Matthew Settles

Managing Director, Bioinformatics
Biochemistry and Biophysics
[email protected]

An extensive two-decade career blending computational and biological realms in genomics under the overarching theme of ’big data.'

Publications: 

High-volume hybridoma sequencing on the NeuroMabSeq platform enables efficient generation of recombinant monoclonal antibodies and scFvs for neuroscience research.

Scientific reports

Mitchell KG, Gong B, Hunter SS, Burkart-Waco D, Gavira-O'Neill CE, Templeton KM, Goethel ME, Bzymek M, MacNiven LM, Murray KD, Settles ML, Froenicke L, Trimmer JS

NeuroMabSeq: high volume acquisition, processing, and curation of hybridoma sequences and their use in generating recombinant monoclonal antibodies and scFvs for neuroscience research.

bioRxiv : the preprint server for biology

Mitchell KG, Gong B, Hunter SS, Burkart-Waco D, Gavira-O'Neill CE, Templeton KM, Goethel ME, Bzymek M, MacNiven LM, Murray KD, Settles ML, Froenicke L, Trimmer JS

Human soft tissue sarcomas harbor an intratumoral viral microbiome which is linked with natural killer cell infiltrate and prognosis.

Journal for immunotherapy of cancer

Perry LM, Cruz SM, Kleber KT, Judge SJ, Darrow MA, Jones LB, Basmaci UN, Joshi N, Settles ML, Durbin-Johnson BP, Gingrich AA, Monjazeb AM, Carr-Ascher J, Thorpe SW, Murphy WJ, Eisen JA, Canter RJ

Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries.

Global health action

Perier C, Nasinghe E, Charles I, Ssetaba LJ, Ahyong V, Bangs D, Beatty PR, Czudnochowski N, Diallo A, Dugan E, Fabius JM, Fong Baker H, Gardner J, Isaacs S, Joanah B, Kalantar K, Kateete D, Knight M, Krasilnikov M, Krogan NJ, Langelier C, Lee E, Li LM, Licht D, Lien K, Lyons Z, Mboowa G, Mwebaza I, Mwesigwa S, Nalwadda G, Nichols R, Penaranda ME, Petnic S, Phelps M, Popper SJ, Rape M, Reingold A, Robbins R, Rosenberg OS, Savage DF, Schildhauer S, Settles ML, Sserwadda I, Stanley S, Tato CM, Tsitsiklis A, Van Dis E, Vanaerschot M, Vinden J, Cox JS, Joloba ML, Schaletzky J

Biofilms preserve the transmissibility of a multi-drug resistance plasmid.

NPJ biofilms and microbiomes

Metzger GA, Ridenhour BJ, France M, Gliniewicz K, Millstein J, Settles ML, Forney LJ, Stalder T, Top EM

A two-stage digestion of whole murine knee joints for single-cell RNA sequencing.

Osteoarthritis and cartilage open

Leale DM, Li L, Settles ML, Mitchell K, Froenicke L, Yik JHN, Haudenschild DR

Comparative Transcriptional Analyses in the Nucleus Accumbens Identifies RGS2 as a Key Mediator of Depression-Related Behavior.

Biological psychiatry

Williams AV, Peña CJ, Ramos-Maciel S, Laman-Maharg A, Ordoñez-Sanchez E, Britton M, Durbin-Johnson B, Settles M, Hao R, Yokoyama S, Xu C, Luo PX, Dwyer T, Bhela S, Black AM, Labonté B, Serafini RA, Ruiz A, Neve RL, Zachariou V, Nestler EJ, Trainor BC

Effects of pairing on color change and central gene expression in lined seahorses.

Genes, brain, and behavior

Mederos SL, Duarte RC, Mastoras M, Dennis MY, Settles ML, Lau AR, Scott A, Woodward K, Johnson C, Seelke AMH, Bales KL

Sex disparate gut microbiome and metabolome perturbations precede disease progression in a mouse model of Rett syndrome.

Communications biology

Neier K, Grant TE, Palmer RL, Chappell D, Hakam SM, Yasui KM, Rolston M, Settles ML, Hunter SS, Madany A, Ashwood P, Durbin-Johnson B, LaSalle JM, Yasui DH

Establishment of quantitative RNAi-based forward genetics in Entamoeba histolytica and identification of genes required for growth.

