pypi: custom | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0195461

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome
Cited by: 80
Author(s): Kris A. Christensen, Jong S. Leong, Dionne Sakhrani, Carlo A. Biagi, David R. Minkley, Ruth E. Withler, Eric B. Rondeau, Ben F. Koop, Robert H. Devlin
Software Mentions: 5
Published: over 6 years ago

10.1534/g3.113.007849

Opposing Activities of DRM and MES-4 Tune Gene Expression and X-Chromosome Repression inCaenorhabditis elegansGerm Cells
Cited by: 8
Author(s): Tomoko M. Tabuchi, Andreas Rechtsteiner, Susan Strome, Kirsten Hagstrom
Software Mentions: 5
Published: almost 11 years ago

10.3389/fpls.2017.00367

Gene Classification and Mining of Molecular Markers Useful in Red Clover (Trifolium pratense) Breeding
Cited by: 14
Author(s): Jan Ištvánek, Jana Dluhošová, Petr Dluhoš, Lenka Pátková, J. Nedĕlník, Jana Řepková
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0042678

The Role of Master Regulators in the Metabolic/Transcriptional Coupling in Breast Carcinomas
Cited by: 19
Author(s): Karol Baca-López, M. Mayorga, Alfredo Hidalgo-Miranda, Nora Gutiérrez-Nájera, Enrique Hernández‐Lemus
Software Mentions: 5
Published: about 12 years ago

10.1534/g3.117.040170

A Chromosome-Scale Assembly of theBactrocera cucurbitaeGenome Provides Insight to the Genetic Basis ofwhite pupae
Cited by: 30
Author(s): Sheina B. Sim, Scott M. Geib
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0119198

Genome-Wide Analysis of Homeobox Gene Family in Legumes: Identification, Gene Duplication and Expression Profiling
Cited by: 47
Author(s): Annapurna Bhattacharjee, Rajesh Ghangal, Rohini Garg, Mukesh Jain
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0237641

Locus of emotion influences psychophysiological reactions to music
Cited by: 7
Author(s): Julia Merrill, Diana Omigie, Melanie Wald-Fuhrmann
Software Mentions: 5
Published: about 4 years ago

10.1038/s41438-019-0146-2

Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard
Cited by: 31
Author(s): Zoë Migicovsky, Zachary N. Harris, Laura L. Klein, Mao Li, Adam McDermaid, Daniel H. Chitwood, Anne Fennell, László Kovács, Misha T. Kwasniewski, Jason P. Londo, Qin Ma, Allison J. Miller
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.69068

Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology
Cited by: 26
Author(s): Joshua H. Siegle, Peter Ledochowitsch, Xiaoxuan Jia, Daniel Millman, Gabriel Koch Ocker, Shiella Caldejon, Linzy Casal, Andy Cho, Daniel J. Denman, Séverine Durand, Peter A. Groblewski, Gregg Heller, India Kato, Sara Kivikas, Jérôme Lecoq, Chelsea Nayan, Kiet Ngo, Philip R. Nicovich, Kat North, Tamina K Ramirez, Jackie Swapp, Xana Waughman, Ali Williford, Shawn R. Olsen, Christof Koch, Michael A. Buice, Saskia E. J. de Vries
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0252457

Lack of parent-of-origin effects in Nasonia jewel wasp: A replication and extension study
Cited by: 1
Author(s): Kimberly C. Olney, Joshua D. Gibson, Heini M. Natri, Avery Underwood, Juergen Gadau, Melissa A. Wilson
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2164-15-1103

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies
Cited by: 75
Author(s): Romain Blanc-Mathieu, Bram Verhelst, Évelyne Derelle, Stéphane Rombauts, François‐Yves Bouget, Isabelle A. Carré, Annie Château, Adam Eyre‐Walker, Nigel Grimsley, Hervé Moreau, Benoît Piégu, Éric Rivals, Wendy Schackwitz, Yves Van de Peer, Gwenaël Piganeau
Software Mentions: 5
Published: almost 10 years ago

10.3389/fmicb.2019.02075

Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis
Cited by: 14
Author(s): Gi Yoon Shin, Jeffrey K. Schachterle, Divine Yufetar Shyntum, Lucy N. Moleleki, Teresa A. Coutinho, George W. Sundin
Software Mentions: 5
Published: about 5 years ago

