pypi: browser | Projects | Ecosyste.ms: Papers

10.1242/dev.175265

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs
Cited by: 21
Author(s): Alexandra L. McCorkindale, Philipp Wahle, Irwin Jungreis, Peter Menzel, Chinmay Shukla, Rúben Lopes Pereira Abreu, Rafael A. Irizarry, Irmtraud M. Meyer, M Kellis, Robert P. Zinzen
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-019-6088-0

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Cited by: 10
Author(s): Jonas Ibn-Salem, Miguel A. Andrade‐Navarro
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12859-018-2086-5

An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data
Cited by: 23
Author(s): W. Garrett Jenkinson, Jordi Abante, Andrew P. Feinberg, John Goutsias
Software Mentions: 4
Published: over 8 years ago

10.1186/gb-2011-12-2-r16

Genomewide characterization of non-polyadenylated RNAs
Cited by: 358
Author(s): Li Yang, Michael O. Duff, Brenton R. Graveley, Gordon G. Carmichael, Lingling Chen
Software Mentions: 4
Published: over 15 years ago

10.1186/1471-2164-13-549

Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes
Cited by: 17
Author(s): Heidrun Sigrid Windisch, Magnus Lucassen, Stephan Frickenhaus
Software Mentions: 4
Published: over 14 years ago

10.1186/gb-2013-14-3-r28

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
Cited by: 272
Author(s): H. Bradley Shaffer, Patrick Minx, Daniel E. Warren, Andrew M. Shedlock, Robert C. Thomson, Nicole Valenzuela, John Abramyan, Chris T. Amemiya, Daleen Badenhorst, Kyle K. Biggar, Glen M. Borchert, Christopher W. Botka, Rachel M. Bowden, Edward L. Braun, Anne M. Bronikowski, Benoit G. Bruneau, Leslie T. Buck, Blanche Capel, Todd A. Castoe, Michael Czerwinski, Kim D. Delehaunty, Scott V. Edwards, Catrina C. Fronick, Matthew K. Fujita, Lucinda A. Fulton, Tina Graves, Edward Green, Wilfried Haerty, Ramkumar Hariharan, Omar Hernández, LaDeana W. Hillier, Alisha K. Holloway, Daniel E. Janes, Fredric J. Janzen, Cyriac Kandoth, Lesheng Kong, A. P. Jason de Koning, Yang Li, Robert Literman, Suzanne E. McGaugh, Lindsey Mork, Michelle O’Laughlin, Ryan T. Paitz, David D. Pollock, Chris P. Ponting, S. Radhakrishnan, Brian J. Raney, Joy M. Richman, John St. John, Tonia S. Schwartz, Arun Sethuraman, Phillip Q. Spinks, Kenneth B. Storey, Nay Thane, Tomáš Vinař, Laura M. Zimmerman, Wesley C. Warren, Elaine R. Mardis, Richard K. Wilson
Software Mentions: 4
Published: over 13 years ago

10.1186/gb-2014-15-2-r21

Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans
Cited by: 46
Author(s): Cristina González-Aguilera, Kohta Ikegami, Cristina de la Cruz Ayuso, Alberto de Luis, María Íñiguez, Juan Cabello, Jason D. Lieb, Peter Askjaer
Software Mentions: 4
Published: over 12 years ago

10.1186/s12864-020-07100-0

Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus
Cited by: 16
Author(s): Marina Athanasouli, Hanh Witte, Christian Weiler, Tobias Loschko, Gabi Eberhardt, Ralf J. Sommer, Christian Rödelsperger
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.2056

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals
Cited by: 9
Author(s): Yevgeny Nikolaichik, Aliaksandr U. Damienikan
Software Mentions: 4
Published: about 10 years ago

10.1186/s12915-019-0659-z

Biological and RNA regulatory function of MOV10 in mammalian germ cells
Cited by: 18
Author(s): Kaiqiang Fu, Suwen Tian, Huanhuan Tan, Caifeng Wang, Hanben Wang, Min Wang, Yuan‐Yuan Wang, Zhen Chen, Yanfeng Wang, Qiuling Yue, Qiushi Xu, Shuya Zhang, Haixin Li, Jie Xie, Mingyan Lin, Mengcheng Luo, Feng Chen, Lan Ye, Ke Zheng
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-79781-2

Novel circRNA discovery in sheep shows evidence of high backsplice junction conservation
Cited by: 7
Author(s): Endika Varela-Martínez, Giulia I. Corsi, Christian Anthon, Jan Gorodkin, Begoña M. Jugo
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0140829

