pypi: cufflinks | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0132450

Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita (Hamilton)
Cited by: 11
Author(s): Dinesh Kumar Sahu, Soumya Prasad Panda, Prem Kumar Meher, Paramananda Das, P. Routray, Jitendra Kumar Sundaray, P. Jayasankar, Samiran Nandi
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2164-14-S1-S9

Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information
Cited by: 2
Author(s): Ellis Patrick, Michael Buckley, David M. Lin, Jean Yee Hwa Yang
Software Mentions: 4
Published: almost 12 years ago

10.1002/cne.24994

Identification of regenerative processes in neonatal spinal cord injury in the opossum ( <scp> Monodelphis domestica </scp> ): A transcriptomic study
Cited by: 6
Author(s): Benjamin Wheaton, Johnny A. Sena, Anitha Sundararajan, Pooja Umale, Faye Schilkey, Robert D. Miller
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-020-07305-3

Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome
Cited by: 12
Author(s): Xiaodong Tan, Ranran Liu, Yonghong Zhang, Xicai Wang, Jie Wang, Hailong Wang, Guiping Zhao, Maiqing Zheng, Jie Wen
Software Mentions: 4
Published: almost 4 years ago

10.3390/cells10030692

CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
Cited by: 2
Author(s): Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, Karla Johanna Ruth Hoyer-Allo, Felix C. Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman‐Ulrich Müller, Christoph Dieterich
Software Mentions: 4
Published: over 3 years ago

10.1093/gigascience/giz136

Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research
Cited by: 20
Author(s): Joeri S. Strijk, Damien Daniel Hinsinger, Fengping Zhang, Kaihua Cao
Software Mentions: 4
Published: about 5 years ago

10.1002/cam4.2581

Clinical candidate and genistein analogue AXP107‐11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein‐coupled estrogen receptor signaling
Cited by: 11
Author(s): Fahmi Mesmar, Bingbing Dai, Ahmed Atef Ibrahim, Linnea Hases, Mohammed Hakim Jafferali, Jithesh J. Augustine, Sebastian DiLorenzo, Ya’an Kang, Yang Zhao, Jing Wang, Michael Kim, Chin Yo Lin, Anders Berkenstam, Jason B. Fleming, Cecilia Williams
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2020.00736

DNA N6-Methyladenine Modification in Wild and Cultivated Soybeans Reveals Different Patterns in Nucleus and Cytoplasm
Cited by: 13
Author(s): Di Yuan, Jian-Feng Xing, Meiwei Luan, Kai-Kai Ji, Jun Guo, Shuang Xie, Yuanming Zhang
Software Mentions: 4
Published: over 4 years ago

10.3390/insects11010004

Comparative Transcriptome Analysis of Thitarodes Armoricanus in Response to the Entomopathogenic Fungi Paecilomyces Hepiali and Ophiocordyceps Sinensis
Cited by: 7
Author(s): Zhongchen Rao, Li Cao, Hua Wu, Xuehong Qiu, Guiqing Liu, Richou Han
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12896-015-0207-z

A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq
Cited by: 22
Author(s): Kevin Lambirth, Adam M. Whaley, Ivory C. Blakley, Jessica A. Schlueter, Kenneth L. Bost, Ann E. Loraine, Kenneth J. Piller
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-017-12401-8

Similarity-Based Segmentation of Multi-Dimensional Signals
Cited by: 14
Author(s): Rainer Machné, Douglas B. Murray, Peter F. Stadler
Software Mentions: 4
Published: about 7 years ago

10.1186/s12870-019-2202-3

Root system traits impact early fire blight susceptibility in apple (Malus × domestica)
Cited by: 11
Author(s): Jugpreet Singh, Jack Fabrizio, Elsa Desnoues, Julliany Pereira Silva, Wolfgang Busch, Awais Khan
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-98907-8

Transcriptomic profiling of the high-vigour maize (Zea mays L.) hybrid variety response to cold and drought stresses during seed germination
Cited by: 12
Author(s): Heqin Li, Haiwang Yue, Jiping Xie, Junzhou Bu, Li Li, Xueying Xin, Yanming Zhao, Haiyan Zhang, Li Yang, Jianhua Wang, Xuwen Jiang
Software Mentions: 4
Published: about 3 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

10.1016/j.stemcr.2020.06.003

Naive Human Embryonic Stem Cells Can Give Rise to Cells with a Trophoblast-like Transcriptome and Methylome
Cited by: 118
Author(s): Jessica Cinkornpumin, Sin Young Kwon, Yixin Guo, Ishtiaque Hossain, Jacinthe Sirois, Colleen S. Russett, Hsin Wei Tseng, Hiroaki Okae, Takahiro Arima, Thomas F. Duchaîne, Wanlu Liu, William A. Pastor
Software Mentions: 4
Published: over 4 years ago