10.15252/msb.20167058

Mechanism for microbial population collapse in a fluctuating resource environment
Cited by: 21
Author(s): Serdar Turkarslan, Arjun V. Raman, Anne Thompson, Christina E. Arens, Mark A. Gillespie, Frederick von Netzer, Kristina L. Hillesland, Sergey Stolyar, Adrián López García de Lomana, David J Reiss, Drew Gorman‐Lewis, Grant M. Zane, Jeffrey A. Ranish, Judy D. Wall, David A. Stahl, Nitin S. Baliga
Software Mentions: 5
Published: over 7 years ago

10.3389/fpls.2019.01439

Genome-Wide Variation in Potyviruses
Cited by: 75
Author(s): Deepti Nigam, Katherine LaTourrette, Pedro Filho Noronha Souza, Hernán García-Ruíz
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2018.02547

Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation
Cited by: 36
Author(s): Athina Soragia Gkazi, Ben Margetts, Teresa Attenborough, Lana Mhaldien, Joseph F. Standing, Theres Oakes, James Heather, John Booth, Marlène Pasquet, Robert Chiesa, Paul Veys, Nigel Klein, Benjamin M. Chain, Robin E. Callard, Stuart Adams
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2019.01386

Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection
Cited by: 17
Author(s): Thomas J. Hall, Douglas Vernimmen, John Andrew Browne, Michael P. Mullen, Stephen V. Gordon, David E. MacHugh, Alan M. O’Doherty
Software Mentions: 5
Published: almost 5 years ago

10.3389/fimmu.2019.02999

Opioids Impair Intestinal Epithelial Repair in HIV-Infected Humanized Mice
Cited by: 37
Author(s): Jingjing Meng, Santanu Banerjee, Li Zhang, Gregory M. Sindberg, Shamsudheen Moidunny, Bin Li, David J. Robbins, Mohit Girotra, Bradley J. Segura, Sundaram Ramakrishnan, Sabita Roy
Software Mentions: 5
Published: almost 5 years ago

10.3389/fpls.2018.00641

Detailed Phytochemical Analysis of High- and Low Artemisinin-Producing Chemotypes of Artemisia annua
Cited by: 22
Author(s): Tomasz Czechowski, Tony R. Larson, Theresa M. Catania, David Harvey, Cenxi Wei, Michel Essome, Geoffrey D. Brown, Ian A. Graham
Software Mentions: 5
Published: over 6 years ago

10.3390/bs10030062

Random Forest Classification of Alcohol Use Disorder Using EEG Source Functional Connectivity, Neuropsychological Functioning, and Impulsivity Measures
Cited by: 15
Author(s): Chella Kamarajan, Babak A. Ardekani, Ashwini K. Pandey, David B. Chorlian, Sivan Kinreich, Gayathri Pandey, Jacquelyn L. Meyers, Jian Zhang, Weipeng Kuang, Arthur T. Stimus, Bernice Porjesz
Software Mentions: 5
Published: over 4 years ago

10.18632/oncotarget.21031

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

10.1111/mec.12833

Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (Lagopus lagopus scotica)
Cited by: 52
Author(s): Marius Wenzel, Stuart B. Piertney
Software Mentions: 5
Published: over 10 years ago

10.3389/fcell.2020.601145

Spontaneous Membrane Nanodomain Formation in the Absence or Presence of the Neurotransmitter Serotonin
Cited by: 11
Author(s): Anna Bochicchio, Astrid F. Brandner, Oskar Engberg, Daniel Huster, Rainer A. Böckmann
Software Mentions: 5
Published: almost 4 years ago

10.1523/JNEUROSCI.0827-19.2019

Mammillothalamic Disconnection Alters Hippocampocortical Oscillatory Activity and Microstructure: Implications for Diencephalic Amnesia
Cited by: 34
Author(s): Christopher M. Dillingham, Michal M. Milczarek, James C. Perry, Bethany E. Frost, Greg D. Parker, Yaniv Assaf, Frank Sengpiel, Shane M. O’Mara, Seralynne Denise Vann
Software Mentions: 5
Published: over 5 years ago

10.1186/s12915-020-00769-5

Multiple links between 5-methylcytosine content of mRNA and translation
Cited by: 71
Author(s): Ulrike Schümann, He-Na Zhang, Tennille Sibbritt, Anyu Pan, Attila Horváth, Simon Gross, Susan J. Clark, Li Yang, Thomas Preiß
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0176596

Evolution of microRNA in primates
Cited by: 31
Author(s): Jennifer C. McCreight, Sean E. Schneider, Damien B. Wilburn, Willie J. Swanson
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pgen.1009010

