterization of a Sterilizing Trematode Parasite (<i>Microphallus</i> sp.) from Two Species of New Zealand Snails
Cited by: 6
Author(s): Laura Bankers, Maurine Neiman
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0002812

Conserved Secondary Structures in Aspergillus
Cited by: 6
Author(s): Abigail Manson McGuire, James E. Galagan
Software Mentions: 1
Published: over 16 years ago

10.1038/s41598-021-88770-y

Diversification, selective sweep, and body size in the invasive Palearctic alfalfa weevil infected with Wolbachia
Cited by: 1
Author(s): Midori Tuda, Shun Ichiro Iwase, K. Kébé, Julien Haran, Jiří Skuhrovec, Ehsan Sanaei, Naomichi Tsuji, Attila Podlussány, Оttó Merkl, A. H. El‐Heneidy, Katsura Morimoto
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2148-8-69

Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera
Cited by: 37
Author(s): Oliver Voigt, Dirk Erpenbeck, Gert Wörheide
Software Mentions: 1
Published: over 16 years ago

10.4056/sigs.3687314

Complete genome sequence of Streptococcus agalactiae strain SA20-06, a fish pathogen associated to meningoencephalitis outbreaks
Cited by: 27
Author(s): Ulisses de Pádua Pereira, Anderson Santos, Syed Shah Hassan, Flávia Figueira Aburjaile, Siomar de Castro Soares, Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Luís Carlos Guimarães, Sintia Silva de Almeida, Carlos Diniz, Maria Silvanira Barbosa, Pablo Gomes de Sá, Amjad Ali, Syeda Marriam Bakhtiar, Fernanda Alves Dorella, Adhemar Zerlotini, Flávio Marcos Gomes Araújo, Laura Hora Rios Leite, Guilherme Oliveira, Anderson Miyoshi, Artur M. S. Silva, Vasco Azevedo, Henrique César Pereira Figueiredo
Software Mentions: 1
Published: over 11 years ago

10.1093/database/baw012

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms
Cited by: 6
Author(s): N. S. Nagpure, Ajey Kumar Pathak, Rameshwar Pati, Iliyas Rashid, Jyoti Sharma, Shri Prakash Singh, Mahender Singh, Uttam Kumar Sarkar, Basdeo Kushwaha, Ravindra Kumar, S. Murali
Software Mentions: 1
Published: almost 9 years ago

10.1128/MRA.01497-18

Complete Endogenous Retrovirus Genome Sequence from a Brazilian Vampire Bat (Desmodus rotundus)
Cited by: 1
Author(s): Luciano Chaves Franco Filho, Rafael Ribeiro Barata, Jedson Ferreira Cardoso, Janaína Mota de Vasconcelos Massafra, Poliana da Silva Lemos, Lívia Medeiros Neves Casseb, Ana Cecília Ribeiro Cruz, Márcio Roberto Teixeira Nunes
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms21228861

Site-Specific Phosphorylation of Histone H1.4 Is Associated with Transcription Activation
Cited by: 6
Author(s): Ankita Saha, Christopher H. Seward, Lisa Stubbs, Craig A. Mizzen
Software Mentions: 1
Published: about 4 years ago

10.1186/1756-0500-2-220

pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis
Cited by: 12
Author(s): Johann Pellet, Laurène Meyniel, Pierre‐Olivier Vidalain, Benoı̂t de Chassey, Lionel Tafforeau, Vincent Lotteau, Chantal Rabourdin–Combe, Vincent Navratil
Software Mentions: 1
Published: almost 16 years ago