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10.1371/journal.ppat.1009796

Cytomegalovirus late transcription factor target sequence diversity orchestrates viral early to late transcription
Cited by: 12
Author(s): Ming Li, Qiaolin Hu, Geoffrey S Collins, Mrutyunjaya Parida, Christopher B. Ball, David H. Price, Jeffery L. Meier
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.41608

In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta
Cited by: 48
Author(s): Maria Pernemalm, AnnSofi Sandberg, Yong Zhu, Jorrit Boekel, Davide Tamburro, Jochen M. Schwenk, Albin Björk, Marie Wahren‐Herlenius, Hanna Åmark, Claes‐Göran Östenson, Magnus Westgren, Janne Lehtiö
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0006074

More than 9,000,000 Unique Genes in Human Gut Bacterial Community: Estimating Gene Numbers Inside a Human Body
Cited by: 127
Author(s): Xing Yang, Lu Xie, Yixue Li, Chaochun Wei
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.ppat.1009615

A parasitoid wasp of Drosophila employs preemptive and reactive strategies to deplete its host’s blood cells
Cited by: 6
Author(s): Johnny R. Ramroop, Mary Ellen Heavner, Zubaidul H. Razzak, Shubha Govind
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.09945

RNA polymerase errors cause splicing defects and can be regulated by differential expression of RNA polymerase subunits
Cited by: 40
Author(s): Lucas B. Carey
Software Mentions: 2
Published: over 10 years ago

10.3389/fgene.2015.00167

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds
Cited by: 56
Author(s): Beatriz Gutiérrez-Gil, Juan José Arranz, Pamela Wiener
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1000081

Genomic Profiling Identifies GATA6 as a Candidate Oncogene Amplified in Pancreatobiliary Cancer
Cited by: 94
Author(s): Kevin Kwei, Murali D. Bashyam, Jennifer L. Kao, Raman Ratheesh, E. Chandrakanth Reddy, Young H. Kim, Kelli Montgomery, Craig P. Giacomini, Yoon La Choi, Sreejata Chatterjee, Collins Karikari, Keyan Salari, Pei Wang, Tina Hernandez‐Boussard, G Swarnalata, Matt van de Rijn, Anirban Maitra, Jonathan R. Pollack
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pgen.1006754

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
Cited by: 52
Author(s): Wareed Ahmed, Claudia Sala, Shubhada R. Hegde, Rajiv Kumar Jha, Stewart T. Cole, Valakunja Nagaraja
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1008694

WHIMP links the actin nucleation machinery to Src-family kinase signaling during protrusion and motility
Cited by: 7
Author(s): Shail Kabrawala, Margaret D. Zimmer, Kenneth Campellone
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2017.00042

Characterization of X-Chromosome Gene Expression in Bovine Blastocysts Derived by In vitro Fertilization and Somatic Cell Nuclear Transfer
Cited by: 10
Author(s): Byungkuk Min, Jung Sun Park, Kyuheum Jeon, Yong‐Kook Kang
Software Mentions: 2
Published: over 9 years ago

10.1093/jxb/eraa550

Abundance of metalloprotease FtsH12 modulates chloroplast development in Arabidopsis thaliana
Cited by: 16
Author(s): Kati Mielke, Raik Wagner, Laxmi S. Mishra, Fatih Demir, Andreas Perrar, Pitter F. Huesgen, Christiane Funk
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.11752

A new view of transcriptome complexity and regulation through the lens of local splicing variations
Cited by: 338
Author(s): Jorge Vaquero-Garcia, Alejandro Barrera, Matthew R. Gazzara, Juan González-Vallinas, Nicholas F. Lahens, John B. Hogenesch, Kristen W. Lynch, Yoseph Barash
Software Mentions: 2
Published: over 10 years ago

10.1186/s13148-018-0470-7

Methylated genomic loci encoding microRNA as a biomarker panel in tissue and saliva for head and neck squamous cell carcinoma
Cited by: 15
Author(s): Yu Cao, Katherine Green, Steve Quattlebaum, Ben Milam, Ling Lu, Dexiang Gao, Hui He, Ningning Li, Liwei Gao, F. De Havilland Hall, Matthew Whinery, Elyse Handley, Yi Ma, Tao Xu, Feng Jin, Jing Xiao, Minjie Wei, Derek E. Smith, Sophia Bornstein, Neil D. Gross, Dohun Pyeon, John I. Song, Shi Lu
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.19942

Genome-wide identification of neuronal activity-regulated genes in Drosophila
Cited by: 67
Author(s): Chen Xiao, Reazur Rahman, Fang Guo, Michael Rosbash
Software Mentions: 2
Published: over 9 years ago