Candidate variants in TUB are associated with familial tremor
Cited by: 2
Author(s): M. Reza Sailani, Fereshteh Jahanbani, Charles W. Abbott, Hayan Lee, Amin Zia, Shannon Rego, Juliane Winkelmann, Franziska Hopfner, Tahir Naeem Khan, Nicholas Katsanis, Stefanie H. Müller, Daniela Berg, Katherine M. Lyman, Christian Mychajliw, G. Deuschl, Jonathan A. Bernstein, Gregor Kuhlenbäumer, M Snyder
Software Mentions: 5
Published: about 4 years ago

10.3390/ijms20143543

Sex-Dimorphic Behavioral Alterations and Altered Neurogenesis in U12 Intron Splicing-Defective Zrsr1 Mutant Mice
Cited by: 9
Author(s): Francisco Alén, Isabel Gómez-Redondo, Patricia Rivera, Juan Suárez, Priscila Ramos‐Ibeas, Eva Pericuesta, Raúl Fernández‐González, Serafín Pérez‐Cerezales, Keiko Horiuchi, Laura Orío, Fernando Rodríguez de Fonseca, Alfonso Gutiérrez‐Adán
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0161476

Evolution of the Exon-Intron Structure in Ciliate Genomes
Cited by: 17
Author(s): Vladyslav Bondarenko, Mikhail S. Gelfand
Software Mentions: 5
Published: about 8 years ago

10.1111/1755-0998.13008

Metabarcoding a diverse arthropod mock community
Cited by: 97
Author(s): Thomas Braukmann, Natalia V. Ivanova, Sean W. J. Prosser, Vasco Elbrecht, Dirk Steinke, Sujeevan Ratnasingham, Jeremy R. de Waard, Jayme E Sones, Evgeny Zakharov, Paul D. N. Hebert
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1008420

Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice
Cited by: 50
Author(s): Rena M. Schweizer, Jonathan P. Velotta, Catherine M. Ivy, Matthew R. Jones, Sarah M. Muir, Gideon S. Bradburd, Jay F. Storz, Graham R. Scott, Zachary A. Cheviron
Software Mentions: 5
Published: about 5 years ago

10.1186/s13756-019-0567-6

Abstracts from the 5th International Conference on Prevention & Infection Control (ICPIC 2019)
Cited by: 10
Author(s):
Software Mentions: 5
Published: about 5 years ago

10.1111/eva.12699

Weed evolution: Genetic differentiation among wild, weedy, and crop radish
Cited by: 16
Author(s): Amanda Charbonneau, David C. Tack, Allison Lale, J. E. Goldston, Mackenzie Caple, Emma Conner, Oz Barazani, Jotham Ziffer-Berger, Ian Dworkin, Jeffrey K. Conner
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.54880

Transient intracellular acidification regulates the core transcriptional heat shock response
Cited by: 45
Author(s): Catherine G. Triandafillou, Christopher D. Katanski, Aaron R. Dinner, D. Allan Drummond
Software Mentions: 5
Published: over 4 years ago

10.1002/ece3.5260

Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization
Cited by: 17
Author(s): Grey T. Gustafson, Alana Alexander, John S. Sproul, James M. Pflug, David R. Maddison, Andrew Edward Z. Short
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.52611

Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides
Cited by: 108
Author(s): Jamie R Wangen, Rachel Green
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12920-020-00838-2

Genome-wide transcriptome study using deep RNA sequencing for myocardial infarction and coronary artery calcification
Cited by: 5
Author(s): Xiaoling Zhang, Jeroen G.J. van Rooij, Y. Wakabayashi, Shih‐Jen Hwang, Yanqin Yang, Mohsen Ghanbari, Daniël Bos, Daniel Levy, Andrew D. Johnson, Joyce B. J. van Meurs, Maryam Kavousi, Jun Zhu, Christopher J. O’Donnell
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-020-3416-y

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes
Cited by: 12
Author(s): Michelle L. Treiber, Diana H. Taft, Ian F Korf, David A. Mills, Danielle G. Lemay
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-018-0417-4

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota
Cited by: 56
Author(s): Jane A. Mullaney, J. Stephens, Mary Ellen Costello, Cai Fong, Brooke E. Geeling, Patrick G. Gavin, Casey M. Wright, Timothy D. Spector, Matthew A. Brown, Emma E. Hamilton‐Williams
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.05255

