pypi: bowtie | Projects | Ecosyste.ms: Papers

10.18632/oncotarget.22130

Systematic analysis of the expression profile of non-coding RNAs involved in ischemia/reperfusion-induced acute kidney injury in mice using RNA sequencing
Cited by: 25
Author(s): Jun Zhou, Hongtao Chen, Yu Fan
Software Mentions: 4
Published: almost 9 years ago

10.15252/embj.2020105564

Integrator is recruited to promoter‐proximally paused RNA Pol II to generate Caenorhabditis elegans piRNA precursors
Cited by: 21
Author(s): Toni Beltran, Eleni Pahita, Subhanita Ghosh, Boris Lenhard, Peter Sarkies
Software Mentions: 4
Published: almost 6 years ago

10.1128/JVI.00589-18

Transcriptional and Translational Landscape of Equine Torovirus
Cited by: 22
Author(s): Hazel Stewart, Katherine A. Brown, Adam M. Dinan, Nerea Irigoyen, Eric J. Snijder, Andrew E. Firth
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-019-3180-z

DEEPSEN: a convolutional neural network based method for super-enhancer prediction
Cited by: 13
Author(s): Hongda Bu, Jiaqi Hao, Yanglan Gan, Shuigeng Zhou, Jihong Guan
Software Mentions: 4
Published: almost 7 years ago

10.1002/embj.201386225

The long non-coding RNA Paupar regulates the expression of both local and distal genes
Cited by: 183
Author(s): Keith W. Vance, Stephen N. Sansom, Sheena Lee, Vladislava Chalei, Lesheng Kong, Sarah Cooper, Peter L. Oliver, Chris P. Ponting
Software Mentions: 4
Published: over 12 years ago

10.1186/s12864-015-1491-7

Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum
Cited by: 53
Author(s): Rafael D. Rosengarten, Balaji Santhanam, Danny Fuller, Mariko Katoh-Kurasawa, William F. Loomis, Blaž Zupan, Gad Shaulsky
Software Mentions: 4
Published: over 11 years ago

10.1186/s12862-020-01739-9

Genomic variation in the American pika: signatures of geographic isolation and implications for conservation
Cited by: 4
Author(s): Kelly B. Klingler, Joshua P. Jahner, Thomas L. Parchman, Chris Ray, Mary M. Peacock
Software Mentions: 4
Published: over 5 years ago

10.1186/s13048-021-00802-3

Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growth
Cited by: 7
Author(s): Derek Toms, Bo Pan, Yinshan Bai, Julang Li
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-018-0515-3

Breast cancer in postmenopausal women is associated with an altered gut metagenome
Cited by: 157
Author(s): Jia Zhu, Ming Liao, Ziting Yao, Wenying Liang, Qibin Li, Jianlun Liu, Huawei Yang, Yinan Ji, Wei Wei, Aihua Tan, Sai Liang, Yang Chen, Haisong Lin, Xinyuan Zhu, Shengzhu Huang, Jiarong Tian, Rongjiang Tang, Qiuyan Wang, Zengnan Mo
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pgen.1008466

Paralog buffering contributes to the variable essentiality of genes in cancer cell lines
Cited by: 59
Author(s): Barbara De Kegel, Colm J. Ryan
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0238546

MITF and TFEB cross-regulation in melanoma cells
Cited by: 12
Author(s): Josué Ballesteros‐Álvarez, Ramile Dilshat, Valerie Fock, Katrín Möller, Ludwig Karl, Lionel Larue, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 4
Published: about 6 years ago

10.18632/oncotarget.13169

Integrated bioinformatics analysis of chromatin regulator EZH2 in regulating mRNA and lncRNA expression by ChIP sequencing and RNA sequencing
Cited by: 6
Author(s): Yuan Li, Mei Luo, Xuejiao Shi, Zhiliang Lu, Shengrong Sun, Jianbing Huang, Zhaoli Chen, Jié He
Software Mentions: 4
Published: almost 10 years ago