10.3389/fnmol.2016.00013

Recombinant Human Myelin-Associated Glycoprotein Promoter Drives Selective AAV-Mediated Transgene Expression in Oligodendrocytes
Cited by: 35
Author(s): Georg von Jonquières, Dominik Fröhlich, Claudia B. Klugmann, Xin Wen, Anne E. Harasta, Roshini Ramkumar, Ziggy H. T. Spencer, Gary D. Housley, Matthias Klugmann
Software Mentions: 2
Published: over 10 years ago

10.1089/cmb.2018.0199

INDEX-db: The Indian Exome Reference Database (Phase I)
Cited by: 11
Author(s): Parvez Ahmed, More Rp, Biju Viswanath, Sanjeev Jain, Rao Ms, Odity Mukherjee
Software Mentions: 2
Published: over 7 years ago

10.3390/jcm9061672

Association Analysis of TP53 rs1042522, MDM2 rs2279744, rs3730485, MDM4 rs4245739 Variants and Acute Myeloid Leukemia Susceptibility, Risk Stratification Scores, and Clinical Features: An Exploratory Study
Cited by: 6
Author(s): Florin Tripon, Mihaela Iancu, Adrian P. Trifa, George Andrei Crauciuc, Alina Bogliş, Beáta Balla, Adriana S Cosma, Delia Dima, Marcela Cândea, Erzsébet Lázár, Laura Jimbu, Claudia Bănescu
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1005117

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis
Cited by: 20
Author(s): Erin Osborne Nishimura, Jay C. Zhang, Adam D. Werts, Bob Goldstein, Jason D. Lieb
Software Mentions: 2
Published: over 11 years ago

10.1111/jcmm.14104

Genetic variant in miR‐21 binding sites is associated with colorectal cancer risk
Cited by: 6
Author(s): Le Xie, Shuwei Li, Jing Jin, Lei He, Kaili Xu, Lingjun Zhu, Mulong Du, Yanqing Liu, Haiyan Chu, Zhengdong Zhang, Meilin Wang, Danni Shi, Dongying Gu, Min Ni
Software Mentions: 2
Published: over 7 years ago

10.1186/s13148-016-0269-3

MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics
Cited by: 10
Author(s): Ram Vinay Pandey, Walter Pulverer, Rainer Kallmeyer, Gabriel Beikircher, Stephan Pabinger, Albert Kriegner, Andreas Weinhäusel
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13326-016-0053-5

Using Semantic Web technologies for the generation of domain-specific templates to support clinical study metadata standards
Cited by: 7
Author(s): Guoqian Jiang, Julie Evans, Cory M. Endle, Harold R. Solbrig, Christopher G. Chute
Software Mentions: 2
Published: over 10 years ago

10.1038/cr.2017.25

De novo DNA methylation during monkey pre-implantation embryogenesis
Cited by: 42
Author(s): Fei Gao, Yuyu Niu, Yi Sun, Hanlin Lu, Yongchang Chen, Siguang Li, Yu Kang, Yuan Luo, Chenyang Si, Juehua Yu, Li Chang, Nianqin Sun, Wei Si, Hong Wang, Weizhi Ji, Tao Tan
Software Mentions: 2
Published: over 9 years ago

10.1186/2041-1480-2-S2-S3

HyQue: evaluating hypotheses using Semantic Web technologies
Cited by: 33
Author(s): Alison Callahan, Michel Dumontier, Nigam H. Shah
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pgen.1000672

Genetic Determinants of Circulating Sphingolipid Concentrations in European Populations
Cited by: 185
Author(s): Andrew A. Hicks, Peter P. Pramstaller, Åsa Johansson, Véronique Vitart, Igor Rudan, Péter Ugocsai, Yurii S. Aulchenko, Christopher S. Franklin, Gerhard Liebisch, Jeanette Erdmann, Inger Jonasson, Irina V. Zorkoltseva, Cristian Pattaro, Caroline Hayward, Aaron Isaacs, Christian Hengstenberg, Susan Campbell, Carsten Gnewuch, A. Cecile J.W. Janssens, A. V. Kirichenko, Inke R. König, Fabio Marroni, Ozren Polašek, Ayşe Demirkan, Ivana Kolčić, Christine Schwienbacher, Wilmar Igl, Zrinka Biloglav, Jacqueline C. M. Witteman, Irene Pichler, Ghazal Zaboli, Tatiana I. Axenovich, Annette Peters, Stefan Schreiber, H‐Erich Wichmann, Heribert Schunkert, Nick Hastie, Ben A. Oostra, Sarah H. Wild, Thomas Meitinger, Ulf Gyllensten, Cornelia M. van Duijn, James F. Wilson, Alan F. Wright, Gerd Schmitz, Harry Campbell
Software Mentions: 2
Published: almost 17 years ago

10.7554/eLife.09571

Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development
Cited by: 95
Author(s): J. Ż̷ylicz, Sabine Dietmann, Ufuk Günesdogan, Jim Hackett, Delphine Cougot, Caroline Lee, M. Azim Surani
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13148-019-0666-5

DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer
Cited by: 20
Author(s): Christoph Weigel, Jittiporn Chaisaingmongkol, Yassen Assenov, Christine Kuhmann, Volker Winkler, Irene Santi, Olga Bogatyrova, Simone Kaucher, Justo Lorenzo Bermejo, Suet Yi Leung, Tsun Leung Chan, Felix Lasitschka, M. Bohrer, Alexander Marx, Roland Heyny-von Haußen, Christel Herold‐Mende, Gerhard Dyckhoff, Petra Boukamp, K.-W. Delank, K. Hörmann, Burkhard M. Lippert, G. Baier, Andreas Dietz, Christopher C. Oakes, Christoph Plass, Heiko Becher, Peter Schmezer, Heribert Ramroth, Odilia Popanda
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.01257

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments
Cited by: 262
Author(s): Liana F. Lareau, Dustin H Hite, Gregory J. Hogan, Patrick O. Brown
Software Mentions: 2
Published: over 12 years ago

10.7554/eLife.00994

A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity
Cited by: 145
Author(s): Alyson Ashe, Tony Bélicard, Jérémie Le Pen, Peter Sarkies, Lise Frézal, Nicolas J Lehrbach, Marie‐Anne Félix, Eric A. Miska
Software Mentions: 2
Published: almost 13 years ago

10.1186/s13148-017-0386-7

CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel
Cited by: 44
Author(s): Luca Morandi, Davide Bartolomeo Gissi, Achille Tarsitano, Sofia Asioli, Andrea Gabusi, Claudio Marchetti, Lucio Montebugnoli, Maria Pia Foschini
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pgen.1001116

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data
Cited by: 484
Author(s): Abigail W. Bigham, Marc Bauchet, Dalila Pinto, Xiaole Mao, Joshua M. Akey, Rui Mei, Stephen W. Scherer, Colleen G. Julian, Megan J. Wilson, David López Herráez, Tom D. Brutsaert, Esteban J. Parra, Lorna G. Moore, Mark D. Shriver
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pgen.1006296

Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer
Cited by: 37
Author(s): Jian Gong, Carolyn M. Hutter, Polly A. Newcomb, Cornelia M. Ulrich, Stephanie A. Bien, Peter T. Campbell, John A. Baron, Sonja I. Berndt, Stéphane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang–Claude, Mengmeng Du, David Duggan, Jane C. Figueiredo, Steven Gallinger, Edward Giovannucci, Robert W. Haile, Tabitha A. Harrison, Richard B. Hayes, Michael Hoffmeister, John L. Hopper, Thomas J. Hudson, Jihyoun Jeon, Mark A. Jenkins, Jonathan Kocarnik, Sébastien Küry, Loı̈c Le Marchand, Yi Lin, Noralane M. Lindor, Reiko Nishihara, Shuji Ogino, John D. Potter, Anja Rudolph, Robert E. Schoen, Petra Schrotz‐King, Daniela Seminara, Martha L. Slattery, Stephen N. Thibodeau, Mark Thornquist, Réka Tóth, Robert B. Wallace, Emily White, Shuo Jiao, Mathieu Lemire, Li Hsu, Ulrike Peters
Software Mentions: 2
Published: almost 10 years ago

10.1007/s13361-015-1269-9

High Resolution Mass Spectrometry of Polyfluorinated Polyether-Based Formulation
Cited by: 36
Author(s): Ian Ken D. Dimzon, Xenia Trier, Tobias Frömel, Rick Helmus, Thomas P. Knepper, P. de Voogt
Software Mentions: 2
Published: almost 11 years ago

10.3390/cells1041029

A Novel Type III Endosome Transmembrane Protein, TEMP
Cited by: 1
Author(s): Rajith Aturaliya, Markus C. Kerr, Rohan D. Teasdale
Software Mentions: 2
Published: almost 14 years ago

10.3390/cancers13133180

Immunity Depletion, Telomere Imbalance, and Cancer-Associated Metabolism Pathway Aberrations in Intestinal Mucosa upon Short-Term Caloric Restriction
Cited by: 0
Author(s): Evan Maestri, Kalina Duszka, Vladimir A. Kuznetsov
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.0020024

SPA: A Probabilistic Algorithm for Spliced Alignment
Cited by: 25
Author(s): Erik van Nimwegen, Nicodème Paul, Robert P. Sheridan, Mihaela Zavolan
Software Mentions: 2
Published: over 20 years ago

10.3390/genes7030011

Genome-Wide Identification and Characterization of Long Non-Coding RNAs from Mulberry (Morus notabilis) RNA-seq Data
Cited by: 35
Author(s): Xin Song, Liang Sun, Haitao Luo, Qingguo Ma, Yi Zhao, Dong Pei
Software Mentions: 2
Published: over 10 years ago

