DNA microarrays in parasitology: strengths and limitations
Boothroyd, J. C., Blader, I., Cleary, M., & Singh, U. (2003). DNA microarrays in parasitology: strengths and limitations. TRENDS IN PARASITOLOGY, 19(10), 470–76.

DNA content analysis on microarrays.
Singh, U., Shah, P. H., & MacFarlane, R. C. (2004). DNA content analysis on microarrays. Methods in Molecular Biology (Clifton, N.J.), 270, 237–48.

The genome of the protist parasite Entamoeba histolytica
Loftus, B., Anderson, I., Davies, R., Alsmark, U. C. M., Samuelson, J., Amedeo, P., … Hall, N. (2005). The genome of the protist parasite Entamoeba histolytica. NATURE, 433(7028), 865–68.

Comparative genomic hybridizations of Entamoeba strains reveal unique genetic fingerprints that correlate with virulence
Shah, P. H., MacFarlane, R. C., Bhattacharya, D., Matese, J. C., Demeter, J., Stroup, S. E., & Singh, U. (2005). Comparative genomic hybridizations of Entamoeba strains reveal unique genetic fingerprints that correlate with virulence. EUKARYOTIC CELL, 4(3), 504–15.

Transcriptional profiling of Entamoeba histolytica trophozoites
MacFarlane, R. C., Shah, P. H., & Singh, U. (2005). Transcriptional profiling of Entamoeba histolytica trophozoites. INTERNATIONAL JOURNAL FOR PARASITOLOGY, 35(5), 533–42.

Genomic DNA microarrays for Entamoeba histolytica: Applications for use in expression profiling and strain genotyping
Macfarlane, R., Bhattacharya, D., & Singh, U. (2005). Genomic DNA microarrays for Entamoeba histolytica: Applications for use in expression profiling and strain genotyping. EXPERIMENTAL PARASITOLOGY, 110(3), 196–202.

Coding and noncoding genomic regions of Entamoeba histolytica have significantly different rates of sequence polymorphisms: Implications for epidemiological studies
Bhattacharya, D., Haque, R., & Singh, U. (2005). Coding and noncoding genomic regions of Entamoeba histolytica have significantly different rates of sequence polymorphisms: Implications for epidemiological studies. JOURNAL OF CLINICAL MICROBIOLOGY, 43(9), 4815–4819.

Disruption of a locus encoding a nucleolar zinc finger protein decreases tachyzoite-to-bradyzoite differentiation in Toxoplasma gondii
Vanchinathan, P., Brewer, J. L., Harb, O. S., Boothroyd, J. C., & Singh, U. (2005). Disruption of a locus encoding a nucleolar zinc finger protein decreases tachyzoite-to-bradyzoite differentiation in Toxoplasma gondii. INFECTION AND IMMUNITY, 73(10), 6680–88.

Identification of differentially expressed genes in virulent and nonvirulent Entamoeba species: Potential implications for amebic pathogenesis
MacFarlane, R. C., & Singh, U. (2006). Identification of differentially expressed genes in virulent and nonvirulent Entamoeba species: Potential implications for amebic pathogenesis. INFECTION AND IMMUNITY, 74(1), 340–351.

Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome
Gilchrist, C. A., Houpt, E., Trapaidze, N., Fei, Z., Crasta, O., Asgharpour, A., … Petri, W. A. (2006). Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome. MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 147(2), 163–76.

Growth of the protozoan parasite Entamoeba histolytica in 5-azacytidine has limited effects on parasite gene expression
Ali, I. K. M., Ehrenkaufer, G. M., Hackney, J. A., & Singh, U. (2007). Growth of the protozoan parasite Entamoeba histolytica in 5-azacytidine has limited effects on parasite gene expression. BMC GENOMICS, 8.

Identification of developmentally regulated genes in Entamoeba histolytica: insights into mechanisms of stage conversion in a protozoan parasite
Ehrenkaufer, G. M., Haque, R., Hackney, J. A., Eichinger, D. J., & Singh, U. (2007). Identification of developmentally regulated genes in Entamoeba histolytica: insights into mechanisms of stage conversion in a protozoan parasite. CELLULAR MICROBIOLOGY, 9(6), 1426–44.

Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference
Hackney, J. A., Ehrenkaufer, G. M., & Singh, U. (2007). Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference. NUCLEIC ACIDS RESEARCH, 35(7), 2141–52.

Functional characterization of spliceosomal introns and identification of U2, U4, and U5 snRNAs in the deep-branching eukaryote Entamoeba histolytica
Davis, C. A., Brown, M. P. S., & Singh, U. (2007). Functional characterization of spliceosomal introns and identification of U2, U4, and U5 snRNAs in the deep-branching eukaryote Entamoeba histolytica. EUKARYOTIC CELL, 6(6), 940–48.