PLoS pathogens

Bettadapur A, Hunter SS, Suleiman RL, Ruyechan MC, Huang W, Barbieri CG, Miller HW, Tam TSY, Settles ML, Ralston KS

Protective heterologous T cell immunity in COVID-19 induced by the trivalent MMR and Tdap vaccine antigens.

Med (New York, N.Y.)

Mysore V, Cullere X, Settles ML, Ji X, Kattan MW, Desjardins M, Durbin-Johnson B, Gilboa T, Baden LR, Walt DR, Lichtman AH, Jehi L, Mayadas TN

Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias).

Systematic biology

Sarver BAJ, Herrera ND, Sneddon D, Hunter SS, Settles ML, Kronenberg Z, Demboski JR, Good JM, Sullivan J

Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis.

Blood cancer discovery

Wang VE, Blaser BW, Patel RK, Behbehani GK, Rao AA, Durbin-Johnson B, Jiang T, Logan AC, Settles M, Mannis GN, Olin R, Damon LE, Martin TG, Sayre PH, Gaensler KM, McMahon E, Flanders M, Weinberg V, Ye CJ, Carbone DP, Munster PN, Fragiadakis GK, McCormick F, Andreadis C

Wilson Disease: Intersecting DNA Methylation and Histone Acetylation Regulation of Gene Expression in a Mouse Model of Hepatic Copper Accumulation.

Cellular and molecular gastroenterology and hepatology

Sarode GV, Neier K, Shibata NM, Shen Y, Goncharov DA, Goncharova EA, Mazi TA, Joshi N, Settles ML, LaSalle JM, Medici V

The auxin-producing Bacillus thuringiensis RZ2MS9 promotes the growth and modifies the root architecture of tomato (Solanum lycopersicum cv. Micro-Tom).

Archives of microbiology

Batista BD, Dourado MN, Figueredo EF, Hortencio RO, Marques JPR, Piotto FA, Bonatelli ML, Settles ML, Azevedo JL, Quecine MC

Protective heterologous T cell immunity in COVID-19 induced by MMR and Tdap vaccine antigens.

bioRxiv : the preprint server for biology

Mysore V, Cullere X, Settles ML, Ji X, Kattan MW, Desjardins M, Durbin-Johnson B, Gilboa T, Baden LR, Walt DR, Lichtman A, Jehi L, Mayadas TN

Disruption of global hypothalamic microRNA (miR) profiles and associated behavioral changes in California mice (Peromyscus californicus) developmentally exposed to endocrine disrupting chemicals.

Hormones and behavior

Kaur S, Kinkade JA, Green MT, Martin RE, Willemse TE, Bivens NJ, Schenk AK, Helferich WG, Trainor BC, Fass J, Settles M, Mao J, Rosenfeld CS

Chromatin accessibility in canine stromal cells and its implications for canine somatic cell reprogramming.

Stem cells translational medicine

Questa M, Moshref M, Jimenez RJ, Lopez-Cervantes V, Crawford CK, Settles ML, Ross PJ, Kol A

Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent.

Frontiers in genetics

Joslin SEK, Durbin-Johnson BP, Britton M, Settles ML, Korf I, Lemay DG

Transcriptomic response to elevated water temperatures in adult migrating Yukon River Chinook salmon (Oncorhynchus tshawytscha).

Conservation physiology

Bowen L, von Biela VR, McCormick SD, Regish AM, Waters SC, Durbin-Johnson B, Britton M, Settles ML, Donnelly DS, Laske SM, Carey MP, Brown RJ, Zimmerman CE

MYBPC3 Haplotype Linked to Hypertrophic Cardiomyopathy in Rhesus Macaques (Macaca mulatta).

Comparative medicine

Oldt RF, Bussey KJ, Settles ML, Fass JN, Roberts JA, Reader JR, Komandoor S, Abrich VA, Kanthaswamy S

Complete Genome Sequence of Bacillus sp. Strain RZ2MS9, a Multitrait Plant Growth Promoter.

Microbiology resource announcements

Bonatelli ML, Li J, Dumaresq A, Quecine MC, Settles ML

Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities.

