A Reproducible Approach to High-Throughput Biological Data Acquisition and Integration
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CHRISTINA “TINA” WARINNER (Last Updated October 18, 2018)
CHRISTINA “TINA” WARINNER (last updated October 18, 2018) Max Planck Institute University of Oklahoma for the Science of Human History (MPI-SHH) Department of Anthropology Department of Archaeogenetics Laboratories of Molecular Anthropology Kahlaische Strasse 10, 07743 Jena, Germany And Microbiome Research (LMAMR) +49 3641686620 101 David L. Boren Blvd, [email protected] Norman, OK 73019 USA www.christinawarinner.com [email protected] http://www.shh.mpg.de/employees/50506/25522 www.lmamr.org APPOINTMENTS W2 Group Leader, Max Planck Institute for the Science of Human History, Germany 2016-present University Professor, Friedrich Schiller University, Jena, Germany 2018-present Presidential Research Professor, Univ. of Oklahoma, USA 2014-present Assistant Professor, Dept. of Anthropology, Univ. of Oklahoma, USA 2014-present Adjunct Professor, Dept. of Periodontics, College of Dentistry, Univ. of Oklahoma, USA 2014-present Visiting Associate Professor, Dept. of Systems Biology, Technical University of Denmark 2015 Research Associate, Dept. of Anthropology, Univ. of Oklahoma, USA 2012-2014 Acting Head of Group, Centre for Evolutionary Medicine, Univ. of Zürich, Switzerland 2011-2012 Research Assistant, Centre for Evolutionary Medicine, Univ. of Zürich, Switzerland 2010-2011 EDUCATION Ph.D., Anthropology, Dept. of Anthropology, Harvard University 2010 Thesis Title: “Life and Death at Teposcolula Yucundaa: Mortuary, Archaeogenetic, and Isotopic Investigations of the Early Colonial Period in Mexico” A.M., Anthropology, Dept. of Anthropology, Harvard University 2008 B.A., with Honors, Anthropology, University of Kansas 2003 B.A., Germanic Literatures and Languages, University of Kansas 2003 SELECTED HONORS, AWARDS, AND FELLOWSHIPS Invited speaker, British Academy, Albert Reckitt Archaeological Lecture (forthcoming) 2019 Invited speaker, EMBL Science and Society (forthcoming, Nov. -
Ayshwarya Subramanian Updated June 10, 2021
Ayshwarya Subramanian Updated June 10, 2021 Contact Kuchroo Lab and Klarman Cell Observatory Information Broad Institute twitter: @ayshwaryas 5407G, 415 Main Street website: ayshwaryas.github.io Cambridge, MA 02412 USA email:[email protected] Areas of Computational Biology (Kidney disease, Cancer, Inflammatory Bowel Disease, RNA Biology), Ge- expertise nomic Data Analysis (Single-cell and Bulk-RNAseq, Metagenomics, Exome and single-nucleus DNA sequencing), Machine Learning, Probabilistic modeling, Phylogenetics, Applied Statistics Education 2013 Ph.D., Biological Sciences Carnegie Mellon University, Pittsburgh, PA USA Doctoral Advisor: Russell Schwartz, Ph.D. Dissertation: Inferring tumor evolution using computational phylogenetics 2007 M.Sc. (Hons), Biological Sciences (Undergraduate degree) Birla Institute of Technology and Science (BITS{Pilani), Rajasthan, India CGPA 9.21/10, Major GPA 10/10, with Distinction Undergraduate Honors Thesis: A mathematical model for phototactic responses in Halobac- terium salinarium, Max Planck Institute for Complex Technical Systems, Germany. Current Computational Scientist, Cambridge MA 2017{Present Appointment Mentors: Aviv Regev, Ph.D. & Vijay Kuchroo, Ph.D., D.V.M Research Summary: Single-cell portraits of disease and normal states using human data, mouse and organoid models Klarman Cell Observatory Broad Institute, Cambridge, MA 02142 Publications Pre-prints/Under review [1] Subramanian A†, Vernon KA†, Zhou Y† et al. Obesity-instructed TREM2high macrophages identified by comparative analysis of diabetic mouse and human kidney at single cell resolution. bioRxiv 2021.05.30.446342; doi: https://doi.org/10.1101/2021.05.30.446342. [2] Subramanian A†,Vernon KA†, Slyper M, Waldman J, et al. RAAS blockade, kidney dis- ease, and expression of ACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells. -
Case Studies in Bayesian Statistics Workshop 9 Poster Session
