Anita Sil, MD, PhD

Transcriptomic atlas of the morphologic development of the fungal pathogen Coccidioides reveals key phase-enriched transcripts.

bioRxiv : the preprint server for biology

Homer CM, Voorhies M, Walcott K, Ochoa E, Sil A

Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing.

bioRxiv : the preprint server for biology

Voorhies M, Joehnk B, Uehling J, Walcott K, Dubin C, Mead HL, Homer CM, Galgiani JN, Barker BM, Brem RB, Sil A

Immediate myeloid depot for SARS-CoV-2 in the human lung.

Science advances

Magnen M, You R, Rao AA, Davis RT, Rodriguez L, Bernard O, Simoneau CR, Hysenaj L, Hu KH, Maishan M, Conrad C, Gbenedio OM, Samad B, Consortium TUC, Love C, Woodruff PG, Erle DJ, Hendrickson CM, Calfee CS, Matthay MA, Roose JP, Sil A, Ott M, Langelier CR, Krummel MF, Looney MR

NF-κB inhibitor alpha controls SARS-CoV-2 infection in ACE2-overexpressing human airway organoids.

Scientific reports

Simoneau CR, Chen PY, Xing GK, Hayashi JM, Chen IP, Khalid MM, Meyers NL, Taha TY, Leon KE, Suryawanshi RK, McCavitt-Malvido M, Ashuach T, Fontaine KA, Rodriguez L, Joehnk B, Walcott K, Vasudevan S, Fang X, Maishan M, Schultz S, Roose JP, Matthay MA, Sil A, Arjomandi M, Yosef N, Ott M

Optimizing in vitro spherulation cues in the fungal pathogen Coccidioides.

bioRxiv : the preprint server for biology

Homer C, Ochoa E, Voorhies M, Sil A

Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora.

PLoS genetics

Wang Z, Wang YW, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend JP

A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.

Nature cell biology

Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S

Recyclable CRISPR/Cas9-mediated gene disruption and deletions in Histoplasma.

mSphere

Joehnk B, Ali N, Voorhies M, Walcott K, Sil A

Recyclable CRISPR/Cas9 mediated gene disruption and deletions in Histoplasma.

bioRxiv : the preprint server for biology

Joehnk B, Ali N, Voorhies M, Walcott K, Sil A

Chemical stimuli override a temperature-dependent morphological program by reprogramming the transcriptome of a fungal pathogen.

bioRxiv : the preprint server for biology

Assa D, Voorhies M, Sil A

Retraction: Opposing signaling pathways regulate morphology in response to temperature in the fungal pathogen Histoplasma capsulatum.

PLoS biology

Rodriguez L, Voorhies M, Gilmore S, Beyhan S, Myint A, Sil A

SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants.

Stem cell reports

Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP

Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii.

Journal of fungi (Basel, Switzerland)

Dubin CA, Voorhies M, Sil A, Teixeira MM, Barker BM, Brem RB

The future of fungi: threats and opportunities.

G3 (Bethesda, Md.)

Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, Glass NL, Gow NAR, Gurr SJ, Hittinger CT, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE

COVID-19-Associated Lung Microvascular Endotheliopathy: A "From the Bench" Perspective.

American journal of respiratory and critical care medicine

Joffre J, Rodriguez L, Matthay ZA, Lloyd E, Fields AT, Bainton RJ, Kurien P, Sil A, Calfee CS, Woodruff PG, Erle DJ, Hendrickson C, Krummel MF, Langelier CR, Matthay MA, Kornblith LZ, Hellman J, COMET consortium and the Co-ACIT Study Group

Genome-scale CRISPR screening reveals that C3aR signaling is critical for rapid capture of fungi by macrophages.

PLoS pathogens

Cohen A, Jeng EE, Voorhies M, Symington J, Ali N, Rodriguez RA, Bassik MC, Sil A

NF-κB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids.

bioRxiv : the preprint server for biology

Simoneau CR, Chen PY, Xing GK, Khalid MM, Meyers NL, Hayashi JM, Taha TY, Leon KE, Ashuach T, Fontaine KA, Rodriguez L, Joehnk B, Walcott K, Vasudevan S, Fang X, Maishan M, Schultz S, Roose J, Matthay MA, Sil A, Arjomandi M, Yosef N, Ott M

Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis.

PLoS pathogens

Azimova D, Herrera N, Duvenage L, Voorhies M, Rodriguez RA, English BC, Hoving JC, Rosenberg O, Sil A

Immediate myeloid depot for SARS-CoV-2 in the human lung.

