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Nicholas Crawford PhD – Computational Biologist and Author

My name is Nicholas (Nick) Crawford. I am a PhD student at Boston University working with Dr. Christopher Schneider. I’m also part of a larger collaboration with the Hoekstra and Losos labs at Harvard University. Many of these colors, yellow and orange in particular, appear to have evolved independently in multiple lineages. Thus, anoles are an ideal model to study convergent evolution of pigmentation. And their variable flanking sequence. I’ve used these markers to investigate questions in mam...If you&...

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Nicholas Crawford

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Cam●●●dge , Massachusetts, 02139

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Nicholas Crawford

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Cam●●●dge , Massachusetts, 02139

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Nicholas Crawford PhD – Computational Biologist and Author | ngcrawford.com Reviews
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My name is Nicholas (Nick) Crawford. I am a PhD student at Boston University working with Dr. Christopher Schneider. I’m also part of a larger collaboration with the Hoekstra and Losos labs at Harvard University. Many of these colors, yellow and orange in particular, appear to have evolved independently in multiple lineages. Thus, anoles are an ideal model to study convergent evolution of pigmentation. And their variable flanking sequence. I’ve used these markers to investigate questions in mam...If you&...
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Nicholas Crawford PhD – Computational Biologist and Author | ngcrawford.com Reviews

https://ngcrawford.com

My name is Nicholas (Nick) Crawford. I am a PhD student at Boston University working with Dr. Christopher Schneider. I’m also part of a larger collaboration with the Hoekstra and Losos labs at Harvard University. Many of these colors, yellow and orange in particular, appear to have evolved independently in multiple lineages. Thus, anoles are an ideal model to study convergent evolution of pigmentation. And their variable flanking sequence. I’ve used these markers to investigate questions in mam...If you&...

INTERNAL PAGES

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1

Nick Crawford | About me

http://www.ngcrawford.com/about-me

A short biography of my life with a scientific emphasis. Getting ready to explore rural Vermont with my cousin. That’s me on the left. I was also a student of Judith Allard, a fantastic high school teacher who provided me with a solid foundation in Biology. After high school I attended Union College. In Schenectady, New York. At Union I majored in Biology. I also managed to work part time in Barbara Pytel’s. Lab where I studied freeze tolerance in grey tree frogs ( Hyla versicolor. On this project, and I...

2

Nick Crawford | Filtering contigs/chromosomes from a multi-fasta file

http://www.ngcrawford.com/2012/07/31/filtering-contigschromosomes-from-a-multi-fasta-file

Python: Adding Read Group (@RG) tags to BAM or SAM files. Designing qPCR primers from just a GTF/GFF file and a genome sequence. Filtering contigs/chromosomes from a multi-fasta file. July 31, 2012. Middot; In Blog. A colleague needed to remove some individual fastas from a multi-fasta file. Googling didn’t reveal a canned way to do it so I hacked up this script. Tagged with →. Filtering contigs/chromosomes from a multi-fasta file. August 29, 2012 at 4:10 pm. 8220;””. 8220;””. From Bio import SeqIO.

3

Nick Crawford | Python: Adding Read Group (@RG) tags to BAM or SAM files

http://www.ngcrawford.com/2012/04/17/python-adding-read-group-rg-tags-to-bam-or-sam-files

Python: Multiprocessing large files. Filtering contigs/chromosomes from a multi-fasta file. Python: Adding Read Group (@RG) tags to BAM or SAM files. April 17, 2012. Middot; In Blog. Now requires @RG tags to be included in all SAM/BAM alignments. If you are using GATK. You have probably noticed that it will not run without them. Since @RG tags weren’t standard until recently, I’ve written a script to add them in post hoc. You’ll need to install pysam. To get it to work. Tagged with →.

4

Nick Crawford | Publications

http://www.ngcrawford.com/publications

Note: I have a google scholar page. That includes citation counts and can be ordered chronologically. Marcus R. Kronforst, Matthew E. B. Hansen, Nicholas G. Crawford. Jason R. Gallant, Wei Zhang, Rob J. Kulathinal, Durrell D. Kapan, Sean P. Mullen. 2013. Hybridization reveals the evolving genomic architecture of speciation. Cell Reports, 5. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology. 13. Nicholas G. Crawford*. In Press. DOI. PLoS ONE. 8.

5

Nick Crawford | Evolution and more...

http://www.ngcrawford.com/blog

Sorting BED files with headers. November 11, 2013. Middot; Add Comment. Middot; In Blog. Cat file.wheader.bed { head -n 1; tail -n 2 sort -k1,1 -k2,2g; } file.wheader.sorted.bed. Getting started with Ultra Conserved Elements. October 1, 2013. Middot; In Blog. From Faircloth et al 2012. Assembled. With current protocols, this can yield close to 5000 unique UCE loci in most amniotes. These loci can then be used to resolve phylogenies from non-model taxa at an unprecedented genomic resolution. April 3, 2013.

