Center for Computational Biology

The Center for Computational Biology provides institute-wide bioinformatics analytics for Scripps Research as well as for external collaborators. We offer scientific support to assist in the experimental design, collection, analysis, integration and dissemination of biomedical data and knowledge. Projects will often vary in time and cost depending on the scientific goals of the work and the desired level of analysis. Our goal is to use existing software and tools developed by the group, along with open source software, to solve a wide range of bioinformatics analyses and support research in a cost-effective manner.

  • Analyst
  • Embla
  • Envision
  • Platemate
  • Tecan M200
  • Wellmate


Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A., A Residue Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions., J Phys Chem B.  2016

Cummins DJ, Espada A, Novick SJ, Molina-Martin M, Stites RE, Espinosa JF, Broughton H, Goswami D, Pascal BD, Dodge JA, Chalmers MJ, Griffin PR., Two-Site Evaluation of the Repeatability and Precision of an Automated Dual-Column Hydrogen/Deuterium Exchange Mass Spectrometry Platform., Anal Chem.  2016

Emmerich, T., Abdullah, L., Ojo, J., Mouzon B, Nguyen T, Laco G, Crynen G, Evans J, Reed J, Mullan M, Crawford F. Mild TBI Results in a Long-Term Decrease inCirculating Phospholipids in a Mouse Model of Injury Neuromol Med. doi:10.1007/s12017-016-8436-4 2016.

Dretsch M , Silverberg N, Gardner A, Panenka W, Emmerich T, Crynen G, Ait-Ghezala G, Chaytow H, Mathura V, Crawford C, Iverson G. Genetics and Other Risk Factors for Past Concussions in Active-Duty Soldiers. Journal of neurotrauma (DOI: 10.1089/neu.2016.4480) 2016.

Tzekov, R., Dawson, C., Orlando, M., Mouzon, B., Reed, J., Evans, J., Crynen, G., Mullan, M. and Crawford, F., Sub-Chronic Neuropathological and Biochemical Changes in Mouse Visual System after Repetitive Mild Traumatic Brain Injury. PloS one, 11(4), p.e0153608. 2016.

Ait-Ghezala, G., S. Hassan, M. Tweed, D. Paris, G. Crynen, Z. Zakirova, S. Crynen, and F. Crawford. Identification of Telomerase-activating Blends From Naturally Occurring Compounds. Alternative therapies in health and medicine 22: 6. 2016.

Marciano DP, Kuruvilla DS, Pascal BD, Griffin PR., Identification of Bexarotene as a PPARγ Antagonist with HDX., PPAR Res.  2015

Mari Y, West GM, Scharager-Tapia C, Pascal BD, Garcia-Ordonez RD, Griffin PR., SERBP1 Is a Component of the Liver Receptor Homologue-1 Transcriptional Complex., J Proteome Res.  2015

Pascal BD, West GM, Scharager-Tapia C, Flefil R, Moroni T, Martinez-Acedo P, Griffin PR, Carvalloza AC., Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications., J Am Soc Mass Spectrom.  2015

Yang L, Yang D, de Graaf C, Moeller A, West GM, Dharmarajan V, Wang C, Siu FY, Song G, Reedtz-Runge S, Pascal BD, Wu B, Potter CS, Zhou H, Griffin PR, Carragher B, Yang H, Wang MW, Stevens RC, Jiang H., Conformational states of the full-length glucagon receptor., Nat Commun.  2015

Goswami D, Tuske S, Pascal BD, Bauman JD, Patel D, Arnold E, Griffin PR., Differential isotopic enrichment to facilitate characterization of asymmetric multimeric proteins using hydrogen/deuterium exchange mass spectrometry., Anal Chem.  2015

Emmerich, T., Abdullah, L., Crynen, G., Dretsch, M., Evans, J., Ait-Ghenzala, G., Martin J, Pelot R, Ferguson S, Bishop A, Phillips J, Mullan M, Crawford F Plasma lipidomic profiling in a military population of mTBI and PTSD with APOE ε4 dependent effect. Journal of neurotrauma, (ja). 2015.

Zakirova, Z., Crynen, G., Hassan, S., Abdullah, L., Horne, L., Mathura, V., Crawford, F. and Ait-Ghezala, G.,  A chronic longitudinal characterization of neurobehavioral and neuropathological cognitive impairment in a mouse model of Gulf War agent exposure. Frontiers in Integrative Neuroscience, 9. e0119579. 2015.