10.1016/j.ebiom.2016.06.048

Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies
Cited by: 33
Author(s): Karin Hellner, Fabrizio Miranda, Donatien Fotso Chedom, Sandra Herrero-González, Daniel M. Hayden, Rick Tearle, Mara Artibani, Mohammad KaramiNejadRanjbar, Ruth M. Williams, Kezia Gaitskell, Samar Elorbany, Ruoyan Xu, Alexandros Laios, Petronela Buiga, Karim Ahmed, Sunanda Dhar, Rebecca Yu Zhang, Leticia Campo, Kevin A. Myers, M. Luz Lozano, Maria Ruiz‐Miró, Sònia Gatius, Alba Mota, Gema Moreno‐Bueno, Xavier Matías‐Guiu, Javier Benı́tez, Lorna Witty, Gil McVean, Simon J. Leedham, Ian Tomlinson, Radoje Drmanac, Jean‐Baptiste Cazier, Robert J. Klein, Kevin Dunne, Robert C. Bast, Stephen Kennedy, A. Bassim Hassan, Stefano Lise, María José García, Brock A. Peters, Christopher Yau, Tatjana Sauka‐Spengler, Ahmed A. Ahmed
Software Mentions: 3
Published: about 10 years ago

10.1186/s12885-017-3711-9

Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma
Cited by: 22
Author(s): Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong’echa, Ann M. Moormann, Jeffrey A. Bailey
Software Mentions: 3
Published: almost 9 years ago

10.3390/ijms21103660

Genome-Wide Dissection of the CRF Gene Family in Brassica napus Indicates that BnaCRF8s Specifically Regulate Root Architecture and Phosphate Homeostasis against Phosphate Fluctuation in Plants
Cited by: 7
Author(s): Sheliang Wang, Hao Zhang, Lei Shi, Fangsen Xu, Guangda Ding
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-4856-x

Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen
Cited by: 25
Author(s): Muhammad Azher Nawaz, Chen Chen, Fareeha Shireen, Zhuhua Zheng, Hamza Sohail, Muhammad Afzal, Muhammad Amjad Ali, Zhilong Bie, Yuan Huang
Software Mentions: 3
Published: over 8 years ago

10.1186/s13062-017-0195-0

ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?
Cited by: 12
Author(s): Adam M. Dinan, John F. Atkins, Andrew E. Firth
Software Mentions: 3
Published: about 9 years ago

10.3390/ijms20225734

A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity
Cited by: 23
Author(s): Ryan Hunt, Gaya Hettiarachchi, Upendra Katneni, Nancy Hernandez, David D. Holcomb, Jacob Kames, Redab Alnifaidy, Brian C. Lin, Nobuko Hamasaki-Katagiri, Aaron Wesley, Tal Kafri, Christina Morris, Laura Bouché, Maria Panico, Tal Schiller, Juan C. Ibla, Haim Bar, Amra Ismail, Howard R. Morris, Anton A. Komar
Software Mentions: 3
Published: almost 7 years ago

10.1093/bioinformatics/btz433

CoCo: RNA-seq read assignment correction for nested genes and multimapped reads
Cited by: 27
Author(s): Gabrielle Deschamps-Francoeur, Vincent Boivin, Sherif Abou Elela, Michelle S. Scott
Software Mentions: 3
Published: over 7 years ago

10.1093/bioinformatics/btt650

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
Cited by: 246
Author(s): Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chávez
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pgen.1005166

Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation
Cited by: 207
Author(s): Wencheng Li, Bo You, Mainul Hoque, Dinghai Zheng, Wenting Luo, Zhe Ji, Ji Yeon Park, Samuel Gunderson, Auinash Kalsotra, James L. Manley, Bin Tian
Software Mentions: 3
Published: over 11 years ago

10.3390/ijms19113354

Transcriptome Profiles Reveal the Crucial Roles of Auxin and Cytokinin in the “Shoot Branching” of Cremastra appendiculata
Cited by: 13
Author(s): Xiang Lv, Mingsheng Zhang, Xiaolan Li, Ye RuiHua, Xiaohong Wang
Software Mentions: 3
Published: almost 8 years ago

10.3390/ijms21218252

Aging Induces Profound Changes in sncRNA in Rat Sperm and These Changes Are Modified by Perinatal Exposure to Environmental Flame Retardant
Cited by: 9
Author(s): Alexander Suvorov, J. Richard Pilsner, В. А. Наумов, Victoria Shtratnikova, Anna Zheludkevich, Evgeny S. Gerasimov, Maria D. Logacheva, Oleg Sergeyev
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.devcel.2017.05.021