Journal of biomolecular techniques : JBT

Dragon JA, Gates C, Sui SH, Hutchinson JN, Karuturi RKM, Kucukural A, Polson S, Riva A, Settles ML, Thimmapuram J, Levine SS

Proximal femoral head transcriptome reveals novel candidate genes related to epiphysiolysis in broiler chickens.

BMC genomics

de Oliveira Peixoto J, Savoldi IR, Ibelli AMG, Cantão ME, Jaenisch FRF, Giachetto PF, Settles ML, Zanella R, Marchesi JAP, Pandolfi JR, Coutinho LL, Ledur MC

Rectal Microbiome Composition Correlates with Humoral Immunity to HIV-1 in Vaccinated Rhesus Macaques.

mSphere

Elizaldi SR, Verma A, Walter KA, Rolston M, Dinasarapu AR, Durbin-Johnson BP, Settles M, Kozlowski PA, Raeman R, Iyer SS

Single-Cell RNA-seq Reveals Profound Alterations in Mechanosensitive Dorsal Root Ganglion Neurons with Vitamin E Deficiency.

iScience

Finno CJ, Peterson J, Kang M, Park S, Bordbari MH, Durbin-Johnson B, Settles M, Perez-Flores MC, Lee JH, Yamoah EN

Additional Evidence for DDB2 T338M as a Genetic Risk Factor for Ocular Squamous Cell Carcinoma in Horses.

International journal of genomics

Singer-Berk MH, Knickelbein KE, Lounsberry ZT, Crausaz M, Vig S, Joshi N, Britton M, Settles ML, Reilly CM, Bentley E, Nunnery C, Dwyer A, Lassaline ME, Bellone RR

Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform.

mSystems

Holm JB, Humphrys MS, Robinson CK, Settles ML, Ott S, Fu L, Yang H, Gajer P, He X, McComb E, Gravitt PE, Ghanem KG, Brotman RM, Ravel J

Transcriptome Analysis of Salmonella Heidelberg after Exposure to Cetylpyridinium Chloride, Acidified Calcium Hypochlorite, and Peroxyacetic Acid.

Journal of food protection

Cadena M, Froenicke L, Britton M, Settles ML, Durbin-Johnson B, Kumimoto E, Gallardo RA, Ferreiro A, Chylkova T, Zhou H, Pitesky M

Fatherhood alters gene expression within the MPOA.

Environmental epigenetics

Seelke AMH, Bond JM, Simmons TC, Joshi N, Settles ML, Stolzenberg D, Rhemtulla M, Bales KL

Obesity treatment by epigallocatechin-3-gallate-regulated bile acid signaling and its enriched Akkermansia muciniphila.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology

Sheng L, Jena PK, Liu HX, Hu Y, Nagar N, Bronner DN, Settles ML, Bäumler AJ, Wan YY

High-Quality Complete Genome Sequences of Three Bovine Shiga Toxin-Producing Escherichia coli O177:H- (fliCH25) Isolates Harboring Virulent stx2 and Multiple Plasmids.

Genome announcements

Sheng H, Duan M, Hunter SS, Minnich SA, Settles ML, New DD, Chase JR, Fagnan MW, Hovde CJ

16S rRNA analysis of diversity of manure microbial community in dairy farm environment.

PloS one

Pandey P, Chiu C, Miao M, Wang Y, Settles M, Del Rio NS, Castillo A, Souza A, Pereira R, Jeannotte R

Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women.

The Journal of nutrition

Williams JE, Carrothers JM, Lackey KA, Beatty NF, York MA, Brooker SL, Shafii B, Price WJ, Settles ML, McGuire MA, McGuire MK

Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis.

Molecular ecology resources

Byrne AQ, Rothstein AP, Poorten TJ, Erens J, Settles ML, Rosenblum EB

Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).

Journal of biomolecular techniques : JBT

Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N, McIntyre A, Ahsanuddin S, Bezdan D, Green SJ, Joye S, Stewart Johnson S, Baldwin DA, Bivens N, Ajami N, Carmical JR, Herriott IC, Colwell R, Donia M, Foox J, Greenfield N, Hunter T, Hoffman J, Hyman J, Jorgensen E, Krawczyk D, Lee J, Levy S, Garcia-Reyero N, Settles M, Thomas K, Gómez F, Schriml L, Kyrpides N, Zaikova E, Penterman J, Mason CE

Erratum to: Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus.

