pypi: bowtie | Projects | Ecosyste.ms: Papers

10.1038/tp.2016.181

Impaired GABA synthesis, uptake and release are associated with depression-like behaviors induced by chronic mild stress
Cited by: 110
Author(s): Kewei Ma, Aidong Xu, Sheng Cui, Sun Mr, Xue Yc, Wang Jh
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0155039

RNA Sequencing of Trigeminal Ganglia in Rattus Norvegicus after Glyceryl Trinitrate Infusion with Relevance to Migraine
Cited by: 7
Author(s): S. Pedersen, Lasse Maretty, Roshni Ramachandran, Jonas Andreas Sibbesen, Victor Yakimov, Rikke Elgaard-Christensen, Thomas Folkmann Hansen, Anders Krogh, Jes Olesen, Inger Jansen‐Olesen
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0094270

Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs
Cited by: 27
Author(s): Nicholas J. Schurch, Christian Callebaut, Alexander Sherstnev, Junfang Song, Céline Duc, Kate G. Storey, Whi McLean, Sara J. Brown, Gordon G. Simpson, Geoffrey J. Barton
Software Mentions: 3
Published: over 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

10.1186/1471-2164-15-733

Integrating dilution-based sequencing and population genotypes for single individual haplotyping
Cited by: 1
Author(s): Hirotaka Matsumoto, Hisanori Kiryu
Software Mentions: 3
Published: almost 13 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

10.7554/eLife.02407

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons
Cited by: 464
Author(s): Iris Jonkers, Ho Young Kwak, John T. Lis
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0041645

Deep Sequencing-Based Transcriptome Analysis of Chicken Spleen in Response to Avian Pathogenic Escherichia coli (APEC) Infection
Cited by: 36
Author(s): Qinghua Nie, Erin Sandford, Xiquan Zhang, Lisa K. Nolan, Susan J. Lamont
Software Mentions: 3
Published: about 14 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

10.1371/journal.pone.0226707

High expression of olfactomedin-4 is correlated with chemoresistance and poor prognosis in pancreatic cancer
Cited by: 15
Author(s): Ryotaro Ohkuma, Erica Yada, Shumpei Ishikawa, Daisuke Komura, Hidenobu Ishizaki, Koji Tamada, Yutaro Kubota, Kazuyuki Hamada, Hiroo Ishida, Yuya Hirasawa, Hirotsugu Ariizumi, Etsuko Satoh, Midori Shida, Makoto Watanabe, Rie Onoue, Kiyohiro Ando, Junji Tsurutani, Kiyoshi Yoshimura, Takehiko Yokobori, Tetsuro Sasada, Takeshi Aoki, Masahiko Murakami, Tomoko Norose, Nobuyuki Ohike, Masafumi Takimoto, Masahiko Izumizaki, Shinichi Kobayashi, Takuya Tsunoda, Satoshi Wada
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-016-3164-6

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
Cited by: 12
Author(s): Peter J. Hansen, Jochen Hecht, Jonas Ibn-Salem, Benjamin S. Menkuec, Sebastian Roskosch, Mathias Truss, Peter N. Robinson
Software Mentions: 3
Published: almost 10 years ago

10.7554/eLife.41927

Nuclear genetic regulation of the human mitochondrial transcriptome
Cited by: 50
Author(s): Ali At, Lena Boehme, Guillermo Carbajosa, Vlad C. Seitan, Kerrin S. Small, Alan Hodgkinson
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0233394

Gene expression regulation by the Chromodomain helicase DNA-binding protein 9 (CHD9) chromatin remodeler is dispensable for murine development
Cited by: 11
Author(s): Andrej Alendar, Jan-Paul Lambooij, Rajith Bhaskaran, Cesare Lancini, Ji‐Ying Song, H. van Vugt, Michiel Snoek, Anton Berns
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.39842

Environmentally-induced epigenetic conversion of a piRNA cluster
Cited by: 23
Author(s): Karine Casier, Valérie Delmarre, Nathalie Gueguen, Catherine Hermant, Elise Viodé, Chantal Vaury, Stéphane Ronsseray, Emilie Brasset, Laure Teysset, Antoine Boivin
Software Mentions: 3
Published: over 7 years ago

