Computational Biology Consulting Core

Overview of Services

The Computational Biology Consulting Core (CBCC) offers state-of-the-art computational biology services to biomedical researchers at the Johns Hopkins University. We offer comprehensive analyses of sequencing data for a variety of genomics and sequencing-based experiments. We can handle most types of data, including Illumina, PacBio, 454, and Sanger reads, and we have experience with a variety of sequencing protocols (RNA-seq, CHiP-seq, whole-genome and whole-exome sequencing, etc).


Examples of analyses:

  • Transcriptomics (RNA-seq)
  • Metagenomics
  • ChIP-seq analysis
  • Genome assembly
  • Sequence alignment
  • SNP and structural variant detection

 For all projects, we can arrange to transfer the data directly from the sequencing facility to our computers. We use best practice bioinformatics solutions and can work with you to design custom algorithms and analyses as needed. 

Core Coins

CBCC is announcing the 2017 Core coins competition here.

Leadership

Faculty Manager:

Liliana Florea, Ph.D.
Associate Professor of Genetic Medicine and Computer Science
florea@jhu.edu

Director:

Steven Salzberg , Ph.D.
Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science and Biostatistics

Location and hours of operation

Hours Location

8:30a-4:00p     

      McKusick-Nathans Institute of Genetic Medicine
      1900 E. Monument St., Welch Medical Library 113
      Baltimore, MD 21205

Links and Resources

  1. Computational Biology Consulting Core

Contacts

Name Role Phone Email Location
Steven Salzberg, Ph.D.
Director
 
(410)614-6112
 
salzberg@jhu.edu
 
Welch Medical Library Rm 107
 
Liliana Florea, Ph.D.
Faculty Manager
 
(443)287-5624
 
florea@jhu.edu
 
Welch Medical Library Rm. 113
 
Corina Antonescu
Bioinformatics Engineer
 
(443)287-0252
 
acorina@jhu.edu
 
Welch Medical Library Rm. 115A
 
Ann Vukelich
Billing and Administration
 
(410)502-7525 am or (443)287-0231 pm
 
avukeli1@jhmi.edu
 
Welch Medical Library Rm. 115
 

Members at Mid-Atlantic Shared Services Consortium

Core Name Primary Contact Email Phone Number/Ext
Center for Proteomics Discovery

Bayview Immunomics Core (BIC)

Behavioral Core of the School of Medicine

Biostatistics, Epidemiology And Data Management (BEAD) Core

Augusta Smith BEADCore@jhmi.edu 410-550-4227
Bloomberg Flow Cytometry and Immunology Core

Tricia Nilles, MS tnilles1@jhu.edu 410-955-4825
CTMI

Gwyndell Duncan gduncan2@jhmi.edu 410.550.6212
Center for Clinical Data Analysis (CCDA) Consulting Service

Center for Infection and Inflammation Imaging Research (Ci3R)

Sanjay K Jain, M.D. sjain5@jhmi.edu (410) 502-8241
Computational Biology Consulting Core

Steven Salzberg, Ph.D. salzberg@jhu.edu (410)614-6112
Deep Sequencing & Microarray Core

Eukaryotic Tissue Culture Facility

Sandra Beatriz Gabelli gabelli@jhmi.edu 410-614-4145
Genetic Resources Core Facility Biorepository & Cell Center

Genetic Resources Core Facility DNA Services

High Throughput Screening (ChemCORE)

Jun Liu joliu@jhu.edu (410)955-4619
IGM Computing Core

Elvin Hsu elvinhsu@jhu.edu (667)208-7189
Integrated Imaging Center

J. Michael McCaffery jmccaffery@jhu.edu (410) 516-3321
Johns Hopkins All Children's Center for Resources in Integrative Biology (CRIB) & Molecular Determinants Core (MDC)

David Graham dgraham@jhmi.edu 410-955-9770
Johns Hopkins Drug Discovery Group

MMI Common Equipment and Glass Washing Facility

Anne Jedlicka ajedlic1@jhu.edu 443-287-5967
MRB Molecular Imaging Service Center and Cancer Functional Imaging Core

Malaria Mosquito & Parasite Core

George Dimopoulos, Ph.D. gdimopo1@jhu.edu 443-287-0128
Mass Spectrometry and Proteomics Core