10.3390/ijms17111848

IBTK Differently Modulates Gene Expression and RNA Splicing in HeLa and K562 Cells
Cited by: 10
Author(s): Giuseppe Fiume, Annarita Scialdone, Francesca Rizzo, Maria Rosaria De Filippo, Carmelo Laudanna, Fabio Albano, Gaetanina Golino, Eleonora Vecchio, Marilena Pontoriero, Selena Mimmi, Simona Ceglia, Antonio Pisano, Enrico Iaccino, Camillo Palmieri, Sergio Paduano, Giuseppe Viglietto, Alessandro Weisz, Giuseppe Scala, Ileana Quinto
Software Mentions: 2
Published: almost 10 years ago

10.1186/1745-7580-2-4

Cited by: 42
Author(s): Emily Wong, Lauren J. Young, Anthony T. Papenfuss, Katherine Belov
Software Mentions: 2
Published: over 20 years ago

10.1371/journal.pgen.1008026

Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency
Cited by: 13
Author(s): Jinli Li, Yi Chen, Tao Zheng, Lingxin Kong, Sucheng Zhu, Yihua Sun, Zixin Deng, Litao Yang, Delin You
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1006682

Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus
Cited by: 37
Author(s): Anchel de Jaime-Soguero, Francesco Aulicino, Gökhan Ertaylan, Anna Griego, Aniello Cerrato, Aravind Tallam, Antonio del Sol, María Pía Cosma, Frederic Lluı́s
Software Mentions: 2
Published: over 9 years ago

10.1038/s41438-020-0336-y

Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral buds
Cited by: 38
Author(s): Hong Zhu, Pao‐Yang Chen, Silin Zhong, Chris Dardick, Ann M. Callahan, Yong-Qiang An, Steve van Knocker, Yingzhen Yang, Gan-Yuan Zhong, Albert G. Abbott, Zongrang Liu
Software Mentions: 2
Published: about 6 years ago

10.3389/fimmu.2015.00616

Bad News: Analysis of the Quality of Information on Influenza Prevention Returned by Google in English and Italian
Cited by: 21
Author(s): Ali Maki, Roger Evans, Pietro Ghezzi
Software Mentions: 2
Published: over 10 years ago

10.1038/s41438-018-0078-2

PGD: Pineapple Genomics Database
Cited by: 22
Author(s): Huimin Xu, Qingyi Yu, Yan Shi, Xiuting Hua, Haibao Tang, Long Yang, Ray Ming, Jisen Zhang
Software Mentions: 2
Published: almost 8 years ago

10.3390/ht9020008

DMETTM Genotyping: Tools for Biomarkers Discovery in the Era of Precision Medicine
Cited by: 11
Author(s): Giuseppe Agapito, Marzia Settino, Francesca Scionti, Emanuela Altomare, Pietro Hiram Guzzi, Pierfrancesco Tassone, Pierosandro Tagliaferri, Mario Cannataro, Mariamena Arbitrio, Maria Teresa Di Martino
Software Mentions: 2
Published: over 6 years ago

10.1016/j.celrep.2015.10.030

Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis
Cited by: 33
Author(s): Mayuri Rege, Vidya Subramanian, Chenchen Zhu, Tsung Han Hsieh, Assaf Weiner, Nir Friedman, Sandra Clauder‐Münster, Lars M. Steinmetz, Oliver J. Rando, Laurie A. Boyer, Craig L. Peterson
Software Mentions: 2
Published: almost 11 years ago

10.3390/ijms19061722

Systematic Analysis of Long Non-Coding RNAs and mRNAs in the Ovaries of Duroc Pigs During Different Follicular Stages Using RNA Sequencing
Cited by: 30
Author(s): Yi Liu, Mengxun Li, Xiaochen Bo, Tao Li, Ligeng Ma, Tenjiao Zhai, Tao Huang
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1007581

Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation
Cited by: 20
Author(s): Patrick Torbey, Elodie Thierion, Samuel Collombet, Anne De Cian, Carole Desmarquet-Trin-Dinh, Mathilde Dura, Jean-Paul Concordet, Patrick Charnay, Pascale Gilardi-Hebenstreit
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1002384

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
Cited by: 892
Author(s): A. P. Jason de Koning, Wanjun Gu, Todd A. Castoe, Mark A. Batzer, David D. Pollock
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pgen.1000163

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq
Cited by: 518
Author(s): Alexandra Sittka, Sacha Lucchini, Kai Papenfort, Cynthia M. Sharma, Katarzyna Rolle, Tim T. Binnewies, Jay C. D. Hinton, Jörg Vogel
Software Mentions: 2
Published: almost 18 years ago