10.3390/toxins12050290

AFB1 Induced Transcriptional Regulation Related to Apoptosis and Lipid Metabolism in Liver of Chicken
Cited by: 27
Author(s): Xueqin Liu, Suchismita Mishra, Tao Wang, Zhongxian Xu, Xiaoling Zhao, Yan Wang, Huadong Yin, Xiaolan Fan, Bo Zeng, Mingyao Yang, Dapeng Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Qing Zhu, Feng Chen, Diyan Li
Software Mentions: 3
Published: over 6 years ago

10.1016/j.ijpddr.2018.03.006

The anti-fecundity effect of 5-azacytidine (5-AzaC) on Schistosoma mansoni is linked to dis-regulated transcription, translation and stem cell activities
Cited by: 18
Author(s): Kathrin K. Geyer, Sabrina E. Munshi, Martin Vickers, Michael Squance, Toby Wilkinson, Daniel Berrar, Cristian Chaparro, Martin Swain, Karl F. Hoffmann
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0233044

Runx3 prevents spontaneous colitis by directing the differentiation of anti-inflammatory mononuclear phagocytes
Cited by: 13
Author(s): Shay Hantisteanu, Yosef Dicken, Varda Negreanu, Dalia Goldenberg, Ori Brenner, Dena Leshkowitz, Joseph Lotem, Ditsa Levanon, Yoram Groner
Software Mentions: 3
Published: over 6 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

10.1371/journal.pone.0237087

Sequencing and assembly of the Egyptian buffalo genome
Cited by: 10
Author(s): Dina A. El-Khishin, Amr Ageez, Mohamed E. Saad, Amr Ibrahim, Moustafa Shokrof, L. Hassan, Mohamed Abouelhoda
Software Mentions: 3
Published: about 6 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

10.1016/j.ijpara.2020.06.002

Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host
Cited by: 15
Author(s): Ruby White, Sujai Kumar, Wang Ngai Chow, E. Graeme Robertson, Kelly S. Hayes, Richard K. Grencis, María A. Duque-Correa, Amy H. Buck
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.18290

Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility
Cited by: 109
Author(s): Chan-Wang Jerry Lio, Jiayuan Zhang, Edahí González-Avalos, Patrick G. Hogan, Xing Chang, Anjana Rao
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0085648

RNA Polymerase III Transcriptomes in Human Embryonic Stem Cells and Induced Pluripotent Stem Cells, and Relationships with Pluripotency Transcription Factors
Cited by: 32
Author(s): Ravi Alla, Bradley R. Cairns
Software Mentions: 3
Published: almost 13 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

10.1371/journal.pone.0151105

Transcriptome Profiling of Two Asparagus Bean (Vigna unguiculata subsp. sesquipedalis) Cultivars Differing in Chilling Tolerance under Cold Stress
Cited by: 23
Author(s): Haidong Tan, Haitao Huang, Manman Tie, Yi Tang, Yunsong Lai, Huanxiu Li
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-016-2995-5

RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.)
Cited by: 57
Author(s): Kazuma Suzuki, Tomohiro Suzuki, Takashi Nakatsuka, Hideo Dohra, Masumi Yamagishi, Kohei Matsuyama, Hideyuki Matsuura
Software Mentions: 3
Published: about 10 years ago

10.1007/s11626-017-0140-7

Relevant principal factors affecting the reproducibility of insect primary culture
Cited by: 2
Author(s): Naoya Ogata, Kikuo Iwabuchi
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0231738

mmannot: How to improve small–RNA annotation?
Cited by: 1
Author(s): Matthias Zytnicki, Christine Gaspin
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-955

Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification
Cited by: 34
Author(s): Victoria Morin-Adeline, Rodrigo Lomas, Denis O’Meally, Colin M. Stack, Ana Conesa, Jan Šlapeta
Software Mentions: 3
Published: almost 12 years ago

10.1093/hmg/ddaa053

DUX4 expressing immortalized FSHD lymphoblastoid cells express genes elevated in FSHD muscle biopsies, correlating with the early stages of inflammation
Cited by: 16
Author(s): Christopher R. S. Banerji, Maryna Panamarova, Peter S. Zammit
Software Mentions: 3
Published: over 6 years ago

10.1186/1751-0473-8-6

RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics
Cited by: 1
Author(s): Izawa Akiko, Jun Sese
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0096105