Journal of molecular evolution

Madison-Villar MJ, Sun C, Lau NC, Settles ML, Mueller RL

Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus.

Journal of molecular evolution

Madison-Villar MJ, Sun C, Lau NC, Settles ML, Mueller RL

Love the one you're with: replicate viral adaptations converge on the same phenotypic change.

PeerJ

Miller CR, Nagel AC, Scott L, Settles M, Joyce P, Wichman HA

Full Mitochondrial Genome Sequence of the Sugar Beet Wireworm Limonius californicus (Coleoptera: Elateridae), a Common Agricultural Pest.

Genome announcements

Gerritsen AT, New DD, Robison BD, Rashed A, Hohenlohe P, Forney L, Rashidi M, Wilson CM, Settles ML

Mitochondrial Genome Sequence of the Galápagos Endemic Land Snail Naesiotus nux.

Genome announcements

Hunter SS, Settles ML, New DD, Parent CE, Gerritsen AT

Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance.

Molecular biology and evolution

Loftie-Eaton W, Yano H, Burleigh S, Simmons RS, Hughes JM, Rogers LM, Hunter SS, Settles ML, Forney LJ, Ponciano JM, Top EM

The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards.

Molecular ecology

Laurent S, Pfeifer SP, Settles ML, Hunter SS, Hardwick KM, Ormond L, Sousa VC, Jensen JD, Rosenblum EB

Fecal Microbial Community Structure Is Stable over Time and Related to Variation in Macronutrient and Micronutrient Intakes in Lactating Women.

The Journal of nutrition

Carrothers JM, York MA, Brooker SL, Lackey KA, Williams JE, Shafii B, Price WJ, Settles ML, McGuire MA, McGuire MK

Draft Genome Sequence of Pseudomonas sp. nov. H2.

Genome announcements

Loftie-Eaton W, Suzuki H, Bashford K, Heuer H, Stragier P, De Vos P, Settles ML, Top EM

Vaginal microbiota of adolescent girls prior to the onset of menarche resemble those of reproductive-age women.

mBio

Hickey RJ, Zhou X, Settles ML, Erb J, Malone K, Hansmann MA, Shew ML, Van Der Pol B, Fortenberry JD, Forney LJ

Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp.

Pathogens and disease

Mendes-Soares H, Krishnan V, Settles ML, Ravel J, Brown CJ, Forney LJ

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures.

Bioresource technology

Liang S, Gliniewicz K, Mendes-Soares H, Settles ML, Forney LJ, Coats ER, McDonald AG

Prenatal exposure to BPA alters the epigenome of the rat mammary gland and increases the propensity to neoplastic development.

PloS one

Dhimolea E, Wadia PR, Murray TJ, Settles ML, Treitman JD, Sonnenschein C, Shioda T, Soto AM

Vaginal microbiome changes with levonorgestrel intrauterine system placement.

Contraception

Jacobson JC, Turok DK, Dermish AI, Nygaard IE, Settles ML

Phase variation in Myxococcus xanthus yields cells specialized for iron sequestration.

PloS one

Dziewanowska K, Settles M, Hunter S, Linquist I, Schilkey F, Hartzell PL

Maternal bisphenol a exposure impacts the fetal heart transcriptome.

PloS one

Chapalamadugu KC, Vandevoort CA, Settles ML, Robison BD, Murdoch GK

Draft Genome Sequence of Pseudomonas moraviensis R28-S.

Genome announcements

Hunter SS, Yano H, Loftie-Eaton W, Hughes J, De Gelder L, Stragier P, De Vos P, Settles ML, Top EM

Microbiota of the seminal fluid from healthy and infertile men.

Fertility and sterility

Hou D, Zhou X, Zhong X, Settles ML, Herring J, Wang L, Abdo Z, Forney LJ, Xu C

SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching.

Journal of data mining in genomics & proteomics

Zhbannikov IY, Hunter SS, Settles ML, Foster JA

MasABK proteins interact with proteins of the type IV pilin system to affect social motility of Myxococcus xanthus.

PloS one

Fremgen S, Williams A, Furusawa G, Dziewanowska K, Settles M, Hartzell P

A forward genetic screen reveals that calcium-dependent protein kinase 3 regulates egress in Toxoplasma.