Robert N. Cole, PhD rcole@jhmi.edu 410-614-6968
Non-iLab JHU KSAS Facilities

Jerry Hicks ghicks@jhu.edu 410-516-6418
Non-iLab, JHU SKCCC Core Facilities

Jeff Smith smithje@jhmi.edu
Non-iLab, JHU SOM Core Facilities

Barbara Daily bdaily@jhmi.edu
Non-iLab, SPH Core Facilities

Kate Calvin kcalvin1@jhu.edu
Phenocore, Phenotyping and Pathology Core

Cory Brayton, DVM cbrayton@jhmi.edu 410-502-3050**
Reference Histology

Lois Anderson lander@jhmi.edu 410-955-2861
Response Evaluation Criteria In Solid Tumors (RECIST) and Special Imaging Reads/Non-RECIST Response Evaluations

Gale Christensen gchrist8@jhmi.edu (443)287-2676
SKCCC IRAT Core (Image Response Assessment Team)

Michael Jacobs mjacobs8@jhmi.edu
SKCCC Immune Monitoring Core (formerly Human Immunology)

Christopher Thoburn cthoburn@jhmi.edu 410-955-8568
SKCCC Specimen Accessioning Core

Robin Stewart rstewa43@jhmi.edu 410 502-0674
The Biomedical Engineering (BME) Machine Shop

The Cardiovascular Physiology and Surgery Core

The Clinical Research Core Laboratory (ICTR)

The Rheumatic Disease Research Core Center (RDRCC)

WSE Center for Brain Imaging Science

WSE Hopkins Extreme Materials Institute (HEMI)

Scott McGhee mcghee@jhu.edu 410-516-7128
WSE Manufacturing (Machine Shop)

WSE The Materials Characterization and Processing Core (MCP)

WSE Whitaker Microfabrication Lab

SKCCC Analytical Pharmacology Core

Michelle Rudek Mrudek2@jhmi.edu 410-614-6321
SKCCC Animal Resources

Eric Davis edavisa@jhmi.edu 410-502-9544
SKCCC Cell Imaging Facility

Lillian Dasko-Vincent ldaskov1@jhmi.edu 410-614-4414
SKCCC Common Equipment Core

Eric Davis edavisa@jhmi.edu
SKCCC Cytogenetics Core Facility

Laura Morsberger lmorsber@jhmi.edu
SKCCC Experimental Irradiator Core

Esteban Velarde evelard2@jhmi.edu
SKCCC Flow Cytometry Core

Julie Nauroth jnaurot1@jhmi.edu 443-287-3952
SKCCC Glassware Washing Core

Eric Davis edavis4@jhmi.edu 410.502.9544
SKCCC Microarray Core

Wayne Yu wyu8@jhmi.edu 410-502-7970
SKCCC Next Generation Sequencing Core

Lauren Ciotti nextgenseq@jhmi.edu 443-287-7341
Core Name Primary Contact Email Phone Number/Ext
Biostatistics and Bioinformatics Shared Service

State-of-the-art statistical science, expert statistical analysis and sound statistical reporting

Susan Holt sholt@som.umaryland.edu (410) 706-8505
Confocal Microscopy Core

Equipment and expertise to assist investigators in applying advanced fluorescence microscopy techniques to their research.

Joseph Mauban, PhD jmauban@som.umaryland.edu 410-706-6170
Core for Translational Research in Imaging (CTRIM)

State-of-the-art technology for animal imaging at the molecular, cellular and systemic level. Services for in-vivo and ex-vivo cross-sectional and functional imaging using MRI, MR-g-FUS, PET, and CT.

Jiachen Zhuo jzhuo@umm.edu (410) 328-6443
Electron Microscopy Core Imaging Facility

‌‌‌‌‌Transmission Electron Microscope, Scanning Electron Microscope, SEM CryoTransfer & Chamber, High Pressure Freezer, Freeze Substitution System, Grid Plunger, CryoUltramicrotome, Gatan 626 cryo holder

Ru-Ching Hsia, PhD rhsia@umaryland.edu 410-7067992
Flow Cytometry AND Mass Cytometry Core (CVD)

<p>Flow &amp; Mass Cytometry: DakoCytomation MoFlo flow cytometer and cell sorter, BD Biosciences LSR II flow cytometer with 16 parameters and CyTOF Mass Cytometer with the capability of measuring over 30 parameters simultaneously in a single tube.</p>

Regina Harley, MS rharley@som.umaryland.edu 410-706-0095
Flow Cytometry Core

Sample acquisition on three analytical flow cytometers, expert data analysis, experimental planning and consultation and perform cell sorting on two high speed cell sorters.</p>