Distinct Roles of RNA Helicases MVH and TDRD9 in PIWI Slicing-Triggered Mammalian piRNA Biogenesis and Function
Cited by: 60
Author(s): Joanna M. Wenda, David Homolka, Zhaolin Yang, Pietro Spinelli, Ravi Sachidanandam, Radha Raman Pandey, Ramesh S. Pillai
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-015-1983-5

Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta
Cited by: 49
Author(s): Shrikant Patil, Sara Moeys, Peter von Dassow, Marie J. J. Huysman, Daniel Mapleson, Lieven De Veylder, Remo Sanges, Wim Vyverman, Marina Montresor, Maria Immacolata Ferrante
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1004143

DNA Sequence Explains Seemingly Disordered Methylation Levels in Partially Methylated Domains of Mammalian Genomes
Cited by: 62
Author(s): Dimos Gaidatzis, Lukas Burger, Rabih Murr, Anita Lerch, Sophie Dessus-Babus, Dirk Schübeler, Michael Stadler
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pgen.1009650

DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence
Cited by: 7
Author(s): Amanda L. Fry, Amy K. Webster, Julia Burnett, Rojin Chitrakar, L. Ryan Baugh, E. Jane Albert Hubbard
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1006179

Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes
Cited by: 83
Author(s): Kyuha Choi, Carsten Reinhard, Heïdi Serra, Piotr A Ziolkowski, Charles J Underwood, Xiaohui Zhao, Thomas J. Hardcastle, Nataliya E. Yelina, Catherine Griffin, Matthew A. Jackson, Christine Mézard, Gil McVean, Gregory P. Copenhaver, Ian Henderson
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-021-86125-1

Fasciola hepatica hijacks host macrophage miRNA machinery to modulate early innate immune responses
Cited by: 19
Author(s): Nham Tran, Alison Ricafrente, Joyce To, Maria E. Lund, Tânia Monteiro Marques, Margarida Gama‐Carvalho, Krystyna Cwiklinski, John P. Dalton, Sheila Donnelly
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1009689

The native cistrome and sequence motif families of the maize ear
Cited by: 13
Author(s): Savannah D Savadel, Thomas Hartwig, Zachary M. Turpin, Daniel Vera, Pei-Yau Lung, Xin Sui, Max Blank, Wolf B. Frommer, Jane A Dennis, Jinfeng Zhang, Hank W. Bass
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2407-14-880

Deep Sequencing the microRNA profile in rhabdomyosarcoma reveals down-regulation of miR-378 family members
Cited by: 55
Author(s): Francesca Megiorni, Samantha Cialfi, Heather P. McDowell, Armando Felsani, Simona Camero, Alessandro Guffanti, Barry Pizer, Aldo Clerico, Alessandra De Grazia, Antonio Pizzuti, Anna Moles, Carlo Dominici
Software Mentions: 3
Published: almost 12 years ago

10.1093/aobpla/plab048

Analyses of open-access multi-omics data sets reveal genetic and expression characteristics of maize ZmCCT family genes
Cited by: 1
Author(s): Ming-You Dong, Lei Ling, Xian‐Wei Fan, Youzhi Li
Software Mentions: 3
Published: about 5 years ago

10.1186/s12870-019-2121-3

Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
Cited by: 14
Author(s): Juan Wang, Yuan Li, Chunjuan Li, Yan Cheng, Xiaobo Zhao, Cuiling Yuan, Quanxi Sun, Chengren Shi, Shiguang Shan
Software Mentions: 3
Published: almost 7 years ago

10.1093/database/baab053

OUP accepted manuscript
Cited by: 3
Author(s): Yi-Wei Lee, Ming Chen, I‐Fang Chung, Ting‐Yu Chang
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1009438

Toxic Y chromosome: Increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome
Cited by: 18
Author(s): Alison H. Nguyen, Doris Bachtrog
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-82905-x

Transcriptional response to the host cell environment of a multidrug-resistant Mycobacterium tuberculosis clonal outbreak Beijing strain reveals its pathogenic features
Cited by: 9
Author(s): Pakorn Aiewsakun, Pinidphon Prombutara, Tegar Adriansyah Putra Siregar, Thanida Laopanupong, Phongthon Kanjanasirirat, Tanawadee Khumpanied, Suparerk Borwornpinyo, Pirut Tong-ngam, Alisa Tubsuwan, Prapaporn Srilohasin, Angkana Chaiprasert, Wuthiwat Ruangchai, Prasit Palittapongarnpim, Therdsak Prammananan, Brian C. VanderVen, Marisa Ponpuak
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1002742