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud
Cited by: 99
Author(s): Enis Afgan, Clare Sloggett, Nuwan Goonasekera, Igor V. Makunin, Derek Benson, Mark L. Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie
Software Mentions: 4
Published: almost 11 years ago

10.1111/acel.13178

The inherited methylome landscape is directly altered with paternal aging and associated with offspring neurodevelopmental disorders
Cited by: 27
Author(s): Michelle M. Denomme, Mary E. Haywood, Jason C. Parks, William B. Schoolcraft, Mandy G. Katz‐Jaffe
Software Mentions: 4
Published: about 6 years ago

10.1186/s12915-019-0679-8

Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response
Cited by: 13
Author(s): Xiaoman Xie, Casey Hanson, Saurabh Sinha
Software Mentions: 3
Published: about 7 years ago

10.18632/aging.101485

Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence
Cited by: 13
Author(s): Qiongye Dong, Lei Wei, Michael Q. Zhang, Xiaowo Wang
Software Mentions: 3
Published: about 8 years ago

10.1186/1741-7007-10-107

Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes
Cited by: 106
Author(s): Christine E. Schnitzler, Kevin Pang, Meghan L. Powers, Adam M. Reitzel, Joseph F. Ryan, David Simmons, Takeshi Tada, Morgan Park, Jyoti Gupta, Shelise Brooks, Robert W. Blakesley, Shozo Yokoyama, Steven H. D. Haddock, Mark Q. Martindale, Andreas D. Baxevanis
Software Mentions: 3
Published: over 13 years ago

10.1038/s41598-017-12335-1

Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts
Cited by: 23
Author(s): Nathan Lawlor, Ahrim Youn, Romy Kursawe, Duygu Ucar, Michael L. Stitzel
Software Mentions: 3
Published: almost 9 years ago

10.1186/1741-7007-5-37

The DNA binding parvulin Par17 is targeted to the mitochondrial matrix by a recently evolved prepeptide uniquely present in Hominidae
Cited by: 31
Author(s): Daniel S. Kessler, Panagiotis Papatheodorou, Tina Stratmann, Elke A. Dian, Cristina Hartmann-Fatu, Joachim Rassow, Peter Bayer, Jonathan Wolf Mueller
Software Mentions: 3
Published: almost 19 years ago

10.1186/s12915-019-0674-0

RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting
Cited by: 24
Author(s): Bharati Jadhav, Ramin Monajemi, Kristina K. Gagalova, Daniel J. Ho, Harmen H.M. Draisma, Mark A. van de Wiel, Lude Franke, Bastiaan T. Heijmans, Joyce B. J. van Meurs, Rick Jansen, Peter A.C. ’t Hoen, Andrew J. Sharp, Szymon M. Kiełbasa
Software Mentions: 3
Published: about 7 years ago

10.18632/aging.202353

Cell lineage-specific methylome and genome alterations in gout
Cited by: 6
Author(s): Chia‐Chun Tseng, Wei‐Ting Liao, Man-Chun Wong, Chung‐Jen Chen, Su-Chen Lee, Jeng-Hsien Yen, Shun‐Jen Chang
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2350-12-55

Geographic differences in allele frequencies of susceptibility SNPs for cardiovascular disease
Cited by: 43
Author(s): Keyue Ding, Iftikhar J. Kullo
Software Mentions: 3
Published: over 15 years ago

10.18632/aging.102652

Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson’s disease
Cited by: 8
Author(s): Chunlei Han, Yunpeng Liu, Yun‐Peng Sui, Ning Chen, Tingting Du, Ying Jiang, Chenjia Guo, Kailiang Wang, Qiao Wang, Shiying Fan, Michio Shimabukuro, Fangang Meng, Yuan Fang, Jianguo Zhang
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-14-18

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
Cited by: 9
Author(s): Phillip Seitzer, Tu Anh Ngoc Huynh, Marc T. Facciotti
Software Mentions: 3
Published: over 13 years ago

10.1186/s12915-018-0580-x

Identification of cell types in a mouse brain single-cell atlas using low sampling coverage
Cited by: 15
Author(s): Aparna Bhaduri, Tomasz J. Nowakowski, Alex A. Pollen, Arnold R. Kriegstein
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0020042