Karen Underwood, BS Flowcore@som.umaryland.edu 410-706-2173
Genomics Core Facility - Formerly Biopolymer Core Facility

DNA Sequencing, Cell Line Authentication, Gene Expression Microarray, Genotyping and more

Nicholas Ambulos, PhD nambulos@som.umaryland.edu 410-706-60665
Mass Spectrometry Center

Strives to accelerate discovery by providing investigators, on campus and beyond, access to cutting-edge technologies in mass spectrometry. Expetise from basic biology and medicine to technology development and translational research

Maureen A. Kane mkane@rx.umaryland.edu 410-706-5097
NMR Core Facility

Nuclear Magnetic Resonance Spectroscopy: 600 MHz Bruker Avance III NMR Spectrometer, 800 MHz Bruker Avance NMR Spectrometer, 950 MHz Bruker Avance III NMR Spectrometer

Kristen M. Varney, PhD kvall001@umaryland.edu 410-706-2110
Pathology Biorepository Shared Service (PBSS)

Provides the collection of high quality banked patient samples while maintaining patient confidentiality. PBSS also provides pathology, histology, & histotechnology consultation services to assist principal investigators in the procurement, analyses, & clinicopathologic correlation of human tissue

Ashley Cellini, P.A. (ASCP) acellini@som.umaryland.edu 410-706-2174
Translational Laboratory Shared Service (UMGCC)

Pre-clinical and clinical experimental support to basic researchers and physicians. We work in areas across the entire spectrum: cell biology, in vitro, in vivo and human trials.

Rena Lapidus, PhD RLapidus@som.umaryland.edu 410-328-8092
University of Maryland Medicine (UMM) Biorepository

A foundation for personalized medicine. Includes banking of blood samples from UMMS patients, collections of various biospecimens from collaborating researchers. State-of-the-art robotic freezer & liquid-handling equipment. Secure & managed environment for processing, storage & distribution.

Coleen M. Damcott, Ph.D. cdamcott@medicine.umaryland.edu 410-706-8968

University of Virginia

Core Name Primary Contact Email Phone Number/Ext
Advanced Microscopy Facility Stacey Criswell sjm7r@virginia.edu 434-924-2524
BioNMR Facility
Biomolecular Analysis Facility
Biorepository and Tissue Research Facility (BTRF) Craig Rumpel, MS crumpel@virginia.edu 434-982-6453
Flow Cytometry Core Facility FCCF Core Email fccf-staff2@virginia.edu
Genetically Engineered Murine Model (GEMM) Core
Merry X-Ray Leslie Yowell lfy8p@virginia.edu (434) 243-6051
Metabolomics Lipidomics Shared Resource Todd Fox tfox@virginia.edu 434-297-6516
MolMart & Tissue Culture Facility Linda Beggerly lkb7h@virginia.edu 434 924 9211
Molecular Electron Microscopy Core Kelly Dryden kdryden@virginia.edu 434.982.0525
Molecular Imaging Core Jack Roy jrr5a@virginia.edu (434) 243-9232
Office of Research Core Administration Alicia Johnson af7sb@virginia.edu 434-982-6565
SOM Clinical Research Unit (CRU)
Stem Cell Core Arazdordi Toumadje AT5KH@virginia.edu 434-297-5302
Surgical Skills Training Center Dana Davis Sikon dds4g@eservices.virginia.edu 434-924-6854
Core Name Primary Contact Email Phone Number/Ext
Biostatistics and Bioinformatics Shared Service

State-of-the-art statistical science, expert statistical analysis and sound statistical reporting

Susan Holt sholt@som.umaryland.edu (410) 706-8505
Confocal Microscopy Core

Equipment and expertise to assist investigators in applying advanced fluorescence microscopy techniques to their research.

Joseph Mauban, PhD jmauban@som.umaryland.edu 410-706-6170
Core for Translational Research in Imaging (CTRIM)

State-of-the-art technology for animal imaging at the molecular, cellular and systemic level. Services for in-vivo and ex-vivo cross-sectional and functional imaging using MRI, MR-g-FUS, PET, and CT.