10.12688/f1000research.15604.1

Androgen-dependent alternative mRNA isoform expression in prostate cancer cells
Cited by: 14
Author(s): Jennifer Munkley, Teresa Maia, Jesús Ibarluzea, Karen E. Livermore, Daniel Vodák, Ingrid Ehrmann, Katherine James, Prabhakar Rajan, Nuno L. Barbosa‐Morais, David Elliott
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2016.01924

Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Setting in Triploid Loquat (Eriobotrya japonica)
Cited by: 25
Author(s): Shuang Jiang, Luo Jun, Fanjie Xu, Xueying Zhang
Software Mentions: 4
Published: almost 8 years ago

10.1093/database/bav047

GraP: platform for functional genomics analysis of Gossypium raimondii
Cited by: 12
Author(s): Liwei Zhang, Jinyan Guo, Qi You, Xin Yi, Yi Ling, Wenying Xu, Jinping Hua, Zhen Su
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pgen.1006589

Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression
Cited by: 52
Author(s): Thomas Stricker, Christopher D. Brown, Chaitanya Bandlamudi, Megan E. McNerney, Ralf Kittler, Vanessa Montoya, April Peterson, Robert L. Grossman, Kevin P. White
Software Mentions: 4
Published: over 7 years ago

10.3389/fphys.2018.00825

Transcriptomics and Fitness Data Reveal Adaptive Plasticity of Thermal Tolerance in Oysters Inhabiting Different Tidal Zones
Cited by: 28
Author(s): Ao Li, Wei Wang, Kai Song, Guofan Zhang
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.14044

PRKAR2B plays an oncogenic role in the castration-resistant prostate cancer
Cited by: 20
Author(s): Jianjun Sha, Wei Xue, Baijun Dong, Jiahua Pan, Xiaorong Wu, Dong Liu, Dongming Liu, Yiran Huang
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.10249

Gene network analysis reveals a novel 22-gene signature of carbon metabolism in hepatocellular carcinoma
Cited by: 16
Author(s): Jinqiang Zhang, Melody Baddoo, Chang Han, Michael J. Strong, Jennifer Cvitanovic, Krzysztof Moroz, Srikanta Dash, Erik K. Flemington, Tong Wu
Software Mentions: 3
Published: over 8 years ago

10.1111/tpj.14468

An ‘ <scp>eFP</scp> ‐Seq Browser’ for visualizing and exploring <scp>RNA</scp> sequencing data
Cited by: 31
Author(s): Alexander Sullivan, Priyank Purohit, Nowlan H. Freese, Asher Pasha, Eddi Esteban, Jamie Waese, Alison Wu, Michelle Chen, Chih Ying Chin, Richard Song, Sneha Ramesh Watharkar, Agnes P. Chan, Vivek Krishnakumar, Matthew Vaughn, Chris Town, Ann E. Loraine, Nicholas J. Provart
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms19092658

Genome-Wide Analysis Elucidates the Role of CONSTANS-like Genes in Stress Responses of Cotton
Cited by: 11
Author(s): Wenqiang Qin, Ya Bo Yu, Yang Jin, Xindong Wang, Ji Liu, Jianping Xi, Zhi Li, Huiqin Li, Ge Zhao, Wei Hu, Chuanjia Chen, Fuguang Li
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms20225724

A Comparative Analysis of Edwardsiella tarda-Induced Transcriptome Profiles in RAW264.7 Cells Reveals New Insights into the Strategy of Bacterial Immune Evasion
Cited by: 16
Author(s): Huili Li, Bo Sun, Xianhui Ning, Shuai Jiang, Li Sun
Software Mentions: 3
Published: about 5 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 7 years ago

10.7717/peerj.8947

Transcriptomic changes across the life cycle of Trypanosoma cruzi II
Cited by: 8
Author(s): Lissa Cruz-Saavedra, Gustavo Adolfo Vallejo, Felipe Guhl, Juan David Ramírez
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.10518

Temporal transcriptomics suggest that twin-peaking genes reset the clock
Cited by: 58
Author(s): William G Pembroke, Arran Babbs, Kay E. Davies, Chris P. Ponting, Peter L. Oliver
Software Mentions: 3
Published: about 9 years ago

10.1186/s12859-018-2546-y

Measures of co-expression for improved function prediction of long non-coding RNAs
Cited by: 10
Author(s): Rezvan Ehsani, Finn Drabløs
Software Mentions: 3
Published: almost 6 years ago