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
Cited by: 402
Author(s): Manu Dubin, Pei Zhang, Dong Meng, Marie Stanislas Remigereau, Edward J. Osborne, Francesco Paolo Casale, Philipp Drewe, André Kahles, Géraldine Jean, Bjarni J. Vilhjálmsson, Joanna Jagoda, Selen Irez, Viktor Voronin, Qiang Song, Quan Long, Gunnar Rätsch, Oliver Stegle, Richard M. Clark, Magnus Nordborg
Software Mentions: 5
Published: over 9 years ago

10.1128/mSystems.00084-18

Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities
Cited by: 33
Author(s): Ashley R. Coenen, Joshua S. Weitz
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.51243

Global genome diversity of the Leishmania donovani complex
Cited by: 77
Author(s): Susanne U. Franssen, Caroline Durrant, Olivia Stark, Bettina A. Moser, Tim Downing, Hideo Imamura, Jean Claude Dujardin, Mandy Sanders, Isabel Maurício, Michael A. Miles, Lionel F. Schnur, Charles L. Jaffe, Abedelmajeed Nasereddin, Henk D. F. H. Schallig, Matthew Yeo, Tapan Bhattacharyya, Mohammad Zahangir Alam, Matthew Berriman, Thierry Wirth, Gabriele Schönian, James A. Cotton
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1002389

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types
Cited by: 340
Author(s): Michael J. Ziller, Fabian Müller, Jing Liao, Yingying Zhang, Hongcang Gu, Christoph Bock, Patrick Boyle, Charles B. Epstein, B Bernstein, Thomas Lengauer, Andreas Gnirke, Alexander Meissner
Software Mentions: 5
Published: almost 13 years ago

10.1038/s42003-021-01799-7

Genomic insights into the host specific adaptation of the Pneumocystis genus
Cited by: 16
Author(s): Ousmane Cissé, Liang Ma, John P. Dekker, Pavel P. Khil, Jung Ho Youn, Jason M. Brenchley, Robert V Blair, Bapi Pahar, Magali Chabé, Koen K. A. Van Rompay, Rebekah I. Keesler, Antti Sukura, Vanessa M. Hirsch, Geetha Kutty, Yueqin Liu, Peng Li, Jie Chen, Jun Song, Christiane Weissenbacher‐Lang, Jie Xu, Nathan S. Upham, Jason E. Stajich, Christina A. Cuomo, Melanie T. Cushion, Joseph A. Kovacs
Software Mentions: 5
Published: over 3 years ago

10.1016/j.celrep.2020.02.093

Biased Connectivity of Brain-wide Inputs to Ventral Subiculum Output Neurons
Cited by: 35
Author(s): Ryan Wee, Andrew F. MacAskill
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-021-02015-2

Imbalanced social-communicative and restricted repetitive behavior subtypes of autism spectrum disorder exhibit different neural circuitry
Cited by: 13
Author(s): Natasha Bertelsen, Isotta Landi, Richard A. I. Bethlehem, Jakob Seidlitz, Elena Maria Busuoli, Veronica Mandelli, Eleonora Satta, Stavros Trakoshis, Bonnie Auyeung, Prantik Kundu, Eva Loth, Guillaume Dumas, Sarah Baumeister, Christian F. Beckmann, Sven Bölte, Thomas Bourgeron, Tony Charman, Sarah Durston, Christine Ecker, Rosemary Holt, Mark H. Johnson, Emily J.H. Jones, Luke Mason, Andreas Meyer‐Lindenberg, Carolin Moessnang, Marianne Oldehinkel, Antonio M. Persico, Julian Tillmann, Steve Williams, Will Spooren, Declan Murphy, Jan K. Buitelaar, Simon Baron‐Cohen, Meng‐Chuan Lai, Michael Lombardo
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-018-29267-z

Intrinsic Rhythmicity Predicts Synchronization-Continuation Entrainment Performance
Cited by: 26
Author(s): Trevor McPherson, Dorita S. Berger, Sankaraleengam Alagapan, Flavio Fröhlich
Software Mentions: 5
Published: over 6 years ago

10.1038/srep23490

Combinatorial microenvironmental regulation of liver progenitor differentiation by Notch ligands, TGFβ and extracellular matrix
Cited by: 33
Author(s): Kerim B. Kaylan, Viktoriya Ermilova, Ravi Chandra Yada, Gregory H. Underhill
Software Mentions: 5
Published: over 8 years ago

