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★★★★★
☆☆☆☆☆
USD 150 /hr
Hire Dr. Alexander D.
United States
USD 150 /hr

Biological Data Analyst with 15 years of experience | Bioinformatics & Machine Learning Expert | C++ & Python

Profile Summary
Subject Matter Expertise
Services
Writing Technical Writing
Research Scientific and Technical Research, Systematic Literature Review
Consulting Scientific and Technical Consulting
Data & AI Predictive Modeling, Statistical Analysis, Algorithm Design-Non ML, Algorithm Design-ML, Data Visualization, Big Data Analytics, Data Mining, Data Cleaning, Data Processing, Data Insights
Work Experience

ASSISTANT PROFESSOR

Cold Spring Harbor Laboratory

May 2018 - Present

Cold Spring Harbor Laboratory

September 2008 - Present

Education

Ph.D. in Theoretical Condensed Matter Physics

University of Minnesota

September 1997 - September 2003

Certifications
  • Certification details not provided.
Publications
PREPRINT
Conserved coexpression at single cell resolution across primate brains <head> <META HTTP-EQUIV="Refresh" CONTENT="0;URL=/servlet/useragent"> </head> .
Alexander Dobin, Benjamin Kaminow, Dinar Yunusov(2021). STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data . Cold Spring Harbor Laboratory
Rozowsky J, Drenkow J, Yang Y, Gursoy G, Galeev T, Borsari B, Epstein C, Xiong K, Xu J, Gao J, et al.(2021). Multi-tissue integrative analysis of personal epigenomes .
Kaminow B, Ballouz S, Gillis J, Dobin A(2020). Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses .
Dobin D, Dobin A(2020). Racial/ethnic and socioeconomic disparities of Covid-19 attacks rates in Suffolk County communities .
Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, et al.(2020). Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse .
Wang L, Lu Z, delaBastide M, Van Buren P, Wang X, Ghiban C, Regulski M, Drenkow J, Xu X, Ortiz-Ramirez C, et al.(2019). Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud .
Breschi A, Mu&#241;oz-Aguirre M, Wucher V, Davis CA, Garrido-Mart&#237;n D, Djebali S, Gillis J, Pervouchine DD, Vlasova A, Dobin A, et al.(2019). A limited set of transcriptional programs define major cell types .
Ballouz S, Dobin A, Gillis J(2019). Is it time to change the reference genome? .
Rahmanian S, Murad R, Breschi A, Zeng W, Mackiewicz M, Williams B, Davis C, Roberts B, Meadows S, Moore D, et al.(2018). Dynamics of microRNA expression during mouse prenatal development .
Alexander Dobin, Sara Ballouz, Thomas Gingeras, Jesse Gillis(2017). The fractured landscape of RNA-seq alignment: The default in our STARs . Cold Spring Harbor Laboratory
Ballouz S, Dobin A, Gingeras T, Gillis J(2017). The fractured landscape of RNA-seq alignment: The default in our STARs .
Haas BJ, Dobin A, Stransky N, Li B, Yang X, Tickle T, Bankapur A, Ganote C, Doak TG, Pochet N, et al.(2017). STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq .
Pervouchine D, Djebali S, Breschi A, Davis CA, Prieto Barja P, Dobin A, Tanzer A, Lagarde J, Zaleski C, See L, et al.(2014). Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes .
Comment on “TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions” by Kim et al. @article{PPR:PPR35568, title = {Comment on “TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions” by Kim et al.}, author = {Dobin A and Gingeras TR}, doi = {10.1101/000851} } .
JOURNAL ARTICLE
Alexander Dobin, Benjamin Kaminow, Sara Ballouz, Jesse Gillis(2022). Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses . Genome Research. 32. (4). p. 738--749. Cold Spring Harbor Laboratory
ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, et al.(2020). Expanded encyclopaedias of DNA elements in the human and mouse genomes . Nature.
ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, et al.(2020). Perspectives on ENCODE . Nature.
Breschi A, Mu&#241;oz-Aguirre M, Wucher V, Davis CA, Garrido-Mart&#237;n D, Djebali S, Gillis J, Pervouchine DD, Vlasova A, Dobin A, et al.(2020). A limited set of transcriptional programs define major cell types . Genome research.
Wang L, Lu Z, delaBastide M, Van Buren P, Wang X, Ghiban C, Regulski M, Drenkow J, Xu X, Ortiz-Ramirez C, et al.(2020). Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud . Frontiers in plant science.
Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A(2019). Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods . Genome biology.
Rahmanian S, Murad R, Breschi A, Zeng W, Mackiewicz M, Williams B, Davis CA, Roberts B, Meadows S, Moore D, et al.(2019). Dynamics of microRNA expression during mouse prenatal development . Genome research.
Ballouz S, Dobin A, Gillis JA(2019). Is it time to change the reference genome? . Genome biology.