Research square

Looney M, Magnen M, You R, Rao A, Davis R, Rodriguez L, Simoneau C, Hysenaj L, Hu K, Love C, Woodruff P, Erle D, Hendrickson C, Calfee C, Matthay M, Roose J, Sil A, Ott M, Langelier C, Krummel M

Immediate myeloid depot for SARS-CoV-2 in the human lung.

bioRxiv : the preprint server for biology

Magnen M, You R, Rao AA, Davis RT, Rodriguez L, Simoneau CR, Hysenaj L, Hu KH, UCSF COMET Consortium, Love C, Woodruff PG, Erle DJ, Hendrickson CM, Calfee CS, Matthay MA, Roose JP, Sil A, Ott M, Langelier CR, Krummel MF, Looney MR

The WOPR family protein Ryp1 is a key regulator of gene expression, development, and virulence in the thermally dimorphic fungal pathogen Coccidioides posadasii.

PLoS pathogens

Mandel MA, Beyhan S, Voorhies M, Shubitz LF, Galgiani JN, Orbach MJ, Sil A

Chromosome-Level Genome Assembly of a Human Fungal Pathogen Reveals Synteny among Geographically Distinct Species.

mBio

Voorhies M, Cohen S, Shea TP, Petrus S, Muñoz JF, Poplawski S, Goldman WE, Michael TP, Cuomo CA, Sil A, Beyhan S

SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator.

bioRxiv : the preprint server for biology

Hysenaj L, Little S, Kulhanek K, Gbenedio OM, Rodriguez L, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Bahl K, Mick E, Li JZ, Ding VW, Matsumoto S, Maishan M, Simoneau C, Fragiadakis G, Jablons DM, Langelier CR, Matthay M, Ott M, Krummel M, Combes AJ, Sil A, Erle DJ, Kratz JR, Roose JP

Protomer alignment modulates specificity of RNA substrate recognition by Ire1.

eLife

Li W, Crotty K, Garrido Ruiz D, Voorhies M, Rivera C, Sil A, Mullins RD, Jacobson MP, Peschek J, Walter P

Correction: Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma.

PLoS genetics

Gilmore SA, Voorhies M, Gebhart D, Sil A

Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses.

Cell

Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano KA, Hayashi JM, Carlson-Stevermer J, Zengel JR, Richards CM, Fozouni P, Oki J, Rodriguez L, Joehnk B, Walcott K, Holden K, Sil A, Carette JE, Krogan NJ, Ott M, Puschnik AS

Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.

Cell

Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M

Recurrent Loss of abaA, a Master Regulator of Asexual Development in Filamentous Fungi, Correlates with Changes in Genomic and Morphological Traits.

Genome biology and evolution

Mead ME, Borowsky AT, Joehnk B, Steenwyk JL, Shen XX, Sil A, Rokas A

Sensing the heat and the host: Virulence determinants of Histoplasma capsulatum.

Virulence

Beyhan S, Sil A

Molecular regulation of Histoplasma dimorphism.

Current opinion in microbiology

Sil A

Opposing signaling pathways regulate morphology in response to temperature in the fungal pathogen Histoplasma capsulatum.

PLoS biology

Rodriguez L, Voorhies M, Gilmore S, Beyhan S, Myint A, Sil A

The transcription factor CHOP, an effector of the integrated stress response, is required for host sensitivity to the fungal intracellular pathogen Histoplasma capsulatum.

PLoS pathogens

English BC, Van Prooyen N, Örd T, Örd T, Sil A

CD103+ Conventional Dendritic Cells Are Critical for TLR7/9-Dependent Host Defense against Histoplasma capsulatum, an Endemic Fungal Pathogen of Humans.

PLoS pathogens

Van Prooyen N, Henderson CA, Hocking Murray D, Sil A

Macrophage cell death and transcriptional response are actively triggered by the fungal virulence factor Cbp1 during H. capsulatum infection.

Molecular microbiology

Isaac DT, Berkes CA, English BC, Murray DH, Lee YN, Coady A, Sil A

Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma.

PLoS genetics

Gilmore SA, Voorhies M, Gebhart D, Sil A

MyD88-dependent signaling drives host survival and early cytokine production during Histoplasma capsulatum infection.

Infection and immunity

Coady A, Sil A

Thermally Dimorphic Human Fungal Pathogens--Polyphyletic Pathogens with a Convergent Pathogenicity Trait.