10.1038/srep27722

Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome
Cited by: 6
Author(s): Natalie C. Fonville, Karthik Raja Velmurugan, Hongseok Tae, Zalman Vaksman, Lauren J. McIver, Harold R. Garner
Software Mentions: 5
Published: over 8 years ago

10.21203/rs.3.rs-25643/v1

Identification of new drug treatments to combat COVID19: A signature-based approach using iLINCS
Cited by: 5
Author(s): Sinead M. O’Donovan, Hunter M. Eby, Nicholas Henkel, Justin Creeden, Ali Sajid Imami, Sophie Asah, Xiaolu Zhang, Xiaojun Wu, Rawan Alnafisah, R Travis Taylor, James Reigle, Alexander W. Thorman, Behrouz Shamsaei, Jarek Meller, Robert E. McCullumsmith
Software Mentions: 5
Published: over 4 years ago

10.1126/sciimmunol.abe4782

Severely ill patients with COVID-19 display impaired exhaustion features in SARS-CoV-2–reactive CD8 + T cells
Cited by: 163
Author(s): Anthony Kusnadi, Ciro Ramírez-Suástegui, Vicente Fajardo, Serena Chee, Benjamin J Meckiff, Hayley Simon, Emanuela Pelosi, Grégory Seumois, Ferhat Ay, Pandurangan Vijayanand, Christian Ottensmeier
Software Mentions: 5
Published: almost 4 years ago

10.3390/cancers13040610

Comprehensive Epstein-Barr Virus Transcriptome by RNA-Sequencing in Angioimmunoblastic T Cell Lymphoma (AITL) and Other Lymphomas
Cited by: 17
Author(s): Nader Bayda, Valentin Tilloy, Alain Chaunavel, Racha Bahri, Mohamad Adnan Halabi, Jean Feuillard, Arnaud Jaccard, Sylvie Ranger-Rogez
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12920-019-0596-2

Transcriptome analysis identified a novel 3-LncRNA regulatory network of transthyretin attenuating glucose induced hRECs dysfunction in diabetic retinopathy
Cited by: 14
Author(s): Jun Shao, Yunbin Zhang, Guangming Fan, Yu Xin, Yong Yao
Software Mentions: 5
Published: about 5 years ago

10.1172/jci.insight.142501

Surfactant protein C mutation links postnatal type 2 cell dysfunction to adult disease
Cited by: 10
Author(s): Sneha Sitaraman, Emily P. Martin, Cheng-Lun Na, Shuyang Zhao, Jenna Green, Hitesh Deshmukh, Anne‐Karina T. Perl, James P. Bridges, Yan Xu, Timothy E. Weaver
Software Mentions: 5
Published: over 3 years ago

10.1186/s40168-020-00966-y

Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation
Cited by: 10
Author(s): Rajesh Kaushal, Peng Li, Sunil Kumar Singh, Mengrui Zhang, Xinlian Zhang, Juan Ignacio Vílchez, Zhen Wang, Danxia He, Yu Ye, Suhui Lv, Zhongtian Xu, Rafael J. L. Morcillo, Wei Wang, Wei-Chang Huang, Paul W. Paré, Chun‐Peng Song, Jian‐Kang Zhu, Renyi Liu, Wenxuan Zhong, Ping Ma, Huiming Zhang
Software Mentions: 5
Published: over 3 years ago

10.1098/rsos.181382

Phenotypic plasticity in the mandibular morphology of Japanese macaques: captive–wild comparison
Cited by: 14
Author(s): Siti Norsyuhada Kamaluddin, Mikiko Tanaka, Hikaru Wakamori, Takeshi Nishimura, Tsuyoshi Ito
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-020-00841-w

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets
Cited by: 49
Author(s): Isabel F. Escapa, Yanmei Huang, Tsute Chen, Maoxuan Lin, Alexis Kokaras, Floyd E. Dewhirst, Katherine P. Lemon
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-016-0982-0

Modeling the integration of bacterial rRNA fragments into the human cancer genome
Cited by: 5
Author(s): Karsten B. Sieber, Pawel Gajer, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 8 years ago

10.1186/s13073-018-0563-0

Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing
Cited by: 25
Author(s): Annie N. Cowell, Hugo O. Valdivia, Danett K. Bishop, Elizabeth A. Winzeler
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-5895-7

Comparative physiology and transcriptome analysis allows for identification of lncRNAs imparting tolerance to drought stress in autotetraploid cassava
Cited by: 21
Author(s): Xiao Liang, Xianwen Shang, Sheng Cao, Xuewen Xie, Wendan Zeng, Lingyun Lu, Songbi Chen, Huabing Yan
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-918