Zhang Q, Chao TC, Patil VS, Qin Y, Tiwari SK, Chiou J, Dobin A, Tsai CM, Li Z, Dang J, et al.(2019). The long noncoding RNA ROCKI regulates inflammatory gene expression . The EMBO journal.
Ballouz S, Dobin A, Gingeras TR, Gillis J(2018). The fractured landscape of RNA-seq alignment: the default in our STARs . Nucleic acids research.
Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, et al.(2016). Erratum to: A benchmark for RNA-seq quantification pipelines . Genome biology.
Breschi A, Djebali S, Gillis J, Pervouchine DD, Dobin A, Davis CA, Gingeras TR, Guig&#243; R(2016). Gene-specific patterns of expression variation across organs and species . Genome biology.
Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, et al.(2016). Erratum to: A benchmark for RNA-seq quantification pipelines . Genome biology.
Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, et al.(2016). A benchmark for RNA-seq quantification pipelines . Genome biology.
Dobin A, Gingeras TR(2016). Optimizing RNA-Seq Mapping with STAR . Methods in molecular biology (Clifton, N.J.).
Dobin A, Gingeras TR(2015). Mapping RNA-seq Reads with STAR . Current protocols in bioinformatics.
Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, et al.(2015). Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression . Nature communications.
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, et al.(2014). A comparative encyclopedia of DNA elements in the mouse genome . Nature.
Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, et al.(2014). Comparison of the transcriptional landscapes between human and mouse tissues . Proceedings of the National Academy of Sciences of the United States of America.
Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, et al.(2014). Principles of regulatory information conservation between mouse and human . Nature.
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, et al.(2014). Comparative analysis of the transcriptome across distant species . Nature.
Engstr&#246;m PG, Steijger T, Sipos B, Grant GR, Kahles A, R&#228;tsch G, Goldman N, Hubbard TJ, Harrow J, Guig&#243; R, et al.(2013). Systematic evaluation of spliced alignment programs for RNA-seq data . Nature methods.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR(2012). STAR: ultrafast universal RNA-seq aligner . Bioinformatics (Oxford, England).
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al.(2012). Landscape of transcription in human cells . Nature.
ENCODE Project Consortium(2012). An integrated encyclopedia of DNA elements in the human genome . Nature.
Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, et al.(2012). An encyclopedia of mouse DNA elements (Mouse ENCODE) . Genome biology.
Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR(2012). High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression . Genome research.
Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, et al.(2012). Evidence for transcript networks composed of chimeric RNAs in human cells . PloS one.
Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, Vergara-Irigaray M, Segura V, Fagegaltier D, Penad&#233;s JR, Valle J, et al.(2011). Genome-wide antisense transcription drives mRNA processing in bacteria . Proceedings of the National Academy of Sciences of the United States of America.
ENCODE Project Consortium(2011). A user's guide to the encyclopedia of DNA elements (ENCODE) . PLoS biology.
Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, et al.(2010). The transcriptional diversity of 25 Drosophila cell lines . Genome research.
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, et al.(2010). The developmental transcriptome of Drosophila melanogaster . Nature.
modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, et al.(2010). Identification of functional elements and regulatory circuits by Drosophila modENCODE . Science (New York, N.Y.).
Stamm C, Tudosa I, Siegmann HC, St&#246;hr J, Dobin AY, Woltersdorf G, Heinrich B, Vaterlaus A(2005). Dissipation of spin angular momentum in magnetic switching . Physical review letters.
Dobin AY, Victora RH(2004). Surface roughness induced extrinsic damping in thin magnetic films . Physical review letters.
Dobin AY, Victora RH(2003). Intrinsic nonlinear ferromagnetic relaxation in thin metallic films . Physical review letters.
Krivorotov IN, Nikolaev KR, Dobin AY, Goldman AM, Dahlberg ED(2001). Exchange field induced magnetoresistance in colossal magnetoresistance manganites . Physical review letters.
Nikolaev KR, Dobin AY, Krivorotov IN, Cooley WK, Bhattacharya A, Kobrinskii AL, Glazman LI, Wentzovitch RM, Dahlberg ED, Goldman AM(2000). Oscillatory exchange coupling and positive magnetoresistance in epitaxial oxide heterostructures . Physical review letters.