Patterns of Genome-Wide VDR Locations
Cited by: 112
Author(s): Pauli Tuoresmäki, Sami Vaïsänen, Antonio Neme, Sami Heikkinen, Carsten Carlberg
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0067788

LOcating Non-Unique matched Tags (LONUT) to Improve the Detection of the Enriched Regions for ChIP-seq Data
Cited by: 11
Author(s): Rui Wang, Hang Kai Hsu, Adam Blattler, Yisong Wang, Xun Lan, Yao Wang, Pei Yin Hsu, Yu Wei Leu, Tim H.M. Huang, Peggy J. Farnham, Victor X. Jin
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0226905

Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells
Cited by: 9
Author(s): Xiangqin Ji, Penglei Jiang, Juntao Luo, Mengjia Li, Yajing Bai, Junfang Zhang, Bingshe Han
Software Mentions: 3
Published: almost 7 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

10.7554/eLife.21964

DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells
Cited by: 25
Author(s): Sarah J. Hainer, Kurtis N. McCannell, Jun Yu, Ly-Sha Ee, Lihua Julie Zhu, Oliver J. Rando, Thomas G. Fazzio
Software Mentions: 3
Published: almost 10 years ago

10.1128/mSystems.00046-17

Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling
Cited by: 179
Author(s): Eva d’Hennezel, Sahar Abubucker, Leon O. Murphy, Thomas W. Cullen
Software Mentions: 3
Published: almost 9 years ago

10.1128/mBio.01053-20

FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo
Cited by: 3
Author(s): Alexandre Duprey, Eduardo A. Groisman
Software Mentions: 3
Published: about 6 years ago

10.1128/mBio.01950-18

Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery
Cited by: 8
Author(s): James T. Van Leuven, Meng Mao, Denghui Xing, Gordon M. Bennett, John P. McCutcheon
Software Mentions: 3
Published: over 7 years ago

10.1128/mBio.02047-18

Nucleotide Resolution Comparison of Transcription of Human Cytomegalovirus and Host Genomes Reveals Universal Use of RNA Polymerase II Elongation Control Driven by Dissimilar Core Promoter Elements
Cited by: 25
Author(s): Mrutyunjaya Parida, Kyle A. Nilson, Ming Li, Christopher B. Ball, Harrison A. Fuchs, Christine Lawson, Donal S. Luse, Jeffery L. Meier, David H. Price
Software Mentions: 3
Published: over 7 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.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

10.3389/fnins.2018.00243

Adar3 Is Involved in Learning and Memory in Mice
Cited by: 48
Author(s): Dessislava Mladenova, Guy Barry, Lyndsey M. Konen, Sandy S. Pineda, Boris Guennewig, Lotta Avesson, Raphael Zinn, Nicole Schönrock, Mainá Bitar, Nicky Jonkhout, Lauren Crumlish, Dominik C. Kaczorowski, Andrew Gong, Mark Pinese, Glória Regina Franco, Carl R. Walkley, Bryce Vissel, John S. Mattick
Software Mentions: 3
Published: over 8 years ago

10.1186/1755-8794-4-19

Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes
Cited by: 40
Author(s): Dominik Beck, Steve Ayers, Jianguo Wen, Miriam Brandl, Tuan D. Pham, Paul Webb, Chung Che Chang, Xiaobo Zhou
Software Mentions: 3
Published: over 15 years ago

10.3389/fmicb.2020.01665

Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger
Cited by: 36
Author(s): Ning Yao, Jianzhao Qi, Michael Dobbins, Xiaobo Liang, Jingxuan Wang, Shiyu Chen, Jingyun Ma, Guangshun Jiang
Software Mentions: 3
Published: about 6 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

10.3389/fonc.2020.00037

Genomic Identification of RNA Editing Through Integrating Omics Datasets and the Clinical Relevance in Hepatocellular Carcinoma
Cited by: 8
Author(s): Juan Chen, Lu Wang, Fangbin Wang, Jian Liu, Zhenyu Bai
Software Mentions: 3
Published: over 6 years ago