10.1016/j.heliyon.2020.e05243

Fast, easy, cheap, robust and safe method of analysis of Sudan dyes in chilli pepper powder
Cited by: 5
Author(s): Joseph Kweku Adjei, Vigil Ahormegah, Alex Kissi Boateng, Harry Kwaku Megbenu, Samuel Asiedu Owusu
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1004885

Interactions of Chromatin Context, Binding Site Sequence Content, and Sequence Evolution in Stress-Induced p53 Occupancy and Transactivation
Cited by: 49
Author(s): Dan Su, Xuting Wang, Michelle R. Campbell, Lingyun Song, Alexias Safi, Gregory E. Crawford, Douglas A. Bell
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1005702

Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish
Cited by: 70
Author(s): Adi Shamay-Ramot, Khen Khermesh, Hagit T. Porath, Michal Barák, Yishay Pinto, Chaim Wachtel, Alona Zilberberg, Tali Lerer-Goldshtein, Sol Efroni, Erez Y. Levanon, Lior Appelbaum
Software Mentions: 2
Published: over 10 years ago

10.3390/ijms21061908

Peripheral Circulating Exosomal miRNAs Potentially Contribute to the Regulation of Molecular Signaling Networks in Aging
Cited by: 13
Author(s): Hongxia Zhang, Kunlin Jin
Software Mentions: 2
Published: over 6 years ago

10.3390/genes5041115

Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential
Cited by: 18
Author(s): Y. Kurihara, Yuko Makita, Mika Kawashima, Hidefumi Hamasaki, Yoshiharu Y. Yamamoto, Minami Matsui
Software Mentions: 2
Published: over 11 years ago

10.1016/j.cellsig.2007.01.010

Genomic tagging of endogenous Type IIβ Phosphatidylinositol 5-phosphate 4-kinase in DT40 cells reveals a nuclear localisation
Cited by: 31
Author(s): Jonathan P. Richardson, Minchuan Wang, Jonathan H. Clarke, Ketan Patel, Robin F. Irvine
Software Mentions: 2
Published: about 19 years ago

10.1534/g3.115.021386

Identification of Genes Uniquely Expressed in the Germ-Line Tissues of the Jewel WaspNasonia vitripennis
Cited by: 15
Author(s): Patrick M. Ferree, Christopher Fang, Mariah Mastrodimos, Bruce A. Hay, Henry Amrhein, Omar S. Akbari
Software Mentions: 2
Published: over 10 years ago

10.3389/fpls.2019.00072

Cold Induced Antisense Transcription of FLOWERING LOCUS C in Distant Grasses
Cited by: 16
Author(s): Fuchao Jiao, Kanchan Pahwa, Murray Manning, Niklas Dochy, Koen Geuten
Software Mentions: 2
Published: over 7 years ago

10.1534/g3.112.003194

Microarray-Based Capture of Novel Expressed Cell Type–Specific Transfrags (CoNECT) to Annotate Tissue-Specific Transcription in Drosophila melanogaster
Cited by: 0
Author(s): Xiaojing Hong, Harshavardhan Doddapaneni, Josep M. Comeron, Matthew J. Rodesch, Heather A. Halvensleben, Chung Yi Nien, F. Bolei, Raghu Metpally, Todd Richmond, Thomas Albert, J. Robert Manak
Software Mentions: 2
Published: about 14 years ago

10.3390/ijms21165831

BrassicaEDB: A Gene Expression Database for Brassica Crops
Cited by: 37
Author(s): Haoyu Chao, Li Tian, Chaoyu Luo, Hualei Huang, Yingfei Ruan, Xiaodong Li, Yue Niu, Yonghai Fan, Wei Sun, Kai Zhang, Jiana Li, Cunmin Qu, Kun Lü
Software Mentions: 2
Published: about 6 years ago

10.1038/s41419-021-04017-8

Tissue-specific expression of p73 and p63 isoforms in human tissues
Cited by: 10
Author(s): Clayton B. Marshall, J. Scott Beeler, Brian D. Lehmann, Paula I. González-Ericsson, Violeta Sánchez, Melinda E. Sanders, Kelli L. Boyd, Jennifer A. Pietenpol
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1005709

Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes
Cited by: 110
Author(s): Thomas Arbogast, Abdel‐Mouttalib Ouagazzal, Claire Chevalier, Maksym V. Kopanitsa, Nurudeen O. Afinowi, Eugenia Migliavacca, Belinda S. Cowling, Marie‐Christine Birling, Marie‐France Champy, Alexandre Reymond, Yann Hérault
Software Mentions: 2
Published: over 10 years ago

10.1038/s41422-021-00477-x

Formative pluripotent stem cells show features of epiblast cells poised for gastrulation
Cited by: 42
Author(s): Xiaoxiao Wang, Yunlong Xiang, Yang Yu, Ran Wang, Yu Zhang, Qianhua Xu, Hao Sun, Zhen Zhao, Xiangxiang Jiang, Xiaoqing Wang, Xukun Lu, Dandan Qin, Yujun Quan, Jiaqi Zhang, Ng Shyh‐Chang, Hongmei Wang, Naihe Jing, Wei Xie, Lei Li
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21249701

