Principal Investigator
PAN Cuiping
Research Direction

Computational Biology, Systems Biology, Bioinformatics, Big Data Computation, Multiomics, Cardiometabolic Diseases, Immune System.


Dr. Pan received her Ph.D. from the Max-Planck Institute for Biochemistry, Germany and trained as a postdoctoral scholar in the Genetics Department, Stanford University, USA. She has extensive experience in using proteomics and genomics technologies and computational strategies to decode cardiometablic diseases, including mapping the critical signal transduction pathways, identifying the signature biomolecules, inferring potential drug targets and effects, and constructing disease risk prediction models. In 2014-2021, she led a bioinformatics team in the Palo Alto Veterans Affairs Healthcare System, USA, where she co-supervised the genomic sequencing initiatives in the US Million Veteran Program and pioneered cloud computing technologies for 100,000s of genomes and 10+ petabytes of data. She joined the GBA-IPM in October 2021 and continued pursuing her scientific interests in cardiometabolic diseases and immune system. She publishes on cardiometabolic diseases, population genetics, and big data computing.


1.    Billing-Ross P, Song J, Tsao PS#, Pan C#.   Trellis for Efficient Data and Task Management in VA Million Veteran Program.  Sci Rep. 2021 Dec; 11, 23229.

2.    Bahmani A*, Ferriter K*, Krishnan V, Alavi A, Alavi A,Tsao PS, Snyder MP#, Pan C#.   Swarm: A Federated Cloud Framework for Large-Scale Variant Analysis.  PLoS Comput Biol. 2021 May 12;17(5):e1008977.

3.    Pan C#, Tsao PS.   Response by Pan and Tsao to Letter Regarding Article,“Genetic Architecture of Abdominal Aortic Aneurysm in the Million Veteran Program”.  Circulation. 2021 Apr 27;143(17):e873-e874.

4.    Bahmani A*, Xing Z*, Krishnan V*, Ray U*, Mueller F, Alavi AA, Tsao PS, Snyder MP#, Pan C#.   Hummingbird: Efficient Performance Prediction for Executing Genomic Applications in the Cloud.  Bioinformatics. 37 (17), 2537-2543.

5.    Ferriter K, Mueller F#, Bahmani A#, Pan C#.   VCFC: Structural and Semantic Compression and Indexing of Genetic Variant Data. (full access) Conference paper for The IEEE International Conference on Bioinformatics and Biomedicine 2020.  BIBM 2020: 200-203. 2020 Dec.

6.    Klarin D, Verma SS, Judy R, Dikilitas O, Wolford B, Paranjpe I, Levin MG, Pan C, Tcheandjieu C, Spin J, Lynch J, Assimes TL, Nyrønning LÅ, Mattsson E, Edwards TL, Denny J, Larson E, Lee MAM, Carrell D, Zhang Y, Jarvik G, Gharavi A, Harley J, Jarvik G, Mentch F, Pacheco JA, Skogholt AH, Thomas L, Gabrielsen ME, Hveem K, Nielsen JB, Zhou W, Fritsche K, Huang J, Natarajan P, Sun YS, DuVall SL, Rader DJ, Cho K, Chang KM, Wilson PWF, O’Donnell CJ, Kathiresan S, Scali ST, Berceli SA, Willer C, Jones GT, Bown MJ, Nadkarni G, Kullo I, Ritchie M, Damrauer SM*, Tsao PS* on behalf of the VA Million Veteran Program.  Genetic Architecture of Abdominal Aortic Aneurysm in the Million Veteran Program.  Circulation. 2020 Sep 28. doi: 10.1161/CIRCULATIONAHA.120.047544.

7.    Hunter-Zinck H, Shi Y, Li M, Gorman BR, Ji SG, Sun N, Webster T, Liem A, Hsieh P, Devineni P, Karnam P, Gong X, Radhakrishnan L, Schmidt J, Assimes TL, Huang J, Pan C, Humphries D, Brophy M, Moser J, Muralidhar S, Huang GD, Przygodzki R, Concato J, Gaziano JM, Gelernter J, O'Donnell CJ, Hauser ER, Zhao H, O'Leary TJ; VA Million Veteran Program, Tsao PS, Pyarajan S.  Genotyping Array Design and Data Quality Control in the Million Veteran Program.  Am J Hum Genet. 2020 Apr 2;106(4):535-548.