Trichostatin A effects on gene expression in the protozoan parasite Entamoeba histolytica
Ehrenkaufer, G. M., Eichinger, D. J., & Singh, U. (2007). Trichostatin A effects on gene expression in the protozoan parasite Entamoeba histolytica. BMC GENOMICS, 8.

Identification of an Entamoeba histolytica serine-, threonine-, and isoleucine-rich protein with roles in adhesion and cytotoxicity
MacFarlane, R. C., & Singh, U. (2007). Identification of an Entamoeba histolytica serine-, threonine-, and isoleucine-rich protein with roles in adhesion and cytotoxicity. EUKARYOTIC CELL, 6(11), 2139–46.

Structure and content of the Entamoeba histolytica genome
Clark, C. G., Alsmark, U. C. M., Tazreiter, M., Saito-Nakano, Y., Ali, V., Marion, S., … Hall, N. (2007). Structure and content of the Entamoeba histolytica genome. ADVANCES IN PARASITOLOGY, VOL 65, 65, 51–190.

Loss of dsRNA-based gene silencing in Entamoeba histolytica: Implications for approaches to genetic analysis
MacFarlane, R. C., & Singh, U. (2008). Loss of dsRNA-based gene silencing in Entamoeba histolytica: Implications for approaches to genetic analysis. EXPERIMENTAL PARASITOLOGY, 119(2), 296–300.

An Entamoeba histolytica rhomboid protease with atypical specificity cleaves a surface lectin involved in phagocytosis and immune evasion
Baxt, L. A., Baker, R. P., Singh, U., & Urban, S. (2008). An Entamoeba histolytica rhomboid protease with atypical specificity cleaves a surface lectin involved in phagocytosis and immune evasion. GENES & DEVELOPMENT, 22(12), 1636–46.

New insights into Entamoeba histolytica pathogenesis
Baxt, L. A., & Singh, U. (2008). New insights into Entamoeba histolytica pathogenesis. CURRENT OPINION IN INFECTIOUS DISEASES, 21(5), 489–94.

Entamoeba histolytica modulates a complex repertoire of novel genes in response to oxidative and nitrosative stresses: implications for amebic pathogenesis
Vicente, J. B., Ehrenkaufer, G. M., Saraiva, L. M., Teixeira, M., & Singh, U. (2009). Entamoeba histolytica modulates a complex repertoire of novel genes in response to oxidative and nitrosative stresses: implications for amebic pathogenesis. CELLULAR MICROBIOLOGY, 11(1), 51–69.

Recent insights into Entamoeba development: Identification of transcriptional networks associated with stage conversion
Singh, U., & Ehrenkaufer, G. M. (2009). Recent insights into Entamoeba development: Identification of transcriptional networks associated with stage conversion. INTERNATIONAL JOURNAL FOR PARASITOLOGY, 39(1), 41–47.

Transcriptional Regulatory Networks in Entamoeba histolytica
Ehrenkaufer, G. M., & Singh, U. (2008). Transcriptional Regulatory Networks in Entamoeba histolytica. CURRENT DRUG TARGETS, 9(11), 931–37.

Small RNAs with 5 '- Polyphosphate Termini Associate with a Piwi-Related Protein and Regulate Gene Expression in the Single-Celled Eukaryote Entamoeba histolytica
Zhang, H., Ehrenkaufer, G. M., Pompey, J. M., Hackney, J. A., & Singh, U. (2008). Small RNAs with 5 '- Polyphosphate Termini Associate with a Piwi-Related Protein and Regulate Gene Expression in the Single-Celled Eukaryote Entamoeba histolytica. PLOS PATHOGENS, 4(11).

A Pseudouridine Synthase Homologue Is Critical to Cellular Differentiation in Toxoplasma gondii
Anderson, M. Z., Brewer, J., Singh, U., & Boothroyd, J. C. (2009). A Pseudouridine Synthase Homologue Is Critical to Cellular Differentiation in Toxoplasma gondii. EUKARYOTIC CELL, 8(3), 398–409.

A developmentally regulated Myb domain protein regulates expression of a subset of stage-specific genes in Entamoeba histolytica
Ehrenkaufer, G. M., Hackney, J. A., & Singh, U. (2009). A developmentally regulated Myb domain protein regulates expression of a subset of stage-specific genes in Entamoeba histolytica. CELLULAR MICROBIOLOGY, 11(6), 898–910.

Downregulation of an Entamoeba histolytica Rhomboid Protease Reveals Roles in Regulating Parasite Adhesion and Phagocytosis
Baxt, L. A., Rastew, E., Bracha, R., Mirelman, D., & Singh, U. (2010). Downregulation of an Entamoeba histolytica Rhomboid Protease Reveals Roles in Regulating Parasite Adhesion and Phagocytosis. EUKARYOTIC CELL, 9(8), 1283–93.

Approaches to characterizing Entamoeba histolytica transcriptional regulation
Pearson, R. J., & Singh, U. (2010). Approaches to characterizing Entamoeba histolytica transcriptional regulation. CELLULAR MICROBIOLOGY, 12(12), 1681–1690.