A Locus on Chromosome 5 Is Associated with Dilated Cardiomyopathy in Doberman Pinschers
Cited by: 44
Author(s): Theresa-Bernadette Mausberg, Gerhard Wess, Julia Simak, Lena Keller, Michaela Drögemüller, Cord Drögemüller, Matthew T. Webster, Hannah Stephenson, J. Dukes‐McEwan, Tosso Leeb
Software Mentions: 3
Published: about 15 years ago

10.1186/1471-2105-13-85

DIPSBC - data integration platform for systems biology collaborations
Cited by: 13
Author(s): Felix Dreher, Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, K. Schellander, Hans Lehrach, Bodo Lange, Ralf Herwig
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0133751

Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes
Cited by: 43
Author(s): Moon Young Lee, Chanjae Park, Robyn M. Berent, Paul J. Park, Robert Fuchs, Syn Hannah, Chin Albert, Jared Townsend, Craig C. Benson, Doug Redelman, Tong Shen, Sang-Youel Park, Joseph M. Miano, Kenton M. Sanders, Seungil Ro
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0239627

Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel
Cited by: 5
Author(s): Gabriel Schneebauer, Constantin Lindemann, Victoria Drechsel, Lasse Marohn, Klaus Wysujack, Elena Santidrian, Ron P. Dirks, Reinhold Hanel, Bernd Pelster
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0247402

DeepSRE: Identification of sterol responsive elements and nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network analysis
Cited by: 0
Author(s): Davide Noto, Antonina Giammanco, Rossella Spina, Francesca Fayer, Angelo B. Cefalù, Maurizio Averna
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-021-07478-5

Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs
Cited by: 13
Author(s): Christine N Goldfarb, David J. Waxman
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-016-1139-x

CerealsDB 3.0: expansion of resources and data integration
Cited by: 38
Author(s): Paul Wilkinson, Mark Winfield, Gary Barker, Simon Tyrrell, Xingdong Bian, Alexandra M. Allen, Amanda Burridge, Jane A. Coghill, Christy Waterfall, Mario Cáccamo, Robert P. Davey, Keith J. Edwards
Software Mentions: 3
Published: about 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: over 12 years ago

10.1128/JVI.00980-17

ZIC2 Is Essential for Maintenance of Latency and Is a Target of an Immediate Early Protein during Kaposi's Sarcoma-Associated Herpesvirus Lytic Reactivation
Cited by: 10
Author(s): Yuanzhi Lyu, K. Nakano, Ryan R. Davis, Clifford G. Tepper, Mel Campbell, Yoshihiro Izumiya
Software Mentions: 3
Published: almost 9 years ago

10.18632/oncotarget.24361

Integrative proteomic and transcriptomic analysis provides evidence for TrkB (NTRK2) as a therapeutic target in combination with tyrosine kinase inhibitors for non-small cell lung cancer
Cited by: 12
Author(s): Daniel R. Gomez, Lauren A. Byers, Monique B. Nilsson, Lixia Diao, Jing Wang, Lerong Li, Pan Tong, Mia Hofstad, Babita Saigal, Ignacio I. Wistuba, Neda Kalhor, Stephen G. Swisher, You-Hong Fan, Waun Ki Hong, Milind Suraokar, Carmen Behrens, César A. Moran, John V. Heymach
Software Mentions: 3
Published: over 8 years ago

10.3791/57633

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Cited by: 3
Author(s): Christoph N. Schlaffner, Georg J. Pirklbauer, Andreas Bender, Judith A. Steen, Jyoti S. Choudhary
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0047216

A Hybrid Distance Measure for Clustering Expressed Sequence Tags Originating from the Same Gene Family
Cited by: 5
Author(s): Keng-Hoong Ng, Chin-Kuan Ho, Somnuk Phon-Amnuaisuk
Software Mentions: 3
Published: almost 14 years ago

10.18632/oncotarget.14843

Relationship between LINC00341 expression and cancer prognosis
Cited by: 13
Author(s): Meijian Liao, Bing Li, Shikuan Zhang, Qing Liu, Weijie Liao, Weidong Xie, Yaou Zhang
Software Mentions: 3
Published: over 9 years ago

10.1523/ENEURO.0108-21.2021

Forebrain Neural Precursor Cells Are Differentially Vulnerable to Zika Virus Infection
Cited by: 1
Author(s): Samantha M Shelton, Alexandra R Soucy, Ronni Kurzion, Ella Zeldich, John H. Connor, Tarik F. Haydar
Software Mentions: 3
Published: about 5 years ago