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selection |

http://www.molecularecologist.com/category/selection

How to …. The Genomics of Rapid Adaptation. 1 August, 2016. Phenology (the timing of life cycle events such as growth, breeding, or migration) is among the most sensitive organismal traits to climate and environmental change. In recent years, phenological shifts have been documented in numerous taxa, in traits such as … Continue reading →. Molecular Ecology, the journal. New insight into the genetic basis of industrial melanism. 9 June, 2016. Catching evolution in the act with the Singleton Density Score.

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natural history |

http://www.molecularecologist.com/category/natural-history

How to …. Category Archives: natural history. Phenotypes in Comparative Phylogeography. 11 August, 2016. Earlier this week, The Molecular Ecologist contributor Bryan McLean posted about the current state of comparative phylogeography (Riddle 2016). He listed several exciting directions that comparative phylogeography is heading, including more research that includes trait data. As a followup to … Continue reading →. A tale of mammoths and a disappearing lake. 4 August, 2016. 15 July, 2016. 11 July, 2016.

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genomics |

http://www.molecularecologist.com/category/genomics

How to …. The trouble with PCR duplicates. 25 August, 2016. The sequencing center just sent your lane of Illumina data. You’re excited. Life is great. You begin to process the data. You align the data. You check for PCR duplicates. 50 percent. Half of your data is garbage. Everything is … Continue reading →. Of microbes and men: Testing the neutral theory with the human microbiome. 22 August, 2016. Understanding the pieces of all those meeces: characterizing mice gut microbiota. 12 August, 2016. STRUCTUR...

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adaptation |

http://www.molecularecologist.com/category/adaptation

How to …. The Genomics of Rapid Adaptation. 1 August, 2016. Phenology (the timing of life cycle events such as growth, breeding, or migration) is among the most sensitive organismal traits to climate and environmental change. In recent years, phenological shifts have been documented in numerous taxa, in traits such as … Continue reading →. Molecular Ecology, the journal. New insight into the genetic basis of industrial melanism. 9 June, 2016. 6 June, 2016. 19 May, 2016. Recent works that attempt to get a...

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How to …. This is a weblog maintained and updated by people interested in the field of molecular ecology. The views and opinions expressed here are their own, and not those of other people, institutions or companies with which they are affiliated, unless stated explicitly. This blog is not affiliated with, neither does it represent the views, position or attitudes of John Wiley and Sons, any of their employees or affiliated companies. Stay up to date. Join 183 other subscribers.

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mokelly's devlog: Bootstrap statistics in Python

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THIS WAS UNCALLED FOR. Python, science and what have you. Tuesday, April 11, 2006. Bootstrap statistics in Python. Bootstrap.py version 0.1. Python didn't seem to have. A straightforward published bootstrap statistics module, so here is my effort. Suppose you had 40 measurements. Array([ 9.95587335, 11.14893547, 12.07186714, 9.06794986,. 1066503852, 10.7564387 , 11.42936871, 9.72575509, …. 8230;11.41262324, 9.28556988, 8.01210309, 9.98832624]). Might the underlying distribution have sigma=1? If we had 1,...

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Molecular Ecology, the journal |

http://www.molecularecologist.com/category/molecol

How to …. Category Archives: Molecular Ecology, the journal. The Genomics of Rapid Adaptation. 1 August, 2016. Phenology (the timing of life cycle events such as growth, breeding, or migration) is among the most sensitive organismal traits to climate and environmental change. In recent years, phenological shifts have been documented in numerous taxa, in traits such as … Continue reading →. Molecular Ecology, the journal. RADseq and missing data: some considerations. 10 May, 2016. 25 March, 2016. Fred All...

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The N=1 Guide to Grad School

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The N=1 guide to grad school (and hopefully, knowledge work). Putting yourself out there. Reach out on Twitter. Last August, I finished my Ph.D. with the help of a bunch of amazing people. I submitted my thesis, and on a bus in Turkey during my post-graduation vacation, I put together a list of practices and mindsets that I sometimes stuck to while working on my Ph.D. Over the last few months, I added some details, and you'll find the finished work below. Got something to say about this document? Finally...

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Nicholas Crawford PhD – Computational Biologist and Author

My name is Nicholas (Nick) Crawford. I am a PhD student at Boston University working with Dr. Christopher Schneider. I’m also part of a larger collaboration with the Hoekstra and Losos labs at Harvard University. Many of these colors, yellow and orange in particular, appear to have evolved independently in multiple lineages. Thus, anoles are an ideal model to study convergent evolution of pigmentation. And their variable flanking sequence. I’ve used these markers to investigate questions in mam...If you&...

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Curriculum Vitae ←

NICHOLAS G. CRAWFORD. Bioinformatics, evolutionary biology, computational biology, population genomics, phylogenomics, speciation, ultra conserved elements, herpetology and entomology. 2013, Postdoctoral Fellow, California Academy of Sciences. Durrell Kapan and Brian Simison. 2007/13, Ph.D. Biology, Boston University. Anolis Lizard Genomics and Phylogenetics. Mammal, Reptile, and Avian Phylogenomics, with Travis Glenn. Butterfly Speciation Genomics, with Sean Mullen. With Academic and Departmental Honors.

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