Case Studies in Bayesian Statistics Workshop 9 Poster Session Following is a tentative list of posters being presented during the workshop: 1. Edoardo Airoldi, Curtis Huttenhower, Olga Troyanskaya and David Botstein 2. Dipankar Bandyopadhyay, Elizabeth Slate, Debajyoti Sinha, Dikpak Dey and Jyotika Fernandes 3. Brenda Betancourt and Maria-Eglee Perez 4. Sham Bhat, Murali Haran, Julio Molineros and Erick Dewolf 5. Jen-hwa Chu, Merlise A. Clyde and Feng Liang 6. Jason Connor, Scott Berry and Don Berry 7. J. Mark Donovan, Michael R. Elliott and Daniel F. Heitjan 8. Elena A. Erosheva, Donatello Telesca, Ross L. Matsueda and Derek Kreager 9. Xiaodan Fan and Jun S. Liu 10. Jairo A. Fuquene and Luis Raul Pericchi 11. Marti Font, Josep Ginebra, Xavier Puig 12. Isobel Claire Gormley and Thomas Brendan Murphy 13. Cari G. Kaufman and Stephan R. Sain 14. Alex Lenkoski 15. Herbie Lee 16. Fei Liu 17. Jingchen Liu, Xiao-Li Meng, Chih-nan Chen, Margarita Alegria 18. Christian Macaro 19. Il-Chul Moon, Eunice J. Kim and Kathleen M. Carley 20. Christopher Paciorek 21. Susan M. Paddock and Patricia Ebener 22. Nicholas M. Pajewski, L. Thomas Johnson, Thomas Radmer, and Purushottam W. Laud 23. Mark W. Perlin, Joseph B. Kadane, Robin W. Cotton and Alexander Sinelnikov 24. Alicia Quiros, Raquel Montes Diez and Dani Gamerman 25. Eiki Satake and Philip Amato 26. James Scott 27. Russell Steele, Robert Platt and Michelle Ross 28. Alejandro Villagran, Gabriel Huerta, Charles S. Jackson and Mrinal K. Sen 29. Dawn Woodard 30. David C. Wheeler, Lance A. Waller and John O. -
Open Dogan Phdthesis Final.Pdf
The Pennsylvania State University The Graduate School Eberly College of Science ELUCIDATING BIOLOGICAL FUNCTION OF GENOMIC DNA WITH ROBUST SIGNALS OF BIOCHEMICAL ACTIVITY: INTEGRATIVE GENOME-WIDE STUDIES OF ENHANCERS A Dissertation in Biochemistry, Microbiology and Molecular Biology by Nergiz Dogan © 2014 Nergiz Dogan Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2014 ii The dissertation of Nergiz Dogan was reviewed and approved* by the following: Ross C. Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee David S. Gilmour Professor of Molecular and Cell Biology Anton Nekrutenko Professor of Biochemistry and Molecular Biology Robert F. Paulson Professor of Veterinary and Biomedical Sciences Philip Reno Assistant Professor of Antropology Scott B. Selleck Professor and Head of the Department of Biochemistry and Molecular Biology *Signatures are on file in the Graduate School iii ABSTRACT Genome-wide measurements of epigenetic features such as histone modifications, occupancy by transcription factors and coactivators provide the opportunity to understand more globally how genes are regulated. While much effort is being put into integrating the marks from various combinations of features, the contribution of each feature to accuracy of enhancer prediction is not known. We began with predictions of 4,915 candidate erythroid enhancers based on genomic occupancy by TAL1, a key hematopoietic transcription factor that is strongly associated with gene induction in erythroid cells. Seventy of these DNA segments occupied by TAL1 (TAL1 OSs) were tested by transient transfections of cultured hematopoietic cells, and 56% of these were active as enhancers. Sixty-six TAL1 OSs were evaluated in transgenic mouse embryos, and 65% of these were active enhancers in various tissues. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
UNIVERSITY of CALIFORNIA SAN DIEGO Making Sense of Microbial
UNIVERSITY OF CALIFORNIA SAN DIEGO Making sense of microbial populations from representative samples A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Computer Science by James T. Morton Committee in charge: Professor Rob Knight, Chair Professor Pieter Dorrestein Professor Rachel Dutton Professor Yoav Freund Professor Siavash Mirarab 2018 Copyright James T. Morton, 2018 All rights reserved. The dissertation of James T. Morton is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California San Diego 2018 iii DEDICATION To my friends and family who paved the road and lit the journey. iv EPIGRAPH The ‘paradox’ is only a conflict between reality and your feeling of what reality ‘ought to be’ —Richard Feynman v TABLE OF CONTENTS Signature Page . iii Dedication . iv Epigraph . .v Table of Contents . vi List of Abbreviations . ix List of Figures . .x List of Tables . xi Acknowledgements . xii Vita ............................................. xiv Abstract of the Dissertation . xvii Chapter 1 Methods for phylogenetic analysis of microbiome data . .1 1.1 Introduction . .2 1.2 Phylogenetic Inference . .4 1.3 Phylogenetic Comparative Methods . .6 1.4 Ancestral State Reconstruction . .9 1.5 Analysis of phylogenetic variables . 11 1.6 Using Phylogeny-Aware Distances . 15 1.7 Challenges of phylogenetic analysis . 18 1.8 Discussion . 19 1.9 Acknowledgements . 21 Chapter 2 Uncovering the horseshoe effect in microbial analyses . 23 2.1 Introduction . 24 2.2 Materials and Methods . 34 2.3 Acknowledgements . 35 Chapter 3 Balance trees reveal microbial niche differentiation . 36 3.1 Introduction . -