10.1038/s41389-020-00285-9

Triptolide targets super-enhancer networks in pancreatic cancer cells and cancer-associated fibroblasts
Cited by: 32
Author(s): Pawan Noel, Shaimaa Hussein, Serina Ng, Corina E. Antal, Wei Lin, Emily Rodela, Priscilla Delgado, Sanna Naveed, Michael Downes, Yin Lin, Ronald M. Evans, Daniel D. Von Hoff, Haiyong Han
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2105-10-26

Identifying differential exon splicing using linear models and correlation coefficients
Cited by: 19
Author(s): Sonia Shah, Jacqueline A. Pallas
Software Mentions: 3
Published: over 17 years ago

10.1371/journal.pone.0193614

A common copy-number variant within SIRPB1 correlates with human Out-of-Africa migration after genetic drift correction
Cited by: 5
Author(s): José Luis Royo, Joan Valls, Rafael D. Acemel, Carlos Gómez-Marín, Mariona Pascual-Pons, Arantxa Lupiañez, José Luis Gómez-Skármeta, Joan Fibla
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-8-113

Discovery and characterization of 91 novel transcripts expressed in cattle placenta
Cited by: 9
Author(s): Charu G. Kumar, Joshua H. Larson, Mark Band, Harris A. Lewin
Software Mentions: 3
Published: over 19 years ago

10.2196/resprot.9639

A Web-Based Telemanagement System for Patients With Complex Inflammatory Bowel Disease: Protocol for a Randomized Controlled Clinical Trial
Cited by: 9
Author(s): Mariam Aguas, Javier del Hoyo, Raquel Faubel, Diana Muñoz, Dana A. Dominguez, Guillermo Bastida, Belén Navarro, Alejandra Barrios, Bernardo Valdivieso, Marisa Correcher, Pilar Nos
Software Mentions: 3
Published: over 7 years ago

10.1038/s41388-018-0659-4

Histoepigenetic analysis of HPV- and tobacco-associated head and neck cancer identifies both subtype-specific and common therapeutic targets despite divergent microenvironments
Cited by: 20
Author(s): Ivenise Carrero, Hsuan-Chen Liu, Andrew G. Sikora, Aleksandar Milosavljevic
Software Mentions: 3
Published: over 7 years ago

10.1523/JNEUROSCI.2836-16.2016

LHX2 Interacts with the NuRD Complex and Regulates Cortical Neuron Subtype DeterminantsFezf2andSox11
Cited by: 52
Author(s): Bhavana Muralidharan, Zeba Khatri, Upasana Maheshwari, Rupesh Gupta, Basabdatta Roy, Saurabh J. Pradhan, Krishanpal Karmodiya, Hari Padmanabhan, Ashwin S. Shetty, Chinthapalli Balaji, Ullas Kolthur‐Seetharam, Jeffrey D. Macklis, Sanjeev Galande, Shubha Tole
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0015392

Identification of De Novo Copy Number Variants Associated with Human Disorders of Sexual Development
Cited by: 133
Author(s): Mounia Tannour‐Louet, Shuo Han, Sean T. Corbett, Jean-François Louet, Svetlana A. Yatsenko, Lindsay Meyers, Chad A. Shaw, Sung-Hae L. Kang, Sau Wai Cheung, Dolores J. Lamb
Software Mentions: 3
Published: almost 16 years ago

10.1128/mBio.00768-21

Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans
Cited by: 7
Author(s): Joel T Steyer, Damien J. Downes, Cameron C. Hunter, Pierre Migeon, Richard B. Todd
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-015-2214-9

Analysis of nucleosome positioning landscapes enables gene discovery in the human malaria parasite Plasmodium falciparum
Cited by: 5
Author(s): Xueqing Maggie Lu, Evelien M. Bunnik, Neeti Pokhriyal, Sara Nasseri, Stefano Lonardi, Karine G. Le Roch
Software Mentions: 3
Published: over 10 years ago