Origin and Evolution of the Human Bcl2-Associated Athanogene-1 (BAG-1)
Cited by: 4
Author(s): Peter Q. Nguyen, Kyle Hess, Larissa Smulders, Dat Le, Carolina Briseno, Christina M Chavez, Nikolas Nikolaidis
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22020602

Transposable Elements and Teleost Migratory Behaviour
Cited by: 8
Author(s): Elisa Carotti, Federica Carducci, Adriana Canapa, Marco Barucca, Samuele Greco, Marco Gerdol, Maria Assunta Biscotti
Software Mentions: 2
Published: over 5 years ago

10.1038/s41421-018-0039-9

DNA methylation reprogramming of functional elements during mammalian embryonic development
Cited by: 43
Author(s): Congru Li, Yong Fan, Guoqiang Li, Xiaocui Xu, Jialei Duan, Rong Li, Xiangjin Kang, Xin Ma, Xuepeng Chen, Youqi Ke, Jie Yan, Ying Lian, Ping Liu, Yue Zhao, Haiquan Zhao, Yaoyong Chen, Yang Yu, Jiang Liu
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2018.00965

Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts
Cited by: 25
Author(s): M. A. Eldarov, Alexey V. Beletsky, Tatiana N. Tanashchuk, Svetlana A. Kishkovskaya, Nikolai V. Ravin, Andrey V. Mardanov
Software Mentions: 2
Published: over 8 years ago

10.3390/cells9010147

IGF-1 Signalling Regulates Mitochondria Dynamics and Turnover through a Conserved GSK-3β–Nrf2–BNIP3 Pathway
Cited by: 46
Author(s): Sarah Riis, Jack Murray, Rosemary O’Connor
Software Mentions: 2
Published: over 6 years ago

10.1038/s41419-019-2201-1

Epigenetic priming by Dot1l in lymphatic endothelial progenitors ensures normal lymphatic development and function
Cited by: 11
Author(s): Hyunjin Yoo, Young Jae Lee, Chanhyeok Park, Dabin Son, Dong Yoon Choi, Ji Hyun Park, Hee-Jin Choi, Hyun Woo La, Yun Jung Choi, Eun Hye Moon, Dieter Saur, Hyung Min Chung, Hyuk Song, Jeong Tae, Hoon Jang, Dong Ryul Lee, Chankyu Park, Ok Hee Lee, Ssang-Goo Cho, Seok Ho Hong, Gu Kong, Jin‐Hoi Kim, Yun‐Sang Choi, Kwonho Hong
Software Mentions: 2
Published: over 6 years ago

10.3390/genes11121486

citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement
Cited by: 8
Author(s): Naveen Duhan, Manish Meshram, Cristian D Loaiza, Rakesh Kaundal
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22168646

PPARγ-Induced Global H3K27 Acetylation Maintains Osteo/Cementogenic Abilities of Periodontal Ligament Fibroblasts
Cited by: 7
Author(s): Hang Yuan, Shigeki Suzuki, Shizu Hirata-Tsuchiya, Akiko Satô, Eiji Nemoto, Masahiro Saito, Hideki Shiba, Satoru Yamada
Software Mentions: 2
Published: about 5 years ago

10.2196/jmir.9644

Online Information Infrastructure Increases Inter-Rater Reliability of Medical Coders: A Quasi-Experimental Study (Preprint)
Cited by: 6
Author(s): Julian Varghese, Sarah Sandmann, Martin Dugas
Software Mentions: 2
Published: over 8 years ago

10.3390/cancers12082137

Epigenetic Targeting of Mcl-1 Is Synthetically Lethal with Bcl-xL/Bcl-2 Inhibition in Model Systems of Glioblastoma
Cited by: 14
Author(s): Enyuan Shang, Trang Nguyen, Chang Shu, Mike‐Andrew Westhoff, Georg Karpel‐Massler, Markus D. Siegelin
Software Mentions: 2
Published: about 6 years ago

10.2196/10227

What People “Like”: Analysis of Social Media Strategies Used by Food Industry Brands, Lifestyle Brands, and Health Promotion Organizations on Facebook and Instagram
Cited by: 106
Author(s): Karen Klassen, Emily S. Borleis, Louis Brennan, Mike Reid, Tracy A. McCaffrey, Megan S C Lim
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1008036

LINE-2 transposable elements are a source of functional human microRNAs and target sites
Cited by: 42
Author(s): Rebecca Petri, Per Ludvik Brattås, Yogita Sharma, Marie E. Jönsson, Karolina Pircs, Johan Bengzon, Johan Jakobsson
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2017.02218