Bioinformatics Opening Workshop September 8 - 12, 2014
Bioinformatics Opening Workshop September 8 - 12, 2014 Mihye Ahn James (Paul) Brooks University of North Carolina Virginia Commonwealth Alexander Alekseyenko Greg Buck New York University Virginia Commonwealth Baiguo An Mark Burch University of North Carolina Ohio State University Jeremy Ash Christopher Burke North Carolina State University University of Cincinnati Deepak Nag Ayyala Hongyuan Cao University of Maryland University of Missouri Keith Baggerly Vincent Carey MD Anderson Center Harvard University Veera Baladandayuthapani Luis Carvalho MD Anderson Center Boston University Pallavi Basu Alberto Cassese University of Southern California Rice University Munni Begum Changgee Chang Ball State University Emory University Emanuel Ben-David Hegang Chen Columbia University University of Maryland Anindya Bhadra Chen Chen Purdue University Purdue University Yuanyuan Bian Mengjie Chen University of Missouri University of North Carolina Huybrechts Frazier Achard Bindele Hyoyoung Choo-Wosoba University of South Alabama University of Louisville Kristen Borchert Pankaj Choudhary BD Technologies University of Texas Russell Bowler Hyonho Chun National Jewish Health Purdue University Bioinformatics Opening Workshop September 8 - 12, 2014 Robert Corty Yang Feng University of North Carolina Columbia University Xinping Cui Hua Feng University of California, Riverside University of Idaho Hongying Dai Jennifer Fettweis Children's Mercy Hospital Virginia Commonwealth Susmita Datta Dayne Filer University of Louisville EPA Sujay Datta Christopher Fowler -
Early-Onset Obesity and Paternal 2Pter Deletion Encompassing the ACP1, TMEM18,Andmyt1l Genes
European Journal of Human Genetics (2014) 22, 471–479 & 2014 Macmillan Publishers Limited All rights reserved 1018-4813/14 www.nature.com/ejhg ARTICLE Early-onset obesity and paternal 2pter deletion encompassing the ACP1, TMEM18,andMYT1L genes Martine Doco-Fenzy*,1, Camille Leroy1, Anouck Schneider2, Florence Petit3, Marie-Ange Delrue4, Joris Andrieux3, Laurence Perrin-Sabourin5, Emilie Landais1, Azzedine Aboura5, Jacques Puechberty2,6, Manon Girard6, Magali Tournaire6, Elodie Sanchez2, Caroline Rooryck4,Agne`s Ameil7, Michel Goossens8, Philippe Jonveaux9, Genevie`ve Lefort2,6, Laurence Taine4, Dorothe´e Cailley4, Dominique Gaillard1, Bruno Leheup10, Pierre Sarda2 and David Genevie`ve2 Obesity is a common but highly, clinically, and genetically heterogeneous disease. Deletion of the terminal region of the short arm of chromosome 2 is rare and has been reported in about 13 patients in the literature often associated with a Prader–Willi-like phenotype. We report on five unrelated patients with 2p25 deletion of paternal origin presenting with early- onset obesity, hyperphagia, intellectual deficiency, and behavioural difficulties. Among these patients, three had de novo pure 2pter deletions, one presented with a paternal derivative der(2)t(2;15)(p25.3;q26) with deletion in the 2pter region and the last patient presented with an interstitial 2p25 deletion. The size of the deletions was characterized by SNP array or array-CGH and was confirmed by fluorescence in situ hybridization (FISH) studies. Four patients shared a 2p25.3 deletion with a minimal critical region estimated at 1.97 Mb and encompassing seven genes, namely SH3HYL1, ACP1, TMEMI8, SNTG2, TPO, PXDN, and MYT1L genes. The fifth patient had a smaller interstitial deletion encompassing the TPO, PXDN, and MYT1L genes. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
A Compendium of Co-Regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events