RNA interference in Entamoeba histolytica: implications for parasite biology and gene silencing
Zhang, H., Pompey, J. M., & Singh, U. (2011). RNA interference in Entamoeba histolytica: implications for parasite biology and gene silencing. FUTURE MICROBIOLOGY, 6(1), 103–17.

Antiparasitic Therapy
Kappagoda, S., Singh, U., & Blackburn, B. G. (2011). Antiparasitic Therapy. MAYO CLINIC PROCEEDINGS, 86(6), 561–83.

Nucleus-localized Antisense Small RNAs with 5 '-Polyphosphate Termini Regulate Long Term Transcriptional Gene Silencing in Entamoeba histolytica G3 Strain
Zhang, H., Alramini, H., Vy Tran, V., & Singh, U. (2011). Nucleus-localized Antisense Small RNAs with 5 '-Polyphosphate Termini Regulate Long Term Transcriptional Gene Silencing in Entamoeba histolytica G3 Strain. JOURNAL OF BIOLOGICAL CHEMISTRY, 286(52), 44467–79.

Transient and stable transfection in the protozoan parasite Entamoeba invadens
Ehrenkaufer, G. M., & Singh, U. (2012). Transient and stable transfection in the protozoan parasite Entamoeba invadens. MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 184(1), 59–62.

Entamoeba histolytica: a snapshot of current research and methods for genetic analysis
Morf, L., & Singh, U. (2012). Entamoeba histolytica: a snapshot of current research and methods for genetic analysis. CURRENT OPINION IN MICROBIOLOGY, 15(4), 469–75.

A Detoxifying Oxygen Reductase in the Anaerobic Protozoan Entamoeba histolytica
Vicente, J. B., Vy Tran, V., Pinto, L., Teixeira, M., & Singh, U. (2012). A Detoxifying Oxygen Reductase in the Anaerobic Protozoan Entamoeba histolytica. EUKARYOTIC CELL, 11(9), 1112–18.

Oxidative stress resistance genes contribute to the pathogenic potential of the anaerobic protozoan parasite, Entamoeba histolytica
Rastew, E., Vicente, J. B., & Singh, U. (2012). Oxidative stress resistance genes contribute to the pathogenic potential of the anaerobic protozoan parasite, Entamoeba histolytica. INTERNATIONAL JOURNAL FOR PARASITOLOGY, 42(11), 1007–15.

Regulation of H2O2 Stress-responsive Genes through a Novel Transcription Factor in the Protozoan Pathogen Entamoeba histolytica
Pearson, R. J., Morf, L., & Singh, U. (2013). Regulation of H2O2 Stress-responsive Genes through a Novel Transcription Factor in the Protozoan Pathogen Entamoeba histolytica. JOURNAL OF BIOLOGICAL CHEMISTRY, 288(6), 4462–74.

Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States.
Lin, A., Bik, E. M., Costello, E. K., Dethlefsen, L., Haque, R., Relman, D. A., & Singh, U. (2013). Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PloS One, 8(1).

Transcription initiation is controlled by three core promoter elements in the hgl5 gene of the protozoan parasite Entamoeba histolytica
Singh, U., Rogers, J. B., Mann, B. J., & Petri, W. A. (1997). Transcription initiation is controlled by three core promoter elements in the hgl5 gene of the protozoan parasite Entamoeba histolytica. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 94(16), 8812–8817.

The novel core promoter element GAAC in the hgl5 gene of Entamoeba histolytica is able to direct a transcription start site independent of TATA or Inr regions.
The novel core promoter element GAAC in the hgl5 gene of Entamoeba histolytica is able to direct a transcription start site independent of TATA or Inr regions. (1998). Journal of Biological Chemistry., (273).

Diagnosis and management of amebiasis.
Diagnosis and management of amebiasis. (1999). Clinical Infectious Diseases., (29).

Investigating amoebic pathogenesis using Entamoeba histolytica DNA microarrays
Singh, U., & Shah, P. (2002). Investigating amoebic pathogenesis using Entamoeba histolytica DNA microarrays. JOURNAL OF BIOSCIENCES, 27(6), 595–601.

Short hairpin RNA-mediated knockdown of protein expression in Entamoeba histolytica
Linford, A. S., Moreno, H., Good, K. R., Zhang, H., Singh, U., & Petri, W. A. (2009). Short hairpin RNA-mediated knockdown of protein expression in Entamoeba histolytica. BMC MICROBIOLOGY, 9.

Diagnosis and management of amebiasis
Petri, W. A., & Singh, U. (1999). Diagnosis and management of amebiasis. CLINICAL INFECTIOUS DISEASES, 29(5), 1117–1125.

Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes
Zhang, H., Ehrenkaufer, G. M., Hall, N., & Singh, U. (2013). Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes. BMC GENOMICS, 14.