8.    Li J*, Pan C*, Zhang S*, Spin JM, Deng A, Leung LLK, Dalman RL, Tsao PS, Snyder M.  Decoding the Genomics of Abdominal Aortic Aneurysm.  Cell. 2018 Sep 174 (6): 1361-1372.

9.    Pan C*, McInnes G*, Deflaux N*, Snyder M, Bingham J, Datta S, Tsao PS.   Cloud-based Interactive Analytics for Terabytes of Genomic Variants Data.   Bioinformatics. 2017 Dec 1;33(23):3709-3715.

10.  Dewey FE, Grove ME, Priest JR, Waggott D, Batra P, Miller CL, Wheeler M, Zia A, Pan C, Karzcewski KJ, Miyake C, Whirl-Carrillo M, Klein TE, Datta S, Altman RB, Snyder M, Quertermous T, Ashley EA.  Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data.  PLoS Genet. 2015 Oct 8;11(10).

11.  Hellmuth S*, Boettger F*, Pan C, Mann M, Stemmann O.   PP2A Delays APC/C-dependent Degradation of Separase-associated but not Free Securin.  EMBO J. 2014 May 16;33(10):1134-47.

12.  Dewey FE*, Grove ME*, Pan C*, Goldstein BA, Bernstein J, Chaib H, Goldfeder RL, Ormond KE, Caleshu C, Kingham K, Klein TE, Whirl-Carillo M, Sakamoto K, Wheeler MT, Butte AJ, Merker JD, Ford J, Boxer L, Loannidis JPA, Yeung AC, Altman RA, Assimes TL, Snyder M*, Ashley EA*, Quertermous T*.   Clinical Interpretation and Implications of Whole Genome Sequencing.  JAMA. 2014;311(10):1035-1045

13.  Merker JD, Roskin KM, Ng D, Pan C, Fisk DG, King JJ, Hoh R, Stadler M, Okumoto LM, Abidi P, Hewitt R, Jones CD, Gojenola L, Clark MJ, Zhang B, Cherry AM, George TI, Cherry M, Snyder M, Boyd SD, Zehnder JL, Fire AZ*, Gotlib J*.  Comprehensive Whole-genome Sequencing of An Early-stage Primary Myelofibrosis Patient Defines Low Mutational Burden and Non-recurrent Candidate Genes.  Haematologica. 2013; Nov;98(11):1689-96

14.  Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M.   Detecting and Annotating Genetic Variations Using the HugeSeq Pipeline.  Nat Biotechnol. 2012; 30 (3): 226-9

15.  Sun N, Pan C, Nickell S, Mann M, Baumeister W, and Nagy I.  Quantitative Proteomic and Transcriptomic Analysis of Thermoplasma Acidophilum Cultured under Aerobic and Anaerobic Conditions.  J Proteome Res. 2010; 9 (9): 4839-50

16.  Pan C, Olsen JV, Daub H, and Mann M.  Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics.  Mol Cell Proteomics. 2009 Dec;8(12):2796-808

17.  Pan C*, Kumar C*, Bohl S, Klingmü U, and Mann M.  Comparative Proteomic Phenotyping of Cell lines and Primary Cells to Assess Preservation of
 Cell Type Specific Functions. Mol Cell Proteomics. Mar 01, 2009; 8: 443-450 (Journal cover story; Highlighted by Journal of Proteome Research, December 2008)

18.  Pan C, Gnad F, Olsen JV, and Mann M.  Quantitative Phosphoproteome Analysis of a Liver Cell Line Reveals Specificity of Phosphatase Inhibitors. Proteomics. 2008 Nov;8(21):4534-46

19.  Schroder B, Wrocklage C, Pan C, Jager R, Kosters B, Schafer H, Elsasser HP, Mann M, Hasilik A.  Integral and Associated Lysosomal Membrane Proteins. Traffic 2007 8:12 1676-86.

20.  Yuan JW, ZhengB, Pan CP, Wu YZ, Trimper S.  Dynamic Scaling Behavior of Human Brain Electroencephalogram. Physica A: Statistical Mechanics and its Applications. 364. 315-323.

21.  Pan CP, Zheng B, Wu YZ, Wang Y, and Tang XW.  Detrended Fluctuation Analysis of Human Brain Electroencephalogram.  Physics Letters A, 2004, Volume 329, Issue 1-2, p.130-135.