10.3389/fphar.2021.596535

The Widely Used Antihelmintic Drug Albendazole is a Potent Inducer of Loss of Heterozygosity
Cited by: 3
Author(s): Luiza Sheyla Evenni Porfírio Will Castro, Wietske Pieters, Mir Farshid Alemdehy, Muhammad Aslam, Olimpia Alessandra Buoninfante, Jonne A. Raaijmakers, Bas Pilzecker, Paul C.M. van den Berk, Hein te Riele, René H. Medema, Rozangela Curi Pedrosa, Heinz Jacobs
Software Mentions: 3
Published: over 5 years ago

10.3389/fphar.2020.622658

Involvement of Circulating Exosomal MicroRNAs in Jian-Pi-Yi-Shen Formula Protection Against Adenine-Induced Chronic Kidney Disease
Cited by: 5
Author(s): Xinhui Liu, Siqi Liu, Denggui Luo, Shiying Huang, Fochang Wang, Bing Zhang, Yulian Chen, Lin Zheng, Jiandong Lu, Shunmin Li
Software Mentions: 3
Published: over 5 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

10.3389/fmicb.2020.02075

Sodium New Houttuyfonate Inhibits Candida albicans Biofilm Formation by Inhibiting the Ras1-cAMP-Efg1 Pathway Revealed by RNA-seq
Cited by: 21
Author(s): Jiadi Wu, Donghui Wu, Yeye Zhao, Yuanqing Si, Longfei Mei, Jing Shao, Tianming Wang, Yan Ge, Changzhong Wang
Software Mentions: 3
Published: about 6 years ago

10.3389/fphys.2015.00286

Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution
Cited by: 30
Author(s): Anita Tripathi, Kavita Goswami, Neeti Sanan-Mishra
Software Mentions: 3
Published: almost 11 years ago

10.7554/eLife.32341

CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
Cited by: 60
Author(s): Gabriel Aughey, Alicia Estacio-Gómez, Jamie Thomson, Hang Yin, Tony D. Southall
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-14-648

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs
Cited by: 80
Author(s): Jeroen Crappé, Wim Van Criekinge, Geert Trooskens, Eisuke Hayakawa, Walter Luyten, Geert Baggerman, Gerben Menschaert
Software Mentions: 3
Published: almost 14 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

10.1186/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

10.1534/g3.117.300318

Pas de deux: An Intricate Dance of Anther Smut and Its Host
Cited by: 5
Author(s): Su San Toh, Zehua Chen, Eric C. Rouchka, David J. Schultz, Christina A. Cuomo, Michael H. Perlin
Software Mentions: 3
Published: over 8 years ago

10.1534/g3.116.035873

First in Vivo Batrachochytrium dendrobatidis Transcriptomes Reveal Mechanisms of Host Exploitation, Host-Specific Gene Expression, and Expressed Genotype Shifts
Cited by: 21
Author(s): Amy Ellison, Graziella V. DiRenzo, Cait A. McDonald, Karen R. Lips, Kelly R. Zamudio
Software Mentions: 3
Published: almost 10 years ago

10.7554/eLife.01439

Coordinated genomic control of ciliogenesis and cell movement by RFX2
Cited by: 115
Author(s): Mei I. Chung, Taejoon Kwon, Fan Tu, Eric Brooks, Ritu Gupta, Matthew D. Meyer, Julie C. Baker, Edward M. Marcotte, John B. Wallingford
Software Mentions: 3
Published: almost 13 years ago

10.1534/g3.116.031120

Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea
Cited by: 12
Author(s): Vairavan Lakshmanan, Dhiru Bansal, Jahnavi Kulkarni, Deepak Poduval, Srikar Krishna, Vidyanand Sasidharan, Praveen Anand, Aswin Sai Narain Seshasayee
Software Mentions: 3
Published: about 10 years ago

10.3389/fmicb.2020.00395

Different Genetic Sources Contribute to the Small RNA Population in the Arbuscular Mycorrhizal Fungus Gigaspora margarita
Cited by: 17
Author(s): Alessandro Silvestri, Massimo Turina, Valentina Fiorilli, Laura Miozzi, Francesco Venice, Paola Bonfante, Luisa Lanfranco
Software Mentions: 3
Published: over 6 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