Nictaba Homologs from Arabidopsis thaliana Are Involved in Plant Stress Responses
Cited by: 13
Author(s): Lore Eggermont, Karolina Stefanowicz, Els J. M. Van Damme
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-14336-6

Unravelling pathways downstream Sox6 induction in K562 erythroid cells by proteomic analysis
Cited by: 6
Author(s): Gloria Barbarani, Antonella Ronchi, Margherita Ruoppolo, Lucia Santorelli, Robert S. Steinfelder, Sudharshan Elangovan, Cristina Fugazza, Marianna Caterino
Software Mentions: 2
Published: almost 9 years ago

10.1111/cmi.12890

Systematic gene overexpression inCandida albicansidentifies a regulator of early adaptation to the mammalian gut
Cited by: 35
Author(s): Sadri Znaidi, Lasse van Wijlick, Arturo Hernández‐Cervantes, Natacha Sertour, Jean‐Luc Desseyn, Frédéric Vincent, Ralitsa Atanassova, Valérie Gouyer, Carol A. Munro, Sophie Bachellier‐Bassi, Frédéric Dalle, Thierry Jouault, Marie‐Elisabeth Bougnoux, Christophe d’Enfert
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.11155

Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway
Cited by: 112
Author(s): Zhiyun Ge, Bao Lin Quek, Karen Beemon, J. Robert Hogg
Software Mentions: 2
Published: over 10 years ago

10.1093/database/bax059

BioSearch: a semantic search engine for Bio2RDF
Cited by: 19
Author(s): Wei Hu, Honglei Qiu, Junhui Huang, Michel Dumontier
Software Mentions: 2
Published: over 9 years ago

10.1038/srep41474

Genome-wide DNA methylation reprogramming in response to inorganic arsenic links inhibition of CTCF binding, DNMT expression and cellular transformation
Cited by: 29
Author(s): Matthew Rea, Meredith Eckstein, Rebekah Eleazer, Caroline N. Smith, Yvonne Fondufe‐Mittendorf
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1005946

MiR144/451 Expression Is Repressed by RUNX1 During Megakaryopoiesis and Disturbed by RUNX1/ETO
Cited by: 17
Author(s): Nicole Kohrs, Stephan Kolodziej, Olga N. Kuvardina, Julia Herglotz, Jasmin Yillah, Stefanie Herkt, Alexander Piechatzek, Gabriela Salinas Riester, Thomas Lingner, Christian Wichmann, Halvard Bönig, Erhard Seifried, Uwe Platzbecker, Hind Medyouf, Manuel Grez, Jörn Lausen
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.29550

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo
Cited by: 76
Author(s): Michael Stadler, Jenna E. Haines, Michael B. Eisen
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.56697

Trait-associated noncoding variant regions affect TBX3 regulation and cardiac conduction
Cited by: 5
Author(s): Jan Hendrik van Weerd, Rajiv A Mohan, Karel van Duijvenboden, Ingeborg B. Hooijkaas, Vincent Wakker, Bastiaan J. Boukens, Phil Barnett, Vincent M. Christoffels
Software Mentions: 2
Published: about 6 years ago

10.1038/srep41598

Genome-wide Regulatory Roles of the C2H2-type Zinc Finger Protein ZNF764 on the Glucocorticoid Receptor
Cited by: 14
Author(s): Abeer A. Fadda, Najeeb Syed, Rafah Mackeh, Anna Papadopoulou, Shigeru Suzuki, Puthen V. Jithesh, Tomoshige Kino
Software Mentions: 2
Published: over 9 years ago

10.1093/database/baz056

LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species
Cited by: 6
Author(s): Leiming You, Jiaqi Chi, Shengfeng Huang, Ting Yu, Guangrui Huang, Yuchao Feng, Xiaopu Sang, Xinhui Gao, Tingan Li, Zirui Yue, Aijie Liu, Shangwu Chen, Anlong Xu
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2021.636284

Antimicrobial Resistance and Genomic Characterization of Two mcr-1-Harboring Foodborne Salmonella Isolates Recovered in China, 2016
Cited by: 4
Author(s): Yujie Hu, Scott V. Nguyen, Wei Wang, Xin Gan, Yinping Dong, Chang Liu, Xiquan Cui, Jin Xu, Fengqin Li, Séamus Fanning
Software Mentions: 2
Published: about 5 years ago

10.1534/g3.118.200901

Genetic, Inflammatory, and Epithelial Cell Differentiation Factors Control Expression of Human Calpain-14
Cited by: 14
Author(s): Daniel Miller, Carmy Forney, Mark Rochman, Stacey A Cranert, Jeffery Habel, Jeffrey K. Rymer, Arthur Lynch, Connor Schroeder, Josh Lee, Amber Sauder, Quinton Smith, Mehak Chawla, Michael Trimarchi, Xiaoming Lu, Ellen Fjellman, Michael Brusilovsky, Artem Barski, Stephen N. Waggoner, Matthew T. Weirauch, Marc E. Rothenberg, Leah C. Kottyan
Software Mentions: 2
Published: over 7 years ago

