A citation-based method for searching scientific literature

Jacqueline Hoare, Dan J Stein, Sarah J Heany, Jean-Paul Fouche, Nicole Phillips, Sebnem Er, Landon Myer, Heather J Zar, Steve Horvath, Andrew J Levine. J Neurovirol 2021
Times Cited: 1







List of co-cited articles
articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


DNA methylation GrimAge strongly predicts lifespan and healthspan.
Ake T Lu, Austin Quach, James G Wilson, Alex P Reiner, Abraham Aviv, Kenneth Raj, Lifang Hou, Andrea A Baccarelli, Yun Li, James D Stewart,[...]. Aging (Albany NY) 2019
274
100

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
100

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.
Belinda Phipson, Jovana Maksimovic, Alicia Oshlack. Bioinformatics 2016
239
100

TRAF6 and IRF7 control HIV replication in macrophages.
Mélissa Sirois, Lynda Robitaille, Robin Allary, Mohak Shah, Christopher H Woelk, Jérôme Estaquier, Jacques Corbeil. PLoS One 2011
28
100

The role of FcεRI expressed in dendritic cells and monocytes.
Jeoung-Sook Shin, Alexandra M Greer. Cell Mol Life Sci 2015
54
100

Type I interferon responses in rhesus macaques prevent SIV infection and slow disease progression.
Netanya G Sandler, Steven E Bosinger, Jacob D Estes, Richard T R Zhu, Gregory K Tharp, Eli Boritz, Doron Levin, Sathi Wijeyesinghe, Krystelle Nganou Makamdop, Gregory Q del Prete,[...]. Nature 2014
309
100

DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty.
Xinyu Zhang, Ying Hu, Amy C Justice, Boyang Li, Zuoheng Wang, Hongyu Zhao, John H Krystal, Ke Xu. Nat Commun 2017
14
100

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
100

Viral kinetics in untreated versus treated acute HIV infection in prospective cohort studies in Thailand.
Jintanat Ananworanich, Leigh Anne Eller, Suteeraporn Pinyakorn, Eugene Kroon, Somchai Sriplenchan, James Lk Fletcher, Duanghathai Suttichom, Christopher Bryant, Rapee Trichavaroj, Peter Dawson,[...]. J Int AIDS Soc 2017
11
100

Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq).
Stephen J Clark, Sébastien A Smallwood, Heather J Lee, Felix Krueger, Wolf Reik, Gavin Kelsey. Nat Protoc 2017
88
100

Single-cell transcriptional landscapes reveal HIV-1-driven aberrant host gene transcription as a potential therapeutic target.
Runxia Liu, Yang-Hui Jimmy Yeh, Ales Varabyou, Jack A Collora, Scott Sherrill-Mix, C Conover Talbot, Sameet Mehta, Kristen Albrecht, Haiping Hao, Hao Zhang,[...]. Sci Transl Med 2020
21
100

Transient detectable viremia and the risk of viral rebound in patients from the Swiss HIV Cohort Study.
Jim Young, Martin Rickenbach, Alexandra Calmy, Enos Bernasconi, Cornelia Staehelin, Patrick Schmid, Matthias Cavassini, Manuel Battegay, Huldrych F Günthard, Heiner C Bucher. BMC Infect Dis 2015
19
100

New signatures of poor CD4 cell recovery after suppressive antiretroviral therapy in HIV-1-infected individuals: involvement of miR-192, IL-6, sCD14 and miR-144.
Francisco Hernández-Walias, María J Ruiz-de-León, Isaac Rosado-Sánchez, Esther Vázquez, Manuel Leal, Santiago Moreno, Francesc Vidal, Julià Blanco, Yolanda M Pacheco, Alejandro Vallejo. Sci Rep 2020
8
100


The Genome-wide Methylation Profile of CD4+ T Cells From Individuals With Human Immunodeficiency Virus (HIV) Identifies Distinct Patterns Associated With Disease Progression.
Sara Moron-Lopez, Victor Urrea, Judith Dalmau, Miguel Lopez, Maria C Puertas, Dan Ouchi, Antonio Gómez, Caroline Passaes, Beatriz Mothe, Christian Brander,[...]. Clin Infect Dis 2021
5
100

Designer epigenome modifiers enable robust and sustained gene silencing in clinically relevant human cells.
Tafadzwa Mlambo, Sandra Nitsch, Markus Hildenbeutel, Marianna Romito, Maximilian Müller, Claudia Bossen, Sven Diederichs, Tatjana I Cornu, Toni Cathomen, Claudio Mussolino. Nucleic Acids Res 2018
31
100

Normalization of Soluble CD163 Levels After Institution of Antiretroviral Therapy During Acute HIV Infection Tracks with Fewer Neurological Abnormalities.
Michelle L D'Antoni, Mary Margaret Byron, Phillip Chan, Napapon Sailasuta, Carlo Sacdalan, Pasiri Sithinamsuwan, Somporn Tipsuk, Suteeraporn Pinyakorn, Eugene Kroon, Bonnie M Slike,[...]. J Infect Dis 2018
21
100