10.1186/1471-2229-14-141

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

10.3389/fpls.2016.01920

Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax
Cited by: 45
Author(s): Alexey A. Dmitriev, George S. Krasnov, Tatiana A. Rozhmina, Natalya V. Kishlyan, Alexander V. Zyablitsin, А. Ф. Садритдинова, Anastasiya V. Snezhkina, Maria Fedorova, Olga Yu. Yurkevich, Olga V. Muravenko, Nadezhda L. Bolsheva, Anna V. Kudryavtseva, Nataliya V. Melnikova
Software Mentions: 3
Published: almost 10 years ago

10.3389/fpls.2018.00497

Massive Loss of DNA Methylation in Nitrogen-, but Not in Phosphorus-Deficient Zea mays Roots Is Poorly Correlated With Gene Expression Differences
Cited by: 28
Author(s): Svenja Mager, Uwe Ludewig
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2020.00176

Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants
Cited by: 14
Author(s): Claudius Grehl, M. Wagner, Ioana Lemnian, Bruno Glaser, Ivo Große
Software Mentions: 3
Published: over 6 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

10.3389/fpls.2017.00468

Transcriptomic Response of Chinese Yew (Taxus chinensis) to Cold Stress
Cited by: 29
Author(s): Delong Meng, YU Xiang-hua, Liyuan Ma, Jin Hu, Yili Liang, Xueduan Liu, Huaqun Yin, Hongwei Liu, Xiaojia He, Diqiang Li
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2017.00322

isomiR2Function: An Integrated Workflow for Identifying MicroRNA Variants in Plants
Cited by: 9
Author(s): Kun Yang, Gaurav Sablok, Guang Hang Qiao, Qiang Nie, Xiaopeng Wen
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-016-2539-z

A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome
Cited by: 117
Author(s): Laurence Ettwiller, John A. Buswell, Erbay Yigit, Ira Schildkraut
Software Mentions: 3
Published: over 10 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

10.1038/s41398-019-0538-y

Temporal dynamics of miRNAs in human DLPFC and its association with miRNA dysregulation in schizophrenia
Cited by: 24
Author(s): Zhonghua Hu, Shaojian Gao, Daniel M. Lindberg, Debabrata Panja, Yoshi Wakabayashi, Keshen Li, Joel E. Kleinman, Jun Zhu, Zheng Li
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.34870

OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development
Cited by: 44
Author(s): Joel Hrit, Leeanne Goodrich, Li Cheng, Bang-An Wang, Ji Nie, Xiaolong Cui, Elizabeth Allene Martin, Eric Simental, Jenna Fernandez, Monica Yun Liu, Joseph R. Nery, Rosa Castanon, Rahul M. Kohli, Natalia Tretyakova, Chuan He, Joseph R. Ecker, Mary Goll, Barbara Panning
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.29494

Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow
Cited by: 23
Author(s): Patrick A. Murphy, Vincent Butty, Paul L. Boutz, Shahinoor Begum, Amy Kimble, Phillip A. Sharp, Christopher B. Burge, Richard O. Hynes
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.71611

A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability
Cited by: 3
Author(s): Michèle Felletti, Cédric Romilly, E. Gerhart H. Wagner, Kristina Jonas
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.35989

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation
Cited by: 129
Author(s): Daniel Fuentes, Tomek Swigut, Joanna Wysocka
Software Mentions: 3
Published: about 8 years ago

10.7554/eLife.14295

Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation
Cited by: 125
Author(s): Ryuta Ishimura, Gábor Nagy, Iván Dotú, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 3
Published: over 10 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

10.1093/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

10.1186/1471-2164-13-50

Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages
Cited by: 68
Author(s): Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynänen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R. Steffensen, Carsten Carlberg
Software Mentions: 3
Published: over 14 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

10.1371/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

10.7554/eLife.26845

Unfolded protein response transducer IRE1-mediated signaling independent of XBP1 mRNA splicing is not required for growth and development of medaka fish
Cited by: 34
Author(s): Tokiro Ishikawa, Makoto Kashima, Atsushi J. Nagano, Tomoko Ishikawa-Fujiwara, Yasuhiro Kamei, Tomoki Todo, Kazutoshi Mori
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

10.7554/eLife.27596

Maturation of selected human mitochondrial tRNAs requires deadenylation
Cited by: 68
Author(s): Sarah F Pearce, Joanna Rorbach, Lindsey Van Haute, Aaron R. D’Souza, Pedro Rebelo-Guiomar, Christopher A. Powell, Ian Brierley, Andrew E. Firth, Michal Minczuk
Software Mentions: 3
Published: about 9 years ago