bioRxiv preprint doi: https://doi.org/10.1101/155333; this version posted June 26, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. A compendium of co-regulated protein complexes in breast cancer reveals collateral loss events Colm J. Ryan*1, Susan Kennedy1, Ilirjana Bajrami2, David Matallanas1, Christopher J. Lord2 1Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland 2The Breast Cancer Now Toby Robins Breast Cancer Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, United Kingdom. * Correspondence: [email protected] Summary Protein complexes are responsible for the bulk of activities within the cell, but how their behavior and composition varies across tumors remains poorly understood. By combining proteomic profiles of breast tumors with a large-scale protein-protein interaction network, we have identified a set of 258 high-confidence protein complexes whose subunits have highly correlated protein abundance across tumor samples. We used this set to identify complexes that are reproducibly under- or over- expressed in specific breast cancer subtypes. We found that mutation or deletion of one subunit of a complex was often associated with a collateral reduction in protein expression of additional complex members. This collateral loss phenomenon was evident from proteomic, but not transcriptomic, profiles suggesting post- transcriptional control. Mutation of the tumor suppressor E-cadherin (CDH1) was associated with a collateral loss of members of the adherens junction complex, an effect we validated using an engineered model of E-cadherin loss. -
Supporting Information Supplementary Methods Patients for Whole Genome Sequencing and Validation Cohort. Heparinized Bone Marrow
Supporting Information Supplementary Methods Patients for whole genome sequencing and validation cohort. Heparinized bone marrow samples were obtained from 8 RAEB patients with informed consent for WGS according to the ethics review board of Shanghai Institute of Hematology. Briefly, these 8 patients were 4 RAEB-1, 4 RAEB-2, 5 males, 3 females, 1 with complex karyotype, 1 with +8, 5 with normal karyotype, and classified as intermediate to very high risk level. 6 patients died 4-23 months after diagnosis of infection, hemorrhage, cerebral infarction or evolution to AML (complete information see Table S1). The validation cohort consisted of 188 various subtypes of MDS patients diagnosed and treated in Shanghai Ruijin Hospital and Shanghai No.6 People’s Hospital. All patients provided written informed consent. Bone marrow and paired buccal samples were obtained after informed consent. DNA sample preparation. Mononuclear cells (MNC) were separated by density gradient centrifugation using Ficoll in 8 RAEB patients and 188 MDS patients from validation cohort. Subsequently, CD34+ cells were isolated by magnetic cell separation (Miltenyi Biotech, Bergisch Gladbach, Germany) to reach a purity of 89-97.7% (average: 93.1%) in 8 RAEB patients. Flow through CD34- cells were also collected for analysis. Skin biopsy was obtained for analysis of normal genome and extracted by DNeasy Blood & Tissue Kit (Qiagen). Genomic DNA of CD34+ cells were isolated by QuickGene DNA whole blood kit L (FUJIFILM, Life Science). Genomic DNA of MNC from validation set was extracted by Wizard® Genomic DNA Purification Kit (Promega). DNA library preparation. Genomic DNA was sheared by sonication 1 and adaptors were ligated to the resulting fragments. -
Integrating Taxonomic, Functional, and Strain-Level Profiling of Diverse
TOOLS AND RESOURCES Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Francesco Beghini1†, Lauren J McIver2†, Aitor Blanco-Mı´guez1, Leonard Dubois1, Francesco Asnicar1, Sagun Maharjan2,3, Ana Mailyan2,3, Paolo Manghi1, Matthias Scholz4, Andrew Maltez Thomas1, Mireia Valles-Colomer1, George Weingart2,3, Yancong Zhang2,3, Moreno Zolfo1, Curtis Huttenhower2,3*, Eric A Franzosa2,3*, Nicola Segata1,5* 1Department CIBIO, University of Trento, Trento, Italy; 2Harvard T.H. Chan School of Public Health, Boston, United States; 3The Broad Institute of MIT and Harvard, Cambridge, United States; 4Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all’Adige, Italy; 5IEO, European Institute of Oncology IRCCS, Milan, Italy Abstract Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and *For correspondence: phylogenetic profiling of metagenomes newly developed to build on the largest set of reference [email protected] (CH); sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of [email protected] (EAF); taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These [email protected] (NS) methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and †These authors contributed IBD (1635 metagenomes and 817 metatranscriptomes).