Cold Spring Harbor perspectives in medicine

Sil A, Andrianopoulos A

N-acetylglucosamine (GlcNAc) triggers a rapid, temperature-responsive morphogenetic program in thermally dimorphic fungi.

PLoS genetics

Gilmore SA, Naseem S, Konopka JB, Sil A

A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen.

PLoS biology

Beyhan S, Gutierrez M, Voorhies M, Sil A

Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum reveals a core set of transcripts that specify infectious and pathogenic states.

Eukaryotic cell

Inglis DO, Voorhies M, Hocking Murray DR, Sil A

The 3-hydroxy-methylglutaryl coenzyme A lyase HCL1 is required for macrophage colonization by human fungal pathogen Histoplasma capsulatum.

Infection and immunity

Isaac DT, Coady A, Van Prooyen N, Sil A

Mouse models for the study of fungal pneumonia: a collection of detailed experimental protocols for the study of Coccidioides, Cryptococcus, Fusarium, Histoplasma and combined infection due to Aspergillus-Rhizopus.

Virulence

Muhammed M, Feldmesser M, Shubitz LF, Lionakis MS, Sil A, Wang Y, Glavis-Bloom J, Lewis RE, Galgiani JN, Casadevall A, Kontoyiannis DP, Mylonakis E

SRE1 regulates iron-dependent and -independent pathways in the fungal pathogen Histoplasma capsulatum.

Eukaryotic cell

Hwang LH, Seth E, Gilmore SA, Sil A

A conserved transcriptional regulator governs fungal morphology in widely diverged species.

Genetics

Cain CW, Lohse MB, Homann OR, Sil A, Johnson AD

Experimental annotation of the human pathogen Histoplasma capsulatum transcribed regions using high-resolution tiling arrays.

BMC microbiology

Voorhies M, Foo CK, Sil A

Conidia but not yeast cells of the fungal pathogen Histoplasma capsulatum trigger a type I interferon innate immune response in murine macrophages.

Infection and immunity

Inglis DO, Berkes CA, Hocking Murray DR, Sil A

Conserved factors Ryp2 and Ryp3 control cell morphology and infectious spore formation in the fungal pathogen Histoplasma capsulatum.

Proceedings of the National Academy of Sciences of the United States of America

Webster RH, Sil A

Histoplasma requires SID1, a member of an iron-regulated siderophore gene cluster, for host colonization.

PLoS pathogens

Hwang LH, Mayfield JA, Rine J, Sil A

Temperature-induced switch to the pathogenic yeast form of Histoplasma capsulatum requires Ryp1, a conserved transcriptional regulator.

Proceedings of the National Academy of Sciences of the United States of America

Nguyen VQ, Sil A

Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii.

Eukaryotic cell

Fraser JA, Stajich JE, Tarcha EJ, Cole GT, Inglis DO, Sil A, Heitman J

Identification of a copper-inducible promoter for use in ectopic expression in the fungal pathogen Histoplasma capsulatum.

Eukaryotic cell

Gebhart D, Bahrami AK, Sil A

Identification of Histoplasma capsulatum transcripts induced in response to reactive nitrogen species.

Molecular biology of the cell

Nittler MP, Hocking-Murray D, Foo CK, Sil A

Identifying phase-specific genes in the fungal pathogen Histoplasma capsulatum using a genomic shotgun microarray.

Molecular biology of the cell

Hwang L, Hocking-Murray D, Bahrami AK, Andersson M, Rine J, Sil A

Vectors allowing amplified expression of the Saccharomyces cerevisiae Gal3p-Gal80p-Gal4p transcription switch: applications to galactose-regulated high-level production of proteins.

Protein expression and purification

Sil AK, Xin P, Hopper JE

The Gal3p-Gal80p-Gal4p transcription switch of yeast: Gal3p destabilizes the Gal80p-Gal4p complex in response to galactose and ATP.

Molecular and cellular biology

Sil AK, Alam S, Xin P, Ma L, Morgan M, Lebo CM, Woods MP, Hopper JE

Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast.

Nature

Takizawa PA, Sil A, Swedlow JR, Herskowitz I, Vale RD

Identification of asymmetrically localized determinant, Ash1p, required for lineage-specific transcription of the yeast HO gene.

Cell

Sil A, Herskowitz I

Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription.

Genes & development

Kruger W, Peterson CL, Sil A, Coburn C, Arents G, Moudrianakis EN, Herskowitz I

Retroviral integration into minichromosomes in vitro.

The EMBO journal

Pryciak PM, Sil A, Varmus HE

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Anita Sil, MD, PhD