10.7554/eLife.36144

TALE factors use two distinct functional modes to control an essential zebrafish gene expression program
Cited by: 21
Author(s): Franck Ladam, William Stanney, Ian J. Donaldson, Ozge Yildiz, Nicoletta Bobola, Charles G. Sagerström
Software Mentions: 3
Published: over 8 years ago

10.1155/2014/462135

miRSeq: A User-Friendly Standalone Toolkit for Sequencing Quality Evaluation and miRNA Profiling
Cited by: 16
Author(s): Pan Cheng, Kuo‐Wang Tsai, Tzu Min Hung, Wei Chen Lin, Chao Pan, Hong‐Ren Yu, Sung Chou Li
Software Mentions: 3
Published: almost 13 years ago

10.1155/2018/2617432

Aberrantly Expressed Genes and miRNAs in Slow Transit Constipation Based on RNA-Seq Analysis
Cited by: 11
Author(s): Shushan Zhao, Qiang Chen, Xianwu Kang, Bin Kong, Zhuo Wang
Software Mentions: 3
Published: about 8 years ago

10.1186/1471-2164-15-808

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes
Cited by: 47
Author(s): Pallavi Chauhan, Bengt Hansson, Ken Kraaijeveld, Peter de Knijff, Erik I. Svensson, Maren Wellenreuther
Software Mentions: 3
Published: almost 13 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

10.1371/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

10.7554/eLife.00011

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation
Cited by: 273
Author(s): Jérôme S. Menet, Joseph Rodriguez, Katharine C. Abruzzi, Michael Rosbash
Software Mentions: 3
Published: almost 14 years ago

10.1186/s13068-017-0825-x

Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters
Cited by: 73
Author(s): Wan-Chen Li, Chien‐Hao Huang, Chia-Ling Chen, Yu-Chien Chuang, Shu-Yun Tung, Ting-Fang Wang
Software Mentions: 3
Published: over 9 years ago

10.1186/s13068-015-0348-2

Phylogeny-structured carbohydrate metabolism across microbiomes collected from different units in wastewater treatment process
Cited by: 16
Author(s): Yu Xia, Francis Y. L. Chin, Yuanqing Chao, Tong Zhang
Software Mentions: 3
Published: about 11 years ago

10.1186/s12870-016-0932-z

Characterization of the cytokinin-responsive transcriptome in rice
Cited by: 34
Author(s): Tracy Raines, Ivory C. Blakley, Yu‐Chang Tsai, Jennifer M. Worthen, José Manuel Franco-Zorrilla, Roberto Solano, G. Schäller, Ann E. Loraine, Joseph J. Kieber
Software Mentions: 3
Published: almost 10 years ago

10.7554/eLife.49314

Kinetics of cytokine receptor trafficking determine signaling and functional selectivity
Cited by: 31
Author(s): Jonathan Martínez-Fábregas, Stephan Wilmes, Luopin Wang, Maximillian Hafer, Elizabeth Pöhler, Juliane Lokau, Christoph Garbers, Adeline Cozzani, Paul K. Fyfe, Jacob Piehler, Majid Kazemian, Suman Mitra, Ignacio Moraga
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.00808

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation
Cited by: 159
Author(s): William S. Kruesi, Leighton J. Core, Colin T. Waters, John T. Lis, Barbara J Meyer
Software Mentions: 3
Published: over 13 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

10.1371/journal.pone.0210273

Identification of whole blood mRNA and microRNA biomarkers of tissue damage and immune function resulting from amphetamine exposure or heat stroke in adult male rats
Cited by: 6
Author(s): Luísa Camacho, Camila S. Silva, Joseph P. Hanig, Robert P. Schleimer, Nysia I. George, John F. Bowyer
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0151522

Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
Cited by: 25
Author(s): Paul Pavlidis, Vignesh Dhandapani, Jana Jeevan Rameneni, Xiaonan Li, Ganesan Sivanandhan, Su Ryun Choi, Wenxing Pang, Subin Im, Yong Pyo Lim
Software Mentions: 3
Published: over 10 years ago

Projects: pypi: bowtie

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Papers Mentioning bowtie 1,566