Academic Unit: Biochemistry and Molecular Biophysics and Systems Biology | Search Results

1. Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis

: Bansal, Mukesh; He, Jing; Peyton, Michael; Kustagi, Manjunath; Iyer, Archana; Comb, Michael; White, Michael; Minna, John D.; Califano, Andrea
: 2019
: Articles
: AdenocarcinomaMolecular biologyLungs--Cancer--Molecular aspectsProteomics

2. Accurate and sensitive quantification of protein-DNA binding affinity

: Rastogi, Chaitanya; Rube, Hans Tomas; Kribelbauer, Judith Franziska; Crocker, Justin; Loker, Ryan Edmund; Martini, Gabriella D.; Laptenko, Oleg; Freed-Pastor, William Allen; Prives, Carol L.; Stern, David L.; Mann, Richard S.; Bussemaker, Harmen J.
: 2018
: Articles
: Transcription factorsDNA-protein interactionsProtein bindingProbabilities--Mathematical models

3. Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

: Yuan, Yuan; Xie, Shirley; Darnell, Jennifer C.; Darnell, Andrew J.; Saito, Yuhki; Phatnani, Hemali P.; Murphy, Elisabeth A.; Zhang, Chaolin; Maniatis, Tom; Darnell, Robert B.
: 2018
: Articles
: Motor neuronsCytoskeletonSeptinsRNA splicingBiology

4. cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg

: Newcomb, Susan Elizabeth; Voutev, Roumen; Jory, Aurelie E.; Delker, Rebecca; Slattery, Matthew; Mann, Richard S.
: 2018
: Articles
: Drosophila melanogaster--GeneticsGrowth factors--ReceptorsCloningBiologyGene expression

5. Graph complexity analysis identifies an ETV5 tumor-specific network in human and murine low-grade glioma

: Pan, Yuan; Duron, Christina; Bush, Erin C.; Ma, Yu; Sims, Peter A.; Gutmann, David H.; Radunskaya, Ami; Hardin, Johanna
: 2018
: Articles
: GliomasGene regulatory networksGene expressionSystem analysisSystems biologyMathematics

6. Precise temporal regulation of alternative splicing during neural development

: Weyn-Vanhentenryck, Sabastien Matthieu; Feng, Huijuan; Ustianenko, Dmytro; Duffié, Rachel; Yan, Qinghong; Jacko, Martin; Martinez, Jose C.; Goodwin, Marianne; Zhang, Xuegong; Hengst, Ulrich; Lomvardas, Stavros; Swanson, Maurice S.; Zhang, Chaolin
: 2018
: Articles
: Genetic regulationNeurologyRNA splicing

7. SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing

: Yuan, Jinzhou; Sheng, Jenny; Sims, Peter A.
: 2018
: Articles
: Imaging systems in biologyNucleotide sequenceMicrofluidicsMolecular biology

8. Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry

: Freddolino, Peter L.; Yang, Jamie Siyu; Momen-Roknabadi, Amir; Tavazoie, Saeed
: 2018
: Articles
: Gene regulatory networksSystems biologyGene expressionStochastic processesEpigenetics

9. Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

: Rao, Satyanarayan; Chiu, Tsu-Pei; Kribelbauer, Judith F.; Mann, Richard S.; Bussemaker, Harmen J.; Rohs, Remo
: 2018
: Articles
: DNA--MethylationEpigeneticsDNA-binding proteinsSystems biology

10. Systematic reconstruction of autism biology from massive genetic mutation profiles

: Luo, Weijun; Zhang, Chaolin; Jiang, Yong-hui; Brouwer, Cory R.
: 2018
: Articles
: Mutation (Biology)Developmental geneticsAutism--ResearchAutism spectrum disorders--Genetic aspectsSystems biology

11. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

: Kribelbauer, Judith F.; Laptenko, Oleg; Chen, Siying; Martini, Gabriella D.; Freed-Pastor, William Allen; Prives, Carol L.; Mann, Richard S.; Bussemaker, Harmen J.
: 2017
: Articles
: DNA--MethylationTranscription factorsGenetic regulationDNA-protein interactionsEpigenetics