10.7554/eLife.02510

MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale
Cited by: 93
Author(s): Ngoc-Hien Du, Alaaddin Bulak Arpat, Mara De Matos, David Gatfield
Software Mentions: 3
Published: over 10 years ago

10.1186/s13567-015-0153-8

Genomic analysis of host – Peste des petits ruminants vaccine viral transcriptome uncovers transcription factors modulating immune regulatory pathways
Cited by: 40
Author(s): Siddappa Manjunath, Girish Kumar, Bishnu Prasad Mishra, Bina Mishra, Aditya Prasad Sahoo, Chaitanya G. Joshi, Ashok Kumar Tiwari, Kaushal Kishor Rajak, Sarath Chandra Janga
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.06974

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites
Cited by: 175
Author(s): Yong Woo, Hifzur Rahman Ansari, Thomas D. Otto, Christen M. Klinger, Martin Kolísko, Jan Michálek, Alka Saxena, Dhanasekaran Shanmugam, Annageldi Tayyrov, Alaguraj Veluchamy, Shahjahan Ali, Axel Bernal, Javier del Campo, Jaromír Cihlář, Pavel Flegontov, Sebastian G. Gornik, Eva Hajdušková, Aleš Horák, Jan Janouškovec, Nicholas J. Katris, Fred D. Mast, Diego Miranda‐Saavedra, Tobias Mourier, Raeece Naeem, Mridul Nair, Aswini K. Panigrahi, Neil D. Rawlings, Eriko Padron-Regalado, Abhinay Ramaprasad, Nadira Samad, Aleš Tomčala, Jonathan M. Wilkes, Daniel E. Neafsey, Christian Doerig, Chris Bowler, Patrick J. Keeling, David S. Roos, Joel B. Dacks, Thomas J. Templeton, Ross F. Waller, Julius Lukeš, Miroslav Oborník, Arnab Pain
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-14-914

Divergent transcription is associated with promoters of transcriptional regulators
Cited by: 91
Author(s): Cyrille Lepoivre, Mohamed Belhocine, Aurélie Bergon, Aurélien Griffon, Miriam Yammine, Laurent Vanhille, Joaquin Zacarías-Cabeza, Marc Garibal, Frank‐Thomas Koch, Muhammad Ahmad Maqbool, Romain Fenouil, Béatrice Loriod, Hélène Holota, Marta Gut, Jean Imbert, Jean-Christophe Andrau, Denis Puthier, Salvatore Spicuglia
Software Mentions: 3
Published: almost 11 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 6 years ago

10.1111/jipb.12862

Identification of plant genes putatively involved in the perception of fungal ergosterol‐squalene
Cited by: 15
Author(s): Laura Lindo, Rosa E. Cardoza, Alicia Lorenzana de la Varga, Pedro A. Casquero, Santiago Gutiérrez
Software Mentions: 3
Published: almost 5 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 4 years ago

10.15252/embj.201899016

miR‐200/375 control epithelial plasticity‐associated alternative splicing by repressing the <scp>RNA</scp> ‐binding protein Quaking
Cited by: 75
Author(s): Katherine A. Pillman, C. Phillips, Suraya Roslan, John Toubia, B Kate Dredge, Andrew G. Bert, Rachael Lumb, Daniel Neumann, Xiaochun Li, Simon J. Conn, Dawei Liu, Cameron P. Bracken, David Lawrence, Nataly Stylianou, Andreas W. Schreiber, Wayne D. Tilley, Brett G. Hollier, Yeesim Khew‐Goodall, Luke A. Selth, Gregory J. Goodall, Philip A. Gregory
Software Mentions: 3
Published: over 6 years ago

10.1002/iub.1887

Alternate splicing of transcripts upon Mycobacterium tuberculosis infection impacts the expression of functional protein domains
Cited by: 13
Author(s): Haroon Kalam, Kartikeya Singh, Komal Chauhan, Mary F. Fontana, Dhiraj Kumar
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-015-1938-x

Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model
Cited by: 69
Author(s): Kyle M. Schachtschneider, Ole Madsen, Chankyu Park, Laurie A. Rund, Martien A. M. Groenen, Lawrence B. Schook
Software Mentions: 3
Published: about 9 years ago

10.3389/fpls.2018.00771

Molecular Profiling of Pierce’s Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection
Cited by: 28
Author(s): Paulo A. Zaini, Rafael Nascimento, Hossein Gouran, Dario Cantu, Sandeep Chakraborty, My L. Phu, Luíz Ricardo Goulart, Abhaya M. Dandekar
Software Mentions: 3
Published: over 6 years ago