Robust gene silencing mediated by antisense small RNAs in the pathogenic protist Entamoeba histolytica.
Morf, L., Pearson, R. J., Wang, A. S., & Singh, U. (2013). Robust gene silencing mediated by antisense small RNAs in the pathogenic protist Entamoeba histolytica. Nucleic Acids Research, 41(20), 9424–37.

The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation.
Ehrenkaufer, G. M., Weedall, G. D., Williams, D., Lorenzi, H. A., Caler, E., Hall, N., & Singh, U. (2013). The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation. Genome Biology, 14(7), R77.

The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation
Ehrenkaufer, G. M., Weedall, G. D., Williams, D., Lorenzi, H. A., Caler, E., Hall, N., & Singh, U. (2013). The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation. GENOME BIOLOGY, 14(7).

Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States
Lin, A., Bik, E. M., Costello, E. K., Dethlefsen, L., Haque, R., Relman, D. A., & Singh, U. (2013). Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States. PLOS ONE, 8(1).

Regulation of gene expression in the protozoan parasite Entamoeba invadens: identification of core promoter elements and promoters with stage-specific expression patterns.
Manna, D., Ehrenkaufer, G. M., & Singh, U. (2014). Regulation of gene expression in the protozoan parasite Entamoeba invadens: identification of core promoter elements and promoters with stage-specific expression patterns. International Journal for Parasitology, 44(11), 837–45.

Destabilization domain approach adapted for regulated protein expression in the protozoan parasite Entamoeba histolytica.
Liu, Y.-C., & Singh, U. (2014). Destabilization domain approach adapted for regulated protein expression in the protozoan parasite Entamoeba histolytica. International Journal for Parasitology, 44(10), 729–35.

RNAi Pathway Genes Are Resistant to Small RNA Mediated Gene Silencing in the Protozoan Parasite Entamoeba histolytica
Pompey, J. M., Morf, L., & Singh, U. (2014). RNAi Pathway Genes Are Resistant to Small RNA Mediated Gene Silencing in the Protozoan Parasite Entamoeba histolytica. PLOS ONE, 9(9).

Regulation of gene expression in the protozoan parasite Entamoeba invadens: identification of core promoter elements and promoters with stage-specific expression patterns
Manna, D., Ehrenkaufer, G. M., & Singh, U. (2014). Regulation of gene expression in the protozoan parasite Entamoeba invadens: identification of core promoter elements and promoters with stage-specific expression patterns. INTERNATIONAL JOURNAL FOR PARASITOLOGY, 44(11), 837–45.

Three conserved cis-acting sequences in the core promoter control gene expression in the protozoan parasite Entamoeba histolytica.
Singh, U., Purdy, J., Mann, B. J., & Petri, W. A. (1997). Three conserved cis-acting sequences in the core promoter control gene expression in the protozoan parasite Entamoeba histolytica. Archives of Medical Research, 28, 41–42.

The novel core promoter element GAAC in the hgl5 gene of Entamoeba histolytica is able to direct a transcription start site independent of TATA or initiator regions
Singh, U., & Rogers, J. B. (1998). The novel core promoter element GAAC in the hgl5 gene of Entamoeba histolytica is able to direct a transcription start site independent of TATA or initiator regions. JOURNAL OF BIOLOGICAL CHEMISTRY, 273(34), 21663–21668.

High Throughput Sequencing of Entamoeba 27nt Small RNA Population Reveals Role in Permanent Gene Silencing But No Effect on Regulating Gene Expression Changes during Stage Conversion, Oxidative, or Heat Shock Stress.
Zhang, H., Ehrenkaufer, G. M., Manna, D., Hall, N., & Singh, U. (2015). High Throughput Sequencing of Entamoeba 27nt Small RNA Population Reveals Role in Permanent Gene Silencing But No Effect on Regulating Gene Expression Changes during Stage Conversion, Oxidative, or Heat Shock Stress. PloS One, 10(8).

Entamoeba histolytica rhomboid protease 1 has a role in migration and motility as validated by two independent genetic approaches
Rastew, E., Morf, L., & Singh, U. (2015). Entamoeba histolytica rhomboid protease 1 has a role in migration and motility as validated by two independent genetic approaches. EXPERIMENTAL PARASITOLOGY, 154, 33–42.

A Single RNaseIII Domain Protein from Entamoeba histolytica Has dsRNA Cleavage Activity and Can Help Mediate RNAi Gene Silencing in a Heterologous System
Pompey, J. M., Foda, B., & Singh, U. (2015). A Single RNaseIII Domain Protein from Entamoeba histolytica Has dsRNA Cleavage Activity and Can Help Mediate RNAi Gene Silencing in a Heterologous System. PLOS ONE, 10(7).

Dimethylated H3K27 Is a Repressive Epigenetic Histone Mark in the Protist Entamoeba histolytica and Is Significantly Enriched in Genes Silenced via the RNAi Pathway
Foda, B. M., & Singh, U. (2015). Dimethylated H3K27 Is a Repressive Epigenetic Histone Mark in the Protist Entamoeba histolytica and Is Significantly Enriched in Genes Silenced via the RNAi Pathway. JOURNAL OF BIOLOGICAL CHEMISTRY, 290(34), 21114–30.