Kang Y, Zhou XE, Gao X, He Y, Liu W, Ishchenko A, Barty A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Ke J, Tan MH, Zhang C, Moeller A, West GM, Pascal BD, Van Eps N, Caro LN, Vishnivetskiy SA, Lee RJ, et al., Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser., Nature.  2015

Rzuczek SG, Southern MR, Disney MD., Studying a Drug-like, RNA-Focused Small Molecule Library Identifies Compounds That Inhibit RNA Toxicity in Myotonic Dystrophy., ACS Chem Biol.  2015

Howe EA, de Souza A, Lahr DL, Chatwin S, Montgomery P, Alexander BR, Nguyen DT, Cruz Y, Stonich DA, Walzer G, Rose JT, Picard SC, Liu Z, Rose JN, Xiang X, Asiedu J, Durkin D, Levine J, Yang JJ, Schürer SC, Braisted JC, Southall N, et al., BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types., Nucleic Acids Res.  2015

Reich A, Dunn C, Akasaka K, Wessel G., Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa., PLoS One.  2015

Lin JR, Fallahi-Sichani M, Sorger PK., Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method., Nat Commun.  2015

Fallahi-Sichani M, Moerke NJ, Niepel M, Zhang T, Gray NS, Sorger PK., Systematic analysis of BRAF(V600E) melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis., Mol Syst Biol.  2015

Kirschner DE, Hunt CA, Marino S, Fallahi-Sichani M, Linderman JJ., Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models., Wiley Interdiscip Rev Syst Biol Med.  2014

Marciano DP, Chang MR, Corzo CA, Goswami D, Lam VQ, Pascal BD, Griffin PR., The therapeutic potential of nuclear receptor modulators for treatment of metabolic disorders: PPARγ, RORs, and Rev-erbs., Cell Metab.  2014

Underbakke ES, Iavarone AT, Chalmers MJ, Pascal BD, Novick S, Griffin PR, Marletta MA., Nitric oxide-induced conformational changes in soluble guanylate cyclase., Structure.  2014

Goswami D, Callaway C, Pascal BD, Kumar R, Edwards DP, Griffin PR., Influence of domain interactions on conformational mobility of the progesterone receptor detected by hydrogen/deuterium exchange mass spectrometry., Structure.  2014

West GM, Willard FS, Sloop KW, Showalter AD, Pascal BD, Griffin PR., Glucagon-like peptide-1 receptor ligand interactions: structural cross talk between ligands and the extracellular domain., PLoS One.  2014

Abdullah, L., Evans, J. E., Ferguson, S., Mouzon, B., Montague, H., Reed, J, Crynen G, Crawford, F. Lipidomic analyses identify injury-specific phospholipid changes 3 mo after traumatic brain injury. The FASEB Journal, fj-14, doi:10.1096/fj.14-258228 2014.

Mouzon B, Bachmeier C, Ferro A, Olubunmi J, Crynen G, Acker C, Davies P,Mullan M, Stewart W, Crawford.  Chronic neuropathological and neurobehavioral changes in a repetitive mTBI model. Annals of Neurology. 75(2):241-254. 2014.

Girardet C, Mavrikaki M, Southern MR, Smith RG, Butler AA., Assessing interactions between Ghsr and Mc3r reveals a role for AgRP in the expression of food anticipatory activity in male mice., Endocrinology.  2014

Amelio AL, Fallahi M, Schaub FX, Zhang M, Lawani MB, Alperstein AS, Southern MR, Young BM, Wu L, Zajac-Kaye M, Kaye FJ, Cleveland JL, Conkright MD., CRTC1/MAML2 gain-of-function interactions with MYC create a gene signature predictive of cancers with CREB-MYC involvement., Proc Natl Acad Sci U S A.  2014

de Souza A, Bittker JA, Lahr DL, Brudz S, Chatwin S, Oprea TI, Waller A, Yang JJ, Southall N, Guha R, Schurer SC, Vempati UD, Southern MR, Dawson ES, Clemons PA, Chung TD., An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines., J Biomol Screen.  2014

Ramos I, Reich A, Wessel GM., Two-pore channels function in calcium regulation in sea star oocytes and embryos., Development.  2014

Swartz SZ, Reich AM, Oulhen N, Raz T, Milos PM, Campanale JP, Hamdoun A, Wessel GM., Deadenylase depletion protects inherited mRNAs in primordial germ cells., Development.  2014