10.1186/s13046-018-0859-3

Chemotherapy-induced niche perturbs hematopoietic reconstitution in B-cell acute lymphoblastic leukemia
Cited by: 15
Author(s): Chao Tang, Minghao Li, Yali Chen, Huiying Sun, Shengli Liu, Weiwei Zheng, Meng-Yi Zhang, Hui Li, Wei Fu, Wenjun Zhang, Aibin Liang, Zhonghua Tang, Dengli Hong, Bin‐Bing S. Zhou, Cai-Wen Duan
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.60481

Identification of PARP-7 substrates reveals a role for MARylation in microtubule control in ovarian cancer cells
Cited by: 35
Author(s): Lori Parsons, Sridevi Challa, Bryan A. Gibson, Tulip Nandu, MiKayla S Stokes, Dan Huang, Jayanthi Lea, W. Lee Kraus
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.dib.2015.10.033

Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model
Cited by: 6
Author(s): Joel B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William Stafford Noble, Christine M. Distèche, Xinxian Deng
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-020-59407-3

MicroRNAs regulate innate immunity against uropathogenic and commensal-like Escherichia coli infections in the surrogate insect model Galleria mellonella
Cited by: 15
Author(s): Krishnendu Mukherjee, Daniel Amsel, Miriam Kalsy, André Billion, Ulrich Dobrindt, Andreas Vilcinskas
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-41457-x

The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination system
Cited by: 25
Author(s): Kang Du, Sven Wuertz, Mateus Contar Adolfi, Susanne Kneitz, Matthias Stöck, Marcos Antônio de Oliveira, Rafael Henrique Nóbrega, Jenny Ormanns, Werner Kloas, Romain Féron, Christophe Klopp, Hugues Parrinello, Laurent Journot, Shunping He, John H. Postlethwait, Axel Meyer, Yann Guiguen, Manfred Schartl
Software Mentions: 3
Published: over 5 years ago

10.1002/cam4.436

Feasibility of implementing molecular‐guided therapy for the treatment of patients with relapsed or refractory neuroblastoma
Cited by: 24
Author(s): Giselle L. Saulnier Sholler, Jeffrey P. Bond, Genevieve Bergendahl, Akshita Dutta, Julie A. Dragon, Kathleen Neville, William S. Ferguson, William Roberts, Don Eslin, Jacqueline M. Kraveka, Joel A. Kaplan, Deanna Mitchell, Nehal S. Parikh, Melinda S. Merchant, Takamaru Ashikaga, Gina Hanna, Pamela J. Lescault, Ashley L. Siniard, Jason J. Corneveaux, Matthew J. Huentelman, Jeffrey M. Trent
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-019-45898-2

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor
Cited by: 19
Author(s): Rajesh Kumar Gazara, Eduardo Alves Gamosa de Oliveira, B. Calderan Rodrigues, Rodrigo Nunes da Fonseca, Antônia Elenir Amâncio Oliveira, Thiago M. Venancio
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-72828-4

Pax6 modulates intra-retinal axon guidance and fasciculation of retinal ganglion cells during retinogenesis
Cited by: 14
Author(s): Soundararajan Lalitha, Budhaditya Basu, Surya Suresh, Vadakkath Meera, Paul Ann Riya, Surendran Parvathy, Ani V. Das, Krishnankutty C. Sivakumar, Shijulal Nelson-Sathi, Jackson James
Software Mentions: 3
Published: about 4 years ago

10.1038/s41422-018-0104-9

Plant HP1 protein ADCP1 links multivalent H3K9 methylation readout to heterochromatin formation
Cited by: 71
Author(s): Shuai Zhao, Lan Cheng, Yifei Gao, Baichao Zhang, Xiangdong Zheng, Liang Wang, Pilong Li, Qianwen Sun, Haitao Li
Software Mentions: 3
Published: about 6 years ago

10.1016/j.celrep.2021.109622

Intra- and extra-cellular environments contribute to the fate of HIV-1 infection
Cited by: 8
Author(s): Sneha Ratnapriya, Miranda Harris, Angela Chov, Zachary T. Herbert, Vladimir Vrbanac, Maud Déruaz, Vasudevan Achuthan, Alan Engelman, Joseph Sodroski, Alon Herschhorn
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-24701-8

A compendium of long non-coding RNAs transcriptional fingerprint in multiple myeloma
Cited by: 33
Author(s): Domenica Ronchetti, Luca Agnelli, Alessandro Pietrelli, Katia Todoerti, Martina Manzoni, Elisa Taìana, Antonino Neri
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2019.01772