High Throughput Sequencing of Entamoeba 27nt Small RNA Population Reveals Role in Permanent Gene Silencing But No Effect on Regulating Gene Expression Changes during Stage Conversion, Oxidative, or Heat Shock Stress
Zhang, H., Ehrenkaufer, G. M., Manna, D., Hall, N., & Singh, U. (2015). High Throughput Sequencing of Entamoeba 27nt Small RNA Population Reveals Role in Permanent Gene Silencing But No Effect on Regulating Gene Expression Changes during Stage Conversion, Oxidative, or Heat Shock Stress. PLOS ONE, 10(8).

RNAi pathway genes are resistant to small RNA mediated gene silencing in the protozoan parasite Entamoeba histolytica.
Pompey, J. M., Morf, L., & Singh, U. (2014). RNAi pathway genes are resistant to small RNA mediated gene silencing in the protozoan parasite Entamoeba histolytica. PloS One, 9(9).

Development of RNA Interference Trigger-Mediated Gene Silencing in Entamoeba invadens.
Suresh, S., Ehrenkaufer, G., Zhang, H., & Singh, U. (2016). Development of RNA Interference Trigger-Mediated Gene Silencing in Entamoeba invadens. Infection and Immunity, 84(4), 964–75.

Technical advances in trigger-induced RNA interference gene silencing in the parasite Entamoeba histolytica
Khalil, M. I., Foda, B. M., Suresh, S., & Singh, U. (2016). Technical advances in trigger-induced RNA interference gene silencing in the parasite Entamoeba histolytica. INTERNATIONAL JOURNAL FOR PARASITOLOGY, 46(3), 205–12.

biology: RNA interference, drug discovery, and gut microbiome.
Morgado, P., Manna, D., & Singh, U. (2016). biology: RNA interference, drug discovery, and gut microbiome. F1000Research, 5, 2578-?

Policy Recommendations for Optimizing the Infectious Diseases Physician-Scientist Workforce.
Singh, U., Levy, J., Armstrong, W., Bedimo, R., Creech, C. B., Lautenbach, E., … Vyas, J. M. (2018). Policy Recommendations for Optimizing the Infectious Diseases Physician-Scientist Workforce. The Journal of Infectious Diseases, 218(suppl_1), S49–S54.

Supporting Research Career Development of Physician-Scientists
Singh, U. (2018). Supporting Research Career Development of Physician-Scientists. JOURNAL OF INFECTIOUS DISEASES, 218, S36–S39.

High-Throughput Screening of Entamoeba Identifies Compounds Which Target Both Life Cycle Stages and Which Are Effective Against Metronidazole Resistant Parasites
Ehrenkaufer, G. M., Suresh, S., Solow-Cordero, D., & Singh, U. (2018). High-Throughput Screening of Entamoeba Identifies Compounds Which Target Both Life Cycle Stages and Which Are Effective Against Metronidazole Resistant Parasites. FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 8.

Entamoeba histolytica Genomic Analyses
Singh, U., & Ehrenkaufer, G. M. (2010). Entamoeba histolytica Genomic Analyses. ANAEROBIC PARASITIC PROTOZOA: GENOMICS AND MOLECULAR BIOLOGY, 157–73.

Identification and characterization of differentiation mutants in the protozoan parasite Toxoplasma gondii
Matrajt, M., Donald, R. G., Singh, U., & Roos, D. S. (2002). Identification and characterization of differentiation mutants in the protozoan parasite Toxoplasma gondii. MOLECULAR MICROBIOLOGY, 44(3), 735–47.

High-Throughput Screening of Entamoeba Identifies Compounds Which Target Both Life Cycle Stages and Which Are Effective Against Metronidazole Resistant Parasites.
Ehrenkaufer, G. M., Suresh, S., Solow-Cordero, D., & Singh, U. (2018). High-Throughput Screening of Entamoeba Identifies Compounds Which Target Both Life Cycle Stages and Which Are Effective Against Metronidazole Resistant Parasites. Frontiers in Cellular and Infection Microbiology, 8, 276.

An NAD+-dependent novel transcription factor controls stage conversion in Entamoeba.
Manna, D., Lentz, C. S., Ehrenkaufer, G. M., Suresh, S., Bhat, A., & Singh, U. (2018). An NAD+-dependent novel transcription factor controls stage conversion in Entamoeba. ELife, 7.

Dimethylated H3K27 Is a Repressive Epigenetic Histone Mark in the Protist Entamoeba histolytica and Is Significantly Enriched in Genes Silenced via the RNAi Pathway.
Foda, B. M., & Singh, U. (2015). Dimethylated H3K27 Is a Repressive Epigenetic Histone Mark in the Protist Entamoeba histolytica and Is Significantly Enriched in Genes Silenced via the RNAi Pathway. The Journal of Biological Chemistry, 290(34), 21114–30.