10.1093/database/bat034

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
Cited by: 120
Author(s): Deeksha Bhartiya, Koustav Pal, Sourav Ghosh, Shruti Kapoor, Saakshi Jalali, Bharat Panwar, Sakshi Jain, Satish Sati, Shantanu Sengupta, Chetana Sachidanandan, Gajendra P. S. Raghava, Sridhar Sivasubbu, Vinod Scaria
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0005008

Transcriptional Network of p63 in Human Keratinocytes
Cited by: 42
Author(s): Silvia Pozzi, Federico Zambelli, Daniele Merico, Giulio Pavesi, Amélie Robert, Peggy Maltère, Xavier Gidrol, Roberto Mantovani, M. Alessandra Viganò
Software Mentions: 2
Published: over 17 years ago

10.7554/eLife.41444

The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci
Cited by: 35
Author(s): Anand Kumar Singh, Subhendu Roy Choudhury, Sandip De, Jie Zhang, Stephen Kissane, Vibha Dwivedi, Preethi Ramanathan, Marija Petrić, Luisa Orsini, Daniel Hebenstreit
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.23670

DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids
Cited by: 101
Author(s): Sebastián Cánovas, Elena Ivanova, Raquel Romar, Soledad García-Martínez, Cristina Soriano‐Úbeda, Francisco Alberto García–Vázquez, Heba Saadeh, Simon Andrews, Gavin Kelsey, Pilar Coy
Software Mentions: 2
Published: over 9 years ago

10.1038/srep33779

SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster
Cited by: 12
Author(s): Jinumary Mathai, Smriti Mittal, Aftab Alam, Payal Ranade, Devraj Mogare, Sonal Patel, Smita Saxena, Suvankar Ghorai, Abhijeet Kulkarni, Samit Chattopadhyay
Software Mentions: 2
Published: almost 10 years ago

10.7554/eLife.53447

Suppressing proteasome mediated processing of topoisomerase II DNA-protein complexes preserves genome integrity
Cited by: 25
Author(s): Nicholas Sciascia, Wei Wu, Dali Zong, Yilun Sun, Nancy Wong, Sam John, Darawalee Wangsa, Thomas Ried, Samuel F. Bunting, Yves Pommier, André Nussenzweig
Software Mentions: 2
Published: over 6 years ago

10.1093/database/baw162

viruSITE—integrated database for viral genomics
Cited by: 47
Author(s): Matej Stano, Gábor Beke, Ľuboš Klučár
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0097568

Genome-Wide Quantitative Analysis of Histone H3 Lysine 4 Trimethylation in Wild House Mouse Liver: Environmental Change Causes Epigenetic Plasticity
Cited by: 12
Author(s): Angelika Börsch-Haubold, Inka Montero, Kathryn Konrad, Bernhard Haubold
Software Mentions: 2
Published: over 12 years ago

10.1038/srep32348

Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection
Cited by: 20
Author(s): Rajesh Pandey, Aniket Bhattacharya, Vivek Bhardwaj, Vineet Jha, Amit Kumar Mandal, Mitali Mukerji
Software Mentions: 2
Published: almost 10 years ago

10.1093/database/bav103

WaspAtlas: aNasonia vitripennisgene database and analysis platform
Cited by: 17
Author(s): Nathaniel J. Davies, Eran Tauber
Software Mentions: 2
Published: over 11 years ago

10.7554/eLife.17061

Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling
Cited by: 121
Author(s): Krzysztof Brzezinka, Simone Altmann, Hjördis Czesnick, Philippe Naveilhan, Michał Górka, Eileen Benke, Tina Kabelitz, Felix Jähne, Alexander Graf, Christian Kappel, Isabel Bäurle
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep25954

CNV analysis in Chinese children of mental retardation highlights a sex differentiation in parental contribution to de novo and inherited mutational burdens
Cited by: 19
Author(s): Binbin Wang, Taoyun Ji, Xueya Zhou, Jing Wang, Xi Wang, Jingmin Wang, Dandan Zhu, Xuejun Zhang, Pak C. Sham, Xuegong Zhang, Xu Ma, Yuwu Jiang
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pgen.1001134

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome
Cited by: 461
Author(s): Robert S. Illingworth, Ulrike Gruenewald-Schneider, Shaun Webb, Alastair Kerr, Keith James, Daniel J. Turner, Colin Smith, David J. Harrison, Robert Andrews, Adrian Bird
Software Mentions: 2
Published: almost 16 years ago

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