Genome-Wide Analysis of GLD-1–Mediated mRNA Regulation Suggests a Role in mRNA Storage
Cited by: 43
Author(s): Claudia Scheckel, Dimos Gaidatzis, Jane E. Wright, Rafal Ciosk
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0195003

Improved methods of DNA extraction from human spermatozoa that mitigate experimentally-induced oxidative DNA damage
Cited by: 5
Author(s): Miguel J Xavier, Brett Nixon, Shaun D. Roman, R. John Aitken
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-82979-7

Transcriptome analysis of arterial and venous circulating miRNAs during hypertension
Cited by: 2
Author(s): Ling Jin, Min Li, Hao Wang, Zhongnan Yin, Li Chen, Yang Zhou, Yongzheng Han, Qinghua Cui, Yuan Zhou, Lixiang Xue
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-60655-6

High-resolution profiling of human cytomegalovirus cell-free DNA in human plasma highlights its exceptionally fragmented nature
Cited by: 3
Author(s): Vikas Peddu, Benjamin T. Bradley, Amanda M. Casto, Raj Shree, Brice G. Colbert, Hong Xie, Tracy K. Santo, Meei‐Li Huang, Edith Cheng, Eric Q. Konnick, Stephen J. Salipante, Keith R. Jerome, Christina M. Lockwood, Alexander L. Greninger
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0113800

ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation
Cited by: 44
Author(s): Tom Sante, Sarah Vergult, Pieter-Jan Volders, Wigard P. Kloosterman, Geert Trooskens, Katleen De Preter, Annelies Dheedene, Franki Speleman, Tim De Meyer, Björn Menten
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-020-63263-6

Circulating MicroRNA Profiling in Non-ST Elevated Coronary Artery Syndrome Highlights Genomic Associations with Serial Platelet Reactivity Measurements
Cited by: 14
Author(s): Kristian C. Becker, Lydia Coulter Kwee, Megan L. Neely, Elizabeth Grass, Joseph A. Jakubowski, Keith Fox, Harvey D. White, Simon Gregory, Paul A. Gurbel, Leonardo de Pinto Carvalho, Richard C. Becker, E. Magnus Ohman, Matthew T. Roe, Svati H. Shah, Mark Y. Chan
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2229-14-141

Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana
Cited by: 86
Author(s): Yong Ding, Laëtitia Virlouvet, Ning Liu, Jean-Jack M. Riethoven, Michael Fromm, Zoya Avramova
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0094646

Post-Translational Decrease in Respiratory Chain Proteins in the Polg Mutator Mouse Brain
Cited by: 12
Author(s): David N. Hauser, Allissa Dillman, Jinhui Ding, Li Yan, Mark Cookson
Software Mentions: 3
Published: over 12 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 11 years ago

10.1186/s12864-021-08010-5

Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses
Cited by: 5
Author(s): Rumana Akter, Charles El-Hage, Fiona M. Sansom, Joan Carrick, Joanne M. Devlin, Alistair R. Legione
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-39608-1

Field transcriptome revealed a novel relationship between nitrate transport and flowering in Japanese beech
Cited by: 16
Author(s): Akiko Satake, Kazutaka Kawatsu, Kenjiro Teshima, Daisuke Kabeya, Qingmin Han
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1006988

Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis
Cited by: 28
Author(s): Daniel Antony Pass, Emily Sornay, Angela Marchbank, Margaret Crawford, Konrad Paszkiewicz, Nicholas A. Kent, James A. H. Murray
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pgen.1004566

Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27 Methylation
Cited by: 174
Author(s): Relja Popovic, Eva Martínez-García, Ευγενία Γιαννοπούλου, Quanwei Zhang, Qingyang Zhang, Teresa Ezponda, Mrinal Y. Shah, Yupeng Zheng, Christine M. Will, Eliza C. Small, Youjia Hua, Marinka Bulic, Yanwen Jiang, Matteo Carrara, Raffaele Calogero, William L. Kath, Neil L. Kelleher, Ji Ping Wang, Olivier Elemento, Jonathan D. Licht
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0211430

Role of CsrA in stress responses and metabolism important for Salmonella virulence revealed by integrated transcriptomics
Cited by: 36
Author(s): Anastasia H. Potts, Yinping Guo, Brian M. M. Ahmer, Tony Romeo
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-017-1187-z