Coexpression of PalbHLH1 and PalMYB90 Genes From Populus alba Enhances Pathogen Resistance in Poplar by Increasing the Flavonoid Content
Cited by: 33
Author(s): Qiuxian Bai, Bingbing Duan, Jianchao Ma, Yannan Fen, Shujiao Sun, Qiming Long, Jiaojiao Lv, Dongshi Wan
Software Mentions: 3
Published: over 4 years ago

10.1038/s41419-021-03760-2

Targeting epigenetic modulation of cholesterol synthesis as a therapeutic strategy for head and neck squamous cell carcinoma
Cited by: 13
Author(s): Xing Xu, Jun Chen, Yán Li, Xiaojie Yang, Qing Wang, Yanjun Wen, Ming Yan, Jianjun Zhang, Qin Xu, Wei Yan, Wantao Chen, Xu Wang
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-23334-1

Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
Cited by: 32
Author(s): Jinfang Zhang, Lijuan Wei, Jun Jiang, Annaliese S. Mason, Haojie Li, Cheng Cui, Linna Chai, Beibei Zheng, Yongqing Zhu, Qing Xia, Long Jiang, Donghui Fu
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-23514-z

Comparative transcriptomics gives insights into the evolution of parasitism in Strongyloides nematodes at the genus, subclade and species level
Cited by: 22
Author(s): Vicky L. Hunt, Akinori Hino, Akemi Yoshida, Taisei Kikuchi
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-81577-x

The combination of the tubulin binding small molecule PTC596 and proteasome inhibitors suppresses the growth of myeloma cells
Cited by: 3
Author(s): Yurie Nagai, Naoya Mimura, Ola Rizq, Yusuke Isshiki, Motohiko Oshima, Mohamed Rizk, Atsunori Saraya, Shuhei Koide, Yaeko Nakajima‐Takagi, Makiko Miyota, Tetsuhiro Chiba, Nagisa Oshima-Hasegawa, Tomoya Muto, Shokichi Tsukamoto, Shio Mitsukawa, Yusuke Takeda, Chikako Ohwada, Masahiro Takeuchi, Tohru Iseki, Chiaki Nakaseko, William Lennox, Josephine Sheedy, Marla Weetall, Koutaro Yokote, Atsushi Iwama, Emiko Sakaida
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-11379-7

RNA-seq analysis of the kidneys of broiler chickens fed diets containing different concentrations of calcium
Cited by: 12
Author(s): Woncheoul Park, Deivendran Rengaraj, Dong Yong Kil, Heebal Kim, Hak-Kyo Lee, Ki Duk Song
Software Mentions: 3
Published: about 7 years ago

10.1038/s41419-020-03201-6

Effective inhibition of MYC-amplified group 3 medulloblastoma by FACT-targeted curaxin drug CBL0137
Cited by: 24
Author(s): Jiajia Wang, Yi Sui, Qifeng Li, Zhao Yang, Dong Xu, Jian Yang, Zhuangzhuang Liang, Yipeng Han, Yujie Tang, Jie Ma
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-016-2976-8

Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.)
Cited by: 28
Author(s): Kathleen M. Martin, Jugpreet Singh, John H. Hill, Steven A. Whitham, Steven B. Cannon
Software Mentions: 3
Published: over 8 years ago

10.3390/cancers12113081

Prognostic Significance of Oxidation Pathway Mutations in Recurrent Laryngeal Squamous Cell Carcinoma
Cited by: 8
Author(s): Molly Heft Neal, Apurva Bhangale, Andrew C. Birkeland, Jonathan B. McHugh, Andrew G. Shuman, Andrew J. Rosko, Paul Swiecicki, Matthew E. Spector, J. Chad Brenner
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-017-07872-8

A Genome-Wide Identification of the WRKY Family Genes and a Survey of Potential WRKY Target Genes in Dendrobium officinale
Cited by: 28
Author(s): Chunmei He, Jaime A. Teixeira da Silva, Jian‐Wen Tan, Jianxia Zhang, Xiaoping Pan, Mingzhi Li, Jian‐Ping Luo, Jun Duan
Software Mentions: 3
Published: over 7 years ago

10.1038/srep13336

Extensive shift in placental transcriptome profile in preeclampsia and placental origin of adverse pregnancy outcomes
Cited by: 81
Author(s): Siim Sõber, Mario Reiman, Triin Kikas, Kristiina Rull, Rain Inno, Pille Vaas, Pille Teesalu, Jesus M. Lopez Marti, Pirkko Mattila, Maris Laan
Software Mentions: 3
Published: over 9 years ago

10.1038/srep18399

Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing
Cited by: 56
Author(s): Aroa Suárez-Vega, Christophe Klopp, Christèle Robert-Granié, Gwenola Tosser‐Klopp, Juan José Arranz
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13104-018-3864-x