Effects of early versus delayed initiation of antiretroviral treatment on clinical outcomes of HIV-1 infection: results from the phase 3 HPTN 052 randomised controlled trial.
Beatriz Grinsztejn, Mina C Hosseinipour, Heather J Ribaudo, Susan Swindells, Joseph Eron, Ying Q Chen, Lei Wang, San-San Ou, Maija Anderson, Marybeth McCauley,[...]. Lancet Infect Dis 2014
320
100

Interferon-alpha drives monocyte gene expression in chronic unsuppressed HIV-1 infection.
Hans Rempel, Bing Sun, Cyrus Calosing, Satish K Pillai, Lynn Pulliam. AIDS 2010
56
100

Virologic failure is uncommon after treatment initiation during acute HIV infection.
Trevor A Crowell, Nittaya Phanuphak, Suteeraporn Pinyakorn, Eugene Kroon, James L K Fletcher, Donn Colby, Somporn Tipsuk, Putthachard Karnsomlap, Naphassanant Laopraynak, Robert J O'Connell,[...]. AIDS 2016
17
100

A peripheral monocyte interferon phenotype in HIV infection correlates with a decrease in magnetic resonance spectroscopy metabolite concentrations.
Lynn Pulliam, Hans Rempel, Bing Sun, Linda Abadjian, Cyrus Calosing, Dieter J Meyerhoff. AIDS 2011
25
100

HIV DNA Set Point is Rapidly Established in Acute HIV Infection and Dramatically Reduced by Early ART.
Jintanat Ananworanich, Nicolas Chomont, Leigh Ann Eller, Eugene Kroon, Sodsai Tovanabutra, Meera Bose, Martin Nau, James L K Fletcher, Somporn Tipsuk, Claire Vandergeeten,[...]. EBioMedicine 2016
129
100

Comparative DNA methylomic analyses reveal potential origins of novel epigenetic biomarkers of insulin resistance in monocytes from virally suppressed HIV-infected adults.
Christian K Dye, Michael J Corley, Dongmei Li, Vedbar S Khadka, Brooks I Mitchell, Razvan Sultana, Annette Lum-Jones, Cecilia M Shikuma, Lishomwa C Ndhlovu, Alika K Maunakea. Clin Epigenetics 2019
6
100

Infection and replication of HIV-1 in purified progenitor cells of normal human bone marrow.
T M Folks, S W Kessler, J M Orenstein, J S Justement, E S Jaffe, A S Fauci. Science 1988
368
100

Reshaping of the Dendritic Cell Chromatin Landscape and Interferon Pathways during HIV Infection.
Jarrod S Johnson, Sasha Y Lucas, Lynn M Amon, Stephanie Skelton, Rodolfo Nazitto, Sara Carbonetti, D Noah Sather, Dan R Littman, Alan Aderem. Cell Host Microbe 2018
16
100

Shift in monocyte apoptosis with increasing viral load and change in apoptosis-related ISG/Bcl2 family gene expression in chronically HIV-1-infected subjects.
Sean C Patro, Sharmistha Pal, Yingtao Bi, Kenneth Lynn, Karam C Mounzer, Jay R Kostman, Ramana V Davuluri, Luis J Montaner. J Virol 2015
15
100

Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA.
Andrew M Gross, Philipp A Jaeger, Jason F Kreisberg, Katherine Licon, Kristen L Jepsen, Mahdieh Khosroheidari, Brenda M Morsey, Susan Swindells, Hui Shen, Cherie T Ng,[...]. Mol Cell 2016
142
100

Enhanced normalisation of CD4/CD8 ratio with early antiretroviral therapy in primary HIV infection.
John Thornhill, Jamie Inshaw, Soonita Oomeer, Pontiano Kaleebu, David Cooper, Gita Ramjee, Mauro Schechter, Giuseppe Tambussi, Julie Fox, Jose Maria Miro,[...]. J Int AIDS Soc 2014
29
100

A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies.
Andrew E Teschendorff, Charles E Breeze, Shijie C Zheng, Stephan Beck. BMC Bioinformatics 2017
109
100

Determinants of suboptimal CD4+ T cell recovery after antiretroviral therapy initiation in a prospective cohort of acute HIV-1 infection.
Ryan Handoko, Donn J Colby, Eugène Kroon, Carlo Sacdalan, Mark de Souza, Suteeraporn Pinyakorn, Peeriya Prueksakaew, Chutharat Munkong, Sasiwimol Ubolyam, Siriwat Akapirat,[...]. J Int AIDS Soc 2020
3
100

Longitudinal analysis of clinical markers following antiretroviral therapy initiated during acute or early HIV type 1 infection.
Sigall Kassutto, Kaveh Maghsoudi, Mary N Johnston, Gregory K Robbins, Nicole C Burgett, Paul E Sax, Daniel Cohen, Eunice Pae, Ben Davis, Kimon Zachary,[...]. Clin Infect Dis 2006
55
100