12. Systematic, network-based characterization of therapeutic target inhibitors

: Shen, Yao; Alvarez, Mariano; Bisikirska, Brygida; Lachmann, Alexander; Realubit, Ronald B.; Pampou, Sergey Yu; Coku, Jorida; Karan Jr., Charles; Califano, Andrea
: 2017
: Articles
: TherapeuticsGene expressionComputational biologyBioinformatics

13. A computational interactome and functional annotation for the human proteome

: Garzon Canas, Jose I.; Deng, Lei; Murray, Diana; Shapira, Sagi; Petrey, Donald S.; Honig, Barry
: 2016
: Articles
: Computational biologyProteomicsProtein-protein interactionsSystems biology

14. A High-Throughput Strategy for Dissecting Mammalian Genetic Interactions

: Stockman, Victoria B.; Ghamsari, Lila; Lasso Cabrera, Gorka; Honig, Barry; Shapira, Sagi; Wang, Harris H.
: 2016
: Articles
: RNAMammals--Molecular geneticsNucleotide sequenceSystems biologyMolecular geneticsCloningGeneticsBiology--Classification

15. An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq

: Yuan, Jinzhou; Sims, Peter A.
: 2016
: Articles
: Nucleotide sequenceGene expression

16. Molecular basis of sidekick-mediated cell-cell adhesion and specificity

: Goodman, Kerry; Yamagata, Masahito; Jin, Xiangshu; Mannepalli, Seetha M.; Katsamba, Phinikoula S.; Ahlsen, Goran; Sergeeva, Alina P.; Honig, Barry; Sanes, Joshua R.; Shapiro, Lawrence S.
: 2016
: Articles
: NeurosciencesCell interactionCell adhesionMolecular biology

17. Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks

: Repunte-Canonigo, Vez; Shin, William Kihoon; Vendruscolo, Leandro F.; Lefebvre, Celine; van der Stap, Lena; Kawamura, Tomoya; Schlosburg, Joel E.; Alvarez, Mariano Javier; Koob, George F.; Califano, Andrea; Sanno, Pietro Paolo
: 2015
: Articles
: Gene regulatory networksAlcoholismBiology--Classification

18. Single-Cell Identity Generated by Combinatorial Homophilic Interactions between α, β, and γ Protocadherins

: Thu, Chan Aye; Chen, Weisheng; Rubinstein, Rotem; Chevee, Maxime; Wolcott, Holly N.; Felsovalyi, Klara O.; Tapia, Juan Carlos; Shapiro, Lawrence S.; Honig, Barry; Maniatis, Tom
: 2014
: Articles
: Cellular recognitionNeuronsCytologyCadherinsNeurosciences

19. Bacterial Adaptation through Loss of Function

: Hottes, Alison K.; Freddolino, Peter L.; Khare, Anupama; Donnell, Zachary N.; Liu, Julia C.; Tavazoie, Saeed
: 2013
: Articles
: Microbial mutationNonsense mutationBacteriaGeneticsMicrobiologyBiology--Classification

20. Tumor-associated T cell receptor repertoires in low- and high-grade gliomas

: Sims, Jennifer S.; Grinshpun, Boris; Amendolara, Benjamin; Shen, Yufeng; Canoll, Peter D.; Sims, Peter A.; Bruce, Jeffrey N.
: 2013
: Presentations (Communicative Events)
: AstrocytomasGliomasT cells--ReceptorsExcision (Surgery)Cancer--SurgeryGlioblastoma multiformeOncologySurgeryMedicine

21. PrePPI: a structure-informed database of protein–protein interactions

: Zhang, Qiangfeng Cliff; Petrey, Donald S.; Garzon Canas, Jose I.; Deng, Lei; Honig, Barry
: 2012
: Articles
: BiochemistryMolecular biologyBiomedical engineering

22. The rate of the molecular clock and the cost of gratuitous protein synthesis

: Plata, Germán Alonso; Gottesman, Maxwell E.; Vitkup, Dennis
: 2010
: Articles
: Molecular biologyBiochemistry

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