Transcriptomic evidence for distinct mechanisms underlying abscission deficiency in the Arabidopsis mutants haesa/haesa-like 2 and nevershed
Cited by: 6
Author(s): Isaiah Taylor, John C. Walker
Software Mentions: 3
Published: about 6 years ago

10.3389/fpls.2014.00615

Bayesian phylogeny of sucrose transporters: ancient origins, differential expansion and convergent evolution in monocots and dicots
Cited by: 39
Author(s): Duo Peng, Xi Gu, Liang‐Jiao Xue, James H. Leebens‐Mack, Chung‐Jui Tsai
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0112102

Isolation of Specific Neurons from C. elegans Larvae for Gene Expression Profiling
Cited by: 84
Author(s): W. Clay Spencer, Rebecca McWhirter, Tyne Miller, Pnina Strasbourger, Owen Thompson, LaDeana W. Hillier, Robert H. Waterston, David M. Miller
Software Mentions: 3
Published: about 10 years ago

10.1038/srep27640

Comprehensive analysis of multi-tissue transcriptome data and the genome-wide investigation of GRAS family in Phyllostachys edulis
Cited by: 11
Author(s): Hansheng Zhao, Lili Dong, Huayu Sun, Lichao Li, Yonggen Lou, Lili Wang, Zuyao Li, Zhimin Gao
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-017-14807-w

Heterogeneous circRNA expression profiles and regulatory functions among HEK293T single cells
Cited by: 5
Author(s): Chunrong Zhong, Shaojun Yu, Maozhen Han, Jiahuan Chen, Kang Ning
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-021-87278-9

Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
Cited by: 8
Author(s): Lingshu Han, Yuena Sun, Yue Cao, Peng Gao, Zijiao Quan, Yaqing Chang, Jun Ding
Software Mentions: 3
Published: over 3 years ago

10.1186/s12870-019-2074-6

Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species
Cited by: 37
Author(s): Ying Hong, Jian Shi, Shanshan Zhang, Gesang Pingcuo, Shuo Wang, Fan Zhao, Yongning Cui, Xiuli Zeng
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2019.00936

Enhancer LncRNAs Influence Chromatin Interactions in Different Ways
Cited by: 32
Author(s): Yue Hou, Rong Xin Zhang, Xiao Sun
Software Mentions: 3
Published: about 5 years ago

10.1186/s12929-020-00642-1

Long-term expansion of directly reprogrammed keratinocyte-like cells and in vitro reconstitution of human skin
Cited by: 2
Author(s): Jie Zheng, Wonjin Yun, Junghyun Park, Phil Jun Kang, Gilju Lee, Gwonhwa Song, In Yong Kim, Seungkwon You
Software Mentions: 3
Published: over 4 years ago

10.3390/biomedicines9060657

An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change
Cited by: 3
Author(s): Tianyi Xu, Liping Wang, Peilin Jia, Xiaofeng Song, Zhongming Zhao
Software Mentions: 3
Published: over 3 years ago

10.1038/s41419-021-04143-3

Pyroptosis inhibition improves the symptom of acute myocardial infarction
Cited by: 26
Author(s): Wenju Liu, Junwei Shen, Yanfei Li, Jiawen Wu, Xiaofeng Luo, Yuanyuan Yu, Yuhan Zhang, Liang Gu, Xiaobai Zhang, Cizhong Jiang, Jue Li
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0149640

Preferentially Expressed Antigen of Melanoma Prevents Lung Cancer Metastasis
Cited by: 14
Author(s): Quan Huang, Haifeng Wei, Zhipeng Wu, Lin Li, Liangfang Yao, Zhengwang Sun, Lei Li, Lin Zx, Wei Xu, Shuai Han, Wenjiao Cao, Yunfei Xu, Dianwen Song, Xianghong Yang, Jianru Xiao
Software Mentions: 3
Published: over 8 years ago

10.1080/19336896.2019.1615197

Rodent models allow BSE discrimination of goat prions and reveal geographical differences in the biological properties of scrapie
Cited by: 4
Author(s): Laura Pirisinu, Olivier Andréoletti, Frédéric Lantier, Pier Luigi Acutis, S. Acin, Wilfred Goldmann, Theodoros Sklaviadis, Loukia Ekateriniadou, Christine Fast, Penelope Papasavva-Stylianou, Stéphanie Simon, J. Spiropoulol, Umberto Agrimi, J.G. Jacobs, Alex Bossers, Lucien van Keulen, Maria Mazza, Romolo Nonno, J.P.M. Langeveld
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2019.00116