Nuclear Factor Y (NF-Y) Modulates Encystation in Entamoeba via Stage-Specific Expression of the NF-YB and NF-YC Subunits.
Manna, D., & Singh, U. (2019). Nuclear Factor Y (NF-Y) Modulates Encystation in Entamoeba via Stage-Specific Expression of the NF-YB and NF-YC Subunits. MBio, 10(3).

Functional Characterization of Entamoeba histolytica Argonaute Proteins Reveals a Repetitive DR-Rich Motif Region That Controls Nuclear Localization.
Zhang, H., Tran, V., Manna, D., Ehrenkaufer, G., & Singh, U. (2019). Functional Characterization of Entamoeba histolytica Argonaute Proteins Reveals a Repetitive DR-Rich Motif Region That Controls Nuclear Localization. MSphere, 4(5).

Identification of plicamycin, TG02, panobinostat, lestaurtinib, and GDC-0084 as promising compounds for the treatment of central nervous system infections caused by the free-living amebae Naegleria, Acanthamoeba and Balamuthia.
Kangussu-Marcolino, M. M., Ehrenkaufer, G. M., Chen, E., Debnath, A., & Singh, U. (2019). Identification of plicamycin, TG02, panobinostat, lestaurtinib, and GDC-0084 as promising compounds for the treatment of central nervous system infections caused by the free-living amebae Naegleria, Acanthamoeba and Balamuthia. International Journal for Parasitology. Drugs and Drug Resistance, 11, 80–94.

Identification of anisomycin, prodigiosin and obatoclax as compounds with broad-spectrum anti-parasitic activity.
Ehrenkaufer, G., Li, P., Stebbins, E. E., Kangussu-Marcolino, M. M., Debnath, A., White, C. V., … Singh, U. (2020). Identification of anisomycin, prodigiosin and obatoclax as compounds with broad-spectrum anti-parasitic activity. PLoS Neglected Tropical Diseases, 14(3), e0008150.

Drug treatment algorithms for water-borne parasitic pathogens
Singh, U. (2019). Drug treatment algorithms for water-borne parasitic pathogens. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 258.

Identification of anisomycin, prodigiosin and obatoclax as compounds with broad-spectrum anti-parasitic activity
Ehrenkaufer, G., Li, P., Stebbins, E. E., Kangussu-Marcolino, M. M., Debnath, A., White, C., … Singh, U. (2020). Identification of anisomycin, prodigiosin and obatoclax as compounds with broad-spectrum anti-parasitic activity. PLOS NEGLECTED TROPICAL DISEASES, 14(3).

Characterization of extracellular vesicles from Entamoeba histolytica identifies roles in intercellular communication that regulates parasite growth and development.
Sharma, M., Morgado, P., Zhang, H., Ehrenkaufer, G., Manna, D., & Singh, U. (2020). Characterization of extracellular vesicles from Entamoeba histolytica identifies roles in intercellular communication that regulates parasite growth and development. Infection and Immunity.

The NAD+ Responsive Transcription Factor ERM-BP Functions Downstream of Cellular Aggregation and Is an Early Regulator of Development and Heat Shock Response in Entamoeba.
Manna, D., Lozano-Amado, D., Ehrenkaufer, G., & Singh, U. (2020). The NAD+ Responsive Transcription Factor ERM-BP Functions Downstream of Cellular Aggregation and Is an Early Regulator of Development and Heat Shock Response in Entamoeba. Frontiers in Cellular and Infection Microbiology, 10, 363.

Entamoeba stage conversion: progress and new insights.
Manna, D., Ehrenkaufer, G. M., Lozano-Amado, D., & Singh, U. (2020). Entamoeba stage conversion: progress and new insights. Current Opinion in Microbiology, 58, 62–68.

Interferon-gamma release assay for accurate detection of SARS-CoV-2 T cell response.
Murugesan, K., Jagannathan, P., Pham, T. D., Pandey, S., Bonilla, H. F., Jacobson, K., … Banaei, N. (2020). Interferon-gamma release assay for accurate detection of SARS-CoV-2 T cell response. Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America.

Proinflammatory IgG Fc structures in patients with severe COVID-19
Chakraborty, S., Gonzales, J., Edwards, K., Mallajosyulla, V., Buzzanco, A. S., Sherwood, R., … Tan, G. S. (2020). Proinflammatory IgG Fc structures in patients with severe COVID-19. Nature Immunology.

Development of a CRISPR/Cas9 system in Entamoeba histolytica: proof of concept.
Kangussu-Marcolino, M. M., Morgado, P., Manna, D., Yee, H., & Singh, U. (2020). Development of a CRISPR/Cas9 system in Entamoeba histolytica: proof of concept. International Journal for Parasitology.