De novo transcriptome assembly from flower buds of dioecious, gynomonoecious and chemically masculinized female Coccinia grandis reveals genes associated with sex expression and modification
Cited by: 16
Author(s): Ravi Suresh Devani, Sangram Sinha, Jayeeta Banerjee, Rabindra Kumar Sinha, Abdelhafid Bendahmane, Anjan K. Banerjee
Software Mentions: 3
Published: almost 9 years ago

10.1371/currents.md.d0c203c018bc024f2f4c9791ecb05f88

Exploratory Profiling of Urine MicroRNAs in the dy2J/dy2J Mouse Model of LAMA2-CMD: Relation to Disease Progression
Cited by: 5
Author(s): Bernardo Moreira Soares Oliveira, Kinga I. Gawlik, Madeleine Durbeej, Johan Holmberg
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0062547

p63 Attenuates Epithelial to Mesenchymal Potential in an Experimental Prostate Cell Model
Cited by: 29
Author(s): Jan Roger Olsen, Anne Margrete Øyan, Kari Rostad, Margrete R. Hellem, Jie Liu, Lisha Li, David Micklem, Hallvard Haugen, James B. Lorens, Varda Rotter, Xisong Ke, Biaoyang Lin, Karl‐Henning Kalland
Software Mentions: 3
Published: over 13 years ago

10.1038/s41598-019-38932-w

Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants
Cited by: 8
Author(s): Kun Yang, Xiaopeng Wen, Suresh B. Mudunuri, G. P. S. Varma, Gaurav Sablok
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-43141-6

CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement
Cited by: 62
Author(s): Joshua K. Young, Gina Zastrow-Hayes, Stéphane Deschamps, Sergei Svitashev, Mindaugas Zaremba, Ananta Acharya, Sushmitha Paulraj, Brooke D. Peterson-Burch, Chris Schwartz, Vesna Djukanovic, Brian Lenderts, Lanie Feigenbutz, Limin Wang, Clara M. Alarcon, Virginijus Šikšnys, Gregory D. May, N. Doane Chilcoat, Sandeep Kumar
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-020-02528-8

Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid
Cited by: 7
Author(s): Weiling Luan, Yan Dai, Xinyu Li, Yan Wang, Tao Xiang, Caixia Li, Ping Mao, Xinrong Ma
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-29604-2

ICAM1 expression is induced by proinflammatory cytokines and associated with TLS formation in aggressive breast cancer subtypes
Cited by: 63
Author(s): Stine Figenschau, Erik Knutsen, Ilona Urbárová, Christopher Graham Fenton, B. Elston, Maria Perander, Elin Mortensen, Kristin Andreassen Fenton
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pcbi.1002714

Confidence-based Somatic Mutation Evaluation and Prioritization
Cited by: 30
Author(s): Martin Löwer, Bernhard Y. Renard, Jos de Graaf, Meike Wagner, Claudia Paret, Kneip Christoph, Özlem Türeci, Mustafa Diken, Cedrik M. Britten, Sebastian Kreiter, Michael Koslowski, John C. Castle, Uğur Şahin
Software Mentions: 3
Published: about 14 years ago

10.1038/s41598-018-19323-z

Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach
Cited by: 16
Author(s): Arne Jacobs, Michele De Noia, Kim Præbel, Øyvind Kanstad-Hanssen, Marta Paterno, David W. Jackson, Philip McGinnity, Armin Sturm, Kathryn R. Elmer, Martin S. Llewellyn
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-22798-5

Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane
Cited by: 14
Author(s): Ratnesh Singh, Tyler Jones, Ching Man Wai, John Jifon, Chifumi Nagai, Ray Ming, Qingyi Yu
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-33947-1

Genome wide mapping of ETV6 binding sites in pre-B leukemic cells
Cited by: 9
Author(s): Benjamin Neveu, Maxime Caron, Karine Lagacé, Chantal Richer, Daniel Sinnett
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12870-019-2166-3

Transcriptomic and proteomic analysis reveals mechanisms of low pollen-pistil compatibility during water lily cross breeding
Cited by: 10
Author(s): Caixia Sun, Fadi Chen, Nianjun Teng, Yue-Mei Yao, Xi Shan, Zhigang Dai
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pcbi.1005706