Juliano CE, Reich A, Liu N, Götzfried J, Zhong M, Uman S, Reenan RA, Wessel GM, Steele RE, Lin H., PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells., Proc Natl Acad Sci U S A.  2014

Fresques T, Zazueta-Novoa V, Reich A, Wessel GM., Selective accumulation of germ-line associated gene products in early development of the sea star and distinct differences from germ-line development in the sea urchin., Dev Dyn.  2014

Wessel GM, Brayboy L, Fresques T, Gustafson EA, Oulhen N, Ramos I, Reich A, Swartz SZ, Yajima M, Zazueta V., The biology of the germ line in echinoderms., Mol Reprod Dev.  2014

Landgraf RR, Goswami D, Rajamohan F, Harris MS, Calabrese MF, Hoth LR, Magyar R, Pascal BD, Chalmers MJ, Busby SA, Kurumbail RG, Griffin PR., Activation of AMP-activated protein kinase revealed by hydrogen/deuterium exchange mass spectrometry., Structure.  2013

Pelot RC, Reed J, Crynen G, Evans J, Hart A, Plate T, Vallabhaneni P, Abdullah L, Mullan M, Crawford F.  Rapid and cost-effective purification of endo-Lys-N from  Maitake mushrooms for proteomic applications. Current Proteomics 10(4):292-297 2013.

Nwachukwu JC, Southern MR, Kiefer JR, Afonine PV, Adams PD, Terwilliger TC, Nettles KW., Improved crystallographic structures using extensive combinatorial refinement., Structure.  2013

Oulhen N, Reich A, Wong JL, Ramos I, Wessel GM., Diversity in the fertilization envelopes of echinoderms., Evol Dev.  2013

Fallahi-Sichani M, Honarnejad S, Heiser LM, Gray JW, Sorger PK., Metrics other than potency reveal systematic variation in responses to cancer drugs., Nat Chem Biol.  2013

Pascal BD, Willis S, Lauer JL, Landgraf RR, West GM, Marciano D, Novick S, Goswami D, Chalmers MJ, Griffin PR., HDX workbench: software for the analysis of H/D exchange MS data., J Am Soc Mass Spectrom.  2012

Fallahi-Sichani M, Flynn JL, Linderman JJ, Kirschner DE., Differential risk of tuberculosis reactivation among anti-TNF therapies is due to drug binding kinetics and permeability., J Immunol.  2012

Mouzon B, Chaytow H, Crynen G, Bachmeier C, Stewart J, Mullan M, Stewart W, Crawford F.  Repetitive mild traumatic brain injury in a mouse model produces learning and memory deficits accompanied by histological changes. Journal of Neurotrauma 10;29(18):2761-73. 2012.

Abdullah L, Evans JE, Bishop A, Reed JM, Crynen G, Phillips J, Pelot R, Mullan MA, Ferro A, Mullan CM, Mullan MJ, Ait-Ghezala G, Crawford FC.  Lipidomic Profiling of Phosphocholine Containing Brain Lipids in Mice with Sensorimotor Deficits and Anxiety- Like Features After Exposure to Gulf War Agents. NeuroMolecular Medicine, 14(4):349-61. 2012.

Crawford F, Crynen GC, Reed J, Mouzon B, Bishop A, Katz B, Ferguson S, Phillips J, Ganapathi V, Mathura V, Roses A, Mullan M. Identification of plasma biomarkers of TBI outcome using proteomic approaches in an APOE mouse model. Journal of Neurotrauma 20;29(2):246-60. 2012.

Canny SA, Cruz Y, Southern MR, Griffin PR., PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem., Bioinformatics.  2012

Reich A, Neretti N, Freiman RN, Wessel GM., Transcriptome variance in single oocytes within, and between, genotypes., Mol Reprod Dev.  2012

Zhang J, Chalmers MJ, Stayrook KR, Burris LL, Wang Y, Busby SA, Pascal BD, Garcia-Ordonez RD, Bruning JB, Istrate MA, Kojetin DJ, Dodge JA, Burris TP, Griffin PR., DNA binding alters coactivator interaction surfaces of the intact VDR-RXR complex., Nat Struct Mol Biol.  2011

Chalmers MJ, Pascal BD, Willis S, Zhang J, Iturria SJ, Dodge JA, Griffin PR., Methods for the Analysis of High Precision Differential Hydrogen Deuterium Exchange Data., Int J Mass Spectrom.  2011