Identification of oligo-adenylated small RNAs in the parasite Entamoeba and a potential role for small RNA control.
Zhang, H., Ehrenkaufer, G. M., Hall, N., & Singh, U. (2020). Identification of oligo-adenylated small RNAs in the parasite Entamoeba and a potential role for small RNA control. BMC Genomics, 21(1), 879.

Patients with uncomplicated COVID-19 have long-term persistent symptoms and functional impairment similar to patients with severe COVID-19: a cautionary tale during a global pandemic.
Jacobson, K. B., Rao, M., Bonilla, H., Subramanian, A., Hack, I., Madrigal, M., … Grant, P. (2021). Patients with uncomplicated COVID-19 have long-term persistent symptoms and functional impairment similar to patients with severe COVID-19: a cautionary tale during a global pandemic. Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America.

Peginterferon Lambda-1a for treatment of outpatients with uncomplicated COVID-19: a randomized placebo-controlled trial.
Jagannathan, P., Andrews, J. R., Bonilla, H., Hedlin, H., Jacobson, K. B., Balasubramanian, V., … Singh, U. (2021). Peginterferon Lambda-1a for treatment of outpatients with uncomplicated COVID-19: a randomized placebo-controlled trial. Nature Communications, 12(1), 1967.

SARS-CoV-2 subgenomic RNA kinetics in longitudinal clinical samples
Verma, R., Kim, E., Martinez, G., Jagannathan, P., Rustagi, A., Parsonnet, J., … Andrews, J. (2021). SARS-CoV-2 subgenomic RNA kinetics in longitudinal clinical samples. Open Forum Infectious Diseases.

The COVID-19 Outpatient Pragmatic Platform Study (COPPS): Study design of a multi-center pragmatic platform trial.
Bunning, B., Hedlin, H., Purington, N., Sundaram, V., Kapphahn, K., Weng, Y., … Desai, M. (2021). The COVID-19 Outpatient Pragmatic Platform Study (COPPS): Study design of a multi-center pragmatic platform trial. Contemporary Clinical Trials, 106509.

RISC in Entamoeba histolytica: Identification of a Protein-Protein Interaction Network for the RNA Interference Pathway in a Deep-Branching Eukaryote.
Zhang, H., Veira, J., Bauer, S. T., Yip, C., & Singh, U. (2021). RISC in Entamoeba histolytica: Identification of a Protein-Protein Interaction Network for the RNA Interference Pathway in a Deep-Branching Eukaryote. MBio, e0154021.

New-onset IgG autoantibodies in hospitalized patients with COVID-19.
Chang, S. E., Feng, A., Meng, W., Apostolidis, S. A., Mack, E., Artandi, M., … Utz, P. J. (2021). New-onset IgG autoantibodies in hospitalized patients with COVID-19. Nature Communications, 12(1), 5417.

Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA.
Natarajan, A., Han, A., Zlitni, S., Brooks, E. F., Vance, S. E., Wolfe, M., … Bhatt, A. S. (2021). Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Nature Communications, 12(1), 5753.

Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA.
Natarajan, A., Han, A., Zlitni, S., Brooks, E. F., Vance, S. E., Wolfe, M., … Bhatt, A. S. (2021). Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. MedRxiv : the Preprint Server for Health Sciences.

Publisher Correction: Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA.
Natarajan, A., Han, A., Zlitni, S., Brooks, E. F., Vance, S. E., Wolfe, M., … Bhatt, A. S. (2021). Publisher Correction: Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Nature Communications, 12(1), 7100.

Ponatinib, Lestaurtinib and mTOR/PI3K inhibitors are promising repurposing candidates against Entamoeba histolytica.
Kangussu-Marcolino, M. M., & Singh, U. (2021). Ponatinib, Lestaurtinib and mTOR/PI3K inhibitors are promising repurposing candidates against Entamoeba histolytica. Antimicrobial Agents and Chemotherapy, AAC0120721.

Inflammatory but not respiratory symptoms are associated with ongoing upper airway viral shedding in outpatients with uncomplicated COVID-19.
Jacobson, K. B., Purington, N., Parsonnet, J., Andrews, J., Balasubramanian, V., Bonilla, H., … Jagannathan, P. (2021). Inflammatory but not respiratory symptoms are associated with ongoing upper airway viral shedding in outpatients with uncomplicated COVID-19. Diagnostic Microbiology and Infectious Disease, 102(3), 115612.

Variation in Severe Acute Respiratory Syndrome Coronavirus 2 Bioaerosol Production in Exhaled Breath.
Verma, R., Kim, E., Degner, N., Walter, K. S., Singh, U., & Andrews, J. R. (2022). Variation in Severe Acute Respiratory Syndrome Coronavirus 2 Bioaerosol Production in Exhaled Breath. Open Forum Infectious Diseases, 9(1), ofab600.

Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses.
Sievers, B. L., Chakraborty, S., Xue, Y., Gelbart, T., Gonzalez, J. C., Cassidy, A. G., … Tan, G. S. (1800). Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses. Science Translational Medicine, eabn7842.