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment
Cited by: 62
Author(s): Julia Fukuyama, Laurie Rumker, Kris Sankaran, P. Jeganathan, Les Dethlefsen, David A. Relman, Susan Holmes
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0077490

Transcriptional Reprogramming of CD11b+Esamhi Dendritic Cell Identity and Function by Loss of Runx3
Cited by: 29
Author(s): Joseph Dicken, Alexander Mildner, Dena Leshkowitz, Ivo P. Touw, Shay Hantisteanu, Steffen Jung, Yoram Groner
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pcbi.1007309

miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs
Cited by: 8
Author(s): Jimmy D. Bell, Maureen K. Larson, Michelle Anne Kutzler, Massimo Bionaz, Christiane V. Löhr, David A. Hendrix
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-017-12989-x

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells
Cited by: 62
Author(s): Simone Rizzetto, Auda A. Eltahla, Peijie Lin, Rowena A. Bull, Andrew R. Lloyd, Joshua W. K. Ho, Vanessa Venturi, Fabio Luciani
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0083723

Function of GATA Factors in the Adult Mouse Liver
Cited by: 39
Author(s): Rena Zheng, Boris Rebolledo‐Jaramillo, Yiwei Zong, Liqing Wang, Pierre Russo, Wayne W. Hancock, Ben Z. Stanger, Ross C. Hardison, Gerd A. Blobel
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41598-018-34243-8

The evolutionary dynamics of microRNAs in domestic mammals
Cited by: 17
Author(s): Luca Penso-Dolfin, Simon Moxon, Wilfried Haerty, Federica Di Palma
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1007543

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
Cited by: 6
Author(s): Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Mitchell D. Probasco, Ning Leng, Bret Duffin, John Steill, Scott Swanson, Brian E. McIntosh, Ron Stewart, Christina Kendziorski, James A. Thomson, Rhonda Bacher
Software Mentions: 3
Published: almost 7 years ago

10.1038/srep42702

Aging and serum exomiR content in women-effects of estrogenic hormone replacement therapy
Cited by: 23
Author(s): Reeta Kangas, Timo Törmäkangas, Vidal Fey, Juha Pursiheimo, Ilkka Miinalainen, Markku Alén, Jaakko Kaprio, Sarianna Sipilä, Anna‐Marja Säämänen, Vuokko Kovanen, Eija K. Laakkonen
Software Mentions: 3
Published: over 9 years ago

10.1038/srep44605

MicroRNA roles in signalling during lactation: an insight from differential expression, time course and pathway analyses of deep sequence data
Cited by: 65
Author(s): Duy Ngoc, Ran Li, Pier-Luc Dudemaine, Eveline M. Ibeagha‐Awemu
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0150591

Analysis of the Phialocephala subalpina Transcriptome during Colonization of Its Host Plant Picea abies
Cited by: 11
Author(s): Vanessa Reininger, Markus Schlegel
Software Mentions: 3
Published: over 10 years ago

10.1186/s12860-020-00251-8

Identification of universal and cell-type specific p53 DNA binding
Cited by: 14
Author(s): Antonina Hafner, Lyubov Kublo, Michael Tsabar, Galit Lahav, Jacob Stewart-Ornstein
Software Mentions: 3
Published: over 6 years ago

10.1038/srep41328

PrimerSuite: A High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR
Cited by: 32
Author(s): Jennifer Lu, Andrew D. Johnston, Philippe Berichon, Kelin Ru, Darren Korbie, Matt Trau
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0142262

High-Throughput Profiling of Caenorhabditis elegans Starvation-Responsive microRNAs
Cited by: 16
Author(s): Laura García-Segura, Cei Abreu‐Goodger, Armando Hernández-Mendoza, Tzvetanka D. Dinkova, Luis Padilla-Noriega, Martha Elva Pérez-Andrade, Juan Miranda-Ríos
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-15-406

Differential gene expression between functionally specialized polyps of the colonial hydrozoan Hydractinia symbiolongicarpus (Phylum Cnidaria)
Cited by: 43
Author(s): Steven M. Sanders, Mariya Shcheglovitova, Paulyn Cartwright
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pbio.2002039

Dual role of starvation signaling in promoting growth and recovery
Cited by: 17
Author(s): Yonat Gurvich, Dena Leshkowitz, Naama Barkai
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12866-015-0370-3