POMO - Plotting Omics analysis results for Multiple Organisms
Cited by: 3
Author(s): Jake Lin, Richard Kreisberg, Aleksi Kallio, Andrew T. Dudley, Matti Nykter, Ilya Shmulevich, Patrick May, Reija Autio
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12863-018-0608-9

RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat & rat
Cited by: 21
Author(s): Xiaoxiao Gao, Jing Ye, Chen Yang, Lei Luo, Ya Liu, Jianping Ding, Yunhai Zhang, Yinghui Ling, Weiping Huang, Xiaorong Zhang, Kaifa Zhang, Xiumei Li, Jie Zhou, Fugui Fang, Zubing Cao
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0127103

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response
Cited by: 31
Author(s): Barbara Blasi, Hakim Tafer, Donatella Tesei, Katja Sterflinger
Software Mentions: 4
Published: over 9 years ago

10.1093/gigascience/giz029

An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies
Cited by: 34
Author(s): Jan Axtner, Alex Crampton‐Platt, Lisa Hörig, Azlan Mohamed, Charles C.Y. Xu, Douglas W. Yu, Andreas Wilting
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-018-1437-x

Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency
Cited by: 63
Author(s): Scott I. Adamson, Lijun Zhan, Brenton R. Graveley
Software Mentions: 4
Published: over 6 years ago

10.1186/gb-2009-10-3-r33

Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions
Cited by: 30
Author(s): Thiago M. Venancio, S. Balaji, Lakshminarayan M. Iyer, L. Aravind
Software Mentions: 4
Published: almost 16 years ago

10.1186/gb-2013-14-12-r147

Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties
Cited by: 77
Author(s): Aurélien A. Sérandour, Gordon D. Brown, Joshua D. Cohen, Jason S. Carroll
Software Mentions: 4
Published: almost 12 years ago

10.3390/plants10010005

Single and Combined Abiotic Stress in Maize Root Morphology
Cited by: 11
Author(s): Rosa Vescio, Maria Rosa Abenavoli, Agostino Sorgonà
Software Mentions: 4
Published: almost 4 years ago

10.1186/gb-2014-15-4-r57

Evidence for the biogenesis of more than 1,000 novel human microRNAs
Cited by: 214
Author(s): Marc R. Friedländer, Esther Lizano, Anna J.S. Houben, Daniela Bezdan, Mónica Báñez-Coronel, Grzegorz Kudla, Elisabet Mateu-Huertas, Birgit Kagerbauer, Justo González, Kevin C. Chen, Emily LeProust, Eulàlia Martı́, Xavier Estivill
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41437-019-0252-9

Conservation of the genome-wide recombination rate in white-footed mice
Cited by: 8
Author(s): April Peterson, Nathan D. Miller, Bret A. Payseur
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0045708

Cooperativity of Stress-Responsive Transcription Factors in Core Hypoxia-Inducible Factor Binding Regions
Cited by: 32
Author(s): Diego Villar, Amaya Ortiz-Barahona, Laura Gómez-Maldonado, Nuria Pescador, Fátima Sánchez-Cabo, Hubert Hackl, Blanca Rodriguez, Zlatko Trajanoski, Ana Dopazo, Tim Hui-Ming Huang, Pearlly S. Yan, Luis del Peso
Software Mentions: 4
Published: about 12 years ago

10.1534/g3.120.401306

Genotypic Characterization of the U.S. Peanut Core Collection
Cited by: 10
Author(s): Paul I. Otyama, R.S. Kulkarni, Kelly D. Chamberlin, Peggy Ozias‐Akins, Ye Chu, Lori M. Lincoln, Gregory E. MacDonald, Noelle L. Anglin, Sudhansu Dash, David J. Bertioli, David Fernández-Baca, Michelle A. Graham, Steven B. Cannon, Ethalinda K. S. Cannon
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0181902

EINCR1 is an EGF inducible lincRNA overexpressed in lung adenocarcinomas
Cited by: 4
Author(s): Karol Nowicki-Osuch, Yaoyong Li, Mairi Challinor, Dave T. Gerrard, Neil A. Hanley, Andrew D. Sharrocks
Software Mentions: 4
Published: over 7 years ago

10.3390/genes9040180

Non-Pleiotropic Coupling of Daily and Seasonal Temporal Isolation in the European Corn Borer
Cited by: 29
Author(s): Rebecca C. Levy, Genevieve M. Kozak, Erik B. Dopman
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.120.401497