10.1101/2021.07.09.21260221

Genetic regulation ofOAS1nonsense-mediated decay underlies association with risk of severe COVID-19
Cited by: 8
Author(s): Abdul Rouf Banday, Megan L. Stanifer, Óscar Flórez-Vargas, Olusegun O. Onabajo, Muhammad Atif Zahoor, Brenen W. Papenberg, Timothy J. Ring, Chia-Han Lee, Evangelos Andreakos, Evgeny Arons, Greg Barsh, Leslie G. Biesecker, David L. Boyle, Andrea N. Burnett‐Hartman, Mary Carrington, Euijin Chang, Pyoeng Gyun Choe, Rex L Chrisholm, Clifton L. Dalgard, Jeff Edberg, Nathan Erdmann, Heather Spencer Feigelson, Gary S. Firestein, Adam J. Gehring, Michelle Ho, Steven M. Holland, Amy Hutchinson, Hogune Im, Michael G. Ison, Hong Bin Kim, Robert J. Kreitman, Bruce R. Korf, Lisa Mirabello, Jennifer A. Pacheco, Michael J. Peluso, Daniel J. Rader, David T. Redden, Marylyn D. Ritchie, Brooke Rosenbloom, Hanaisa P. Sant Anna, Sharon A. Savage, E. Siouti, Vasiliki Triantafyllia, Joselin M. Vargas, Anurag Verma, Vibha Vij, Duane R. Wesemann, Meredith Yeager, Xu G. Yu, Yu Zhang, Steeve Boulant, Stephen J. Chanock, Jordan J. Feld, Ludmila Prokunina–Olsson
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0094187

ZBED6 Modulates the Transcription of Myogenic Genes in Mouse Myoblast Cells
Cited by: 19
Author(s): Lin Jiang, Ola Wallerman, Shady Younis, Carl-Johan Rubin, Elizabeth R. Gilbert, Elisabeth Sundström, Awaisa Ghazal, Xiaolan Zhang, Li Wang, Tarjei S. Mikkelsen, Gerhard Andersson, Leif Andersson
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0105685

Analysis of Papaya Cell Wall-Related Genes during Fruit Ripening Indicates a Central Role of Polygalacturonases during Pulp Softening
Cited by: 56
Author(s): João Paulo Fabi, Sabrina Garcia Broetto, Sarah Lígia Garcia Leme da Silva, Silin Zhong, Franco Maria Lajolo, João Roberto Oliveira do Nascimento
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0222432

The intermediate proteasome is constitutively expressed in pancreatic beta cells and upregulated by stimulatory, low concentrations of interleukin 1 β
Cited by: 13
Author(s): Muhammad Saad Khilji, Danielle Verstappen, Tina Dahlby, Michala Prause, Celina Pihl, Sophie Emilie Bresson, Tenna Holgersen Bryde, Phillip Alexander Keller Andersen, Kristian Klindt, Dušan Živković, Marie‐Pierre Bousquet, Björn Tyrberg, Thomas Mandrup‐Poulsen, Michał Marzec
Software Mentions: 3
Published: over 6 years ago

10.1186/1756-8722-6-25

Structurally differentiated cis-elements that interact with PU.1 are functionally distinguishable in acute promyelocytic leukemia
Cited by: 12
Author(s): Maoxiang Qian, Ji Wen, Xuehua Zhu, Xiaohong Jia, Xian‐Wen Yang, Yanzhi Du, Kankan Wang, Ji Zhang
Software Mentions: 3
Published: over 13 years ago

10.1186/1751-0473-6-2

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format
Cited by: 55
Author(s): Guiyin Xu, Nan Deng, Zhiyu Zhao, Thair Judeh, Erik K. Flemington, Dongxiao Zhu
Software Mentions: 3
Published: over 15 years ago

10.1186/s12859-014-0422-y

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
Cited by: 9
Author(s): Shi Tan, Avirup Dutta, Nicholas S. Jakubovics, Mia Yang Ang, Cheuk Chuen Siow, Naresh V.R. Mutha, Hamed Heydari, Wei Yee Wee, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: over 11 years ago

10.18632/oncotarget.20098

Robust diagnosis of Ewing sarcoma by immunohistochemical detection of super-enhancer-driven EWSR1-ETS targets
Cited by: 60
Author(s): Michaela C. Baldauf, Martin F. Orth, Marlene Dallmayer, Aruna Marchetto, Julia S. Gerke, Rebeca Alba Rubío, Merve Meryem Kıran, Julian Musa, Max Knott, Shunya Ohmura, Jing Li, Nusret Akpolat, Ayşe Nur Akatlı, Özlem Özen, Uta Dirksen, Wolfgang Hartmann, Enrique de Álava, Daniel Baumhoer, Giuseppina Sannino, Thomas Kirchner, Thomas G.P. Grünewald
Software Mentions: 3
Published: about 9 years ago