Early non-neutralizing, afucosylated antibody responses are associated with COVID-19 severity.
Chakraborty, S., Gonzalez, J. C., Sievers, B. L., Mallajosyula, V., Chakraborty, S., Dubey, M., … Wang, T. T. (1800). Early non-neutralizing, afucosylated antibody responses are associated with COVID-19 severity. Science Translational Medicine, eabm7853.

Long Term Accuracy of SARS-CoV-2 Interferon-? Release Assay and its Application in Household Investigation.
Murugesan, K., Jagannathan, P., Altamirano, J., Maldonado, Y. A., Bonilla, H. F., Jacobson, K. B., … Banaei, N. (2022). Long Term Accuracy of SARS-CoV-2 Interferon-? Release Assay and its Application in Household Investigation. Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America.

New-Onset IgG Autoantibodies in Hospitalized Patients with COVID-19
Chang, S., Feng, A., Meng, W., Apostolidis, S., Mack, E., Artandi, M., … Utz, P. (2021). New-Onset IgG Autoantibodies in Hospitalized Patients with COVID-19. ARTHRITIS & RHEUMATOLOGY. WILEY.

SARS-CoV-2 Neutralizing Monoclonal Antibodies for the Treatment of COVID-19 in Kidney Transplant Recipients.
Wang, A. X., Busque, S., Kuo, J., Singh, U., Roeltgen, K., Pinsky, B. A., … Lenihan, C. R. (2022). SARS-CoV-2 Neutralizing Monoclonal Antibodies for the Treatment of COVID-19 in Kidney Transplant Recipients. Kidney360, 3(1), 133–143.

Favipiravir for treatment of outpatients with asymptomatic or uncomplicated COVID-19: a double-blind randomized, placebo-controlled, phase 2 trial.
Holubar, M., Subramanian, A., Purington, N., Hedlin, H., Bunning, B., Walter, K. S., … Maldonado, Y. (2022). Favipiravir for treatment of outpatients with asymptomatic or uncomplicated COVID-19: a double-blind randomized, placebo-controlled, phase 2 trial. Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America.

Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection.
Natarajan, A., Zlitni, S., Brooks, E. F., Vance, S. E., Dahlen, A., Hedlin, H., … Bhatt, A. S. (2022). Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection. Med (New York, N.Y.).

TNF-alpha+ CD4+ Tcells dominate the SARS-CoV-2 specific T cell response in COVID-19 outpatients and are associated with durable antibodies.
van der Ploeg, K., Kirosingh, A. S., Mori, D. A., Chakraborty, S., Hu, Z., Sievers, B. L., … Jagannathan, P. (2022). TNF-alpha+ CD4+ Tcells dominate the SARS-CoV-2 specific T cell response in COVID-19 outpatients and are associated with durable antibodies. Cell Reports. Medicine, 100640.

Successful recruitment of monolingual Spanish speaking Latinos to university phase II and III outpatient COVID-19 clinical treatment trials in Northern California.
Levy, V., Bengoa, R. Y., Romero, P. P., Bollyky, J., & Singh, U. (2022). Successful recruitment of monolingual Spanish speaking Latinos to university phase II and III outpatient COVID-19 clinical treatment trials in Northern California. Contemporary Clinical Trials, 106891.

Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study.
Hu, Z., van der Ploeg, K., Chakraborty, S., Arunachalam, P. S., Mori, D. A., Jacobson, K. B., … Jagannathan, P. (2022). Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study. ELife, 11.

Turning the page: a welcome from the new leadership of the Journal of Infectious Diseases.
Sears, C. L., Li, J. Z., & Singh, U. (2022). Turning the page: a welcome from the new leadership of the Journal of Infectious Diseases. The Journal of Infectious Diseases, 227(1), 1–3.

Effect of Fluvoxamine vs Placebo on Time to Sustained Recovery in Outpatients With Mild to Moderate COVID-19: A Randomized Clinical Trial.
McCarthy, M. W., Naggie, S., Boulware, D. R., Lindsell, C. J., Stewart, T. G., Felker, G. M., … Hernandez, A. F. (2023). Effect of Fluvoxamine vs Placebo on Time to Sustained Recovery in Outpatients With Mild to Moderate COVID-19: A Randomized Clinical Trial. JAMA.

Stress Response in Entamoeba histolytica Is Associated with Robust Processing of tRNA to tRNA Halves.
Sharma, M., Zhang, H., Ehrenkaufer, G., & Singh, U. (2023). Stress Response in Entamoeba histolytica Is Associated with Robust Processing of tRNA to tRNA Halves. MBio, e0345022.

Transparent Reporting at the Journal of Infectious Diseases.
Clancy, C. J., Li, J. Z., Singh, U., & Sears, C. L. (2023). Transparent Reporting at the Journal of Infectious Diseases. The Journal of Infectious Diseases.