Comparative Genomic Analyses and a Novel Linkage Map for Cisco (Coregonus artedi) Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids
Cited by: 13
Author(s): Danielle M. Blumstein, Matthew A. Campbell, Matthew C. Hale, Ben J. G. Sutherland, Garrett J. McKinney, Wendylee Stott, Wesley A. Larson
Software Mentions: 4
Published: over 4 years ago

10.1590/1678-4685-GMB-2017-0164

Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells
Cited by: 5
Author(s): Zhizhong Gong, Jianyun Liu, Xin Xie, Xiaoyuan Xu, Ping Wu, Huimin Li, Yaqin Wang, Weidong Li, Jianjun Xiong
Software Mentions: 4
Published: over 6 years ago

10.3389/fpsyg.2020.02154

HIIT the Road Jack: An Exploratory Study on the Effects of an Acute Bout of Cardiovascular High-Intensity Interval Training on Piano Learning
Cited by: 3
Author(s): Dana Swarbrick, Alex Kiss, Sandra E. Trehub, Luc Tremblay, David A. Alter, Joyce L. Chen
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0088950

Widespread FRA1-Dependent Control of Mesenchymal Transdifferentiation Programs in Colorectal Cancer Cells
Cited by: 68
Author(s): Jeannine Diesch, Elaine Sanij, Omer Gilan, Christopher G. Love, Hoanh Tran, Nicholas I. Fleming, Jason Ellul, Amalia Marcia, Izhak Haviv, Richard B. Pearson, Eugene Tulchinsky, John M. Mariadason, Oliver M. Sieber, Ross D. Hannan, Amardeep S. Dhillon
Software Mentions: 4
Published: over 10 years ago

10.3389/fpls.2020.567249

Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon
Cited by: 7
Author(s): Kanae Masuda, Naoko Fujita, Ho Wen Yang, Koichiro Ushijima, Yasutaka Kubo, Ryutaro Tao, Takashi Akagi
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0180647

Assessment of circulating copy number variant detection for cancer screening
Cited by: 30
Author(s): Bhuvan Molparia, Eshaan Nichani, Ali Torkamani
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0228722

Iron metabolic pathways in the processes of sponge plasticity
Cited by: 8
Author(s): Alexander D. Finoshin, Kim I. Adameyko, Kirill V. Mikhailov, О. И. Кравчук, Anton Georgiev, Н. Г. Горностаев, Igor A. Kosevich, Victor S. Mikhailov, Guzel Gazizova, Elena Shagimardanova, Oleg Gusev, Yu. V. Lyupina
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.3569

Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?
Cited by: 42
Author(s): Malvina Kadlec, Baoheng Du, Nicholas C Le Maitre, Michael D. Pirie
Software Mentions: 4
Published: over 7 years ago

10.1111/acel.13443

The antagonistic pleiotropy of insulin‐like growth factor 1
Cited by: 22
Author(s): William B. Zhang, Kenny Ye, Nir Barzilai, Sofiya Milman
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0150094

Development of the Intestinal RNA Virus Community of Healthy Broiler Chickens
Cited by: 8
Author(s): Jigna Shah, Prerak Desai, Ying Zhang, Sarah K. Scharber, Joshua A. Baller, Zheng Xing, Carol J. Cardona
Software Mentions: 4
Published: over 8 years ago

10.1534/g3.117.300550

Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (Lolium perenne L.)
Cited by: 8
Author(s): Rachel F. Begheyn, Steven Yates, Timothy Sykes, Bruno Studer
Software Mentions: 4
Published: over 6 years ago

10.1534/genetics.119.302757

Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection
Cited by: 26
Author(s): Marnin D. Wolfe, Guillaume Bauchet, A. M. C. Chan, Roberto Lozano, Punna Ramu, Chiedozie Egesi, Robert Kawuki, Peter Kulakow, Ismail Rabbi, Jean‐Luc Jannink
Software Mentions: 4
Published: almost 5 years ago

10.1186/s40462-017-0108-y

Three-dimensional space use during the bottom phase of southern elephant seal dives
Cited by: 15
Author(s): Yves Le Bras, Joffrey Jouma’a, Christophe Guinet
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2019.02886

Microbial Communities in Human Milk Relate to Measures of Maternal Weight
Cited by: 26
Author(s): Sara Lundgren, Juliette C. Madan, Margaret R. Karagas, Hilary G. Morrison, Anne G. Hoen, Brock C. Christensen
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2020.00490

Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races
Cited by: 12
Author(s): Thomas M. Adams, Andrew D. Armitage, Maria K. Sobczyk, Helen Bates, Javier F. Tabima, Brent Kronmiller, Brett M. Tyler, Niklaus J. Grünwald, Jim M. Dunwell, Charlotte F. Nellist, Richard J. Harrison
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2016.00434

Restructuring of Epibacterial Communities on Fucus vesiculosus forma mytili in Response to Elevated pCO2 and Increased Temperature Levels
Cited by: 26
Author(s): Birte Mensch, Sven C. Neulinger, Angelika Graiff, Andreas Pansch, Sven Künzel, Martin Fischer, Ruth A. Schmitz
Software Mentions: 4
Published: over 8 years ago

10.3390/v10100576

Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
Cited by: 10
Author(s): Phillip Seitzer, Adrien Jeanniard, Fangrui Ma, James L. Van Etten, Marc T. Facciotti, David D. Dunigan
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2017.01808

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses
Cited by: 36
Author(s): François Thomas, Philippe Bordron, Damien Eveillard, Gurvan Michel
Software Mentions: 4
Published: about 7 years ago

10.1093/bioinformatics/btab263

Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited
Cited by: 1
Author(s): Wei Wang, Ahmad Hejasebazzi, Julia Zheng, Kevin J. Liu
Software Mentions: 4
Published: over 3 years ago

10.1186/s13024-021-00423-w

Methods to investigate intrathecal adaptive immunity in neurodegeneration
Cited by: 11
Author(s): Hamilton Oh, Olivia Leventhal, Divya Channappa, Victor W. Henderson, Tony Wyss‐Coray, Benoit Lehallier, David Gate
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2164-15-1179

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis
Cited by: 34
Author(s): Kate J. Howell, Lucy A. Weinert, Roy R. Chaudhuri, Shi-Lu Luan, Sarah Peters, Jukka Corander, David Harris, Øystein Angen, Virginia Aragón, Albert Bensaid, Susanna Williamson, Julian Parkhill, Paul R. Langford, Andrew N. Rycroft, Brendan W. Wren, Matthew T. G. Holden, Alexander W. Tucker, Duncan J. Maskell
Software Mentions: 4
Published: almost 11 years ago

10.3389/fonc.2018.00482

Transcriptomic Alterations in Lung Adenocarcinoma Unveil New Mechanisms Targeted by the TBX2 Subfamily of Tumor Suppressor Genes
Cited by: 10
Author(s): Athar Khalil, Batoul Dekmak, Fouad Boulos, Jake Kantrowitz, Avrum Spira, Junya Fujimoto, Humam Kadara, Nehmé El-Hachem, Georges Nemer
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1004660

Widespread Genome Reorganization of an Obligate Virus Mutualist
Cited by: 66
Author(s): Gaelen R. Burke, Kimberly K. O. Walden, James B. Whitfield, Hugh M. Robertson, Michael R. Strand
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-015-1374-y

Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals
Cited by: 29
Author(s): Vincent A. Streva, Vallmer E Jordan, Sara B. Linker, Dale J. Hedges, Prescott L. Deininger
Software Mentions: 4
Published: over 9 years ago

10.1186/s12915-021-00991-9

Long-term persistence of supernumerary B chromosomes in multiple species of Astyanax fish
Cited by: 6
Author(s): Duílio Mazzoni Zerbinato de Andrade Silva, Francisco J. Ruíz-Ruano, Ricardo Utsunomia, María Martín-Peciña, Jonathan Pena Castro, Paula Paccielli Freire, Robson Francisco Carvalho, Diogo Teruo Hashimoto, Alexander Suh, Cláudio Oliveira, Fábio Porto‐Foresti, Roberto Ferreira Artoni, Fausto Foresti, Juan Pedro M. Camacho
Software Mentions: 4
Published: over 3 years ago

10.1111/mec.13146

Heterogeneity of genetic architecture of body size traits in a free‐living population
Cited by: 69
Author(s): Camillo Bérénos, Philip A Ellis, Jill G. Pilkington, Sang Lee, Jacob Gratten, Josephine M. Pemberton
Software Mentions: 4
Published: over 9 years ago

10.1186/s12870-015-0632-0

Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet
Cited by: 10
Author(s): Fei Yi, Jian Chen, Jingjuan Yu
Software Mentions: 4
Published: about 9 years ago

Projects: pypi: custom

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