Chalmers MJ, Busby SA, Pascal BD, West GM, Griffin PR., Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions., Expert Rev Proteomics.  2011

Fallahi-Sichani M, El-Kebir M, Marino S, Kirschner DE, Linderman JJ., Multiscale computational modeling reveals a critical role for TNF-α receptor 1 dynamics in tuberculosis granuloma formation., J Immunol.  2011

Southern MR, Griffin PR., A Java API for working with PubChem datasets., Bioinformatics.  2011

Reich A, Klatsky P, Carson S, Wessel G., The transcriptome of a human polar body accurately reflects its sibling oocyte., J Biol Chem.  2011

Kayihan GC, Wood M, Mouzon B, Ferguson S, Margenthaler E, Mathura V, Mullan M, Crawford F. Gulf War agents trigger discrete transcriptional changes in human neuronal cells. Toxicological & Environmental Chemistry 92:9, 1783-1799. 2010

Kayihan GC, Nelson DC, Huber DA, Amerson HV,White TL Davis JM. Clonal Evaluation for Fusiform Rust Disease Resistance: Effects of Pathogen Virulence and Disease Escape. Canadian Journal of Forestry 40:6, 1042-1050. 2010

Wessel GM, Reich AM, Klatsky PC., Use of sea stars to study basic reproductive processes., Syst Biol Reprod Med.  2010

Fallahi-Sichani M, Schaller MA, Kirschner DE, Kunkel SL, Linderman JJ., Identification of key processes that control tumor necrosis factor availability in a tuberculosis granuloma., PLoS Comput Biol.  2010

Fallahi-Sichani M, Linderman JJ., Lipid raft-mediated regulation of G-protein coupled receptor signaling by ligands which influence receptor dimerization: a computational study., PLoS One.  2009

Chalmers MJ, Busby SA, Pascal BD, Southern MR, Griffin PR., A two-stage differential hydrogen deuterium exchange method for the rapid characterization of protein/ligand interactions., J Biomol Tech.  2007

Pascal BD, Chalmers MJ, Busby SA, Mader CC, Southern MR, Tsinoremas NF, Griffin PR., The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data., BMC Bioinformatics.  2007

Fallahi-Sichani M, Soleimani M, Najafi SM, Kiani J, Arefian E, Atashi A., In vitro differentiation of cord blood unrestricted somatic stem cells expressing dopamine-associated genes into neuron-like cells., Cell Biol Int.  2007

Mohammadi Y, Soleimani M, Fallahi-Sichani M, Gazme A, Haddadi-Asl V, Arefian E, Kiani J, Moradi R, Atashi A, Ahmadbeigi N., Nanofibrous poly(epsilon-caprolactone)/poly(vinyl alcohol)/chitosan hybrid scaffolds for bone tissue engineering using mesenchymal stem cells., Int J Artif Organs.  2007

Kayihan GC, Onde S, Kandemir GE, Kaya Z. The genetic structure of Cedrus libani A. Rich seed stands determined by random amplified polymorphic DNA markers. Forest Genetics 12:3, 181–190. 2006

Schwartz R, Engel I, Fallahi-Sichani M, Petrie HT, Murre C., Gene expression patterns define novel roles for E47 in cell cycle progression, cytokine-mediated signaling, and T lineage development., Proc Natl Acad Sci U S A.  2006

Hamuro Y, Coales SJ, Morrow JA, Molnar KS, Tuske SJ, Southern MR, Griffin PR., Hydrogen/deuterium-exchange (H/D-Ex) of PPARgamma LBD in the presence of various modulators., Protein Sci.  2006

Kayihan GC, Huber DA, Morse AM, White TL Davis JM Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine. Theoretical and Applied Genetics 110, 948–958. 2005.

Tabrizifard S, Olaru A, Plotkin J, Fallahi-Sichani M, Livak F, Petrie HT., Analysis of transcription factor expression during discrete stages of postnatal thymocyte differentiation., J Immunol.  2004

Hamuro Y, Coales SJ, Southern MR, Nemeth-Cawley JF, Stranz DD, Griffin PR., Rapid analysis of protein structure and dynamics by hydrogen/deuterium exchange mass spectrometry., J Biomol Tech.  2003

Southern MR, Lewis AP., JavaShade: multiple sequence alignment box-and-shading on the World Wide Web., Bioinformatics.  1998

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