Jiachen Zhuo jzhuo@umm.edu (410) 328-6443
Electron Microscopy Core Imaging Facility

‌‌‌‌‌Transmission Electron Microscope, Scanning Electron Microscope, SEM CryoTransfer & Chamber, High Pressure Freezer, Freeze Substitution System, Grid Plunger, CryoUltramicrotome, Gatan 626 cryo holder

Ru-Ching Hsia, PhD rhsia@umaryland.edu 410-7067992
Flow Cytometry Core

Sample acquisition on three analytical flow cytometers, expert data analysis, experimental planning and consultation and perform cell sorting on two high speed cell sorters.</p>

Karen Underwood, BS Flowcore@som.umaryland.edu 410-706-2173
Genomics Core Facility - Formerly Biopolymer Core Facility

DNA Sequencing, Cell Line Authentication, Gene Expression Microarray, Genotyping and more

Nicholas Ambulos, PhD nambulos@som.umaryland.edu 410-706-60665
Mass Spectrometry Center

Strives to accelerate discovery by providing investigators, on campus and beyond, access to cutting-edge technologies in mass spectrometry. Expetise from basic biology and medicine to technology development and translational research

Maureen A. Kane mkane@rx.umaryland.edu 410-706-5097
Pathology Biorepository Shared Service (PBSS)

Provides the collection of high quality banked patient samples while maintaining patient confidentiality. PBSS also provides pathology, histology, & histotechnology consultation services to assist principal investigators in the procurement, analyses, & clinicopathologic correlation of human tissue

Ashley Cellini, P.A. (ASCP) acellini@som.umaryland.edu 410-706-2174
Translational Laboratory Shared Service (UMGCC)

Pre-clinical and clinical experimental support to basic researchers and physicians. We work in areas across the entire spectrum: cell biology, in vitro, in vivo and human trials.

Rena Lapidus, PhD RLapidus@som.umaryland.edu 410-328-8092
Core Name Primary Contact Email Phone Number/Ext
Non-iLab, JHU SKCCC Core Facilities

Jeff Smith smithje@jhmi.edu
SKCCC IRAT Core (Image Response Assessment Team)

Michael Jacobs mjacobs8@jhmi.edu
SKCCC Immune Monitoring Core (formerly Human Immunology)

Christopher Thoburn cthoburn@jhmi.edu 410-955-8568
SKCCC Specimen Accessioning Core

Robin Stewart rstewa43@jhmi.edu 410 502-0674
SKCCC Analytical Pharmacology Core

Michelle Rudek Mrudek2@jhmi.edu 410-614-6321
SKCCC Animal Resources

Eric Davis edavisa@jhmi.edu 410-502-9544
SKCCC Cell Imaging Facility

Lillian Dasko-Vincent ldaskov1@jhmi.edu 410-614-4414
SKCCC Common Equipment Core

Eric Davis edavisa@jhmi.edu
SKCCC Cytogenetics Core Facility

Laura Morsberger lmorsber@jhmi.edu
SKCCC Experimental Irradiator Core

Esteban Velarde evelard2@jhmi.edu
SKCCC Flow Cytometry Core

Julie Nauroth jnaurot1@jhmi.edu 443-287-3952
SKCCC Microarray Core

Wayne Yu wyu8@jhmi.edu 410-502-7970
SKCCC Next Generation Sequencing Core

Lauren Ciotti nextgenseq@jhmi.edu 443-287-7341

University of Virginia

Core Name Primary Contact Email Phone Number/Ext
Advanced Microscopy Facility Stacey Criswell sjm7r@virginia.edu 434-924-2524
BioNMR Facility
Biomolecular Analysis Facility
Biorepository and Tissue Research Facility (BTRF) Craig Rumpel, MS crumpel@virginia.edu 434-982-6453
Flow Cytometry Core Facility FCCF Core Email fccf-staff2@virginia.edu
Genetically Engineered Murine Model (GEMM) Core
Merry X-Ray Leslie Yowell lfy8p@virginia.edu (434) 243-6051
Metabolomics Lipidomics Shared Resource Todd Fox tfox@virginia.edu 434-297-6516
MolMart & Tissue Culture Facility Linda Beggerly lkb7h@virginia.edu 434 924 9211
Molecular Electron Microscopy Core Kelly Dryden kdryden@virginia.edu 434.982.0525
Molecular Imaging Core Jack Roy jrr5a@virginia.edu (434) 243-9232
Office of Research Core Administration Alicia Johnson af7sb@virginia.edu 434-982-6565
SOM Clinical Research Unit (CRU)
Stem Cell Core Arazdordi Toumadje AT5KH@virginia.edu 434-297-5302
Surgical Skills Training Center Dana Davis Sikon dds4g@eservices.virginia.edu 434-924-6854