PLoS pathogens

Garrison E, Treeck M, Ehret E, Butz H, Garbuz T, Oswald BP, Settles M, Boothroyd J, Arrizabalaga G

Epigenetic transgenerational inheritance of vinclozolin induced mouse adult onset disease and associated sperm epigenome biomarkers.

Reproductive toxicology (Elmsford, N.Y.)

Guerrero-Bosagna C, Covert TR, Haque MM, Settles M, Nilsson EE, Anway MD, Skinner MK

Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio).

BMC genomics

Drew RE, Settles ML, Churchill EJ, Williams SM, Balli S, Robison BD

The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation.

mBio

Hughes JM, Lohman BK, Deckert GE, Nichols EP, Settles M, Abdo Z, Top EM

mcaGUI: microbial community analysis R-Graphical User Interface (GUI).

Bioinformatics (Oxford, England)

Copeland WK, Krishnan V, Beck D, Settles M, Foster JA, Cho KC, Day M, Hickey R, Schütte UM, Zhou X, Williams CJ, Forney LJ, Abdo Z

Meta-analysis of two genome-wide association studies of bovine paratuberculosis.

PloS one

Minozzi G, Williams JL, Stella A, Strozzi F, Luini M, Settles ML, Taylor JF, Whitlock RH, Zanella R, Neibergs HL

Only skin deep: shared genetic response to the deadly chytrid fungus in susceptible frog species.

Molecular ecology

Rosenblum EB, Poorten TJ, Settles M, Murdoch GK

Genome-wide scan identifies loci associated with classical BSE occurrence.

PloS one

Murdoch BM, Murdoch GK, Settles M, McKay S, Williams JL, Moore SS

Global analysis of phase variation in Myxococcus xanthus.

Molecular microbiology

Furusawa G, Dziewanowska K, Stone H, Settles M, Hartzell P

OTUbase: an R infrastructure package for operational taxonomic unit data.

Bioinformatics (Oxford, England)

Beck D, Settles M, Foster JA

PRNP haplotype associated with classical BSE incidence in European Holstein cattle.

PloS one

Murdoch BM, Clawson ML, Yue S, Basu U, McKay S, Settles M, Capoferri R, Laegreid WW, Williams JL, Moore SS

GSEA-SNP identifies genes associated with Johne's disease in cattle.

Mammalian genome : official journal of the International Mammalian Genome Society

Neibergs HL, Settles ML, Whitlock RH, Taylor JF

Alterations in the developing testis transcriptome following embryonic vinclozolin exposure.

Reproductive toxicology (Elmsford, N.Y.)

Clement TM, Savenkova MI, Settles M, Anway MD, Skinner MK

A 2cM genome-wide scan of European Holstein cattle affected by classical BSE.

BMC genetics

Murdoch BM, Clawson ML, Laegreid WW, Stothard P, Settles M, McKay S, Prasad A, Wang Z, Moore SS, Williams JL

Genome-wide transcriptional response of Silurana (Xenopus) tropicalis to infection with the deadly chytrid fungus.

PloS one

Rosenblum EB, Poorten TJ, Settles M, Murdoch GK, Robert J, Maddox N, Eisen MB

Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio).

Physiological genomics

Drew RE, Rodnick KJ, Settles M, Wacyk J, Churchill E, Powell MS, Hardy RW, Murdoch GK, Hill RA, Robison BD

Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

Coram TE, Settles ML, Wang M, Chen X

Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio).

Comparative biochemistry and physiology. Part D, Genomics & proteomics

Robison BD, Drew RE, Murdoch GK, Powell M, Rodnick KJ, Settles M, Stone D, Churchill E, Hill RA, Papasani MR, Lewis SS, Hardy RW

Referencing the CAT Core and Publications

When submitting manuscripts, please acknowledge the CAT by including the text: “Sequencing was performed at the UCSF CAT, supported by UCSF PBBR, RRP IMIA, and NIH 1S10OD028511-01 grants.” 

 

To aid our facility in future grant submissions, it helps to reference labs and publications that have benefited from our core please notify us of your achievement by emailing catcore [at] ucsf.edu the PMID number, lab, and the piece of equipment used in the paper.