Genome-Wide Identification, Sequence Variation, and Expression of the Glycerol-3-Phosphate Acyltransferase (GPAT) Gene Family in Gossypium
Cited by: 14
Author(s): Yupeng Cui, Jianjiang Ma, Guoyuan Liu, Nuohan Wang, Wenfeng Pei, Man Wu, Xingli Li, Jinfa Zhang, Jie-Ae Yu
Software Mentions: 3
Published: almost 6 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 7 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 10 years ago

10.1371/journal.pone.0229513

The RNA-seq transcriptomic analysis reveals genes mediating salt tolerance through rapid triggering of ion transporters in a mutant barley
Cited by: 24
Author(s): Sareh Yousefirad, Hassan Soltanloo, Seyedeh Sanaz Ramezanpour, Khalil Zaynali Nezhad, Vahid Shariati
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2021.671650

A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi)
Cited by: 7
Author(s): Weidong Ding, Xinhui Zhang, Xiaomeng Zhao, Jing Wu, Zhen Cao, Jia Li, Yu Huang, Xinxin You, Min Wang, Qiong Shi, Xuwen Bing
Software Mentions: 3
Published: over 3 years ago

10.1016/j.stem.2018.12.001

The BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC Differentiation
Cited by: 26
Author(s): Wensheng Zhang, Constantinos Chronis, Xi Chen, Heyao Zhang, Rapolas Spalinskas, Mercedes Pardo, Liangliang Chen, Guangming Wu, Zhexin Zhu, Yong Yu, Lu Yu, Jyoti S. Choudhary, Jennifer Nichols, Mana M. Parast, Boris Greber, Pelin Sahlén, Kathrin Plath
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2018.01845

Quantitative RNA-seq Analysis Unveils Osmotic and Thermal Adaptation Mechanisms Relevant for Ectoine Production in Chromohalobacter salexigens
Cited by: 17
Author(s): Manuel Salvador, Montserrat Argandoña, Emilia Naranjo, Francine Piubeli, Joaquı́n J. Nieto, L.N. Csonka, Carmen Regla Vargas
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-017-1251-x

Dynamic DNA methylation reconfiguration during seed development and germination
Cited by: 187
Author(s): Taiji Kawakatsu, Joseph R. Nery, Rosa Castanon, Joseph R. Ecker
Software Mentions: 3
Published: about 7 years ago

10.1093/gbe/evu067

Comparative Genomics of Taphrina Fungi Causing Varying Degrees of Tumorous Deformity in Plants
Cited by: 29
Author(s): Isheng Jason Tsai, Eiji Tanaka, Hayato Masuya, Ryusei Tanaka, Y. Hirooka, Rikiya Endoh, Norio Sahashi, Taisei Kikuchi
Software Mentions: 3
Published: over 10 years ago

10.3389/fncel.2021.626192

The Human ApoE4 Variant Reduces Functional Recovery and Neuronal Sprouting After Incomplete Spinal Cord Injury in Male Mice
Cited by: 7
Author(s): Carlos A. Toro, Jens Hansen, Mustafa M Siddiq, Kaitlin Johnson, Wei Zhao, Daniella Azulai, Dibash Kumar Das, William A. Bauman, Robert Sebra, Dongming Cai, Ravi Iyengar, Christopher P. Cardozo
Software Mentions: 3
Published: almost 4 years ago

10.1002/2211-5463.12737

Transcriptome analysis of roots from resistant and susceptible rice varieties infected with Hirschmanniella mucronata
Cited by: 7
Author(s): Xiaotang Sun, Lei Zhang, Ziqing Tang, Xugen Shi, Jian Ma, Ruqiang Cui
Software Mentions: 3
Published: about 5 years ago

10.1186/s13073-017-0452-y

Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability
Cited by: 28
Author(s): Claudio Reggiani, Sandra Coppens, Tayeb Sékhara, Ivan K. Dimov, Bruno Pichon, Nicolas Lufin, Marie Claude Addor, Elga Fabia Belligni, María Cristina Digilio, Flavio Faletra, Giovanni Battista Ferrero, Marion Gérard, Bertrand Isidor, Shelagh Joss, Florence Niel-Bütschi, Maria Dolores Perrone, Florence Petit, Alessandra Renieri, Serge Romana, Alexandra Topa, Joris Robert Vermeesch, Tom Lenaerts, Georges Casimir, Marc Abramowicz, Gianluca Bontempi, Catheline Vilain, Nicolas Deconinck, Guillaume Smits
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pntd.0007850

A glance of the blood stage transcriptome of a Southeast Asian Plasmodium ovale isolate
Cited by: 5
Author(s): Awtum Brashear, Wanlapa Roobsoong, Faiza Amber Siddiqui, Wang Nguitragool, Jetsumon Sattabongkot, Margarita M. López‐Uribe, Jun Miao, Liwang Cui
Software Mentions: 3
Published: about 5 years ago