10.1016/j.jsb.2016.02.012

Web-based volume slicer for 3D electron-microscopy data from EMDB
Cited by: 14
Author(s): José Salavert-Torres, A. Iudin, Ingvar Lagerstedt, Eduardo Sanz-García, Gerard J. Kleywegt, Ardan Patwardhan
Software Mentions: 3
Published: over 10 years ago

10.1186/s12859-020-03934-3

Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays
Cited by: 9
Author(s): Vandhana Krishnan, Sowmithri Utiramerur, Zena Ng, Somalee Datta, M Snyder, Euan A. Ashley
Software Mentions: 3
Published: over 5 years ago

10.1016/j.stemcr.2020.01.004

Activin A and BMP4 Signaling Expands Potency of Mouse Embryonic Stem Cells in Serum-Free Media
Cited by: 13
Author(s): Baojiang Wu, Lin Li, Bojiang Li, Junpeng Gao, Yanglin Chen, Mengyi Wei, Zhiqing Yang, Baojing Zhang, Shudong Li, Kexin Li, Changshan Wang, M. Azim Surani, Xihe Li, Fuchou Tang, Siqin Bao
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-10-148

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes
Cited by: 17
Author(s): Wonhoon Lee, Jongsun Park, Jaeyoung Choi, Ki Won Jung, Bong Soo Park, Donghan Kim, Jae-Young Lee, Kyohun Ahn, Wonho Song, Seogchan Kang, Yong Hwan Lee, Seung Hwan Lee
Software Mentions: 3
Published: over 17 years ago

10.1128/AEM.01741-18

Response of the Biocontrol Agent Pseudomonas pseudoalcaligenes AVO110 to Rosellinia necatrix Exudate
Cited by: 5
Author(s): Clara Pliego, José Ignacio Crespo-Gómez, Adrián Pintado, Isabel Pérez‐Martínez, Antonio de Vicente, Francisco M. Cazorla, Cayo Ramos
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0094101

Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter
Cited by: 52
Author(s): Florian Maumus, Hadi Quesneville
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-021-98708-z

AGO CLIP-based imputation of potent siRNA sequences targeting SARS-CoV-2 with antifibrotic miRNA-like activity
Cited by: 6
Author(s): Seung Hyun Ahn, Dowoon Gu, Yongjun Koh, Hye-Sook Lee, Sung Wook
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-016-2457-0

Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster
Cited by: 18
Author(s): Mei-Ju May Chen, Li-Kai Chen, Yu-Shing Lai, Yu-Yu Lin, Dung-Chi Wu, Yi-Chung Tung, Kwei-Yan Liu, Hsueh‐Tzu Shih, Yi-Jyun Chen, Yen‐Ting Lin, Li‐Ting Ma, Jun Huang, Po-Chun Wu, Hong Mei, Fang-Hua Chu, June‐Tai Wu, Wen-Hsiung Li, Chien‐Yu Chen
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-021-91503-w

Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
Cited by: 12
Author(s): Jessica Gray, P. Scott Chandry, Mandeep Kaur, Chawalit Kocharunchitt, Séamus Fanning, John P. Bowman, Edward M. Fox
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0102968

Role of Polycomb Group Proteins in the DNA Damage Response – A Reassessment
Cited by: 12
Author(s): Hollie Chandler, Harshil Patel, Richard D. Palermo, Sharon Brookes, Nik Matthews, Gordon Peters
Software Mentions: 3
Published: about 12 years ago

10.1186/s12920-018-0453-8

Identification of exon skipping events associated with Alzheimer’s disease in the human hippocampus
Cited by: 17
Author(s): Seonggyun Han, Jason E. Miller, Seyoun Byun, Dokyoon Kim, Shannon L. Risacher, Andrew J. Saykin, Younghee Lee, Kwangsik Nho
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-021-89798-w

Genomic selection signatures in autism spectrum disorder identifies cognitive genomic tradeoff and its relevance in paradoxical phenotypes of deficits versus potentialities
Cited by: 3
Author(s): Anil Prakash, Moinak Banerjee
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0015688

High-Definition Mapping of Retroviral Integration Sites Defines the Fate of Allogeneic T Cells After Donor Lymphocyte Infusion
Cited by: 40
Author(s): Claudia Cattoglio, Giulietta Maruggi, Cynthia C. Bartholomae, Nirav Malani, Danilo Pellin, Fabienne Cocchiarella, Zulma Magnani, Fabio Ciceri, Alessandro Ambrosi, Christof von Kalle, Frederic D. Bushman, Chiara Bonini, Manfred Schmidt, Fulvio Mavilio, Alessandra Recchia
Software Mentions: 3
Published: over 15 years ago