Integrated systems approach defines the antiviral pathways conferring protection by the RV144 HIV vaccine.
Slim Fourati, Susan Pereira Ribeiro, Filipa Blasco Tavares Pereira Lopes, Aarthi Talla, Francois Lefebvre, Mark Cameron, J Kaewkungwal, P Pitisuttithum, S Nitayaphan, S Rerks-Ngarm,[...]. Nat Commun 2019
16
100

An Epigenetic Clock Measures Accelerated Aging in Treated HIV Infection.
Konstantinos Boulias, Judy Lieberman, Eric Lieberman Greer. Mol Cell 2016
16
100

Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality.
Xinyu Zhang, Ying Hu, Bradley E Aouizerat, Gang Peng, Vincent C Marconi, Michael J Corley, Todd Hulgan, Kendall J Bryant, Hongyu Zhao, John H Krystal,[...]. Clin Epigenetics 2018
12
100

Virological and immunological characteristics of HIV-infected individuals at the earliest stage of infection.
Jintanat Ananworanich, Carlo P Sacdalan, Suteeraporn Pinyakorn, Nicolas Chomont, Mark de Souza, Tassanee Luekasemsuk, Alexandra Schuetz, Shelly J Krebs, Robin Dewar, Linda Jagodzinski,[...]. J Virus Erad 2016
45
100

Epigenetic age acceleration changes 2 years after antiretroviral therapy initiation in adults with HIV: a substudy of the NEAT001/ANRS143 randomised trial.
Andrés Esteban-Cantos, Javier Rodríguez-Centeno, Pilar Barruz, Belén Alejos, Gabriel Saiz-Medrano, Julián Nevado, Artur Martin, Francisco Gayá, Rosa De Miguel, Jose I Bernardino,[...]. Lancet HIV 2021
5
100

Methylation regulation of Antiviral host factors, Interferon Stimulated Genes (ISGs) and T-cell responses associated with natural HIV control.
Bruna Oriol-Tordera, Maria Berdasco, Anuska Llano, Beatriz Mothe, Cristina Gálvez, Javier Martinez-Picado, Jorge Carrillo, Julià Blanco, Clara Duran-Castells, Carmela Ganoza,[...]. PLoS Pathog 2020
11
100

EWAS Atlas: a curated knowledgebase of epigenome-wide association studies.
Mengwei Li, Dong Zou, Zhaohua Li, Ran Gao, Jian Sang, Yuansheng Zhang, Rujiao Li, Lin Xia, Tao Zhang, Guangyi Niu,[...]. Nucleic Acids Res 2019
61
100

An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray.
Lucas A Salas, Devin C Koestler, Rondi A Butler, Helen M Hansen, John K Wiencke, Karl T Kelsey, Brock C Christensen. Genome Biol 2018
66
100

DNA methylation as a transcriptional regulator of the immune system.
Luisa Morales-Nebreda, Fred S McLafferty, Benjamin D Singer. Transl Res 2019
44
100


Editing DNA Methylation in the Mammalian Genome.
X Shawn Liu, Hao Wu, Xiong Ji, Yonatan Stelzer, Xuebing Wu, Szymon Czauderna, Jian Shu, Daniel Dadon, Richard A Young, Rudolf Jaenisch. Cell 2016
562
100


Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation.
Gero Hütter, Daniel Nowak, Maximilian Mossner, Susanne Ganepola, Arne Müssig, Kristina Allers, Thomas Schneider, Jörg Hofmann, Claudia Kücherer, Olga Blau,[...]. N Engl J Med 2009
100

CD34+ bone marrow cells are infected with HIV in a subset of seropositive individuals.
S K Stanley, S W Kessler, J S Justement, S M Schnittman, J J Greenhouse, C C Brown, L Musongela, K Musey, B Kapita, A S Fauci. J Immunol 1992
146
100

ChAMP: updated methylation analysis pipeline for Illumina BeadChips.
Yuan Tian, Tiffany J Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, Andrew E Teschendorff. Bioinformatics 2017
181
100

SciPy 1.0: fundamental algorithms for scientific computing in Python.
Pauli Virtanen, Ralf Gommers, Travis E Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright,[...]. Nat Methods 2020
100

Virological Blips and Predictors of Post Treatment Viral Control After Stopping ART Started in Primary HIV Infection.
Sarah Fidler, Ashley D Olson, Heiner C Bucher, Julie Fox, John Thornhill, Charles Morrison, Roberto Muga, Andrew Phillips, John Frater, Kholoud Porter. J Acquir Immune Defic Syndr 2017
21
100

HIV downregulates interferon-stimulated genes in primary macrophages.
Seong-Heon Wie, Pinyi Du, Tiffany Q Luong, Steffney E Rought, Nadejda Beliakova-Bethell, Jean Lozach, Jacques Corbeil, Richard S Kornbluth, Douglas D Richman, Christopher H Woelk. J Interferon Cytokine Res 2013
21
100


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.