10.1186/gb-2014-15-2-r39

Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis
Cited by: 226
Author(s): Linhai Wang, Shanlin Yu, Chaobo Tong, Yingzhong Zhao, Yan Liu, Chi Song, Yanxin Zhang, Xudong Zhang, Ying Wang, Wei Hua, Donghua Li, Dan Li, Fang Li, Jingyin Yu, Chunyan Xu, Xuelian Han, Shunmou Huang, Shuaishuai Tai, Junyi Wang, Xun Xu, Yingrui Li, Liu S, Rajeev K. Varshney, Jun Wang, Xiurong Zhang
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1005924

BRR2a Affects Flowering Time via FLC Splicing
Cited by: 49
Author(s): Walid Mahrez, Juhyun Shin, Rafael Muñoz‐Viana, Duarte D. Figueiredo, Minerva S. Trejo-Arellano, Vivien Exner, Alexey Siretskiy, Wilhelm Gruissem, Claudia Köhler, Lars Hennig
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-020-07040-9

Developmentally regulated activation of defense allows for rapid inhibition of infection in age-related resistance to Phytophthora capsici in cucumber fruit
Cited by: 8
Author(s): Ben N. Mansfeld, Marivi Colle, Chunqiu Zhang, Ying-Zu Lin, Rebecca Grumet
Software Mentions: 3
Published: about 4 years ago

10.3389/fgene.2019.01268

Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism
Cited by: 10
Author(s): Mette Juul Jacobsen, Jakob Hull Havgaard, Christian Anthon, Caroline M. Junker Mentzel, Susanna Cirera, Poula Maltha Krogh, Sachin Pundhir, Peter Karlskov-Mortensen, Camilla S. Bruun, Philippe Lesnik, Maryse Guérin, Jan Gorodkin, Claus B. Jørgensen, Merete Fredholm, Romain Barrès
Software Mentions: 3
Published: almost 5 years ago

10.1002/2211-5463.13226

Set2‐mediated H3K36 methylation states redundantly repress the production of antisense transcripts: role in transcription regulation
Cited by: 1
Author(s): Yu-Chao Mei, Jun Feng, Fei He, Yumin Li, Yafei Liu, Feng Li, Yu Chen, Hai-Ning Du
Software Mentions: 3
Published: over 3 years ago

10.1038/sdata.2017.67

Single-cell transcriptome of early embryos and cultured embryonic stem cells of cynomolgus monkeys
Cited by: 40
Author(s): Tomonori Nakamura, Yukihiro Yabuta, Ikuhiro Okamoto, Kotaro Sasaki, Chizuru Iwatani, Hideaki Tsuchiya, Mitinori Saitou
Software Mentions: 3
Published: over 7 years ago

10.15252/emmm.201707565

The cardiac microenvironment uses non‐canonical <scp>WNT</scp> signaling to activate monocytes after myocardial infarction
Cited by: 48
Author(s): Ingmar Sören Meyer, Andreas Jungmann, Christoph Dieterich, Min Zhang, Felix Lasitschka, Susann Werkmeister, Jan Haas, Oliver Müller, Michael Boutros, Matthias Nahrendorf, Hugo A. Katus, Stefan E. Hardt, Florian Leuschner
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-021-97430-0

Comparative transcriptional profiling of canine acanthomatous ameloblastoma and homology with human ameloblastoma
Cited by: 6
Author(s): Santiago Peralta, G Duhamel, William P. Katt, Kristiina Heikinheimo, Andrew D. Miller, Faraz Ahmed, Angela L. McCleary‐Wheeler, Jennifer K. Grenier
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pgen.1007130

Gene duplicates cause hybrid lethality between sympatric species of Mimulus
Cited by: 56
Author(s): Matthew P. Zuellig, Andrea L. Sweigart
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-018-0394-2

Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling
Cited by: 13
Author(s): Yonggang Zhang, Gustavo Arango, Fang Li, Xiao Xiao, Raj Putatunda, Jun Yu, Xiao Feng Yang, Hong Wang, Layne T. Watson, Liqing Zhang, Wenhui Hu
Software Mentions: 2
Published: about 6 years ago

10.1186/s12920-018-0414-2

Gene Ontology-based function prediction of long non-coding RNAs using bi-random walk
Cited by: 18
Author(s): Jingpu Zhang, Shuai Zou, Lei Deng
Software Mentions: 2
Published: about 6 years ago

Projects: pypi: cufflinks

Papers Mentioning cufflinks 415