10.1186/s12920-017-0301-2

Analysis of viral diversity for vaccine target discovery
Cited by: 12
Author(s): Mohammad Asif Khan, Yongli Hu, Olivo Miotto, Natascha May Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J. Thomas August
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2350-7-18

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions
Cited by: 24
Author(s): Raihan K. Uddin, Yang Zhang, Victoria Mok Siu, Yao Shan Fan, Richard O’Reilly, Jay Rao, Shiva M. Singh
Software Mentions: 3
Published: over 20 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: about 6 years ago

10.1038/s41598-021-97350-z

Genetic predisposition to tinnitus in the UK Biobank population
Cited by: 1
Author(s): Madeleine E Urbanek, Jian Zuo
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41398-021-01360-4

Genome wide association study identifies four loci for early onset schizophrenia
Cited by: 12
Author(s): Shuxia Guo, Jiewei Liu, Wenqiang Li, Yongfeng Yang, Luxian Lv, Xiao Xiao, Ming Li, Fanglin Guan, Xiong‐Jian Luo
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-34864-z

Interactome determination of a Long Noncoding RNA implicated in Embryonic Stem Cell Self-Renewal
Cited by: 14
Author(s): Keriayn N. Smith, Joshua Starmer, Terry Magnuson
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-22284-y

Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis
Cited by: 19
Author(s): Li Jin, Peng Yu
Software Mentions: 3
Published: over 8 years ago

10.1186/s13073-017-0481-6

Nuclear Wiskott–Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells
Cited by: 16
Author(s): Nikolai V. Kuznetsov, Bader Almuzzaini, Joanna S. Kritikou, Marisa A. P. Baptista, Mariana M.S. Oliveira, Márton Keszei, Scott B. Snapper, Piergiorgio Percipalle, Lisa S. Westerberg
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0078032

Fine-Mapping an Association of FSHR with Preterm Birth in a Finnish Population
Cited by: 16
Author(s): Sung Chun, Jevon Plunkett, Kari Teramo, Louis J. Muglia, Justin C. Fay
Software Mentions: 3
Published: almost 13 years ago

10.1093/gbe/evaa228

Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification
Cited by: 5
Author(s): Alex Dornburg, Zheng Wang, Junrui Wang, Elizabeth S. Mo, Francesc López-Giráldez, Jeffrey P. Townsend
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-42686-w

Enhanced early-life nutrition upregulates cholesterol biosynthetic gene expression and Sertoli cell maturation in testes of pre-pubertal Holstein bulls
Cited by: 12
Author(s): Chinju Johnson, Alysha Dance, Igor Kovalchuk, John P. Kastelic, Jacob C. Thundathil
Software Mentions: 3
Published: over 7 years ago

10.1186/s13059-020-02201-1

Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
Cited by: 28
Author(s): Yue Feng, Yao Wang, Xiangnan Wang, Xiaohong He, Chen Yang, Ardalan Naseri, Thoru Pederson, Jing Zheng, Shaojie Zhang, Xiao Xiao, Wei Xie, Hanhui Ma
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-020-02186-x

Cis-acting lnc-eRNA SEELA directly binds histone H4 to promote histone recognition and leukemia progression
Cited by: 17
Author(s): Ke Fang, Wei Huang, Yu-Meng Sun, Tian-Qi Chen, Zhan-Cheng Zeng, Qianqian Yang, Qi Pan, Cai Han, Lin-Yu Sun, Xue-Qun Luo, Wen-Tao Wang, Yue‐Qin Chen
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-021-02409-9

Evolution of mouse circadian enhancers from transposable elements
Cited by: 29
Author(s): Julius Judd, Hayley Sanderson, Cédric Feschotte
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0079402

Linear Decay of Retrotransposon Antisense Bias across Genes Is Contingent upon Tissue Specificity
Cited by: 1
Author(s): Sara B. Linker, Dale J. Hedges
Software Mentions: 3
Published: almost 13 years ago

10.1186/1471-2164-13-412

Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data
Cited by: 34
Author(s): Peter D. Tonner, Vinodh Srinivasasainagendra, Shaojie Zhang, Degui Zhi
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12864-016-2948-z

Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy
Cited by: 8
Author(s): Candice Brinkmeyer-Langford, Cynthia Balog-Alvarez, James J. Cai, Brian W. Davis, Joe N. Kornegay
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13059-016-1023-z

Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells
Cited by: 54
Author(s): Xiaoli Zhang, Jun Wu, Jian Wang, Tingting Shen, Hua Li, Jun Lü, Yunzhao Gu, Yani Kang, Chee-Hong Wong, Chew Yee Ngan, Zongshu Shao, Ji Wu, Xiaodong Zhao
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pbio.1000238

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA
Cited by: 376
Author(s): David G. Hendrickson, Daniel J. Hogan, Heather McCullough, Jason W. Myers, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: almost 17 years ago

10.1371/journal.pbio.3000580

12-h clock regulation of genetic information flow by XBP1s
Cited by: 34
Author(s): Yinghong Pan, Heather Ballance, Huan Meng, Naomi Gonzalez, Sam-Moon Kim, Leymaan Abdurehman, Brian York, Xi Chen, Yisrael Schnytzer, Oren Levy, Clifford C. Dacso, Colleen A. McClung, Bert W. O’Malley, Silvia Liu, Bokai Zhu
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-016-0924-1

JBrowse: a dynamic web platform for genome visualization and analysis
Cited by: 595
Author(s): Robert Buels, Eric Yao, Colin Diesh, Richard D. Hayes, Monica Muñoz-Torres, Gregg Helt, David Goodstein, Christine G. Elsik, Suzanna Lewis, Lincoln Stein, Ian Holmes
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-11-42

Evolution and diversity of secretome genes in the apicomplexan parasite Theileria annulata
Cited by: 36
Author(s): William Weir, Tülin Karagenç, Margaret Baird, Andy Tait, Brian Shiels
Software Mentions: 3
Published: over 16 years ago

10.1186/s13059-014-0414-2

Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes
Cited by: 67
Author(s): Antony M. Chettoor, Scott A. Givan, Rex A. Cole, Clayton T Coker, Erica Unger-Wallace, Zuzana Vejlupkova, Erik Vollbrecht, John E. Fowler, Evans Mulenga
Software Mentions: 3
Published: about 12 years ago

10.1186/gb-2014-15-1-r3

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
Cited by: 76
Author(s): Ian M. Silverman, Liancheng Fan, A Vinogradov Alexander, Loyal A. Goff, Cole Trapnell, John L. Rinn, Brian D. Gregory
Software Mentions: 3
Published: over 12 years ago

10.7717/peerj.4106

Transcriptomic profiling of mTOR and ryanodine receptor signaling molecules in developing zebrafish in the absence and presence of PCB 95
Cited by: 6
Author(s): Daniel F. Frank, Galen W. Miller, Richard E. Connon, Juergen Geist, Pamela J. Lein
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.1310

Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
Cited by: 25
Author(s): Rakesh Kumar Majhi, S. K. Saha, Ashutosh Kumar, Arijit Ghosh, Nirlipta Swain, Luna Goswami, Pratyush P. Mohapatra, Apratim Maity, Vivek Kumar Sahoo, Abhishek Kumar, Chandan Goswami
Software Mentions: 3
Published: almost 11 years ago

10.7717/peerj.8592

fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool
Cited by: 2
Author(s): Allen Hubbard, Matthew Bomhoff, Carl J. Schmidt
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-14-818

Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data
Cited by: 67
Author(s): Nameeta Shah, Michael Lankerovich, Hwahyung Lee, Jae-Geun Yoon, Brett Schroeder, Greg Foltz
Software Mentions: 3
Published: over 13 years ago

10.1186/gb-2009-10-4-r39

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
Cited by: 64
Author(s): Jessica Severin, Andrew Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J. Balwierz, Michiel de Hoon, David Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O. Daub, Alistair R.R. Forrest
Software Mentions: 3
Published: over 17 years ago

10.1186/gb-2012-13-11-r102

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs
Cited by: 63
Author(s): Ana C. Marques, Jennifer Y. Tan, Sheena Lee, Lesheng Kong, Andreas Heger, Chris P. Ponting
Software Mentions: 3
Published: over 14 years ago

10.1186/gb-2007-8-12-r269

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction
Cited by: 90
Author(s): Samuel S. Gross, B. Chuong, Marina Sirota, Serafim Batzoglou
Software Mentions: 3
Published: over 19 years ago

Projects: pypi: browser

Enhanced Analysis

Science Score: 65/100

Penalties:

Papers Mentioning browser 2,125