New insights into the fungal community from the raw genomic sequence data of fig wasp Ceratosolen solmsi
Cited by: 5
Author(s): Lihua Niu, Xiufeng Song, Shunmin He, Peng Zhang, Ningxin Wang, Yi Li, Dawei Huang
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pbio.3000689

Telomeric TART elements target the piRNA machinery in Drosophila
Cited by: 7
Author(s): Chris Ellison, Meenakshi S. Kagda, Weihuan Cao
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12915-020-00897-y

Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression
Cited by: 7
Author(s): Ulfar Bergthorsson, Caroline J. Sheeba, Anke Konrad, Tony Bélicard, Toni Beltran, Vaishali Katju, Peter Sarkies
Software Mentions: 3
Published: almost 6 years ago

10.1038/srep16324

Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference
Cited by: 42
Author(s): Juan Pablo Isaza, Ana Luz Galván, Víctor Polanco, Bernice Huang, Andrey V. Matveyev, Myrna G. Serrano, Patrício Manque, Gregory A. Buck, Juan F. Alzate
Software Mentions: 3
Published: almost 11 years ago

10.1126/sciadv.aau8317

The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice
Cited by: 387
Author(s): Peng Zheng, Benhua Zeng, Meiling Liu, Jianjun Chen, Junxi Pan, Han Yu, Yiyun Liu, Ke Cheng, Chanjuan Zhou, Haiyang Wang, Xinyu Zhou, Siwen Gui, Seth W. Perry, Ma‐Li Wong, Júlio Licinio, Hong Wei, Peng Xie
Software Mentions: 3
Published: over 7 years ago

10.1038/sdata.2017.161

Nasopharyngeal metagenomic deep sequencing data, Lancaster, UK, 2014–2015
Cited by: 2
Author(s): Kate V. Atkinson, L.A. Bishop, Glenn Rhodes, Nicolas Salez, Neil McEwan, Matthew J. Hegarty, Julie Robey, Nicola Harding, Simon Wetherell, Robert M. Lauder, Roger W. Pickup, Mark Wilkinson, Derek Gatherer
Software Mentions: 3
Published: almost 9 years ago

10.1186/1746-4811-8-12

Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis
Cited by: 18
Author(s): Kun-Hsiang Liu, Matthew McCormack, Jenq-Yunn Sheen
Software Mentions: 3
Published: almost 15 years ago

10.1186/1471-2350-15-43

Identification of transcription factors and single nucleotide polymorphisms of Lrh1 and its homologous genes in Lrh1-knockout pancreas of mice
Cited by: 1
Author(s): Maochun Tang, Li Cheng, Rongrong Jia, Lei Qiu, Hua Liu, Zhou Shu, Xiaolong Ma, Guoyong Hu, Xingpeng Wang, Yan Zhao
Software Mentions: 3
Published: over 12 years ago

10.1186/gb-2013-14-7-r72

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design
Cited by: 18
Author(s): Robin P. Smith, Samantha J. Riesenfeld, Alisha K. Holloway, Qiang Li, Karl K. Murphy, Natalie M. Feliciano, Lorenzo Orecchia, Nir Oksenberg, Katherine S. Pollard, Nadav Ahituv
Software Mentions: 3
Published: almost 14 years ago

10.1111/tpj.14632

Translational regulation contributes to the elevated CO 2 response in two Solanum species
Cited by: 12
Author(s): Sharon B. Gray, Joel Rodríguez-Medina, Samuel Rusoff, Ted Toal, Kaisa Kajala, Daniel E. Runcie, Siobhán M. Brady
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-015-2214-9

Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum
Cited by: 5
Author(s): Xueqing Maggie Lu, Evelien M. Bunnik, Neeti Pokhriyal, Sara Nasseri, Stefano Lonardi, Karine G. Le Roch
Software Mentions: 3
Published: almost 11 years ago

10.1111/pbi.12742

Assembly and comparison of two closely related Brassica napus genomes
Cited by: 129
Author(s): Philipp E. Bayer, Bhavna Hurgobin, Agnieszka A. Golicz, Chon‐Kit Kenneth Chan, Yuxuan Yuan, HueyTyng Lee, Michael Renton, Jianghong Meng, Ruiyuan Li, Yan Long, Jun Zou, Ian Bancroft, Boulos Chalhoub, Graham J. King, Jacqueline Batley, David Edwards
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-12-199

Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems
Cited by: 115
Author(s): Shanshan Yang, Zheng Jin Tu, Foo Cheung, Wayne Xu, J. F. S. Lamb, H. G. Jung, Carroll P. Vance, John W. Gronwald
Software Mentions: 3
Published: over 15 years ago

10.1038/s41597-020-0480-0

An improved high-quality genome assembly and annotation of Tibetan hulless barley
Cited by: 23
Author(s): Xingquan Zeng, Tong Xu, Zhihao Ling, Yulin Wang, Xiangfeng Li, Shuqing Xu, Qijun Xu, Zha Sang, Wangmu Qimei, Yuzhen Basang, Jiabu Dunzhu, Mingzhai Yu, Hongjun Yuan, Nyima Tashi
Software Mentions: 3
Published: over 6 years ago

10.1111/pbi.12988

Multi‐omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process
Cited by: 81
Author(s): Jianying Li, Maojun Wang, Yajun Li, Qinghua Zhang, Keith Lindsey, Henry Daniell, Shuangxia Jin, Xianlong Zhang
Software Mentions: 3
Published: about 8 years ago

10.1111/pbi.13136

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection
Cited by: 83
Author(s): Shan Wu, Xin Wang, Umesh K. Reddy, Honghe Sun, Kan Bao, Lei Gao, Linyong Mao, Takshay Patel, Carlos E. Ortíz, Venkata Lakshmi Abburi, Padma Nimmakayala, Sandra Branham, Patrick Wechter, Laura Massey, Kai-Shu Ling, Chandrasekar S. Kousik, Sue A. Hammar, Yaakov Tadmor, Vitaly Portnoy, Amit Gur, Nurit Katzir, Nihat Guner, Angela R. Davis, Alvaro G. Hernandez, Chris Wright, Cecilia McGregor, Robert L. Jarret, Xingping Zhang, Yong Xu, Todd C. Wehner, Rebecca Grumet, Amnon Levi, Zhangjun Fei
Software Mentions: 3
Published: over 7 years ago

10.1186/gb-2011-12-5-r44

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
Cited by: 309
Author(s): Christopher S. Miller, Brett J. Baker, Brian C. Thomas, Steven W. Singer, Jillian F. Banfield
Software Mentions: 3
Published: over 15 years ago

10.3390/genes8100237

Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin
Cited by: 45
Author(s): Mayra Eduardoff, Catarina Xavier, Christina Strobl, Andrea Casas-Vargas, Walther Parson
Software Mentions: 3
Published: about 9 years ago

10.3390/genes10100795

Identification of Long Non-Coding RNA-Associated Competing Endogenous RNA Network in the Differentiation of Chicken Preadipocytes
Cited by: 21
Author(s): Lan Chen, Tao Zhang, Shanshan Zhang, Jen‐Wei Huang, Genxi Zhang, Kaizhou Xie, Jinyu Wang, Haiqing Wang, Guojun Dai
Software Mentions: 3
Published: about 7 years ago

10.1534/g3.119.400365

Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression
Cited by: 38
Author(s): Adam J. Bewick, Yinwen Zhang, Jered M. Wendte, Xiaoyu Zhang, Robert J. Schmitz
Software Mentions: 3
Published: about 7 years ago

10.1534/g3.118.200872

A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting inDrosophilaFollicular Somatic Cells
Cited by: 4
Author(s): Nelson Martins, Aurélie Lemoine, Estelle Santiago, Simona Paro, Jean‐Luc Imler, Carine Meignin
Software Mentions: 3
Published: over 7 years ago

10.3390/ani10091640

Effect of Concentrate Supplementation on the Expression Profile of miRNA in the Ovaries of Yak during Non-Breeding Season
Cited by: 5
Author(s): Jiancheng Xie, Qudratullah Kalwar, Ping Yan, Xian Guo
Software Mentions: 3
Published: about 6 years ago

10.7717/peerj.1828

The myogenic electric organ ofSternopygus macrurus: a non-contractile tissue with a skeletal muscle transcriptome
Cited by: 10
Author(s): Matthew Pinch, Robert Güth, Manoj P. Samanta, Alexander Chaidez, Graciela A. Unguez
Software Mentions: 3
Published: over 10 years ago

Projects: pypi: bowtie

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Papers Mentioning bowtie 1,566